Transcriptional differences in interleukin-11 (IL11) after antidepressant treatment have been found to correspond to clinical response in major depressive disorder (MDD) patients. Expression differences were partly mediated by a single-nucleotide polymorphism (rs1126757), identified as a predictor of antidepressant response as part of a genome-wide association study. Here we attempt to identify whether DNA methylation, another baseline factor known to affect transcription factor binding, might also predict antidepressant response, using samples collected from the Genome-based Therapeutic Drugs for Depression project (GENDEP). DNA samples from 113 MDD individuals from the GENDEP project, who were treated with either escitalopram (n=80) or nortriptyline (n=33) for 12 weeks, were randomly selected. Percentage change in Montgomery–Åsberg Depression Rating Scale scores between baseline and week 12 were utilized as our measure of antidepressant response. The Sequenom EpiTYPER platform was used to assess DNA methylation across the only CpG island located in the IL11 gene. Regression analyses were then used to explore the relationship between CpG unit methylation and antidepressant response. We identified a CpG unit predictor of general antidepressant response, a drug by CpG unit interaction predictor of response, and a CpG unit by rs1126757 interaction predictor of antidepressant response. The current study is the first to investigate the potential utility of pharmaco-epigenetic biomarkers for the prediction of antidepressant response. Our results suggest that DNA methylation in IL11 might be useful in identifying those patients likely to respond to antidepressants, and if so, the best drug suited to each individual.
Epigenetic profiling of ADHD symptoms trajectories: a prospective, methylome-wide study
E Walton, J -B Pingault, C A M Cecil, T R Gaunt, C L Relton, J Mill, E D Barker
E Walton,
J -B Pingault,
C A M Cecil,
T R Gaunt,
C L Relton,
J Mill,
E D Barker
Attention-deficit/hyperactivity disorder (ADHD) is a prevalent developmental disorder, associated with a range of long-term impairments. Variation in DNA methylation, an epigenetic mechanism, is implicated in both neurobiological functioning and psychiatric health. However, the potential role of DNA methylation in ADHD symptoms is currently unclear. In this study, we examined data from the Avon Longitudinal Study of Parents and Children (ALSPAC)—specifically the subsample forming the Accessible Resource for Integrated Epigenomics Studies (ARIES)—that includes (1) peripheral measures of DNA methylation (Illumina 450k) at birth (n=817, 49% male) and age 7 (n=892, 50% male) and (2) trajectories of ADHD symptoms (7–15 years). We first employed a genome-wide analysis to test whether DNA methylation at birth associates with later ADHD trajectories; and then followed up at age 7 to investigate the stability of associations across early childhood. We found that DNA methylation at birth differentiated ADHD trajectories across multiple genomic locations, including probes annotated to SKI (involved in neural tube development), ZNF544 (previously implicated in ADHD), ST3GAL3 (linked to intellectual disability) and PEX2 (related to perixosomal processes). None of these probes maintained an association with ADHD trajectories at age 7. Findings lend novel insights into the epigenetic landscape of ADHD symptoms, highlighting the potential importance of DNA methylation variation in genes related to neurodevelopmental and peroxisomal processes that play a key role in the maturation and stability of cortical circuits.
Methylomic analysis of monozygotic twins discordant for autism spectrum disorder and related behavioural traits
C C Y Wong,
E L Meaburn,
A Ronald,
T S Price,
A R Jeffries,
L C Schalkwyk,
R Plomin
+ 1 more
C C Y Wong,
E L Meaburn,
A Ronald,
T S Price,
A R Jeffries,
L C Schalkwyk,
R Plomin,
J Mill
Autism spectrum disorder (ASD) defines a group of common, complex neurodevelopmental disorders. Although the aetiology of ASD has a strong genetic component, there is considerable monozygotic (MZ) twin discordance indicating a role for non-genetic factors. Because MZ twins share an identical DNA sequence, disease-discordant MZ twin pairs provide an ideal model for examining the contribution of environmentally driven epigenetic factors in disease. We performed a genome-wide analysis of DNA methylation in a sample of 50 MZ twin pairs (100 individuals) sampled from a representative population cohort that included twins discordant and concordant for ASD, ASD-associated traits and no autistic phenotype. Within-twin and between-group analyses identified numerous differentially methylated regions associated with ASD. In addition, we report significant correlations between DNA methylation and quantitatively measured autistic trait scores across our sample cohort. This study represents the first systematic epigenomic analyses of MZ twins discordant for ASD and implicates a role for altered DNA methylation in autism.
Histone Acetylome-wide Association Study of Autism Spectrum Disorder
Wenjie Sun,
Jeremie Poschmann,
Rosario Ricardo Cruz-Herrera del,
Neelroop N. Parikshak,
Hajira Shreen Hajan,
Vibhor Kumar,
Ramalakshmi Ramasamy
+ 6 more
Wenjie Sun,
Jeremie Poschmann,
Rosario Ricardo Cruz-Herrera del,
Neelroop N. Parikshak,
Hajira Shreen Hajan,
Vibhor Kumar,
Ramalakshmi Ramasamy,
T. Grant Belgard,
Bavani Elanggovan,
Chloe Chung Yi Wong,
Jonathan Mill,
Daniel H. Geschwind,
Shyam Prabhakar
The association of histone modification changes with autism spectrum disorder (ASD) has not been systematically examined. We conducted a histone acetylome-wide association study (HAWAS) by performing H3K27ac chromatin immunoprecipitation sequencing (ChIP-seq) on 257 postmortem samples from ASD and matched control brains. Despite etiological heterogeneity, ≥68% of syndromic and idiopathic ASD cases shared a common acetylome signature at >5,000 cis-regulatory elements in prefrontal and temporal cortex. Similarly, multiple genes associated with rare genetic mutations in ASD showed common "epimutations." Acetylome aberrations in ASD were not attributable to genetic differentiation at cis-SNPs and highlighted genes involved in synaptic transmission, ion transport, epilepsy, behavioral abnormality, chemokinesis, histone deacetylation, and immunity. By correlating histone acetylation with genotype, we discovered >2,000 histone acetylation quantitative trait loci (haQTLs) in human brain regions, including four candidate causal variants for psychiatric diseases. Due to the relative stability of histone modifications postmortem, we anticipate that the HAWAS approach will be applicable to multiple diseases.
Epigenome-Wide DNA Methylation Analysis of Monozygotic Twins Discordant for Diurnal Preference
Chloe C. Y. Wong,
Michael J. Parsons,
Kathryn J. Lester,
Joe Burrage,
Thalia C. Eley,
Jonathan Mill,
Emma L. Dempster
+ 1 more
Chloe C. Y. Wong,
Michael J. Parsons,
Kathryn J. Lester,
Joe Burrage,
Thalia C. Eley,
Jonathan Mill,
Emma L. Dempster,
Alice M. Gregory
Diurnal preference is an individual's preference for daily activities and sleep timing and is strongly correlated with the underlying circadian clock and the sleep-wake cycle validating its use as an indirect circadian measure in humans. Recent research has implicated DNA methylation as a mechanism involved in the regulation of the circadian clock system in humans and other mammals. In order to evaluate the extent of epigenetic differences associated with diurnal preference, we examined genome-wide patterns of DNA methylation in DNA from monozygotic (MZ) twin-pairs discordant for diurnal preference. MZ twins were selected from a longitudinal twin study designed to investigate the interplay of genetic and environmental factors in the development of emotional and behavioral difficulties. Fifteen pairs of MZ twins were identified in which one member scored considerably higher on the Horne-Ostberg Morningness-Eveningness Questionnaire (MEQ) than the other. Genome-wide DNA methylation patterns were assessed in twins' buccal cell DNA using the Illumina Infinium HumanMethylation450 BeadChips. Quality control and data pre-processing was undertaken using the wateRmelon package. Differentially methylated probes (DMPs) were identified using an analysis strategy taking into account both the significance and the magnitude of DNA methylation differences. Our data indicate that DNA methylation differences are detectable in MZ twins discordant for diurnal preference. Moreover, downstream gene ontology (GO) enrichment analysis on the top-ranked diurnal preference associated DMPs revealed significant enrichment of pathways that have been previously associated with circadian rhythm regulation, including cell adhesion processes and calcium ion binding.
Epigenetic regulation of mitochondrial function in neurodegenerative disease: New insights from advances in genomic technologies
Matthew Devall, Janou Roubroeks, Jonathan Mill, Michael Weedon, Katie Lunnon
Matthew Devall,
Janou Roubroeks,
Jonathan Mill,
Michael Weedon,
Katie Lunnon
The field of mitochondrial epigenetics has received increased attention in recent years and changes in mitochondrial DNA (mtDNA) methylation has been implicated in a number of diseases, including neurodegenerative diseases such as amyotrophic lateral sclerosis. However, current publications have been limited by the use of global or targeted methods of measuring DNA methylation. In this review, we discuss current findings in mitochondrial epigenetics as well as its potential role as a regulator of mitochondria within the brain. Finally, we summarize the current technologies best suited to capturing mtDNA methylation, and how a move towards whole epigenome sequencing of mtDNA may help to advance our current understanding of the field.
O2‐06‐02: Genome‐Wide Meta‐Analysis of Transcriptome Profiling Identifies Novel Dysregulated Genes Implicated in Alzheimer's Disease
Kwangsik Nho,
Sungeun Kim,
Shannon L. Risacher,
Liana G. Apostolova,
Kuang Lin,
Aoife Keohane,
Katie Lunnon
+ 19 more
Kwangsik Nho,
Sungeun Kim,
Shannon L. Risacher,
Liana G. Apostolova,
Kuang Lin,
Aoife Keohane,
Katie Lunnon,
Angela Hodges,
Mariet Allen,
Xue Wang,
Jeremy D. Burgess,
Nilufer Ertekin-Taner,
Ronald C. Petersen,
Holly Soares,
Parul Singh,
Lisu Wang,
Zhenhao Qi,
Aiqing He,
Isaac Neuhaus,
Vishal Patel,
Tatiana M. Foroud,
Kelley Faber,
Simon Lovestone,
Andrew Simmons,
Michael W. Weiner,
Andrew J. Saykin
Increased understanding about the functional complexity of the genome has led to growing recognition about the role of epigenetic variation in the etiology of schizophrenia. Epigenetic processes act to dynamically control gene expression independently of DNA sequence variation and are known to regulate key neurobiological and cognitive processes in the brain. To date, our knowledge about the role of epigenetic processes in schizophrenia is limited and based on analyses of small numbers of samples obtained from a range of different cell and tissue types. Moving forward, it will be important to establish cause and effect in epigenetic studies of schizophrenia and broaden our horizons beyond DNA methylation. Rather than investigating genetic and epigenetic factors independently, an integrative etiological research paradigm based on the combination of genomic, transcriptomic, and epigenomic analyses is required.
How Can Pharmacogenomics Biomarkers Be Translated into Patient Benefit
D. Collier,
E. Achilla,
G. Breen,
S. Curran,
D. Dima,
R. Flanagan,
J. Frank
+ 13 more
D. Collier,
E. Achilla,
G. Breen,
S. Curran,
D. Dima,
R. Flanagan,
J. Frank,
S. Frangou,
C. Gasse,
I. Giegling,
M. Rietschel,
D. Rujescu,
J. Maccabe,
P. McCrone,
J. Mill,
E. Sigurdsson,
H. Stefansson,
J. Walters,
M. Verbelen,
M. Helthuis
Treatment resistant schizophrenia (TRS) is one of the most disabling of psychiatric disorders, affecting about 1/3 of patients. First-line treatments include both atypical and typical antipsychotics. The original atypical, clozapine, is a final option, and although it has been shown to be the only effective treatment for TRS, many patients do not respond well to clozapine. Clozapine use is related to adverse events, most notably agranulocytosis, a potentially fatal blood disorder which affects about 1% of those prescribed clozapine and requires regular blood monitoring. This as a barrier to prescription and there is a long delay in access for TRS patients, of five or more years, from first antipsychotic prescription. Better tools to predict treatment resistance and to identify risk of adverse events would allow faster and safer access to clozapine for patients who are likely to benefit from it. The CRESTAR project (www.crestar-project.eu) is a European Framework 7 collaborative project that aims to develop tools to predict i) treatment response, particularly patients who are less likely to respond to usual antipsychotics, indicating treatment with clozapine as early as possible, ii) patients who are at high or low risk of adverse events and side effects, iii) extreme TRS patients so that they can be stratified in clinical trials for novel treatments. CRESTAR has addressed these questions by examining genome-wide association data, genome sequence, epigenetic biomarkers and epidemiological data in European patient cohorts characterized for treatment response, and adverse drug reaction using data from clozapine therapeutic drug monitoring and linked National population medical and pharmacy databases, to identify predictive factors. In parallel CRESTAR will perform health economic research on potential benefits, and ethics and patient-centred research with stakeholders.
TEMPORARY REMOVAL: Blood methylomic signatures of presymptomatic dementia in elderly subjects with type 2 diabetes mellitus
Katie Lunnon, Rebecca G. Smith, Itzik Cooper, Lior Greenbaum, Jonathan Mill, Michal Schnaider Beeri
Katie Lunnon,
Rebecca G. Smith,
Itzik Cooper,
Lior Greenbaum,
Jonathan Mill,
Michal Schnaider Beeri
The authors discuss strategies and challenges of population-based studies of epigenetic variation. Such studies should contribute to our understanding of the contribution of epigenetic factors to human disease, but need to be performed and interpreted with consideration of their limitations.
Mitochondrial genes are altered in blood early in Alzheimer's disease
Katie Lunnon,
Aoife Keohane,
Ruth Pidsley,
Stephen Newhouse,
Joanna Riddoch-Contreras,
Elisabeth B. Thubron,
Matthew Devall
+ 12 more
Katie Lunnon,
Aoife Keohane,
Ruth Pidsley,
Stephen Newhouse,
Joanna Riddoch-Contreras,
Elisabeth B. Thubron,
Matthew Devall,
Hikka Soininen,
Iwona Kłoszewska,
Patrizia Mecocci,
Magda Tsolaki,
Bruno Vellas,
Leonard Schalkwyk,
Richard Dobson,
Afshan N. Malik,
John Powell,
Simon Lovestone,
Angela Hodges,
AddNeuroMed Consortium
Although mitochondrial dysfunction is a consistent feature of Alzheimer's disease in the brain and blood, the molecular mechanisms behind these phenomena are unknown. Here we have replicated our previous findings demonstrating reduced expression of nuclear-encoded oxidative phosphorylation (OXPHOS) subunits and subunits required for the translation of mitochondrial-encoded OXPHOS genes in blood from people with Alzheimer's disease and mild cognitive impairment. Interestingly this was accompanied by increased expression of some mitochondrial-encoded OXPHOS genes, namely those residing closest to the transcription start site of the polycistronic heavy chain mitochondrial transcript (MT-ND1, MT-ND2, MT-ATP6, MT-CO1, MT-CO2, MT-C03) and MT-ND6 transcribed from the light chain. Further we show that mitochondrial DNA copy number was unchanged suggesting no change in steady-state numbers of mitochondria. We suggest that an imbalance in nuclear and mitochondrial genome-encoded OXPHOS transcripts may drive a negative feedback loop reducing mitochondrial translation and compromising OXPHOS efficiency, which is likely to generate damaging reactive oxygen species.
Profiling Regulatory Variation in the Brain: Methods for Exploring the Neuronal Epigenome
Clonal level random allelic expression imbalance and random monoallelic expression provides cellular heterogeneity within tissues by modulating allelic dosage. Although such expression patterns have been observed in multiple cell types, little is known about when in development these stochastic allelic choices are made. We examine allelic expression patterns in human neural progenitor cells before and after epigenetic reprogramming to induced pluripotency, observing that loci previously characterized by random allelic expression imbalance (0.63% of expressed genes) are generally reset to a biallelic state in induced pluripotent stem cells (iPSCs). We subsequently neuralized the iPSCs and profiled isolated clonal neural stem cells, observing that significant random allelic expression imbalance is reestablished at 0.65% of expressed genes, including novel loci not found to show allelic expression imbalance in the original parental neural progenitor cells. Allelic expression imbalance was associated with altered DNA methylation across promoter regulatory regions, with clones characterized by skewed allelic expression being hypermethylated compared to their biallelic sister clones. Our results suggest that random allelic expression imbalance is established during lineage commitment and is associated with increased DNA methylation at the gene promoter.
Hypermethylation in the ZBTB20 gene is associated with major depressive disorder
Matthew N Davies,
Lutz Krause,
Jordana T Bell,
Fei Gao,
Kirsten J Ward,
Honglong Wu,
Hanlin Lu
+ 16 more
Matthew N Davies,
Lutz Krause,
Jordana T Bell,
Fei Gao,
Kirsten J Ward,
Honglong Wu,
Hanlin Lu,
Yuan Liu,
Pei-Chein Tsai,
David A Collier,
Therese Murphy,
Emma Dempster,
Jonathan Mill,
UK Brain Expression Consortium,
Alexis Battle,
Sara Mostafavi,
Xiaowei Zhu,
Anjali Henders,
Enda Byrne,
Naomi R Wray,
Nicholas G Martin,
Tim D Spector,
Jun Wang
BackgroundAlthough genetic variation is believed to contribute to an individual’s susceptibility to major depressive disorder, genome-wide association studies have not yet identified associations that could explain the full etiology of the disease. Epigenetics is increasingly believed to play a major role in the development of common clinical phenotypes, including major depressive disorder.ResultsGenome-wide MeDIP-Sequencing was carried out on a total of 50 monozygotic twin pairs from the UK and Australia that are discordant for depression. We show that major depressive disorder is associated with significant hypermethylation within the coding region of ZBTB20, and is replicated in an independent cohort of 356 unrelated case-control individuals. The twins with major depressive disorder also show increased global variation in methylation in comparison with their unaffected co-twins. ZBTB20 plays an essential role in the specification of the Cornu Ammonis-1 field identity in the developing hippocampus, a region previously implicated in the development of major depressive disorder.ConclusionsOur results suggest that aberrant methylation profiles affecting the hippocampus are associated with major depressive disorder and show the potential of the epigenetic twin model in neuro-psychiatric disease.
The PsychENCODE project
Schahram Akbarian,
Chunyu Liu,
James A Knowles,
Flora M Vaccarino,
Peggy J Farnham,
Gregory E Crawford,
Andrew E Jaffe
+ 77 more
Schahram Akbarian,
Chunyu Liu,
James A Knowles,
Flora M Vaccarino,
Peggy J Farnham,
Gregory E Crawford,
Andrew E Jaffe,
Dalila Pinto,
Stella Dracheva,
Daniel H Geschwind,
Jonathan Mill,
Angus C Nairn,
Alexej Abyzov,
Sirisha Pochareddy,
Shyam Prabhakar,
Sherman Weissman,
Patrick F Sullivan,
Matthew W State,
Zhiping Weng,
Mette A Peters,
Kevin P White,
Mark B Gerstein,
Anahita Amiri,
Chris Armoskus,
Allison E Ashley-Koch,
Taejeong Bae,
Andrea Beckel-Mitchener,
Benjamin P Berman,
Gerhard A Coetzee,
Gianfilippo Coppola,
Nancy Francoeur,
Menachem Fromer,
Robert Gao,
Kay Grennan,
Jennifer Herstein,
David H Kavanagh,
Nikolay A Ivanov,
Yan Jiang,
Robert R Kitchen,
Alexey Kozlenkov,
Marija Kundakovic,
Mingfeng Li,
Zhen Li,
Shuang Liu,
Lara M Mangravite,
Eugenio Mattei,
Eirene Markenscoff-Papadimitriou,
Fábio C P Navarro,
Nicole North,
Larsson Omberg,
David Panchision,
Neelroop Parikshak,
Jeremie Poschmann,
Amanda J Price,
Michael Purcaro,
Timothy E Reddy,
Panos Roussos,
Shannon Schreiner,
Soraya Scuderi,
Robert Sebra,
Mikihito Shibata,
Annie W Shieh,
Mario Skarica,
Wenjie Sun,
Vivek Swarup,
Amber Thomas,
Junko Tsuji,
Bakel Harm van,
Daifeng Wang,
Yongjun Wang,
Kai Wang,
Donna M Werling,
A Jeremy Willsey,
Heather Witt,
Hyejung Won,
Chloe C Y Wong,
Gregory A Wray,
Emily Y Wu,
Xuming Xu,
Lijing Yao,
Geetha Senthil,
Thomas Lehner,
Pamela Sklar,
Nenad Sestan
Recent research on disparate psychiatric disorders has implicated rare variants in genes involved in global gene regulation and chromatin modification, as well as many common variants located primarily in regulatory regions of the genome. Understanding precisely how these variants contribute to disease will require a deeper appreciation for the mechanisms of gene regulation in the developing and adult human brain. The PsychENCODE project aims to produce a public resource of multidimensional genomic data using tissue- and cell type–specific samples from approximately 1,000 phenotypically well-characterized, high-quality healthy and disease-affected human post-mortem brains, as well as functionally characterize disease-associated regulatory elements and variants in model systems. We are beginning with a focus on autism spectrum disorder, bipolar disorder and schizophrenia, and expect that this knowledge will apply to a wide variety of psychiatric disorders. This paper outlines the motivation and design of PsychENCODE.
Epigenetic regulation of adult neural stem cells: implications for Alzheimer’s disease
Carlos P Fitzsimons,
Bodegraven Emma van,
Marijn Schouten,
Roy Lardenoije,
Konstantinos Kompotis,
Gunter Kenis,
den Hurk Mark van
+ 11 more
Carlos P Fitzsimons,
Bodegraven Emma van,
Marijn Schouten,
Roy Lardenoije,
Konstantinos Kompotis,
Gunter Kenis,
den Hurk Mark van,
Marco P Boks,
Caroline Biojone,
Samia Joca,
Harry WM Steinbusch,
Katie Lunnon,
Diego F Mastroeni,
Jonathan Mill,
Paul J Lucassen,
Paul D Coleman,
den Hove Daniel LA van,
Bart PF Rutten
Experimental evidence has demonstrated that several aspects of adult neural stem cells (NSCs), including their quiescence, proliferation, fate specification and differentiation, are regulated by epigenetic mechanisms. These control the expression of specific sets of genes, often including those encoding for small non-coding RNAs, indicating a complex interplay between various epigenetic factors and cellular functions.Previous studies had indicated that in addition to the neuropathology in Alzheimer’s disease (AD), plasticity-related changes are observed in brain areas with ongoing neurogenesis, like the hippocampus and subventricular zone. Given the role of stem cells e.g. in hippocampal functions like cognition, and given their potential for brain repair, we here review the epigenetic mechanisms relevant for NSCs and AD etiology. Understanding the molecular mechanisms involved in the epigenetic regulation of adult NSCs will advance our knowledge on the role of adult neurogenesis in degeneration and possibly regeneration in the AD brain.
DNA methylation at the Igf2/H19 imprinting control region is associated with cerebellum mass in outbred mice
Ruth Pidsley,
Cathy Fernandes,
Joana Viana,
Jose L Paya-Cano,
Lin Liu,
Rebecca G Smith,
Leonard C Schalkwyk
+ 1 more
Ruth Pidsley,
Cathy Fernandes,
Joana Viana,
Jose L Paya-Cano,
Lin Liu,
Rebecca G Smith,
Leonard C Schalkwyk,
Jonathan Mill
BackgroundInsulin-like growth factor 2 (Igf2) is a paternally expressed imprinted gene regulating fetal growth, playing an integral role in the development of many tissues including the brain. The parent-of-origin specific expression of Igf2 is largely controlled by allele-specific DNA methylation at CTCF-binding sites in the imprinting control region (ICR), located immediately upstream of the neighboring H19 gene. Previously we reported evidence of a negative correlation between DNA methylation in this region and cerebellum weight in humans.ResultsWe quantified cerebellar DNA methylation across all four CTCF binding sites spanning the murine Igf2/H19 ICR in an outbred population of Heterogeneous Stock (HS) mice (n = 48). We observe that DNA methylation at the second and third CTCF binding sites in the Igf2/H19 ICR shows a negative relationship with cerebellar mass, reflecting the association observed in human post-mortem cerebellum tissue.ConclusionsGiven the important role of the cerebellum in motor control and cognition, and the link between structural cerebellar abnormalities and neuropsychiatric phenotypes, the identification of epigenetic factors associated with cerebellum growth and development may provide important insights about the etiology of psychiatric disorders.
O3‐04‐03: CROSS‐TISSUE METHYLOMIC PROFILING IN ALZHEIMER'S DISEASE
Katie Lunnon,
Rebecca Smith,
Eilis Hannon,
Manuela Volta,
Claire Troakes,
Vahram Haroutunian,
Pavel Katsel
+ 4 more
Katie Lunnon,
Rebecca Smith,
Eilis Hannon,
Manuela Volta,
Claire Troakes,
Vahram Haroutunian,
Pavel Katsel,
Safa Al‐Sarraj,
Simon Lovestone,
Leonard Schalkwyk,
Jonathan Mill
Major depressive disorder (MDD) represents a major social and economic health issue and constitutes a major risk factor for suicide. The molecular pathology of suicidal depression remains poorly understood, although it has been hypothesised that regulatory genomic processes are involved in the pathology of both MDD and suicidality. In this study, genome-wide patterns of DNA methylation were assessed in depressed suicide completers (n=20) and compared with non-psychiatric, sudden-death controls (n=20) using tissue from two cortical brain regions (Brodmann Area 11 (BA11) and Brodmann Area 25 (BA25)). Analyses focused on identifying differentially methylated regions (DMRs) associated with suicidal depression and epigenetic variation were explored in the context of polygenic risk scores for major depression and suicide. Weighted gene co-methylation network analysis was used to identify modules of co-methylated loci associated with depressed suicide completers and polygenic burden for MDD and suicide attempt. We identified a DMR upstream of the PSORS1C3 gene, subsequently validated using bisulfite pyrosequencing and replicated in a second set of suicide samples, which is characterised by significant hypomethylation in both cortical brain regions in MDD suicide cases. We also identified discrete modules of co-methylated loci associated with polygenic risk burden for suicide attempt, but not major depression. Suicide-associated co-methylation modules were enriched among gene networks implicating biological processes relevant to depression and suicidality, including nervous system development and mitochondria function. Our data suggest that there are coordinated changes in DNA methylation associated with suicide that may offer novel insights into the molecular pathology associated with depressed suicide completers.
Childhood maternal care is associated with DNA methylation of the genes for brain-derived neurotrophic factor (BDNF) and oxytocin receptor (OXTR) in peripheral blood cells in adult men and women
Eva Unternaehrer,
Andrea Hans Meyer,
Susan C. A. Burkhardt,
Emma Dempster,
Simon Staehli,
Nathan Theill,
Roselind Lieb
+ 1 more
Eva Unternaehrer,
Andrea Hans Meyer,
Susan C. A. Burkhardt,
Emma Dempster,
Simon Staehli,
Nathan Theill,
Roselind Lieb,
Gunther Meinlschmidt
In adults, reporting low and high maternal care in childhood, we compared DNA methylation in two stress-associated genes (two target sequences in the oxytocin receptor gene, OXTR; one in the brain-derived neurotrophic factor gene, BDNF) in peripheral whole blood, in a cross-sectional study (University of Basel, Switzerland) during 2007-2008. We recruited 89 participants scoring < 27 (n = 47, 36 women) or > 33 (n = 42, 35 women) on the maternal care subscale of the Parental Bonding Instrument (PBI) at a previous assessment of a larger group (N = 709, range PBI maternal care = 0-36, age range = 19-66 years; median 24 years). 85 participants gave blood for DNA methylation analyses (Sequenom(R) EpiTYPER, San Diego, CA) and cell count (Sysmex PocH-100i™, Kobe, Japan). Mixed model statistical analysis showed greater DNA methylation in the low versus high maternal care group, in the BDNF target sequence [Likelihood-Ratio (1) = 4.47; p = 0.035] and in one OXTR target sequence Likelihood-Ratio (1) = 4.33; p = 0.037], but not the second OXTR target sequence [Likelihood-Ratio (1) < 0.001; p = 0.995). Mediation analyses indicated that differential blood cell count did not explain associations between low maternal care and BDNF (estimate = -0.005, 95% CI = -0.025 to 0.015; p = 0.626) or OXTR DNA methylation (estimate = -0.015, 95% CI = -0.038 to 0.008; p = 0.192). Hence, low maternal care in childhood was associated with greater DNA methylation in an OXTR and a BDNF target sequence in blood cells in adulthood. Although the study has limitations (cross-sectional, a wide age range, only three target sequences in two genes studied, small effects, uncertain relevance of changes in blood cells to gene methylation in brain), the findings may indicate components of the epiphenotype from early life stress.
Bisphenol A causes reproductive toxicity, decreases dnmt1 transcription, and reduces global DNA methylation in breeding zebrafish (Danio rerio)
L. V. Laing,
J. Viana,
E. L. Dempster,
M. Trznadel,
L. A. Trunkfield,
T. M. Uren Webster,
Aerle R. van
+ 4 more
L. V. Laing,
J. Viana,
E. L. Dempster,
M. Trznadel,
L. A. Trunkfield,
T. M. Uren Webster,
Aerle R. van,
G. C. Paull,
R. J. Wilson,
J. Mill,
E. M. Santos
Bisphenol A (BPA) is a commercially important high production chemical widely used in epoxy resins and polycarbonate plastics, and is ubiquitous in the environment. Previous studies demonstrated that BPA activates estrogenic signaling pathways associated with adverse effects on reproduction in vertebrates and that exposure can induce epigenetic changes. We aimed to investigate the reproductive effects of BPA in a fish model and to document its mechanisms of toxicity. We exposed breeding groups of zebrafish (Danio rerio) to 0.01, 0.1, and 1 mg/L BPA for 15 d. We observed a significant increase in egg production, together with a reduced rate of fertilization in fish exposed to 1 mg/L BPA, associated with significant alterations in the transcription of genes involved in reproductive function and epigenetic processes in both liver and gonad tissue at concentrations representing hotspots of environmental contamination (0.1 mg/L) and above. Of note, we observed reduced expression of DNA methyltransferase 1 (dnmt1) at environmentally relevant concentrations of BPA, along with a significant reduction in global DNA methylation, in testes and ovaries following exposure to 1 mg/L BPA. Our findings demonstrate that BPA disrupts reproductive processes in zebrafish, likely via estrogenic mechanisms, and that environmentally relevant concentrations of BPA are associated with altered transcription of key enzymes involved in DNA methylation maintenance. These findings provide evidence of the mechanisms of action of BPA in a model vertebrate and advocate for its reduction in the environment.
Is treatment-resistant schizophrenia categorically distinct from treatment-responsive schizophrenia? a systematic review
Amy L. Gillespie, Ruta Samanaite, Jonathan Mill, Alice Egerton, James H. MacCabe
Amy L. Gillespie,
Ruta Samanaite,
Jonathan Mill,
Alice Egerton,
James H. MacCabe
BackgroundSchizophrenia is a highly heterogeneous disorder, and around a third of patients are treatment-resistant. The only evidence-based treatment for these patients is clozapine, an atypical antipsychotic with relatively weak dopamine antagonism. It is plausible that varying degrees of response to antipsychotics reflect categorically distinct illness subtypes, which would have significant implications for research and clinical practice. If these subtypes could be distinguished at illness onset, this could represent a first step towards personalised medicine in psychiatry. This systematic review investigates whether current evidence supports conceptualising treatment-resistant and treatment-responsive schizophrenoa as categorically distinct subtypes.MethodA systematic literature search was conducted, using PubMed, EMBASE, PsycInfo, CINAHL and OpenGrey databases, to identify all studies which compared treatment-resistant schizophrenia (defined as either a lack of response to two antipsychotic trials or clozapine prescription) to treatment-responsive schizophrenia (defined as known response to non-clozapine antipsychotics).ResultsNineteen studies of moderate quality met inclusion criteria. The most robust findings indicate that treatment-resistant patients show glutamatergic abnormalities, a lack of dopaminergic abnormalities, and significant decreases in grey matter compared to treatment-responsive patients. Treatment-resistant patients were also reported to have higher familial loading; however, no individual gene-association study reported their findings surviving correction for multiple comparisons.ConclusionsTentative evidence supports conceptualising treatment-resistant schizophrenia as a categorically different illness subtype to treatment-responsive schizophrenia. However, research is limited and confirmation will require replication and rigorously controlled studies with large sample sizes and prospective study designs.
DNA methylation and substance-use risk: a prospective, genome-wide study spanning gestation to adolescence
C A M Cecil,
E Walton,
R G Smith,
E Viding,
E J McCrory,
C L Relton,
M Suderman
+ 5 more
C A M Cecil,
E Walton,
R G Smith,
E Viding,
E J McCrory,
C L Relton,
M Suderman,
J-B Pingault,
W McArdle,
T R Gaunt,
J Mill,
E D Barker
Epigenetic processes have been implicated in addiction; yet, it remains unclear whether these represent a risk factor and/or a consequence of substance use. Here, we believe we conducted the first genome-wide, longitudinal study to investigate whether DNA methylation patterns in early life prospectively associate with substance use in adolescence. The sample comprised of 244 youth (51% female) from the Avon Longitudinal Study of Parents and Children (ALSPAC), with repeated assessments of DNA methylation (Illumina 450k array; cord blood at birth, whole blood at age 7) and substance use (tobacco, alcohol and cannabis use; age 14–18). We found that, at birth, epigenetic variation across a tightly interconnected genetic network (n=65 loci; q<0.05) associated with greater levels of substance use during adolescence, as well as an earlier age of onset amongst users. Associations were specific to the neonatal period and not observed at age 7. Key annotated genes included PACSIN1, NEUROD4 and NTRK2, implicated in neurodevelopmental processes. Several of the identified loci were associated with known methylation quantitative trait loci, and consequently likely to be under significant genetic control. Collectively, these 65 loci were also found to partially mediate the effect of prenatal maternal tobacco smoking on adolescent substance use. Together, findings lend novel insights into epigenetic correlates of substance use, highlight birth as a potentially sensitive window of biological vulnerability and provide preliminary evidence of an indirect epigenetic pathway linking prenatal tobacco exposure and adolescent substance use.
Blood methylomic signatures of presymptomatic dementia in elderly subjects with type 2 diabetes mellitus
Katie Lunnon, Rebecca G. Smith, Itzik Cooper, Lior Greenbaum, Jonathan Mill, Michal Schnaider Beeri
Katie Lunnon,
Rebecca G. Smith,
Itzik Cooper,
Lior Greenbaum,
Jonathan Mill,
Michal Schnaider Beeri
Due to an aging population, the incidence of dementia is steadily rising. The ability to identify early markers in blood, which appear before the onset of clinical symptoms is of considerable interest to allow early intervention, particularly in "high risk" groups such as those with type 2 diabetes. Here, we present a longitudinal study of genome-wide DNA methylation in whole blood from 18 elderly individuals with type 2 diabetes who developed presymptomatic dementia within an 18-month period following baseline assessment and 18 age-, sex-, and education-matched controls who maintained normal cognitive function. We identified a significant overlap in methylomic differences between groups at baseline and follow-up, with 8 CpG sites being consistently differentially methylated above our nominal significance threshold before symptoms at baseline and at 18 months follow up, after a diagnosis of presymptomatic dementia. Finally, we report a significant overlap between DNA methylation differences identified in converters, only after they develop symptoms of dementia, with differences at the same loci in blood samples from patients with clinically diagnosed Alzheimer's disease compared with unaffected control subjects.
Stress-induced gene expression and behavior are controlled by DNA methylation and methyl donor availability in the dentate gyrus
Emily A. Saunderson,
Helen Spiers,
Karen R. Mifsud,
Maria Gutierrez-Mecinas,
Alexandra F. Trollope,
Abeera Shaikh,
Jonathan Mill
+ 1 more
Emily A. Saunderson,
Helen Spiers,
Karen R. Mifsud,
Maria Gutierrez-Mecinas,
Alexandra F. Trollope,
Abeera Shaikh,
Jonathan Mill,
Johannes M. H. M. Reul
Proceedings of the National Academy of Sciences of the United States of America
Stressful events evoke long-term changes in behavioral responses; however, the underlying mechanisms in the brain are not well understood. Previous work has shown that epigenetic changes and immediate-early gene (IEG) induction in stress-activated dentate gyrus (DG) granule neurons play a crucial role in these behavioral responses. Here, we show that an acute stressful challenge [i.e., forced swimming (FS)] results in DNA demethylation at specific CpG (5'-cytosine-phosphate-guanine-3') sites close to the c-Fos (FBJ murine osteosarcoma viral oncogene homolog) transcriptional start site and within the gene promoter region of Egr-1 (early growth response protein 1) specifically in the DG. Administration of the (endogenous) methyl donor S-adenosyl methionine (SAM) did not affect CpG methylation and IEG gene expression at baseline. However, administration of SAM before the FS challenge resulted in an enhanced CpG methylation at the IEG loci and suppression of IEG induction specifically in the DG and an impaired behavioral immobility response 24 h later. The stressor also specifically increased the expression of the de novo DNA methyltransferase Dnmt3a [DNA (cytosine-5-)-methyltransferase 3 alpha] in this hippocampus region. Moreover, stress resulted in an increased association of Dnmt3a enzyme with the affected CpG loci within the IEG genes. No effects of SAM were observed on stress-evoked histone modifications, including H3S10p-K14ac (histone H3, phosphorylated serine 10 and acetylated lysine-14), H3K4me3 (histone H3, trimethylated lysine-4), H3K9me3 (histone H3, trimethylated lysine-9), and H3K27me3 (histone H3, trimethylated lysine-27). We conclude that the DNA methylation status of IEGs plays a crucial role in FS-induced IEG induction in DG granule neurons and associated behavioral responses. In addition, the concentration of available methyl donor, possibly in conjunction with Dnmt3a, is critical for the responsiveness of dentate neurons to environmental stimuli in terms of gene expression and behavior.
Methylomic profiling implicates cortical deregulation of ANK1 in Alzheimer's disease
Katie Lunnon,
Rebecca Smith,
Eilis Hannon,
Jager Philip L De,
Gyan Srivastava,
Manuela Volta,
Claire Troakes
+ 14 more
Katie Lunnon,
Rebecca Smith,
Eilis Hannon,
Jager Philip L De,
Gyan Srivastava,
Manuela Volta,
Claire Troakes,
Safa Al-Sarraj,
Joe Burrage,
Ruby Macdonald,
Daniel Condliffe,
Lorna W Harries,
Pavel Katsel,
Vahram Haroutunian,
Zachary Kaminsky,
Catharine Joachim,
John Powell,
Simon Lovestone,
David A Bennett,
Leonard C Schalkwyk,
Jonathan Mill
Alzheimer's disease (AD) is a chronic neurodegenerative disorder characterized by progressive neuropathology and cognitive decline. Here the authors describe an epigenome-wide association study (EWAS) of human post-mortem brain samples across multiple independent AD cohorts. They find consistent hypermethylation of the ANK1 gene associated with neuropathology.
Genome-wide Methylomic Analysis of Monozygotic Twins Discordant for Adolescent Depression
Emma L. Dempster, Chloe C.Y. Wong, Kathryn J. Lester, Joe Burrage, Alice M. Gregory, Jonathan Mill, Thalia C. Eley
Emma L. Dempster,
Chloe C.Y. Wong,
Kathryn J. Lester,
Joe Burrage,
Alice M. Gregory,
Jonathan Mill,
Thalia C. Eley
BACKGROUND: Adolescent depression is a common neuropsychiatric disorder that often continues into adulthood and is associated with a wide range of poor outcomes including suicide. Although numerous studies have looked at genetic markers associated with depression, the role of epigenetic variation remains relatively unexplored.
METHODS: Monozygotic (MZ) twins were selected from an adolescent twin study designed to investigate the interplay of genetic and environmental factors in the development of emotional and behavioral difficulties. There were 18 pairs of MZ twins identified in which one member scored consistently higher (group mean within the clinically significant range) on self-rated depression than the other. We assessed genome-wide patterns of DNA methylation in twin buccal cell DNA using the Infinium HumanMethylation450 BeadChip from Illumina. Quality control and data preprocessing was undertaken using the wateRmelon package. Differentially methylated probes (DMPs) were identified using an analysis strategy taking into account both the significance and the magnitude of DNA methylation differences. The top differentially methylated DMP was successfully validated by bisulfite-pyrosequencing, and identified DMPs were tested in postmortem brain samples obtained from patients with major depressive disorder (n = 14) and matched control subjects (n = 15).
RESULTS: Two reproducible depression-associated DMPs were identified, including the top-ranked DMP that was located within STK32C, which encodes a serine/threonine kinase, of unknown function.
CONCLUSIONS: Our data indicate that DNA methylation differences are apparent in MZ twins discordant for adolescent depression and that some of the disease-associated variation observed in buccal cell DNA is mirrored in adult brain tissue obtained from individuals with clinical depression.
Alzheimer's disease susceptibility variants in the MS4A6A gene are associated with altered levels of MS4A6A expression in blood
Petroula Proitsi,
Sang Hyuck Lee,
Katie Lunnon,
Aoife Keohane,
John Powell,
Claire Troakes,
Safa Al-Sarraj
+ 9 more
Petroula Proitsi,
Sang Hyuck Lee,
Katie Lunnon,
Aoife Keohane,
John Powell,
Claire Troakes,
Safa Al-Sarraj,
Simon Furney,
Hilkka Soininen,
Iwona Kłoszewska,
Patrizia Mecocci,
Magda Tsolaki,
Bruno Vellas,
Simon Lovestone,
Angela Hodges,
AddNeuroMed Consortium
An increased risk of developing Alzheimer's disease (AD) has previously been found to be associated with variants at the MS4A6A locus. We sought to identify which genes and transcripts in this region have altered expression in AD and mild cognitive impairment (MCI) and are influenced by the AD risk variant(s), as a first step to understanding the molecular basis of AD susceptibility at this locus. Common variants located within highly expressed MS4A6A transcripts were significantly associated with AD and MS4A6A expression levels in blood from MCI and AD subjects (p < 0.05, rs610932, rs7232, rs583791). More copies of the protective (minor) allele were associated with lower MS4A6A expression of each transcript (e.g., p = 0.019; rs610932-total MS4A6A). Furthermore, in heterozygous AD subjects, relative expression of the protective allele of V4-MS4A6A transcripts was lower (p < 0.008). Irrespective of genotype, MS4A6A transcripts were increased in blood from people with AD (p < 0.003), whereas lower expression of full length V1-MS4A6A (p = 0.002) and higher expression of V4-MS4A6A (p = 1.8 × 10(-4)) were observed in MCI, relative to elderly controls. The association between genotype and expression was less consistent in brain, although BA9 did have a similar genotype association with V4-MS4A6A transcripts as in blood. MS4A6A transcripts were widely expressed in tissues and cells, with the exception of V4-MS4A6A, which was not expressed in neuronal cells. Together these results suggest that high levels of MS4A6A in emerging AD pathology are detrimental. Persons with MCI may lower MS4A6A expression to minimize detrimental disease associated MS4A6A activity. However, those with the susceptibility allele appear unable to decrease expression sufficiently, which may explain their increased risk for developing AD. Inhibiting MS4A6A may therefore promote a more neuroprotective phenotype, although further work is needed to establish whether this is the case.
ABCA7 p.G215S as potential protective factor for Alzheimer's disease
Celeste Sassi,
Michael A. Nalls,
Perry G. Ridge,
Jesse R. Gibbs,
Jinhui Ding,
Michelle K. Lupton,
Claire Troakes
+ 44 more
Celeste Sassi,
Michael A. Nalls,
Perry G. Ridge,
Jesse R. Gibbs,
Jinhui Ding,
Michelle K. Lupton,
Claire Troakes,
Katie Lunnon,
Safa Al-Sarraj,
Kristelle S. Brown,
Christopher Medway,
Naomi Clement,
Jenny Lord,
James Turton,
Jose Bras,
Maria R. Almeida,
ARUK Consortium,
Peter Passmore,
David Craig,
Janet Johnston,
Bernadette McGuinness,
Stephen Todd,
Reinhard Heun,
Heike Kölsch,
Patrick G. Kehoe,
Emma R.L.C. Vardy,
Nigel M. Hooper,
David M. Mann,
Stuart Pickering-Brown,
Kristelle Brown,
James Lowe,
Kevin Morgan,
A. David Smith,
Gordon Wilcock,
Donald Warden,
Clive Holmes,
Henne Holstege,
Eva Louwersheimer,
der Flier Wiesje M. van,
Philip Scheltens,
Swieten John C. Van,
Isabel Santana,
Catarina Oliveira,
Kevin Morgan,
John F. Powell,
John S. Kauwe,
Carlos Cruchaga,
Alison M. Goate,
Andrew B. Singleton,
Rita Guerreiro,
John Hardy
Genome-wide association studies (GWASs) have been effective approaches to dissect common genetic variability underlying complex diseases in a systematic and unbiased way. Recently, GWASs have led to the discovery of over 20 susceptibility loci for Alzheimer's disease (AD). Despite the evidence showing the contribution of these loci to AD pathogenesis, their genetic architecture has not been extensively investigated, leaving the possibility that low frequency and rare coding variants may also occur and contribute to the risk of disease. We have used exome and genome sequencing data to analyze the single independent and joint effect of rare and low-frequency protein coding variants in 9 AD GWAS loci with the strongest effect sizes after APOE (BIN1, CLU, CR1, PICALM, MS4A6A, ABCA7, EPHA1, CD33, and CD2AP) in a cohort of 332 sporadic AD cases and 676 elderly controls of British and North-American ancestry. We identified coding variability in ABCA7 as contributing to AD risk. This locus harbors a low-frequency coding variant (p.G215S, rs72973581, minor allele frequency = 4.3%) conferring a modest but statistically significant protection against AD (p-value = 0.024, odds ratio = 0.57, 95% confidence interval = 0.41-0.80). Notably, our results are not driven by an enrichment of loss of function variants in ABCA7, recently reported as main pathogenic factor underlying AD risk at this locus. In summary, our study confirms the role of ABCA7 in AD and provides new insights that should address functional studies.
Genetic variation at 16q24.2 is associated with small vessel stroke
Matthew Traylor,
Rainer Malik,
Mike A. Nalls,
Ioana Cotlarciuc,
Farid Radmanesh,
Gudmar Thorleifsson,
Ken B. Hanscombe
+ 62 more
Matthew Traylor,
Rainer Malik,
Mike A. Nalls,
Ioana Cotlarciuc,
Farid Radmanesh,
Gudmar Thorleifsson,
Ken B. Hanscombe,
Carl Langefeld,
Danish Saleheen,
Natalia S. Rost,
Idil Yet,
Tim D. Spector,
Jordana T. Bell,
Eilis Hannon,
Jonathan Mill,
Ganesh Chauhan,
Stephanie Debette,
Joshua C. Bis,
W.T. Longstreth,
M. Arfan Ikram,
Lenore J. Launer,
Sudha Seshadri,
Young Lacunar DNA Study METASTROKE,
Monica Anne Hamilton‐Bruce,
Jordi Jimenez‐Conde,
John W. Cole,
Reinhold Schmidt,
Agnieszka Słowik,
Robin Lemmens,
Arne Lindgren,
Olle Melander,
Raji P. Grewal,
Ralph L. Sacco,
Tatjana Rundek,
Kathryn Rexrode,
Donna K. Arnett,
Julie A. Johnson,
Oscar R. Benavente,
Sylvia Wasssertheil‐Smoller,
Jin‐Moo Lee,
Sara L. Pulit,
Quenna Wong,
Stephen S. Rich,
Bakker Paul I.W. de,
Patrick F. McArdle,
Daniel Woo,
Christopher D. Anderson,
Huichun Xu,
Laura Heitsch,
Myriam Fornage,
Christina Jern,
Kari Stefansson,
Unnur Thorsteinsdottir,
Solveig Gretarsdottir,
Cathryn M. Lewis,
Pankaj Sharma,
Cathie L.M. Sudlow,
Peter M. Rothwell,
Giorgio B. Boncoraglio,
Vincent Thijs,
Chris Levi,
James F. Meschia,
Jonathan Rosand,
Steven J. Kittner,
Braxton D. Mitchell,
Martin Dichgans,
Bradford B. Worrall,
Hugh S. Markus,
on behalf of the International Stroke Genetics Consortium
OBJECTIVE: Genome-wide association studies (GWAS) have been successful at identifying associations with stroke and stroke subtypes, but have not yet identified any associations solely with small vessel stroke (SVS). SVS comprises one quarter of all ischemic stroke and is a major manifestation of cerebral small vessel disease, the primary cause of vascular cognitive impairment. Studies across neurological traits have shown that younger-onset cases have an increased genetic burden. We leveraged this increased genetic burden by performing an age-at-onset informed GWAS meta-analysis, including a large younger-onset SVS population, to identify novel associations with stroke.
METHODS: We used a three-stage age-at-onset informed GWAS to identify novel genetic variants associated with stroke. On identifying a novel locus associated with SVS, we assessed its influence on other small vessel disease phenotypes, as well as on messenger RNA (mRNA) expression of nearby genes, and on DNA methylation of nearby CpG sites in whole blood and in the fetal brain.
RESULTS: We identified an association with SVS in 4,203 cases and 50,728 controls on chromosome 16q24.2 (odds ratio [OR; 95% confidence interval {CI}] = 1.16 [1.10-1.22]; p = 3.2 × 10-9 ). The lead single-nucleotide polymorphism (rs12445022) was also associated with cerebral white matter hyperintensities (OR [95% CI] = 1.10 [1.05-1.16]; p = 5.3 × 10-5 ; N = 3,670), but not intracerebral hemorrhage (OR [95% CI] = 0.97 [0.84-1.12]; p = 0.71; 1,545 cases, 1,481 controls). rs12445022 is associated with mRNA expression of ZCCHC14 in arterial tissues (p = 9.4 × 10-7 ) and DNA methylation at probe cg16596957 in whole blood (p = 5.3 × 10-6 ).
INTERPRETATION: 16q24.2 is associated with SVS. Associations of the locus with expression of ZCCHC14 and DNA methylation suggest the locus acts through changes to regulatory elements. Ann Neurol 2017;81:383-394.
Elucidating novel dysfunctional pathways in Alzheimer's disease by integrating loci identified in genetic and epigenetic studies
Adam R. Smith, Jonathan Mill, Rebecca G. Smith, Katie Lunnon
Adam R. Smith,
Jonathan Mill,
Rebecca G. Smith,
Katie Lunnon
Alzheimer's disease is a complex neurodegenerative disorder. A large number of genome-wide association studies have been performed, which have been supplemented more recently by the first epigenome-wide association studies, leading to the identification of a number of novel loci altered in disease. Twin studies have shown monozygotic twin discordance for Alzheimer's disease (Gatz et al., 2006), leading to the conclusion that a combination of genetic and epigenetic mechanisms is likely to be involved in disease etiology (Lunnon & Mill, 2013). This review focuses on identifying overlapping pathways between published genome-wide association studies and epigenome-wide association studies, highlighting dysfunctional synaptic, lipid metabolism, plasma membrane/cytoskeleton, mitochondrial, and immune cell activation pathways. Identifying common pathways altered in genetic and epigenetic studies will aid our understanding of disease mechanisms and identify potential novel targets for pharmacological intervention.
Measuring adolescents' exposure to victimization: The Environmental Risk (E-Risk) Longitudinal Twin Study
Helen L. Fisher,
Avshalom Caspi,
Terrie E. Moffitt,
Jasmin Wertz,
Rebecca Gray,
Joanne Newbury,
Antony Ambler
+ 7 more
Helen L. Fisher,
Avshalom Caspi,
Terrie E. Moffitt,
Jasmin Wertz,
Rebecca Gray,
Joanne Newbury,
Antony Ambler,
Helena Zavos,
Andrea Danese,
Jonathan Mill,
Candice L. Odgers,
Carmine Pariante,
Chloe C. Y. Wong,
Louise Arseneault
This paper presents multilevel findings on adolescents' victimization exposure from a large longitudinal cohort of twins. Data were obtained from the Environmental Risk (E-Risk) Longitudinal Twin Study, an epidemiological study of 2,232 children (1,116 twin pairs) followed to 18 years of age (with 93% retention). To assess adolescent victimization, we combined best practices in survey research on victimization with optimal approaches to measuring life stress and traumatic experiences, and introduce a reliable system for coding severity of victimization. One in three children experienced at least one type of severe victimization during adolescence (crime victimization, peer/sibling victimization, Internet/mobile phone victimization, sexual victimization, family violence, maltreatment, or neglect), and most types of victimization were more prevalent among children from low socioeconomic backgrounds. Exposure to multiple victimization types was common, as was revictimization; over half of those physically maltreated in childhood were also exposed to severe physical violence in adolescence. Biometric twin analyses revealed that environmental factors had the greatest influence on most types of victimization, while severe physical maltreatment from caregivers during adolescence was predominantly influenced by heritable factors. The findings from this study showcase how distinct levels of victimization measurement can be harmonized in large-scale studies of health and development.
Long-Term Effects of Gestational Nicotine Exposure and Food-Restriction on Gene Expression in the Striatum of Adolescent Rats
Nicholas E. Ilott,
Tomasz Schneider,
Jonathan Mill,
Leonard Schalkwyk,
Giovana Brolese,
Lisiane Bizarro,
Ian P. Stolerman
+ 2 more
Nicholas E. Ilott,
Tomasz Schneider,
Jonathan Mill,
Leonard Schalkwyk,
Giovana Brolese,
Lisiane Bizarro,
Ian P. Stolerman,
Emma Dempster,
Philip Asherson
Gestational exposure to environmental toxins such as nicotine may result in detectable gene expression changes in later life. To investigate the direct toxic effects of prenatal nicotine exposure on later brain development, we have used transcriptomic analysis of striatal samples to identify gene expression differences between adolescent Lister Hooded rats exposed to nicotine in utero and controls. Using an additional group of animals matched for the reduced food intake experienced in the nicotine group, we were also able to assess the impact of imposed food-restriction on gene expression profiles. We found little evidence for a role of gestational nicotine exposure on altered gene expression in the striatum of adolescent offspring at a significance level of p<0.01 and |log2 fold change >0.5|, although we cannot exclude the possibility of nicotine-induced changes in other brain regions, or at other time points. We did, however, find marked gene expression differences in response to imposed food-restriction. Food-restriction resulted in significant group differences for a number of immediate early genes (IEGs) including Fos, Fosb, Fosl2, Arc, Junb, Nr4a1 and Nr4a3. These genes are associated with stress response pathways and therefore may reflect long-term effects of nutritional deprivation on the development of the stress system.
Integrated Genetic and Epigenetic Analysis Identifies Haplotype-Specific Methylation in the FTO Type 2 Diabetes and Obesity Susceptibility Locus
Christopher G. Bell,
Sarah Finer,
Cecilia M. Lindgren,
Gareth A. Wilson,
Vardhman K. Rakyan,
Andrew E. Teschendorff,
Pelin Akan
+ 12 more
Christopher G. Bell,
Sarah Finer,
Cecilia M. Lindgren,
Gareth A. Wilson,
Vardhman K. Rakyan,
Andrew E. Teschendorff,
Pelin Akan,
Elia Stupka,
Thomas A. Down,
Inga Prokopenko,
Ian M. Morison,
Jonathan Mill,
Ruth Pidsley,
,
Panos Deloukas,
Timothy M. Frayling,
Andrew T. Hattersley,
Mark I. McCarthy,
Stephan Beck
Graham A. Hitman
Recent multi-dimensional approaches to the study of complex disease have revealed powerful insights into how genetic and epigenetic factors may underlie their aetiopathogenesis. We examined genotype-epigenotype interactions in the context of Type 2 Diabetes (T2D), focussing on known regions of genomic susceptibility. We assayed DNA methylation in 60 females, stratified according to disease susceptibility haplotype using previously identified association loci. CpG methylation was assessed using methylated DNA immunoprecipitation on a targeted array (MeDIP-chip) and absolute methylation values were estimated using a Bayesian algorithm (BATMAN). Absolute methylation levels were quantified across LD blocks, and we identified increased DNA methylation on the FTO obesity susceptibility haplotype, tagged by the rs8050136 risk allele A (p = 9.40×10(-4), permutation p = 1.0×10(-3)). Further analysis across the 46 kb LD block using sliding windows localised the most significant difference to be within a 7.7 kb region (p = 1.13×10(-7)). Sequence level analysis, followed by pyrosequencing validation, revealed that the methylation difference was driven by the co-ordinated phase of CpG-creating SNPs across the risk haplotype. This 7.7 kb region of haplotype-specific methylation (HSM), encapsulates a Highly Conserved Non-Coding Element (HCNE) that has previously been validated as a long-range enhancer, supported by the histone H3K4me1 enhancer signature. This study demonstrates that integration of Genome-Wide Association (GWA) SNP and epigenomic DNA methylation data can identify potential novel genotype-epigenotype interactions within disease-associated loci, thus providing a novel route to aid unravelling common complex diseases.
The mitochondrial epigenome: a role in Alzheimer's disease?
Considerable evidence suggests that mitochondrial dysfunction occurs early in Alzheimer's disease, both in affected brain regions and in leukocytes, potentially precipitating neurodegeneration through increased oxidative stress. Epigenetic processes are emerging as a dynamic mechanism through which environmental signals may contribute to cellular changes, leading to neuropathology and disease. Until recently, little attention was given to the mitochondrial epigenome itself, as preliminary studies indicated an absence of DNA modifications. However, recent research has demonstrated that epigenetic changes to the mitochondrial genome do occur, potentially playing an important role in several disorders characterized by mitochondrial dysfunction. This review explores the potential role of mitochondrial epigenetic dysfunction in Alzheimer's disease etiology and discusses some technical issues pertinent to the study of these processes.
Differential methylation of the TRPA1 promoter in pain sensitivity
J.T. Bell,
A.K. Loomis,
L.M. Butcher,
F. Gao,
B. Zhang,
C.L. Hyde,
J. Sun
+ 15 more
J.T. Bell,
A.K. Loomis,
L.M. Butcher,
F. Gao,
B. Zhang,
C.L. Hyde,
J. Sun,
H. Wu,
K. Ward,
J. Harris,
S. Scollen,
M.N. Davies,
L.C. Schalkwyk,
J. Mill,
F.M.K. Williams,
N. Li,
P. Deloukas,
S. Beck,
S.B. McMahon,
J. Wang,
S.L. John,
T.D. Spector
Chronic pain is a global public health problem, but the underlying molecular mechanisms are not fully understood. Here we examine genome-wide DNA methylation, first in 50 identical twins discordant for heat pain sensitivity and then in 50 further unrelated individuals. Whole-blood DNA methylation was characterized at 5.2 million loci by MeDIP sequencing and assessed longitudinally to identify differentially methylated regions associated with high or low pain sensitivity (pain DMRs). Nine meta-analysis pain DMRs show robust evidence for association (false discovery rate 5%) with the strongest signal in the pain gene TRPA1 (P=1.2 × 10−13). Several pain DMRs show longitudinal stability consistent with susceptibility effects, have similar methylation levels in the brain and altered expression in the skin. Our approach identifies epigenetic changes in both novel and established candidate genes that provide molecular insights into pain and may generalize to other complex traits.
Methylomic analysis of salivary DNA in childhood ADHD identifies altered DNA methylation in VIPR2
Beth Wilmot, Rebecca Fry, Lisa Smeester, Erica D Musser, Jonathan Mill, Joel T Nigg
Beth Wilmot,
Rebecca Fry,
Lisa Smeester,
Erica D Musser,
Jonathan Mill,
Joel T Nigg
BACKGROUND: Peripheral epigenetic marks hold promise for understanding psychiatric illness and may represent fingerprints of gene-environment interactions. We conducted an initial examination of CpG methylation variation in children with or without attention-deficit/hyperactivity disorder (ADHD).
METHODS: Children age 7-12 were recruited, screened, evaluated and assigned to ADHD or non-ADHD groups by defined research criteria. Two independent age-matched samples were examined, a discovery set (n = 92, all boys, half control, half ADHD) and a confirmation set (n = 20, half ADHD, all boys). 5-methylcytosine levels were quantified in salivary DNA using the Illumina 450 K HumanMethylation array. Genes for which multiple probes were nominally significant and had a beta difference of at least 2% were evaluated for biological relevance and prioritized for confirmation and sequence validation. Gene pathways were explored and described.
RESULTS: Two genes met the criteria for confirmation testing, VIPR2 and MYT1L; both had multiple probes meeting cutoffs and strong biological relevance. Probes on VIPR2 passed FDR correction in the confirmation set and were confirmed through bisulfite sequencing. Enrichment analysis suggested involvement of gene sets or pathways related to inflammatory processes and modulation of monoamine and cholinergic neurotransmission.
CONCLUSIONS: Although it is unknown to what extent CpG methylation seen in peripheral tissue reflect transcriptomic changes in the brain, these initial results indicate that peripheral DNA methylation markers in ADHD may be promising and suggest targeted hypotheses for future study in larger samples.
Age-associated changes in DNA methylation across multiple tissues in an inbred mouse model
Helen Spiers, Eilis Hannon, Sara Wells, Brenda Williams, Cathy Fernandes, Jonathan Mill
Helen Spiers,
Eilis Hannon,
Sara Wells,
Brenda Williams,
Cathy Fernandes,
Jonathan Mill
Epigenetic disruption has been implicated in many diseases of aging, and age-associated DNA methylation changes at specific genomic loci in humans are strongly correlated with chronological age. The aim of this study was to explore the specificity of selected age-associated differentially methylated positions (aDMPs) identified in human epidemiological studies by quantifying DNA methylation across multiple tissues in homologous regions of the murine genome. We selected four high-confidence aDMPs (located in the vicinity of the ELOVL2, GLRA1, MYOD1 and PDE4C genes) and quantified DNA methylation across these regions in four tissues (blood, lung, cerebellum and hippocampus) from male and female C57BL/6J mice, ranging in age from fetal (embryonic day 17) to 630 days. We observed tissue-specific age-associated changes in DNA methylation that was directionally consistent with those observed in humans. These findings lend further support to the notion that changes in DNA methylation are associated with chronological age and suggest that these processes are often conserved across tissues and between mammalian species. Our data highlight the relevance of utilizing model systems, in which environmental and genetic influences can be carefully controlled, for the further study of these phenomena.
Epigenetic studies in Alzheimer's disease: Current findings, caveats, and considerations for future studies
Katie Lunnon, Jonathan Mill
Katie Lunnon,
Jonathan Mill
American Journal of Medical Genetics Part B Neuropsychiatric Genetics
Alzheimer's disease (AD) is a sporadic, chronic neurodegenerative disease, usually occurring late in life. The last decade has witnessed tremendous advances in our understanding about the genetic basis of AD, but a large amount of the variance in disease risk remains to be explained. Epigenetic mechanisms, which developmentally regulate gene expression via modifications to DNA, histone proteins, and chromatin, have been hypothesized to play a role in other complex neurobiological diseases, and studies to identify genome-wide epigenetic changes in AD are currently under way. However, the simple brute-force approach that has been successfully employed in genome-wide association studies is unlikely to be successful in epigenome-wide association studies of neurodegeneration. A more academic approach to understanding the role of epigenetic variation in AD is required, with careful consideration of study design, methodological approaches, tissue-specificity, and causal inference. In this article, we review the empirical literature supporting a role for epigenetic processes in AD, and discuss important considerations and future directions for this new and emerging field of research.
Variation in 5-hydroxymethylcytosine across human cortex and cerebellum
Katie Lunnon,
Eilis Hannon,
Rebecca G. Smith,
Emma Dempster,
Chloe Wong,
Joe Burrage,
Claire Troakes
+ 4 more
Katie Lunnon,
Eilis Hannon,
Rebecca G. Smith,
Emma Dempster,
Chloe Wong,
Joe Burrage,
Claire Troakes,
Safa Al-Sarraj,
Agnieszka Kepa,
Leonard Schalkwyk,
Jonathan Mill
BackgroundThe most widely utilized approaches for quantifying DNA methylation involve the treatment of genomic DNA with sodium bisulfite; however, this method cannot distinguish between 5-methylcytosine (5mC) and 5-hydroxymethylcytosine (5hmC). Previous studies have shown that 5hmC is enriched in the brain, although little is known about its genomic distribution and how it differs between anatomical regions and individuals. In this study, we combine oxidative bisulfite (oxBS) treatment with the Illumina Infinium 450K BeadArray to quantify genome-wide patterns of 5hmC in two distinct anatomical regions of the brain from multiple individuals.ResultsWe identify 37,145 and 65,563 sites passing our threshold for detectable 5hmC in the prefrontal cortex and cerebellum respectively, with 23,445 loci common across both brain regions. Distinct patterns of 5hmC are identified in each brain region, with notable differences in the genomic location of the most hydroxymethylated loci between these brain regions. Tissue-specific patterns of 5hmC are subsequently confirmed in an independent set of prefrontal cortex and cerebellum samples.ConclusionsThis study represents the first systematic analysis of 5hmC in the human brain, identifying tissue-specific hydroxymethylated positions and genomic regions characterized by inter-individual variation in DNA hydroxymethylation. This study demonstrates the utility of combining oxBS-treatment with the Illumina 450k methylation array to systematically quantify 5hmC across the genome and the potential utility of this approach for epigenomic studies of brain disorders.
Epigenetic signatures of childhood abuse and neglect: Implications for psychiatric vulnerability
Charlotte A.M. Cecil, Rebecca G. Smith, Esther Walton, Jonathan Mill, Eamon J. McCrory, Essi Viding
Charlotte A.M. Cecil,
Rebecca G. Smith,
Esther Walton,
Jonathan Mill,
Eamon J. McCrory,
Essi Viding
Childhood maltreatment is a key risk factor for poor mental and physical health. Recently, variation in epigenetic processes, such as DNA methylation, has emerged as a potential pathway mediating this association; yet, the extent to which different forms of maltreatment may be characterized by unique vs shared epigenetic signatures is currently unknown. In this study, we quantified DNA methylation across the genome in buccal epithelial cell samples from a high-risk sample of inner-city youth (n = 124; age = 16-24; 53% female), 68% of whom reported experiencing at least one form of maltreatment while growing up. Our analyses aimed to identify methylomic variation associated with exposure to five major types of childhood maltreatment. We found that: (i) maltreatment types differ in the extent to which they associate with methylomic variation, with physical exposures showing the strongest associations; (ii) many of the identified loci are annotated to genes previously implicated in stress-related outcomes, including psychiatric and physical disorders (e.g. GABBR1, GRIN2D, CACNA2D4, PSEN2); and (iii) based on gene ontology analyses, maltreatment types not only show unique methylation patterns enriched for specific biological processes (e.g. physical abuse and cardiovascular function), but also share a 'common' epigenetic signature enriched for biological processes related to neural development and organismal growth. A stringent set of sensitivity analyses were also run to identify high-confidence associations. Together, findings lend novel insights into epigenetic signatures of childhood abuse and neglect, point to novel potential biomarkers for future investigation and support a molecular link between maltreatment and poor health outcomes. Nevertheless, it will be important in future to replicate findings, as the use of cross-sectional data and high rates of polyvictimization in our study make it difficult to fully disentangle the shared vs unique epigenetic signatures of maltreatment types. Furthermore, studies will be needed to test the role of potential moderators in the identified associations, including age of onset and chronicity of maltreatment exposure.
DNA Modification Study of Major Depressive Disorder: Beyond Locus-by-Locus Comparisons
Gabriel Oh,
Sun-Chong Wang,
Mrinal Pal,
Zheng Fei Chen,
Tarang Khare,
Mamoru Tochigi,
Catherine Ng
+ 20 more
Gabriel Oh,
Sun-Chong Wang,
Mrinal Pal,
Zheng Fei Chen,
Tarang Khare,
Mamoru Tochigi,
Catherine Ng,
Yeqing A. Yang,
Andrew Kwan,
Zachary A. Kaminsky,
Jonathan Mill,
Cerisse Gunasinghe,
Jennifer L. Tackett,
Irving I. Gottesman,
Gonneke Willemsen,
Geus Eco J.C. de,
Jacqueline M. Vink,
P. Eline Slagboom,
Naomi R. Wray,
Andrew C. Heath,
Grant W. Montgomery,
Gustavo Turecki,
Nicholas G. Martin,
Dorret I. Boomsma,
Peter McGuffin,
Rafal Kustra,
Art Petronis
BACKGROUND: Major depressive disorder (MDD) exhibits numerous clinical and molecular features that are consistent with putative epigenetic misregulation. Despite growing interest in epigenetic studies of psychiatric diseases, the methodologies guiding such studies have not been well defined.
METHODS: We performed DNA modification analysis in white blood cells from monozygotic twins discordant for MDD, in brain prefrontal cortex, and germline (sperm) samples from affected individuals and control subjects (total N = 304) using 8.1K CpG island microarrays and fine mapping. In addition to the traditional locus-by-locus comparisons, we explored the potential of new analytical approaches in epigenomic studies.
RESULTS: In the microarray experiment, we detected a number of nominally significant DNA modification differences in MDD and validated selected targets using bisulfite pyrosequencing. Some MDD epigenetic changes, however, overlapped across brain, blood, and sperm more often than expected by chance. We also demonstrated that stratification for disease severity and age may increase the statistical power of epimutation detection. Finally, a series of new analytical approaches, such as DNA modification networks and machine-learning algorithms using binary and quantitative depression phenotypes, provided additional insights on the epigenetic contributions to MDD.
CONCLUSIONS: Mapping epigenetic differences in MDD (and other psychiatric diseases) is a complex task. However, combining traditional and innovative analytical strategies may lead to identification of disease-specific etiopathogenic epimutations.
Methylomic markers of persistent childhood asthma: a longitudinal study of asthma-discordant monozygotic twins
Therese M. Murphy,
Chloe C. Y. Wong,
Louise Arseneault,
Joe Burrage,
Ruby Macdonald,
Eilis Hannon,
Helen L. Fisher
+ 4 more
Therese M. Murphy,
Chloe C. Y. Wong,
Louise Arseneault,
Joe Burrage,
Ruby Macdonald,
Eilis Hannon,
Helen L. Fisher,
Antony Ambler,
Terrie E. Moffitt,
Avshalom Caspi,
Jonathan Mill
BackgroundAsthma is the most common chronic inflammatory disorder in children. The aetiology of asthma pathology is complex and highly heterogeneous, involving the interplay between genetic and environmental risk factors that is hypothesized to involve epigenetic processes. Our aim was to explore whether methylomic variation in early childhood is associated with discordance for asthma symptoms within monozygotic (MZ) twin pairs recruited from the Environmental Risk (E-Risk) longitudinal twin study. We also aimed to identify differences in DNA methylation that are associated with asthma that develops in childhood and persists into early adulthood as these may represent useful prognostic biomarkers.ResultsWe examined genome-wide patterns of DNA methylation in buccal cell samples collected from 37 MZ twin pairs discordant for asthma at age 10. DNA methylation at individual CpG sites demonstrated significant variability within discordant MZ twin pairs with the top-ranked nominally significant differentially methylated position (DMP) located in the HGSNAT gene. We stratified our analysis by assessing DNA methylation differences in a sub-group of MZ twin pairs who remained persistently discordant for asthma at age 18. The top-ranked nominally significant DMP associated with persisting asthma is located in the vicinity of the HLX gene, which has been previously implicated in childhood asthma.ConclusionsWe identified DNA methylation differences associated with childhood asthma in peripheral DNA samples from discordant MZ twin pairs. Our data suggest that differences in DNA methylation associated with childhood asthma which persists into early adulthood are distinct from those associated with asthma which remits.
P3‐087: Gene Expression of ABCA7 Dysregulated in Peripheral Blood is Associated With Decreased Metabolic Activity in Hippocampus
Kwangsik Nho,
Sungeun Kim,
Emrin Horgousluoglu,
Shannon L. Risacher,
Liana G. Apostolova,
Kuang Lin,
Aoife Keohane
+ 20 more
Kwangsik Nho,
Sungeun Kim,
Emrin Horgousluoglu,
Shannon L. Risacher,
Liana G. Apostolova,
Kuang Lin,
Aoife Keohane,
Katie Lunnon,
Angela Hodges,
Mariet Allen,
Xue Wang,
Jeremy D. Burgess,
Nilufer Ertekin-Taner,
Ronald C. Petersen,
Holly Soares,
Parul Singh,
Lisu Wang,
Zhenhao Qi,
Aiqing He,
Isaac Neuhaus,
Vishal Patel,
Tatiana M. Foroud,
Kelley Faber,
Simon Lovestone,
Andrew Simmons,
Michael W. Weiner,
Andrew J. Saykin
Mapping epigenetic changes to the host cell genome induced by Burkholderia pseudomallei reveals pathogen-specific and pathogen-generic signatures of infection
Deniz Cizmeci,
Emma L. Dempster,
Olivia L. Champion,
Sariqa Wagley,
Ozgur E. Akman,
Joann L. Prior,
Orkun S. Soyer
+ 2 more
Deniz Cizmeci,
Emma L. Dempster,
Olivia L. Champion,
Sariqa Wagley,
Ozgur E. Akman,
Joann L. Prior,
Orkun S. Soyer,
Jonathan Mill,
Richard W. Titball
The potential for epigenetic changes in host cells following microbial infection has been widely suggested, but few examples have been reported. We assessed genome-wide patterns of DNA methylation in human macrophage-like U937 cells following infection with Burkholderia pseudomallei, an intracellular bacterial pathogen and the causative agent of human melioidosis. Our analyses revealed significant changes in host cell DNA methylation, at multiple CpG sites in the host cell genome, following infection. Infection induced differentially methylated probes (iDMPs) showing the greatest changes in DNA methylation were found to be in the vicinity of genes involved in inflammatory responses, intracellular signalling, apoptosis and pathogen-induced signalling. A comparison of our data with reported methylome changes in cells infected with M. tuberculosis revealed commonality of differentially methylated genes, including genes involved in T cell responses (BCL11B, FOXO1, KIF13B, PAWR, SOX4, SYK), actin cytoskeleton organisation (ACTR3, CDC42BPA, DTNBP1, FERMT2, PRKCZ, RAC1) and cytokine production (FOXP1, IRF8, MR1). Overall our findings show that pathogenic-specific and pathogen-common changes in the methylome occur following infection.
Cross-region reduction in 5-hydroxymethylcytosine in Alzheimer's disease brain
Daniel Condliffe,
Andrew Wong,
Claire Troakes,
Petroula Proitsi,
Yogen Patel,
Leonidas Chouliaras,
Cathy Fernandes
+ 5 more
Daniel Condliffe,
Andrew Wong,
Claire Troakes,
Petroula Proitsi,
Yogen Patel,
Leonidas Chouliaras,
Cathy Fernandes,
Jonathan Cooper,
Simon Lovestone,
Leonard Schalkwyk,
Jonathan Mill,
Katie Lunnon
Epigenetic processes play a key role in the central nervous system and altered levels of 5-methylcytosine have been associated with a number of neurologic phenotypes, including Alzheimer's disease (AD). Recently, 3 additional cytosine modifications have been identified (5-hydroxymethylcytosine, 5-formylcytosine, and 5-carboxylcytosine), which are thought to be intermediate steps in the demethylation of 5-methylcytosine to unmodified cytosine. Little is known about the frequency of these modifications in the human brain during health or disease. In this study, we used immunofluorescence to confirm the presence of each modification in human brain and investigate their cross-tissue abundance in AD patients and elderly control samples. We identify a significant AD-associated decrease in global 5-hydroxymethylcytosine in entorhinal cortex and cerebellum, and differences in 5-formylcytosine levels between brain regions. Our study further implicates a role for epigenetic alterations in AD.
Epigenetics in health and disease: heralding the EWAS era
Epigenetic processes play a key role in orchestrating transcriptional regulation during development. The importance of DNA methylation in fetal brain development is highlighted by the dynamic expression of de novo DNA methyltransferases during the perinatal period and neurodevelopmental deficits associated with mutations in the methyl-CpG binding protein 2 (MECP2) gene. However, our knowledge about the temporal changes to the epigenome during fetal brain development has, to date, been limited. We quantified genome-wide patterns of DNA methylation at ∼ 400,000 sites in 179 human fetal brain samples (100 male, 79 female) spanning 23 to 184 d post-conception. We identified highly significant changes in DNA methylation across fetal brain development at >7% of sites, with an enrichment of loci becoming hypomethylated with fetal age. Sites associated with developmental changes in DNA methylation during fetal brain development were significantly underrepresented in promoter regulatory regions but significantly overrepresented in regions flanking CpG islands (shores and shelves) and gene bodies. Highly significant differences in DNA methylation were observed between males and females at a number of autosomal sites, with a small number of regions showing sex-specific DNA methylation trajectories across brain development. Weighted gene comethylation network analysis (WGCNA) revealed discrete modules of comethylated loci associated with fetal age that are significantly enriched for genes involved in neurodevelopmental processes. This is, to our knowledge, the most extensive study of DNA methylation across human fetal brain development to date, confirming the prenatal period as a time of considerable epigenomic plasticity.
Plasma proteins predict conversion to dementia from prodromal disease
Abdul Hye,
Joanna Riddoch‐Contreras,
Alison L. Baird,
Nicholas J. Ashton,
Chantal Bazenet,
Rufina Leung,
Eric Westman
+ 20 more
Abdul Hye,
Joanna Riddoch‐Contreras,
Alison L. Baird,
Nicholas J. Ashton,
Chantal Bazenet,
Rufina Leung,
Eric Westman,
Andrew Simmons,
Richard Dobson,
Martina Sattlecker,
Michelle Lupton,
Katie Lunnon,
Aoife Keohane,
Malcolm Ward,
Ian Pike,
Hans Dieter Zucht,
Danielle Pepin,
Wei Zheng,
Alan Tunnicliffe,
Jill Richardson,
Serge Gauthier,
Hilkka Soininen,
Iwona Kłoszewska,
Patrizia Mecocci,
Magda Tsolaki,
Bruno Vellas,
Simon Lovestone
BACKGROUND: The study aimed to validate previously discovered plasma biomarkers associated with AD, using a design based on imaging measures as surrogate for disease severity and assess their prognostic value in predicting conversion to dementia.
METHODS: Three multicenter cohorts of cognitively healthy elderly, mild cognitive impairment (MCI), and AD participants with standardized clinical assessments and structural neuroimaging measures were used. Twenty-six candidate proteins were quantified in 1148 subjects using multiplex (xMAP) assays.
RESULTS: Sixteen proteins correlated with disease severity and cognitive decline. Strongest associations were in the MCI group with a panel of 10 proteins predicting progression to AD (accuracy 87%, sensitivity 85%, and specificity 88%).
CONCLUSIONS: We have identified 10 plasma proteins strongly associated with disease severity and disease progression. Such markers may be useful for patient selection for clinical trials and assessment of patients with predisease subjective memory complaints.
Epigenetic Research in Neuropsychiatric Disorders: the “Tissue Issue”
Kelly M. Bakulski, Alycia Halladay, Valerie W. Hu, Jonathan Mill, M. Daniele Fallin
Kelly M. Bakulski,
Alycia Halladay,
Valerie W. Hu,
Jonathan Mill,
M. Daniele Fallin
Purpose of ReviewEvidence has linked neuropsychiatric disorders with epigenetic marks as either a biomarker of disease, biomarker of exposure, or mechanism of disease processes. Neuropsychiatric epidemiologic studies using either target brain tissue or surrogate blood tissue each have methodological challenges and distinct advantages.Recent findingsBrain tissue studies are challenged by small sample sizes of cases and controls, incomplete phenotyping, post-mortem timing, and cellular heterogeneity, but the use of a primary disease relevant tissue is critical. Blood-based studies have access to much larger sample sizes and more replication opportunities, as well as the potential for longitudinal measurements, both prior to onset and during the course of treatments. Yet, blood studies also are challenged by cell-type heterogeneity, and many question the validity of using peripheral tissues as a brain biomarker. Emerging evidence suggests that these limitations to blood-based epigenetic studies are surmountable, but confirmation in target tissue remains important.SummaryEpigenetic mechanisms have the potential to help elucidate biology connecting experiential risk factors with neuropsychiatric disease manifestation. Cross-tissue studies as well as advanced epidemiologic methods should be employed to more effectively conduct neuropsychiatric epigenetic research.
ISDN2014_0171: Dynamic and sex‐specific changes in DNA methylation during human fetal brain development
H. Spiers,
N.J. Bray,
E. Hannon,
L.C. Schalkwyk,
C.C. Wong,
R. Pidsley,
R.G. Smith
+ 1 more
H. Spiers,
N.J. Bray,
E. Hannon,
L.C. Schalkwyk,
C.C. Wong,
R. Pidsley,
R.G. Smith,
J. Mill
International Journal of Developmental Neuroscience
Alzheimer's disease: early alterations in brain DNA methylation at ANK1, BIN1, RHBDF2 and other loci
Jager Philip L De,
Gyan Srivastava,
Katie Lunnon,
Jeremy Burgess,
Leonard C Schalkwyk,
Lei Yu,
Matthew L Eaton
+ 22 more
Jager Philip L De,
Gyan Srivastava,
Katie Lunnon,
Jeremy Burgess,
Leonard C Schalkwyk,
Lei Yu,
Matthew L Eaton,
Brendan T Keenan,
Jason Ernst,
Cristin McCabe,
Anna Tang,
Towfique Raj,
Joseph Replogle,
Wendy Brodeur,
Stacey Gabriel,
High S Chai,
Curtis Younkin,
Steven G Younkin,
Fanggeng Zou,
Moshe Szyf,
Charles B Epstein,
Julie A Schneider,
Bradley E Bernstein,
Alex Meissner,
Nilufer Ertekin-Taner,
Lori B Chibnik,
Manolis Kellis,
Jonathan Mill,
David A Bennett
Aging can lead to cognitive decline associated with neural pathology and Alzheimer's disease (AD). Here the authors scan the methylation status of CpGs across the entire genome of brain samples from aged subjects in an epigenome-wide association study (EWAS). Several loci, including ANK1, were associated with AD pathology, gene expression and AD genetic risk networks.
A Pathway Based Classification Method for Analyzing Gene Expression for Alzheimer’s Disease Diagnosis
Nicola Voyle,
Aoife Keohane,
Stephen Newhouse,
Katie Lunnon,
Caroline Johnston,
Hilkka Soininen,
Iwona Kloszewska
+ 7 more
Nicola Voyle,
Aoife Keohane,
Stephen Newhouse,
Katie Lunnon,
Caroline Johnston,
Hilkka Soininen,
Iwona Kloszewska,
Patrizia Mecocci,
Magda Tsolaki,
Bruno Vellas,
Simon Lovestone,
Angela Hodges,
Steven Kiddle,
Richard JB. Dobson
BACKGROUND: Recent studies indicate that gene expression levels in blood may be able to differentiate subjects with Alzheimer's disease (AD) from normal elderly controls and mild cognitively impaired (MCI) subjects. However, there is limited replicability at the single marker level. A pathway-based interpretation of gene expression may prove more robust.
OBJECTIVES: This study aimed to investigate whether a case/control classification model built on pathway level data was more robust than a gene level model and may consequently perform better in test data. The study used two batches of gene expression data from the AddNeuroMed (ANM) and Dementia Case Registry (DCR) cohorts.
METHODS: Our study used Illumina Human HT-12 Expression BeadChips to collect gene expression from blood samples. Random forest modeling with recursive feature elimination was used to predict case/control status. Age and APOE ɛ4 status were used as covariates for all analysis.
RESULTS: Gene and pathway level models performed similarly to each other and to a model based on demographic information only.
CONCLUSIONS: Any potential increase in concordance from the novel pathway level approach used here has not lead to a greater predictive ability in these datasets. However, we have only tested one method for creating pathway level scores. Further, we have been able to benchmark pathways against genes in datasets that had been extensively harmonized. Further work should focus on the use of alternative methods for creating pathway level scores, in particular those that incorporate pathway topology, and the use of an endophenotype based approach.
IC‐P‐072: Gene Expression Of ABCA7 Dysregulated in Peripheral Blood is Associated With Decreased Metabolic Activity in Hippocampus
Kwangsik Nho,
Sungeun Kim,
Emrin Horgousluoglu,
Shannon L. Risacher,
Liana G. Apostolova,
Kuang Lin,
Aoife Keohane
+ 20 more
Kwangsik Nho,
Sungeun Kim,
Emrin Horgousluoglu,
Shannon L. Risacher,
Liana G. Apostolova,
Kuang Lin,
Aoife Keohane,
Katie Lunnon,
Angela Hodges,
Mariet Allen,
Xue Wang,
Jeremy D. Burgess,
Nilufer Ertekin-Taner,
Ronald C. Petersen,
Holly Soares,
Parul Singh,
Lisu Wang,
Zhenhao Qi,
Aiqing He,
Isaac Neuhaus,
Vishal Patel,
Tatiana M. Foroud,
Kelley Faber,
Simon Lovestone,
Andrew Simmons,
Michael W. Weiner,
Andrew J. Saykin
IC‐P‐074: Genome‐Wide Meta‐Analysis of Transcriptome Profiling Identifies Novel Dysregulated Genes Implicated in Alzheimer’s Disease
Kwangsik Nho,
Sungeun Kim,
Shannon L. Risacher,
Liana G. Apostolova,
Kuang Lin,
Aoife Keohane,
Katie Lunnon
+ 19 more
Kwangsik Nho,
Sungeun Kim,
Shannon L. Risacher,
Liana G. Apostolova,
Kuang Lin,
Aoife Keohane,
Katie Lunnon,
Angela Hodges,
Mariet Allen,
Xue Wang,
Jeremy D. Burgess,
Nilufer Ertekin-Taner,
Ronald C. Petersen,
Holly Soares,
Parul Singh,
Lisu Wang,
Zhenhao Qi,
Aiqing He,
Isaac Neuhaus,
Vishal Patel,
Tatiana M. Foroud,
Kelley Faber,
Simon Lovestone,
Andrew Simmons,
Michael W. Weiner,
Andrew J. Saykin
Methylation QTLs in the developing brain and their enrichment in schizophrenia risk loci
Eilis Hannon,
Helen Spiers,
Joana Viana,
Ruth Pidsley,
Joe Burrage,
Therese M Murphy,
Claire Troakes
+ 5 more
Eilis Hannon,
Helen Spiers,
Joana Viana,
Ruth Pidsley,
Joe Burrage,
Therese M Murphy,
Claire Troakes,
Gustavo Turecki,
Michael C O'Donovan,
Leonard C Schalkwyk,
Nicholas J Bray,
Jonathan Mill
There are widespread genetic effects on DNA methylation in the developing brain. Fetal brain mQTLs are enriched in regulatory domains, overlapping with variants influencing gene expression. Most are developmentally stable, but some are fetal specific. These mQTLs are enriched in genomic regions associated with schizophrenia, a neuropsychiatric disorder with neurodevelopmental origins.
Effects of advanced paternal age on trajectories of social behavior in offspring
M Janecka,
A Manduca,
M Servadio,
V Trezza,
R Smith,
J Mill,
L C Schalkwyk
+ 2 more
M Janecka,
A Manduca,
M Servadio,
V Trezza,
R Smith,
J Mill,
L C Schalkwyk,
A Reichenberg,
C Fernandes
Our study is the first investigation of the effects of advanced paternal age (APA) on the developmental trajectory of social behavior in rodent offspring. Given the strong epidemiological association between APA and sexually dimorphic neurodevelopmental disorders that are characterized by abnormalities in social behavior (autism, schizophrenia), we assessed sociability in male and female inbred mice (C57BL/6J) across postnatal development (N = 104) in relation to paternal age. We found differences in early social behavior in both male and female offspring of older breeders, with differences in this social domain persisting into adulthood in males only. We showed that these social deficits were not present in the fathers of these offspring, confirming a de novo origin of an altered social trajectory in the offspring generation. Our results, highly novel in rodent research, support the epidemiological observations in humans and provide evidence for a causal link between APA, age-related changes in the paternal sperm DNA and neurodevelopmental disorders in their offspring.
Methylomic profiling of human brain tissue supports a neurodevelopmental origin for schizophrenia
Ruth Pidsley,
Joana Viana,
Eilis Hannon,
Helen Spiers,
Claire Troakes,
Safa Al-Saraj,
Naguib Mechawar
+ 4 more
Ruth Pidsley,
Joana Viana,
Eilis Hannon,
Helen Spiers,
Claire Troakes,
Safa Al-Saraj,
Naguib Mechawar,
Gustavo Turecki,
Leonard C Schalkwyk,
Nicholas J Bray,
Jonathan Mill
BackgroundSchizophrenia is a severe neuropsychiatric disorder that is hypothesized to result from disturbances in early brain development. There is mounting evidence to support a role for developmentally regulated epigenetic variation in the molecular etiology of the disorder. Here, we describe a systematic study of schizophrenia-associated methylomic variation in the adult brain and its relationship to changes in DNA methylation across human fetal brain development.ResultsWe profile methylomic variation in matched prefrontal cortex and cerebellum brain tissue from schizophrenia patients and controls, identifying disease-associated differential DNA methylation at multiple loci, particularly in the prefrontal cortex, and confirming these differences in an independent set of adult brain samples. Our data reveal discrete modules of co-methylated loci associated with schizophrenia that are enriched for genes involved in neurodevelopmental processes and include loci implicated by genetic studies of the disorder. Methylomic data from human fetal cortex samples, spanning 23 to 184 days post-conception, indicates that schizophrenia-associated differentially methylated positions are significantly enriched for loci at which DNA methylation is dynamically altered during human fetal brain development.ConclusionsOur data support the hypothesis that schizophrenia has an important early neurodevelopmental component, and suggest that epigenetic mechanisms may mediate these effects.
Erratum to: Variation in 5-hydroxymethylcytosine across human cortex and cerebellum
Katie Lunnon,
Eilis Hannon,
Rebecca G.Smith,
Emma Dempster,
Chloe Wong,
Joe Burrage,
Claire Troakes
+ 4 more
Katie Lunnon,
Eilis Hannon,
Rebecca G.Smith,
Emma Dempster,
Chloe Wong,
Joe Burrage,
Claire Troakes,
Safa Al-Sarraj,
Agnieszka Kepa,
Leonard Schalkwyk,
Jonathan Mill
Even though the etiology of Alzheimer’s disease (AD) remains unknown, it is suggested that an interplay among genetic, epigenetic and environmental factors is involved. An increasing body of evidence pinpoints that dysregulation in the epigenetic machinery plays a role in AD. Recent developments in genomic technologies have allowed for high throughput interrogation of the epigenome, and epigenome-wide association studies have already identified unique epigenetic signatures for AD in the cortex. Considerable evidence suggests that early dysregulation in the brainstem, more specifically in the raphe nuclei and the locus coeruleus, accounts for the most incipient, non-cognitive symptomatology, indicating a potential causal relationship with the pathogenesis of AD. Here we review the advancements in epigenomic technologies and their application to the AD research field, particularly with relevance to the brainstem. In this respect, we propose the assessment of epigenetic signatures in the brainstem as the cornerstone of interrogating causality in AD. Understanding how epigenetic dysregulation in the brainstem contributes to AD susceptibility could be of pivotal importance for understanding the etiology of the disease and for the development of novel diagnostic and therapeutic strategies.
Collapsed methylation quantitative trait loci analysis for low frequency and rare variants
Tom G. Richardson,
Hashem A. Shihab,
Gibran Hemani,
Jie Zheng,
Eilis Hannon,
Jonathan Mill,
Elena Carnero-Montoro
+ 10 more
Tom G. Richardson,
Hashem A. Shihab,
Gibran Hemani,
Jie Zheng,
Eilis Hannon,
Jonathan Mill,
Elena Carnero-Montoro,
Jordana T. Bell,
Oliver Lyttleton,
Wendy L. McArdle,
Susan M. Ring,
Santiago Rodriguez,
Colin Campbell,
George Davey Smith,
Caroline L. Relton,
Nicholas J. Timpson,
Tom R. Gaunt
BACKGROUND: Single variant approaches have been successful in identifying DNA methylation quantitative trait loci (mQTL), although as with complex traits they lack the statistical power to identify the effects from rare genetic variants. We have undertaken extensive analyses to identify regions of low frequency and rare variants that are associated with DNA methylation levels.
METHODS: We used repeated measurements of DNA methylation from five different life stages in human blood, taken from the Avon Longitudinal Study of Parents and Children (ALSPAC) cohort. Variants were collapsed across CpG islands and their flanking regions to identify variants collectively associated with methylation, where no single variant was individually responsible for the observed signal. All analyses were undertaken using the sequence kernel association test.
RESULTS: For loci where no individual variant mQTL was observed based on a single variant analysis, we identified 95 unique regions where the combined effect of low frequency variants (MAF ≤ 5%) provided strong evidence of association with methylation. For loci where there was previous evidence of an individual variant mQTL, a further 3 regions provided evidence of association between multiple low frequency variants and methylation levels. Effects were observed consistently across 5 different time points in the lifecourse and evidence of replication in the TwinsUK and Exeter cohorts was also identified.
CONCLUSION: We have demonstrated the potential of this novel approach to mQTL analysis by analysing the combined effect of multiple low frequency or rare variants. Future studies should benefit from applying this approach as a complementary follow up to single variant analyses.
Intermediate DNA methylation is a conserved signature of genome regulation
GiNell Elliott,
Chibo Hong,
Xiaoyun Xing,
Xin Zhou,
Daofeng Li,
Cristian Coarfa,
Robert J.A. Bell
+ 17 more
GiNell Elliott,
Chibo Hong,
Xiaoyun Xing,
Xin Zhou,
Daofeng Li,
Cristian Coarfa,
Robert J.A. Bell,
Cecile L. Maire,
Keith L. Ligon,
Mahvash Sigaroudinia,
Philippe Gascard,
Thea D. Tlsty,
R. Alan Harris,
Leonard C. Schalkwyk,
Misha Bilenky,
Jonathan Mill,
Peggy J. Farnham,
Manolis Kellis,
Marco A. Marra,
Aleksandar Milosavljevic,
Martin Hirst,
Gary D. Stormo,
Ting Wang,
Joseph F. Costello
The role of intermediate methylation states in DNA is unclear. Here, to comprehensively identify regions of intermediate methylation and their quantitative relationship with gene activity, we apply integrative and comparative epigenomics to 25 human primary cell and tissue samples. We report 18,452 intermediate methylation regions located near 36% of genes and enriched at enhancers, exons and DNase I hypersensitivity sites. Intermediate methylation regions average 57% methylation, are predominantly allele-independent and are conserved across individuals and between mouse and human, suggesting a conserved function. These regions have an intermediate level of active chromatin marks and their associated genes have intermediate transcriptional activity. Exonic intermediate methylation correlates with exon inclusion at a level between that of fully methylated and unmethylated exons, highlighting gene context-dependent functions. We conclude that intermediate DNA methylation is a conserved signature of gene regulation and exon usage.
A role for CaV1 and calcineurin signaling in depolarization-induced changes in neuronal DNA methylation
Eilis Hannon, Annisa N. Chand, Mark D. Evans, Chloe C.Y. Wong, Matthew S. Grubb, Jonathan Mill
Eilis Hannon,
Annisa N. Chand,
Mark D. Evans,
Chloe C.Y. Wong,
Matthew S. Grubb,
Jonathan Mill
Direct manipulations of neuronal activity have been shown to induce changes in DNA methylation (DNAm), although little is known about the cellular signaling pathways involved. Using reduced representation bisulfite sequencing, we identify DNAm changes associated with moderate chronic depolarization in dissociated rat hippocampal cultures. Consistent with previous findings, these changes occurred primarily in the vicinity of loci implicated in neuronal function, being enriched in intergenic regions and underrepresented in CpG-rich promoter regulatory regions. We subsequently used 2 pharmacological interventions (nifedipine and FK-506) to test whether the identified changes depended on 2 interrelated signaling pathways known to mediate multiple forms of neuronal plasticity. Both pharmacological manipulations had notable effects on the extent and magnitude of depolarization-induced DNAm changes indicating that a high proportion of activity-induced changes are likely to be mediated by calcium entry through L-type CaV1 channels and/or downstream signaling via the calcium-dependent phosphatase calcineurin.
Epigenetically regulated microRNAs in Alzheimer's disease
den Hove Daniel L. Van,
Konstantinos Kompotis,
Roy Lardenoije,
Gunter Kenis,
Jonathan Mill,
Harry W. Steinbusch,
Klaus-Peter Lesch
+ 3 more
den Hove Daniel L. Van,
Konstantinos Kompotis,
Roy Lardenoije,
Gunter Kenis,
Jonathan Mill,
Harry W. Steinbusch,
Klaus-Peter Lesch,
Carlos P. Fitzsimons,
Strooper Bart De,
Bart P.F. Rutten
Alzheimer's disease (AD) is a complex neurodegenerative disorder involving dysregulation of many biological pathways at multiple levels. Classical epigenetic mechanisms, including DNA methylation and histone modifications, and regulation by microRNAs (miRNAs), are among the major regulatory elements that control these pathways at the molecular level, with epigenetic modifications regulating gene expression transcriptionally and miRNAs suppressing gene expression posttranscriptionally. Epigenetic mechanisms and miRNAs have recently been shown to closely interact with each other, thereby creating reciprocal regulatory circuits, which appear to be disrupted in neuronal and glial cells affected by AD. Here, we review those miRNAs implicated in AD that are regulated by promoter DNA methylation and/or chromatin modifications and, which frequently direct the expression of constituents of the epigenetic machinery, concluding with the delineation of a complex epigenetic-miRNA regulatory network and its alterations in AD.
Genome-wide DNA methylation levels and altered cortisol stress reactivity following childhood trauma in humans
Lotte C. Houtepen,
Christiaan H. Vinkers,
Tania Carrillo-Roa,
Marieke Hiemstra,
Lier Pol A. van,
Wim Meeus,
Susan Branje
+ 9 more
Lotte C. Houtepen,
Christiaan H. Vinkers,
Tania Carrillo-Roa,
Marieke Hiemstra,
Lier Pol A. van,
Wim Meeus,
Susan Branje,
Christine M. Heim,
Charles B. Nemeroff,
Jonathan Mill,
Leonard C. Schalkwyk,
Menno P. Creyghton,
René S. Kahn,
Marian Joëls,
Elisabeth B. Binder,
Marco P. M. Boks
DNA methylation likely plays a role in the regulation of human stress reactivity. Here we show that in a genome-wide analysis of blood DNA methylation in 85 healthy individuals, a locus in the Kit ligand gene (KITLG; cg27512205) showed the strongest association with cortisol stress reactivity (P=5.8 × 10−6). Replication was obtained in two independent samples using either blood (N=45, P=0.001) or buccal cells (N=255, P=0.004). KITLG methylation strongly mediates the relationship between childhood trauma and cortisol stress reactivity in the discovery sample (32% mediation). Its genomic location, a CpG island shore within an H3K27ac enhancer mark, and the correlation between methylation in the blood and prefrontal cortex provide further evidence that KITLG methylation is functionally relevant for the programming of stress reactivity in the human brain. Our results extend preclinical evidence for epigenetic regulation of stress reactivity to humans and provide leads to enhance our understanding of the neurobiological pathways underlying stress vulnerability.
Epigenetic processes such as DNA methylation have been implicated in the pathophysiology of neurodevelopmental disorders including schizophrenia and autism. Epigenetic changes can be induced by environmental exposures such as inflammation. Here we tested the hypothesis that prenatal inflammation, a recognized risk factor for schizophrenia and related neurodevelopmental conditions, alters DNA methylation in key brain regions linked to schizophrenia, namely the dopamine rich striatum and endocrine regulatory centre, the hypothalamus. DNA methylation across highly repetitive elements (long interspersed element 1 (LINE1) and intracisternal A-particles (IAPs)) were used to proxy global DNA methylation. We also investigated the Mecp2 gene because it regulates transcription of LINE1 and has a known association with neurodevelopmental disorders. Brain tissue was harvested from 6 week old offspring of mice exposed to the viral analog PolyI:C or saline on gestation day 9. We used Sequenom EpiTYPER assay to quantitatively analyze differences in DNA methylation at IAPs, LINE1 elements and the promoter region of Mecp2. In the hypothalamus, prenatal exposure to PolyI:C caused significant global DNA hypomethylation (t=2.44, P=0.019, PolyI:C mean 69.67%, saline mean 70.19%), especially in females, and significant hypomethylation of the promoter region of Mecp2, (t=3.32, P=0.002; PolyI:C mean 26.57%, saline mean 34.63%). IAP methylation was unaltered. DNA methylation in the striatum was not significantly altered. This study provides the first experimental evidence that exposure to inflammation during prenatal life is associated with epigenetic changes, including Mecp2 promoter hypomethylation. This suggests that environmental and genetic risk factors associated with neurodevelopmental disorders may act upon similar pathways. This is important because epigenetic changes are potentially modifiable and their investigation may open new avenues for treatment.
Environmental risk, Oxytocin Receptor Gene (OXTR) methylation and youth callous-unemotional traits: a 13-year longitudinal study
C A M Cecil,
L J Lysenko,
S R Jaffee,
J-B Pingault,
R G Smith,
C L Relton,
G Woodward
+ 3 more
C A M Cecil,
L J Lysenko,
S R Jaffee,
J-B Pingault,
R G Smith,
C L Relton,
G Woodward,
W McArdle,
J Mill,
E D Barker
Youth with high callous-unemotional traits (CU) are at risk for early-onset and persistent conduct problems. Research suggests that there may be different developmental pathways to CU (genetic/constitutional vs environmental), and that the absence or presence of co-occurring internalizing problems is a key marker. However, it is unclear whether such a distinction is valid. Intermediate phenotypes such as DNA methylation, an epigenetic modification regulating gene expression, may help to clarify etiological pathways. This is the first study to examine prospective inter-relationships between environmental risk (prenatal/postnatal) and DNA methylation (birth, age 7 and 9) in the prediction of CU (age 13), for youth low vs high in internalizing problems. We focused on DNA methylation in the vicinity of the oxytocin receptor (OXTR) gene as it has been previously implicated in CU. Participants were 84 youth with early-onset and persistent conduct problems drawn from the Avon Longitudinal Study of Parents and Children. For youth with low internalizing problems (46%), we found that (i) OXTR methylation at birth associated with higher CU (age 13) as well as decreased experience of victimization during childhood (evocative epigenetic-environment correlation; birth–age 7), (ii) higher prenatal parental risks (maternal psychopathology, criminal behaviors, substance use) associated with higher OXTR methylation at birth and (iii) OXTR methylation levels were more stable across time (birth–age 9). In contrast, for youth with high internalizing problems, CU were associated with prenatal risks of an interpersonal nature (that is, intimate partner violence, family conflict) but not OXTR methylation. Findings support the existence of distinct developmental pathways to CU.
An integrated genetic-epigenetic analysis of schizophrenia: evidence for co-localization of genetic associations and differential DNA methylation
Eilis Hannon,
Emma Dempster,
Joana Viana,
Joe Burrage,
Adam R. Smith,
Ruby Macdonald,
Clair David St
+ 17 more
Eilis Hannon,
Emma Dempster,
Joana Viana,
Joe Burrage,
Adam R. Smith,
Ruby Macdonald,
Clair David St,
Colette Mustard,
Gerome Breen,
Sebastian Therman,
Jaakko Kaprio,
Timothea Toulopoulou,
Hilleke E. Hulshoff Pol,
Marc M. Bohlken,
Rene S. Kahn,
Igor Nenadic,
Christina M. Hultman,
Robin M. Murray,
David A. Collier,
Nick Bass,
Hugh Gurling,
Andrew McQuillin,
Leonard Schalkwyk,
Jonathan Mill
BackgroundSchizophrenia is a highly heritable, neuropsychiatric disorder characterized by episodic psychosis and altered cognitive function. Despite success in identifying genetic variants associated with schizophrenia, there remains uncertainty about the causal genes involved in disease pathogenesis and how their function is regulated.ResultsWe performed a multi-stage epigenome-wide association study, quantifying genome-wide patterns of DNA methylation in a total of 1714 individuals from three independent sample cohorts. We have identified multiple differentially methylated positions and regions consistently associated with schizophrenia across the three cohorts; these effects are independent of important confounders such as smoking. We also show that epigenetic variation at multiple loci across the genome contributes to the polygenic nature of schizophrenia. Finally, we show how DNA methylation quantitative trait loci in combination with Bayesian co-localization analyses can be used to annotate extended genomic regions nominated by studies of schizophrenia, and to identify potential regulatory variation causally involved in disease.ConclusionsThis study represents the first systematic integrated analysis of genetic and epigenetic variation in schizophrenia, introducing a methodological approach that can be used to inform epigenome-wide association study analyses of other complex traits and diseases. We demonstrate the utility of using a polygenic risk score to identify molecular variation associated with etiological variation, and of using DNA methylation quantitative trait loci to refine the functional and regulatory variation associated with schizophrenia risk variants. Finally, we present strong evidence for the co-localization of genetic associations for schizophrenia and differential DNA methylation.
Genome-wide analysis of genetic correlation in dementia with Lewy bodies, Parkinson's and Alzheimer's diseases
Rita Guerreiro,
Valentina Escott-Price,
Lee Darwent,
Laura Parkkinen,
Olaf Ansorge,
Dena G. Hernandez,
Michael A. Nalls
+ 41 more
Rita Guerreiro,
Valentina Escott-Price,
Lee Darwent,
Laura Parkkinen,
Olaf Ansorge,
Dena G. Hernandez,
Michael A. Nalls,
Lorraine Clark,
Lawrence Honig,
Karen Marder,
der Flier Wiesje van,
Henne Holstege,
Eva Louwersheimer,
Afina Lemstra,
Philip Scheltens,
Ekaterina Rogaeva,
George-Hyslop Peter St,
Elisabet Londos,
Henrik Zetterberg,
Sara Ortega-Cubero,
Pau Pastor,
Tanis J. Ferman,
Neill R. Graff-Radford,
Owen A. Ross,
Imelda Barber,
Anne Braae,
Kristelle Brown,
Kevin Morgan,
Walter Maetzler,
Daniela Berg,
Claire Troakes,
Safa Al-Sarraj,
Tammaryn Lashley,
Yaroslau Compta,
Tamas Revesz,
Andrew Lees,
Nigel J. Cairns,
Glenda M. Halliday,
David Mann,
Stuart Pickering-Brown,
John Powell,
Katie Lunnon,
Michelle K. Lupton,
International Parkinson's Disease Genomics Consortium,
Dennis Dickson,
John Hardy,
Andrew Singleton,
Jose Bras
The similarities between dementia with Lewy bodies (DLB) and both Parkinson's disease (PD) and Alzheimer's disease (AD) are many and range from clinical presentation, to neuropathological characteristics, to more recently identified, genetic determinants of risk. Because of these overlapping features, diagnosing DLB is challenging and has clinical implications since some therapeutic agents that are applicable in other diseases have adverse effects in DLB. Having shown that DLB shares some genetic risk with PD and AD, we have now quantified the amount of sharing through the application of genetic correlation estimates, and show that, from a purely genetic perspective, and excluding the strong association at the APOE locus, DLB is equally correlated to AD and PD.
A data-driven approach to preprocessing Illumina 450K methylation array data
Ruth Pidsley, Wong Chloe C Y, Manuela Volta, Katie Lunnon, Jonathan Mill, Leonard C Schalkwyk
Ruth Pidsley,
Wong Chloe C Y,
Manuela Volta,
Katie Lunnon,
Jonathan Mill,
Leonard C Schalkwyk
BackgroundAs the most stable and experimentally accessible epigenetic mark, DNA methylation is of great interest to the research community. The landscape of DNA methylation across tissues, through development and in disease pathogenesis is not yet well characterized. Thus there is a need for rapid and cost effective methods for assessing genome-wide levels of DNA methylation. The Illumina Infinium HumanMethylation450 (450K) BeadChip is a very useful addition to the available methods for DNA methylation analysis but its complex design, incorporating two different assay methods, requires careful consideration. Accordingly, several normalization schemes have been published. We have taken advantage of known DNA methylation patterns associated with genomic imprinting and X-chromosome inactivation (XCI), in addition to the performance of SNP genotyping assays present on the array, to derive three independent metrics which we use to test alternative schemes of correction and normalization. These metrics also have potential utility as quality scores for datasets.ResultsThe standard index of DNA methylation at any specific CpG site is β = M/(M + U + 100) where M and U are methylated and unmethylated signal intensities, respectively. Betas (βs) calculated from raw signal intensities (the default GenomeStudio behavior) perform well, but using 11 methylomic datasets we demonstrate that quantile normalization methods produce marked improvement, even in highly consistent data, by all three metrics. The commonly used procedure of normalizing betas is inferior to the separate normalization of M and U, and it is also advantageous to normalize Type I and Type II assays separately. More elaborate manipulation of quantiles proves to be counterproductive.ConclusionsCareful selection of preprocessing steps can minimize variance and thus improve statistical power, especially for the detection of the small absolute DNA methylation changes likely associated with complex disease phenotypes. For the convenience of the research community we have created a user-friendly R software package called wateRmelon, downloadable from bioConductor, compatible with the existing methylumi, minfi and IMA packages, that allows others to utilize the same normalization methods and data quality tests on 450K data.
No Evidence to Suggest that the Use of Acetylcholinesterase Inhibitors Confounds the Results of Two Blood-Based Biomarker Studies in Alzheimer’s Disease
Justin Tao Wen Chiam,
Katie Lunnon,
Nicola Voyle,
Petroula Proitsi,
Giovanni Coppola,
Daniel Geschwind,
Sally Nelson
+ 12 more
Justin Tao Wen Chiam,
Katie Lunnon,
Nicola Voyle,
Petroula Proitsi,
Giovanni Coppola,
Daniel Geschwind,
Sally Nelson,
Caroline Johnston,
Hilkka Soininen,
Iwona Kłoszewska,
Patrizia Mecocci,
Magda Tsolaki,
Bruno Vellas,
Angela Hodges,
Simon Lovestone,
Stephen Newhouse,
Richard James Butler Dobson,
Steven John Kiddle,
Martina Sattlecker
BACKGROUND: There is an urgent need to discover Alzheimer's disease (AD) biomarkers that are both easily measured and reliable. Research into blood-based biomarkers for AD using transcriptomics and proteomics has been an attractive and promising area of research. However, to date researchers have not looked into the possibility of AD medication being a confounding factor in these studies.
OBJECTIVE: This study explored whether acetylcholinesterase inhibitors (AChEIs), the main class of AD medication, are a confounding factor in AD blood biomarker studies.
METHODS: The most promising blood transcriptomic and proteomic biomarkers from two recent studies were analyzed to determine if they were differentially expressed between AD subjects on AChEIs and subjects that were not.
RESULTS: None of the gene or protein biomarkers analyzed were found to be significantly altered between subjects in either group.
CONCLUSION: This study found no evidence that AChEIs are a confounding factor in these published AD blood biomarker studies. Further work is needed to confirm that this is also the case for other proposed biomarkers.
Severe psychosocial deprivation in early childhood is associated with increased DNA methylation across a region spanning the transcription start site of CYP2E1
R Kumsta,
S J Marzi,
J Viana,
E L Dempster,
B Crawford,
M Rutter,
J Mill
+ 1 more
R Kumsta,
S J Marzi,
J Viana,
E L Dempster,
B Crawford,
M Rutter,
J Mill,
E J S Sonuga-Barke
Exposure to adverse rearing environments including institutional deprivation and severe childhood abuse is associated with an increased risk for mental and physical health problems across the lifespan. Although the mechanisms mediating these effects are not known, recent work in rodent models suggests that epigenetic processes may be involved. We studied the impact of severe early-life adversity on epigenetic variation in a sample of adolescents adopted from the severely depriving orphanages of the Romanian communist era in the 1980s. We quantified buccal cell DNA methylation at ~400 000 sites across the genome in Romanian adoptees exposed to either extended (6–43 months; n=16) or limited duration (<6 months; n=17) of severe early-life deprivation, in addition to a matched sample of UK adoptees (n=16) not exposed to severe deprivation. Although no probe-wise differences remained significant after controlling for the number of probes tested, we identified an exposure-associated differentially methylated region (DMR) spanning nine sequential CpG sites in the promoter-regulatory region of the cytochrome P450 2E1 gene (CYP2E1) on chromosome 10 (corrected P=2.98 × 10−5). Elevated DNA methylation across this region was also associated with deprivation-related clinical markers of impaired social cognition. Our data suggest that environmental insults of sufficient biological impact during early development are associated with long-lasting epigenetic changes, potentially reflecting a biological mechanism linking the effects of early-life adversity to cognitive and neurobiological phenotypes.
Genetic variants near MLST8 and DHX57 affect the epigenetic age of the cerebellum
Ake T. Lu,
Eilis Hannon,
Morgan E. Levine,
Ke Hao,
Eileen M. Crimmins,
Katie Lunnon,
Alexey Kozlenkov
+ 3 more
Ake T. Lu,
Eilis Hannon,
Morgan E. Levine,
Ke Hao,
Eileen M. Crimmins,
Katie Lunnon,
Alexey Kozlenkov,
Jonathan Mill,
Stella Dracheva,
Steve Horvath
DNA methylation (DNAm) levels lend themselves for defining an epigenetic biomarker of aging known as the ‘epigenetic clock’. Our genome-wide association study (GWAS) of cerebellar epigenetic age acceleration identifies five significant (P<5.0 × 10−8) SNPs in two loci: 2p22.1 (inside gene DHX57) and 16p13.3 near gene MLST8 (a subunit of mTOR complex 1 and 2). We find that the SNP in 16p13.3 has a cis-acting effect on the expression levels of MLST8 (P=6.9 × 10−18) in most brain regions. In cerebellar samples, the SNP in 2p22.1 has a cis-effect on DHX57 (P=4.4 × 10−5). Gene sets found by our GWAS analysis of cerebellar age acceleration exhibit significant overlap with those of Alzheimer’s disease (P=4.4 × 10−15), age-related macular degeneration (P=6.4 × 10−6), and Parkinson’s disease (P=2.6 × 10−4). Overall, our results demonstrate the utility of a new paradigm for understanding aging and age-related diseases: it will be fruitful to use epigenetic tissue age as endophenotype in GWAS.
A novel multi-tissue RNA diagnostic of healthy ageing relates to cognitive health status
Sanjana Sood,
Iain J. Gallagher,
Katie Lunnon,
Eric Rullman,
Aoife Keohane,
Hannah Crossland,
Bethan E. Phillips
+ 10 more
Sanjana Sood,
Iain J. Gallagher,
Katie Lunnon,
Eric Rullman,
Aoife Keohane,
Hannah Crossland,
Bethan E. Phillips,
Tommy Cederholm,
Thomas Jensen,
Loon Luc JC van,
Lars Lannfelt,
William E. Kraus,
Philip J. Atherton,
Robert Howard,
Thomas Gustafsson,
Angela Hodges,
James A. Timmons
BackgroundDiagnostics of the human ageing process may help predict future healthcare needs or guide preventative measures for tackling diseases of older age. We take a transcriptomics approach to build the first reproducible multi-tissue RNA expression signature by gene-chip profiling tissue from sedentary normal subjects who reached 65 years of age in good health.ResultsOne hundred and fifty probe-sets form an accurate classifier of young versus older muscle tissue and this healthy ageing RNA classifier performed consistently in independent cohorts of human muscle, skin and brain tissue (n = 594, AUC = 0.83–0.96) and thus represents a biomarker for biological age. Using the Uppsala Longitudinal Study of Adult Men birth-cohort (n = 108) we demonstrate that the RNA classifier is insensitive to confounding lifestyle biomarkers, while greater gene score at age 70 years is independently associated with better renal function at age 82 years and longevity. The gene score is ‘up-regulated’ in healthy human hippocampus with age, and when applied to blood RNA profiles from two large independent age-matched dementia case–control data sets (n = 717) the healthy controls have significantly greater gene scores than those with cognitive impairment. Alone, or when combined with our previously described prototype Alzheimer disease (AD) RNA ‘disease signature’, the healthy ageing RNA classifier is diagnostic for AD.ConclusionsWe identify a novel and statistically robust multi-tissue RNA signature of human healthy ageing that can act as a diagnostic of future health, using only a peripheral blood sample. This RNA signature has great potential to assist research aimed at finding treatments for and/or management of AD and other ageing-related conditions.
Transcriptomic changes in the frontal cortex associated with paternal age
Rebecca G Smith, Cathy Fernandes, Rachel Kember, Leonard C Schalkwyk, Joseph Buxbaum, Abraham Reichenberg, Jonathan Mill
Rebecca G Smith,
Cathy Fernandes,
Rachel Kember,
Leonard C Schalkwyk,
Joseph Buxbaum,
Abraham Reichenberg,
Jonathan Mill
BackgroundAdvanced paternal age is robustly associated with several human neuropsychiatric disorders, particularly autism. The precise mechanism(s) mediating the paternal age effect are not known, but they are thought to involve the accumulation of de novo (epi)genomic alterations. In this study we investigate differences in the frontal cortex transcriptome in a mouse model of advanced paternal age.FindingsTranscriptomic profiling was undertaken for medial prefrontal cortex tissue dissected from the male offspring of young fathers (2 month old, 4 sires, n = 16 offspring) and old fathers (10 month old, 6 sires, n = 16 offspring) in a mouse model of advancing paternal age. We found a number of differentially expressed genes in the offspring of older fathers, many previously implicated in the aetiology of autism. Pathway analysis highlighted significant enrichment for changes in functional networks involved in inflammation and inflammatory disease, which are also implicated in autism.ConclusionsWe observed widespread alterations to the transcriptome associated with advanced paternal age with an enrichment of genes associated with inflammation, an interesting observation given previous evidence linking the immune system to several neuropsychiatric disorders including autism.
Increased DNA methylation near TREM2 is consistently seen in the superior temporal gyrus in Alzheimer's disease brain
Adam R. Smith, Rebecca G. Smith, Daniel Condliffe, Eilis Hannon, Leonard Schalkwyk, Jonathan Mill, Katie Lunnon
Adam R. Smith,
Rebecca G. Smith,
Daniel Condliffe,
Eilis Hannon,
Leonard Schalkwyk,
Jonathan Mill,
Katie Lunnon
Although mutations within the TREM2 gene have been robustly associated with Alzheimer's disease, it is not known whether alterations in the regulation of this gene are also involved in pathogenesis. Here, we present data demonstrating increased DNA methylation in the superior temporal gyrus in Alzheimer's disease brain at a CpG site located 289 bp upstream of the transcription start site of the TREM2 gene in 3 independent study cohorts using 2 different technologies (Illumina Infinium 450K methylation beadchip and pyrosequencing). A meta-analysis across all 3 cohorts reveals consistent AD-associated hypermethylation (p = 3.47E-08). This study highlights that extending genetic studies of TREM2 in AD to investigate epigenetic changes may nominate additional mechanisms by which disruption to this gene increases risk.
Methylomic analysis of monozygotic twins discordant for childhood psychotic symptoms
Helen L Fisher,
Therese M Murphy,
Louise Arseneault,
Avshalom Caspi,
Terrie E Moffitt,
Joana Viana,
Eilis Hannon
+ 6 more
Helen L Fisher,
Therese M Murphy,
Louise Arseneault,
Avshalom Caspi,
Terrie E Moffitt,
Joana Viana,
Eilis Hannon,
Ruth Pidsley,
Joe Burrage,
Emma L Dempster,
Chloe C Y Wong,
Carmine M Pariante,
Jonathan Mill
Childhood psychotic symptoms are associated with increased rates of schizophrenia, other psychiatric disorders, and suicide attempts in adulthood; thus, elucidating early risk indicators is crucial to target prevention efforts. There is considerable discordance for psychotic symptoms between monozygotic twins, indicating that child-specific non-genetic factors must be involved. Epigenetic processes may constitute one of these factors and have not yet been investigated in relation to childhood psychotic symptoms. Therefore, this study explored whether differences in DNA methylation at age 10 were associated with monozygotic twin discordance for psychotic symptoms at age 12. The Environmental Risk (E-Risk) Longitudinal Twin Study cohort of 2,232 children (1,116 twin pairs) was assessed for age-12 psychotic symptoms and 24 monozygotic twin pairs discordant for symptoms were identified for methylomic comparison. Children provided buccal samples at ages 5 and 10. DNA was bisulfite modified and DNA methylation was quantified using the Infinium HumanMethylation450 array. Differentially methylated positions (DMPs) associated with psychotic symptoms were subsequently tested in post-mortem prefrontal cortex tissue from adult schizophrenia patients and age-matched controls. Site-specific DNA methylation differences were observed at age 10 between monozygotic twins discordant for age-12 psychotic symptoms. Similar DMPs were not found at age 5. The top-ranked psychosis-associated DMP (cg23933044), located in the promoter of the C5ORF42 gene, was also hypomethylated in post-mortem prefrontal cortex brain tissue from schizophrenia patients compared to unaffected controls. These data tentatively suggest that epigenetic variation in peripheral tissue is associated with childhood psychotic symptoms and may indicate susceptibility to schizophrenia and other mental health problems.
Interindividual methylomic variation across blood, cortex, and cerebellum: implications for epigenetic studies of neurological and neuropsychiatric phenotypes
Eilis Hannon, Katie Lunnon, Leonard Schalkwyk, Jonathan Mill
Eilis Hannon,
Katie Lunnon,
Leonard Schalkwyk,
Jonathan Mill
Given the tissue-specific nature of epigenetic processes, the assessment of disease-relevant tissue is an important consideration for epigenome-wide association studies (EWAS). Little is known about whether easily accessible tissues, such as whole blood, can be used to address questions about interindividual epigenomic variation in inaccessible tissues, such as the brain. We quantified DNA methylation in matched DNA samples isolated from whole blood and 4 brain regions (prefrontal cortex, entorhinal cortex, superior temporal gyrus, and cerebellum) from 122 individuals. We explored co-variation between tissues and the extent to which methylomic variation in blood is predictive of interindividual variation identified in the brain. For the majority of DNA methylation sites, interindividual variation in whole blood is not a strong predictor of interindividual variation in the brain, although the relationship with cortical regions is stronger than with the cerebellum. Variation at a subset of probes is strongly correlated across tissues, even in instances when the actual level of DNA methylation is significantly different between them. A substantial proportion of this co-variation, however, is likely to result from genetic influences. Our data suggest that for the majority of the genome, a blood-based EWAS for disorders where brain is presumed to be the primary tissue of interest will give limited information relating to underlying pathological processes. These results do not, however, discount the utility of using a blood-based EWAS to identify biomarkers of disease phenotypes manifest in the brain. We have generated a searchable database for the interpretation of data from blood-based EWAS analyses ( http://epigenetics.essex.ac.uk/bloodbrain/).
Tissue-specific patterns of allelically-skewed DNA methylation
Sarah J. Marzi,
Emma L. Meaburn,
Emma L. Dempster,
Katie Lunnon,
Jose L. Paya-Cano,
Rebecca G. Smith,
Manuela Volta
+ 3 more
Sarah J. Marzi,
Emma L. Meaburn,
Emma L. Dempster,
Katie Lunnon,
Jose L. Paya-Cano,
Rebecca G. Smith,
Manuela Volta,
Claire Troakes,
Leonard C. Schalkwyk,
Jonathan Mill
While DNA methylation is usually thought to be symmetrical across both alleles, there are some notable exceptions. Genomic imprinting and X chromosome inactivation are two well-studied sources of allele-specific methylation (ASM), but recent research has indicated a more complex pattern in which genotypic variation can be associated with allelically-skewed DNA methylation in cis. Given the known heterogeneity of DNA methylation across tissues and cell types we explored inter- and intra-individual variation in ASM across several regions of the human brain and whole blood from multiple individuals. Consistent with previous studies, we find widespread ASM with > 4% of the ∼220,000 loci interrogated showing evidence of allelically-skewed DNA methylation. We identify ASM flanking known imprinted regions, and show that ASM sites are enriched in DNase I hypersensitivity sites and often located in an extended genomic context of intermediate DNA methylation. We also detect examples of genotype-driven ASM, some of which are tissue-specific. These findings contribute to our understanding of the nature of differential DNA methylation across tissues and have important implications for genetic studies of complex disease. As a resource to the community, ASM patterns across each of the tissues studied are available in a searchable online database: http://epigenetics.essex.ac.uk/ASMBrainBlood.
An epigenome-wide association meta-analysis of prenatal maternal stress in neonates: A model approach for replication
Jolien Rijlaarsdam,
Irene Pappa,
Esther Walton,
Marian J. Bakermans-Kranenburg,
Viara R. Mileva-Seitz,
Ralph C.A. Rippe,
Sabine J. Roza
+ 11 more
Jolien Rijlaarsdam,
Irene Pappa,
Esther Walton,
Marian J. Bakermans-Kranenburg,
Viara R. Mileva-Seitz,
Ralph C.A. Rippe,
Sabine J. Roza,
Vincent W.V. Jaddoe,
Frank C. Verhulst,
Janine F. Felix,
Charlotte A.M. Cecil,
Caroline L. Relton,
Tom R. Gaunt,
Wendy McArdle,
Jonathan Mill,
Edward D. Barker,
Henning Tiemeier,
IJzendoorn Marinus H. van
Prenatal maternal stress exposure has been associated with neonatal differential DNA methylation. However, the available evidence in humans is largely based on candidate gene methylation studies, where only a few CpG sites were evaluated. The aim of this study was to examine the association between prenatal exposure to maternal stress and offspring genome-wide cord blood methylation using different methods. First, we conducted a meta-analysis and follow-up pathway analyses. Second, we used novel region discovery methods [i.e., differentially methylated regions (DMRs) analyses]. To this end, we used data from two independent population-based studies, the Generation R Study (n = 912) and the Avon Longitudinal Study of Parents and Children (ALSPAC, n = 828), to (i) measure genome-wide DNA methylation in cord blood and (ii) extract a prenatal maternal stress composite. The meta-analysis (ntotal = 1,740) revealed no epigenome-wide (meta P <1.00e-07) associations of prenatal maternal stress exposure with neonatal differential DNA methylation. Follow-up analyses of the top hits derived from our epigenome-wide meta-analysis (meta P <1.00e-04) indicated an over-representation of the methyltransferase activity pathway. We identified no Bonferroni-corrected (P <1.00e-06) DMRs associated with prenatal maternal stress exposure. Combining data from two independent population-based samples in an epigenome-wide meta-analysis, the current study indicates that there are no large effects of prenatal maternal stress exposure on neonatal DNA methylation. Such replication efforts are essential in the search for robust associations, whether derived from candidate gene methylation or epigenome-wide studies.
DNA Methylation Profiling in Inflammatory Bowel Disease Provides New Insights into Disease Pathogenesis
Edel McDermott,
Elizabeth J. Ryan,
Miriam Tosetto,
David Gibson,
Joe Burrage,
Denise Keegan,
Kathryn Byrne
+ 10 more
Edel McDermott,
Elizabeth J. Ryan,
Miriam Tosetto,
David Gibson,
Joe Burrage,
Denise Keegan,
Kathryn Byrne,
Eimear Crowe,
Gillian Sexton,
Kevin Malone,
R. Alan Harris,
Richard Kellermayer,
Jonathan Mill,
Garret Cullen,
Glen A. Doherty,
Hugh Mulcahy,
Therese M. Murphy
BACKGROUND AND AIMS: Inflammatory bowel diseases (IBDs) are heterogeneous disorders with complex aetiology. Quantitative genetic studies suggest that only a small proportion of the disease variance observed in IBD is accounted for by genetic variation, indicating a potential role for differential epigenetic regulation in disease aetiology. The aim of this study was to assess genome-wide DNA methylation changes specifically associated with ulcerative colitis (UC), Crohn's disease (CD) and IBD activity.
METHODS: DNA methylation was quantified in peripheral blood mononuclear cells (PBMCs) from 149 IBD cases (61 UC, 88 CD) and 39 controls using the Infinium HumanMethylation450 BeadChip. Technical and functional validation was performed using pyrosequencing and the real-time polymerase chain reaction. Cross-tissue replication of the top differentially methylated positions (DMPs) was tested in colonic mucosa tissue samples obtained from paediatric IBD cases and controls.
RESULTS: A total of 3196 probes were differentially methylated between CD cases and controls, while 1481 probes were differentially methylated between UC cases and controls. There was considerable (45%) overlap between UC and CD DMPs. The top-ranked IBD-associated PBMC differentially methylated region (promoter region of TRIM39-RPP2) was also significantly hypomethylated in colonic mucosa from paediatric UC patients. In addition, we confirmed TRAF6 hypermethylation using pyrosequencing and found reduced TRAF6 gene expression in PBMCs of IBD patients.
CONCLUSIONS: Our data provide new insights into differential epigenetic regulation of genes and molecular pathways, which may contribute to the pathogenesis and activity of IBD.
Schizophrenia-associated methylomic variation: molecular signatures of disease and polygenic risk burden across multiple brain regions
Joana Viana,
Eilis Hannon,
Emma Dempster,
Ruth Pidsley,
Ruby Macdonald,
Olivia Knox,
Helen Spiers
+ 5 more
Joana Viana,
Eilis Hannon,
Emma Dempster,
Ruth Pidsley,
Ruby Macdonald,
Olivia Knox,
Helen Spiers,
Claire Troakes,
Safa Al-Saraj,
Gustavo Turecki,
Leonard C. Schalkwyk,
Jonathan Mill
Genetic association studies provide evidence for a substantial polygenic component to schizophrenia, although the neurobiological mechanisms underlying the disorder remain largely undefined. Building on recent studies supporting a role for developmentally regulated epigenetic variation in the molecular aetiology of schizophrenia, this study aimed to identify epigenetic variation associated with both a diagnosis of schizophrenia and elevated polygenic risk burden for the disease across multiple brain regions. Genome-wide DNA methylation was quantified in 262 post-mortem brain samples, representing tissue from four brain regions (prefrontal cortex, striatum, hippocampus and cerebellum) from 41 schizophrenia patients and 47 controls. We identified multiple disease-associated and polygenic risk score-associated differentially methylated positions and regions, which are not enriched in genomic regions identified in genetic studies of schizophrenia and do not reflect direct genetic effects on DNA methylation. Our study represents the first analysis of epigenetic variation associated with schizophrenia across multiple brain regions and highlights the utility of polygenic risk scores for identifying molecular pathways associated with aetiological variation in complex disease.
Maternal adversities during pregnancy and cord blood oxytocin receptor (OXTR) DNA methylation
Eva Unternaehrer,
Margarete Bolten,
Irina Nast,
Simon Staehli,
Andrea H. Meyer,
Emma Dempster,
Dirk H. Hellhammer
+ 2 more
Eva Unternaehrer,
Margarete Bolten,
Irina Nast,
Simon Staehli,
Andrea H. Meyer,
Emma Dempster,
Dirk H. Hellhammer,
Roselind Lieb,
Gunther Meinlschmidt
The aim of this study was to investigate whether maternal adversities and cortisol levels during pregnancy predict cord blood DNA methylation of the oxytocin receptor (OXTR). We collected cord blood of 39 babies born to mothers participating in a cross-sectional study (N = 100) conducted in Basel, Switzerland (2007-10). Mothers completed the Inventory of Life Events (second trimester: T2), the Edinburgh Postnatal Depression Scale (EPDS, third trimester: T3), the Trier Inventory of Chronic Stress (TICS-K, 1-3 weeks postpartum) and provided saliva samples (T2, T3) for maternal cortisol profiles, as computed by the area under the curve with respect to ground (AUCg) or increase (AUCi) for the cortisol awakening response (CAR) and for diurnal cortisol profiles (DAY). OXTR DNA methylation was quantified using Sequenom EpiTYPER. The number of stressful life events (P = 0.032), EPDS score (P = 0.007) and cortisol AUCgs at T2 (CAR: P = 0.020; DAY: P = 0.024) were negatively associated with OXTR DNA methylation. Our findings suggest that distinct prenatal adversities predict decreased DNA methylation in a gene that is relevant for childbirth, maternal behavior and wellbeing of mother and offspring. If a reduced OXTR methylation increases OXTR expression, our findings could suggest an epigenetic adaptation to an adverse early environment.
A comparison of mitochondrial DNA isolation methods in frozen post-mortem human brain tissueapplications for studies of mitochondrial genetics in brain disorders
Matthew Devall,
Joe Burrage,
Richard Caswell,
Matthew Johnson,
Claire Troakes,
Safa Al-Sarraj,
Aaron R Jeffries
+ 2 more
Matthew Devall,
Joe Burrage,
Richard Caswell,
Matthew Johnson,
Claire Troakes,
Safa Al-Sarraj,
Aaron R Jeffries,
Jonathan Mill,
Katie Lunnon
Given that many brain disorders are characterized by mitochondrial dysfunction, there is a growing interest in investigating genetic and epigenetic variation in mitochondrial DNA (mtDNA). One major caveat for such studies is the presence of nuclear-mitochondrial pseudogenes (NUMTs), which are regions of the mitochondrial genome that have been inserted into the nuclear genome over evolution and, if not accounted for, can confound genetic studies of mtDNA. Here we provide the first systematic comparison of methods for isolating mtDNA from frozen post-mortem human brain tissue. Our data show that a commercial method from Miltenyi Biotec, which magnetically isolates mitochondria using antibodies raised against the mitochondrial import receptor subunit TOM22, gives significant mtDNA enrichment and should be considered the method of choice for mtDNA studies in frozen brain tissue.
Epigenomic and transcriptomic signatures of a Klinefelter syndrome (47,XXY) karyotype in the brain
Joana Viana,
Ruth Pidsley,
Claire Troakes,
Helen Spiers,
Chloe CY Wong,
Safa Al-Sarraj,
Ian Craig
+ 2 more
Joana Viana,
Ruth Pidsley,
Claire Troakes,
Helen Spiers,
Chloe CY Wong,
Safa Al-Sarraj,
Ian Craig,
Leonard Schalkwyk,
Jonathan Mill
Klinefelter syndrome (KS) is the most common sex-chromosome aneuploidy in humans. Most affected individuals carry one extra X-chromosome (47,XXY karyotype) and the condition presents with a heterogeneous mix of reproductive, physical and psychiatric phenotypes. Although the mechanism(s) by which the supernumerary X-chromosome determines these features of KS are poorly understood, skewed X-chromosome inactivation (XCI), gene-dosage dysregulation, and the parental origin of the extra X-chromosome have all been implicated, suggesting an important role for epigenetic processes. We assessed genomic, methylomic and transcriptomic variation in matched prefrontal cortex and cerebellum samples identifying an individual with a 47,XXY karyotype who was comorbid for schizophrenia and had a notably reduced cerebellum mass compared with other individuals in the study (n = 49). We examined methylomic and transcriptomic differences in this individual relative to female and male samples with 46,XX or 46,XY karyotypes, respectively, and identified numerous locus-specific differences in DNA methylation and gene expression, with many differences being autosomal and tissue-specific. Furthermore, global DNA methylation, assessed via the interrogation of LINE-1 and Alu repetitive elements, was significantly altered in the 47,XXY patient in a tissue-specific manner with extreme hypomethylation detected in the prefrontal cortex and extreme hypermethylation in the cerebellum. This study provides the first detailed molecular characterization of the prefrontal cortex and cerebellum from an individual with a 47,XXY karyotype, identifying widespread tissue-specific epigenomic and transcriptomic alterations in the brain.
Advanced paternal age effects in neurodevelopmental disorders—review of potential underlying mechanisms
M Janecka,
J Mill,
M A Basson,
A Goriely,
H Spiers,
A Reichenberg,
L Schalkwyk
+ 1 more
M Janecka,
J Mill,
M A Basson,
A Goriely,
H Spiers,
A Reichenberg,
L Schalkwyk,
C Fernandes
Multiple epidemiological studies suggest a relationship between advanced paternal age (APA) at conception and adverse neurodevelopmental outcomes in offspring, particularly with regard to increased risk for autism and schizophrenia. Conclusive evidence about how age-related changes in paternal gametes, or age-independent behavioral traits affect neural development is still lacking. Recent evidence suggests that the origins of APA effects are likely to be multidimensional, involving both inherited predisposition and de novo events. Here we provide a review of the epidemiological and molecular findings to date. Focusing on the latter, we present the evidence for genetic and epigenetic mechanisms underpinning the association between late fatherhood and disorder in offspring. We also discuss the limitations of the APA literature. We propose that different hypotheses relating to the origins of the APA effects are not mutually exclusive. Instead, multiple mechanisms likely contribute, reflecting the etiological complexity of neurodevelopmental disorders.
Genome-wide meta-analysis of DNA methylation changes associated with antidepressant effects of Electroconvulsive Therapy
E. Pishva,
G. Kenis,
E. Hannon,
W. Viechtbauer,
A. Jeffries,
R. Lardenoije,
P. Sienaert
+ 3 more
E. Pishva,
G. Kenis,
E. Hannon,
W. Viechtbauer,
A. Jeffries,
R. Lardenoije,
P. Sienaert,
Os J. van,
M.L. Stek,
B.P.F. Rutten
Paternal Age Alters Social Development in Offspring
Magdalena Janecka,
Claire M.A. Haworth,
Angelica Ronald,
Eva Krapohl,
Francesca Happé,
Jonathan Mill,
Leonard C. Schalkwyk
+ 3 more
Magdalena Janecka,
Claire M.A. Haworth,
Angelica Ronald,
Eva Krapohl,
Francesca Happé,
Jonathan Mill,
Leonard C. Schalkwyk,
Cathy Fernandes,
Abraham Reichenberg,
Frühling Rijsdijk
Journal of the American Academy of Child & Adolescent Psychiatry
OBJECTIVE: Advanced paternal age (APA) at conception has been linked with autism and schizophrenia in offspring, neurodevelopmental disorders that affect social functioning. The current study explored the effects of paternal age on social development in the general population.
METHOD: We used multilevel growth modeling to investigate APA effects on socioemotional development from early childhood until adolescence, as measured by the Strengths and Difficulties Questionnaire (SDQ) in the Twins Early Development Study (TEDS) sample. We also investigated genetic and environmental underpinnings of the paternal age effects on development, using the Additive genetics, Common environment, unique Environment (ACE) and gene-environment (GxE) models.
RESULTS: In the general population, both very young and advanced paternal ages were associated with altered trajectory of social development (intercept: p = .01; slope: p = .03). No other behavioral domain was affected by either young or advanced age at fatherhood, suggesting specificity of paternal age effects. Increased importance of genetic factors in social development was recorded in the offspring of older but not very young fathers, suggesting distinct underpinnings of the paternal age effects at these two extremes.
CONCLUSION: Our findings highlight that the APA-related deficits that lead to autism and schizophrenia are likely continuously distributed in the population.
Regional differences in mitochondrial DNA methylation in human post-mortem brain tissue
Matthew Devall,
Rebecca G. Smith,
Aaron Jeffries,
Eilis Hannon,
Matthew N. Davies,
Leonard Schalkwyk,
Jonathan Mill
+ 2 more
Matthew Devall,
Rebecca G. Smith,
Aaron Jeffries,
Eilis Hannon,
Matthew N. Davies,
Leonard Schalkwyk,
Jonathan Mill,
Michael Weedon,
Katie Lunnon
BackgroundDNA methylation is an important epigenetic mechanism involved in gene regulation, with alterations in DNA methylation in the nuclear genome being linked to numerous complex diseases. Mitochondrial DNA methylation is a phenomenon that is receiving ever-increasing interest, particularly in diseases characterized by mitochondrial dysfunction; however, most studies have been limited to the investigation of specific target regions. Analyses spanning the entire mitochondrial genome have been limited, potentially due to the amount of input DNA required. Further, mitochondrial genetic studies have been previously confounded by nuclear-mitochondrial pseudogenes. Methylated DNA Immunoprecipitation Sequencing is a technique widely used to profile DNA methylation across the nuclear genome; however, reads mapped to mitochondrial DNA are often discarded. Here, we have developed an approach to control for nuclear-mitochondrial pseudogenes within Methylated DNA Immunoprecipitation Sequencing data. We highlight the utility of this approach in identifying differences in mitochondrial DNA methylation across regions of the human brain and pre-mortem blood.ResultsWe were able to correlate mitochondrial DNA methylation patterns between the cortex, cerebellum and blood. We identified 74 nominally significant differentially methylated regions (p < 0.05) in the mitochondrial genome, between anatomically separate cortical regions and the cerebellum in matched samples (N = 3 matched donors). Further analysis identified eight significant differentially methylated regions between the total cortex and cerebellum after correcting for multiple testing. Using unsupervised hierarchical clustering analysis of the mitochondrial DNA methylome, we were able to identify tissue-specific patterns of mitochondrial DNA methylation between blood, cerebellum and cortex.ConclusionsOur study represents a comprehensive analysis of the mitochondrial methylome using pre-existing Methylated DNA Immunoprecipitation Sequencing data to identify brain region-specific patterns of mitochondrial DNA methylation.
5-hydroxymethylcytosine is highly dynamic across human fetal brain development
Helen Spiers, Eilis Hannon, Leonard C. Schalkwyk, Nicholas J. Bray, Jonathan Mill
Helen Spiers,
Eilis Hannon,
Leonard C. Schalkwyk,
Nicholas J. Bray,
Jonathan Mill
ABSTRACT Background Epigenetic processes play a key role in orchestrating transcriptional regulation during the development of the human central nervous system. We previously described dynamic changes in DNA methylation (5mC) occurring during human fetal brain development, but other epigenetic processes operating during this period have not been extensively explored. Of particular interest is DNA hydroxymethylation (5hmC), a modification that is enriched in the human brain and hypothesized to play an important role in neuronal function, learning and memory. In this study, we quantify 5hmC across the genome of 71 human fetal brain samples spanning 23 to 184 days post-conception. Results We identify widespread changes in 5hmC occurring during human brain development, notable sex-differences in 5hmC in the fetal brain, and interactions between 5mC and 5hmC at specific sites. Finally, we identify loci where 5hmC in the fetal brain is associated with genetic variation. Conclusions This study represents the first systematic analysis of dynamic changes in 5hmC across neurodevelopment and highlights the potential importance of this modification in the human brain. A searchable database of our fetal brain 5hmC data is available as a resource to the research community at http://epigenetics.essex.ac.uk/fetalbrain2/ .
Genetic architecture of epigenetic and neuronal ageing rates in human brain regions
Ake T. Lu,
Eilis Hannon,
Morgan E. Levine,
Eileen M. Crimmins,
Katie Lunnon,
Jonathan Mill,
Daniel H. Geschwind
+ 1 more
Ake T. Lu,
Eilis Hannon,
Morgan E. Levine,
Eileen M. Crimmins,
Katie Lunnon,
Jonathan Mill,
Daniel H. Geschwind,
Steve Horvath
Identifying genes regulating the pace of epigenetic ageing represents a new frontier in genome-wide association studies (GWASs). Here using 1,796 brain samples from 1,163 individuals, we carry out a GWAS of two DNA methylation-based biomarkers of brain age: the epigenetic ageing rate and estimated proportion of neurons. Locus 17q11.2 is significantly associated (P=4.5 × 10−9) with the ageing rate across five brain regions and harbours a cis-expression quantitative trait locus for EFCAB5 (P=3.4 × 10−20). Locus 1p36.12 is significantly associated (P=2.2 × 10−8) with epigenetic ageing of the prefrontal cortex, independent of the proportion of neurons. Our GWAS of the proportion of neurons identified two genome-wide significant loci (10q26 and 12p13.31) and resulted in a gene set that overlaps significantly with sets found by GWAS of age-related macular degeneration (P=1.4 × 10−12), ulcerative colitis (P<1.0 × 10−20), type 2 diabetes (P=2.8 × 10−13), hip/waist circumference in men (P=1.1 × 10−9), schizophrenia (P=1.6 × 10−9), cognitive decline (P=5.3 × 10−4) and Parkinson’s disease (P=8.6 × 10−3).
Pleiotropic Effects of Trait-Associated Genetic Variation on DNA Methylation: Utility for Refining GWAS Loci
Eilis Hannon, Mike Weedon, Nicholas Bray, Michael O’Donovan, Jonathan Mill
Eilis Hannon,
Mike Weedon,
Nicholas Bray,
Michael O’Donovan,
Jonathan Mill
Most genetic variants identified in genome-wide association studies (GWASs) of complex traits are thought to act by affecting gene regulation rather than directly altering the protein product. As a consequence, the actual genes involved in disease are not necessarily the most proximal to the associated variants. By integrating data from GWAS analyses with those from genetic studies of regulatory variation, it is possible to identify variants pleiotropically associated with both a complex trait and measures of gene regulation. In this study, we used summary-data-based Mendelian randomization (SMR), a method developed to identify variants pleiotropically associated with both complex traits and gene expression, to identify variants associated with complex traits and DNA methylation. We used large DNA methylation quantitative trait locus (mQTL) datasets generated from two different tissues (blood and fetal brain) to prioritize genes for >40 complex traits with robust GWAS data and found considerable overlap with the results of SMR analyses performed with expression QTL (eQTL) data. We identified multiple examples of variable DNA methylation associated with GWAS variants for a range of complex traits, demonstrating the utility of this approach for refining genetic association signals.
Longitudinal analyses of the DNA methylome in deployed military servicemen identify susceptibility loci for post-traumatic stress disorder
B P F Rutten,
E Vermetten,
C H Vinkers,
G Ursini,
N P Daskalakis,
E Pishva,
Nijs L de
+ 21 more
B P F Rutten,
E Vermetten,
C H Vinkers,
G Ursini,
N P Daskalakis,
E Pishva,
Nijs L de,
L C Houtepen,
L Eijssen,
A E Jaffe,
G Kenis,
W Viechtbauer,
den Hove D van,
K G Schraut,
K-P Lesch,
J E Kleinman,
T M Hyde,
D R Weinberger,
L Schalkwyk,
K Lunnon,
J Mill,
H Cohen,
R Yehuda,
D G Baker,
A X Maihofer,
C M Nievergelt,
E Geuze,
M P M Boks
In order to determine the impact of the epigenetic response to traumatic stress on post-traumatic stress disorder (PTSD), this study examined longitudinal changes of genome-wide blood DNA methylation profiles in relation to the development of PTSD symptoms in two prospective military cohorts (one discovery and one replication data set). In the first cohort consisting of male Dutch military servicemen (n=93), the emergence of PTSD symptoms over a deployment period to a combat zone was significantly associated with alterations in DNA methylation levels at 17 genomic positions and 12 genomic regions. Evidence for mediation of the relation between combat trauma and PTSD symptoms by longitudinal changes in DNA methylation was observed at several positions and regions. Bioinformatic analyses of the reported associations identified significant enrichment in several pathways relevant for symptoms of PTSD. Targeted analyses of the significant findings from the discovery sample in an independent prospective cohort of male US marines (n=98) replicated the observed relation between decreases in DNA methylation levels and PTSD symptoms at genomic regions in ZFP57, RNF39 and HIST1H2APS2. Together, our study pinpoints three novel genomic regions where longitudinal decreases in DNA methylation across the period of exposure to combat trauma marks susceptibility for PTSD.
SU116. Longitudinal Epigenetic Analysis of Clozapine Use in Treatment-Resistant Schizophrenia
Amy Gillespie, Eilis Hannon, Emma Dempster, David Collier, Alice Egerton, Jonathan Mill, James MacCabe
Amy Gillespie,
Eilis Hannon,
Emma Dempster,
David Collier,
Alice Egerton,
Jonathan Mill,
James MacCabe
Background: Approximately one-third of patients with schizophrenia are considered treatment resistant. For these patients, the atypical antipsychotic drug clozapine is recommended as the only evidence-based treatment available. However, there is still significant variability in treatment response and many patients suffer side effects. Animal studies have demonstrated that clozapine influences histone modification and DNA methylation, and a recent EWAS study in humans identified multiple differentially methylated positions (DMPs) and differentially methylated regions (DMRs) in clozapine-exposed samples. In the current study, we used a longitudinal, within-participant design to conduct genome-wide analysis of DNA methylation changes in treatment-resistant patients over 6 months of clozapine use. Methods: We recruited 26 participants with a diagnosis of treatment-resistant schizophrenia, before they were prescribed clozapine. We then collected whole-blood samples at baseline and follow-up (6 or 8 wks, 12 wks, and 6 mo after clozapine start date), alongside clinical assessments. This included assessment of treatment response (defined as at least a 20% reduction in PANSS score) and side effects. We quantified DNA methylation at ~480 000 sites across the genome using the Illumina 450K HumanMethylation array and following preprocessing, normalization, and quality control; an epigenome-wide association study was performed comparing DNA methylation over the 4 time points. The trajectories of those with different treatment response/side effects will also be compared. Results: There was a reduction in overall global DNA methylation associated with length of time on clozapine, and multiple individual CpG sites show changes in DNA methylation that were found to be significantly associated with length of time exposed to clozapine. Numerous sites within the top twenty are located within the body of genes associated with immune system and antibodies. Conclusion: This is the first study to identify longitudinal epigenetic changes following clozapine exposure in human subjects. Recruitment and analysis are ongoing, with plans to compare DNA methylation between clozapine responders and nonresponders. Ultimately, these data will help us understand the mechanisms involved in clozapine, potentially providing biomarkers to predict response to clozapine.
ANK1 is up-regulated in laser captured microglia in Alzheimer’s brain; the importance of addressing cellular heterogeneity
Diego Mastroeni,
Shobana Sekar,
Jennifer Nolz,
Elaine Delvaux,
Katie Lunnon,
Jonathan Mill,
Winnie S. Liang
+ 1 more
Diego Mastroeni,
Shobana Sekar,
Jennifer Nolz,
Elaine Delvaux,
Katie Lunnon,
Jonathan Mill,
Winnie S. Liang,
Paul D. Coleman
Recent epigenetic association studies have identified a new gene, ANK1, in the pathogenesis of Alzheimer's disease (AD). Although strong associations were observed, brain homogenates were used to generate the data, introducing complications because of the range of cell types analyzed. In order to address the issue of cellular heterogeneity in homogenate samples we isolated microglial, astrocytes and neurons by laser capture microdissection from CA1 of hippocampus in the same individuals with a clinical and pathological diagnosis of AD and matched control cases. Using this unique RNAseq data set, we show that in the hippocampus, ANK1 is significantly (p<0.0001) up-regulated 4-fold in AD microglia, but not in neurons or astrocytes from the same individuals. These data provide evidence that microglia are the source of ANK1 differential expression previously identified in homogenate samples in AD.
Epigenetics and DNA methylomic profiling in Alzheimer's disease and other neurodegenerative diseases
Janou A. Y. Roubroeks, Rebecca G. Smith, den Hove Daniel L. A. van, Katie Lunnon
Janou A. Y. Roubroeks,
Rebecca G. Smith,
den Hove Daniel L. A. van,
Katie Lunnon
Recent studies have suggested a role for epigenetic mechanisms in the complex etiology of various neurodegenerative diseases. In this review, we discuss advances that have been made toward understanding the role of epigenetic processes in neurodegenerative disorders, with a particular focus on Alzheimer's disease, where the most extensive studies have been undertaken to date. We provide a brief overview of DNA modifications, followed by a summarization of studies of DNA modifications in Alzheimer's disease and other neurodegenerative diseases.
T50 Longitudinal Epigenetic Analysis Of Clozapine Use In Treatment-Resistant Schizophrenia: Data From The Crestar Consortium
Amy Gillespie, Eilis Hannon, Emma Dempster, David Collier, Alice Egerton, Jonathan Mill, James MacCabe
Amy Gillespie,
Eilis Hannon,
Emma Dempster,
David Collier,
Alice Egerton,
Jonathan Mill,
James MacCabe
BackgroundApproximately one-third of patients with schizophrenia are considered treatment-resistant. For these patients, the atypical antipsychotic drug clozapine is recommended as the only evidence based treatment available. However, there is still significant variability in treatment-response. Animal studies have demonstrated that clozapine influences histone modification and DNA methylation, and a recent EWAS study in humans identified multiple differentially methylated positions (DMPs) and differentially methylated regions (DMRs) in clozapine-exposed samples. We used a longitudinal, within-participant design to conduct genome-wide analysis of DNA methylation changes in treatment resistant patients over 6 months of clozapine use.MethodsWe recruited 20 participants with a diagnosis of treatment-resistant schizophrenia, before they were prescribed clozapine. We then collected whole-blood samples at baseline and follow-up (6 weeks, 12 weeks and 6 months after clozapine start date), alongside clinical assessments. We quantified DNA methylation at ~ 480,000 sites across the genome using the Illumina 450 K HumanMethylation array and following pre-processing, normalization and quality control, an epigenome-wide association study was performed comparing DNA methylation at each time point.ResultsPreliminary data demonstrates an overall reduction in DNA methylation in the 6 months of clozapine use, with multiple individual CpG sites showing changes in DNA methylation that were found to be significantly associated with length of time exposed to clozapine. During analysis of the first 10 patients, the most significant CpG site was located in the gene body of CRB1; CRB1 is expressed exclusively in the eye, and the central nervous system, and has been previously associated with Lever’s congenital amaurosis and retinitis pigmentosa. The findings and analysis for all 20 participants will be presented at the meeting.DiscussionThis is the first study to identify longitudinal epigenetic changes following clozapine exposure in human subjects, replicating findings in animal studies of decreased methylation. Recruitment is ongoing and further analysis will look at whether epigenetic changes are associated with treatment-response/adverse reactions. Ultimately, these data will help us understand the mechanisms involved in clozapine, potentially providing biomarkers to predict clozapine response.
A histone acetylome-wide association study of Alzheimer’s disease: neuropathology-associated regulatory variation in the human entorhinal cortex
Sarah J. Marzi,
Teodora Ribarska,
Adam R. Smith,
Eilis Hannon,
Jeremie Poschmann,
Karen Moore,
Claire Troakes
+ 6 more
Sarah J. Marzi,
Teodora Ribarska,
Adam R. Smith,
Eilis Hannon,
Jeremie Poschmann,
Karen Moore,
Claire Troakes,
Safa Al-Sarraj,
Stephan Beck,
Stuart Newman,
Katie Lunnon,
Leonard C. Schalkwyk,
Jonathan Mill
Abstract Alzheimer’s disease (AD) is a chronic neurodegenerative disorder characterized by the progressive accumulation of amyloid-β (Aβ) plaques and neurofibrillary tangles in the neocortex. Recent studies have implicated a role for regulatory genomic variation in AD progression, finding widespread evidence for altered DNA methylation associated with neuropathology. To date, however, no study has systematically examined other types of regulatory genomic modifications in AD. In this study, we quantified genome-wide patterns of lysine H3K27 acetylation (H3K27ac) - a robust mark of active enhancers and promoters that is strongly correlated with gene expression and transcription factor binding - in entorhinal cortex samples from AD cases and matched controls (n = 47) using chromatin immunoprecipitation followed by highly parallel sequencing (ChIP-seq). Across ~182,000 robustly detected H3K27ac peak regions, we found widespread acetylomic variation associated with AD neuropathology, identifying 4,162 differential peaks (FDR < 0.05) between AD cases and controls. These differentially acetylated peaks are enriched in disease-specific biological pathways and include regions annotated to multiple genes directly involved in the progression of Aβ and tau pathology (e.g. APP , PSEN1 , PSEN2 , MAPT ), as well as genomic regions containing variants associated with sporadic late-onset AD. This is the first study of variable H3K27ac yet undertaken in AD and the largest study investigating this modification in the entorhinal cortex. In addition to identifying molecular pathways associated with AD neuropathology, we present a framework for genome-wide studies of histone modifications in complex disease, integrating our data with results obtained from genome-wide association studies as well as other epigenetic marks profiled on the same samples.
5-hydroxymethylcytosine is highly dynamic across human fetal brain development
Helen Spiers, Eilis Hannon, Leonard C. Schalkwyk, Nicholas J. Bray, Jonathan Mill
Helen Spiers,
Eilis Hannon,
Leonard C. Schalkwyk,
Nicholas J. Bray,
Jonathan Mill
BackgroundEpigenetic processes play a key role in orchestrating transcriptional regulation during the development of the human central nervous system. We previously described dynamic changes in DNA methylation (5mC) occurring during human fetal brain development, but other epigenetic processes operating during this period have not been extensively explored. Of particular interest is DNA hydroxymethylation (5hmC), a modification that is enriched in the human brain and hypothesized to play an important role in neuronal function, learning and memory. In this study, we quantify 5hmC across the genome of 71 human fetal brain samples spanning 23 to 184 days post-conception.ResultsWe identify widespread changes in 5hmC occurring during human brain development, notable sex-differences in 5hmC in the fetal brain, and interactions between 5mC and 5hmC at specific sites. Finally, we identify loci where 5hmC in the fetal brain is associated with genetic variation.ConclusionsThis study represents the first systematic analysis of dynamic changes in 5hmC across human neurodevelopment and highlights the potential importance of this modification in the human brain. A searchable database of our fetal brain 5hmC data is available as a resource to the research community at http://www.epigenomicslab.com/online-data-resources.
Using induced pluripotent stem cells to explore genetic and epigenetic variation associated with Alzheimer's disease
Jennifer Imm, Talitha L Kerrigan, Aaron Jeffries, Katie Lunnon
Jennifer Imm,
Talitha L Kerrigan,
Aaron Jeffries,
Katie Lunnon
It is thought that both genetic and epigenetic variation play a role in Alzheimer's disease initiation and progression. With the advent of somatic cell reprogramming into induced pluripotent stem cells it is now possible to generate patient-derived cells that are able to more accurately model and recapitulate disease. Furthermore, by combining this with recent advances in (epi)genome editing technologies, it is possible to begin to examine the functional consequence of previously nominated genetic variants and infer epigenetic causality from recently identified epigenetic variants. In this review, we explore the role of genetic and epigenetic variation in Alzheimer's disease and how the functional relevance of nominated loci can be investigated using induced pluripotent stem cells and (epi)genome editing techniques.
TRANSCRIPTIONAL AND EPIGENOMIC PROFILING IN THE ENTORHINAL CORTEX IN AMYLOID AND TAU MOUSE MODELS OF ALZHEIMER's DISEASE
Isabel M.S. Castanho,
Tracey K. Murray,
Audrey Farbos,
Katie Lunnon,
David A. Collier,
Zeshan Ahmed,
Konrad Paszkiewicz
+ 2 more
Isabel M.S. Castanho,
Tracey K. Murray,
Audrey Farbos,
Katie Lunnon,
David A. Collier,
Zeshan Ahmed,
Konrad Paszkiewicz,
Michael J. O'Neill,
Jonathan Mill
A SYSTEMATIC REVIEW OF MENDELIAN RANDOMIZATION STUDIES INVESTIGATING CAUSAL ASSOCIATIONS BETWEEN RISK FACTORS AND DEMENTIA
Elzbieta Kuzma,
Eilis Hannon,
Ang Zhou,
Ilianna Lourida,
Alison Bethel,
Deborah Levine,
Katie Lunnon
+ 3 more
Elzbieta Kuzma,
Eilis Hannon,
Ang Zhou,
Ilianna Lourida,
Alison Bethel,
Deborah Levine,
Katie Lunnon,
Jo Thompson‐Coon,
Elina Hyppönen,
David J. Llewellyn
Elevated polygenic burden for autism is associated with differential DNA methylation at birth
Eilis Hannon,
Diana Schendel,
Christine Ladd-Acosta,
Jakob Grove,
iPSYCH-Broad ASD Group,
Christine Søholm Hansen,
Shan V. Andrews
+ 16 more
Eilis Hannon,
Diana Schendel,
Christine Ladd-Acosta,
Jakob Grove,
iPSYCH-Broad ASD Group,
Christine Søholm Hansen,
Shan V. Andrews,
David Michael Hougaard,
Michaeline Bresnahan,
Ole Mors,
Mads Vilhelm Hollegaard,
Marie Bækvad-Hansen,
Mady Hornig,
Preben Bo Mortensen,
Anders D. Børglum,
Thomas Werge,
Marianne Giørtz Pedersen,
Merete Nordentoft,
Joseph Buxbaum,
M Daniele Fallin,
Jonas Bybjerg-Grauholm,
Abraham Reichenberg,
Jonathan Mill
ABSTRACT Background Autism spectrum disorder (ASD) is a severe neurodevelopmental disorder characterized by deficits in social communication and restricted, repetitive behaviors, interests, or activities. The etiology of ASD involves both inherited and environmental risk factors, with epigenetic processes hypothesized as one mechanism by which both genetic and non-genetic variation influence gene regulation and pathogenesis. Methods We quantified neonatal methylomic variation in 1,263 infants - of whom ~50% went on to subsequently develop ASD – using DNA isolated from a unique collection of archived blood spots taken shortly after birth. We used matched genetic data from the same individuals to examine the molecular consequences of ASD genetic risk variants, identifying methylomic variation associated with elevated polygenic burden for ASD. In addition, we performed DNA methylation quantitative trait loci (mQTL) mapping to prioritize target genes from ASD GWAS findings. Results Although we did not identify specific loci showing consistent changes in neonatal DNA methylation associated with later ASD, we found a significant association between increased polygenic burden for autism and methylomic variation at two CpG sites located proximal to a robust GWAS signal for ASD on chromosome 8. Conclusions This study is the largest analysis of DNA methylation in ASD yet undertaken and the first to integrate both genetic and epigenetic variation at birth in ASD. We demonstrate the utility of using a polygenic risk score to identify molecular variation associated with disease, and of using mQTL to refine the functional and regulatory variation associated with ASD risk variants.
Meta-analysis of epigenome-wide association studies of cognitive abilities
Riccardo E. Marioni,
Allan F. McRae,
Jan Bressler,
Elena Colicino,
Eilis Hannon,
Shuo Li,
Diddier Prada
+ 40 more
Riccardo E. Marioni,
Allan F. McRae,
Jan Bressler,
Elena Colicino,
Eilis Hannon,
Shuo Li,
Diddier Prada,
Jennifer A Smith,
Letizia Trevisi,
Pei-Chien Tsai,
Dina Vojinovic,
Jeannette Simino,
Daniel Levy,
Chunyu Liu,
Michael Mendelson,
Claudia L. Satizabal,
Qiong Yang,
Min A. Jhun,
Sharon L. R. Kardia,
Wei Zhao,
Stefania Bandinelli,
Luigi Ferrucci,
Dena G. Hernandez,
Andrew B. Singleton,
Sarah E. Harris,
John M. Starr,
Douglas P. Kiel,
Robert R. McLean,
Allan C. Just,
Joel Schwartz,
Avron Spiro,
Pantel Vokonas,
Najaf Amin,
M. Arfan Ikram,
Andre G. Uitterlinden,
Meurs Joyce B. J. van,
Tim D. Spector,
Claire Steves,
Andrea A. Baccarelli,
Jordana T. Bell,
Duijn Cornelia M. van,
Myriam Fornage,
Yi-Hsiang Hsu,
Jonathan Mill,
Thomas H. Mosley,
Sudha Seshadri,
Ian J. Deary
Cognitive functions are important correlates of health outcomes across the life-course. Individual differences in cognitive functions are partly heritable. Epigenetic modifications, such as DNA methylation, are susceptible to both genetic and environmental factors and may provide insights into individual differences in cognitive functions. Epigenome-wide meta-analyses for blood-based DNA methylation levels at ~420,000 CpG sites were performed for seven measures of cognitive functioning using data from 11 cohorts. CpGs that passed a Bonferroni correction, adjusting for the number of CpGs and cognitive tests, were assessed for: longitudinal change; being under genetic control (methylation QTLs); and associations with brain health (structural MRI), brain methylation and Alzheimer's disease pathology. Across the seven measures of cognitive functioning (meta-analysis n range: 2557–6809), there were epigenome-wide significant (P < 1.7 × 10-8) associations for global cognitive function (cg21450381, P = 1.6 × 10-8), and phonemic verbal fluency (cg12507869, P = 2.5 × 10-9). The CpGs are located in an intergenic region on chromosome 12 and the INPP5A gene on chromosome 10, respectively. Both probes have moderate correlations (~0.4) with brain methylation in Brodmann area 20 (ventral temporal cortex). Neither probe showed evidence of longitudinal change in late-life or associations with white matter brain MRI measures in one cohort with these data. A methylation QTL analysis suggested that rs113565688 was a cis methylation QTL for cg12507869 (P = 5 × 10-5 and 4 × 10-13 in two lookup cohorts). We demonstrate a link between blood-based DNA methylation and measures of phonemic verbal fluency and global cognitive ability. Further research is warranted to understand the mechanisms linking genomic regulatory changes with cognitive function to health and disease.
Analysis of DNA Methylation in Young People: Limited Evidence for an Association Between Victimization Stress and Epigenetic Variation in Blood
Sarah J Marzi,
Karen Sugden,
Louise Arseneault,
Daniel W Belsky,
Joe Burrage,
David L Corcoran,
Andrea Danese
+ 10 more
Sarah J Marzi,
Karen Sugden,
Louise Arseneault,
Daniel W Belsky,
Joe Burrage,
David L Corcoran,
Andrea Danese,
Helen L Fisher,
Eilis Hannon,
Terrie E Moffitt,
Candice L Odgers,
Carmine Pariante,
Richie Poulton,
Benjamin S Williams,
Chloe C Y Wong,
Jonathan Mill,
Avshalom Caspi
OBJECTIVE: DNA methylation has been proposed as an epigenetic mechanism by which early-life experiences become "embedded" in the genome and alter transcriptional processes to compromise health. The authors sought to investigate whether early-life victimization stress is associated with genome-wide DNA methylation.
METHOD: The authors tested the hypothesis that victimization is associated with DNA methylation in the Environmental Risk (E-Risk) Longitudinal Study, a nationally representative 1994-1995 birth cohort of 2,232 twins born in England and Wales and assessed at ages 5, 7, 10, 12, and 18 years. Multiple forms of victimization were ascertained in childhood and adolescence (including physical, sexual, and emotional abuse; neglect; exposure to intimate-partner violence; bullying; cyber-victimization; and crime).
RESULTS: Epigenome-wide analyses of polyvictimization across childhood and adolescence revealed few significant associations with DNA methylation in peripheral blood at age 18, but these analyses were confounded by tobacco smoking and/or did not survive co-twin control tests. Secondary analyses of specific forms of victimization revealed sparse associations with DNA methylation that did not replicate across different operationalizations of the same putative victimization experience. Hypothesis-driven analyses of six candidate genes in the stress response (NR3C1, FKBP5, BDNF, AVP, CRHR1, SLC6A4) did not reveal predicted associations with DNA methylation in probes annotated to these genes.
CONCLUSIONS: Findings from this epidemiological analysis of the epigenetic effects of early-life stress do not support the hypothesis of robust changes in DNA methylation in victimized young people. We need to come to terms with the possibility that epigenetic epidemiology is not yet well matched to experimental, nonhuman models in uncovering the biological embedding of stress.
Mendelian adult-onset leukodystrophy genes in Alzheimer's disease: critical influence of CSF1R and NOTCH3
Celeste Sassi,
Michael A. Nalls,
Perry G. Ridge,
Jesse R. Gibbs,
Michelle K. Lupton,
Claire Troakes,
Katie Lunnon
+ 43 more
Celeste Sassi,
Michael A. Nalls,
Perry G. Ridge,
Jesse R. Gibbs,
Michelle K. Lupton,
Claire Troakes,
Katie Lunnon,
Safa Al-Sarraj,
Kristelle S. Brown,
Christopher Medway,
Jenny Lord,
James Turton,
Jose Bras,
ARUK Consortium,
Peter Passmore,
David Craig,
Janet Johnston,
Bernadette McGuinness,
Stephen Todd,
Reinhard Heun,
Heike Kölsch,
Patrick G. Kehoe,
Emma R.L.C. Vardy,
Nigel M. Hooper,
David M. Mann,
Stuart Pickering-Brown,
Kristelle Brown,
James Lowe,
Kevin Morgan,
A. David Smith,
Gordon Wilcock,
Donald Warden,
Clive Holmes,
Sonja Blumenau,
Mareike Thielke,
Christa Josties,
Dorette Freyer,
Annette Dietrich,
Monia Hammer,
Michael Baier,
Ulrich Dirnagl,
Kevin Morgan,
John F. Powell,
John S. Kauwe,
Carlos Cruchaga,
Alison M. Goate,
Andrew B. Singleton,
Rita Guerreiro,
Angela Hodges,
John Hardy
Mendelian adult-onset leukodystrophies are a spectrum of rare inherited progressive neurodegenerative disorders affecting the white matter of the central nervous system. Among these, cerebral autosomal dominant and recessive arteriopathy with subcortical infarcts and leukoencephalopathy, cerebroretinal vasculopathy, metachromatic leukodystrophy, hereditary diffuse leukoencephalopathy with spheroids, and vanishing white matter disease present with rapidly progressive dementia as dominant feature and are caused by mutations in NOTCH3, HTRA1, TREX1, ARSA, CSF1R, EIF2B1, EIF2B2, EIF2B3, EIF2B4, and EIF2B5, respectively. Given the rare incidence of these disorders and the lack of unequivocally diagnostic features, leukodystrophies are frequently misdiagnosed with common sporadic dementing diseases such as Alzheimer's disease (AD), raising the question of whether these overlapping phenotypes may be explained by shared genetic risk factors. To investigate this intriguing hypothesis, we have combined gene expression analysis (1) in 6 different AD mouse strains (APPPS1, HOTASTPM, HETASTPM, TPM, TAS10, and TAU) at 5 different developmental stages (embryo [E15], 2, 4, 8, and 18 months), (2) in APPPS1 primary cortical neurons under stress conditions (oxygen-glucose deprivation) and single-variant-based and single-gene-based (c-alpha test and sequence kernel association test (SKAT)) genetic screening in a cohort composed of 332 Caucasian late-onset AD patients and 676 Caucasian elderly controls. Csf1r was significantly overexpressed (log2FC > 1, adj. p-value < 0.05) in the cortex and hippocampus of aged HOTASTPM mice with extensive Aβ dense-core plaque pathology. We identified 3 likely pathogenic mutations in CSF1R TK domain (p.L868R, p.Q691H, and p.H703Y) in our discovery and validation cohort, composed of 465 AD and mild cognitive impairment (MCI) Caucasian patients from the United Kingdom. Moreover, NOTCH3 was a significant hit in the c-alpha test (adj p-value = 0.01). Adult-onset Mendelian leukodystrophy genes are not common factors implicated in AD. Nevertheless, our study suggests a potential pathogenic link between NOTCH3, CSF1R, and sporadic late-onset AD, which warrants further investigation.
Elevated DNA methylation across a 48‐kb region spanning the HOXA gene cluster is associated with Alzheimer's disease neuropathology
Rebecca G. Smith,
Eilis Hannon,
Jager Philip L. De,
Lori Chibnik,
Simon J. Lott,
Daniel Condliffe,
Adam R. Smith
+ 9 more
Rebecca G. Smith,
Eilis Hannon,
Jager Philip L. De,
Lori Chibnik,
Simon J. Lott,
Daniel Condliffe,
Adam R. Smith,
Vahram Haroutunian,
Claire Troakes,
Safa Al‐Sarraj,
David A. Bennett,
John Powell,
Simon Lovestone,
Leonard Schalkwyk,
Jonathan Mill,
Katie Lunnon
INTRODUCTION: Alzheimer's disease is a neurodegenerative disorder that is hypothesized to involve epigenetic dysregulation of gene expression in the brain.
METHODS: We performed an epigenome-wide association study to identify differential DNA methylation associated with neuropathology in prefrontal cortex and superior temporal gyrus samples from 147 individuals, replicating our findings in two independent data sets (N = 117 and 740).
RESULTS: We identify elevated DNA methylation associated with neuropathology across a 48-kb region spanning 208 CpG sites within the HOXA gene cluster. A meta-analysis of the top-ranked probe within the HOXA3 gene (cg22962123) highlighted significant hypermethylation across all three cohorts (P = 3.11 × 10-18).
DISCUSSION: We present robust evidence for elevated DNA methylation associated with Alzheimer's disease neuropathology spanning the HOXA gene cluster on chromosome 7. These data add to the growing evidence highlighting a role for epigenetic variation in Alzheimer's disease, implicating the HOX gene family as a target for future investigation.
Elevated polygenic burden for autism is associated with differential DNA methylation at birth
Eilis Hannon,
Diana Schendel,
Christine Ladd-Acosta,
Jakob Grove,
iPSYCH-Broad ASD Group,
Christine Søholm Hansen,
Shan V. Andrews
+ 16 more
Eilis Hannon,
Diana Schendel,
Christine Ladd-Acosta,
Jakob Grove,
iPSYCH-Broad ASD Group,
Christine Søholm Hansen,
Shan V. Andrews,
David Michael Hougaard,
Michaeline Bresnahan,
Ole Mors,
Mads Vilhelm Hollegaard,
Marie Bækvad-Hansen,
Mady Hornig,
Preben Bo Mortensen,
Anders D. Børglum,
Thomas Werge,
Marianne Giørtz Pedersen,
Merete Nordentoft,
Joseph Buxbaum,
Fallin M. Daniele,
Jonas Bybjerg-Grauholm,
Abraham Reichenberg,
Jonathan Mill
BackgroundAutism spectrum disorder (ASD) is a severe neurodevelopmental disorder characterized by deficits in social communication and restricted, repetitive behaviors, interests, or activities. The etiology of ASD involves both inherited and environmental risk factors, with epigenetic processes hypothesized as one mechanism by which both genetic and non-genetic variation influence gene regulation and pathogenesis. The aim of this study was to identify DNA methylation biomarkers of ASD detectable at birth.MethodsWe quantified neonatal methylomic variation in 1263 infants—of whom ~ 50% went on to subsequently develop ASD—using DNA isolated from archived blood spots taken shortly after birth. We used matched genotype data from the same individuals to examine the molecular consequences of ASD-associated genetic risk variants, identifying methylomic variation associated with elevated polygenic burden for ASD. In addition, we performed DNA methylation quantitative trait loci (mQTL) mapping to prioritize target genes from ASD GWAS findings.ResultsWe identified robust epigenetic signatures of gestational age and prenatal tobacco exposure, confirming the utility of DNA methylation data generated from neonatal blood spots. Although we did not identify specific loci showing robust differences in neonatal DNA methylation associated with later ASD, there was a significant association between increased polygenic burden for autism and methylomic variation at specific loci. Each unit of elevated ASD polygenic risk score was associated with a mean increase in DNA methylation of − 0.14% at two CpG sites located proximal to a robust GWAS signal for ASD on chromosome 8.ConclusionsThis study is the largest analysis of DNA methylation in ASD undertaken and the first to integrate genetic and epigenetic variation at birth. We demonstrate the utility of using a polygenic risk score to identify molecular variation associated with disease, and of using mQTL to refine the functional and regulatory variation associated with ASD risk variants.
EPIGENETIC SIGNATURES OF CHILDHOOD AND ADOLESCENT VICTIMISATION USING A GENETICALLY SENSITIVE LONGITUDINAL COHORT STUDY.
Helen Fisher,
Sarah Marzi,
Louise Arseneault,
Chloe Wong,
Radhika Kandaswamy,
Terrie Moffitt,
Susanna Roberts
+ 2 more
Helen Fisher,
Sarah Marzi,
Louise Arseneault,
Chloe Wong,
Radhika Kandaswamy,
Terrie Moffitt,
Susanna Roberts,
Jonathan Mill,
Avshalom Caspi
Stress is a normal, adaptive response to stressors (e.g. events that make a person feel threatened or upset). However, healthy development can be derailed by excessive or prolonged exposure to stress especially during important developmental periods such as childhood and adolescence. Exposure to severe stress may have immediate as well as long-lasting damaging effects on learning, behaviour, and health, and has been implicated in the development of psychosis. One way these may occur is via changes to epigenetic processes (e.g. alterations in DNA methylation). Initial studies have shown that individuals exposed to severe psychosocial stress have different patterns of DNA methylation (epigenetic ‘signatures’) compared to individuals exposed to no/minimal stressful life events, but these studies are methodologically limited. This paper describes our examination of the potential link between exposure to multiple forms of severe victimisation (poly-victimisation) during childhood adolescence and DNA methylation differences utilising data from the Environmental Risk (E-Risk) Longitudinal Twin Study, an epidemiological study of 2,232 children (1,116 twin pairs) born in 1994–1995 in England and Wales and followed to 18 years of age (with 93% retention). Multiple forms of victimisation were ascertained in childhood and adolescence (including physical, sexual and emotional abuse, neglect, exposure to intimate-partner violence, bullying, cyber- and crime victimization) by combining the best practices in survey research with comprehensive interview-based approaches. Whole blood samples were collected from participants at age 18, and the extracted DNA was used to quantify genome-wide patterns of DNA methylation. Epigenome-wide analyses of poly-victimisation across childhood and adolescence revealed several significant associations with DNA methylation in peripheral blood at age 18 years, but these were confounded by tobacco smoking and/or did not survive co-twin control tests. Secondary analyses of specific forms of victimisation revealed sparse associations with DNA methylation that did not replicate across different operationalisations of the same putative victimization experience. Hypothesis-driven analyses of six candidate genes in the stress response (NR3C1, FKBP5, BDNF, AVP, CRHR1, SLC6A4) did not reveal predicted associations with DNA methylation in probes annotated to these genes. Findings from this epidemiological analysis of the epigenetic effects of early-life stress do not support the hypothesis of robust changes in DNA methylation in victimised young people. It is possible that epigenetic epidemiology is not yet well matched to experimental, non-human models in uncovering the biological embedding of stress.
Sex-specific transcription and DNA methylation profiles of reproductive and epigenetic associated genes in the gonads and livers of breeding zebrafish
L.V. Laing, J. Viana, E.L. Dempster, T.M. Uren Webster, Aerle R. van, J. Mill, E.M. Santos
L.V. Laing,
J. Viana,
E.L. Dempster,
T.M. Uren Webster,
Aerle R. van,
J. Mill,
E.M. Santos
Comparative Biochemistry and Physiology Part A Molecular & Integrative Physiology
Reproduction is an essential process for life and is regulated by complex hormone networks and environmental factors. To date, little is known about the contribution of epigenetic mechanisms to the regulation of reproduction, particularly in lower vertebrates. We used the zebrafish (Danio rerio) model to investigate the sex-specific transcription and DNA methylation profiles for genes involved in the regulation of reproduction and in epigenetic signalling in the livers and gonads. We found evidence for associations between DNA promotor methylation and transcription for esr1 (gonads and female livers), amh (gonads) and dnmt1 (livers). In the liver, esr1 was shown to be significantly over-expressed in females compared to males, and its promoter was significantly hypo-methylated in females compared to males. In the gonads, genes involved in epigenetic processes including dnmt1, dnmt3 and hdac1 were over-expressed in the ovary compared to the testis. In addition, dnmt1 and dnmt3 transcription in the testis was found to be strongly correlated with global DNA methylation. These data provide evidence of the sex-specific epigenetic regulation and transcription of genes involved in reproduction and epigenetic signalling in a commonly used vertebrate model.
Leveraging DNA methylation quantitative trait loci to characterize the relationship between methylomic variation, gene expression and complex traits
Eilis Hannon,
Tyler J Gorrie-Stone,
Melissa C Smart,
Joe Burrage,
Amanda Hughes,
Yanchun Bao,
Meena Kumari
+ 2 more
Eilis Hannon,
Tyler J Gorrie-Stone,
Melissa C Smart,
Joe Burrage,
Amanda Hughes,
Yanchun Bao,
Meena Kumari,
Leonard C Schalkwyk,
Jonathan Mill
ABSTRACT
Characterizing the complex relationship between genetic, epigenetic and transcriptomic variation has the potential to increase understanding about the mechanisms underpinning health and disease phenotypes. In this study, we describe the most comprehensive analysis of common genetic variation on DNA methylation (DNAm) to date, using the Illumina EPIC array to profile samples from the UK Household Longitudinal study. We identified 12,689,548 significant DNA methylation quantitative trait loci (mQTL) associations (P < 6.52x10
-14
) occurring between 2,907,234 genetic variants and 93,268 DNAm sites, including a large number not identified using previous DNAm-profiling methods. We demonstrate the utility of these data for interpreting the functional consequences of common genetic variation associated with > 60 human traits, using
S
ummary data–based
M
endelian
R
andomization (SMR) to identify 1,662 pleiotropic associations between 36 complex traits and 1,246 DNAm sites. We also use SMR to characterize the relationship between DNAm and gene expression, identifying 6,798 pleiotropic associations between 5,420 DNAm sites and the transcription of 1,702 genes. Our mQTL database and SMR results are available via a searchable online database (
http://www.epigenomicslab.com/online-data-resources/
) as a resource to the research community.
Peripheral DNA methylation, cognitive decline and brain aging: pilot findings from the Whitehall II imaging study
Leonidas Chouliaras,
Ehsan Pishva,
Rita Haapakoski,
Eniko Zsoldos,
Abda Mahmood,
Nicola Filippini,
Joe Burrage
+ 4 more
Leonidas Chouliaras,
Ehsan Pishva,
Rita Haapakoski,
Eniko Zsoldos,
Abda Mahmood,
Nicola Filippini,
Joe Burrage,
Jonathan Mill,
Mika Kivimki,
Katie Lunnon,
Klaus P Ebmeier
AIM: The present study investigated the link between peripheral DNA methylation (DNAm), cognitive impairment and brain aging.
METHODS: We tested the association between blood genome-wide DNAm profiles using the Illumina 450K arrays, cognitive dysfunction and brain MRI measures in selected participants of the Whitehall II imaging sub-study.
RESULTS: Eight differentially methylated regions were associated with cognitive impairment. Accelerated aging based on the Hannum epigenetic clock was associated with mean diffusivity and global fractional anisotropy. We also identified modules of co-methylated loci associated with white matter hyperintensities. These co-methylation modules were enriched among pathways relevant to β-amyloid processing and glutamatergic signaling.
CONCLUSION: Our data support the notion that blood DNAm changes may have utility as a biomarker for cognitive dysfunction and brain aging.
Genome-wide association analyses identify 44 risk variants and refine the genetic architecture of major depression
Naomi R. Wray,
Stephan Ripke,
Manuel Mattheisen,
Maciej Trzaskowski,
Enda M. Byrne,
Abdel Abdellaoui,
Mark J. Adams
+ 212 more
Naomi R. Wray,
Stephan Ripke,
Manuel Mattheisen,
Maciej Trzaskowski,
Enda M. Byrne,
Abdel Abdellaoui,
Mark J. Adams,
Esben Agerbo,
Tracy M. Air,
Till M. F. Andlauer,
Silviu-Alin Bacanu,
Marie Bækvad-Hansen,
Aartjan F. T. Beekman,
Tim B. Bigdeli,
Elisabeth B. Binder,
Douglas R. H. Blackwood,
Julien Bryois,
Henriette N. Buttenschøn,
Jonas Bybjerg-Grauholm,
Na Cai,
Enrique Castelao,
Jane Hvarregaard Christensen,
Toni-Kim Clarke,
Jonathan I. R. Coleman,
Lucía Colodro-Conde,
Baptiste Couvy-Duchesne,
Nick Craddock,
Gregory E. Crawford,
Cheynna A. Crowley,
Hassan S. Dashti,
Gail Davies,
Ian J. Deary,
Franziska Degenhardt,
Eske M. Derks,
Nese Direk,
Conor V. Dolan,
Erin C. Dunn,
Thalia C. Eley,
Nicholas Eriksson,
Valentina Escott-Price,
Farnush Hassan Farhadi Kiadeh,
Hilary K. Finucane,
Andreas J. Forstner,
Josef Frank,
Héléna A. Gaspar,
Michael Gill,
Paola Giusti-Rodríguez,
Fernando S. Goes,
Scott D. Gordon,
Jakob Grove,
Lynsey S. Hall,
Eilis Hannon,
Christine Søholm Hansen,
Thomas F. Hansen,
Stefan Herms,
Ian B. Hickie,
Per Hoffmann,
Georg Homuth,
Carsten Horn,
Jouke-Jan Hottenga,
David M. Hougaard,
Ming Hu,
Craig L. Hyde,
Marcus Ising,
Rick Jansen,
Fulai Jin,
Eric Jorgenson,
James A. Knowles,
Isaac S. Kohane,
Julia Kraft,
Warren W. Kretzschmar,
Jesper Krogh,
Zoltán Kutalik,
Jacqueline M. Lane,
Yihan Li,
Yun Li,
Penelope A. Lind,
Xiaoxiao Liu,
Leina Lu,
Donald J. MacIntyre,
Dean F. MacKinnon,
Robert M. Maier,
Wolfgang Maier,
Jonathan Marchini,
Hamdi Mbarek,
Patrick McGrath,
Peter McGuffin,
Sarah E. Medland,
Divya Mehta,
Christel M. Middeldorp,
Evelin Mihailov,
Yuri Milaneschi,
Lili Milani,
Jonathan Mill,
Francis M. Mondimore,
Grant W. Montgomery,
Sara Mostafavi,
Niamh Mullins,
Matthias Nauck,
Bernard Ng,
Michel G. Nivard,
Dale R. Nyholt,
Paul F. O’Reilly,
Hogni Oskarsson,
Michael J. Owen,
Jodie N. Painter,
Carsten Bøcker Pedersen,
Marianne Giørtz Pedersen,
Roseann E. Peterson,
Erik Pettersson,
Wouter J. Peyrot,
Giorgio Pistis,
Danielle Posthuma,
Shaun M. Purcell,
Jorge A. Quiroz,
Per Qvist,
John P. Rice,
Brien P. Riley,
Margarita Rivera,
Saira Saeed Mirza,
Richa Saxena,
Robert Schoevers,
Eva C. Schulte,
Ling Shen,
Jianxin Shi,
Stanley I. Shyn,
Engilbert Sigurdsson,
Grant B. C. Sinnamon,
Johannes H. Smit,
Daniel J. Smith,
Hreinn Stefansson,
Stacy Steinberg,
Craig A. Stockmeier,
Fabian Streit,
Jana Strohmaier,
Katherine E. Tansey,
Henning Teismann,
Alexander Teumer,
Wesley Thompson,
Pippa A. Thomson,
Thorgeir E. Thorgeirsson,
Chao Tian,
Matthew Traylor,
Jens Treutlein,
Vassily Trubetskoy,
André G. Uitterlinden,
Daniel Umbricht,
Sandra Van der Auwera,
Albert M. van Hemert,
Alexander Viktorin,
Peter M. Visscher,
Yunpeng Wang,
Bradley T. Webb,
Shantel Marie Weinsheimer,
Jürgen Wellmann,
Gonneke Willemsen,
Stephanie H. Witt,
Yang Wu,
Hualin S. Xi,
Jian Yang,
Futao Zhang,
eQTLGen,
23andMe,
Volker Arolt,
Bernhard T. Baune,
Klaus Berger,
Dorret I. Boomsma,
Sven Cichon,
Udo Dannlowski,
E. C. J. de Geus,
J. Raymond DePaulo,
Enrico Domenici,
Katharina Domschke,
Tõnu Esko,
Hans J. Grabe,
Steven P. Hamilton,
Caroline Hayward,
Andrew C. Heath,
David A. Hinds,
Kenneth S. Kendler,
Stefan Kloiber,
Glyn Lewis,
Qingqin S. Li,
Susanne Lucae,
Pamela F. A. Madden,
Patrik K. Magnusson,
Nicholas G. Martin,
Andrew M. McIntosh,
Andres Metspalu,
Ole Mors,
Preben Bo Mortensen,
Bertram Müller-Myhsok,
Merete Nordentoft,
Markus M. Nöthen,
Michael C. O’Donovan,
Sara A. Paciga,
Nancy L. Pedersen,
Brenda W. J. H. Penninx,
Roy H. Perlis,
David J. Porteous,
James B. Potash,
Martin Preisig,
Marcella Rietschel,
Catherine Schaefer,
Thomas G. Schulze,
Jordan W. Smoller,
Kari Stefansson,
Henning Tiemeier,
Rudolf Uher,
Henry Völzke,
Myrna M. Weissman,
Thomas Werge,
Ashley R. Winslow,
Cathryn M. Lewis,
Douglas F. Levinson,
Gerome Breen,
Anders D. Børglum,
Patrick F. Sullivan,
the Major Depressive Disorder Working Group of the Psychiatric Genomics Consortium
Major depressive disorder (MDD) is a common illness accompanied by considerable morbidity, mortality, costs, and heightened risk of suicide. We conducted a genome-wide association meta-analysis based in 135,458 cases and 344,901 controls and identified 44 independent and significant loci. The genetic findings were associated with clinical features of major depression and implicated brain regions exhibiting anatomical differences in cases. Targets of antidepressant medications and genes involved in gene splicing were enriched for smaller association signal. We found important relationships of genetic risk for major depression with educational attainment, body mass, and schizophrenia: lower educational attainment and higher body mass were putatively causal, whereas major depression and schizophrenia reflected a partly shared biological etiology. All humans carry lesser or greater numbers of genetic risk factors for major depression. These findings help refine the basis of major depression and imply that a continuous measure of risk underlies the clinical phenotype.
DNA methylation and inflammation marker profiles associated with a history of depression
Bethany Crawford,
Zoe Craig,
Georgina Mansell,
Isobel White,
Adam Smith,
Steve Spaull,
Jennifer Imm
+ 9 more
Bethany Crawford,
Zoe Craig,
Georgina Mansell,
Isobel White,
Adam Smith,
Steve Spaull,
Jennifer Imm,
Eilis Hannon,
Andrew Wood,
Hanieh Yaghootkar,
Yingjie Ji,
Major Depressive Disorder Working Group of the Psychiatric Genomics Consortium,
Niamh Mullins,
Cathryn M Lewis,
Jonathan Mill,
Therese M Murphy
Depression is a common and disabling disorder, representing a major social and economic health issue. Moreover, depression is associated with the progression of diseases with an inflammatory etiology including many inflammatory-related disorders. At the molecular level, the mechanisms by which depression might promote the onset of these diseases and associated immune-dysfunction are not well understood. In this study we assessed genome-wide patterns of DNA methylation in whole blood-derived DNA obtained from individuals with a self-reported history of depression (n = 100) and individuals without a history of depression (n = 100) using the Illumina 450K microarray. Our analysis identified six significant (Šidák corrected P < 0.05) depression-associated differentially methylated regions (DMRs); the top-ranked DMR was located in exon 1 of the LTB4R2 gene (Šidák corrected P = 1.27 × 10-14). Polygenic risk scores (PRS) for depression were generated and known biological markers of inflammation, telomere length (TL) and IL-6, were measured in DNA and serum samples, respectively. Next, we employed a systems-level approach to identify networks of co-methylated loci associated with a history of depression, in addition to depression PRS, TL and IL-6 levels. Our analysis identified one depression-associated co-methylation module (P = 0.04). Interestingly, the depression-associated module was highly enriched for pathways related to immune function and was also associated with TL and IL-6 cytokine levels. In summary, our genome-wide DNA methylation analysis of individuals with and without a self-reported history of depression identified several candidate DMRs of potential relevance to the pathogenesis of depression and its associated immune-dysfunction phenotype.
Which Risk Factors Causally Influence Dementia? A Systematic Review of Mendelian Randomization Studies
Elżbieta Kuźma,
Eilis Hannon,
Ang Zhou,
Ilianna Lourida,
Alison Bethel,
Deborah A. Levine,
Katie Lunnon
+ 3 more
Elżbieta Kuźma,
Eilis Hannon,
Ang Zhou,
Ilianna Lourida,
Alison Bethel,
Deborah A. Levine,
Katie Lunnon,
Jo Thompson-Coon,
Elina Hyppönen,
David J. Llewellyn
BACKGROUND: Numerous risk factors for dementia are well established, though the causal nature of these associations remains unclear.
OBJECTIVE: To systematically review Mendelian randomization (MR) studies investigating causal relationships between risk factors and global cognitive function or dementia.
METHODS: We searched five databases from inception to February 2017 and conducted citation searches including MR studies investigating the association between any risk factor and global cognitive function, all-cause dementia or dementia subtypes. Two reviewers independently assessed titles and abstracts, full-texts, and study quality.
RESULTS: We included 18 MR studies investigating education, lifestyle factors, cardiovascular factors and related biomarkers, diabetes related and other endocrine factors, and telomere length. Studies were of predominantly good quality, however eight received low ratings for sample size and statistical power. The most convincing causal evidence was found for an association of shorter telomeres with increased risk of Alzheimer's disease (AD). Causal evidence was weaker for smoking quantity, vitamin D, homocysteine, systolic blood pressure, fasting glucose, insulin sensitivity, and high-density lipoprotein cholesterol. Well-replicated associations were not present for most exposures and we cannot fully discount survival and diagnostic bias, or the potential for pleiotropic effects.
CONCLUSIONS: Genetic evidence supported a causal association between telomere length and AD, whereas limited evidence for other risk factors was largely inconclusive with tentative evidence for smoking quantity, vitamin D, homocysteine, and selected metabolic markers. The lack of stronger evidence for other risk factors may reflect insufficient statistical power. Larger well-designed MR studies would therefore help establish the causal status of these dementia risk factors.
Dynamic expression of risk genes for schizophrenia and bipolar disorder across development
Nicholas E Clifton,
Eilís Hannon,
Florio Arianna Di,
Kerrie L Thomas,
Peter A Holmans,
James TR Walters,
Michael C O’Donovan
+ 3 more
Nicholas E Clifton,
Eilís Hannon,
Florio Arianna Di,
Kerrie L Thomas,
Peter A Holmans,
James TR Walters,
Michael C O’Donovan,
Michael J Owen,
Andrew J Pocklington,
Jeremy Hall
A
BSTRACT
Common genetic variation contributes a substantial proportion of risk for both schizophrenia and bipolar disorder. Furthermore, there is evidence of significant, but not complete, overlap in genetic risk between schizophrenia and bipolar disorder. It has been hypothesised that genetic variants conferring risk for these disorders do so by influencing brain development, leading to the later emergence of symptoms. The comparative profile of risk gene expression for schizophrenia and bipolar disorder across development over different brain regions however remains unclear. Using genotypes derived from genome wide associations studies of the largest available cohorts of patients and control subjects, we investigated whether genes enriched for schizophrenia and bipolar disorder association show a bias for expression across any of 13 developmental stages in prefrontal cortical and subcortical brain regions. We show that genes associated with schizophrenia have a strong bias towards increased expression in the prefrontal cortex during early midfetal development and early infancy, and decreased expression during late childhood which normalises in adolescence. Risk-associated genes for bipolar disorder shared this postnatal expression profile but did not exhibit a bias towards expression at any prenatal stage. These results emphasise the dynamic expression of genes harbouring risk for schizophrenia and bipolar disorder across prefrontal cortex development and support the view that prenatal neurodevelopmental events are more strongly associated with schizophrenia than bipolar disorder.
Prenatal immune activation alters the adult neural epigenome but can be partly stabilised by a n-3 polyunsaturated fatty acid diet
Paul Basil,
Qi Li,
Hongsheng Gui,
Tomy C. K. Hui,
Vicki H. M. Ling,
Chloe C. Y. Wong,
Jonathan Mill
+ 2 more
Paul Basil,
Qi Li,
Hongsheng Gui,
Tomy C. K. Hui,
Vicki H. M. Ling,
Chloe C. Y. Wong,
Jonathan Mill,
Grainne M. McAlonan,
Pak-Chung Sham
An unstable epigenome is implicated in the pathophysiology of neurodevelopmental disorders such as schizophrenia and autism. This is important because the epigenome is potentially modifiable. We have previously reported that adult offspring exposed to maternal immune activation (MIA) prenatally have significant global DNA hypomethylation in the hypothalamus. However, what genes had altered methylation state, their functional effects on gene expression and whether these changes can be moderated, have not been addressed. In this study, we used next-generation sequencing (NGS) for methylome profiling in a MIA rodent model of neurodevelopmental disorders. We assessed whether differentially methylated regions (DMRs) affected the chromatin state by mapping known DNase I hypersensitivity sites (DHSs), and selected overlapping genes to confirm a functional effect of MIA on gene expression using qPCR. Finally, we tested whether methylation differences elicited by MIA could be limited by post-natal dietary (omega) n-3 polyunsaturated fatty acid (PUFA) supplementation. These experiments were conducted using hypothalamic brain tissue from 12-week-old offspring of mice injected with viral analogue PolyI:C on gestation day 9 of pregnancy or saline on gestation day 9. Half of the animals from each group were fed a diet enriched with n-3 PUFA from weaning (MIA group, n = 12 units, n = 39 mice; Control group, n = 12 units, n = 38 mice). The results confirmed our previous finding that adult offspring exposed to MIA prenatally had significant global DNA hypomethylation. Furthermore, genes linked to synaptic plasticity were over-represented among differentially methylated genes following MIA. More than 80% of MIA-induced hypomethylated sites, including those affecting chromatin state and MECP2 binding, were stabilised by the n-3 PUFA intervention. MIA resulted in increased expression of two of the ‘top five’ genes identified from an integrated analysis of DMRs, DHSs and MECP2 binding sites, namely Abat (t = 2.46, p < 0.02) and Gnas9 (t = 2.96, p < 0.01), although these changes were not stabilised by dietary intervention. Thus, prenatal MIA exposure impacts upon the epigenomic regulation of gene pathways linked to neurodevelopmental conditions; and many of the changes can be attenuated by a low-cost dietary intervention.
Properties of the epigenetic clock and age acceleration
Louis El Khoury,
Tyler Gorrie-Stone,
Melissa Smart,
Amanda Hughes,
Yanchun Bao,
Alexandria Andrayas,
Joe Burrage
+ 4 more
Louis El Khoury,
Tyler Gorrie-Stone,
Melissa Smart,
Amanda Hughes,
Yanchun Bao,
Alexandria Andrayas,
Joe Burrage,
Eilis Hannon,
Meena Kumari,
Jonathan Mill,
Leonard C Schalkwyk
Abstract
Background
The methylation status of numerous CpG sites in the human genome varies with age. The Horvath epigenetic clock used a wide variety of published DNA methylation data to produce an age prediction that has been widely used to, predict age in unknown samples, and draw conclusions about speed of ageing in various tissues, environments, and diseases. Despite its utility, there are a number of assumptions in the model that require examination. We explore the characteristics of the model in whole blood and multiple brain regions from older people, who are not well represented in the original training data, and in blood from a cross-sectional population study.
Results
We find that the model systematically underestimates age in tissues from older people. A decrease in slope of the predicted ages were observed at approximately 60 years, indicating that some loci in the model may change differently with age, and that age acceleration measures will themselves be age-dependent. This is seen most strongly in the cerebellum but is also present in other examined tissues, and is consistently observed in multiple datasets. An apparent association of Alzheimer’s disease with age acceleration disappears when age is used as a covariate. Association tests in the literature use a variety of methods for calculating age acceleration and often do not use age as a covariate. This is a potential cause of misleading findings.
Conclusions
Associations of phenotypes with age acceleration should be evaluated cautiously, and chronological age should be included as a covariate in all analyses.
Application of a novel molecular method to age free‐living wild Bechstein's bats
Patrick G. R. Wright,
Fiona Mathews,
Henry Schofield,
Colin Morris,
Joe Burrage,
Adam Smith,
Emma L. Dempster
+ 1 more
Patrick G. R. Wright,
Fiona Mathews,
Henry Schofield,
Colin Morris,
Joe Burrage,
Adam Smith,
Emma L. Dempster,
Patrick B. Hamilton
The age profile of populations fundamentally affects their conservation status. Yet, age is frequently difficult to assess in wild animals. Here, we assessed the use of DNA methylation of homologous genes to establish the age structure of a rare and elusive wild mammal: the Bechstein's bat (Myotis bechsteinii). We collected 62 wing punches from individuals whose ages were known as a result of a long-term banding study. DNA methylation was measured at seven CpG sites from three genes, which have previously shown age-associated changes in humans and laboratory mice. All CpG sites from the tested genes showed a significant relationship between DNA methylation and age, both individually and in combination (multiple linear regression R2 = 0.58, p < 0.001). Despite slight approximation around estimates, the approach is sufficiently precise to place animals into practically useful age cohorts. This method is of considerable practical benefit as it can reliably age individual bats. It is also much faster than traditional capture-mark-recapture techniques, with the potential to collect information on the age structure of an entire colony from a single sampling session to better inform conservation actions for Bechstein's bats. By identifying three genes where DNA methylation correlates with age across distantly related species, this study also suggests that the technique can potentially be applied across a wide range of mammals.
Genome-wide methylomic analysis in individuals with HNF1B intragenic mutation and 17q12 microdeletion
Rhian L. Clissold,
Beth Ashfield,
Joe Burrage,
Eilis Hannon,
Coralie Bingham,
Jonathan Mill,
Andrew Hattersley
+ 1 more
Rhian L. Clissold,
Beth Ashfield,
Joe Burrage,
Eilis Hannon,
Coralie Bingham,
Jonathan Mill,
Andrew Hattersley,
Emma L. Dempster
Heterozygous mutation of the transcription factor HNF1B is the most common cause of monogenetic developmental renal disease. Disease-associated mutations fall into two categories: HNF1B intragenic mutations and a 1.3 Mb deletion at chromosome 17q12. An increase in neurodevelopmental disorders has been observed in individuals harbouring the 17q12 deletion but not in patients with HNF1B coding mutations.Previous investigations have concentrated on identifying a genetic cause for the increase in behavioural problems seen in 17q12 deletion carriers. We have taken the alternative approach of investigating the DNA methylation profile of these two HNF1B genotype groups along with controls matched for age, gender and diabetes status using the Illumina 450K DNA methylation array (total sample n = 60).We identified a number of differentially methylated probes (DMPs) that were associated with HNF1B-associated disease and passed our stringent experiment-wide significance threshold. These associations were largely driven by the deletion patients and the majority of the significant probes mapped to the 17q12 deletion locus. The observed changes in DNA methylation at this locus were not randomly dispersed and occurred in clusters, suggesting a regulatory mechanism reacting to haploinsufficiency across the entire deleted region.Along with these deletion-specific changes in DNA methylation, we also identified a shared DNA methylation signature in both mutation and deletion patient groups indicating that haploinsufficiency of HNF1B impacts on the methylome of a number of genes, giving further insight to the role of HNF1B.
Genetics & the Geography of Health, Behavior, and Attainment
Daniel W Belsky,
Avshalom Caspi,
Louise Arseneault,
David L Corcoran,
Benjamin W Domingue,
Kathleen Mullan Harris,
Renate M Houts
+ 7 more
Daniel W Belsky,
Avshalom Caspi,
Louise Arseneault,
David L Corcoran,
Benjamin W Domingue,
Kathleen Mullan Harris,
Renate M Houts,
Jonathan S Mill,
Terrie E Moffitt,
Joseph Prinz,
Karen Sugden,
Jasmin Wertz,
Benjamin Williams,
Candice L Odgers
Abstract
People’s life chances can be predicted by their neighborhoods. This observation is driving efforts to improve lives by changing neighborhoods. Some neighborhood effects may be causal, supporting neighborhood-level interventions. Other neighborhood effects may reflect selection of families with different characteristics into different neighborhoods, supporting interventions that target families/individuals directly. To test how selection affects different neighborhood-linked problems, we linked neighborhood data with genetic, health, and social-outcome data for >7,000 European-descent UK and US young people in the E-Risk and Add Health Studies. We tested selection/concentration of genetic risks for obesity, schizophrenia, teen-pregnancy, and poor educational outcomes in high-risk neighborhoods, including genetic analysis of neighborhood mobility. Findings argue against genetic selection/concentration as an explanation for neighborhood gradients in obesity and mental-health problems, suggesting neighborhoods may be causal. In contrast, modest genetic selection/concentration was evident for teen-pregnancy and poor educational outcomes, suggesting neighborhood effects for these outcomes should be interpreted with care.
Characterizing genetic and environmental influences on variable DNA methylation using monozygotic and dizygotic twins
Eilis Hannon,
Olivia Knox,
Karen Sugden,
Joe Burrage,
Chloe C. Y. Wong,
Daniel W. Belsky,
David L. Corcoran
+ 4 more
Eilis Hannon,
Olivia Knox,
Karen Sugden,
Joe Burrage,
Chloe C. Y. Wong,
Daniel W. Belsky,
David L. Corcoran,
Louise Arseneault,
Terrie E. Moffitt,
Avshalom Caspi,
Jonathan Mill
Variation in DNA methylation is being increasingly associated with health and disease outcomes. Although DNA methylation is hypothesized to be a mechanism by which both genetic and non-genetic factors can influence the regulation of gene expression, little is known about the extent to which DNA methylation at specific sites is influenced by heritable as well as environmental factors. We quantified DNA methylation in whole blood at age 18 in a birth cohort of 1,464 individuals comprising 426 monozygotic (MZ) and 306 same-sex dizygotic (DZ) twin pairs. Site-specific levels of DNA methylation were more strongly correlated across the genome between MZ than DZ twins. Structural equation models revealed that although the average contribution of additive genetic influences on DNA methylation across the genome was relatively low, it was notably elevated at the highly variable sites characterized by intermediate levels of DNAm that are most relevant for epigenetic epidemiology. Sites at which variable DNA methylation was most influenced by genetic factors were significantly enriched for DNA methylation quantitative trait loci (mQTL) effects, and overlapped with sites where inter-individual variation correlates across tissues. Finally, we show that DNA methylation at sites robustly associated with environmental exposures such as tobacco smoking and obesity is also influenced by additive genetic effects, highlighting the need to control for genetic background in analyses of exposure-associated DNA methylation differences. Estimates of the contribution of genetic and environmental influences to DNA methylation at all sites profiled in this study are available as a resource for the research community (http://www.epigenomicslab.com/online-data-resources).
Genome-wide DNA methylation profiling identifies convergent molecular signatures associated with idiopathic and syndromic forms of autism in post-mortem human brain tissue
Chloe C.Y. Wong,
Rebecca G. Smith,
Eilis Hannon,
Gokul Ramaswami,
Neelroop N. Parikshak,
Elham Assary,
Claire Troakes
+ 6 more
Chloe C.Y. Wong,
Rebecca G. Smith,
Eilis Hannon,
Gokul Ramaswami,
Neelroop N. Parikshak,
Elham Assary,
Claire Troakes,
Jeremie Poschmann,
Leonard C. Schalkwyk,
Wenjie Sun,
Shyam Prabhakar,
Daniel H. Geschwind,
Jonathan Mill
Abstract
Autism spectrum disorder (ASD) encompasses a collection of complex neuropsychiatric disorders characterized by deficits in social functioning, communication and repetitive behavior. Building on recent studies supporting a role for developmentally moderated regulatory genomic variation in the molecular etiology of ASD, we quantified genome-wide patterns of DNA methylation in 233 post-mortem tissues samples isolated from three brain regions (prefrontal cortex, temporal cortex and cerebellum) dissected from 43 ASD patients and 38 non-psychiatric control donors. We identified widespread differences in DNA methylation associated with idiopathic ASD (iASD), with consistent signals in both cortical regions that were distinct to those observed in the cerebellum. Individuals carrying a duplication on chromosome 15q (dup15q), representing a genetically-defined subtype of ASD, were characterized by striking differences in DNA methylation across a discrete domain spanning an imprinted gene cluster within the duplicated region. In addition to the dramatic cis-effects on DNA methylation observed in dup15q carriers, we identified convergent methylomic signatures associated with both iASD and dup15q, reflecting the findings from previous studies of gene expression and H3K27ac. Cortical co-methylation network analysis identified a number of co-methylated modules significantly associated with ASD that are enriched for genomic regions annotated to genes involved in the immune system, synaptic signalling and neuronal regulation. Our study represents the first systematic analysis of DNA methylation associated with ASD across multiple brain regions, providing novel evidence for convergent molecular signatures associated with both idiopathic and syndromic autism.
Bigmelon: tools for analysing large DNA methylation datasets
Tyler J Gorrie-Stone,
Melissa C Smart,
Ayden Saffari,
Karim Malki,
Eilis Hannon,
Joe Burrage,
Jonathan Mill
+ 2 more
Tyler J Gorrie-Stone,
Melissa C Smart,
Ayden Saffari,
Karim Malki,
Eilis Hannon,
Joe Burrage,
Jonathan Mill,
Meena Kumari,
Leonard C Schalkwyk
MOTIVATION: The datasets generated by DNA methylation analyses are getting bigger. With the release of the HumanMethylationEPIC micro-array and datasets containing thousands of samples, analyses of these large datasets using R are becoming impractical due to large memory requirements. As a result there is an increasing need for computationally efficient methodologies to perform meaningful analysis on high dimensional data.
RESULTS: Here we introduce the bigmelon R package, which provides a memory efficient workflow that enables users to perform the complex, large scale analyses required in epigenome wide association studies (EWAS) without the need for large RAM. Building on top of the CoreArray Genomic Data Structure file format and libraries packaged in the gdsfmt package, we provide a practical workflow that facilitates the reading-in, preprocessing, quality control and statistical analysis of DNA methylation data.We demonstrate the capabilities of the bigmelon package using a large dataset consisting of 1193 human blood samples from the Understanding Society: UK Household Longitudinal Study, assayed on the EPIC micro-array platform.
AVAILABILITY AND IMPLEMENTATION: The bigmelon package is available on Bioconductor (http://bioconductor.org/packages/bigmelon/). The Understanding Society dataset is available at https://www.understandingsociety.ac.uk/about/health/data upon request.
SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.
Using three-dimensional regulatory chromatin interactions from adult and fetal cortex to interpret genetic results for psychiatric disorders and cognitive traits
Paola Giusti-Rodríguez,
Leina Lu,
Yuchen Yang,
Cheynna A Crowley,
Xiaoxiao Liu,
Ivan Juric,
Joshua S Martin
+ 35 more
Paola Giusti-Rodríguez,
Leina Lu,
Yuchen Yang,
Cheynna A Crowley,
Xiaoxiao Liu,
Ivan Juric,
Joshua S Martin,
Armen Abnousi,
S. Colby Allred,
NaEshia Ancalade,
Nicholas J Bray,
Gerome Breen,
Julien Bryois,
Cynthia M Bulik,
James J Crowley,
Jerry Guintivano,
Philip R Jansen,
George J Jurjus,
Yan Li,
Gouri Mahajan,
Sarah Marzi,
Jonathan Mill,
Michael C O’Donovan,
James C Overholser,
Michael J Owen,
Antonio F Pardiñas,
Sirisha Pochareddy,
Danielle Posthuma,
Grazyna Rajkowska,
Gabriel Santpere,
Jeanne E Savage,
Nenad Sestan,
Yurae Shin,
Craig A Stockmeier,
James TR Walters,
Shuyang Yao,
Eating Disorders Working Group of the Psychiatric Genomics Consortium Bipolar Disorder Working Group of the Psychiatric Genomics Consortium,
Gregory E Crawford,
Fulai Jin,
Ming Hu,
Yun Li,
Patrick F Sullivan
Genome-wide association studies have identified hundreds of genetic associations for complex psychiatric disorders and cognitive traits. However, interpretation of most of these findings is complicated by the presence of many significant and highly correlated genetic variants located in non-coding regions. Here, we address this issue by creating a high-resolution map of the three-dimensional (3D) genome organization by applying Hi-C to adult and fetal brain cortex with concomitant RNA-seq, open chromatin (ATAC-seq), and ChIP-seq data (H3K27ac, H3K4me3, and CTCF). Extensive analyses established the quality, information content, and salience of these new Hi-C data. We used these data to connect 938 significant genetic loci for schizophrenia, intelligence, ADHD, alcohol dependence, Alzheimer's disease, anorexia nervosa, autism spectrum disorder, bipolar disorder, major depression, and educational attainment to 8,595 genes (with 42.1% of these genes implicated more than once). We show that assigning genes to traits based on proximity provides a limited view of the complexity of GWAS findings and that gene set analyses based on functional genomic data provide an expanded view of the biological processes involved in the etiology of schizophrenia and other complex brain traits.
Autosomal genetic variation is associated with DNA methylation in regions variably escaping X-chromosome inactivation
René Luijk,
Haoyu Wu,
Cavin K Ward-Caviness,
Eilis Hannon,
Elena Carnero-Montoro,
Josine L. Min,
Pooja Mandaviya
+ 22 more
René Luijk,
Haoyu Wu,
Cavin K Ward-Caviness,
Eilis Hannon,
Elena Carnero-Montoro,
Josine L. Min,
Pooja Mandaviya,
Martina Müller-Nurasyid,
Hailiang Mei,
der Maarel Silvere M. van,
BIOS Consortium,
Caroline Relton,
Jonathan Mill,
Melanie Waldenberger,
Jordana T. Bell,
Rick Jansen,
Alexandra Zhernakova,
Lude Franke,
Hoen Peter A. C. ‘t,
Dorret I. Boomsma,
Duijn Cornelia M. van,
Greevenbroek Marleen M. J. van,
Jan H. Veldink,
Cisca Wijmenga,
Meurs Joyce van,
Lucia Daxinger,
P. Eline Slagboom,
Zwet Erik W. van,
Bastiaan T. Heijmans
X-chromosome inactivation (XCI), i.e., the inactivation of one of the female X chromosomes, restores equal expression of X-chromosomal genes between females and males. However, ~10% of genes show variable degrees of escape from XCI between females, although little is known about the causes of variable XCI. Using a discovery data-set of 1867 females and 1398 males and a replication sample of 3351 females, we show that genetic variation at three autosomal loci is associated with female-specific changes in X-chromosome methylation. Through cis-eQTL expression analysis, we map these loci to the genes SMCHD1/METTL4, TRIM6/HBG2, and ZSCAN9. Low-expression alleles of the loci are predominantly associated with mild hypomethylation of CpG islands near genes known to variably escape XCI, implicating the autosomal genes in variable XCI. Together, these results suggest a genetic basis for variable escape from XCI and highlight the potential of a population genomics approach to identify genes involved in XCI.
Mis-expression of the Alzheimer’s disease associated gene Ankyrin causes memory loss and shortened lifespan in Drosophila
James P Higham, Bilal R Malik, Edgar Buhl, Jenny Dawson, Anna S Ogier, Katie Lunnon, James JL Hodge
James P Higham,
Bilal R Malik,
Edgar Buhl,
Jenny Dawson,
Anna S Ogier,
Katie Lunnon,
James JL Hodge
ABSTRACT
Alzheimer’s disease (AD) is the most common form of dementia and is characterized by the accumulation of extracellular amyloid beta (Aβ) plaques and intracellular neurofibrillary tangles of hyperphosphorylated Tau, including the 4R0N isoform. Recent epigenome-wide association studies (EWAS) of AD have identified a number of loci that are differentially methylated in AD cortex. Indeed, hypermethylation of the
Ankyrin 1
(
ANK1
) gene in AD has been reported in the cortex in numerous different post-mortem brain cohorts. Little is known about the normal function of ANK1 in the healthy brain, nor the role it may play in AD. We have generated
Drosophila
models to allow us to functionally characterize
Drosophila Ank2
, the ortholog of human
ANK1
. These models have targeted reduction in the expression of
Ank2
in neurons. We find that
Drosophila
with reduced neuronal
Ank2
expression have shortened lifespan, reduced locomotion, reduced memory and reduced neuronal excitability similar to flies overexpressing either human mutant
APP
(that leads to Aβ42 production) and
MAPT
(that leads to 0N4R Tau). Therefore, we show that the mis-expression of
Ank2
can drive disease relevant processes and phenocopy some features of AD and we propose targeting ANK1 may have therapeutic potential. This represents the first study to characterize a gene implicated in AD, which was nominated from EWAS.
Author summary
The majority (>95%) of Alzheimer’s disease (AD) cases are sporadic, with their incidence attributed to common genetic mutations, epigenetic variation, aging and the environment. There is no cure for AD and only limited treatment options which only treat the symptoms of AD and only work in some people. Recent epigenome-wide association studies (EWAS) in AD have highlighted hypermethylation of the Ankyrin1 (
ANK1
) gene in AD cortex. Little is known of the normal role of the gene in the brain. Here, we have demonstrated that
Drosophila
with reduced neuronal expression of the
Drosophila
ortholog of human
ANK1 (Ank2)
, can drive AD relevant processes including locomotor difficulties, memory loss and shortened lifespan similar to expression of human amyloid-Beta or tau mutant proteins. Furthermore, increasing
Ank2
expression reversed the memory loss caused by expression of human amyloid-Beta or tau mutant proteins, suggesting that targeting
ANK1
may have therapeutic potential. This represents the first study to characterize a gene implicated in AD, which was nominated from EWAS.
A histone acetylome-wide association study of Alzheimer’s disease identifies disease-associated H3K27ac differences in the entorhinal cortex
Sarah J. Marzi,
Szi Kay Leung,
Teodora Ribarska,
Eilis Hannon,
Adam R. Smith,
Ehsan Pishva,
Jeremie Poschmann
+ 8 more
Sarah J. Marzi,
Szi Kay Leung,
Teodora Ribarska,
Eilis Hannon,
Adam R. Smith,
Ehsan Pishva,
Jeremie Poschmann,
Karen Moore,
Claire Troakes,
Safa Al-Sarraj,
Stephan Beck,
Stuart Newman,
Katie Lunnon,
Leonard C. Schalkwyk,
Jonathan Mill
We quantified genome-wide patterns of lysine H3K27 acetylation (H3K27ac) in entorhinal cortex samples from Alzheimer’s disease (AD) cases and matched controls using chromatin immunoprecipitation and highly parallel sequencing. We observed widespread acetylomic variation associated with AD neuropathology, identifying 4,162 differential peaks (false discovery rate < 0.05) between AD cases and controls. Differentially acetylated peaks were enriched in disease-related biological pathways and included regions annotated to genes involved in the progression of amyloid-β and tau pathology (for example, APP, PSEN1, PSEN2, and MAPT), as well as regions containing variants associated with sporadic late-onset AD. Partitioned heritability analysis highlighted a highly significant enrichment of AD risk variants in entorhinal cortex H3K27ac peak regions. AD-associated variable H3K27ac was associated with transcriptional variation at proximal genes including CR1, GPR22, KMO, PIM3, PSEN1, and RGCC. In addition to identifying molecular pathways associated with AD neuropathology, we present a framework for genome-wide studies of histone modifications in complex disease.
A cross-brain regions study of ANK1 DNA methylation in different neurodegenerative diseases
Adam R. Smith,
Rebecca G. Smith,
Joe Burrage,
Claire Troakes,
Safa Al-Sarraj,
Rajesh N. Kalaria,
Carolyn Sloan
+ 3 more
Adam R. Smith,
Rebecca G. Smith,
Joe Burrage,
Claire Troakes,
Safa Al-Sarraj,
Rajesh N. Kalaria,
Carolyn Sloan,
Andrew C. Robinson,
Jonathan Mill,
Katie Lunnon
Recent epigenome-wide association studies in Alzheimer's disease have highlighted consistent robust neuropathology-associated DNA hypermethylation of the ankyrin 1 (ANK1) gene in the cortex. The extent to which altered ANK1 DNA methylation is also associated with other neurodegenerative diseases is not currently known. In the present study, we used bisulfite pyrosequencing to quantify DNA methylation across 8 CpG sites within a 118 bp region of the ANK1 gene across multiple brain regions in Alzheimer's disease, Vascular dementia, Dementia with Lewy bodies, Huntington's disease, and Parkinson's disease. We demonstrate disease-associated ANK1 hypermethylation in the entorhinal cortex in Alzheimer's disease, Huntington's disease, and Parkinson's disease, whereas in donors with Vascular dementia and Dementia with Lewy bodies, we observed elevated ANK1 DNA methylation only in individuals with coexisting Alzheimer's disease pathology. We did not observe any disease-associated differential ANK1 DNA methylation in the striatum in Huntington's disease or the substantia nigra in Parkinson's disease. Our data suggest that ANK1 is characterized by region and disease-specific differential DNA methylation in multiple neurodegenerative diseases.
P3‐123: MAPPING GENOMIC CONSEQUENCES OF ALZHEIMER'S DISEASE PATHOLOGY IN AMYLOID AND TAU MOUSE MODELS
Isabel M.S. Castanho,
Tracey K. Murray,
Audrey Farbos,
Katie Lunnon,
David A. Collier,
Zeshan Ahmed,
Karen Moore
+ 2 more
Isabel M.S. Castanho,
Tracey K. Murray,
Audrey Farbos,
Katie Lunnon,
David A. Collier,
Zeshan Ahmed,
Karen Moore,
Michael J. O'Neill,
Jonathan Mill
F1‐02‐04: GENOMICS AND EPIGENOMICS ANALYSES IN THE EMIF‐AD MULTIMODAL BIOMARKER DISCOVERY STUDY
Shengjun Hong,
Valerija Dobricic,
Rebecca G. Smith,
Fahri Küçükali,
Fabian Kilpert,
Isabelle Bos,
Stephanie J.B. Vos
+ 25 more
Shengjun Hong,
Valerija Dobricic,
Rebecca G. Smith,
Fahri Küçükali,
Fabian Kilpert,
Isabelle Bos,
Stephanie J.B. Vos,
Rik Vandenberghe,
Philip Scheltens,
Sebastiaan Engelborghs,
Giovanni B. Frisoni,
Olivier Blin,
Jill Richardson,
Régis Bordet,
Magda Tsolaki,
Frans R.J. Verhey,
Julius Popp,
Pablo Martinez-Lage,
Alberto Lleó,
Peter Johannsen,
Lutz Frölich,
Alison L. Baird,
Frederik Barkhof,
Cristina Legido Quigley,
Simon Lovestone,
Johannes Streffer,
Pieter Jelle Visser,
Henrik Zetterberg,
Kristel Sleegers,
Broeckhoven Christine Van,
Katie Lunnon,
Lars Bertram
Characterizing the complex relationship between genetic, epigenetic, and transcriptomic variation has the potential to increase understanding about the mechanisms underpinning health and disease phenotypes. We undertook a comprehensive analysis of common genetic variation on DNA methylation (DNAm) by using the Illumina EPIC array to profile samples from the UK Household Longitudinal study. We identified 12,689,548 significant DNA methylation quantitative trait loci (mQTL) associations (p < 6.52 × 10-14) occurring between 2,907,234 genetic variants and 93,268 DNAm sites, including a large number not identified by previous DNAm-profiling methods. We demonstrate the utility of these data for interpreting the functional consequences of common genetic variation associated with > 60 human traits by using summary-data-based Mendelian randomization (SMR) to identify 1,662 pleiotropic associations between 36 complex traits and 1,246 DNAm sites. We also use SMR to characterize the relationship between DNAm and gene expression and thereby identify 6,798 pleiotropic associations between 5,420 DNAm sites and the transcription of 1,702 genes. Our mQTL database and SMR results are available via a searchable online database as a resource to the research community.
THE AUTHORS REPLY
Amanda Hughes,
Yanchun Bao,
Melissa Smart,
Tyler Gorrie-Stone,
Eilis Hannon,
Jonathan Mill,
Joe Burrage
+ 2 more
Amanda Hughes,
Yanchun Bao,
Melissa Smart,
Tyler Gorrie-Stone,
Eilis Hannon,
Jonathan Mill,
Joe Burrage,
Leo Schalkwyk,
Meena Kumari
Expression quantitative trait loci in the developing human brain and their enrichment in neuropsychiatric disorders
Heath E. O’Brien,
Eilis Hannon,
Matthew J. Hill,
Carolina C. Toste,
Matthew J. Robertson,
Joanne E. Morgan,
Gemma McLaughlin
+ 8 more
Heath E. O’Brien,
Eilis Hannon,
Matthew J. Hill,
Carolina C. Toste,
Matthew J. Robertson,
Joanne E. Morgan,
Gemma McLaughlin,
Cathryn M. Lewis,
Leonard C. Schalkwyk,
Lynsey S. Hall,
Antonio F. Pardiñas,
Michael J. Owen,
Michael C. O’Donovan,
Jonathan Mill,
Nicholas J. Bray
BackgroundGenetic influences on gene expression in the human fetal brain plausibly impact upon a variety of postnatal brain-related traits, including susceptibility to neuropsychiatric disorders. However, to date, there have been no studies that have mapped genome-wide expression quantitative trait loci (eQTL) specifically in the human prenatal brain.ResultsWe performed deep RNA sequencing and genome-wide genotyping on a unique collection of 120 human brains from the second trimester of gestation to provide the first eQTL dataset derived exclusively from the human fetal brain. We identify high confidence cis-acting eQTL at the individual transcript as well as whole gene level, including many mapping to a common inversion polymorphism on chromosome 17q21. Fetal brain eQTL are enriched among risk variants for postnatal conditions including attention deficit hyperactivity disorder, schizophrenia, and bipolar disorder. We further identify changes in gene expression within the prenatal brain that potentially mediate risk for neuropsychiatric traits, including increased expression of C4A in association with genetic risk for schizophrenia, increased expression of LRRC57 in association with genetic risk for bipolar disorder, and altered expression of multiple genes within the chromosome 17q21 inversion in association with variants influencing the personality trait of neuroticism.ConclusionsWe have mapped eQTL operating in the human fetal brain, providing evidence that these confer risk to certain neuropsychiatric disorders, and identifying gene expression changes that potentially mediate susceptibility to these conditions.
Sex differences in gene expression in the human fetal brain
Heath E. O’Brien,
Eilis Hannon,
Aaron R. Jeffries,
William Davies,
Matthew J. Hill,
Richard J. Anney,
Michael C. O’Donovan
+ 2 more
Heath E. O’Brien,
Eilis Hannon,
Aaron R. Jeffries,
William Davies,
Matthew J. Hill,
Richard J. Anney,
Michael C. O’Donovan,
Jonathan Mill,
Nicholas J. Bray
ABSTRACT
Widespread structural, chemical and molecular differences have been reported between the male and female human brain. Although several neurodevelopmental disorders are more commonly diagnosed in males, little is known regarding sex differences in early human brain development. Here, we used RNA sequencing data from a large collection of human brain samples from the second trimester of gestation (N = 120) to assess sex biases in gene expression within the human fetal brain. In addition to 43 genes (102 Ensembl transcripts) transcribed from the Y-chromosome in males, we detected sex differences in the expression of 2558 autosomal genes (2723 Ensembl transcripts) and 155 genes on the X-chromosome (207 Ensembl transcripts) at a false discovery rate (FDR) < 0.1. Genes exhibiting sex-biased expression in human fetal brain are enriched for high-confidence risk genes for autism and other developmental disorders. Male-biased genes are enriched for expression in neural progenitor cells, whereas female-biased genes are enriched for expression in Cajal-Retzius cells and glia. All gene- and transcript-level data are provided as an online resource (available at
http://fgen.psycm.cf.ac.uk/FBSeq1
) through which researchers can search, download and visualize data pertaining to sex biases in gene expression during early human brain development.
Integrated genetic and methylomic analyses identify shared biology between autism and autistic traits
Aicha Massrali, Helena Brunel, Eilis Hannon, Chloe Wong, iPSYCH-MINERvA Epigenetics Group, Simon Baron-Cohen, Varun Warrier
Aicha Massrali,
Helena Brunel,
Eilis Hannon,
Chloe Wong,
iPSYCH-MINERvA Epigenetics Group,
Simon Baron-Cohen,
Varun Warrier
Abstract
Previous studies have identified differences in DNA methylation in autistic individuals compared to neurotypical individuals. Yet, it is unclear if this extends to autistic traits – subclinical manifestation of autism features in the general population. Here, we investigate the association between DNA methylation at birth (cord blood), and scores on the Social and Communication Disorders Checklist (SCDC), a measure of autistic traits, in 701 8-year olds, by conducting a methylome-wide association study (MWAS) using DNA methylation data from cord-blood. Whilst did not identify significant loci demonstrating differential methylation, we observe a degree of overlap between the SCDC MWAS and post-mortem brain methylation signature in autism. Validating this, we observe an enrichment for genes that are dysregulated in the post-mortem autism brain. Finally, integrating genome-wide data from more than 40,000 individuals and mQTL maps from cord-blood, we demonstrate that mQTLs of CpGs associated with SCDC scores at different P-value thresholds are significantly shifted towards lower P-values in a GWAS for autism. We validate this using a GWAS of SCDC, and demonstrate a lack of enrichment in a GWAS of Alzheimer’s disease. Our results highlight the shared cross-tissue epigenetic architecture of autism and autistic traits, and demonstrate that mQTLs associated with methylation changes in childhood autistic traits are enriched for common genetic variants associated with autism and autistic traits.
Epigenetic studies of schizophrenia: current status and future directions
Schizophrenia is a chronic neuropsychiatric disorder characterized by episodes of psychosis and altered cognitive functioning. Epigenetic processes, which developmentally regulate gene expression via modifications to DNA, histone proteins, and chromatin, have been widely heralded as the ‘missing piece’ of the etiological puzzle for many neuropsychiatric and neurodevelopmental disorders, including schizophrenia. In this review, we discuss the current state of knowledge of epigenetic mechanisms in schizophrenia, highlighting how future work integrating these data with recent genetic findings will facilitate our understanding of schizophrenia pathophysiology.
Genetic risk variants for brain disorders are enriched in cortical H3K27ac domains
Eilis Hannon, Sarah J. Marzi, Leonard S. Schalkwyk, Jonathan Mill
Eilis Hannon,
Sarah J. Marzi,
Leonard S. Schalkwyk,
Jonathan Mill
Most variants associated with complex phenotypes in genome-wide association studies (GWAS) do not directly index coding changes affecting protein structure. Instead they are hypothesized to influence gene regulation, with common variants associated with disease being enriched in regulatory domains including enhancers and regions of open chromatin. There is interest, therefore, in using epigenomic annotation data to identify the specific regulatory mechanisms involved and prioritize risk variants. We quantified lysine H3K27 acetylation (H3K27ac) - a robust mark of active enhancers and promoters that is strongly correlated with gene expression and transcription factor binding – across the genome in entorhinal cortex samples using chromatin immunoprecipitation followed by highly parallel sequencing (ChIP-seq). H3K27ac peaks were called using high quality reads combined across all samples and formed the basis of partitioned heritability analysis using LD score regression along with publicly-available GWAS results for seven psychiatric and neurodegenerative traits. Heritability for all seven brain traits was significantly enriched in these H3K27ac peaks (enrichment ranging from 1.09–2.13) compared to regions of the genome containing other active regulatory and functional elements across multiple cell types and tissues. The strongest enrichments were for amyotrophic lateral sclerosis (ALS) (enrichment = 2.19; 95% CI = 2.12–2.27), autism (enrichment = 2.11; 95% CI = 2.05–2.16) and major depressive disorder (enrichment = 2.04; 95% CI = 1.92–2.16). Much lower enrichments were observed for 14 non-brain disorders, although we identified enrichment in cortical H3K27ac domains for body mass index (enrichment = 1.16; 95% CI = 1.13–1.19), ever smoked (enrichment = 2.07; 95% CI = 2.04–2.10), HDL (enrichment = 1.53; 95% CI = 1.45–1.62) and trigylcerides (enrichment = 1.33; 95% CI = 1.24–1.42). These results indicate that risk alleles for brain disorders are preferentially located in regions of regulatory/enhancer function in the cortex, further supporting the hypothesis that genetic variants for these phenotypes influence gene regulation in the brain.
Dynamic expression of genes associated with schizophrenia and bipolar disorder across development
Nicholas E. Clifton,
Eilís Hannon,
Janet C. Harwood,
Florio Arianna Di,
Kerrie L. Thomas,
Peter A. Holmans,
James T. R. Walters
+ 4 more
Nicholas E. Clifton,
Eilís Hannon,
Janet C. Harwood,
Florio Arianna Di,
Kerrie L. Thomas,
Peter A. Holmans,
James T. R. Walters,
Michael C. O’Donovan,
Michael J. Owen,
Andrew J. Pocklington,
Jeremy Hall
Common genetic variation contributes a substantial proportion of risk for both schizophrenia and bipolar disorder. Furthermore, there is evidence of significant, but not complete, overlap in genetic risk between the two disorders. It has been hypothesised that genetic variants conferring risk for these disorders do so by influencing brain development, leading to the later emergence of symptoms. The comparative profile of risk gene expression for schizophrenia and bipolar disorder across development over different brain regions however remains unclear. Using genotypes derived from genome-wide associations studies of the largest available cohorts of patients and control subjects, we investigated whether genes enriched for schizophrenia and bipolar disorder association show a bias for expression across any of 13 developmental stages in prefrontal cortical and subcortical brain regions. We show that genetic association with schizophrenia is positively correlated with expression in the prefrontal cortex during early midfetal development and early infancy, and negatively correlated with expression during late childhood, which stabilises in adolescence. In contrast, risk-associated genes for bipolar disorder did not exhibit a bias towards expression at any prenatal stage, although the pattern of postnatal expression was similar to that of schizophrenia. These results highlight the dynamic expression of genes harbouring risk for schizophrenia and bipolar disorder across prefrontal cortex development and support the hypothesis that prenatal neurodevelopmental events are more strongly associated with schizophrenia than bipolar disorder.
Longitudinal investigation of DNA methylation changes preceding adolescent psychotic experiences
Susanna Roberts,
Matthew Suderman,
Stanley Zammit,
Sarah H. Watkins,
Eilis Hannon,
Jonathan Mill,
Caroline Relton
+ 3 more
Susanna Roberts,
Matthew Suderman,
Stanley Zammit,
Sarah H. Watkins,
Eilis Hannon,
Jonathan Mill,
Caroline Relton,
Louise Arseneault,
Chloe C. Y. Wong,
Helen L. Fisher
Childhood psychotic experiences (PEs), such as seeing or hearing things that others do not, or extreme paranoia, are relatively common with around 1 in 20 children reporting them at age 12. Childhood PEs are often distressing and can be predictive of schizophrenia, other psychiatric disorders, and suicide attempts in adulthood, particularly if they persist during adolescence. Previous research has demonstrated that methylomic signatures in blood could be potential biomarkers of psychotic phenomena. This study explores the association between DNA methylation (DNAm) and the emergence, persistence, and remission of PEs in childhood and adolescence. DNAm profiles were obtained from the ALSPAC cohort at birth, age 7, and age 15/17 (n = 901). PEs were assessed through interviews with participants at ages 12 and 18. We identified PE-associated probes (p < 5 × 10−5) and regions (corrected p < 0.05) at ages 12 and 18. Several of the differentially methylated probes were also associated with the continuity of PEs across adolescence. One probe (cg16459265), detected consistently at multiple timepoints in the study sample, was replicated in an independent sample of twins (n = 1658). Six regions, including those spanning the HLA-DBP2 and GDF7 genes, were consistently differentially methylated at ages 7 and 15–17. Findings from this large, population-based study suggest that DNAm at multiple stages of development may be associated with PEs in late childhood and adolescence, though further replication is required. Research uncovering biomarkers associated with pre-clinical PEs is important as it has the potential to facilitate early identification of individuals at increased risk who could benefit from preventive interventions.
Transcriptional signatures of progressive neuropathology in transgenic tau and amyloid mouse models
Isabel Castanho,
Tracey K. Murray,
Eilis Hannon,
Aaron Jeffries,
Emma Walker,
Emma Laing,
Hedley Baulf
+ 9 more
Isabel Castanho,
Tracey K. Murray,
Eilis Hannon,
Aaron Jeffries,
Emma Walker,
Emma Laing,
Hedley Baulf,
Joshua Harvey,
Andrew Randall,
Karen Moore,
Paul O’Neill,
Katie Lunnon,
David A. Collier,
Zeshan Ahmed,
Michael J. O’Neil,
Jonathan Mill
Abstract
The onset and progression of Alzheimer’s disease (AD) is characterized by increasing intracellular aggregation of hyperphosphorylated tau protein and accumulation of β-amyloid (Aβ) in the neocortex. Despite recent success in identifying genetic risk factors for AD the transcriptional mechanisms involved in disease progression are not fully understood. We used transgenic mice harbouring human tau (rTg4510) and amyloid precursor protein (J20) mutations to investigate transcriptional changes associated with the development of both tau and amyloid pathology. Using highly-parallel RNA sequencing we profiled transcriptional variation in the entorhinal cortex at four time points identifying robust genotype-associated differences in entorhinal cortex gene expression in both models. We quantified neuropathological burden across multiple brain regions in the same individual mice, identifying widespread changes in gene expression paralleling the development of tau pathology in rTg4510 mice. Differentially expressed transcripts included genes associated with familial AD from genetic studies of human patients, and genes annotated to both common and rare variants identified in GWAS and exome-sequencing studies of late-onset sporadic AD. Systems-level analyses identified discrete co-expression networks associated with the progressive accumulation of tau, with these enriched for genes and pathways previously implicated in the neuro-immunological and neurodegenerative processes driving AD pathology. Finally, we report considerable overlap between tau-associated networks and AD-associated co-expression modules identified in the human cortex. Our data provide further support for an immune-response component in the accumulation of tau, and reveal novel molecular pathways associated with the progression of AD neuropathology.
Establishing a generalized polyepigenetic biomarker for tobacco smoking
Karen Sugden,
Eilis J. Hannon,
Louise Arseneault,
Daniel W. Belsky,
Jonathan M. Broadbent,
David L. Corcoran,
Robert J. Hancox
+ 9 more
Karen Sugden,
Eilis J. Hannon,
Louise Arseneault,
Daniel W. Belsky,
Jonathan M. Broadbent,
David L. Corcoran,
Robert J. Hancox,
Renate M. Houts,
Terrie E. Moffitt,
Richie Poulton,
Joseph A. Prinz,
W. Murray Thomson,
Benjamin S. Williams,
Chloe C. Y. Wong,
Jonathan Mill,
Avshalom Caspi
Large-scale epigenome-wide association meta-analyses have identified multiple ‘signatures’’ of smoking. Drawing on these findings, we describe the construction of a polyepigenetic DNA methylation score that indexes smoking behavior and that can be utilized for multiple purposes in population health research. To validate the score, we use data from two birth cohort studies: The Dunedin Longitudinal Study, followed to age-38 years, and the Environmental Risk Study, followed to age-18 years. Longitudinal data show that changes in DNA methylation accumulate with increased exposure to tobacco smoking and attenuate with quitting. Data from twins discordant for smoking behavior show that smoking influences DNA methylation independently of genetic and environmental risk factors. Physiological data show that changes in DNA methylation track smoking-related changes in lung function and gum health over time. Moreover, DNA methylation changes predict corresponding changes in gene expression in pathways related to inflammation, immune response, and cellular trafficking. Finally, we present prospective data about the link between adverse childhood experiences (ACEs) and epigenetic modifications; these findings document the importance of controlling for smoking-related DNA methylation changes when studying biological embedding of stress in life-course research. We introduce the polyepigenetic DNA methylation score as a tool both for discovery and theory-guided research in epigenetic epidemiology.
Variable DNA methylation in neonates mediates the association between prenatal smoking and birth weight
Eilis Hannon,
Diana Schendel,
Christine Ladd-Acosta,
Jakob Grove,
Christine Søholm Hansen,
David Michael Hougaard,
Michaeline Bresnahan
+ 14 more
Eilis Hannon,
Diana Schendel,
Christine Ladd-Acosta,
Jakob Grove,
Christine Søholm Hansen,
David Michael Hougaard,
Michaeline Bresnahan,
Ole Mors,
Mads Vilhelm Hollegaard,
Marie Bækvad-Hansen,
Mady Hornig,
Preben Bo Mortensen,
Anders D. Børglum,
Thomas Werge,
Marianne Giørtz Pedersen,
Merete Nordentoft,
Joseph D. Buxbaum,
M. Daniele Fallin,
Jonas Bybjerg-Grauholm,
Abraham Reichenberg,
Jonathan Mill
Philosophical Transactions of the Royal Society B Biological Sciences
There is great interest in the role epigenetic variation induced by non-genetic exposures may play in the context of health and disease. In particular, DNA methylation has previously been shown to be highly dynamic during the earliest stages of development and is influenced by in utero exposures such as maternal smoking and medication. In this study we sought to identify the specific DNA methylation differences in blood associated with prenatal and birth factors, including birth weight, gestational age and maternal smoking. We quantified neonatal methylomic variation in 1263 infants using DNA isolated from a unique collection of archived blood spots taken shortly after birth (mean = 6.08 days; s.d. = 3.24 days). An epigenome-wide association study (EWAS) of gestational age and birth weight identified 4299 and 18 differentially methylated positions (DMPs) respectively, at an experiment-wide significance threshold of p < 1 × 10-7. Our EWAS of maternal smoking during pregnancy identified 110 DMPs in neonatal blood, replicating previously reported genomic loci, including AHRR. Finally, we tested the hypothesis that DNA methylation mediates the relationship between maternal smoking and lower birth weight, finding evidence that methylomic variation at three DMPs may link exposure to outcome. These findings complement an expanding literature on the epigenomic consequences of prenatal exposures and obstetric factors, confirming a link between the maternal environment and gene regulation in neonates. This article is part of the theme issue 'Developing differences: early-life effects and evolutionary medicine'.
Epigenome-wide Association Study of Attention-Deficit/Hyperactivity Disorder Symptoms in Adults
Dongen Jenny van,
Nuno R. Zilhão,
Karen Sugden,
Eilis J. Hannon,
Jonathan Mill,
Avshalom Caspi,
Jessica Agnew-Blais
+ 70 more
Dongen Jenny van,
Nuno R. Zilhão,
Karen Sugden,
Eilis J. Hannon,
Jonathan Mill,
Avshalom Caspi,
Jessica Agnew-Blais,
Louise Arseneault,
David L. Corcoran,
Terrie E. Moffitt,
Richie Poulton,
Lude Franke,
Dorret I. Boomsma,
Bastiaan T. Heijmans,
Peter A.C. ’t Hoen,
Meurs Joyce van,
Aaron Isaacs,
Rick Jansen,
Barbara Franke,
Dorret I. Boomsma,
René Pool,
Dongen Jenny van,
Jouke J. Hottenga,
Greevenbroek Marleen M.J. van,
Coen D.A. Stehouwer,
der Kallen Carla J.H. van,
Casper G. Schalkwijk,
Cisca Wijmenga,
Lude Franke,
Sasha Zhernakova,
Ettje F. Tigchelaar,
P. Eline Slagboom,
Marian Beekman,
Joris Deelen,
Heemst Diana van,
Jan H. Veldink,
den Berg Leonard H. van,
Duijn Cornelia M. van,
Bert A. Hofman,
Aaron Isaacs,
André G. Uitterlinden,
Meurs Joyce van,
P. Mila Jhamai,
Michael Verbiest,
H. Eka D. Suchiman,
Marijn Verkerk,
der Breggen Ruud van,
Rooij Jeroen van,
Nico Lakenberg,
Hailiang Mei,
Iterson Maarten van,
Galen Michiel van,
Jan Bot,
Dasha V. Zhernakova,
Rick Jansen,
’t Hof Peter van,
Patrick Deelen,
Irene Nooren,
Peter-Bram ’t Hoen,
Bastiaan T. Heijmans,
Matthijs Moed,
Lude Franke,
Martijn Vermaat,
Dasha V. Zhernakova,
René Luijk,
Marc Jan Bonder,
Iterson Maarten van,
Patrick Deelen,
Dijk Freerk van,
Galen Michiel van,
Wibowo Arindrarto,
Szymon M. Kielbasa,
Morris A. Swertz,
Zwet Erik. W. van,
Rick Jansen,
Peter-Bram ’t Hoen,
Bastiaan T. Heijmans
BACKGROUND: Previous studies have reported associations between attention-deficit/hyperactivity disorder symptoms and DNA methylation in children. We report the first epigenome-wide association study meta-analysis of adult attention-deficit/hyperactivity disorder symptoms, based on peripheral blood DNA methylation (Infinium HumanMethylation450K array) in three population-based adult cohorts.
METHODS: An epigenome-wide association study was performed in the Netherlands Twin Register (N = 2258, mean age 37 years), Dunedin Multidisciplinary Health and Development Study (N = 800, age 38 years), and Environmental Risk Longitudinal Twin Study (N = 1631, age 18 years), and results were combined through meta-analysis (total sample size N = 4689). Region-based analyses accounting for the correlation between nearby methylation sites were also performed.
RESULTS: One epigenome-wide significant differentially methylated position was detected in the Dunedin study, but meta-analysis did not detect differentially methylated positions that were robustly associated across cohorts. In region-based analyses, six significant differentially methylation regions (DMRs) were identified in the Netherlands Twin Register, 19 in the Dunedin study, and none in the Environmental Risk Longitudinal Twin Study. Of these DMRs, 92% were associated with methylation quantitative trait loci, and 68% showed moderate to large blood-brain correlations for DNA methylation levels. DMRs included six nonoverlapping DMRs (three in the Netherlands Twin Register, three in the Dunedin study) in the major histocompatibility complex, which were associated with expression of genes in the major histocompatibility complex, including C4A and C4B, previously implicated in schizophrenia.
CONCLUSIONS: Our findings point at new candidate loci involved in immune and neuronal functions that await further replication. Our work also illustrates the need for further research to examine to what extent epigenetic associations with psychiatric traits depend on characteristics such as age, comorbidities, exposures, and genetic background.
Genome-wide DNA methylation profiling identifies convergent molecular signatures associated with idiopathic and syndromic autism in post-mortem human brain tissue
Chloe C Y Wong,
Rebecca G Smith,
Eilis Hannon,
Gokul Ramaswami,
Neelroop N Parikshak,
Elham Assary,
Claire Troakes
+ 6 more
Chloe C Y Wong,
Rebecca G Smith,
Eilis Hannon,
Gokul Ramaswami,
Neelroop N Parikshak,
Elham Assary,
Claire Troakes,
Jeremie Poschmann,
Leonard C Schalkwyk,
Wenjie Sun,
Shyam Prabhakar,
Daniel H Geschwind,
Jonathan Mill
Autism spectrum disorder (ASD) encompasses a collection of complex neuropsychiatric disorders characterized by deficits in social functioning, communication and repetitive behaviour. Building on recent studies supporting a role for developmentally moderated regulatory genomic variation in the molecular aetiology of ASD, we quantified genome-wide patterns of DNA methylation in 223 post-mortem tissues samples isolated from three brain regions [prefrontal cortex, temporal cortex and cerebellum (CB)] dissected from 43 ASD patients and 38 non-psychiatric control donors. We identified widespread differences in DNA methylation associated with idiopathic ASD (iASD), with consistent signals in both cortical regions that were distinct to those observed in the CB. Individuals carrying a duplication on chromosome 15q (dup15q), representing a genetically defined subtype of ASD, were characterized by striking differences in DNA methylationacross a discrete domain spanning an imprinted gene cluster within the duplicated region. In addition to the dramatic cis-effects on DNA methylation observed in dup15q carriers, we identified convergent methylomic signatures associated with both iASD and dup15q, reflecting the findings from previous studies of gene expression and H3K27ac. Cortical co-methylation network analysis identified a number of co-methylated modules significantly associated with ASD that are enriched for genomic regions annotated to genes involved in the immune system, synaptic signalling and neuronal regulation. Our study represents the first systematic analysis of DNA methylation associated with ASD across multiple brain regions, providing novel evidence for convergent molecular signatures associated with both idiopathic and syndromic autism.
Parallel profiling of DNA methylation and hydroxymethylation highlights neuropathology-associated epigenetic variation in Alzheimer’s disease
Adam R. Smith,
Rebecca G. Smith,
Ehsan Pishva,
Eilis Hannon,
Janou A. Y. Roubroeks,
Joe Burrage,
Claire Troakes
+ 5 more
Adam R. Smith,
Rebecca G. Smith,
Ehsan Pishva,
Eilis Hannon,
Janou A. Y. Roubroeks,
Joe Burrage,
Claire Troakes,
Safa Al-Sarraj,
Carolyn Sloan,
Jonathan Mill,
den Hove Daniel L. van,
Katie Lunnon
BackgroundAlzheimer’s disease is a progressive neurodegenerative disorder that is hypothesized to involve epigenetic dysfunction. Previous studies of DNA modifications in Alzheimer’s disease have been unable to distinguish between DNA methylation and DNA hydroxymethylation. DNA hydroxymethylation has been shown to be enriched in the human brain, although its role in Alzheimer’s disease has not yet been fully explored. Here, we utilize oxidative bisulfite conversion, in conjunction with the Illumina Infinium Human Methylation 450K microarray, to identify neuropathology-associated differential DNA methylation and DNA hydroxymethylation in the entorhinal cortex.ResultsWe identified one experiment-wide significant differentially methylated position residing in the WNT5B gene. Next, we investigated pathology-associated regions consisting of multiple adjacent loci. We identified one significant differentially hydroxymethylated region consisting of four probes spanning 104 bases in the FBXL16 gene. We also identified two significant differentially methylated regions: one consisting of two probes in a 93 base-pair region in the ANK1 gene and the other consisting of six probes in a 99-base pair region in the ARID5B gene. We also highlighted three regions that show alterations in unmodified cytosine: two probes in a 39-base pair region of ALLC, two probes in a 69-base pair region in JAG2, and the same six probes in ARID5B that were differentially methylated. Finally, we replicated significant ANK1 disease-associated hypermethylation and hypohydroxymethylation patterns across eight CpG sites in an extended 118-base pair region in an independent cohort using oxidative-bisulfite pyrosequencing.ConclusionsOur study represents the first epigenome-wide association study of both DNA methylation and hydroxymethylation in Alzheimer’s disease entorhinal cortex. We demonstrate that previous estimates of DNA hypermethylation in ANK1 in Alzheimer’s disease were underestimates as it is confounded by hypohydroxymethylation.
Functional Genomic Regulation In The Brain: (Epi)Genetic Variation, Neurodevelopment and Psychiatric Disease
Overall Abstract Epigenetic mechanisms play a role in the dynamic regulation of various genomic functions through covalent modifications to DNA and histones. These mechanisms establish and maintain cell-specific gene expression programs to orchestrate brain development, adult neurogenesis and synaptic plasticity. Given their role in the development and function of the brain, there is increasing awareness about the involvement of altered gene regulatory processes in the etiology of many neuropsychiatric phenotypes. This symposium will highlight how studies from different areas of epigenetics research can provide important insights into the molecular etiology of schizophrenia and cognitive function, and enable the identification of potential therapeutic targets. The first presentation will discuss a study of the NuRD nucleosome remodeling complex that mediates the projection of neurons across the cerebral hemispheres during development. SATB2, BCL11B and GATAD2A encode proteins within this complex and contain genome-wide significant risk SNPs for schizophrenia. Beyond these individually associated genes, this study will describe a gene set analysis of 127 genes involved in this process during cortical development that indicates strong enrichment of association signals in both schizophrenia and educational attainment GWAS data. These data point to a role for this chromatin remodeling process in the biology of schizophrenia and cognition. The second presentation will describe an analysis of dynamic DNA modifications (5mC and 5hmC) across human brain development, highlighting how the prenatal period is a time of considerable epigenomic plasticity in the brain, and the importance of neurodevelopmentally-dynamic loci in psychiatric phenotypes. It will highlight the impact of genetic variation on the epigenome during brain development showing that although most DNA methylation quantitative trait loci (mQTLs) are developmentally stable, a subset are characterized by fetal-specific effects and enriched amongst risk loci identified in recent schizophrenia GWAS. We will highlight the utility of integrating genetic and epigenetic data to fine-map GWAS regions using co-localization approaches. The third presentation will highlight results from a study of cell type-specific genome-wide maps of chromatin accessibility, which are critical resources to complement genomic sequence data and to correlate functional and genetic brain architecture. This study will describe the generation and analysis of an open chromatin atlas of different cell types in the adult human brain generated across multiple brain regions. Transcription factor-gene regulome networks were generated for each cell type and brain region and subnetworks affected by schizophrenia risk loci were identified. The final presentation will describe a study of non-coding RNAs in neuronal function. This study will highlight how epigenetic processes are potential therapeutic targets in neuropsychiatric disorders and will then detail research work showing that non-coding RNAs regulate epigenetic dynamics in neuronal systems to support cognitive function.
M55 PLEIOTROPIC EFFECTS OF GENETIC VARIATION ASSOCIATED WITH PSYCHIATRIC DISORDERS ON DNA METHYLATION
Eilis Hannon,
Nick Bray,
Micheal Weedon,
Tyler Gorrie-Stone,
Melissa Smart,
Meena Kumari,
Leo Schalkwyk
+ 2 more
Eilis Hannon,
Nick Bray,
Micheal Weedon,
Tyler Gorrie-Stone,
Melissa Smart,
Meena Kumari,
Leo Schalkwyk,
Michael O'Donovan,
Jonathan Mill
Background Success in the identification of genetic variants associated with neuropsychiatric disorders is one of the major achievements in contemporary biomedical research. Most genetic variants identified in Genome-Wide Association Studies (GWAS) of complex traits are thought to act via effects on gene regulation rather than directly altering the protein product. As a consequence, the actual genes involved in disease are not necessarily the most proximal to the associated variants. By integrating data from GWAS analyses with that from genetic studies of regulatory variation, it is possible to identify variants pleiotropically-associated with both a complex trait and measures of gene regulation. Methods In this study, we use data–based Mendelian Randomization (SMR), a method developed to identify variants pleiotropically associated with both complex traits and gene expression, to identify associations between neuropsychiatric disorders and DNA methylation. Building on our previous efforts, we increased our catalogue of DNA Methylation Quantitative Trait Loci (mQTL) in whole blood using the Illumina EPIC HumanMethylation array that interrogates over 800,000 genomic loci. These data along with mQTL data identified previously in human fetal brain were used to prioritize genes for psychiatric disorders using GWAS data from the Psychiatric Genomics Consortium (PGC). Results In this study, we apply the SMR approach to test 129,469 DNA methylation sites against five psychiatric phenotypes (schizophrenia, bipolar disorder, major depressive disorder, autism, ADHD) with robust GWAS data available from the PGC using mQTLs identified in whole blood (n=1,175; mQTL P < 1×10-10) to identify novel associations with psychiatric traits. In addition, we tested 9,261 DNA methylation sites using mQTL identified in fetal brain (n=166; mQTL P < 1×10-8). In total, we identified 107 associations with 37 satisfied addition criteria to be defined as pleiotropic and not an artefact of linkage disequilibrium. Discussion We identify multiple examples of variable DNA methylation associated with GWAS variants across the five psychiatric disorders, demonstrating the utility of the SMR approach for refining genetic association signals.
M58 FUNCTIONAL ANALYSIS OF THE SCHIZOPHRENIA ASSOCIATED GENE AS3MT IN SH-SY5Y NEUROBLASTOMA CELLS
Sam Washer, Joe Burrage, Jonathan Mill, Aaron Jeffries, Emma Dempster
Sam Washer,
Joe Burrage,
Jonathan Mill,
Aaron Jeffries,
Emma Dempster
Background Schizophrenia is a neuropsychiatric disorder with a prevalence of 1%, characterised by episodes of psychosis and an alteration in cognitive function. The aetiology of Schizophrenia is still largely unknown but evidence suggests an underlying neurodevelopmental aspect despite onset occurring in adulthood as well as a considerable genetic burden. Recently 108 genomic loci have robustly been associated with Schizophrenia. However, of these identified genes, very few have been characterised for their role in brain development. Arsenite Methyltransferase (AS3MT) is located in the10q24.32 GWAS locus, which is the most statistically significant locus outside the Major Histocompatibility Complex (MHC) region associated with schizophrenia. Furthermore, both mQTLs and expression quantitative trait loci (eQTL) map to this gene and a recent publication has identified an alternative splice variant which is increased in schizophrenia brain. AS3MT encodes for a methyltransferase involved in arsenic metabolism, however the role of AS3MT in brain development has not been explored. Methods CRISPR-Cas9 technology was used to create a knockout cell line of AS3MT in SH-SY5Y neuroblastoma cells. Two guide RNAs (gRNA) were designed, one to cut in exon 4 and one in exon 6 of the AS3MT gene, where the methyltransferase domain is located. These guides were cloned into two expression vectors which express the gRNA, Cas9 enzyme and either EGFP or mCherry. These vectors were transfected into P11 SH-SY5Y (neuroblastoma) cell line and screened for double fluorescence and sorted into single cells by Fluorescent Activated Cell Sorting after 24hours. These cells were allowed to clonally expand for 3 weeks before DNA was extracted for genotyping by PCR. Protein expression of AS3MT was measured by western blotting, gene expression by RT-PCR and DNA methylation by the Ilumina EPIC array. Immunocytochemistry techniques will be used to identify any alterations in cell morphology. Results Of the cells transfected with EGPF and mCherry expressing CRISPR-Cas9 vectors 15.5% of the single sorted cells expressed both EGPF and mCherry and were sorted into 96 well plates. Following a week of clonal expansion approximately 38% of wells contained colonies, where 41% un-transfected control sorted cells had colonies. Following genotyping 27.8% (5/18) were identified as heterozygous mutants, 16.7% (3/18) were homozygous mutants and 55.6% (10/18) were wild type. Discussion We have developed a robust protocol for creating deletion mutants using CRISPR-Cas9 technology and a functional domain of AS3MT has been deleted in the neuroblastoma cell line SH-SY5Y using CRISPR-Cas9 technology, further work is ongoing to characterise the molecular consequences of this mutation.
M61 SITES OF ACTIVE GENE REGULATION IN THE DEVELOPING HUMAN BRAIN AND THEIR ROLE IN NEUROPSYCHIATRIC DISORDERS
Manuela Kouakou, Jonathan Mill, Matthew Hill, Nick Bray
Manuela Kouakou,
Jonathan Mill,
Matthew Hill,
Nick Bray
Background Neuropsychiatric conditions such as schizophrenia and autism are complex disorders with a neurodevelopmental origin. Most common risk loci for these disorders are located in non-coding regions of the genome and are likely to index functional variants that alter gene regulation rather than protein structure. Identifying regulatory genomic regions active in the developing human brain will therefore be important for elucidating genetic mechanisms underpinning these conditions. Methods We sought to identify sites of open chromatin, indicative of active regulatory regions, in frontal lobe from two samples from the 2nd trimester of gestation using the Assay for Transposase-Accessible Chromatin with high throughput sequencing (ATAC-seq). Nuclei from frozen brain tissue were isolated by ultracentrifugation, followed by FACS to separate NeuN+ and Ki67+ cells. ATAC-seq libraries were sequenced on a HiSeq. 4000 and data analyzed following the ENCODE pipeline. Results We have identified regulatory genomic regions that are active in the prenatal human brain. We will test for enrichment of polygenic signal for psychiatric disorders such as schizophrenia within these regions. Discussion These data advance our understanding of gene regulation within cells from the developing human brain. Identifying risk variants for psychiatric disorders within regulatory regions active in the human fetal brain will help elucidate neurodevelopmental risk mechanisms for these conditions.
AN INTEGRATED GENETIC-EPIGENETIC ANALYSIS OF SCHIZOPHRENIA: EVIDENCE FOR CO-LOCALIZATION OF GENETIC ASSOCIATIONS AND DIFFERENTIAL DNA METHYLATION FROM A LARGE META-ANALYSIS OF WHOLE BLOOD DNA
Eilis Hannon,
Emma Dempster,
Joe Burrage,
Andrew McQuillin,
Clair David St.,
Derek Morris,
Forti Marta Di
+ 7 more
Eilis Hannon,
Emma Dempster,
Joe Burrage,
Andrew McQuillin,
Clair David St.,
Derek Morris,
Forti Marta Di,
Fiona Gaughran,
James MacCabe,
Gerome Breen,
David Collier,
Robin Murray,
Leo Schalkwyk,
Jonathan Mill
Background Schizophrenia is a severe, highly heritable, neuropsychiatric disorder characterized by episodic psychosis and altered cognitive function. Despite recent successes in identifying genetic variants robustly associated with susceptibility, there remains uncertainty about the causal genes involved in disease pathogenesis and how their function is regulated. There is growing interest in the role of developmentally regulated epigenetic variation in the molecular etiology of schizophrenia, with studies of disease-discordant monozygotic twins, clinical sample cohorts and post-mortem brain tissue identifying methylomic variation associated with disease. Leveraging on the considerable investment in genome-wide association studies (GWAS) we are examining genome-wide patterns of DNA methylation across multiple cohorts with the aim of undertaking an integrated genetic-epigenetic approach to schizophrenia. Methods DNA methylation profiled in whole blood samples from five schizophrenia case-control cohorts using the Illumina 450K HumanMethylation array (total n = ~3,200 samples). Each sample was also genotyped and polygenic scores for schizophrenia calculated. We performed two parallel epigenome-wide association studies (EWAS) to identify methylomic variation associated with 1) schizophrenia diagnosis and 2) polygenic burden calculated from the results of latest PGC schizophrenia GWAS, combing the results from each individual cohort by meta-analysis. Results Differentially methylated positions (DMPs) associated with schizophrenia identified in each cohort showed consistent direction of effects across other datasets. Combing the results across the five cohorts, we identified 3,911 schizophrenia-associated DMPs annotated to 2,307 genes. This included further replication of 305/365 DMPs identified in our previous schizophrenia EWAS and an additional 2,434 novel DMPs. Furthermore, we identify overlap in regions characterized by differential DNA methylation and loci nominated in the largest GWAS of schizophrenia conducted by the PGC. Finally, we show how DNA methylation quantitative trait loci in combination with Bayesian co-localization analyses can be used to annotate extended genomic regions nominated by studies of schizophrenia, and to identify potential regulatory variation causally involved in disease. Discussion This study represents the largest integrated analysis of genetic and epigenetic variation in schizophrenia. Combining data from multiple cohorts has enabled us to identify novel DMPs associated with both diagnosis and elevated polygenic burden for schizophrenia. We demonstrate the utility of using a polygenic risk score to identify molecular variation associated with etiological variation, and of using DNA methylation quantitative trait loci to refine the functional and regulatory variation associated with schizophrenia risk variants. Finally, we present strong evidence for the co-localization of genetic associations for schizophrenia and differential DNA methylation.
M52 CONVERGENT METHYLOMIC SIGNATURES BETWEEN AUTISM ASSOCIATED WITH DUPLICATIONS OF CHROMOSOME 15Q AND IDIOPATHIC AUTISM
Chloe Chung Yi Wong,
Rebecca G. Smith,
Eilis Hannon,
Elham Assary,
Neelroop Parikshak,
Shyam Prabhakar,
Daniel Geschwind
+ 1 more
Chloe Chung Yi Wong,
Rebecca G. Smith,
Eilis Hannon,
Elham Assary,
Neelroop Parikshak,
Shyam Prabhakar,
Daniel Geschwind,
Jonathan Mill
Background Autism Spectrum Disorder (ASD) includes a spectrum of genetically and clinically complex neurodevelopmental disorders. Findings from recent discordant monozygotic twins and post-mortem brain studies suggest that altered epigenetic processes, including DNA methylation and histone acetylation, are involved in the etiology of ASD. This study presents, to our knowledge, the largest post-mortem genome-wide DNA methylation analyses of autism patients, including idiopathic ASD and chromosome 15q11.2-13.1 duplication syndrome (dup15q) carriers, and matched controls. Methods We performed methylomic profiling in human post-mortem brain tissues using samples from three brain regions (dorsolateral prefrontal cortex, primary auditory cortex and cerebellum) of idiopathic autism cases, dup15q cariers and matched controls using the Illumina Infinium HumanMethylation450 array. Following stringent quality control and data pre-processing ASD-associated differential methylation analyses were performed at both probe-wise and region-wise levels. Results Our analyses revealed ASD-associated dysregulation of DNA methylation at multiple loci, with a large number of cross-cortex significant differentially methylated probes. In addition, although the differential methylation observed in dup15q samples were much more pronounced than those from iASD samples, we observed a convergent of methylomic signatures between autism associated with duplications of chromosome 15q and idiopathic autism. Discussion This epigenome-wide study of autism using post-mortem tissues represents the most comprehensive study to date. Findings from this study further support a role of altered epigenetics signatures in ASD and provide novel insight that idiopathic ASD and a genetically defined form of ASD (i.e. dup15q) carry similar underlying epigenetics changes.
SA54 DNA METHYLATION AND ADOLESCENT TRAJECTORIES OF PSYCHOTIC SYMPTOMS
Susanna Roberts,
Matthew Suderman,
Stanley Zammit,
Sarah H. Watkins,
Eilis Hannon,
Caroline Relton,
Jonathan Mill
+ 1 more
Susanna Roberts,
Matthew Suderman,
Stanley Zammit,
Sarah H. Watkins,
Eilis Hannon,
Caroline Relton,
Jonathan Mill,
Helen Fisher
Background Psychotic Symptoms (PS) are often distressing and can be predictive of schizophrenia, other psychiatric disorders and suicide attempts in adulthood, particularly if they persist during adolescence. Previous research in diagnosis-discordant monozygotic twin-pairs and patient-control samples has demonstrated that changes in epigenetic processes could be potential biomarkers of the emergence and persistence of PS. Investigation in large, pre-clinical population-based samples is urgently required. The aim of this study is to explore the association between DNA methylation and the emergence, persistence, and remission of PS in childhood and adolescence. Methods DNA methylation data (Illumina 450k) were obtained from the ARIES subsample of the ALSPAC birth cohort at birth, age 7, and age 15/17 (N=901). PS were assessed in private interviews with the participants at ages 12 and 18. EWAS were conducted to determine the association between DNA methylation at each time-point and reports of PS at ages 12 and 18, controlling for pregnancy and birth-related covariates and cell-type composition. Gene Ontology (GO) term enrichment analyses of the top probes were performed to identify important pathways. The top probes from each EWAS were used to investigate the role of DNA methylation in the persistence and remission of PS by comparing individuals with no history of PS, those whose symptoms persisted, and those whose symptoms remitted. Multilevel models were then constructed to test the association between the longitudinal methylomic trajectory of the top CpG sites and the trajectory of psychotic symptoms. Results from a replication of the top findings in an independent cohort will also be presented. Results A number of probes were differentially methylated (p<5×10-5) at each time-point between those who experienced PS at age 12 and age 18, although these were not significant after applying stringent correction for multiple testing (p<1.3×10-7). The top ranked GO terms from enrichment analyses at each time-point included those related to neuronal development, immune processes, and the Wnt signalling pathway. Investigation of the top probes revealed differences in DNA methylation profiles between PS trajectories in adolescence, in both a time-point specific manner and longitudinally across development. At many of these probes, individuals whose symptoms remitted between 12 and 18 showed DNA methylation profiles more similar to those with no history of PS, and those whose symptoms persisted showed the largest difference in DNA methylation. Discussion Findings from this large, population-based study suggest that epigenetic processes at multiple stages of development may be associated with the emergence, remission, and persistence of PS in late childhood and adolescence. Research uncovering biomarkers associated with pre-clinical PS is important as it has the potential to facilitate early identification of individuals at increased risk and target preventive interventions.
A ZEBRAFISH MODEL OF CLOZAPINE EXPOSURE: DRUG-INDUCED TRANSCRIPTOMIC CHANGES IN THE BRAIN
Joana Viana, Eilis Hannon, Aerle Ronny van, Emma Dempster, Gregory Paull, Eduarda Santos, Jonathan Mill
Joana Viana,
Eilis Hannon,
Aerle Ronny van,
Emma Dempster,
Gregory Paull,
Eduarda Santos,
Jonathan Mill
Background Schizophrenia (SZ) is a severe neuropsychiatric disorder characterized by episodic psychosis and altered cognitive function. About 20% of SZ patients are resistant to the commonly-prescribed antipsychotic medications used to treat disease symptoms. Clozapine is an atypical antipsychotic drug often prescribed to treatment-resistant SZ patients, although the functional pathways mediating its action are not well understood. Importantly, 40–70% of patients treated with clozapine show an inadequate response and there are sever side-effects. Understanding the molecular pathways involved in antipsychotic response will help in the development of new improved therapeutics that act on pathogenicity rather than just treating the acute manifestations of SZ. Methods We exposed wild type zebrafish to high and low doses of the antipsychotic drug clozapine over 72hours. Relevant controls were included at all stages of the experiment. We recorded the animals and analysed changes in behavior associated with clozapine exposure. We then performed RNA-sequencing in the brain and identified changes in gene expression in response to clozapine exposure. Network analysis was performed to identify modules of co-expressed genes sensitive to clozapine exposure and pathway analysis was employed to identify overrepresentation of GO terms in each of the clozapine exposure-associated modules Results The fish showed a dose-sensitive shift in behaviour in response to clozapine. We identified five genes showing significant gene expression changes in response to clozapine, including ODC1, a gene previously implicated in SZ which shows changes in expression during brain development. Using network analysis, we identified fifteen modules of co-expressed genes which present a striking change in module connectivity in response to the drug. These modules show overrepresentation of key gene ontology terms, implicating processes such as calcium ion transport, cell-cell signalling, G-protein coupled receptor activity, ribosomal activity, and the regulation of transcription. Discussion Our study highlights the utility of zebrafish as a model for assessing the molecular consequences of antipsychotic medications. Our data show marked behavioural effects induced by clozapine and significant transcriptomic alterations in important functional pathways in the brain.
Regulatory Genomic Variation In The Developing Brain: Relevance To Neuropsychiatric Phenotypes
Jonathan Mill,
Eilis Hannon,
Helen Spiers,
Chloe Chung Yi Wong,
Joana Viana,
Michael O'Donovan,
Leo Schalkwyk
+ 1 more
Jonathan Mill,
Eilis Hannon,
Helen Spiers,
Chloe Chung Yi Wong,
Joana Viana,
Michael O'Donovan,
Leo Schalkwyk,
Nick Bray
Epigenetic processes play a key role in orchestrating transcriptional regulation during the development of the human central nervous system. We have quantified dynamic changes in DNA methylation (5mC) and DNA hydroxymethylation (5hmC) occurring during human fetal brain development, using a unique collection of human fetal brain samples spanning 23 to 184 days post-conception. We identify widespread changes in both modifications occurring during human brain development, notable sex-differences, and interactions between 5mC and 5hmC at specific sites. We also identify loci where DNA modifications in the fetal brain are associated with genetic variation, highlighting the utility of mQTLs and hmQTLs for fine-mapping GWAS loci of neurodevelopmental phenotypes. Finally, we have examined variation in both 5mC and 5hmC across multiple regions of the adult brain in neurodevelopmental phenotypes including schizophrenia and autism, identifying disease-associated DNA modifications and relating these to neurodevelopmental trajectories of gene regulation. A searchable database of our fetal brain regulatory genomic data is available as a resource to the research community at http://epigenetics.essex.ac.uk/fetalbrain2/.
TRANSCRIPTOMIC STUDIES OF THE HUMAN PRENATAL BRAIN
Heath O'Brien,
Eilis Hannon,
Helen Spiers,
Aaron Jeffries,
Gemma McLaughlin,
William Davies,
Richard Anney
+ 4 more
Heath O'Brien,
Eilis Hannon,
Helen Spiers,
Aaron Jeffries,
Gemma McLaughlin,
William Davies,
Richard Anney,
Matthew Hill,
Michael O'Donovan,
Jon Mill,
Nick Bray
Background Several neuropsychiatric disorders are thought to have an early developmental component, which could be partly conferred by individual differences in gene expression. In order to explore sex and genotypic effects on gene expression in the human prenatal brain, we have performed whole transcriptome sequencing and genome-wide genotyping on a large collection (N > 120) of human fetal brain samples from the second trimester of gestation. Methods Strand-specific whole transcriptome RNA-seq libraries were prepared from total RNA following ribosomal RNA depletion and deeply sequenced on an Illumina HiSeq. Genomic DNA from each sample was genotyped using Illumina arrays followed by SNP and indel imputation. Sex effects on gene expression were assessed by likelihood ratio tests. Expression quantitative trait loci (eQTL) in the human fetal brain will be identified using measures of total and allele-specific gene expression. Results We have identified hundreds of autosomal as well sex-linked genes exhibiting sex differences in expression or splicing in the prenatal human brain. Details of fetal brain eQTL and their association with neuropsychiatric disorders will also be presented. Discussion Our findings of sex differences in gene expression highlight an early stage of sexual differentiation of the human brain, which could have relevance to sex-biased neurodevelopmental disorders. Identification of fetal brain eQTL associated with neuropsychiatric disorders will help elucidate neurodevelopmental mechanisms contributing to these conditions.
Genetics and the geography of health, behaviour and attainment
Daniel W. Belsky,
Avshalom Caspi,
Louise Arseneault,
David L. Corcoran,
Benjamin W. Domingue,
Kathleen Mullan Harris,
Renate M. Houts
+ 7 more
Daniel W. Belsky,
Avshalom Caspi,
Louise Arseneault,
David L. Corcoran,
Benjamin W. Domingue,
Kathleen Mullan Harris,
Renate M. Houts,
Jonathan S. Mill,
Terrie E. Moffitt,
Joseph Prinz,
Karen Sugden,
Jasmin Wertz,
Benjamin Williams,
Candice L. Odgers
Young people’s life chances can be predicted by characteristics of their neighbourhood1. Children growing up in disadvantaged neighbourhoods exhibit worse physical and mental health and suffer poorer educational and economic outcomes than children growing up in advantaged neighbourhoods. Increasing recognition that aspects of social inequalities tend, in fact, to be geographical inequalities2–5 is stimulating research and focusing policy interest on the role of place in shaping health, behaviour and social outcomes. Where neighbourhood effects are causal, neighbourhood-level interventions can be effective. Where neighbourhood effects reflect selection of families with different characteristics into different neighbourhoods, interventions should instead target families or individuals directly. To test how selection may affect different neighbourhood-linked problems, we linked neighbourhood data with genetic, health and social outcome data for >7,000 European-descent UK and US young people in the E-Risk and Add Health studies. We tested selection/concentration of genetic risks for obesity, schizophrenia, teen pregnancy and poor educational outcomes in high-risk neighbourhoods, including genetic analysis of neighbourhood mobility. Findings argue against genetic selection/concentration as an explanation for neighbourhood gradients in obesity and mental health problems. By contrast, modest genetic selection/concentration was evident for teen pregnancy and poor educational outcomes, suggesting that neighbourhood effects for these outcomes should be interpreted with care.
DNA METHYLATION PROFILING MIGHT SHED LIGHT ON THE BIOLOGY OF CANNABIS ASSOCIATED PSYCHOSIS
Forti Marta Di,
Emma Dempster,
Diego Quattrone,
Giada Tripoli,
Radhika Kandaswamy,
Craig Morgan,
Os Jim van
+ 5 more
Forti Marta Di,
Emma Dempster,
Diego Quattrone,
Giada Tripoli,
Radhika Kandaswamy,
Craig Morgan,
Os Jim van,
Bart Rutten,
Robin Murray,
Jonathan Mill,
Chloe Wong,
Rajiv Radhakrishnan
Epigenetic mechanisms are emerging as potential important players that underlie the interactions between genetic and environmental risk factors in the aetiology of psychiatric disorders. Cannabis is the most widely used recreational drug and its use, with a dose relationship pattern, has consistently been associated with an increased risk to develop Psychotic Disorders. Consistent with animal data, it has been shown that regular cannabis users show higher levels of CB1 mRNA expression and promoter methylation status in peripheral blood cells than non-users. We are the first to investigate if cannabis use leaves a distinct DNA methylation signature across the genome and if this overlaps with biological pathways already associated with Psychotic Disorders. Genome-wide DNA methylomic (EWAS) profiling using the Illumina Infinium MethylationEPIC array in human peripheral blood tissue from 413 First episode Psychosis and 521 healthy population controls part of the EUGEI (European network of national schizophrenia networks studying Gene-Environment Interactions) study. Samples were randomized with respect to phenotypic status, age, sex and study site to avoid batch effects. Stringent QC pipeline checks (i.e. signal intensity, duplicates, sex, bisulphite conversion, genotypes) with cross-reactive and non-reliable probes removed. Our analyses focused on probes with a minimum range of methylation values of 5% within the middle 80% of samples, resulting in 618,048 probes5. Covariates: 1) tobacco smoking score; 2) age; 3) cell type proportions and 4) study sites Linear model was used to compare across the DNA methylomic profiling of a) Lifetime cannabis users (YES) and b) daily cannabis users with never users. Our preliminary analyses revealed regular cannabis use-associated dysregulation of DNA methylation at multiple loci across the epigenome that also include CpGs previously associated with Schizophrenia. Downstream pathway analysis revealed enrichment of genomic regions that are highly disease relevant. Our preliminary findings in a sample of healthy controls suggest: Difference in DNA Methylation profiling between individuals who have tried cannabis at some point in their life and more significantly so in daily users compared to never users; 2) these differences were detected taking into account important confounders including the epigenetic tobacco scoring. Most of these DMS are in protein coding genes including BDNF,SHANK2 and CACNA2D2, which are involved in important neurodevelopmental processes. BDNF and CACNA2D2 have also been indicated as susceptibility genes for Schizophrenia and Bipolar Disorders. Finally, our pathway analysis indicated significant enrichment for these DMSs in pathways involved in biological processing such as neuronal migration and development and glutamate receptor binding, a possible hint towards the unravelling of the biology linking adolescence cannabis use with psychosis.
Transcriptional Signatures of Progressive Neuropathology in Transgenic Models of Tau and Amyloid Pathology
Isabel Castanho,
Tracey Murray,
Eilis Hannon,
Aaron Jeffries,
Emma Walker,
Emma Laing,
Hedley Baulf
+ 8 more
Isabel Castanho,
Tracey Murray,
Eilis Hannon,
Aaron Jeffries,
Emma Walker,
Emma Laing,
Hedley Baulf,
Joshua Harvey,
Andrew Randall,
Karen Moore,
Paul O’Neill,
David Collier,
Zeshan Ahmed,
Michael J. O’Neil,
Jonathan Mill
The onset and progression of Alzheimer’s disease (AD) is characterized by increasing intracellular aggregation of hyperphosphorylated tau protein and the accumulation of β-amyloid (Aβ) in the neocortex. Despite recent success in identifying genetic risk factors for AD, the transcriptional mechanisms involved in disease progression are not fully understood. We used transgenic mice harbouring human tau (rTg4510) and amyloid precursor protein (J20) mutations to investigate transcriptional changes associated with the development of both tau and amyloid pathology. Using highly-parallel RNA sequencing we profiled transcriptional variation in the entorhinal cortex at four time points identifying robust genotype-associated differences in entorhinal cortex gene expression in both models. We quantified neuropathological burden across multiple brain regions in the same individual mice, identifying widespread changes in gene expression paralleling the development of tau pathology in rTg4510 mice. There was a striking overlap between differentially expressed transcripts and genes associated with familial AD from genetic studies of human patients, and genes annotated to both common and rare variants identified in genome-wide association and exome-sequencing studies of late-onset sporadic AD. Systems-level analyses identified discrete co-expression networks associated with the progressive accumulation of tau, with these enriched for genes and pathways previously implicated in the neuro-immunological and neurodegenerative processes driving AD pathology. Finally, we report a highly-significant overlap between tau-associated networks and AD-associated co-expression modules identified in analyses of post-mortem human cortex. This study represents the most systematic analysis of progressive changes in gene expression in mouse models of AD pathology and the first to focus specifically on the entorhinal cortex, a key region affected early in human Alzheimer’s disease (AD). Our data provide further strong for an immune-response component in the accumulation of tau, and reveal novel molecular pathways associated with the progression of AD neuropathology.
Independent Methylome-Wide Association Studies of Schizophrenia Detect Consistent Case–Control Differences
Robin F Chan,
Andrey A Shabalin,
Carolina Montano,
Eilis Hannon,
Christina M Hultman,
Margaret D Fallin,
Andrew P Feinberg
+ 3 more
Robin F Chan,
Andrey A Shabalin,
Carolina Montano,
Eilis Hannon,
Christina M Hultman,
Margaret D Fallin,
Andrew P Feinberg,
Jonathan Mill,
den Oord Edwin J C G van,
Karolina A Aberg
Methylome-wide association studies (MWASs) are promising complements to sequence variation studies. We used existing sequencing-based methylation data, which assayed the majority of all 28 million CpGs in the human genome, to perform an MWAS for schizophrenia in blood, while controlling for cell-type heterogeneity with a recently generated platform-specific reference panel. Next, we compared the MWAS results with findings from 3 existing large-scale array-based schizophrenia methylation studies in blood that assayed up to ~450 000 CpGs. Our MWAS identified 22 highly significant loci (P < 5 × 10-8) and 852 suggestively significant loci (P < 1 × 10-5). The top finding (P = 5.62 × 10-11, q = 0.001) was located in MFN2, which encodes mitofusin-2 that regulates Ca2+ transfer from the endoplasmic reticulum to mitochondria in cooperation with DISC1. The second-most significant site (P = 1.38 × 10-9, q = 0.013) was located in ALDH1A2, which encodes an enzyme for astrocyte-derived retinoic acid-a key neuronal morphogen with relevance for schizophrenia. Although the most significant MWAS findings were not assayed on the arrays, we observed significant enrichment of overlapping findings with 2 of the 3 array datasets (P = 0.0315, 0.0045, 0.1946). Overrepresentation analysis of Gene Ontology terms for the genes in the significant overlaps suggested high similarity in the biological functions detected by the different datasets. Top terms were related to immune and/or stress responses, cell adhesion and motility, and a broad range of processes essential for neurodevelopment.
T40. Alzheimer’s Disease DNA (Hydroxy)Methylome in the Brain and Blood: Evidence for OXT Methylation as a Preclinical Marker
Roy Lardenoije,
Janou Roubroeks,
Ehsan Pishva,
Markus Leber,
Holger Wagner,
Artemis Iatrou,
Adam Smith
+ 21 more
Roy Lardenoije,
Janou Roubroeks,
Ehsan Pishva,
Markus Leber,
Holger Wagner,
Artemis Iatrou,
Adam Smith,
Rebecca Smith,
Lars Eijssen,
Luca Kleineidam,
Amit Kawalia,
Per Hoffmann,
Tobias Luck,
Steffi Riedel-Heller,
Frank Jessen,
Wolfgang Maier,
Michael Wagner,
Gunter Kenis,
Muhammad Ali,
Sol Antonio del,
Diego Mastroeni,
Elaine Delvaux,
Paul Coleman,
Jonathan Mill,
Bart Rutten,
Katie Lunnon,
Alfredo Ramirez,
den Hove Daniël van
BackgroundThere has been a steady increase in the number of studies aiming to identify DNA methylation differences associated with complex phenotypes. Many of the challenges of epigenetic epidemiology regarding study design and interpretation have been discussed in detail, however there are analytical concerns that are outstanding and require further exploration. In this study we seek to address three analytical issues. First, we quantify the multiple testing burden and propose a standard statistical significance threshold for identifying DNA methylation sites that are associated with an outcome. Second, we establish whether linear regression, the chosen statistical tool for the majority of studies, is appropriate and whether it is biased by the underlying distribution of DNA methylation data. Finally, we assess the sample size required for adequately powered DNA methylation association studies.ResultsWe quantified DNA methylation in the Understanding Society cohort (n = 1175), a large population based study, using the Illumina EPIC array to assess the statistical properties of DNA methylation association analyses. By simulating null DNA methylation studies, we generated the distribution of p-values expected by chance and calculated the 5% family-wise error for EPIC array studies to be 9 × 10− 8. Next, we tested whether the assumptions of linear regression are violated by DNA methylation data and found that the majority of sites do not satisfy the assumption of normal residuals. Nevertheless, we found no evidence that this bias influences analyses by increasing the likelihood of affected sites to be false positives. Finally, we performed power calculations for EPIC based DNA methylation studies, demonstrating that existing studies with data on ~ 1000 samples are adequately powered to detect small differences at the majority of sites.ConclusionWe propose that a significance threshold of P < 9 × 10− 8 adequately controls the false positive rate for EPIC array DNA methylation studies. Moreover, our results indicate that linear regression is a valid statistical methodology for DNA methylation studies, despite the fact that the data do not always satisfy the assumptions of this test. These findings have implications for epidemiological-based studies of DNA methylation and provide a framework for the interpretation of findings from current and future studies.
Methylation age acceleration does not predict mortality in schizophrenia
Kaarina Kowalec,
Eilis Hannon,
Georgina Mansell,
Joe Burrage,
Anil P. S. Ori,
Roel A. Ophoff,
Jonathan Mill
+ 1 more
Kaarina Kowalec,
Eilis Hannon,
Georgina Mansell,
Joe Burrage,
Anil P. S. Ori,
Roel A. Ophoff,
Jonathan Mill,
Patrick F. Sullivan
Schizophrenia (SCZ) is associated with high mortality. DNA methylation levels vary over the life course, and pre-selected combinations of methylation array probes can be used to estimate “methylation age” (mAge). mAge correlates highly with chronological age but when it differs, termed mAge acceleration, it has been previously associated with all-cause mortality. We tested the association between mAge acceleration and mortality in SCZ and controls. We selected 190 SCZ cases and 190 controls from the Sweden Schizophrenia Study. Cases were identified from the Swedish Hospital Discharge Register with ≥5 specialist treatment contacts and ≥5 antipsychotic prescriptions. Controls had no psychotic disorder or antipsychotics. Subjects were selected if they had died or survived during follow-up (2:1 oversampling). Extracted DNA was assayed on the Illumina MethylationEPIC array. mAge was regressed on age at sampling to obtain mAge acceleration. Using Cox proportional hazards regression, the association between mAge acceleration and mortality was tested. After quality control, the following were available: n = 126 SCZ died, 63 SCZ alive, 127 controls died, 62 controls alive. In the primary analyses, we did not find a significant association between mAge acceleration and SCZ mortality (adjusted p > 0.005). Sensitivity analyses excluding SCZ cases with pre-existing cancer demonstrated a significant association between the Hannum mAge acceleration and mortality (hazard ratio = 1.13, 95% confidence interval = 1.04–1.22, p = 0.005). Per our pre-specified criteria, we did not confirm our primary hypothesis that mAge acceleration would predict subsequent mortality in people with SCZ, but we cannot rule out smaller effects or effects in patient subsets.
Growth disrupting mutations in epigenetic regulatory molecules are associated with abnormalities of epigenetic aging
Aaron R. Jeffries,
Reza Maroofian,
Claire G. Salter,
Barry A. Chioza,
Harold E. Cross,
Michael A. Patton,
Emma Dempster
+ 19 more
Aaron R. Jeffries,
Reza Maroofian,
Claire G. Salter,
Barry A. Chioza,
Harold E. Cross,
Michael A. Patton,
Emma Dempster,
I. Karen Temple,
Deborah J.G. Mackay,
Faisal I. Rezwan,
Lise Aksglaede,
Diana Baralle,
Tabib Dabir,
Matthew F. Hunter,
Arveen Kamath,
Ajith Kumar,
Ruth Newbury-Ecob,
Angelo Selicorni,
Amanda Springer,
Maldergem Lionel Van,
Vinod Varghese,
Naomi Yachelevich,
Katrina Tatton-Brown,
Jonathan Mill,
Andrew H. Crosby,
Emma L. Baple
Germline mutations in fundamental epigenetic regulatory molecules including DNA methyltransferase 3 alpha (DNMT3A) are commonly associated with growth disorders, whereas somatic mutations are often associated with malignancy. We profiled genome-wide DNA methylation patterns in DNMT3A c.2312G > A; p.(Arg771Gln) carriers in a large Amish sibship with Tatton-Brown-Rahman syndrome (TBRS), their mosaic father, and 15 TBRS patients with distinct pathogenic de novo DNMT3A variants. This defined widespread DNA hypomethylation at specific genomic sites enriched at locations annotated as genes involved in morphogenesis, development, differentiation, and malignancy predisposition pathways. TBRS patients also displayed highly accelerated DNA methylation aging. These findings were most marked in a carrier of the AML-associated driver mutation p.Arg882Cys. Our studies additionally defined phenotype-related accelerated and decelerated epigenetic aging in two histone methyltransferase disorders: NSD1 Sotos syndrome overgrowth disorder and KMT2D Kabuki syndrome growth impairment. Together, our findings provide fundamental new insights into aberrant epigenetic mechanisms, the role of epigenetic machinery maintenance, and determinants of biological aging in these growth disorders.
Alzheimer’s Disease Associated Genes Ankyrin and Tau Cause Shortened Lifespan and Memory Loss in Drosophila
James P. Higham, Bilal R. Malik, Edgar Buhl, Jennifer M. Dawson, Anna S. Ogier, Katie Lunnon, James J. L. Hodge
James P. Higham,
Bilal R. Malik,
Edgar Buhl,
Jennifer M. Dawson,
Anna S. Ogier,
Katie Lunnon,
James J. L. Hodge
Alzheimer's disease (AD) is the most common form of dementia and is characterized by intracellular neurofibrillary tangles of hyperphosphorylated Tau, including the 0N4R isoform and accumulation of extracellular amyloid beta (Aβ) plaques. However, less than 5% of AD cases are familial, with many additional risk factors contributing to AD including aging, lifestyle, the environment and epigenetics. Recent epigenome-wide association studies (EWAS) of AD have identified a number of loci that are differentially methylated in the AD cortex. Indeed, hypermethylation and reduced expression of the Ankyrin 1 (ANK1) gene in AD has been reported in the cortex in numerous different post-mortem brain cohorts. Little is known about the normal function of ANK1 in the healthy brain, nor the role it may play in AD. We have generated Drosophila models to allow us to functionally characterize Drosophila Ank2, the ortholog of human ANK1 and to determine its interaction with human Tau and Aβ. We show expression of human Tau 0N4R or the oligomerizing Aβ 42 amino acid peptide caused shortened lifespan, degeneration, disrupted movement, memory loss, and decreased excitability of memory neurons with co-expression tending to make the pathology worse. We find that Drosophila with reduced neuronal Ank2 expression have shortened lifespan, reduced locomotion, reduced memory and reduced neuronal excitability similar to flies overexpressing either human Tau 0N4R or Aβ42. Therefore, we show that the mis-expression of Ank2 can drive disease relevant processes and phenocopy some features of AD. Therefore, we propose targeting human ANK1 may have therapeutic potential. This represents the first study to characterize an AD-relevant gene nominated from EWAS.
Association of Lifestyle and Genetic Risk With Incidence of Dementia
Ilianna Lourida, Eilis Hannon, Thomas J. Littlejohns, Kenneth M. Langa, Elina Hyppönen, Elżbieta Kuźma, David J. Llewellyn
Ilianna Lourida,
Eilis Hannon,
Thomas J. Littlejohns,
Kenneth M. Langa,
Elina Hyppönen,
Elżbieta Kuźma,
David J. Llewellyn
IMPORTANCE: Genetic factors increase risk of dementia, but the extent to which this can be offset by lifestyle factors is unknown.
OBJECTIVE: To investigate whether a healthy lifestyle is associated with lower risk of dementia regardless of genetic risk.
DESIGN, SETTING, AND PARTICIPANTS: A retrospective cohort study that included adults of European ancestry aged at least 60 years without cognitive impairment or dementia at baseline. Participants joined the UK Biobank study from 2006 to 2010 and were followed up until 2016 or 2017.
EXPOSURES: A polygenic risk score for dementia with low (lowest quintile), intermediate (quintiles 2 to 4), and high (highest quintile) risk categories and a weighted healthy lifestyle score, including no current smoking, regular physical activity, healthy diet, and moderate alcohol consumption, categorized into favorable, intermediate, and unfavorable lifestyles.
MAIN OUTCOMES AND MEASURES: Incident all-cause dementia, ascertained through hospital inpatient and death records.
RESULTS: A total of 196 383 individuals (mean [SD] age, 64.1 [2.9] years; 52.7% were women) were followed up for 1 545 433 person-years (median [interquartile range] follow-up, 8.0 [7.4-8.6] years). Overall, 68.1% of participants followed a favorable lifestyle, 23.6% followed an intermediate lifestyle, and 8.2% followed an unfavorable lifestyle. Twenty percent had high polygenic risk scores, 60% had intermediate risk scores, and 20% had low risk scores. Of the participants with high genetic risk, 1.23% (95% CI, 1.13%-1.35%) developed dementia compared with 0.63% (95% CI, 0.56%-0.71%) of the participants with low genetic risk (adjusted hazard ratio, 1.91 [95% CI, 1.64-2.23]). Of the participants with a high genetic risk and unfavorable lifestyle, 1.78% (95% CI, 1.38%-2.28%) developed dementia compared with 0.56% (95% CI, 0.48%-0.66%) of participants with low genetic risk and favorable lifestyle (hazard ratio, 2.83 [95% CI, 2.09-3.83]). There was no significant interaction between genetic risk and lifestyle factors (P = .99). Among participants with high genetic risk, 1.13% (95% CI, 1.01%-1.26%) of those with a favorable lifestyle developed dementia compared with 1.78% (95% CI, 1.38%-2.28%) with an unfavorable lifestyle (hazard ratio, 0.68 [95% CI, 0.51-0.90]).
CONCLUSIONS AND RELEVANCE: Among older adults without cognitive impairment or dementia, both an unfavorable lifestyle and high genetic risk were significantly associated with higher dementia risk. A favorable lifestyle was associated with a lower dementia risk among participants with high genetic risk.
Integrated genetic and methylomic analyses identify shared biology between autism and autistic traits
Aicha Massrali, Helena Brunel, Eilis Hannon, Chloe Wong, Simon Baron-Cohen, Varun Warrier
Aicha Massrali,
Helena Brunel,
Eilis Hannon,
Chloe Wong,
Simon Baron-Cohen,
Varun Warrier
Previous studies have identified differences in DNA methylation in autistic individuals compared to neurotypical individuals. Yet, it is unclear if this extends to autistic traits—subclinical manifestation of autism features in the general population. Here, we investigate the association between DNA methylation at birth (cord blood), and scores on the Social and Communication Disorders Checklist (SCDC), a measure of autistic traits, in 701 8-year-olds, by conducting a methylome-wide association study (MWAS). We did not identify significant CpGs associated with SCDC. The most significant CpG site was cg14379490, on chromosome 9 (MWAS beta = − 1.78 ± 0.35, p value = 5.34 × 10−7). Using methylation data for autism in peripheral tissues, we did not identify a significant concordance in effect direction of CpGs with p value < 10−4 in the SCDC MWAS (binomial sign test, p value > 0.5). In contrast, using methylation data for autism from post-mortem brain tissues, we identify a significant concordance in effect direction of CpGs with a p value < 10−4 in the SCDC MWAS (binomial sign test, p value = 0.004). Supporting this, we observe an enrichment for genes that are dysregulated in the post-mortem autism brain (one-sided Wilcoxon rank-sum test, p value = 6.22 × 10−5). Finally, integrating genome-wide association study (GWAS) data for autism (n = 46,350) with mQTL maps from cord-blood (n = 771), we demonstrate that mQTLs of CpGs associated with SCDC scores at p value thresholds of 0.01 and 0.005 are significantly shifted toward lower p values in the GWAS for autism (p < 5 × 10−3). We provide additional support for this using a GWAS of SCDC, and demonstrate a lack of enrichment in a GWAS of Alzheimer’s disease. Our results highlight the shared cross-tissue methylation architecture of autism and autistic traits, and demonstrate that mQTLs associated with differences in DNA methylation associated with childhood autistic traits are enriched for common genetic variants associated with autism and autistic traits.
Major surgery induces acute changes in DNA methylation associated with activation of the immune response
Ryoichi Sadahiro,
Bridget Knight,
Ffion James,
Eilis Hannon,
John Charity,
Ian R. Daniels,
Joe Burrage
+ 4 more
Ryoichi Sadahiro,
Bridget Knight,
Ffion James,
Eilis Hannon,
John Charity,
Ian R. Daniels,
Joe Burrage,
Olivia Knox,
Bethany Crawford,
Neil J. Smart,
Jonathan Mill
Abstract
Background
Surgery is an invasive procedure evoking acute inflammatory and immune responses that are believed to mediate risk for postoperative complications including cognitive dysfunction and delirium. Although the specific mechanisms driving these responses have not been well-characterized, they are hypothesized to involve the epigenetic regulation of gene expression. We quantified genome-wide levels of DNA methylation in purified peripheral blood mononuclear cells (PBMCs) longitudinally collected from 55 elderly patients undergoing three types of major surgery (elective colorectal and hip replacement surgery, and emergency hip fracture surgery), comparing samples collected at baseline to those collected immediately post-operatively and at discharge from hospital.
Results
Major surgery was associated with acute changes in DNA methylation at sites annotated to immune system genes, paralleling changes in serum-levels of markers including C-reactive protein (CRP) and Interleukin 6 (IL-6) measured in the same individuals. Although many of the observed changes in DNA methylation are consistent across the three types of surgery, there is notable heterogeneity between surgery types at certain loci. The acute changes in DNA methylation induced by surgery are relatively stable in the postoperative period, generally persisting until discharge from hospital.
Conclusions
Our results highlight the dramatic alterations in gene regulation induced by invasive surgery, primarily reflecting upregulation of the immune system in response to trauma, wound healing and anaesthesia.
SA73SITES OF ACTIVE GENE REGULATION IN THE DEVELOPING HUMAN BRAIN AND THEIR ROLE IN NEUROPSYCHIATRIC DISORDERS
Manuela Kouakou, Jonathan Mill, Matthew Hill, Nick Bray
Manuela Kouakou,
Jonathan Mill,
Matthew Hill,
Nick Bray
SU40DNA METHYLATION AND INFLAMMATION MARKER PROFILES ASSOCIATED WITH A HISTORY OF DEPRESSION
Bethany Crawford,
Zoe Craig,
Georgina Mansell,
Isobel White,
Adam Smith,
Steve Spaull,
Jennifer Imm
+ 9 more
Bethany Crawford,
Zoe Craig,
Georgina Mansell,
Isobel White,
Adam Smith,
Steve Spaull,
Jennifer Imm,
Eilis Hannon,
Andrew Wood,
Hanieh Yaghootkar,
Yingjie Ji,
Major Depressive Disorder Working Group,
Niamh Mullins,
Cathryn Lewis,
Jonathan Mill,
Therese Murphy
METHYLOMIC BIOMARKERS OF SCHIZOPHRENIA AND ANTIPSYCHOTIC MEDICATION EXPOSURE
Eilis Hannon,
Emma Dempster,
Georgina Mansell,
Leo Schalkwyk,
Robin Murray,
Andrew McQuillin,
Kaarina Kowalec
+ 8 more
Eilis Hannon,
Emma Dempster,
Georgina Mansell,
Leo Schalkwyk,
Robin Murray,
Andrew McQuillin,
Kaarina Kowalec,
Clair David St.,
Derek Morris,
Patrick Sullivan,
Michael O'Donovan,
James MacCabe,
CRESTAR Consortium,
David Collier,
Jonathan Mill
EXPRESSION QUANTITATIVE TRAIT LOCI IN THE DEVELOPING HUMAN BRAIN AND THEIR ENRICHMENT IN NEUROPSYCHIATRIC DISORDERS
Heath O'Brien,
Eilis Hannon,
Matthew Hill,
Carolina Toste,
Matthew Robertson,
Joanne Morgan,
Gemma McLaughlin
+ 7 more
Heath O'Brien,
Eilis Hannon,
Matthew Hill,
Carolina Toste,
Matthew Robertson,
Joanne Morgan,
Gemma McLaughlin,
Cathryn Lewis,
Leonard Schalkwyk,
Antonio Pardinas,
Michael Owen,
Michael O'Donovan,
Jonathan Mill,
Nick Bray
SA65DNA METHYLOME MARKS OF EXPOSURE TO PSYCHOSOCIAL STRESS DURING ADOLESCENCE: ANALYSIS OF A NOVEL LONGITUDINAL MZ DISCORDANT TWIN STUDY
Radhika Kandaswamy,
Eilis Hannon,
Georgina Mansell,
Ben Williams,
Joe Burrage,
Susanna Roberts,
Andrea Danese
+ 4 more
Radhika Kandaswamy,
Eilis Hannon,
Georgina Mansell,
Ben Williams,
Joe Burrage,
Susanna Roberts,
Andrea Danese,
Jonathan Mill,
Louise Arseneault,
Helen Fisher,
Chloe Chung Yi Wong
SA61CAN DNA METHYLATION PROFILING SHED LIGHT ON THE BIOLOGY OF CANNABIS ASSOCIATED PSYCHOSIS? PRELIMINARY DATA ON THE EWAS CANNABIS USE SIGNATURE IN THE EUGEI CASE-CONTROL STUDY
Forti Marta Di,
Emma Dempster,
Diego Quattrone,
Eilis Hannon,
Joe Burrage,
Georgina Mansell,
Bart Rutten
+ 7 more
Forti Marta Di,
Emma Dempster,
Diego Quattrone,
Eilis Hannon,
Joe Burrage,
Georgina Mansell,
Bart Rutten,
Os Jim van,
Michael O'Donovan,
Alexander Richards,
Craig Morgan,
Robin Murray,
Chloe Chung Yi Wong,
Jonathan Mill
SU103A ZEBRAFISH MODEL OF CLOZAPINE EXPOSURE: DRUG-INDUCED TRANSCRIPTOMIC CHANGES IN THE BRAIN
Joana Viana,
Nick Wildman,
Eilis Hannon,
Audrey Farbos,
Paul O'Neill,
Karen Moore,
Konrad Paszkiewicz
+ 4 more
Joana Viana,
Nick Wildman,
Eilis Hannon,
Audrey Farbos,
Paul O'Neill,
Karen Moore,
Konrad Paszkiewicz,
Aerle Ronny van,
Gregory Paull,
Eduarda Santos,
Jonathan Mill
Integrative genomics identifies a convergent molecular subtype that links epigenomic with transcriptomic differences in autism
Gokul Ramaswami,
Hyejung Won,
Michael J. Gandal,
Jillian Haney,
Jerry C. Wang,
Chloe C.Y. Wong,
Wenjie Sun
+ 3 more
Gokul Ramaswami,
Hyejung Won,
Michael J. Gandal,
Jillian Haney,
Jerry C. Wang,
Chloe C.Y. Wong,
Wenjie Sun,
Shyam Prabhakar,
Jonathan Mill,
Daniel H. Geschwind
Abstract
Autism spectrum disorder (ASD) is a phenotypically and genetically heterogeneous neurodevelopmental disorder. Despite this heterogeneity, previous studies have shown patterns of molecular convergence in post-mortem brain tissue from autistic subjects. Here, we integrate genome-wide measures of mRNA expression, miRNA expression, DNA methylation, and histone acetylation from ASD and control brains to identify a convergent molecular subtype of ASD with shared dysregulation across both the epigenome and transcriptome. Focusing on this convergent subtype, we substantially expand the repertoire of differentially expressed genes in ASD and identify a component of upregulated immune processes that are associated with hypomethylation. We utilize eQTL and chromosome conformation datasets to link differentially acetylated regions with their cognate genes and identify an enrichment of ASD genetic risk variants in hyperacetylated noncoding regulatory regions linked to neuronal genes. These findings help elucidate how diverse genetic risk factors converge onto specific molecular processes in ASD.
Epigenetic age is accelerated in schizophrenia with age- and sex-specific effects and associated with polygenic disease risk
Anil P.S. Ori,
Loes M. Olde Loohuis,
Jerry Guintivano,
Eilis Hannon,
Emma Dempster,
Clair David St.,
Nick J Bass
+ 6 more
Anil P.S. Ori,
Loes M. Olde Loohuis,
Jerry Guintivano,
Eilis Hannon,
Emma Dempster,
Clair David St.,
Nick J Bass,
Andrew McQuillin,
Jonathan Mill,
Patrick F Sullivan,
Rene S. Kahn,
Steve Horvath,
Roel A. Ophoff
Abstract Background The study of biological age acceleration may help identify at-risk individuals and contribute to reduce the rising global burden of age-related diseases. Using DNA methylation (DNAm) clocks, we investigated biological aging in schizophrenia (SCZ), a severe mental illness that is associated with an increased prevalence of age-related disabilities and morbidities. In a multi-cohort whole blood sample consisting of 1,090 SCZ cases and 1,206 controls, we investigated differential aging using three DNAm clocks (i.e. Hannum, Horvath, Levine). These clocks are highly predictive of chronological age and are known to capture different processes of biological aging. Results We found that blood-based DNAm aging is significantly altered in SCZ with age- and sex-specific effects that differ between clocks and map to distinct chronological age windows. Most notably, differential phenotypic age (Levine clock) was most pronounced in female SCZ patients in later adulthood compared to matched controls. Female patients with high SCZ polygenic risk scores (PRS) present the highest age acceleration in this age group with +4.30 years (CI: 2.40-6.20, P=1.3E-05). Phenotypic age and SCZ PRS contribute additively to the illness and together explain up to 22.4% of the variance in disease status in this study. This suggests that combining genetic and epigenetic predictors may improve predictions of disease outcomes. Conclusions Since increased phenotypic age is associated with increased risk of all-cause mortality, our findings indicate that specific and identifiable patient groups are at increased mortality risk as measured by the Levine clock. These results provide new biological insights into the aging landscape of SCZ with age- and sex-specific effects and warrant further investigations into the potential of DNAm clocks as clinical biomarkers that may help with disease management in schizophrenia.
SCHIZOPHRENIA IS CHARACTERIZED BY AGE- AND SEX-SPECIFIC EFFECTS ON EPIGENETIC AGING
Anil Ori,
Loes Olde Loohuis,
Jerry Guintivano,
Clair David St.,
Andrew McQuillin,
Jonathan Mill,
Patrick Sullivan
+ 3 more
Anil Ori,
Loes Olde Loohuis,
Jerry Guintivano,
Clair David St.,
Andrew McQuillin,
Jonathan Mill,
Patrick Sullivan,
Rene Kahn,
Steve Horvath,
Roel Ophoff
O4‐10‐06: INTEGRATED GENETIC‐EPIGENETIC ANALYSES OF ALZHEIMER'S DISEASE
Rebecca G. Smith,
Ehsan Pishva,
Gemma Shireby,
Adam R. Smith,
Eilis Hannon,
Andrew J. Sharp,
Diego f Mastroeni
+ 8 more
Rebecca G. Smith,
Ehsan Pishva,
Gemma Shireby,
Adam R. Smith,
Eilis Hannon,
Andrew J. Sharp,
Diego f Mastroeni,
Leonard C. Schalkwyk,
Vahram Haroutunian,
Paul D. Coleman,
David A. Bennett,
den Hove Daniel L.A. van,
Jager Philip L. De,
Jonathan Mill,
Katie Lunnon
BackgroundA gap exists in our mechanistic understanding of how genetic and environmental risk factors converge at the molecular level to result in the emergence of autism symptoms. We compared blood-based gene expression signatures in identical twins concordant and discordant for autism spectrum condition (ASC) to differentiate genetic and environmentally driven transcription differences, and establish convergent evidence for biological mechanisms involved in ASC.MethodsGenome-wide gene expression data were generated using RNA-seq on whole blood samples taken from 16 pairs of monozygotic (MZ) twins and seven twin pair members (39 individuals in total), who had been assessed for ASC and autism traits at age 12. Differential expression (DE) analyses were performed between (a) affected and unaffected subjects (N = 36) and (b) within discordant ASC MZ twin pairs (total N = 11) to identify environmental-driven DE. Gene set enrichment and pathway testing was performed on DE gene lists. Finally, an integrative analysis using DNA methylation data aimed to identify genes with consistent evidence for altered regulation in cis.ResultsIn the discordant twin analysis, three genes showed evidence for DE at FDR < 10%: IGHG4, EVI2A and SNORD15B. In the case-control analysis, four DE genes were identified at FDR < 10% including IGHG4, PRR13P5, DEPDC1B, and ZNF501. We find enrichment for DE of genes curated in the SFARI human gene database. Pathways showing evidence of enrichment included those related to immune cell signalling and immune response, transcriptional control and cell cycle/proliferation. Integrative methylomic and transcriptomic analysis identified a number of genes showing suggestive evidence for cis dysregulation.LimitationsIdentical twins stably discordant for ASC are rare, and as such the sample size was limited and constrained to the use of peripheral blood tissue for transcriptomic and methylomic profiling. Given these primary limitations, we focused on transcript-level analysis.ConclusionsUsing a cohort of ASC discordant and concordant MZ twins, we add to the growing body of transcriptomic-based evidence for an immune-based component in the molecular aetiology of ASC. Whilst the sample size was limited, the study demonstrates the utility of the discordant MZ twin design combined with multi-omics integration for maximising the potential to identify disease-associated molecular signals.
Alzheimer’s disease-associated (hydroxy)methylomic changes in the brain and blood
Roy Lardenoije,
Janou A. Y. Roubroeks,
Ehsan Pishva,
Markus Leber,
Holger Wagner,
Artemis Iatrou,
Adam R. Smith
+ 22 more
Roy Lardenoije,
Janou A. Y. Roubroeks,
Ehsan Pishva,
Markus Leber,
Holger Wagner,
Artemis Iatrou,
Adam R. Smith,
Rebecca G. Smith,
Lars M. T. Eijssen,
Luca Kleineidam,
Amit Kawalia,
Per Hoffmann,
Tobias Luck,
Steffi Riedel-Heller,
Frank Jessen,
Wolfgang Maier,
Michael Wagner,
René Hurlemann,
Gunter Kenis,
Muhammad Ali,
Sol Antonio del,
Diego Mastroeni,
Elaine Delvaux,
Paul D. Coleman,
Jonathan Mill,
Bart P. F. Rutten,
Katie Lunnon,
Alfredo Ramirez,
den Hove Daniël L. A. van
BackgroundLate-onset Alzheimer’s disease (AD) is a complex multifactorial affliction, the pathogenesis of which is thought to involve gene-environment interactions that might be captured in the epigenome. The present study investigated epigenome-wide patterns of DNA methylation (5-methylcytosine, 5mC) and hydroxymethylation (5-hydroxymethylcytosine, 5hmC), as well as the abundance of unmodified cytosine (UC), in relation to AD.ResultsWe identified epigenetic differences in AD patients (n = 45) as compared to age-matched controls (n = 35) in the middle temporal gyrus, pertaining to genomic regions close to or overlapping with genes such as OXT (− 3.76% 5mC, pŠidák = 1.07E−06), CHRNB1 (+ 1.46% 5hmC, pŠidák = 4.01E−04), RHBDF2 (− 3.45% UC, pŠidák = 4.85E−06), and C3 (− 1.20% UC, pŠidák = 1.57E−03). In parallel, in an independent cohort, we compared the blood methylome of converters to AD dementia (n = 54) and non-converters (n = 42), at a preclinical stage. DNA methylation in the same region of the OXT promoter as found in the brain was found to be associated with subsequent conversion to AD dementia in the blood of elderly, non-demented individuals (+ 3.43% 5mC, pŠidák = 7.14E−04).ConclusionsThe implication of genome-wide significant differential methylation of OXT, encoding oxytocin, in two independent cohorts indicates it is a promising target for future studies on early biomarkers and novel therapeutic strategies in AD.
Systematic underestimation of the epigenetic clock and age acceleration in older subjects
Khoury Louis Y. El,
Tyler Gorrie-Stone,
Melissa Smart,
Amanda Hughes,
Yanchun Bao,
Alexandria Andrayas,
Joe Burrage
+ 4 more
Khoury Louis Y. El,
Tyler Gorrie-Stone,
Melissa Smart,
Amanda Hughes,
Yanchun Bao,
Alexandria Andrayas,
Joe Burrage,
Eilis Hannon,
Meena Kumari,
Jonathan Mill,
Leonard C. Schalkwyk
BackgroundThe Horvath epigenetic clock is widely used. It predicts age quite well from 353 CpG sites in the DNA methylation profile in unknown samples and has been used to calculate “age acceleration” in various tissues and environments.ResultsThe model systematically underestimates age in tissues from older people. This is seen in all examined tissues but most strongly in the cerebellum and is consistently observed in multiple datasets. Age acceleration is thus age-dependent, and this can lead to spurious associations. The current literature includes examples of association tests with age acceleration calculated in a wide variety of ways.ConclusionsThe concept of an epigenetic clock is compelling, but caution should be taken in interpreting associations with age acceleration. Association tests of age acceleration should include age as a covariate.
Psychosis-associated DNA methylomic variation in Alzheimer's disease cortex
Ehsan Pishva,
Byron Creese,
Adam R Smith,
Wolfgang Viechtbauer,
Petroula Proitsi,
den Hove Daniel L A van,
Clive Ballard
+ 2 more
Ehsan Pishva,
Byron Creese,
Adam R Smith,
Wolfgang Viechtbauer,
Petroula Proitsi,
den Hove Daniel L A van,
Clive Ballard,
Jonathan Mill,
Katie Lunnon
Psychotic symptoms are a common and debilitating feature of Alzheimer's disease (AD) and are associated with a more rapid course of decline. Current evidence from postmortem and neuroimaging studies implicates frontal, temporal, and parietal lobes, with reported disruptions in monoaminergic pathways. However, the molecular mechanisms underlying this remain unclear. In the present study, we investigated methylomic variation associated with AD psychosis in 3 key brain regions implicated in the etiology of psychosis (prefrontal cortex, entorhinal cortex, and superior temporal gyrus) in postmortem brain samples from 29 AD donors with psychosis and 18 matched AD donors without psychosis. We identified psychosis-associated methylomic changes in a number of loci, with these genes being enriched in known schizophrenia-associated genetic and epigenetic variants. One of these known loci resided in the AS3MT gene-previously implicated in schizophrenia in a large GWAS meta-analysis. We used bisulfite-pyrosequencing to confirm hypomethylation across 4 neighboring CpG sites in the ASM3T gene. Finally, our regional analysis nominated multiple CpG sites in TBX15 and WT1, which are genes that have been previously implicated in AD. Thus one potential implication from our study is whether psychosis-associated variation drives reported associations in AD case-control studies.
P.118 Longitudinal DNA methylation changes associated with improvement of psychotic symptoms during clozapine treatment
A. Gillespie, E. Hannon, A. Egerton, J. Mill, J. MacCabe
A. Gillespie,
E. Hannon,
A. Egerton,
J. Mill,
J. MacCabe
Genome-Wide DNA Methylation Patterns in Persistent Attention-Deficit/Hyperactivity Disorder and in Association With Impulsive and Callous Traits
Mandy Meijer,
Marieke Klein,
Eilis Hannon,
der Meer Dennis van,
Catharina Hartman,
Jaap Oosterlaan,
Dirk Heslenfeld
+ 4 more
Mandy Meijer,
Marieke Klein,
Eilis Hannon,
der Meer Dennis van,
Catharina Hartman,
Jaap Oosterlaan,
Dirk Heslenfeld,
Pieter J. Hoekstra,
Jan Buitelaar,
Jonathan Mill,
Barbara Franke
Attention-deficit/hyperactivity disorder (ADHD) is a neurodevelopmental disorder that often persists into adulthood. ADHD and related personality traits, such as impulsivity and callousness, are caused by genetic and environmental factors and their interplay. Epigenetic modifications of DNA, including methylation, are thought to mediate between such factors and behavior and may behave as biomarkers for disorders. Here, we set out to study DNA methylation in persistent ADHD and related traits. We performed epigenome-wide association studies (EWASs) on peripheral whole blood from participants in the NeuroIMAGE study (age range 12-23 years). We compared participants with persistent ADHD (n = 35) with healthy controls (n = 19) and with participants with remittent ADHD (n = 19). Additionally, we performed EWASs of impulsive and callous traits derived from the Conners Parent Rating Scale and the Callous-Unemotional Inventory, respectively, across all participants. For every EWAS, the linear regression model analyzed included covariates for age, sex, smoking scores, and surrogate variables reflecting blood cell type composition and genetic background. We observed no epigenome-wide significant differences in single CpG site methylation between participants with persistent ADHD and healthy controls or participants with remittent ADHD. However, epigenome-wide analysis of differentially methylated regions provided significant findings showing that hypermethylated regions in the APOB and LPAR5 genes were associated with ADHD persistence compared to ADHD remittance (p = 1.68 * 10-24 and p = 9.06 * 10-7, respectively); both genes are involved in cholesterol signaling. Both findings appeared to be linked to genetic variation in cis. We found neither significant epigenome-wide single CpG sites nor regions associated with impulsive and callous traits; the top-hits from these analyses were annotated to genes involved in neurotransmitter release and the regulation of the biological clock. No link to genetic variation was observed for these findings, which thus might reflect environmental influences. In conclusion, in this pilot study with a small sample size, we observed several DNA-methylation-disorder/trait associations of potential significance for ADHD and the related behavioral traits. Although we do not wish to draw conclusions before replication in larger, independent samples, cholesterol signaling and metabolism may be of relevance for the onset and/or persistence of ADHD.
Clozapine-induced transcriptional changes in the zebrafish brain
Joana Viana,
Nick Wildman,
Eilis Hannon,
Audrey Farbos,
Paul O’ Neill,
Karen Moore,
Aerle Ronny van
+ 3 more
Joana Viana,
Nick Wildman,
Eilis Hannon,
Audrey Farbos,
Paul O’ Neill,
Karen Moore,
Aerle Ronny van,
Greg Paull,
Eduarda Santos,
Jonathan Mill
Clozapine is an atypical antipsychotic medication that is used to treat schizophrenia patients who are resistant to other antipsychotic drugs. The molecular mechanisms mediating the effects of clozapine are not well understood and its use is often associated with severe side-effects. In this study, we exposed groups of wild-type zebrafish to two doses of clozapine (‘low’ (20 µg/L) and ‘high’ (70 µg/L)) over a 72-h period, observing dose-dependent effects on behaviour. Using RNA sequencing (RNA-seq) we identified multiple genes differentially expressed in the zebrafish brain following exposure to clozapine. Network analysis identified co-expression modules characterised by striking changes in module connectivity in response to clozapine, and these were enriched for regulatory pathways relevant to the etiology of schizophrenia. Our study highlights the utility of zebrafish as a model for assessing the molecular consequences of antipsychotic medications and identifies genomic networks potentially involved in schizophrenia.
Quantification of the pace of biological aging in humans through a blood test: The DunedinPoAm DNA methylation algorithm
DW Belsky,
A Caspi,
L Arseneault,
A Baccarelli,
D Corcoran,
X Gao,
E Hannon
+ 15 more
DW Belsky,
A Caspi,
L Arseneault,
A Baccarelli,
D Corcoran,
X Gao,
E Hannon,
HL Harrington,
LJH Rasmussen,
R Houts,
K Huffman,
WE Kraus,
D Kwon,
J Mill,
CF Pieper,
J Prinz,
R Poulton,
J Schwartz,
K Sugden,
P Vokonas,
BS Williams,
TE Moffitt
ABSTRACT Biological aging is the gradual, progressive decline in system integrity that occurs with advancing chronological age, causing morbidity and disability. Measurements of the pace of aging are needed to serve as surrogate endpoints in trials of therapies designed to prevent disease by slowing biological aging. We report a blood DNA-methylation measure that is sensitive to variation in the pace of biological aging among individuals born the same year. We first modeled longitudinal change in 18 biomarkers tracking organ-system integrity across 12 years of follow-up in the Dunedin birth cohort. Rates of change in each biomarker were composited to form a measure of aging-related decline, termed Pace of Aging. Elastic-net regression was used to develop a DNA-methylation predictor of Pace of Aging, called DunedinPoAm for Dunedin (P)ace (o)f (A)ging (m)ethylation. Validation analyses showed DunedinPoAm was associated with functional decline in the Dunedin Study and more advanced biological age in the Understanding Society Study, predicted chronic disease and mortality in the Normative Aging Study, was accelerated by early-life adversity in the E-risk Study, and DunedinPoAm prediction was disrupted by caloric restriction in the CALERIE trial. DunedinPoAm generally outperformed epigenetic clocks. Findings provide proof-of-principle for DunedinPoAm as a single-time-point measure of a person’s pace of biological aging.
Evidence that Telomere Length is Causal for Idiopathic Pulmonary Fibrosis but not Chronic Obstructive Pulmonary Disease: A Mendelian Randomisation Study
Anna Duckworth,
Michael A. Gibbons,
Richard J. Allen,
Howard Almond,
Robin N. Beaumont,
Andrew R. Wood,
Katie Lunnon
+ 4 more
Anna Duckworth,
Michael A. Gibbons,
Richard J. Allen,
Howard Almond,
Robin N. Beaumont,
Andrew R. Wood,
Katie Lunnon,
Mark A. Lindsay,
Louise V. Wain,
Jess Tyrrell,
Chris J. Scotton
Summary Background Idiopathic pulmonary fibrosis (IPF) is a fatal lung disease accounting for 1% of UK deaths. In the familial form of pulmonary fibrosis, causal genes have been identified in ∼30% of cases, and a majority relate to telomere maintenance. Prematurely shortened leukocyte telomere length has also been associated with IPF, as well as chronic obstructive pulmonary disease (COPD), a disease with a similar demographic and shared risk factors. Using Mendelian randomisation (MR), our study aimed to determine whether short telomeres cause IPF or COPD. Methods We performed an MR study for telomere length causality in IPF and COPD with up to 1,369 IPF cases, 14,103 COPD cases and 435,866 controls of European ancestry in UK Biobank. Initial studies using polygenic risk scores followed by two-sample MR analyses were carried out using seven genetic variants previously associated with telomere length, with replication analysis in an IPF cohort of 2,668 IPF cases and 8,591 controls and a COPD cohort of 15,256 cases and 47,936 controls. Findings Meta-analysis of the two-sample MR results provided evidence that shorter telomeres cause IPF, with a genetically instrumented one standard deviation shorter telomere length associated with 5.81 higher odds of IPF ([95% CI: 3.56-9.50], P=2.19×10 −12 . Despite being an age-related lung disease with overlapping risk, there was no evidence that telomere length caused COPD (OR 1.07, [95% CI 0.90-1.27], P = 0.46). Interpretation Cellular senescence is hypothesised as a major driving force in both IPF and COPD; telomere shortening may be a contributory factor in IPF, suggesting divergent mechanisms in COPD. This enables greater focus in telomere-related diagnostics, treatments and the search for a cure in IPF. Therapies manifesting improvements in telomere length, including safe telomere activation therapy, may warrant investigation.
Transcriptional Signatures of Tau and Amyloid Neuropathology
Isabel Castanho,
Tracey K. Murray,
Eilis Hannon,
Aaron Jeffries,
Emma Walker,
Emma Laing,
Hedley Baulf
+ 10 more
Isabel Castanho,
Tracey K. Murray,
Eilis Hannon,
Aaron Jeffries,
Emma Walker,
Emma Laing,
Hedley Baulf,
Joshua Harvey,
Lauren Bradshaw,
Andrew Randall,
Karen Moore,
Paul O’Neill,
Katie Lunnon,
David A. Collier,
Zeshan Ahmed,
Michael J. O’Neill,
Jonathan Mill
Alzheimer's disease (AD) is associated with the intracellular aggregation of hyperphosphorylated tau and the accumulation of β-amyloid in the neocortex. We use transgenic mice harboring human tau (rTg4510) and amyloid precursor protein (J20) mutations to investigate transcriptional changes associated with the progression of tau and amyloid pathology. rTg4510 mice are characterized by widespread transcriptional differences in the entorhinal cortex with changes paralleling neuropathological burden across multiple brain regions. Differentially expressed transcripts overlap with genes identified in genetic studies of familial and sporadic AD. Systems-level analyses identify discrete co-expression networks associated with the progressive accumulation of tau that are enriched for genes and pathways previously implicated in AD pathology and overlap with co-expression networks identified in human AD cortex. Our data provide further evidence for an immune-response component in the accumulation of tau and reveal molecular pathways associated with the progression of AD neuropathology.
Large epigenome-wide association study of childhood ADHD identifies peripheral DNA methylation associated with disease and polygenic risk burden
Michael A. Mooney, Peter Ryabinin, Beth Wilmot, Priya Bhatt, Jonathan Mill, Joel T. Nigg
Michael A. Mooney,
Peter Ryabinin,
Beth Wilmot,
Priya Bhatt,
Jonathan Mill,
Joel T. Nigg
Epigenetic variation in peripheral tissues is being widely studied as a molecular biomarker of complex disease and disease-related exposures. To date, few studies have examined differences in DNA methylation associated with attention-deficit hyperactivity disorder (ADHD). In this study, we profiled genetic and methylomic variation across the genome in saliva samples from children (age 7–12 years) with clinically established ADHD (N = 391) and nonpsychiatric controls (N = 213). We tested for differentially methylated positions (DMPs) associated with both ADHD diagnosis and ADHD polygenic risk score, by using linear regression models including smoking, medication effects, and other potential confounders in our statistical models. Our results support previously reported associations between ADHD and DNA methylation levels at sites annotated to VIPR2, and identify several novel disease-associated DMPs (p < 1e–5), although none of them were genome-wide significant. The two top-ranked, ADHD-associated DMPs (cg17478313 annotated to SLC7A8 and cg21609804 annotated to MARK2) are also significantly associated with nearby SNPs (p = 1.2e–46 and p = 2.07e–59), providing evidence that disease-associated DMPs are under genetic control. We also report a genome-wide significant association between ADHD polygenic risk and variable DNA methylation at a site annotated to the promoter of GART and SON (p = 6.71E–8). Finally, we show that ADHD-associated SNPs colocalize with SNPs associated with methylation levels in saliva. This is the first large-scale study of DNA methylation in children with ADHD. Our results represent novel epigenetic biomarkers for ADHD that may be useful for patient stratification, reinforce the importance of genetic effects on DNA methylation, and provide plausible molecular mechanisms for ADHD risk variants.
Genome-wide DNA methylation meta-analysis in the brains of suicide completers
Stefania Policicchio,
Sam Washer,
Joana Viana,
Artemis Iatrou,
Joe Burrage,
Eilis Hannon,
Gustavo Turecki
+ 4 more
Stefania Policicchio,
Sam Washer,
Joana Viana,
Artemis Iatrou,
Joe Burrage,
Eilis Hannon,
Gustavo Turecki,
Zachary Kaminsky,
Jonathan Mill,
Emma L. Dempster,
Therese M. Murphy
Suicide is the second leading cause of death globally among young people representing a significant global health burden. Although the molecular correlates of suicide remains poorly understood, it has been hypothesised that epigenomic processes may play a role. The objective of this study was to identify suicide-associated DNA methylation changes in the human brain by utilising previously published and unpublished methylomic datasets. We analysed prefrontal cortex (PFC, n = 211) and cerebellum (CER, n = 114) DNA methylation profiles from suicide completers and non-psychiatric, sudden-death controls, meta-analysing data from independent cohorts for each brain region separately. We report evidence for altered DNA methylation at several genetic loci in suicide cases compared to controls in both brain regions with suicide-associated differentially methylated positions enriched among functional pathways relevant to psychiatric phenotypes and suicidality, including nervous system development (PFC) and regulation of long-term synaptic depression (CER). In addition, we examined the functional consequences of variable DNA methylation within a PFC suicide-associated differentially methylated region (PSORS1C3 DMR) using a dual luciferase assay and examined expression of nearby genes. DNA methylation within this region was associated with decreased expression of firefly luciferase but was not associated with expression of nearby genes, PSORS1C3 and POU5F1. Our data suggest that suicide is associated with DNA methylation, offering novel insights into the molecular pathology associated with suicidality.
Significant out-of-sample classification from methylation profile scoring for amyotrophic lateral sclerosis
Marta F. Nabais,
Tian Lin,
Beben Benyamin,
Kelly L. Williams,
Fleur C. Garton,
Anna A. E. Vinkhuyzen,
Futao Zhang
+ 30 more
Marta F. Nabais,
Tian Lin,
Beben Benyamin,
Kelly L. Williams,
Fleur C. Garton,
Anna A. E. Vinkhuyzen,
Futao Zhang,
Costanza L. Vallerga,
Restuadi Restuadi,
Anna Freydenzon,
Ramona A. J. Zwamborn,
Paul J. Hop,
Matthew R. Robinson,
Jacob Gratten,
Peter M. Visscher,
Eilis Hannon,
Jonathan Mill,
Matthew A. Brown,
Nigel G. Laing,
Karen A. Mather,
Perminder S. Sachdev,
Shyuan T. Ngo,
Frederik J. Steyn,
Leanne Wallace,
Anjali K. Henders,
Merrilee Needham,
Jan H. Veldink,
Susan Mathers,
Garth Nicholson,
Dominic B. Rowe,
Robert D. Henderson,
Pamela A. McCombe,
Roger Pamphlett,
Jian Yang,
Ian P. Blair,
Allan F. McRae,
Naomi R. Wray
We conducted DNA methylation association analyses using Illumina 450K data from whole blood for an Australian amyotrophic lateral sclerosis (ALS) case–control cohort (782 cases and 613 controls). Analyses used mixed linear models as implemented in the OSCA software. We found a significantly higher proportion of neutrophils in cases compared to controls which replicated in an independent cohort from the Netherlands (1159 cases and 637 controls). The OSCA MOMENT linear mixed model has been shown in simulations to best account for confounders. When combined in a methylation profile score, the 25 most-associated probes identified by MOMENT significantly classified case–control status in the Netherlands sample (area under the curve, AUC = 0.65, CI95% = [0.62–0.68], p = 8.3 × 10−22). The maximum AUC achieved was 0.69 (CI95% = [0.66–0.71], p = 4.3 × 10−34) when cell-type proportion was included in the predictor.
A meta-analysis of epigenome-wide association studies in Alzheimer’s disease highlights novel differentially methylated loci across cortex
Rebecca G. Smith,
Ehsan Pishva,
Gemma Shireby,
Adam R. Smith,
Janou A.Y. Roubroeks,
Eilis Hannon,
Gregory Wheildon
+ 21 more
Rebecca G. Smith,
Ehsan Pishva,
Gemma Shireby,
Adam R. Smith,
Janou A.Y. Roubroeks,
Eilis Hannon,
Gregory Wheildon,
Diego Mastroeni,
Gilles Gasparoni,
Matthias Riemenschneider,
Armin Giese,
Andrew J. Sharp,
Leonard Schalkwyk,
Vahram Haroutunian,
Wolfgang Viechtbauer,
den Hove Daniel L.A. van,
Michael Weedon,
Danielle Brokaw,
Paul T. Francis,
Alan J Thomas,
Seth Love,
Kevin Morgan,
Jörn Walter,
Paul D. Coleman,
David A. Bennett,
Jager Philip L. De,
Jonathan Mill,
Katie Lunnon
ABSTRACT Epigenome-wide association studies of Alzheimer’s disease have highlighted neuropathology-associated DNA methylation differences, although existing studies have been limited in sample size and utilized different brain regions. Here, we combine data from six DNA methylomic studies of Alzheimer’s disease (N=1,453 unique individuals) to identify differential methylation associated with Braak stage in different brain regions and across cortex. We identify 236 CpGs in the prefrontal cortex, 95 CpGs in the temporal gyrus and ten CpGs in the entorhinal cortex at Bonferroni significance, with none in the cerebellum. Our cross-cortex meta-analysis (N=1,408 donors) identifies 220 CpGs associated with neuropathology, annotated to 121 genes, of which 84 genes have not been previously reported at this significance threshold. We have replicated our findings using two further DNA methylomic datasets consisting of a further > 600 unique donors. The meta-analysis summary statistics are available in our online data resource ( www.epigenomicslab.com/ad-meta-analysis/ ).
Non-neuronal expression of SARS-CoV-2 entry genes in the olfactory system suggests mechanisms underlying COVID-19-associated anosmia
David H. Brann,
Tatsuya Tsukahara,
Caleb Weinreb,
Marcela Lipovsek,
den Berge Koen Van,
Boying Gong,
Rebecca Chance
+ 18 more
David H. Brann,
Tatsuya Tsukahara,
Caleb Weinreb,
Marcela Lipovsek,
den Berge Koen Van,
Boying Gong,
Rebecca Chance,
Iain C. Macaulay,
Hsin-jung Chou,
Russell Fletcher,
Diya Das,
Kelly Street,
Bezieux Hector Roux de,
Yoon-Gi Choi,
Davide Risso,
Sandrine Dudoit,
Elizabeth Purdom,
Jonathan S. Mill,
Ralph Abi Hachem,
Hiroaki Matsunami,
Darren W. Logan,
Bradley J. Goldstein,
Matthew S. Grubb,
John Ngai,
Sandeep Robert Datta
Abstract Altered olfactory function is a common symptom of COVID-19, but its etiology is unknown. A key question is whether SARS-CoV-2 (CoV-2) – the causal agent in COVID-19 – affects olfaction directly by infecting olfactory sensory neurons or their targets in the olfactory bulb, or indirectly, through perturbation of supporting cells. Here we identify cell types in the olfactory epithelium and olfactory bulb that express SARS-CoV-2 cell entry molecules. Bulk sequencing revealed that mouse, non-human primate and human olfactory mucosa expresses two key genes involved in CoV-2 entry, ACE2 and TMPRSS2. However, single cell sequencing and immunostaining demonstrated ACE2 expression in support cells, stem cells, and perivascular cells; in contrast, neurons in both the olfactory epithelium and bulb did not express ACE2 message or protein. These findings suggest that CoV-2 infection of non-neuronal cell types leads to anosmia and related disturbances in odor perception in COVID-19 patients.
Major surgery induces acute changes in measured DNA methylation associated with immune response pathways
Ryoichi Sadahiro,
Bridget Knight,
Ffion James,
Eilis Hannon,
John Charity,
Ian R. Daniels,
Joe Burrage
+ 4 more
Ryoichi Sadahiro,
Bridget Knight,
Ffion James,
Eilis Hannon,
John Charity,
Ian R. Daniels,
Joe Burrage,
Olivia Knox,
Bethany Crawford,
Neil J. Smart,
Jonathan Mill
Surgery is an invasive procedure evoking acute inflammatory and immune responses that can influence risk for postoperative complications including cognitive dysfunction and delirium. Although the specific mechanisms driving these responses have not been well-characterized, they are hypothesized to involve the epigenetic regulation of gene expression. We quantified genome-wide levels of DNA methylation in peripheral blood mononuclear cells (PBMCs) longitudinally collected from a cohort of elderly patients undergoing major surgery, comparing samples collected at baseline to those collected immediately post-operatively and at discharge from hospital. We identified acute changes in measured DNA methylation at sites annotated to immune system genes, paralleling changes in serum-levels of markers including C-reactive protein (CRP) and Interleukin 6 (IL-6) measured in the same individuals. Many of the observed changes in measured DNA methylation were consistent across different types of major surgery, although there was notable heterogeneity between surgery types at certain loci. The acute changes in measured DNA methylation induced by surgery are relatively stable in the post-operative period, generally persisting until discharge from hospital. Our results highlight the dramatic alterations in gene regulation induced by invasive surgery, primarily reflecting upregulation of the immune system in response to trauma, wound healing and anaesthesia.
Large-scale analysis of DNA methylation identifies cellular alterations in blood from psychosis patients and molecular biomarkers of treatment-resistant schizophrenia
Eilis Hannon,
Emma L Dempster,
Georgina Mansell,
Joe Burrage,
Nick Bass,
Marc M Bohlken,
Aiden Corvin
+ 41 more
Eilis Hannon,
Emma L Dempster,
Georgina Mansell,
Joe Burrage,
Nick Bass,
Marc M Bohlken,
Aiden Corvin,
Charles J Curtis,
David Dempster,
Forta Marta Di,
Timothy G Dinan,
Gary Donohoe,
Fiona Gaughran,
Michael Gill,
Amy Gillespie,
Cerisse Gunasinghe,
Hilleke E Hulshoff,
Christina M Hultman,
Viktoria Johansson,
Rene S Kahn,
Jaakko Kaprio,
Gunter Kenis,
Kaarina Kowalec,
James MacCabe,
Colm McDonald,
Andew McQuillin,
Derek W Morris,
Kieran C Murphy,
Collette Mustard,
Igor Nenadic,
Michael C O’Donovan,
Diego Quattrone,
Alexander L Richards,
Bart PF Rutten,
Clair David St,
Sebastian Therman,
Timothea Toulopoulou,
Os Jim Van,
John L Waddington,
Wellcome Trust Case Control Consortium,
CREeTable AR consortium,
Patrick Sullivan,
Evangelos Vassos,
Gerome Breen,
David Andrew Collier,
Robin Murray,
Leonard S Schalkwyk,
Jonathan Mill
ABSTRACT Objective Psychosis - a complex and heterogeneous neuropsychiatric condition characterized by hallucinations and delusions - is a common feature of schizophrenia. There is evidence for altered DNA methylation (DNAm) associated with schizophrenia in both brain and peripheral tissues. We aimed to undertake a systematic analysis of variable DNAm associated with psychosis, schizophrenia, and treatment-resistant schizophrenia, also exploring measures of biological ageing, smoking, and blood cell composition derived from DNAm data to identify molecular biomarkers of disease. Methods We quantified DNAm across the genome in blood samples from 4,483 participants from seven case-control cohorts including patients with schizophrenia or first-episode psychosis. Measures of biological age, cellular composition and smoking status were derived from DNAm data using established algorithms. DNAm and derived measures were analyzed within each cohort and the results combined by meta-analysis. Results Psychosis cases were characterized by significant differences in measures of blood cell proportions and elevated smoking exposure derived from the DNAm data, with the largest differences seen in treatment-resistant schizophrenia patients. DNAm at 95 CpG sites was significantly different between psychosis cases and controls, with 1,048 differentially methylated positions (DMPs) identified between schizophrenia cases and controls. Schizophrenia-associated DMPs colocalize to regions identified in genetic association studies, with genes annotated to these sites enriched for pathways relevant to disease. Finally, a number of the schizophrenia associated differences were only present in the treatment-resistant schizophrenia subgroup. Conclusions We show that DNAm data can be leveraged to derive measures of blood cell counts and smoking that are strongly associated with psychosis. Our DNAm meta-analysis identified multiple DMPs associated with both psychosis and a more refined diagnosis of schizophrenia, with evidence for differential methylation associated with treatment-resistant schizophrenia that potentially reflects exposure to clozapine.
Whole transcriptome in-silico screening implicates cardiovascular and infectious disease in the mechanism of action underlying atypical antipsychotic side-effects
Yasaman Malekizadeh,
Gareth Williams,
Mark Kelson,
David Whitfield,
Jonathan Mill,
David A Collier,
Clive Ballard
+ 2 more
Yasaman Malekizadeh,
Gareth Williams,
Mark Kelson,
David Whitfield,
Jonathan Mill,
David A Collier,
Clive Ballard,
Aaron R Jeffries,
Byron Creese
Abstract INTRODUCTION Stroke/thromboembolic events, infections and death are all significantly increased by antipsychotics in dementia but little is known about why they can be harmful. Using a novel application of a drug repurposing paradigm, we aimed to identify potential mechanisms underlying adverse events. METHOD Whole transcriptome signatures were generated for SH-SY5Y cells treated with amisulpride, risperidone and volinanserin using RNA-sequencing. Bioinformatic analysis was performed which scored the association between antipsychotic signatures and expression data from 415,252 samples in the NCBI GEO repository. RESULTS Atherosclerosis, venous thromboembolism and influenza NCBI GEO-derived samples scored positively against antipsychotic signatures. Pathways enriched in antipsychotic signatures were linked to the cardiovascular and immune systems (e.g. BDNF, PDGFR-beta, TNF, TGF-beta, selenoamino acid metabolism and influenza infection). CONCLUSION These findings for the first time mechanistically link antipsychotics to specific cardiovascular and infectious diseases which are known side effects of their use in dementia, providing new information to explain related adverse events.
Whole transcriptome in-silico screening implicates cardiovascular and infectious disease in the mechanism of action underlying atypical antipsychotic side-effects
Yasaman Malekizadeh,
Gareth Williams,
Mark Kelson,
David R Whitfield,
Jonathan Mill,
David A Collier,
Clive Ballard
+ 2 more
Yasaman Malekizadeh,
Gareth Williams,
Mark Kelson,
David R Whitfield,
Jonathan Mill,
David A Collier,
Clive Ballard,
Aaron R Jeffries,
Byron Creese
BACKGROUND Stroke/thromboembolic events, infections and death are all significantly increased by antipsychotics in dementia but little is known about why they can be harmful. Using a novel application of a drug repurposing paradigm, we aimed to identify potential mechanisms underlying adverse events.
METHODS Whole transcriptome signatures were generated for SH-SY5Y cells treated with amisulpride, risperidone and volinanserin using RNA-sequencing. Bioinformatic analysis was performed which scored the association between antipsychotic signatures and expression data from 415,252 samples in the NCBI GEO repository.
RESULTS Atherosclerosis, venous thromboembolism and influenza NCBI GEO-derived samples scored positively against antipsychotic signatures. Pathways enriched in antipsychotic signatures were linked to the cardiovascular and immune systems (e.g. BDNF, PDGFR-beta, TNF, TGF-beta, selenoamino acid metabolism and influenza infection).
CONCLUSIONS These findings for the first time mechanistically link antipsychotics to specific cardiovascular and infectious diseases which are known side effects of their use in dementia, providing new information to explain related adverse events.
Patterns of Reliability: Assessing the Reproducibility and Integrity of DNA Methylation Measurement
Karen Sugden,
Eilis J. Hannon,
Louise Arseneault,
Daniel W. Belsky,
David L. Corcoran,
Helen L. Fisher,
Renate M. Houts
+ 9 more
Karen Sugden,
Eilis J. Hannon,
Louise Arseneault,
Daniel W. Belsky,
David L. Corcoran,
Helen L. Fisher,
Renate M. Houts,
Radhika Kandaswamy,
Terrie E. Moffitt,
Richie Poulton,
Joseph A. Prinz,
Line J.H. Rasmussen,
Benjamin S. Williams,
Chloe C.Y. Wong,
Jonathan Mill,
Avshalom Caspi
DNA methylation plays an important role in both normal human development and risk of disease. The most utilized method of assessing DNA methylation uses BeadChips, generating an epigenome-wide "snapshot" of >450,000 observations (probe measurements) per assay. However, the reliability of each of these measurements is not equal, and little consideration is paid to consequences for research. We correlated repeat measurements of the same DNA samples using the Illumina HumanMethylation450K and the Infinium MethylationEPIC BeadChips in 350 blood DNA samples. Probes that were reliably measured were more heritable and showed consistent associations with environmental exposures, gene expression, and greater cross-tissue concordance. Unreliable probes were less replicable and generated an unknown volume of false negatives. This serves as a lesson for working with DNA methylation data, but the lessons are equally applicable to working with other data: as we advance toward generating increasingly greater volumes of data, failure to document reliability risks harming reproducibility.
Recalibrating the Epigenetic Clock: Implications for Assessing Biological Age in the Human Cortex
Gemma L Shireby,
Jonathan P Davies,
Paul T Francis,
Joe Burrage,
Emma M Walker,
Grant W A Neilson,
Aisha Dahir
+ 10 more
Gemma L Shireby,
Jonathan P Davies,
Paul T Francis,
Joe Burrage,
Emma M Walker,
Grant W A Neilson,
Aisha Dahir,
Alan J Thomas,
Seth Love,
Rebecca G Smith,
Katie Lunnon,
Meena Kumari,
Leonard C Schalkwyk,
Kevin Morgan,
Keeley Brookes,
Eilis J Hannon,
Jonathan Mill
Abstract Human DNA-methylation data have been used to develop biomarkers of ageing - referred to ‘epigenetic clocks’ - that have been widely used to identify differences between chronological age and biological age in health and disease including neurodegeneration, dementia and other brain phenotypes. Existing DNA methylation clocks are highly accurate in blood but are less precise when used in older samples or on brain tissue. We aimed to develop a novel epigenetic clock that performs optimally in human cortex tissue and has the potential to identify phenotypes associated with biological ageing in the brain. We generated an extensive dataset of human cortex DNA methylation data spanning the life-course (n = 1,397, ages = 1 to 104 years). This dataset was split into ‘training’ and ‘testing’ samples (training: n = 1,047; testing: n = 350). DNA methylation age estimators were derived using a transformed version of chronological age on DNA methylation at specific sites using elastic net regression, a supervised machine learning method. The cortical clock was subsequently validated in a novel human cortex dataset (n = 1,221, ages = 41 to 104 years) and tested for specificity in a large whole blood dataset (n = 1,175, ages = 28 to 98 years). We identified a set of 347 DNA methylation sites that, in combination optimally predict age in the human cortex. The sum of DNA methylation levels at these sites weighted by their regression coefficients provide the cortical DNA methylation clock age estimate. The novel clock dramatically out-performed previously reported clocks in additional cortical datasets. Our findings suggest that previous associations between predicted DNA methylation age and neurodegenerative phenotypes might represent false positives resulting from clocks not robustly calibrated to the tissue being tested and for phenotypes that become manifest in older ages. The age distribution and tissue type of samples included in training datasets need to be considered when building and applying epigenetic clock algorithms to human epidemiological or disease cohorts.
Quantification of the pace of biological aging in humans through a blood test, The DunedinPoAm DNA methylation algorithm
Daniel W W Belsky,
Avshalom Caspi,
Louise Arseneault,
Andrea Baccarelli,
David L Corcoran,
Xu Gao,
Eiliss Hannon
+ 15 more
Daniel W W Belsky,
Avshalom Caspi,
Louise Arseneault,
Andrea Baccarelli,
David L Corcoran,
Xu Gao,
Eiliss Hannon,
Hona Lee Harrington,
Line J H Rasmussen,
Renate Houts,
Kim Huffman,
William E Kraus,
Dayoon Kwon,
Jonathan Mill,
Carl F Pieper,
Joseph A Prinz,
Richie Poulton,
Joel Schwartz,
Karen Sugden,
Pantel Vokonas,
Benjamin S Williams,
Terrie E Moffitt
Biological aging is the gradual, progressive decline in system integrity that occurs with advancing chronological age, causing morbidity and disability. Measurements of the pace of aging are needed as surrogate endpoints in trials of therapies designed to prevent disease by slowing biological aging. We report a blood-DNA-methylation measure that is sensitive to variation in pace of biological aging among individuals born the same year. We first modeled change-over-time in 18 biomarkers tracking organ-system integrity across 12 years of follow-up in n = 954 members of the Dunedin Study born in 1972-1973. Rates of change in each biomarker over ages 26-38 years were composited to form a measure of aging-related decline, termed Pace-of-Aging. Elastic-net regression was used to develop a DNA-methylation predictor of Pace-of-Aging, called DunedinPoAm for Dunedin(P)ace(o)f(A)ging(m)ethylation. Validation analysis in cohort studies and the CALERIE trial provide proof-of-principle for DunedinPoAm as a single-time-point measure of a person's pace of biological aging.
Epigenetic regulation in the pathophysiology of Lewy body dementia
Leonidas Chouliaras, Gautham S Kumar, Alan J Thomas, Katie Lunnon, Patrick F Chinnery, John T O'Brien
Leonidas Chouliaras,
Gautham S Kumar,
Alan J Thomas,
Katie Lunnon,
Patrick F Chinnery,
John T O'Brien
Lewy body dementia encompasses both dementia with Lewy bodies and Parkinson's disease dementia. Although both are common causes of dementia, they remain relatively understudied. The review summarises the clinico-pathologic characteristics of Lewy Body dementia and discusses the genetic and environmental evidence contributing to the risk of developing the condition. Considering that the pathophysiology of Lewy body dementia is not yet fully understood, here we focus on the role of epigenetic mechanisms as potential key mediators of gene-environment interactions in the development of the disease. We examine available important data on genomics, epigenomics, gene expression and proteomic studies in Lewy body dementia on human post-mortem brain and peripheral tissues. Genetic variation and epigenetic modifications in key genes involved in the disorder, such as apolipoprotein E (APOE), α-synuclein (SNCA) and glucocerobrosidase (GBA), suggest a central involvement of epigenetics in DLB but conclusive evidence is scarce. This is due to limitations of existing literature, such as small sample sizes, lack of replication and lack of studies interrogating cell-type specific epigenetic modifications in the brain. Future research in the field can improve the understanding of this common but complex and rapidly progressing type of dementia and potentially open early diagnostic and effective therapeutic targets.
Assessing the co-variability of DNA methylation across peripheral cells and tissues: implications for the interpretation of findings in epigenetic epidemiology
Eilis Hannon,
Georgina Mansell,
Joe Burrage,
Agnieszka Kepa,
Janis Best-Lane,
Anna Rose,
Suzanne Heck
+ 4 more
Eilis Hannon,
Georgina Mansell,
Joe Burrage,
Agnieszka Kepa,
Janis Best-Lane,
Anna Rose,
Suzanne Heck,
Terrie Moffitt,
Avshalom Caspi,
Louise Arseneault,
Jonathan Mill
Summary/Abstract Background Most epigenome-wide association studies (EWAS) quantify DNA methylation (DNAm) in peripheral tissues such as whole blood to identify positions in the genome where variation is statistically associated with a trait or exposure. As whole blood comprises a mix of cell types, it is unclear whether trait-associated variation is specific to an individual cellular population. Methods We collected three peripheral tissues (whole blood, buccal and nasal epithelial cells) from thirty individuals. Whole blood samples were subsequently processed using fluorescence-activated cell sorting (FACS) to purify five constituent cell-types (monocytes, granulocytes, CD4 + T cells, CD8 + T cells, and B cells). DNAm was profiled in all eight sample-types from each individual using the Illumina EPIC array. Results We identified significant differences in both the level and variability of DNAm between different tissues and cell types, and DNAm data-derived estimates of age and smoking were found to differ dramatically across sample types from the same individual. We found that for the majority of loci variation in DNAm in individual blood cell types was only weakly predictive of variance in DNAm measured in whole blood, however, the proportion of variance explained was greater than that explained by either buccal or nasal tissues. Instead we observe that DNAm variation in whole blood is additively influenced by a combination of the major blood cell types. For a subset of sites variable DNAm detected in whole blood can be attributed to variation in a single blood cell type providing potential mechanistic insight. Conclusions We identified major differences in DNAm between blood cell types and peripheral tissues, with each sample type being characterized by a unique DNAm signature across multiple loci. Our results suggest that associations between whole blood DNAm and traits or exposures reflect differences in multiple cell types and provide important insights for the interpretation of EWAS performed in whole blood. Key Messages We identified major differences in DNA methylation between blood cell types and peripheral tissues, with each sample type being characterized by a unique DNA methylation signature across multiple loci. Estimates of DNAmAge and tobacco smoking from DNA methylation data can be highly variable across different sample types collected from the same individual at the same time. While individual blood cell types did predict more of the variation in whole blood compared to buccal epithelial and nasal epithelial cells, the percentage of variance explained was still small. Instead our data indicate that at the majority of sites, variation in multiple blood cell types additively combines to drive variation in DNA methylation in whole blood. There are subset of sites where variable DNA methylation detected in whole blood can be attributed to variation in a single blood cell type.
Association of Neighborhood Disadvantage in Childhood With DNA Methylation in Young Adulthood
Aaron Reuben,
Karen Sugden,
Louise Arseneault,
David L. Corcoran,
Andrea Danese,
Helen L. Fisher,
Terrie E. Moffitt
+ 7 more
Aaron Reuben,
Karen Sugden,
Louise Arseneault,
David L. Corcoran,
Andrea Danese,
Helen L. Fisher,
Terrie E. Moffitt,
Joanne B. Newbury,
Candice Odgers,
Joey Prinz,
Line J. H. Rasmussen,
Ben Williams,
Jonathan Mill,
Avshalom Caspi
Importance: DNA methylation has been proposed as an epigenetic mechanism by which the childhood neighborhood environment may have implications for the genome that compromise adult health.
Objective: To ascertain whether childhood neighborhood socioeconomic disadvantage is associated with differences in DNA methylation by age 18 years.
Design, Setting, and Participants: This longitudinal cohort study analyzed data from the Environmental Risk (E-Risk) Longitudinal Twin Study, a nationally representative birth cohort of children born between 1994 and 1995 in England and Wales and followed up from age 5 to 18 years. Data analysis was performed from March 15, 2019, to June 30, 2019.
Exposures: High-resolution neighborhood data (indexing deprivation, dilapidation, disconnection, and dangerousness) collected across childhood.
Main Outcomes and Measures: DNA methylation in whole blood was drawn at age 18 years. Associations between neighborhood socioeconomic disadvantage and methylation were tested using 3 prespecified approaches: (1) testing probes annotated to candidate genes involved in biological responses to growing up in socioeconomically disadvantaged neighborhoods and investigated in previous epigenetic research (stress reactivity-related and inflammation-related genes), (2) polyepigenetic scores indexing differential methylation in phenotypes associated with growing up in disadvantaged neighborhoods (obesity, inflammation, and smoking), and (3) a theory-free epigenome-wide association study.
Results: A total of 1619 participants (806 female individuals [50%]) had complete neighborhood and DNA methylation data. Children raised in socioeconomically disadvantaged neighborhoods exhibited differential DNA methylation in genes involved in inflammation (β = 0.12; 95% CI, 0.06-0.19; P < .001) and smoking (β = 0.18; 95% CI, 0.11-0.25; P < .001) but not obesity (β = 0.05; 95% CI, -0.01 to 0.11; P = .12). An epigenome-wide association study identified multiple CpG sites at an arraywide significance level of P < 1.16 × 10-7 in genes involved in the metabolism of hydrocarbons. Associations between neighborhood disadvantage and methylation were small but robust to family-level socioeconomic factors and to individual-level tobacco smoking.
Conclusions and Relevance: Children raised in more socioeconomically disadvantaged neighborhoods appeared to enter young adulthood epigenetically distinct from their less disadvantaged peers. This finding suggests that epigenetic regulation may be a mechanism by which the childhood neighborhood environment alters adult health.
Epigenome-wide association study of attention-deficit/hyperactivity disorder in adults
Paula Rovira,
Cristina Sánchez-Mora,
Mireia Pagerols,
Vanesa Richarte,
Montserrat Corrales,
Christian Fadeuilhe,
Laura Vilar-Ribó
+ 8 more
Paula Rovira,
Cristina Sánchez-Mora,
Mireia Pagerols,
Vanesa Richarte,
Montserrat Corrales,
Christian Fadeuilhe,
Laura Vilar-Ribó,
Lorena Arribas,
Gemma Shireby,
Eilis Hannon,
Jonathan Mill,
Miquel Casas,
Josep Antoni Ramos-Quiroga,
Artigas María Soler,
Marta Ribasés
Attention-deficit/hyperactivity disorder (ADHD) is a highly heritable neurodevelopmental disorder that often persists into adulthood. There is growing evidence that epigenetic dysregulation participates in ADHD. Given that only a limited number of epigenome-wide association studies (EWASs) of ADHD have been conducted so far and they have mainly focused on pediatric and population-based samples, we performed an EWAS in a clinical sample of adults with ADHD. We report one CpG site and four regions differentially methylated between patients and controls, which are located in or near genes previously involved in autoimmune diseases, cancer or neuroticism. Our sensitivity analyses indicate that smoking status is not responsible for these results and that polygenic risk burden for ADHD does not greatly impact the signatures identified. Additionally, we show an overlap of our EWAS findings with genetic signatures previously described for ADHD and with epigenetic signatures for smoking behavior and maternal smoking. These findings support a role of DNA methylation in ADHD and emphasize the need for additional efforts in larger samples to clarify the role of epigenetic mechanisms on ADHD across the lifespan.
An epigenome-wide association study of Alzheimer's disease blood highlights robust DNA hypermethylation in the HOXB6 gene
Janou A.Y. Roubroeks,
Adam R. Smith,
Rebecca G. Smith,
Ehsan Pishva,
Zina Ibrahim,
Martina Sattlecker,
Eilis J. Hannon
+ 15 more
Janou A.Y. Roubroeks,
Adam R. Smith,
Rebecca G. Smith,
Ehsan Pishva,
Zina Ibrahim,
Martina Sattlecker,
Eilis J. Hannon,
Iwona Kłoszewska,
Patrizia Mecocci,
Hilkka Soininen,
Magda Tsolaki,
Bruno Vellas,
Lars-Olof Wahlund,
Dag Aarsland,
Petroula Proitsi,
Angela Hodges,
Simon Lovestone,
Stephen J. Newhouse,
Richard J.B. Dobson,
Jonathan Mill,
den Hove Daniël L.A. van,
Katie Lunnon
A growing number of epigenome-wide association studies have demonstrated a role for DNA methylation in the brain in Alzheimer's disease. With the aim of exploring peripheral biomarker potential, we have examined DNA methylation patterns in whole blood collected from 284 individuals in the AddNeuroMed study, which included 89 nondemented controls, 86 patients with Alzheimer's disease, and 109 individuals with mild cognitive impairment, including 38 individuals who progressed to Alzheimer's disease within 1 year. We identified significant differentially methylated regions, including 12 adjacent hypermethylated probes in the HOXB6 gene in Alzheimer's disease, which we validated using pyrosequencing. Using weighted gene correlation network analysis, we identified comethylated modules of genes that were associated with key variables such as APOE genotype and diagnosis. In summary, this study represents the first large-scale epigenome-wide association study of Alzheimer's disease and mild cognitive impairment using blood. We highlight the differences in various loci and pathways in early disease, suggesting that these patterns relate to cognitive decline at an early stage.
Analysis of the transcriptome and DNA methylome in response to acute and recurrent low glucose in human primary astrocytes
Paul G Weightman Potter, Sam Washer, Aaron R Jeffries, Janet E Holley, Nick J Gutowski, Emma Dempster, Craig Beall
Paul G Weightman Potter,
Sam Washer,
Aaron R Jeffries,
Janet E Holley,
Nick J Gutowski,
Emma Dempster,
Craig Beall
ABSTRACT Aims/hypothesis Recurrent hypoglycaemia (RH) is a major side-effect of intensive insulin therapy for people with diabetes. Changes in hypoglycaemia sensing by the brain contribute to the development of impaired counterregulatory responses to and awareness of hypoglycaemia. Little is known about the intrinsic changes in human astrocytes in response to acute and recurrent low glucose (RLG) exposure. Methods Human primary astrocytes (HPA) were exposed to zero, one, three or four bouts of low glucose (0.1 mmol/l) for three hours per day for four days to mimic RH. On the fourth day, DNA and RNA were collected. Differential gene expression and ontology analyses were performed using DESeq2 and GOseq respectively. DNA methylation was assessed using the Infinium MethylationEPIC BeadChip platform. Results 24 differentially expressed genes (DEGs) were detected (after correction for multiple comparisons). One bout of low glucose exposure had the largest effect on gene expression. Pathway analyses revealed that endoplasmic-reticulum (ER) stress-related genes such as HSPA5 , XBP1 , and MANF , involved in the unfolded protein response (UPR), were all significantly increased following LG exposure, which was diminished following RLG. There was little correlation between differentially methylated positions and changes in gene expression yet the number of bouts of LG exposure produced distinct methylation signatures. Conclusions/interpretation These data suggest that exposure of human astrocytes to transient LG triggers activation of genes involved in the UPR linked to endoplasmic reticulum (ER) stress. Following RLG, the activation of UPR related genes was diminished, suggesting attenuated ER stress. This may be mediated by metabolic adaptations to better preserve intracellular and/or ER ATP levels, but this requires further investigation.
Applying gene‐editing technology to elucidate the functional consequence of genetic and epigenetic variation in Alzheimer’s disease
Recent studies have highlighted a potential role of genetic and epigenetic variation in the development of Alzheimer's disease. Application of the CRISPR-Cas genome-editing platform has enabled investigation of the functional impact that Alzheimer's disease-associated gene mutations have on gene expression. Moreover, recent advances in the technology have led to the generation of CRISPR-Cas-based tools that allow for high-throughput interrogation of different risk variants to elucidate the interplay between genomic regulatory features, epigenetic modifications, and chromatin structure. In this review, we examine the various iterations of the CRISPR-Cas system and their potential application for exploring the complex interactions and disruptions in gene regulatory circuits that contribute to Alzheimer's disease.
Alzheimer's disease (AD) is a growing global healthcare epidemic. Owing to advances in technology, genome-scale studies of various layers of molecular information have been undertaken in recent years and robust variation in key loci have now been published and reproduced by others. This mini-symposium highlights four key areas of current research in the field of molecular biology in AD, including articles focused on large-scale genomic profiling, epigenetic research, integrative multi-omic approaches and how these can be appropriately modeled to address reverse causality. This mini-symposium provides a timely update on research focused on elucidating the molecular etiology of AD to date and highlights new methodological advances that could enable neuroscientists to identify novel therapeutic targets.
Tissue-Biased Expansion of DNMT3A-Mutant Clones in a Mosaic Individual Is Associated with Conserved Epigenetic Erosion
Ayala Tovy,
Jaime M Reyes,
Michael C Gundry,
Lorenzo Brunetti,
Henry Lee-Six,
Mia Petljak,
Hyun Jung Park
+ 17 more
Ayala Tovy,
Jaime M Reyes,
Michael C Gundry,
Lorenzo Brunetti,
Henry Lee-Six,
Mia Petljak,
Hyun Jung Park,
Anna G Guzman,
Carina Rosas,
Aaron R Jeffries,
Emma Baple,
Jonathan Mill,
Andrew H Crosby,
Valerie Sency,
Baozhong Xin,
Heather E Machado,
Danielle Castillo,
Jeffrey N Weitzel,
Wei Li,
Michael R Stratton,
Peter J Campbell,
Heng Wang,
Mathijs A Sanders,
Margaret A Goodell
DNA methyltransferase 3A (DNMT3A) is the most commonly mutated gene in clonal hematopoiesis (CH). Somatic DNMT3A mutations arise in hematopoietic stem cells (HSCs) many years before malignancies develop, but difficulties in comparing their impact before malignancy with wild-type cells have limited the understanding of their contributions to transformation. To circumvent this limitation, we derived normal and DNMT3A mutant lymphoblastoid cell lines from a germline mosaic individual in whom these cells co-existed for nearly 6 decades. Mutant cells dominated the blood system, but not other tissues. Deep sequencing revealed similar mutational burdens and signatures in normal and mutant clones, while epigenetic profiling uncovered the focal erosion of DNA methylation at oncogenic regulatory regions in mutant clones. These regions overlapped with those sensitive to DNMT3A loss after DNMT3A ablation in HSCs and in leukemia samples. These results suggest that DNMT3A maintains a conserved DNA methylation pattern, the erosion of which provides a distinct competitive advantage to hematopoietic cells.
Genetic risk for Alzheimer’s disease influences neuropathology and cognition via multiple biological pathways
Eilis Hannon,
Gemma L Shireby,
Keeley Brookes,
Johannes Attems,
Rebecca Sims,
Nigel J Cairns,
Seth Love
+ 4 more
Eilis Hannon,
Gemma L Shireby,
Keeley Brookes,
Johannes Attems,
Rebecca Sims,
Nigel J Cairns,
Seth Love,
Alan J Thomas,
Kevin Morgan,
Paul T Francis,
Jonathan Mill
Abstract Alzheimer’s disease is a highly heritable, common neurodegenerative disease characterised neuropathologically by the accumulation of β-amyloid plaques and tau-containing neurofibrillary tangles. In addition to the well-established risk associated with the APOE locus, there has been considerable success in identifying additional genetic variants associated with Alzheimer’s disease. Major challenges in understanding how genetic risk influences the development of Alzheimer’s disease are clinical and neuropathological heterogeneity, and the high level of accompanying comorbidities. We report a multimodal analysis integrating longitudinal clinical and cognitive assessment with neuropathological data collected as part of the Brains for Dementia Research (BDR) study to understand how genetic risk factors for Alzheimer’s disease influence the development of neuropathology and clinical performance. 693 donors in the BDR cohort with genetic data, semi-quantitative neuropathology measurements, cognitive assessments and established diagnostic criteria were included in this study. We tested the association of APOE genotype and Alzheimer’s disease polygenic risk score - a quantitative measure of genetic burden - with survival, four common neuropathological features in Alzheimer’s disease brains (neurofibrillary tangles, β-amyloid plaques, Lewy bodies and TDP-43 proteinopathy), clinical status (clinical dementia rating) and cognitive performance (Mini-Mental State Exam, Montreal Cognitive Assessment). The APOE ε4 allele was significantly associated with younger age of death in the BDR cohort. Our analyses of neuropathology highlighted two independent pathways from APOE ε4, one where β-amyloid accumulation mediates the development of tauopathy, and a second characterized by direct effects on tauopathy independent of β-amyloidosis. Although we also detected association between APOE ε4 and dementia status and cognitive performance, these were all mediated by tauopathy, highlighting that they are a consequence of the neuropathological changes. Analyses of polygenic risk score identified associations with tauopathy and β-amyloidosis, which appeared to have both shared and unique contributions, suggesting that different genetic variants associated with Alzheimer’s disease affect different features of neuropathology to different degrees. Taken together, our results provide insight into how genetic risk for Alzheimer’s disease influences both the clinical and pathological features of dementia, increasing our understanding about the interplay between APOE genotype and other genetic risk factors.
DNA methylation signatures of aggression and closely related constructs: A meta-analysis of epigenome-wide studies across the lifespan
Dongen Jenny van,
Fiona A. Hagenbeek,
Matthew Suderman,
Peter Roetman,
Karen Sugden,
Andreas G. Chiocchetti,
Khadeeja Ismail
+ 82 more
Dongen Jenny van,
Fiona A. Hagenbeek,
Matthew Suderman,
Peter Roetman,
Karen Sugden,
Andreas G. Chiocchetti,
Khadeeja Ismail,
Rosa H. Mulder,
Jonathan Hafferty,
Mark J. Adams,
Rosie M. Walker,
Stewart W. Morris,
Jari Lahti,
Leanne K. Küpers,
Georgia Escaramis,
Silvia Alemany,
Marc Jan Bonder,
Mandy Meijer,
Hill F. Ip,
Rick Jansen,
Bart M. L. Baselmans,
Priyanka Parmar,
Estelle Lowry,
Fabian Streit,
Lea Sirignano,
Tabea Send,
Josef Frank,
Juulia Jylhävä,
Yunzhang Wang,
Pashupati Prasad Mishra,
Olivier F. Colins,
David Corcoran,
Richie Poulton,
Jonathan Mill,
Eilis J. Hannon,
Louise Arseneault,
Tellervo Korhonen,
Eero Vuoksimaa,
Janine Felix,
Marian Bakermans-Kranenburg,
Archie Campbell,
Darina Czamara,
Elisabeth Binder,
Eva Corpeleijn,
Juan Ramon González,
Regina Grazuleviciene,
Kristine B. Gutzkow,
Jorunn Evandt,
Marina Vafeiadi,
Marieke Klein,
der Meer Dennis van,
Lannie Ligthart,
BIOS Consortium,
Cornelis Kluft,
Gareth E. Davies,
Christian Hakulinen,
Liisa Keltikangas-Järvinen,
Barbara Franke,
Christine M. Freitag,
Kerstin Konrad,
Amaia Hervas,
Aranzazu Fernández-Rivas,
Agnes Vetro,
Olli Raitakari,
Terho Lehtimäki,
Robert Vermeiren,
Timo Strandberg,
Katri Räikkönen,
Harold Snieder,
Stephanie H. Witt,
Michael Deuschle,
Nancy L. Pedersen,
Sara Hägg,
Jordi Sunyer,
Lude Franke,
Jaakko Kaprio,
Miina Ollikainen,
Terrie E. Moffitt,
Henning Tiemeier,
Ijzendoorn Marinus H. van,
Caroline Relton,
Martine Vrijheid,
Sylvain Sebert,
Marjo-Riitta Jarvelin,
Avshalom Caspi,
Kathryn L. Evans,
Andrew M. McIntosh,
Meike Bartels,
Dorret Boomsma
Abstract DNA methylation profiles of aggressive behavior may capture lifetime cumulative effects of genetic, stochastic, and environmental influences associated with aggression. Here, we report the first large meta-analysis of epigenome-wide association studies (EWAS) of aggressive behavior (N=15,324 participants). In peripheral blood samples of 14,434 participants from 18 cohorts with mean ages ranging from 7 to 68 years, 13 methylation sites were significantly associated with aggression (alpha=1.2×10 −7 ; Bonferroni correction). In cord blood samples of 2,425 children from five cohorts with aggression assessed at mean ages ranging from 4 to 7 years, 83% of these sites showed the same direction of association with childhood aggression ( r =0.74, p=0.006) but no epigenome-wide significant sites were found. Top-sites (48 at a false discovery rate of 5% in the peripherl blood meta-analysis or in a combined meta-analysis of peripheral blood and cord blood) have been associated with chemical exposures, smoking, cognition, metabolic traits, and genetic variation (mQTLs). Three genes whose expression levels were associated with top-sites were previously linked to schizophrenia and general risk tolerance. At six CpGs, DNA methylation variation in blood mirrors variation in the brain. On average 44% (range=3-82%) of the aggression–methylation association was explained by current and former smoking and BMI. These findings point at loci that are sensitive to chemical exposures with potential implications for neuronal functions. We hope these results to be a starting point for studies leading to applications as peripheral biomarkers and to reveal causal relationships with aggression and related traits.
Non-neuronal expression of SARS-CoV-2 entry genes in the olfactory system suggests mechanisms underlying COVID-19-associated anosmia
David H. Brann,
Tatsuya Tsukahara,
Caleb Weinreb,
Marcela Lipovsek,
den Berge Koen Van,
Boying Gong,
Rebecca Chance
+ 18 more
David H. Brann,
Tatsuya Tsukahara,
Caleb Weinreb,
Marcela Lipovsek,
den Berge Koen Van,
Boying Gong,
Rebecca Chance,
Iain C. Macaulay,
Hsin-Jung Chou,
Russell B. Fletcher,
Diya Das,
Kelly Street,
Bezieux Hector Roux de,
Yoon-Gi Choi,
Davide Risso,
Sandrine Dudoit,
Elizabeth Purdom,
Jonathan Mill,
Ralph Abi Hachem,
Hiroaki Matsunami,
Darren W. Logan,
Bradley J. Goldstein,
Matthew S. Grubb,
John Ngai,
Sandeep Robert Datta
Altered olfactory function is a common symptom of COVID-19, but its etiology is unknown. A key question is whether SARS-CoV-2 (CoV-2) - the causal agent in COVID-19 - affects olfaction directly, by infecting olfactory sensory neurons or their targets in the olfactory bulb, or indirectly, through perturbation of supporting cells. Here we identify cell types in the olfactory epithelium and olfactory bulb that express SARS-CoV-2 cell entry molecules. Bulk sequencing demonstrated that mouse, non-human primate and human olfactory mucosa expresses two key genes involved in CoV-2 entry, ACE2 and TMPRSS2. However, single cell sequencing revealed that ACE2 is expressed in support cells, stem cells, and perivascular cells, rather than in neurons. Immunostaining confirmed these results and revealed pervasive expression of ACE2 protein in dorsally-located olfactory epithelial sustentacular cells and olfactory bulb pericytes in the mouse. These findings suggest that CoV-2 infection of non-neuronal cell types leads to anosmia and related disturbances in odor perception in COVID-19 patients.
Invited Review – A 5‐year update on epigenome‐wide association studies of DNA modifications in Alzheimer’s disease: progress, practicalities and promise
In late 2014, the first epigenome-wide association studies of DNA modifications in Alzheimer's disease brain samples were published. Over the last 5 years, further studies have been reported in the field and have highlighted consistent and robust alterations in DNA modifications in AD cortex. However, there are some caveats associated with the majority of studies undertaken to date; for example, they are predominantly restricted to profiling a limited number of loci, are principally focused on DNA methylation, are performed on bulk tissue at the end stage of disease and are restricted to nominating associations rather than demonstrating causal relationships. Consequently, the downstream interpretation of these studies is limited. Owing to recent advances in state-of-the-art cell profiling techniques, long-read genomic technologies and genetic engineering methodologies, identifying cell-type-specific causal epigenetic changes is becoming feasible. This review seeks to provide an overview of the last 5 years of epigenomic studies of DNA modifications in Alzheimer's disease brain samples and propose new avenues for future research.
Exploring Beyond the DNA Sequence: A Review of Epigenomic Studies of DNA and Histone Modifications in Dementia
Purpose of ReviewAlthough genome-scale studies have identified many genetic variants associated with dementia, these do not account for all of disease incidence and so recently attention has turned to studying mechanisms of genome regulation. Epigenetic processes such as modifications to the DNA and histones alter transcriptional activity and have been hypothesized to be involved in the etiology of dementia. Here, we review the growing body of literature on dementia epigenomics, with a focus on novel discoveries, current limitations, and future directions for the field.Recent FindingsIt is through advances in genomic technology that large-scale quantification of epigenetic modifications is now possible in dementia. Most of the literature in the field has primarily focussed on exploring DNA modifications, namely DNA methylation, in postmortem brain samples from individuals with Alzheimer’s disease. However, recent studies have now begun to explore other epigenetic marks, such as histone modifications, investigating these signatures in both the brain and blood, and in a range of other dementias.SummaryThere is still a demand for more epigenomic studies to be conducted in the dementia field, particularly those assessing chromatin dynamics and a broader range of histone modifications. The field faces limitations in sample accessibility with many studies lacking power. Furthermore, the frequent use of heterogeneous bulk tissue containing multiple cell types further hinders data interpretation. Looking to the future, multi-omic studies, integrating many different epigenetic marks, with matched genetic, transcriptomic, and proteomic data, will be vital, particularly when undertaken in isolated cell populations, or ideally at the level of the single cell. Ultimately these studies could identify novel dysfunctional pathways and biomarkers for disease, which could lead to new therapeutic avenues.
Kwangsik Nho,
Kelly Nudelman,
Mariet Allen,
Angela Hodges,
Sungeun Kim,
Shannon L. Risacher,
Liana G. Apostolova
+ 18 more
Kwangsik Nho,
Kelly Nudelman,
Mariet Allen,
Angela Hodges,
Sungeun Kim,
Shannon L. Risacher,
Liana G. Apostolova,
Kuang Lin,
Katie Lunnon,
Xue Wang,
Jeremy D. Burgess,
Nilüfer Ertekin‐Taner,
Ronald C. Petersen,
Lisu Wang,
Zhenhao Qi,
Aiqing He,
Isaac Neuhaus,
Vishal Patel,
Tatiana Foroud,
Kelley M. Faber,
Simon Lovestone,
Andrew Simmons,
Michael W. Weiner,
Andrew J. Saykin,
for the Alzheimer's Disease Neuroimaging Initiative
INTRODUCTION: Abnormal gene expression patterns may contribute to the onset and progression of late-onset Alzheimer's disease (LOAD).
METHODS: We performed transcriptome-wide meta-analysis (N = 1440) of blood-based microarray gene expression profiles as well as neuroimaging and cerebrospinal fluid (CSF) endophenotype analysis.
RESULTS: We identified and replicated five genes (CREB5, CD46, TMBIM6, IRAK3, and RPAIN) as significantly dysregulated in LOAD. The most significantly altered gene, CREB5, was also associated with brain atrophy and increased amyloid beta (Aβ) accumulation, especially in the entorhinal cortex region. cis-expression quantitative trait loci mapping analysis of CREB5 detected five significant associations (P < 5 × 10-8 ), where rs56388170 (most significant) was also significantly associated with global cortical Aβ deposition measured by [18 F]Florbetapir positron emission tomography and CSF Aβ1-42 .
DISCUSSION: RNA from peripheral blood indicated a differential gene expression pattern in LOAD. Genes identified have been implicated in biological processes relevant to Alzheimer's disease. CREB, in particular, plays a key role in nervous system development, cell survival, plasticity, and learning and memory.
Whole transcriptome in silico screening implicates cardiovascular and infectious disease in the mechanism of action underlying atypical antipsychotic side effects
Yasaman Malekizadeh,
Gareth Williams,
Mark Kelson,
David Whitfield,
Jonathan Mill,
David A. Collier,
Clive Ballard
+ 2 more
Yasaman Malekizadeh,
Gareth Williams,
Mark Kelson,
David Whitfield,
Jonathan Mill,
David A. Collier,
Clive Ballard,
Aaron R. Jeffries,
Byron Creese
Alzheimer's & Dementia: Translational Research & Clinical Interventions
BACKGROUND: Stroke/thromboembolic events, infections, and death are all significantly increased by antipsychotics in dementia but little is known about why they can be harmful. Using a novel application of a drug repurposing paradigm, we aimed to identify potential mechanisms underlying adverse events.
METHODS: Whole transcriptome signatures were generated for SH-SY5Y cells treated with amisulpride, risperidone, and volinanserin using RNA sequencing. Bioinformatic analysis was performed that scored the association between antipsychotic signatures and expression data from 415,252 samples in the National Center for Biotechnology Information Gene Expression Omnibus (NCBI GEO) repository.
RESULTS: Atherosclerosis, venous thromboembolism, and influenza NCBI GEO-derived samples scored positively against antipsychotic signatures. Pathways enriched in antipsychotic signatures were linked to the cardiovascular and immune systems (eg, brain derived neurotrophic factor [BDNF], platelet derived growth factor receptor [PDGFR]-beta, tumor necrosis factor [TNF], transforming growth factor [TGF]-beta, selenoamino acid metabolism, and influenza infection).
CONCLUSIONS: These findings for the first time mechanistically link antipsychotics to specific cardiovascular and infectious diseases which are known side effects of their use in dementia, providing new information to explain related adverse events.
Altered DNA methylation profiles in blood from patients with sporadic Creutzfeldt-Jakob disease
Luke Dabin,
Fernando Guntoro,
Tracy Campbell,
Tony Bélicard,
Adam R. Smith,
Rebecca G. Smith,
Rachel Raybould
+ 6 more
Luke Dabin,
Fernando Guntoro,
Tracy Campbell,
Tony Bélicard,
Adam R. Smith,
Rebecca G. Smith,
Rachel Raybould,
Jonathan M. Schott,
Katie Lunnon,
Peter Sarkies,
John Collinge,
Simon Mead,
Emmanuelle Viré
Abstract Prion diseases are fatal and transmissible neurodegenerative disorders caused by the misfolding and aggregation of prion protein. Although recent studies have implicated epigenetic variation in common neurodegenerative disorders, no study has yet explored their role in human prion diseases. Here we profiled genome-wide blood DNA methylation in the most common human prion disease, sporadic Creutzfeldt-Jakob disease (sCJD). Our case-control study (n=219), when accounting for differences in cell type composition between individuals, identified 38 probes at genome-wide significance (p < 1.24×0 -7 ). Nine of these sites were taken forward in a replication study, performed in an independent case-control (n=186) cohort using pyrosequencing. Sites in or close to FKBP5, AIM2 (2 probes), UHRF1, KCNAB2, PRNP, ANK1 successfully replicated. The blood-based DNA methylation signal was tissue- and disease-specific, in that the replicated probe signals were unchanged in case-control studies using sCJD frontal-cortex (n=84), blood samples from patients with Alzheimer’s disease, and from inherited and acquired prion diseases. Machine learning algorithms using blood DNA methylation array profiles accurately distinguished sCJD patients and controls. Finally, we identified sites whose methylation levels associated with prolonged survival in sCJD patients. Altogether, this study has identified a peripheral DNA methylation signature of sCJD with a variety of potential biomarker applications.
Genomic and phenomic insights from an atlas of genetic effects on DNA methylation
Josine L. Min,
Gibran Hemani,
Eilis Hannon,
Koen F. Dekkers,
Juan Castillo-Fernandez,
René Luijk,
Elena Carnero-Montoro
+ 149 more
Josine L. Min,
Gibran Hemani,
Eilis Hannon,
Koen F. Dekkers,
Juan Castillo-Fernandez,
René Luijk,
Elena Carnero-Montoro,
Daniel J. Lawson,
Kimberley Burrows,
Matthew Suderman,
Andrew D. Bretherick,
Tom G Richardson,
Johanna Klughammer,
Valentina Iotchkova,
Gemma Sharp,
Ahmad Al Khleifat,
Aleksey Shatunov,
Alfredo Iacoangeli,
Wendy L McArdle,
Karen M Ho,
Ashish Kumar,
Cilla Söderhäll,
Carolina Soriano-Tárraga,
Eva Giralt-Steinhauer,
Nabila Kazmi,
Dan Mason,
Allan F McRae,
David L Corcoran,
Karen Sugden,
Silva Kasela,
Alexia Cardona,
Felix R. Day,
Giovanni Cugliari,
Clara Viberti,
Simonetta Guarrera,
Michael Lerro,
Richa Gupta,
Sailalitha Bollepalli,
Pooja Mandaviya,
Yanni Zeng,
Toni-Kim Clarke,
Rosie M Walker,
Vanessa Schmoll,
Darina Czamara,
Carlos Ruiz-Arenas,
Faisal I Rezwan,
Riccardo E Marioni,
Tian Lin,
Yvonne Awaloff,
Marine Germain,
Dylan Aïssi,
Ramona Zwamborn,
Kristel van Eijk,
Annelot Dekker,
Jenny van Dongen,
Jouke-Jan Hottenga,
Gonneke Willemsen,
Cheng-Jian Xu,
Guillermo Barturen,
Francesc Català-Moll,
Martin Kerick,
Carol Wang,
Phillip Melton,
Hannah R Elliott,
Jean Shin,
Manon Bernard,
Idil Yet,
Melissa Smart,
Tyler Gorrie-Stone,
BIOS Consortium,
Chris Shaw,
Ammar Al Chalabi,
Susan M Ring,
Göran Pershagen,
Erik Melén,
Jordi Jiménez-Conde,
Jaume Roquer,
Debbie A Lawlor,
John Wright,
Nicholas G Martin,
Grant W Montgomery,
Terrie E Moffitt,
Richie Poulton,
Tõnu Esko,
Lili Milani,
Andres Metspalu,
John R. B. Perry,
Ken K. Ong,
Nicholas J Wareham,
Giuseppe Matullo,
Carlotta Sacerdote,
Avshalom Caspi,
Louise Arseneault,
France Gagnon,
Miina Ollikainen,
Jaakko Kaprio,
Janine F Felix,
Fernando Rivadeneira,
Henning Tiemeier,
Marinus H van IJzendoorn,
André G Uitterlinden,
Vincent WV Jaddoe,
Chris Haley,
Andrew M McIntosh,
Kathryn L Evans,
Alison Murray,
Katri Räikkönen,
Jari Lahti,
Ellen A Nohr,
Thorkild IA Sørensen,
Torben Hansen,
Camilla Schmidt Morgen,
Elisabeth B Binder,
Susanne Lucae,
Juan Ramon Gonzalez,
Mariona Bustamante,
Jordi Sunyer,
John W Holloway,
Wilfried Karmaus,
Hongmei Zhang,
Ian J Deary,
Naomi R Wray,
John M Starr,
Marian Beekman,
Diana van Heemst,
P Eline Slagboom,
Pierre-Emmanuel Morange,
David-Alexandre Trégouët,
Jan H. Veldink,
Gareth E Davies,
Eco JC de Geus,
Dorret I Boomsma,
Judith M Vonk,
Bert Brunekreef,
Gerard H. Koppelman,
Marta E Alarcón-Riquelme,
Rae-Chi Huang,
Craig Pennell,
Joyce van Meurs,
M. Arfan Ikram,
Alun D Hughes,
Therese Tillin,
Nish Chaturvedi,
Zdenka Pausova,
Tomas Paus,
Timothy D Spector,
Meena Kumari,
Leonard C Schalkwyk,
Peter M Visscher,
George Davey Smith,
Christoph Bock,
Tom R Gaunt,
Jordana T Bell,
Bastiaan T. Heijmans,
Jonathan Mill,
Caroline L Relton
Abstract Characterizing genetic influences on DNA methylation (DNAm) provides an opportunity to understand mechanisms underpinning gene regulation and disease. Here we describe results of DNA methylation-quantitative trait loci (mQTL) analyses on 32,851 participants, identifying genetic variants associated with DNAm at 420,509 DNAm sites in blood. We present a database of >270,000 independent mQTL of which 8.5% comprise long-range ( trans ) associations. Identified mQTL associations explain 15-17% of the additive genetic variance of DNAm. We reveal that the genetic architecture of DNAm levels is highly polygenic and DNAm exhibits signatures of negative and positive natural selection. Using shared genetic control between distal DNAm sites we construct networks, identifying 405 discrete genomic communities enriched for genomic annotations and complex traits. Shared genetic factors are associated with both blood DNAm levels and complex diseases but in most cases these associations do not reflect causal relationships from DNAm to trait or vice versa indicating a more complex genotype-phenotype map than has previously been hypothesised.
Reduced mitochondrial D-loop methylation levels in sporadic amyotrophic lateral sclerosis
Andrea Stoccoro,
Adam R. Smith,
Lorena Mosca,
Alessandro Marocchi,
Francesca Gerardi,
Christian Lunetta,
Cristina Cereda
+ 4 more
Andrea Stoccoro,
Adam R. Smith,
Lorena Mosca,
Alessandro Marocchi,
Francesca Gerardi,
Christian Lunetta,
Cristina Cereda,
Stella Gagliardi,
Katie Lunnon,
Lucia Migliore,
Fabio Coppedè
BackgroundMitochondrial dysregulation and aberrant epigenetic mechanisms have been frequently reported in neurodegenerative diseases, including amyotrophic lateral sclerosis (ALS), and several researchers suggested that epigenetic dysregulation in mitochondrial DNA (mtDNA) could contribute to the neurodegenerative process. We recently screened families with mutations in the major ALS causative genes, namely C9orf72, SOD1, FUS, and TARDBP, observing reduced methylation levels of the mtDNA regulatory region (D-loop) only in peripheral lymphocytes of SOD1 carriers. However, until now no studies investigated the potential role of mtDNA methylation impairment in the sporadic form of ALS, which accounts for the majority of disease cases. The aim of the current study was to investigate the D-loop methylation levels and the mtDNA copy number in sporadic ALS patients and compare them to those observed in healthy controls and in familial ALS patients. Pyrosequencing analysis of D-loop methylation levels and quantitative analysis of mtDNA copy number were performed in peripheral white blood cells from 36 sporadic ALS patients, 51 age- and sex-matched controls, and 27 familial ALS patients with germinal mutations in SOD1 or C9orf72 that represent the major familial ALS forms.ResultsIn the total sample, D-loop methylation levels were significantly lower in ALS patients compared to controls, and a significant inverse correlation between D-loop methylation levels and the mtDNA copy number was observed. Stratification of ALS patients into different subtypes revealed that both SOD1-mutant and sporadic ALS patients showed lower D-loop methylation levels compared to controls, while C9orf72-ALS patients showed similar D-loop methylation levels than controls. In healthy controls, but not in ALS patients, D-loop methylation levels decreased with increasing age at sampling and were higher in males compared to females.ConclusionsPresent data reveal altered D-loop methylation levels in sporadic ALS and confirm previous evidence of an inverse correlation between D-loop methylation levels and the mtDNA copy number, as well as differences among the major familial ALS subtypes. Overall, present results suggest that D-loop methylation and mitochondrial replication are strictly related to each other and could represent compensatory mechanisms to counteract mitochondrial impairment in sporadic and SOD1-related ALS forms.
Altered DNA methylation profiles in blood from patients with sporadic Creutzfeldt–Jakob disease
Luke C. Dabin,
Fernando Guntoro,
Tracy Campbell,
Tony Bélicard,
Adam R. Smith,
Rebecca G. Smith,
Rachel Raybould
+ 6 more
Luke C. Dabin,
Fernando Guntoro,
Tracy Campbell,
Tony Bélicard,
Adam R. Smith,
Rebecca G. Smith,
Rachel Raybould,
Jonathan M. Schott,
Katie Lunnon,
Peter Sarkies,
John Collinge,
Simon Mead,
Emmanuelle Viré
Prion diseases are fatal and transmissible neurodegenerative disorders caused by the misfolding and aggregation of prion protein. Although recent studies have implicated epigenetic variation in common neurodegenerative disorders, no study has yet explored their role in human prion diseases. Here we profiled genome-wide blood DNA methylation in the most common human prion disease, sporadic Creutzfeldt–Jakob disease (sCJD). Our case–control study (n = 219), when accounting for differences in cell type composition between individuals, identified 38 probes at genome-wide significance (p < 1.24 × 10–7). Nine of these sites were taken forward in a replication study, performed in an independent case–control (n = 186) cohort using pyrosequencing. Sites in or close to FKBP5, AIM2 (2 probes), UHRF1, KCNAB2 successfully replicated. The blood-based DNA methylation signal was tissue- and disease-specific, in that the replicated probe signals were unchanged in case–control studies using sCJD frontal-cortex (n = 84), blood samples from patients with Alzheimer’s disease, and from inherited and acquired prion diseases. Machine learning algorithms using blood DNA methylation array profiles accurately distinguished sCJD patients and controls. Finally, we identified sites whose methylation levels associated with prolonged survival in sCJD patients. Altogether, this study has identified a peripheral DNA methylation signature of sCJD with a variety of potential biomarker applications.
Recalibrating the epigenetic clock: implications for assessing biological age in the human cortex
Gemma L Shireby,
Jonathan P Davies,
Paul T Francis,
Joe Burrage,
Emma M Walker,
Grant W A Neilson,
Aisha Dahir
+ 10 more
Gemma L Shireby,
Jonathan P Davies,
Paul T Francis,
Joe Burrage,
Emma M Walker,
Grant W A Neilson,
Aisha Dahir,
Alan J Thomas,
Seth Love,
Rebecca G Smith,
Katie Lunnon,
Meena Kumari,
Leonard C Schalkwyk,
Kevin Morgan,
Keeley Brookes,
Eilis Hannon,
Jonathan Mill
Human DNA methylation data have been used to develop biomarkers of ageing, referred to as 'epigenetic clocks', which have been widely used to identify differences between chronological age and biological age in health and disease including neurodegeneration, dementia and other brain phenotypes. Existing DNA methylation clocks have been shown to be highly accurate in blood but are less precise when used in older samples or in tissue types not included in training the model, including brain. We aimed to develop a novel epigenetic clock that performs optimally in human cortex tissue and has the potential to identify phenotypes associated with biological ageing in the brain. We generated an extensive dataset of human cortex DNA methylation data spanning the life course (n = 1397, ages = 1 to 108 years). This dataset was split into 'training' and 'testing' samples (training: n = 1047; testing: n = 350). DNA methylation age estimators were derived using a transformed version of chronological age on DNA methylation at specific sites using elastic net regression, a supervised machine learning method. The cortical clock was subsequently validated in a novel independent human cortex dataset (n = 1221, ages = 41 to 104 years) and tested for specificity in a large whole blood dataset (n = 1175, ages = 28 to 98 years). We identified a set of 347 DNA methylation sites that, in combination, optimally predict age in the human cortex. The sum of DNA methylation levels at these sites weighted by their regression coefficients provide the cortical DNA methylation clock age estimate. The novel clock dramatically outperformed previously reported clocks in additional cortical datasets. Our findings suggest that previous associations between predicted DNA methylation age and neurodegenerative phenotypes might represent false positives resulting from clocks not robustly calibrated to the tissue being tested and for phenotypes that become manifest in older ages. The age distribution and tissue type of samples included in training datasets need to be considered when building and applying epigenetic clock algorithms to human epidemiological or disease cohorts.
Integrative genomic strategies applied to a lymphoblast cell line model reveal specific transcriptomic signatures associated with clozapine response
With SAJ de,
APS Ori,
T Wang,
SL Pulit,
E Strengman,
J Viana,
J Mill
+ 2 more
With SAJ de,
APS Ori,
T Wang,
SL Pulit,
E Strengman,
J Viana,
J Mill,
Jong S de,
RA Ophoff
Abstract Clozapine is an important antipsychotic drug. However, its use is often accompanied by metabolic adverse effects and, in rare instances, agranulocytosis. The molecular mechanisms underlying these adverse events are unclear. To gain more insights into the response to clozapine at the molecular level, we exposed lymphoblastoid cell lines (LCLs) to increasing concentrations of clozapine and measured genome-wide gene expression and DNA methylation profiles. We observed robust and significant changes in gene expression levels due to clozapine (n = 463 genes at FDR < 0.05) affecting cholesterol and cell cycle pathways. At the level of DNA methylation, we find significant changes upstream of the LDL receptor, in addition to global enrichments of regulatory, immune and developmental pathways. By integrating these data with human tissue gene expression levels obtained from the Genotype-Tissue Expression project (GTEx), we identified specific tissues, including liver and several tissues involved in immune, endocrine and metabolic functions, that clozapine treatment may disproportionately affect. Notably, differentially expressed genes were not enriched for genome-wide disease risk of schizophrenia or for known psychotropic drug targets. However, we did observe a nominally significant association of genetic signals related to total cholesterol and low-density lipoprotein levels. Together, these results shed light on the biological mechanisms through which clozapine functions. The observed associations with cholesterol pathways, its genetic architecture and specific tissue effects may be indicative of the metabolic adverse effects observed in clozapine users. LCLs may thus serve as a useful tool to study these molecular mechanisms further.
Integrative genomics identifies a convergent molecular subtype that links epigenomic with transcriptomic differences in autism
Gokul Ramaswami,
Hyejung Won,
Michael J. Gandal,
Jillian Haney,
Jerry C. Wang,
Chloe C. Y. Wong,
Wenjie Sun
+ 3 more
Gokul Ramaswami,
Hyejung Won,
Michael J. Gandal,
Jillian Haney,
Jerry C. Wang,
Chloe C. Y. Wong,
Wenjie Sun,
Shyam Prabhakar,
Jonathan Mill,
Daniel H. Geschwind
Autism spectrum disorder (ASD) is a phenotypically and genetically heterogeneous neurodevelopmental disorder. Despite this heterogeneity, previous studies have shown patterns of molecular convergence in post-mortem brain tissue from autistic subjects. Here, we integrate genome-wide measures of mRNA expression, miRNA expression, DNA methylation, and histone acetylation from ASD and control brains to identify a convergent molecular subtype of ASD with shared dysregulation across both the epigenome and transcriptome. Focusing on this convergent subtype, we substantially expand the repertoire of differentially expressed genes in ASD and identify a component of upregulated immune processes that are associated with hypomethylation. We utilize eQTL and chromosome conformation datasets to link differentially acetylated regions with their cognate genes and identify an enrichment of ASD genetic risk variants in hyperacetylated noncoding regulatory regions linked to neuronal genes. These findings help elucidate how diverse genetic risk factors converge onto specific molecular processes in ASD.
Epigenomic features related to microglia are associated with attenuated effect of APOE ε4 on alzheimer’s disease risk in humans
Yiyi Ma,
Lei Yu,
Marta Olah,
Rebecca Smith,
Stephanie R. Oatman,
Mariet Allen,
Ehsan Pishva
+ 7 more
Yiyi Ma,
Lei Yu,
Marta Olah,
Rebecca Smith,
Stephanie R. Oatman,
Mariet Allen,
Ehsan Pishva,
Bin Zhang,
Vilas Menon,
Nilüfer Ertekin-Taner,
Katie Lunnon,
David A. Bennett,
Hans-Ulrich Klein,
Jager Philip L. De
Abstract INTRODUCTION Not all APOE ε4 carriers who survive to advanced age develop Alzheimer’s disease (AD); factors attenuating the risk of ε4 on AD may exist. METHODS Guided by the top ε4-attenuating signals from methylome-wide association analyses (N=572, ε4+ and ε4-) of neurofibrillary tangles and neuritic plaques, we conducted a meta-analysis for pathological AD within the ε4+ subgroups (N=235) across four independent collections of brains. Cortical RNA-seq and microglial morphology measurements were used in functional analyses. RESULTS Three out of the four significant CpG dinucleotides were captured by one principle component (PC1), which interacts with ε4 on AD, and is associated with expression of innate immune genes and activated microglia. In ε4 carriers, reduction in each unit of PC1 attenuated the odds of AD by 58% (OR=2.39, 95%CI=[1.64,3.46], P =7.08×10 −6 ). DISCUSSION An epigenomic factor associated with a reduced proportion of activated microglia appears to attenuate the risk of ε4 on AD.
Anterior cingulate cortex hypofunction causes anti-social aggression in mice
Heukelum S. van,
K. Tulva,
F. Geers,
Dulm S. van,
I. H. Ruisch,
J. Mill,
J. F. Viana
+ 7 more
Heukelum S. van,
K. Tulva,
F. Geers,
Dulm S. van,
I. H. Ruisch,
J. Mill,
J. F. Viana,
C. F. Beckmann,
J. K. Buitelaar,
G. Poelmans,
J. C. Glennon,
B. A. Vogt,
M. N. Havenith,
A. S. C. França
Abstract Controlling aggression is a crucial skill in social species like rodents and humans, and has been associated with anterior cingulate cortex (ACC). Here, we demonstrate a causal link between ACC hypofunction and failed aggression control in BALB/cJ mice. We first show that ACC in BALB/cJ mice is structurally degraded: Neuron density is decreased, with pervasive neuron death and neuro-toxic astroglia. Gene-set enrichment analysis suggested that this process is driven by neuronal degeneration, which then causes toxic astrogliosis. cFos expression across ACC indicated functional consequences: During aggressive encounters, ACC was engaged in control mice, but not BALB/cJ mice. Chemogenetically activating ACC during aggressive encounters drastically suppressed anti-social aggression but left adaptive aggression intact. The network effects of our chemogenetic perturbation suggest that this behavioural rescue is mediated by suppression of amygdala and hypothalamus and activation of mediodorsal thalamus. Together, these findings highlight the causal role of ACC in curbing anti-social aggression.
Increased isoform-specific phosphodiesterase 4D expression is associated with pathology and cognitive impairment in Alzheimer’s disease
Dean Paes,
Roy Lardenoije,
Riccardo M Carollo,
Janou A Y Roubroeks,
Melissa Schepers,
Paul Coleman,
Diego Mastroeni
+ 6 more
Dean Paes,
Roy Lardenoije,
Riccardo M Carollo,
Janou A Y Roubroeks,
Melissa Schepers,
Paul Coleman,
Diego Mastroeni,
Elaine Delvaux,
Ehsan Pishva,
Katie Lunnon,
Tim Vanmierlo,
den Hove Daniel van,
Jos Prickaerts
Pharmacological phosphodiesterase 4D (PDE4D) inhibition shows therapeutic potential to restore memory function in Alzheimer's disease (AD), but will likely evoke adverse side effects. As PDE4D encodes multiple isoforms, targeting specific isoforms may improve treatment efficacy and safety. Here, we investigated whether PDE4D isoform expression and PDE4D DNA methylation is affected in AD and whether expression changes are associated with severity of pathology and cognitive impairment. In post-mortem temporal lobe brain material from AD patients (n = 42) and age-matched controls (n = 40), we measured PDE4D isoform expression and PDE4D DNA (hydroxy)methylation using quantitative polymerase chain reaction and Illumina 450k Beadarrays, respectively. Linear regression revealed increased PDE4D1, -D3, -D5, and -D8 expression in AD with concurrent (hydroxy)methylation changes in associated promoter regions. Moreover, increased PDE4D1 and -D3 expression was associated with higherplaque and tau pathology levels, higher Braak stages, and progressed cognitive impairment. Future studies should indicate functional roles of specific PDE4D isoforms and the efficacy and safety of their selective inhibition to restore memory function in AD.
Genetic risk for Alzheimer’s disease influences neuropathology via multiple biological pathways
Eilis Hannon,
Gemma L Shireby,
Keeley Brookes,
Johannes Attems,
Rebecca Sims,
Nigel J Cairns,
Seth Love
+ 4 more
Eilis Hannon,
Gemma L Shireby,
Keeley Brookes,
Johannes Attems,
Rebecca Sims,
Nigel J Cairns,
Seth Love,
Alan J Thomas,
Kevin Morgan,
Paul T Francis,
Jonathan Mill
Alzheimer's disease is a highly heritable, common neurodegenerative disease characterized neuropathologically by the accumulation of β-amyloid plaques and tau-containing neurofibrillary tangles. In addition to the well-established risk associated with the APOE locus, there has been considerable success in identifying additional genetic variants associated with Alzheimer's disease. Major challenges in understanding how genetic risk influences the development of Alzheimer's disease are clinical and neuropathological heterogeneity, and the high level of accompanying comorbidities. We report a multimodal analysis integrating longitudinal clinical and cognitive assessment with neuropathological data collected as part of the Brains for Dementia Research study to understand how genetic risk factors for Alzheimer's disease influence the development of neuropathology and clinical performance. Six hundred and ninety-three donors in the Brains for Dementia Research cohort with genetic data, semi-quantitative neuropathology measurements, cognitive assessments and established diagnostic criteria were included in this study. We tested the association of APOE genotype and Alzheimer's disease polygenic risk score-a quantitative measure of genetic burden-with survival, four common neuropathological features in Alzheimer's disease brains (neurofibrillary tangles, β-amyloid plaques, Lewy bodies and transactive response DNA-binding protein 43 proteinopathy), clinical status (clinical dementia rating) and cognitive performance (Mini-Mental State Exam, Montreal Cognitive Assessment). The APOE ε4 allele was significantly associated with younger age of death in the Brains for Dementia Research cohort. Our analyses of neuropathology highlighted two independent pathways from APOE ε4, one where β-amyloid accumulation co-occurs with the development of tauopathy, and a second characterized by direct effects on tauopathy independent of β-amyloidosis. Although we also detected association between APOE ε4 and dementia status and cognitive performance, these were all mediated by tauopathy, highlighting that they are a consequence of the neuropathological changes. Analyses of polygenic risk score identified associations with tauopathy and β-amyloidosis, which appeared to have both shared and unique contributions, suggesting that different genetic variants associated with Alzheimer's disease affect different features of neuropathology to different degrees. Taken together, our results provide insight into how genetic risk for Alzheimer's disease influences both the clinical and pathological features of dementia, increasing our understanding about the interplay between APOE genotype and other genetic risk factors.
Novel epigenetic clock for fetal brain development predicts prenatal age for cellular stem cell models and derived neurons
Leonard C. Steg,
Gemma L. Shireby,
Jennifer Imm,
Jonathan P. Davies,
Alice Franklin,
Robert Flynn,
Seema C. Namboori
+ 18 more
Leonard C. Steg,
Gemma L. Shireby,
Jennifer Imm,
Jonathan P. Davies,
Alice Franklin,
Robert Flynn,
Seema C. Namboori,
Akshay Bhinge,
Aaron R. Jeffries,
Joe Burrage,
Grant W. A. Neilson,
Emma M. Walker,
Leo W. Perfect,
Jack Price,
Grainne McAlonan,
Deepak P. Srivastava,
Nicholas J. Bray,
Emma L. Cope,
Kimberly M. Jones,
Nicholas D. Allen,
Ehsan Pishva,
Emma L. Dempster,
Katie Lunnon,
Jonathan Mill,
Eilis Hannon
Abstract Induced pluripotent stem cells (iPSCs) and their differentiated neurons (iPSC-neurons) are a widely used cellular model in the research of the central nervous system. However, it is unknown how well they capture age-associated processes, particularly given that pluripotent cells are only present during the earliest stages of mammalian development. Epigenetic clocks utilize coordinated age-associated changes in DNA methylation to make predictions that correlate strongly with chronological age. It has been shown that the induction of pluripotency rejuvenates predicted epigenetic age. As existing clocks are not optimized for the study of brain development, we developed the fetal brain clock (FBC), a bespoke epigenetic clock trained in human prenatal brain samples in order to investigate more precisely the epigenetic age of iPSCs and iPSC-neurons. The FBC was tested in two independent validation cohorts across a total of 194 samples, confirming that the FBC outperforms other established epigenetic clocks in fetal brain cohorts. We applied the FBC to DNA methylation data from iPSCs and iPSC-derived neuronal precursor cells and neurons, finding that these cell types are epigenetically characterized as having an early fetal age. Furthermore, while differentiation from iPSCs to neurons significantly increases epigenetic age, iPSC-neurons are still predicted as being fetal. Together our findings reiterate the need to better understand the limitations of existing epigenetic clocks for answering biological research questions and highlight a limitation of iPSC-neurons as a cellular model of age-related diseases.
Full-length transcript sequencing of human and mouse identifies widespread isoform diversity and alternative splicing in the cerebral cortex
A.R. Jeffries,
SK. Leung,
I. Castanho,
K. Moore,
J.P. Davies,
E.L. Dempster,
N.J. Bray
+ 9 more
A.R. Jeffries,
SK. Leung,
I. Castanho,
K. Moore,
J.P. Davies,
E.L. Dempster,
N.J. Bray,
P. O‘Neill,
E. Tseng,
Z. Ahmed,
D. Collier,
S. Prabhakar,
L. Schalkwyk,
M.J Gandal,
E. Hannon,
J. Mill
Abstract Alternative splicing is a post-transcriptional regulatory mechanism producing multiple distinct mRNA molecules from a single pre-mRNA. Alternative splicing has a prominent role in the central nervous system, impacting neurodevelopment and various neuronal functions as well as being increasingly implicated in brain disorders including autism, schizophrenia and Alzheimer’s disease. Standard short-read RNA-Seq approaches only sequence fragments of the mRNA molecule, making it difficult to accurately characterize the true nature of RNA isoform diversity. In this study, we used long-read isoform sequencing (Iso-Seq) to generate full-length cDNA sequences and map transcript diversity in the human and mouse cerebral cortex. We identify widespread RNA isoform diversity amongst expressed genes in the cortex, including many novel transcripts not present in existing genome annotations. Alternative splicing events were found to make a major contribution to RNA isoform diversity in the cortex, with intron retention being a relatively common event associated with nonsense-mediated decay and reduced transcript expression. Of note, we found evidence for transcription from novel (unannotated genes) and fusion events between neighbouring genes. Although global patterns of RNA isoform diversity were found to be generally similar between human and mouse cortex, we identified some notable exceptions. We also identified striking developmental changes in transcript diversity, with differential transcript usage between human adult and fetal cerebral cortex. Finally, we found evidence for extensive isoform diversity in genes associated with autism, schizophrenia and Alzheimer’s disease. Our data confirm the importance of alternative splicing in the cerebral cortex, dramatically increasing transcriptional diversity and representing an important mechanism underpinning gene regulation in the brain. We provide this transcript level data as a resource to the scientific community.
DNA methylation-based sex classifier to predict sex and identify sex chromosome aneuploidy
Yucheng Wang,
Eilis Hannon,
Olivia A Grant,
Tyler J Gorrie-Stone,
Meena Kumari,
Jonathan Mill,
Xiaojun Zhai
+ 2 more
Yucheng Wang,
Eilis Hannon,
Olivia A Grant,
Tyler J Gorrie-Stone,
Meena Kumari,
Jonathan Mill,
Xiaojun Zhai,
Klaus D McDonald-Maier,
Leonard C Schalkwyk
Abstract Sex is an important covariate of epigenome-wide association studies due to its strong influence on DNA methylation patterns across numerous genomic positions. Nevertheless, many samples on the Gene Expression Omnibus (GEO) frequently lack a sex annotation or are incorrectly labelled. Considering the influence that sex imposes on DNA methylation patterns, it is necessary to ensure that methods for filtering poor samples and checking of sex assignment are accurate and widely applicable. In this paper, we presented a novel method to predict sex using only DNA methylation density signals, which can be readily applied to almost all DNA methylation datasets of different formats (raw IDATs or text files with only density signals) uploaded to GEO. We identified 4345 significantly ( p < 0.01) sex-associated CpG sites present on both 450K and EPIC arrays, and constructed a sex classifier based on the two first components of PCAs from the two sex chromosomes. The proposed method is constructed using whole blood samples and exhibits good performance across a wide range of tissues. We further demonstrated that our method can be used to identify samples with sex chromosome aneuploidy, this function is validated by five Turner syndrome cases and one Klinefelter syndrome case. The proposed method has been integrated into the wateRmelon Bioconductor package.
Telomere length and risk of idiopathic pulmonary fibrosis and chronic obstructive pulmonary disease: a mendelian randomisation study
Anna Duckworth,
Michael A Gibbons,
Richard J Allen,
Howard Almond,
Robin N Beaumont,
Andrew R Wood,
Katie Lunnon
+ 4 more
Anna Duckworth,
Michael A Gibbons,
Richard J Allen,
Howard Almond,
Robin N Beaumont,
Andrew R Wood,
Katie Lunnon,
Mark A Lindsay,
Louise V Wain,
Jess Tyrrell,
Chris J Scotton
BACKGROUND: Idiopathic pulmonary fibrosis (IPF) is a fatal lung disease accounting for 1% of UK deaths. In the familial form of pulmonary fibrosis, causal genes have been identified in about 30% of cases, and a majority of these causal genes are associated with telomere maintenance. Prematurely shortened leukocyte telomere length is associated with IPF and chronic obstructive pulmonary disease (COPD), a disease with similar demographics and shared risk factors. Using mendelian randomisation, we investigated evidence supporting a causal role for short telomeres in IPF and COPD.
METHODS: Mendelian randomisation inference of telomere length causality was done for IPF (up to 1369 cases) and COPD (13 538 cases) against 435 866 controls of European ancestry in UK Biobank. Polygenic risk scores were calculated and two-sample mendelian randomisation analyses were done using seven genetic variants previously associated with telomere length, with replication analysis in an IPF cohort (2668 cases vs 8591 controls) and COPD cohort (15 256 cases vs 47 936 controls).
FINDINGS: In the UK Biobank, a genetically instrumented one-SD shorter telomere length was associated with higher odds of IPF (odds ratio [OR] 4·19, 95% CI 2·33-7·55; p=0·0031) but not COPD (1·07, 0·88-1·30; p=0·51). Similarly, an association was found in the IPF replication cohort (12·3, 5·05-30·1; p=0·0015) and not in the COPD replication cohort (1·04, 0·71-1·53; p=0·83). Meta-analysis of the two-sample mendelian randomisation results provided evidence inferring that shorter telomeres cause IPF (5·81 higher odds of IPF, 95% CI 3·56-9·50; p=2·19 × 10-12). There was no evidence to infer that telomere length caused COPD (OR 1·07, 95% CI 0·90-1·27; p=0·46).
INTERPRETATION: Cellular senescence is hypothesised as a major driving force in IPF and COPD; telomere shortening might be a contributory factor in IPF, suggesting divergent mechanisms in COPD. Defining a key role for telomere shortening enables greater focus in telomere-related diagnostics, treatments, and the search for a cure in IPF. Investigation of therapies that improve telomere length is warranted.
FUNDING: Medical Research Council.
Patterns of Reliability: Assessing the Reproducibility and Integrity of DNA Methylation Measurement
Karen Sugden,
Eilis J. Hannon,
Louise Arseneault,
Daniel W. Belsky,
David L. Corcoran,
Helen L. Fisher,
Renate M. Houts
+ 9 more
Karen Sugden,
Eilis J. Hannon,
Louise Arseneault,
Daniel W. Belsky,
David L. Corcoran,
Helen L. Fisher,
Renate M. Houts,
Radhika Kandaswamy,
Terrie E. Moffitt,
Richie Poulton,
Joseph A. Prinz,
Line J.H. Rasmussen,
Benjamin S. Williams,
Chloe C.Y. Wong,
Jonathan Mill,
Avshalom Caspi
DNA methylation is an important mechanism of gene regulation. The most popular method to measure methylation is to use BeadChips that contain probes to index hundreds of thousands of methylation sites at once. However, these probes are not equally reliable. In blood DNA, unreliable probes were less heritable and less likely to index gene expression, and associations were less replicable. This has serious downstream consequences for reproducible science and should serve as a caution for all data scientists regardless of discipline.
A comparison of blood and brain-derived ageing and inflammation-related DNA methylation signatures and their association with microglial burdens
Anna J. Stevenson,
Daniel L. McCartney,
Gemma L. Shireby,
Robert F. Hillary,
Declan King,
Makis Tzioras,
Nicola Wrobel
+ 15 more
Anna J. Stevenson,
Daniel L. McCartney,
Gemma L. Shireby,
Robert F. Hillary,
Declan King,
Makis Tzioras,
Nicola Wrobel,
Sarah McCafferty,
Lee Murphy,
Barry W. McColl,
Paul Redmond,
Adele M. Taylor,
Sarah E. Harris,
Tom C. Russ,
Eilis J Hannon,
Andrew M. McIntosh,
Jonathan Mill,
Colin Smith,
Ian J. Deary,
Simon R. Cox,
Riccardo E. Marioni,
Tara L. Spires-Jones
Abstract Inflammation and ageing-related DNA methylation patterns in the blood have been linked to a variety of morbidities, including cognitive decline and neurodegenerative disease. However, it is unclear how these blood-based patterns relate to patterns within the brain, and how each associates with central cellular profiles. In this study, we profiled DNA methylation in both the blood and in five post-mortem brain regions (BA17, BA20/21, BA24, BA46 and hippocampus) in 14 individuals from the Lothian Birth Cohort 1936. Microglial burdens were additionally quantified in the same brain regions. DNA methylation signatures of five epigenetic ageing biomarkers (‘epigenetic clocks’), and two inflammatory biomarkers (DNA methylation proxies for C-reactive protein and interleukin-6) were compared across tissues and regions. Divergent correlations between the inflammation and ageing signatures in the blood and brain were identified, depending on region assessed. Four out of the five assessed epigenetic age acceleration measures were found to be highest in the hippocampus (β range=0.83-1.14, p≤0.02). The inflammation-related DNA methylation signatures showed no clear variation across brain regions. Reactive microglial burdens were found to be highest in the hippocampus (β=1.32, p=5×10 -4 ); however, the only association identified between the blood- and brain-based methylation signatures and microglia was a significant positive association with acceleration of one epigenetic clock (termed DNAm PhenoAge) averaged over all five brain regions (β=0.40, p=0.002). This work highlights a potential vulnerability of the hippocampus to epigenetic ageing and provides preliminary evidence of a relationship between DNA methylation signatures in the brain and differences in microglial burdens.
Genetic risk, education and incidence of dementia
Janice M Ranson,
Ilianna Lourida,
Eilis Hannon,
Thomas J Littlejohns,
Clive Ballard,
Kenneth M Langa,
Elina Hyppönen
+ 2 more
Janice M Ranson,
Ilianna Lourida,
Eilis Hannon,
Thomas J Littlejohns,
Clive Ballard,
Kenneth M Langa,
Elina Hyppönen,
Elzbieta Kuzma,
David J Llewellyn
Abstract Background There is evidence that educational attainment increases cognitive reserve, and may prevent or delay the development of dementia. However, the extent to which education offsets or interacts with genetic risk is unknown. We therefore investigated the relationship between education and genetic risk for dementia. Method In this cohort study, we used data from UK Biobank including adults aged 60 years and older of European ancestry without cognitive impairment or dementia at baseline. Participants joined the study between 2006 and 2010 and were followed until 2016 or 2017. Genetic risk was estimated using a polygenic score for dementia incorporating 249,273 single‐nucleotide polymorphisms with low (lowest quintile), intermediate (quintiles 2 to 4), and high (highest quintile) categories. Education was categorized as low (no/other qualifications), intermediate (secondary/vocational qualifications), or high (college/university degree or other professional qualifications). The outcome was incident all‐cause dementia, ascertained through hospital inpatient and death records. Result 196,383 individuals (mean [SD] age, 64.1 [2.9] years; 52.7% were women) were followed up for 1,545,433 person‐years (median [interquartile range] follow‐up, 8.0 [7.4‐8.6] years). Overall, 41.5% had low education, 31.0% had intermediate education and 27.5% had high levels of education. 20.0% had high polygenic risk scores, 60.0% had intermediate risk scores, and 20.0% had low risk scores. Of the participants with high genetic risk, 1.2% developed dementia compared with 0.6% of the participants with low genetic risk (adjusted hazard ratio, 1.92 [95% CI, 1.64‐2.24]). Of the participants with low education, 1.3% developed dementia compared with 0.7% of participants with high levels of education (adjusted hazard ratio, 1.51 [95% CI, 1.35‐1.70]). Of the participants with a high genetic risk and low education, 1.5% developed dementia compared with 0.4% of participants with low genetic risk and high education (adjusted hazard ratio, 2.79 [95% CI, 2.12‐3.68]). There was no significant interaction between genetic risk and education ( p = 0.108). Conclusion Among older adults without cognitive impairment or dementia, high education was independently associated with lower dementia risk when accounting for genetic risk. Education may increase cognitive reserve even in those with a high genetic risk of dementia.
Characterization of mRNA isoform diversity in a transgenic model of tau pathology using targeted long‐read sequencing
Szi Kay Leung,
Aaron Jeffries,
Eilis Hannon,
Isabel Castanho,
Karen Moore,
Tracey K. Murray,
Zeshan Ahmed
+ 2 more
Szi Kay Leung,
Aaron Jeffries,
Eilis Hannon,
Isabel Castanho,
Karen Moore,
Tracey K. Murray,
Zeshan Ahmed,
David A. Collier,
Jonathan Mill
Abstract Background An increasing number of studies implicate a role for alternative splicing in the development and neuropathology of Alzheimer’s disease (AD). However, it has been historically challenging to characterise splicing events, due to the limitations of short‐read RNA‐sequencing (RNA‐Seq) for the capture full‐length transcripts critical for transcriptome assembly. In this study, we used Pacific Biosciences long‐read isoform sequencing (Iso‐Seq) to enrich and comprehensively characterise isoform diversity for AD‐associated genes in entorhinal cortex samples from a well‐validated AD transgenic mouse model. Method We used Pacific Biosciences Targeted Iso‐Seq to investigate splicing of 20 AD‐associated genes (including TREM2, BIN1 , and APOE ) in entorhinal cortex of a well‐characterised mouse model of tau pathology, rTg4510. Sequence data was processed using the Iso‐Seq3 pipeline, followed by downstream analysis using other publically available resources and customised scripts. The same samples have additionally been sequenced using whole transcriptome Iso‐Seq and RNA‐Seq as validation. Result We obtained deep sequencing coverage of full‐length transcripts for each of the AD genes, revealing complex usage of alternative start sites and splicing events, as well as many novel 5′starts and 3’ends not previously annotated in existing genomic datasets. We identified differential transcript expression and isoform usage between transgenic and wild‐type mice, with highly‐correlated gene expression between Iso‐Seq and short‐read RNA‐seq data. Conclusion This study highlights the application of long‐read sequencing approaches to assess splicing variation and isoform diversity in AD by selective gene enrichment. Results suggest differential splicing events associated with AD pathology, supporting a role for transcriptomic dysregulation in development of AD. Further work will be undertaken to characterise other AD‐associated genes, and to extend these analyses to human post‐mortem brain samples.
An integrated epigenetic‐genetic study of neuropathology in the Brains for Dementia Research cohort
Eilis Hannon,
Gemma Shireby,
Keeley J. Brookes,
Grant Neilson,
Aisha Dahir,
Emma Walker,
Katie Lunnon
+ 5 more
Eilis Hannon,
Gemma Shireby,
Keeley J. Brookes,
Grant Neilson,
Aisha Dahir,
Emma Walker,
Katie Lunnon,
Seth Love,
Alan J. Thomas,
Kevin Morgan,
Paul T. Francis,
Jonathan Mill
Abstract Background In addition to the APOE locus, there has been considerable success in identifying genetic variants associated with an increased risk of developing Alzheimer’s disease (AD). However, there remains considerable uncertainty about the causal genes involved in AD neuropathology and the way in which these loci are functionally regulated by AD risk variants. As the majority of genetic variants are hypothesised to act via disruptions to gene regulation, there is increasing interest in the role of the epigenome, which encompasses a diverse number of chemical modifications to DNA and nucleosomal histone proteins that directly influence gene expression. Methods We have profiled DNA methylation in 1,284 brain samples from up to two regions (prefrontal cortex and occipital cortex) from 656 individuals in the Brains for Dementia Research (BDR) cohort. After stringent quality control, we performed epigenome‐wide association studies of four quantitative measures of neuropathology, Braak stage, Thal amyloid stage, Lewy Body stage and Cerad stage. Using matched genetic data available for these samples, performed a genome‐wide association study of methylomic variation to identify DNAm quantitative trait loci (mQTLs). These mQTL were then were integrated with results from AD GWAS, using summary data‐based Mendelian randomisation, to identify loci where DNA methylation is associated with AD. Finally, we generated polygenic risk scores for these samples and performed an epigenome‐wide study of genetic risk for AD. Results We identified multiple differentially methylated positions (DMPs) associated with neuropathology and AD polygenic risk score, replicating previous findings at known loci and implicating genes linked to known neuropathological pathways. Integrating our database of mQTLs with summary data from a recent AD GWAS, we report pleiotropic associations between AD and DNA methylation at several sites in the genome, including associations annotated to genes implicated in AD (e.g. SLC39A13, SPI1, MS4A6A, and BCL3). Conclusions We identified epigenetic differences associated with detailed measures of neuropathology providing insights on the molecular processes that underlie the disease progression. Furthermore, we characterised the complex relationship between genetic and epigenetic variation, identifying molecular consequences of high genetic risk for AD and prioritising candidate genes for functional follow up.
Assessment of the contribution of common genetic variants associated with Alzheimer’s disease on neuropathological burden and clinical characteristics in the Brains for Dementia Research cohort
Eilis Hannon,
Keeley J. Brookes,
Gemma Shireby,
Johannes Attems,
Rebecca Sims,
Nigel J. Cairns,
Kevin Morgan
+ 3 more
Eilis Hannon,
Keeley J. Brookes,
Gemma Shireby,
Johannes Attems,
Rebecca Sims,
Nigel J. Cairns,
Kevin Morgan,
Alan J. Thomas,
Paul T. Francis,
Jonathan Mill
Abstract Background In addition to the well‐established risk associated with the APOE locus, there has been considerable success in identifying additional genetic variants associated with Alzheimer’s disease (AD). Individually these variants confer only a small increase on an individual’s overall risk; however, combined into a polygenic risk score (PRS), they represent a powerful tool in genetic epidemiology for the investigation of correlates of high genetic risk. We investigated the clinical and neuropathological outcomes associated with high PRS for AD in the Brains for Dementia Research (BDR) cohort. Method 693 individuals in the BDR cohort with high quality genetic data and neuropathology measurements, including staging assessments (Braak and Thal) and established diagnostic criteria were included in this study. PRS were calculated for each individual as the number of genetic risk alleles, weighted by the log odds ratio, using the results of the largest available GWAS of AD. Statistical analysis was performed using regression models whilst controlling for age at death, sex and brain bank. Result We report statistically significant associations between APOE genotype and Braak neurofibrillary tangle stage, a measure of tauopathy, and Thal stage, a measure of Aβ plaque propagation. We also found significant associations between AD PRS and multiple measures of neuropathology (Braak stage, Thal stage, Lewy body stage, and severe cerebral amyloid angiopathy). In order to determine if APOE and AD PRS represent independent predictors of tauopathy (Braak stage) and b‐amyloidosis (Thal stage), we performed a joint analysis finding that APOE and PRS combine in an additive manner to influence both measures of neuropathology. Conclusion The results from this study characterise how genetic risk for AD influence both the clinical and pathological features of dementia and increases our understanding of the interaction between APOE status and other genetic risk factors.
Genome‐wide DNA methylation signatures of tau and amyloid neuropathology
Isabel Castanho,
Tracey K. Murray,
Szi Kay Leung,
Eilis Hannon,
Aaron Jeffries,
Katie Lunnon,
Zeshan Ahmed
+ 1 more
Isabel Castanho,
Tracey K. Murray,
Szi Kay Leung,
Eilis Hannon,
Aaron Jeffries,
Katie Lunnon,
Zeshan Ahmed,
Jonathan Mill
Abstract Background The onset and progression of Alzheimer’s disease (AD) is characterized by increasing intracellular aggregation of hyperphosphorylated tau protein and the accumulation of β‐amyloid (Aβ) in the neocortex. Despite recent success in identifying genetic risk factors for AD, the regulatory genomic mechanisms involved in disease progression are not fully understood. DNA methylation (DNAm) is the most widely studied epigenetic modification in human disease, with recent work by our group robustly linking methylomic variation to AD and other neurodegenerative disorders. To date, no study has systematically profiled DNAm in mouse models of AD. This study aimed to relate progressive changes in DNAm to AD neuropathology in the cortex, using transgenic models of amyloid and tau pathology. Method We used transgenic mice harboring human microtubule‐associated protein tau ( MAPT , rTg4510) and amyloid precursor protein ( APP , J20) mutations to investigate epigenomic and transcriptional changes associated with the development of tau and amyloid pathology. Using sequencing‐based approaches, we quantified changes in DNAm and gene expression identifying genomic signatures paralleling the progression of tau and amyloid across multiple brain regions. Methylomic and transcriptomic changes associated with amyloid and tau pathology were compared to similar data generated from human AD brain. Result We identified progressive changes in gene regulation associated with the development of AD neuropathology, including changes in DNA methylation and gene expression at loci previously identified in previous and ongoing human AD studies ( Ank1 , Hoxa , Abca7 , Bin1 ). Of note, significantly upregulated genes were strikingly enriched for genes involved in immune regulation, and significantly downregulated genes were enriched for synaptic function pathways related to AD. This study represents the most systematic analysis of progressive changes in gene expression and DNA modifications in mouse models of AD pathology and the first to focus specifically on the entorhinal cortex, a key region affected early in human AD. Conclusion Our data provide further evidence for an immune‐response to the accumulation of tau and Aβ, and reveal novel genomic pathways associated with the progression of AD neuropathology.
DNA methylation differences associated with peripheral biomarkers in the EMIF‐AD cohort
Rebecca G. Smith,
Isabelle Bos,
Stephanie J.B. Vos,
Frans R.J. Verhey,
Philip Scheltens,
Sebastiaan Engelborghs,
Giovanni B. Frisoni
+ 19 more
Rebecca G. Smith,
Isabelle Bos,
Stephanie J.B. Vos,
Frans R.J. Verhey,
Philip Scheltens,
Sebastiaan Engelborghs,
Giovanni B. Frisoni,
Olivier Blin,
Jill Richardson,
Régis Bordet,
Magda Tsolaki,
Julius Popp,
Pablo Martinez‐Lage,
Alberto Lleó,
Peter Johannsen,
Yvonne Freund,
Lutz Frölich,
Rik Vandenberghe,
Simon Lovestone,
Johannes Streffer,
Ulf Andreasson,
Kaj Blennow,
Pieter Jelle Visser,
Henrik Zetterberg,
Lars Bertram,
Katie Lunnon
Abstract Background Alzheimer’s disease is associated with increases in amyloid β and hyperphosphorylated tau which is thought to occur decades before the onset of clinical symptoms, leading to cell loss and inhibition. Finding biomarkers to detect these changes before neuronal loss and therefore permanent damage has occurred is integral. Current biomarkers using cerebrospinal fluid (CSF) measures and positron‐emission tomography (PET) imaging are invasive or expensive to perform. In this study we use the European Medical Information Framework Alzheimer’s disease (EMIF‐AD) cohort to looks for blood related epigenetic (DNA methylation) changes which relate to CSF and existing peripheral biomarkers. Method Whole blood samples from EMIF‐AD were accessed for DNA methylation on Illumina EPIC arrays. We assessed DNA methylation levels in 886 individuals with > 10 central and local biomarker measures, including amyloid, tau, neurogranin and YKL‐40. We also performed regional analysis to look for regions of significant DNA methylation change and identified specific pathways that show methylomic changes in association with specific biomarkers. Result We identified epigenome‐wide significant probes associated with many of our biomarker measures including most notably central amyloid β‐42, amyloid β‐40/42 ratio, neurogranin and YKL‐40 CSF levels as well as with local phosphorylated tau and total tau measurements. We also are able to use collections of CpG sites to create classifiers that predict high levels of CSF biomarkers. Conclusion In the future, identified sites and collections of sites could be used as a proxy for other biomarker measures due to the less invasive and less expensive nature of blood collection DNA methylation analysis. We are currently undertaking further analysis of this cohort using imaging and clinical measures.
In‐silico high throughput whole transcriptome screening implicates cardiovascular disease and the immune system in the mechanism of action underlying adverse effects of atypical antipsychotics
Byron Creese,
Yasaman Malekizadeh,
Gareth Williams,
David Whitfield,
Mark Kelson,
Clive Ballard,
Jonathan Mill
+ 1 more
Byron Creese,
Yasaman Malekizadeh,
Gareth Williams,
David Whitfield,
Mark Kelson,
Clive Ballard,
Jonathan Mill,
Aaron Jeffries
Abstract Background Risks of stroke/thromboembolic events, infections and death are all significantly increased by antipsychotics in people with dementia but specific mechanisms are unclear. In a novel application of a drug repurposing paradigm, we aimed to identify candidate underlying mechanisms in‐silico by leveraging publicly available transcriptomic data. Methods Whole transcriptome signatures were first generated for three antipsychotics (amisulpride, risperidone and volinanserin) using RNA‐sequencing in SHSY‐5Y cell lines. These compounds were chosen to represent a range of mechanisms of action relevant to clinically used compounds and novel compounds in development. An unbiased high throughput screen generated correlations between each compound and a public repository of over 100,000 human disease samples. From a long list of statistically significant hits, correlations between each antipsychotic and conditions/diseases related to known side effects of antipsychotic use in dementia were identified and gene set enrichment analysis performed. Results Statistically significant associations were found between antipsychotic transcriptional signatures and atherosclerosis (amisulpride p=0.002; risperidone p=6.98x10 ‐6 ; volinanserin p=5.5x10 ‐8 ), venous thromboembolism (risperidone p=8.13x10 ‐7 ; volinanserin p=0.002) and influenza (amisulpride p=0.002). Pathways enriched in antipsychotic signatures were linked to the cardiovascular system, the immune system and inflammation (including brain derived neurotrophic factor, platelet derived growth factor receptor beta, tumor necrosis factor alpha signalling). Conclusion Using a novel, high throughput approach, these findings implicate cardiovascular disease and the immune system in the mechanisms of action of atypical antipsychotics, providing a list of priority candidate mechanisms of harm relevant to dementia research. This approach could have implications for drug safety screening of psychotropic drugs in dementia.
Epigenomic features related to microglia are associated with attenuated effect of APOE ε4 on Alzheimer’s disease risk in humans
Yiyi Ma,
Lei Yu,
Marta Olah,
Rebecca Smith,
Stephanie R Oatman,
Mariet Allen,
Ehsan Pishva
+ 7 more
Yiyi Ma,
Lei Yu,
Marta Olah,
Rebecca Smith,
Stephanie R Oatman,
Mariet Allen,
Ehsan Pishva,
Bin Zhang,
Vilas Menon,
Nilüfer Ertekin-Taner,
Katie Lunnon,
David A Bennett,
Hans-Ulrich Klein,
Jager Philip L De
Not all APOE ε4 carriers who survive to advanced age develop Alzheimer's disease (AD); factors attenuating the risk of ε4 on AD may exist. Guided by the top ε4-attenuating signals from methylome-wide association analyses (N=572, ε4+ and ε4-) of neurofibrillary tangles and neuritic plaques, we conducted a meta-analysis for pathological AD within the ε4+ subgroups (N=235) across four independent collections of brains. Cortical RNA-seq and microglial morphology measurements were used in functional analyses. Three out of the four significant CpG dinucleotides were captured by one principle component (PC1), which interacts with ε4 on AD, and is associated with expression of innate immune genes and activated microglia. In ε4 carriers, reduction in each unit of PC1 attenuated the odds of AD by 58% (OR=2.39, 95%CI=[1.64,3.46], P=7.08x10-6). An epigenomic factor associated with a reduced proportion of activated microglia (microglial epigenomic factor 1) appears to attenuate the risk of ε4 on AD.
Global shifts in DNA methylation and DNA hydroxymethylation across multiple brain regions in transgenic models of tau and amyloid pathology
Isabel Castanho, Tracey K. Murray, Joshua Harvey, Szi Kay Leung, Katie Lunnon, Zeshan Ahmed, Jonathan Mill
Isabel Castanho,
Tracey K. Murray,
Joshua Harvey,
Szi Kay Leung,
Katie Lunnon,
Zeshan Ahmed,
Jonathan Mill
Abstract Background There is increasing evidence to support a role for altered DNA modifications in Alzheimer’s disease (AD). Global changes in both DNA methylation (5mC) and DNA hydroxymethylation (5hmC) have been robustly reported in cancer, but not widely studied in AD. We quantified global levels of 5mC and 5hmC across multiple brain regions in two transgenic models of AD pathology, relating these to the progressive changes in tau and amyloid observed in the same samples. Method We investigated global DNA modification levels in brain tissue from rTg4510 and J20 mice using two independent approaches. We quantified hippocampal global DNA methylation in rTg4510 and J20 transgenic (TG) and wild‐type (WT) littermate control mice using an enzymatic‐based methylation assay combined with pyrosequencing. Using immunohistochemistry, we directly quantified levels of both 5‐methylcytosine (5mC) and 5‐hydroxymethylcytosine (5hmC) in multiple brain regions in rTg4510 and J20 mice. Result We identified both genotype‐associated and progressive temporal changes (interaction between genotype and age) in 5mC and 5hmC in rTg4510 TG and J20 TG mice compared to WT littermate controls in several brain regions. Levels of both 5mC and 5hmc were negatively correlated with levels of tau and amyloid pathology, reflecting some evidence from human AD brain. Conclusion We identified decreased levels of two DNA modifications (5mC and 5hmC) associated with accumulation of tau and amyloid pathology. Both genotype‐associated and progressive changes in 5mC and 5hmC measured by immunohistochemistry were observed, with these changes notably stronger in rTg4510 TG relatively to J20 TG mice, particularly in the hippocampus.
Stroke, genetic risk and incidence of dementia
Janice M Ranson,
Ilianna Lourida,
Eilis Hannon,
Thomas J Littlejohns,
Clive Ballard,
Kenneth M Langa,
Elina Hyppönen
+ 2 more
Janice M Ranson,
Ilianna Lourida,
Eilis Hannon,
Thomas J Littlejohns,
Clive Ballard,
Kenneth M Langa,
Elina Hyppönen,
Elzbieta Kuzma,
David J Llewellyn
Abstract Background Stroke is a strong, independent and modifiable risk factor for all‐cause dementia. However, the extent to which stroke adds to or moderates genetic risk is unknown. Method In this cohort study, we used data from UK Biobank including adults aged 60 years and older of European ancestry without cognitive impairment or dementia at baseline. Participants joined the study between 2006 and 2010 and were followed until 2016 or 2017. Genetic risk was estimated using a polygenic score for dementia incorporating 249,273 single‐nucleotide polymorphisms with low (lowest quintile), intermediate (quintiles 2‐4), and high (highest quintile) categories. Stroke was a binary variable based upon history of stroke occurring before dementia diagnosis or end of follow‐up in participants who remained dementia‐free. The outcome was incident all‐cause dementia, ascertained through hospital inpatient and death records. Result 196,383 individuals (mean [SD] age, 64.1 [2.9] years; 52.7% were women) were followed up for 1,545,433 person‐years (median [interquartile range] follow‐up, 8.0 [7.4‐8.6] years). Overall, 3.8% of participants had a history of stroke. 20.0% had high polygenic risk scores, 60.0% had intermediate risk scores, and 20.0% had low risk scores. Of the participants with high genetic risk, 1.2% developed dementia compared with 0.63% of the participants with low genetic risk (adjusted hazard ratio, 1.94 [95% CI, 1.66‐2.27]). Of the participants with stroke, 2.7% developed dementia compared with 0.8% of participants without a stroke (adjusted hazard ratio, 2.73 [95% CI, 2.35‐3.17]). Of the participants with a high genetic risk and stroke, 3.4% developed dementia compared with 0.57% of participants with low genetic risk and no stroke (adjusted hazard ratio, 5.02 [95% CI, 3.67‐6.86]). There was no significant interaction between genetic risk and stroke (P = 0.633). Among participants with high genetic risk, 1.2% of those without stroke developed dementia compared with 3.4% of those with stroke (hazard ratio, 0.40 [95% CI, 0.29‐0.53]). Conclusion Among older adults without cognitive impairment or dementia, both stroke and high genetic risk were significantly associated with higher dementia risk. Stroke prevention should be a key element of risk reduction strategies for the prevention of dementia, particularly amongst those with a high genetic risk.
A Mendelian randomisation study of smoking causality in IPF compared with COPD
Anna Duckworth,
Michael A. Gibbons,
Robin N Beaumont,
Andrew R Wood,
Howard Almond,
Katie Lunnon,
Mark A. Lindsay
+ 2 more
Anna Duckworth,
Michael A. Gibbons,
Robin N Beaumont,
Andrew R Wood,
Howard Almond,
Katie Lunnon,
Mark A. Lindsay,
Chris J Scotton,
Jess Tyrrell
Abstract
In a normal year, the fatal lung disease Idiopathic Pulmonary Fibrosis (IPF) accounts for ∼1% of UK deaths. Smoking is a recognised risk factor for IPF but the question of causality remains unanswered. Here, we used data from the UK Biobank (UKBB) and the well-established genetic technique of Mendelian randomisation (MR) methods to investigate whether smoking is causal for IPF compared with COPD, where causality is established.
We looked at observational associations in unrelated Europeans, with 871 IPF cases, 11,413 COPD cases and 366,942 controls. We performed analyses using one-sample MR to test for inferred smoking causality in ever smokers using genetic variants that have a previously demonstrated association with smoking heaviness.
Strong associations between disease status and ever having smoked were found in both IPF (OR = 1.52; 95%CI:1.32-1.74; P=2.4×10
−8
) and COPD (OR= 5.77; 95%CI:5.48-6.07; P<1×10
−15
). Using MR, a one allele increase in smoking volume genetic risk score was associated with higher odds of COPD in ever smokers, (OR = 4.32; 95%CI:3.37-5.54; P<1×10
−15
), but no association was seen in IPF (OR=0.55; 95%CI: 0.17-1.81; P=0.33). No association was found between the genetic risk score and disease prevalence in never smokers with IPF (OR = 1.00; 95%CI:0.98-1.02; P=1.00) or COPD (OR = 1.00; 95%CI:0.99-1.01; P=0.53).
Although both IPF and COPD are observationally associated with smoking, our analysis provides evidence inferring that the association is causal in COPD but there is no such evidence in IPF. This suggests that other environmental exposures also need consideration in IPF.
Cross-reactive probes on Illumina DNA methylation arrays: a large study on ALS shows that a cautionary approach is warranted in interpreting epigenome-wide association studies
Paul J Hop,
Ramona A J Zwamborn,
Eilis J Hannon,
Annelot M Dekker,
Eijk Kristel R van,
Emma M Walker,
Alfredo Iacoangeli
+ 13 more
Paul J Hop,
Ramona A J Zwamborn,
Eilis J Hannon,
Annelot M Dekker,
Eijk Kristel R van,
Emma M Walker,
Alfredo Iacoangeli,
Ashley R Jones,
Aleksey Shatunov,
Khleifat Ahmad Al,
Sarah Opie-Martin,
Christopher E Shaw,
Karen E Morrison,
Pamela J Shaw,
Russell L McLaughlin,
Orla Hardiman,
Ammar Al-Chalabi,
Den Berg Leonard H Van,
Jonathan Mill,
Jan H Veldink
Illumina DNA methylation arrays are a widely used tool for performing genome-wide DNA methylation analyses. However, measurements obtained from these arrays may be affected by technical artefacts that result in spurious associations if left unchecked. Cross-reactivity represents one of the major challenges, meaning that probes may map to multiple regions in the genome. Although several studies have reported on this issue, few studies have empirically examined the impact of cross-reactivity in an epigenome-wide association study (EWAS). In this paper, we report on cross-reactivity issues that we discovered in a large EWAS on the presence of the C9orf72 repeat expansion in ALS patients. Specifically, we found that that the majority of the significant probes inadvertently cross-hybridized to the C9orf72 locus. Importantly, these probes were not flagged as cross-reactive in previous studies, leading to novel insights into the extent to which cross-reactivity can impact EWAS. Our findings are particularly relevant for epigenetic studies into diseases associated with repeat expansions and other types of structural variation. More generally however, considering that most spurious associations were not excluded based on pre-defined sets of cross-reactive probes, we believe that the presented data-driven flag and consider approach is relevant for any type of EWAS.
DNA methylation signatures of adolescent victimization: analysis of a longitudinal monozygotic twin sample
Radhika Kandaswamy,
Eilis Hannon,
Louise Arseneault,
Georgina Mansell,
Karen Sugden,
Benjamin Williams,
Joe Burrage
+ 8 more
Radhika Kandaswamy,
Eilis Hannon,
Louise Arseneault,
Georgina Mansell,
Karen Sugden,
Benjamin Williams,
Joe Burrage,
James R Staley,
Ehsan Pishva,
Aisha Dahir,
Susanna Roberts,
Andrea Danese,
Jonathan Mill,
Helen L Fisher,
Chloe C. Y. Wong
Accumulating evidence suggests that individuals exposed to victimization at key developmental stages may have different epigenetic fingerprints compared to those exposed to no/minimal stressful events, however results are inconclusive. This study aimed to strengthen causal inference regarding the impact of adolescent victimization on the epigenome by controlling for genetic variation, age, gender, and shared environmental exposures. We conducted longitudinal epigenome-wide association analyses (EWAS) on DNA methylation (DNAm) profiles of 118 monozygotic (MZ) twin pairs from the Environmental Risk study with and without severe adolescent victimization generated using buccal DNA collected at ages 5, 10 and 18, and the Illumina EPIC array. Additionally, we performed cross-sectional EWAS on age-18 blood and buccal DNA from the same individuals to elucidate tissue-specific signatures of severe adolescent victimization. Our analyses identified 20 suggestive differentially methylated positions (DMPs) (P < 5e-05), with altered DNAm trajectories between ages 10-18 associated with severe adolescent victimization (∆Beta range = -5.5%-5.3%). Age-18 cross-sectional analyses revealed 72 blood (∆Beta range = -2.2%-3.4%) and 42 buccal (∆Beta range = -3.6%-4.6%) suggestive severe adolescent victimization-associated DMPs, with some evidence of convergent signals between these two tissue types. Downstream regional analysis identified significant differentially methylated regions (DMRs) in LGR6 and ANK3 (Šidák P = 5e-09 and 4.07e-06), and one upstream of CCL27 (Šidák P = 2.80e-06) in age-18 blood and buccal EWAS, respectively. Our study represents the first longitudinal MZ twin analysis of DNAm and severe adolescent victimization, providing initial evidence for altered DNA methylomic signatures in individuals exposed to adolescent victimization.
Characterizing the properties of bisulfite sequencing data: maximizing power and sensitivity to identify between-group differences in DNA methylation
Abstract Background The combination of sodium bisulfite treatment with highly-parallel sequencing is a common method for quantifying DNA methylation across the genome. The power to detect between-group differences in DNA methylation using bisulfite-sequencing approaches is influenced by both experimental (e.g. read depth, missing data and sample size) and biological (e.g. mean level of DNA methylation and difference between groups) parameters. There is, however, no consensus about the optimal thresholds for filtering bisulfite sequencing data with implications for the reproducibility of findings in epigenetic epidemiology. Results We used a large reduced representation bisulfite sequencing (RRBS) dataset to assess the distribution of read depth across DNA methylation sites and the extent of missing data. To investigate how various study variables influence power to identify DNA methylation differences between groups, we developed a framework for simulating bisulfite sequencing data. As expected, sequencing read depth, group size, and the magnitude of DNA methylation difference between groups all impacted upon statistical power. The influence on power was not dependent on one specific parameter, but reflected the combination of study-specific variables. As a resource to the community, we have developed a tool, POWEREDBiSeq, which utilizes our simulation framework to predict study-specific power for the identification of DNAm differences between groups, taking into account user-defined read depth filtering parameters and the minimum sample size per group. Conclusions Our data-driven approach highlights the importance of filtering bisulfite-sequencing data by minimum read depth and illustrates how the choice of threshold is influenced by the specific study design and the expected differences between groups being compared. The POWEREDBiSeq tool can help users identify the level of data filtering needed to optimize power and aims to improve the reproducibility of bisulfite sequencing studies.
The histone modification H3K4me3 is altered at the ANK1 locus in Alzheimer's disease brain
Adam R Smith,
Rebecca G Smith,
Ruby Macdonald,
Sarah J Marzi,
Joe Burrage,
Claire Troakes,
Safa Al-Sarraj
+ 2 more
Adam R Smith,
Rebecca G Smith,
Ruby Macdonald,
Sarah J Marzi,
Joe Burrage,
Claire Troakes,
Safa Al-Sarraj,
Jonathan Mill,
Katie Lunnon
Several epigenome-wide association studies of DNA methylation have highlighted altered DNA methylation in the ANK1 gene in Alzheimer's disease (AD) brain samples. However, no study has specifically examined ANK1 histone modifications in the disease. We use chromatin immunoprecipitation-qPCR to quantify tri-methylation at histone 3 lysine 4 (H3K4me3) and 27 (H3K27me3) in the ANK1 gene in entorhinal cortex from donors with high (n = 59) or low (n = 29) Alzheimer's disease pathology. We demonstrate decreased levels of H3K4me3, a marker of active gene transcription, with no change in H3K27me3, a marker of inactive genes. H3K4me3 is negatively correlated with DNA methylation in specific regions of the ANK1 gene. Our study suggests that the ANK1 gene shows altered epigenetic marks indicative of reduced gene activation in Alzheimer's disease.
DNA methylation meta-analysis reveals cellular alterations in psychosis and markers of treatment-resistant schizophrenia
Eilis Hannon,
Emma L Dempster,
Georgina Mansell,
Joe Burrage,
Nick Bass,
Marc M Bohlken,
Aiden Corvin
+ 39 more
Eilis Hannon,
Emma L Dempster,
Georgina Mansell,
Joe Burrage,
Nick Bass,
Marc M Bohlken,
Aiden Corvin,
Charles J Curtis,
David Dempster,
Forti Marta Di,
Timothy G Dinan,
Gary Donohoe,
Fiona Gaughran,
Michael Gill,
Amy Gillespie,
Cerisse Gunasinghe,
Hilleke E Hulshoff,
Christina M Hultman,
Viktoria Johansson,
René S Kahn,
Jaakko Kaprio,
Gunter Kenis,
Kaarina Kowalec,
James MacCabe,
Colm McDonald,
Andrew McQuillin,
Derek W Morris,
Kieran C Murphy,
Colette J Mustard,
Igor Nenadic,
Michael C O'Donovan,
Diego Quattrone,
Alexander L Richards,
Bart PF Rutten,
Clair David St,
Sebastian Therman,
Timothea Toulopoulou,
Os Jim Van,
John L Waddington,
,
,
Patrick Sullivan,
Evangelos Vassos,
Gerome Breen,
David Andrew Collier,
Robin M Murray
Leonard S Schalkwyk
Jonathan Mill
We performed a systematic analysis of blood DNA methylation profiles from 4483 participants from seven independent cohorts identifying differentially methylated positions (DMPs) associated with psychosis, schizophrenia, and treatment-resistant schizophrenia. Psychosis cases were characterized by significant differences in measures of blood cell proportions and elevated smoking exposure derived from the DNA methylation data, with the largest differences seen in treatment-resistant schizophrenia patients. We implemented a stringent pipeline to meta-analyze epigenome-wide association study (EWAS) results across datasets, identifying 95 DMPs associated with psychosis and 1048 DMPs associated with schizophrenia, with evidence of colocalization to regions nominated by genetic association studies of disease. Many schizophrenia-associated DNA methylation differences were only present in patients with treatment-resistant schizophrenia, potentially reflecting exposure to the atypical antipsychotic clozapine. Our results highlight how DNA methylation data can be leveraged to identify physiological (e.g., differential cell counts) and environmental (e.g., smoking) factors associated with psychosis and molecular biomarkers of treatment-resistant schizophrenia.
Interaction Between Genetic Predisposition, Smoking, and Dementia Risk: A Population-based Cohort Study
Na Zhang,
Janice Ranson,
Zhi-Jie Zheng,
Eilis Hannon,
Zhenwei Zhou,
Xuejun Kong,
David Llewellyn
+ 2 more
Na Zhang,
Janice Ranson,
Zhi-Jie Zheng,
Eilis Hannon,
Zhenwei Zhou,
Xuejun Kong,
David Llewellyn,
Daniel King,
Jie Huang
We conducted a population-based retrospective cohort study to evaluate whether the association between cigarette smoking and dementia risk is modified by genetic predisposition including apolipoprotein E (APOE) genotype and polygenic risk (without APOE gene). We included 193,198 UK Biobank participants aged 60 to 73 years without dementia at baseline who were recruited from 2006 to 2010 and followed until 2018. Hazard ratios (HRs) and 95% confidence intervals (CIs) were estimated using Cox proportional hazards model. The cohort was followed up for 1,700,886 person-years (median [interquartile range] follow-up, 9.0 [8.3-9.7] years). 1788 participants with incident dementia cases were detected. Of non-APOE-ε4 carriers, 0.89% (95% CI, 0.73%-1.08%) current smokers developed dementia compared with 0.49% (95% CI, 0.44%-0.55%) of never smokers (adjusted HR 1.78; 95% CI, 1.39-2.29). Of participants with high polygenic risk, 1.77% (95% CI, 1.35%-2.27%) current smokers developed dementia compared with 1.05% (95% CI, 0.91%-1.21%) of never smokers (adjusted HR 1.63; 95% CI, 1.16-2.28). A significant interaction was found between APOE genotype and smoking status (P = 0.002) while no significant interaction was identified between polygenic risk and smoking status on risk of dementia (P = 0.25). APOE genotype while not polygenic risk modified the effect of smoking on dementia risk.
Common and rare variant association analyses in Amyotrophic Lateral Sclerosis identify 15 risk loci with distinct genetic architectures and neuron-specific biology
Wouter van Rheenen,
Rick A.A. van der Spek,
Mark K. Bakker,
Joke J.F.A. van Vugt,
Paul J. Hop,
Ramona A.J. Zwamborn,
Niek de Klein
+ 190 more
Wouter van Rheenen,
Rick A.A. van der Spek,
Mark K. Bakker,
Joke J.F.A. van Vugt,
Paul J. Hop,
Ramona A.J. Zwamborn,
Niek de Klein,
Harm-Jan Westra,
Olivier B. Bakker,
Patrick Deelen,
Gemma Shireby,
Eilis Hannon,
Matthieu Moisse,
Denis Baird,
Restuadi Restuadi,
Egor Dolzhenko,
Annelot M. Dekker,
Klara Gawor,
Henk-Jan Westeneng,
Gijs H.P. Tazelaar,
Kristel R. van Eijk,
Maarten Kooyman,
Ross P. Byrne,
Mark Doherty,
Mark Heverin,
Ahmad Al Khleifat,
Alfredo Iacoangeli,
Aleksey Shatunov,
Nicola Ticozzi,
Johnathan Cooper-Knock,
Bradley N. Smith,
Marta Gromicho,
Siddharthan Chandran,
Suvankar Pal,
Karen E. Morrison,
Pamela J. Shaw,
John Hardy,
Richard W. Orrell,
Michael Sendtner,
Thomas Meyer,
Nazli Başak,
Anneke J. van der Kooi,
Antonia Ratti,
Isabella Fogh,
Cinzia Gellera,
Giuseppe Lauria Pinter,
Stefania Corti,
Cristina Cereda,
Daisy Sproviero,
Sandra D’Alfonso,
Gianni Sorarù,
Gabriele Siciliano,
Massimiliano Filosto,
Alessandro Padovani,
Adriano Chiò,
Andrea Calvo,
Cristina Moglia,
Maura Brunetti,
Antonio Canosa,
Maurizio Grassano,
Ettore Beghi,
Elisabetta Pupillo,
Giancarlo Logroscino,
Beatrice Nefussy,
Alma Osmanovic,
Angelica Nordin,
Yossef Lerner,
Michal Zabari,
Marc Gotkine,
Robert H. Baloh,
Shaughn Bell,
Patrick Vourc’h,
Philippe Corcia,
Philippe Couratier,
Stéphanie Millecamps,
Vincent Meininger,
François Salachas,
Jesus S. Mora Pardina,
Abdelilah Assialioui,
Ricardo Rojas-García,
Patrick Dion,
Jay P. Ross,
Albert C. Ludolph,
Jochen H. Weishaupt,
David Brenner,
Axel Freischmidt,
Gilbert Bensimon,
Alexis Brice,
Alexandra Dürr,
Christine A.M. Payan,
Safa Saker-Delye,
Nicholas Wood,
Simon Topp,
Rosa Rademakers,
Lukas Tittmann,
Wolfgang Lieb,
Andre Franke,
Stephan Ripke,
Alice Braun,
Julia Kraft,
David C. Whiteman,
Catherine M. Olsen,
Andre G. Uitterlinden,
Albert Hofman,
Marcella Rietschel,
Sven Cichon,
Markus M. Nöthen,
Philippe Amouyel,
SLALOM Consortium,
PARALS Consortium,
SLAGEN Consortium,
SLAP Consortium,
Bryan Traynor,
Adrew B. Singleton,
Miguel Mitne Neto,
Ruben J. Cauchi,
Roel A. Ophoff,
Martina Wiedau-Pazos,
Catherine Lomen-Hoerth,
Vivianna M. van Deerlin,
Julian Grosskreutz,
Annekathrin Rödiger,
Nayana Gaur,
Alexander Jörk,
Tabea Barthel,
Erik Theele,
Benjamin Ilse,
Beatrice Stubendorff,
Otto W. Witte,
Robert Steinbach,
Christian A. Hübner,
Caroline Graff,
Lev Brylev,
Vera Fominykh,
Vera Demeshonok,
Anastasia Ataulina,
Boris Rogelj,
Blaž Koritnik,
Janez Zidar,
Metka Ravnik-Glavač,
Damjan Glavač,
Zorica Stević,
Vivian Drory,
Monica Povedano,
Ian P. Blair,
Matthew C. Kiernan,
Beben Benyamin,
Robert D. Henderson,
Sarah Furlong,
Susan Mathers,
Pamela A. McCombe,
Merrilee Needham,
Shyuan T. Ngo,
Garth A. Nicholson,
Roger Pamphlett,
Dominic B. Rowe,
Frederik J. Steyn,
Kelly L. Williams,
Karen Mather,
Perminder S. Sachdev,
Anjali K. Henders,
Leanne Wallace,
Mamede de Carvalho,
Susana Pinto,
Susanne Petri,
Alma Osmanovic,
Markus Weber,
Guy A. Rouleau,
Vincenzo Silani,
Charles Curtis,
Gerome Breen,
Jonathan Glass,
Robert H. Brown,
John E. Landers,
Christopher E. Shaw,
Peter M. Andersen,
Ewout J.N. Groen,
Michael A. van Es,
R. Jeroen Pasterkamp,
Dongsheng Fan,
Fleur C. Garton,
Allan F. McRae,
George Davey Smith,
Tom R. Gaunt,
Michael A. Eberle,
Jonathan Mill,
Russell L. McLaughlin,
Orla Hardiman,
Kevin P. Kenna,
Naomi R. Wray,
Ellen Tsai,
Heiko Runz,
Lude Franke,
Ammar Al-Chalabi,
Philip Van Damme,
Leonard H. van den Berg,
Jan H. Veldink
Abstract
Amyotrophic lateral sclerosis (ALS) is a fatal neurodegenerative disease with a life-time risk of 1 in 350 people and an unmet need for disease-modifying therapies. We conducted a cross-ancestry GWAS in ALS including 29,612 ALS patients and 122,656 controls which identified 15 risk loci in ALS. When combined with 8,953 whole-genome sequenced individuals (6,538 ALS patients, 2,415 controls) and the largest cortex-derived eQTL dataset (MetaBrain), analyses revealed locus-specific genetic architectures in which we prioritized genes either through rare variants, repeat expansions or regulatory effects. ALS associated risk loci were shared with multiple traits within the neurodegenerative spectrum, but with distinct enrichment patterns across brain regions and cell-types. Across environmental and life-style risk factors obtained from literature, Mendelian randomization analyses indicated a causal role for high cholesterol levels. All ALS associated signals combined reveal a role for perturbations in vesicle mediated transport and autophagy, and provide evidence for cell-autonomous disease initiation in glutamatergic neurons.
Common and rare variant association analyses in Amyotrophic Lateral Sclerosis identify 15 risk loci with distinct genetic architectures and neuron-specific biology
Wouter van Rheenen,
Rick van der Spek,
Mark Bakker,
Leonard van den Berg,
Jan Veldink,
Joke van Vugt,
Paul Hop
+ 185 more
Wouter van Rheenen,
Rick van der Spek,
Mark Bakker,
Leonard van den Berg,
Jan Veldink,
Joke van Vugt,
Paul Hop,
Ramona Zwamborn,
Niek de Klein,
Harm-Jan Westra,
Olivier Bakker,
Patrick Deelen,
Gemma Shireby,
Eilis Hannon,
Matthieu Moisse,
Denis Baird,
Restuadi Restuadi,
Egor Dolzhenko,
Annelot Dekker,
Klara Gawor,
Henk-Jan Westeneng,
Gijs Tazelaar,
Kristel van Eijk,
Maarten Kooyman,
Ross Byrne,
Mark Doherty,
Mark Heverin,
Ahmad Al Khleifat,
Alfredo Iacoangeli,
Aleksey Shatunov,
Nicola Ticozzi,
Johnathan Cooper-Knock,
Bradley Smith,
Marta Gromicho,
Siddharthan Chandran,
Suvankar Pal,
Karen Morrison,
Pamela Shaw,
John Hardy,
Richard Orrell,
Michael Sendtner,
Thomas Meyer,
Nazli Basak,
Anneke van der Kooi,
Antonia Ratti,
Isabella Fogh,
Cinzia Gellera,
Guiseppe Lauria Pinter,
Stefania Corti,
Cristina Cereda,
Daisy Sproviero,
Sandra D'Alfonso,
Gianni Soraru,
Gabriele Siciliano,
Massimiliano Filosto,
Alessandro Padovani,
Adriano Chio,
Andrea Calvo,
Cristina Moglia,
Maura Brunetti,
Antonio Canosa,
Maurizio Grassano,
Ettore Beghi,
Elisabetta Pupillo,
Giancarlo Logroscino,
Beatrice Nefussy,
Alma Osmanovic,
Angelica Nordin,
Yossef Lerner,
Michal Zabari,
Marc Gotkine,
Robert Baloh,
Shaugn Bell,
Patrick Vourc'h,
Philippe Corcia,
Philippe Couratier,
Stephanie Millecamps,
Vincent Meininger,
Francois Salachas,
Jesus Mora Pardina,
Abdelilah Assialioui,
Ricardo Rojas-García,
Patrick Dion,
Jay Ross,
Albert Ludolph,
Jochen Weishaupt,
David Brenner,
Axel Freischmidt,
Gilbert Bensimon,
Alexis Brice,
Alexandra Durr,
Christine Payan,
Safa Saker-Delye,
Nicholas Wood,
Simon Topp,
Rosa Rademakers,
Lukas Tittmann,
Wolfgang Lieb,
Andre Franke,
Stephan Ripke,
Alice Braun,
Julia Kraft,
David Whiteman,
Catherine Olsen,
André Uitterlinden,
Albert Hofman,
Marcella Rietschel,
Sven Cichon,
Markus Nöthen,
Philippe Amouyel,
Bryan Traynor,
Andrew Singleton,
Miguel Mitne Neto,
Ruben Cauchi,
Roel Ophoff,
Martina Wiedau-Pazos,
Catherine Lomen-Hoerth,
Vivianna Van Deerlin,
Julian Grosskreutz,
Annekathrin Rödiger,
Alexander Jörk,
Tabea Barthel,
Erik Theele,
Berjamin Ilse,
Beatrice Stubendorff,
Otto Witte,
Robert Steinbach,
Christian Hübner,
Caroline Graff,
Lev Brylev,
Vera Fominykh,
Vera Demeshonok,
Anastasia Ataulina,
Boris Rogelj,
Blaž Koritnik,
Janez Zidar,
Metka Ravnik-Glavač,
Damjan Glavač,
Zorica Stević,
Vivian Drory,
Mónica Povedano,
Ian Blair,
Matthew Kiernan,
Beben Benyamin,
Robert Henderson,
Sarah Furlong,
Susan Mathers,
Pamela McCombe,
Merrilee Needham,
Shyuan Ngo,
Garth Nicholson,
Roger Pamphlett,
Dominic Rowe,
Frederik Steyn,
Kelly Williams,
Karen Mather,
Perminder Sachdev,
Anjali Henders,
Leanne Wallace,
Mamede de Carvalho,
Susana Pinto,
Susanne Petri,
Markus Weber,
Guy Rouleau,
Vincenzo Silani,
Charles Curtis,
Gerome Breen,
Jonathan Glass,
Robert Brown,
John Landers,
Christopher Shaw,
Peter Andersen,
Ewout Groen,
Michael van Es,
Jeroen Pasterkamp,
Dongsheng Fan,
Fleur Garton,
Allan McRae,
George Davey Smith,
Tom Gaunt,
Michael Eberle,
Jonathan Mill,
Russell McLaughlin,
Orla Hardiman,
Kevin Kenna,
Naomi Wray,
Ellen Tsai,
Heiko Runz,
Lude Franke,
Ammar Al-Chalabi,
Philip Van Damme,
Nayana Gaur
Amyotrophic lateral sclerosis (ALS) is a fatal neurodegenerative disease with a life-time risk of 1 in 350 people and an unmet need for disease-modifying therapies. We conducted a cross-ancestry GWAS in ALS including 29,612 ALS patients and 122,656 controls which identified 15 risk loci in ALS. When combined with 8,953 whole-genome sequenced individuals (6,538 ALS patients, 2,415 controls) and the largest cortex-derived eQTL dataset (MetaBrain), analyses revealed locus-specific genetic architectures in which we prioritized genes either through rare variants, repeat expansions or regulatory effects. ALS associated risk loci were shared with multiple traits within the neurodegenerative spectrum, but with distinct enrichment patterns across brain regions and cell-types. Of the environmental and life-style risk factors obtained from literature, Mendelian randomization analyses indicated a causal role for high cholesterol levels. All ALS associated signals combined reveal a role for perturbations in vesicle mediated transport and autophagy, and provide evidence for cell-autonomous disease initiation in glutamatergic neurons.
Assessing the co-variability of DNA methylation across peripheral cells and tissues: Implications for the interpretation of findings in epigenetic epidemiology
Eilis Hannon,
Georgina Mansell,
Emma Walker,
Marta F. Nabais,
Joe Burrage,
Agnieszka Kepa,
Janis Best-Lane
+ 6 more
Eilis Hannon,
Georgina Mansell,
Emma Walker,
Marta F. Nabais,
Joe Burrage,
Agnieszka Kepa,
Janis Best-Lane,
Anna Rose,
Suzanne Heck,
Terrie E. Moffitt,
Avshalom Caspi,
Louise Arseneault,
Jonathan Mill
Most epigenome-wide association studies (EWAS) quantify DNA methylation (DNAm) in peripheral tissues such as whole blood to identify positions in the genome where variation is statistically associated with a trait or exposure. As whole blood comprises a mix of cell types, it is unclear whether trait-associated DNAm variation is specific to an individual cellular population. We collected three peripheral tissues (whole blood, buccal epithelial and nasal epithelial cells) from thirty individuals. Whole blood samples were subsequently processed using fluorescence-activated cell sorting (FACS) to purify five constituent cell-types (monocytes, granulocytes, CD4+ T cells, CD8+ T cells, and B cells). DNAm was profiled in all eight sample-types from each individual using the Illumina EPIC array. We identified significant differences in both the level and variability of DNAm between different sample types, and DNAm data-derived estimates of age and smoking were found to differ dramatically across sample types from the same individual. We found that for the majority of loci variation in DNAm in individual blood cell types was only weakly predictive of variance in DNAm measured in whole blood, although the proportion of variance explained was greater than that explained by either buccal or nasal epithelial samples. Covariation across sample types was much higher for DNAm sites influenced by genetic factors. Overall, we observe that DNAm variation in whole blood is additively influenced by a combination of the major blood cell types. For a subset of sites, however, variable DNAm detected in whole blood can be attributed to variation in a single blood cell type providing potential mechanistic insight about EWAS findings. Our results suggest that associations between whole blood DNAm and traits or exposures reflect differences in multiple cell types and our data will facilitate the interpretation of findings in epigenetic epidemiology.
Genome-wide study of DNA methylation in Amyotrophic Lateral Sclerosis identifies differentially methylated loci and implicates metabolic, inflammatory and cholesterol pathways
Paul J. Hop,
Ramona A.J. Zwamborn,
Eilis Hannon,
Gemma L. Shireby,
Marta F. Nabais,
Emma M. Walker,
Rheenen Wouter van
+ 78 more
Paul J. Hop,
Ramona A.J. Zwamborn,
Eilis Hannon,
Gemma L. Shireby,
Marta F. Nabais,
Emma M. Walker,
Rheenen Wouter van,
Vugt Joke J.F.A. van,
Annelot M. Dekker,
Henk-Jan Westeneng,
Gijs H.P. Tazelaar,
Eijk Kristel R. van,
Matthieu Moisse,
Denis Baird,
Khleifat Ahmad Al,
Alfredo Iacoangeli,
Nicola Ticozzi,
Antonia Ratti,
Jonathan Cooper-Knock,
Karen E. Morrison,
Pamela J. Shaw,
A. Nazli Basak,
Adriano Chiò,
Andrea Calvo,
Cristina Moglia,
Antonio Canosa,
Maura Brunetti,
Maurizio Grassano,
Marc Gotkine,
Yossef Lerner,
Michal Zabari,
Patrick Vourc’h,
Philippe Corcia,
Philippe Couratier,
Jesus S. Mora Pardina,
Teresa Salas,
Patrick Dion,
Jay P. Ross,
Robert D. Henderson,
Susan Mathers,
Pamela A. McCombe,
Merrilee Needham,
Garth Nicholson,
Dominic B. Rowe,
Roger Pamphlett,
Karen A. Mather,
Perminder S. Sachdev,
Sarah Furlong,
Fleur C. Garton,
Anjali K. Henders,
Tian Lin,
Shyuan T. Ngo,
Frederik J. Steyn,
Leanne Wallace,
Kelly L. Williams,
BIOS Consortium,
Brain MEND Consortium,
Miguel Mitne Neto,
Ruben J. Cauchi,
Ian P. Blair,
Matthew C. Kiernan,
Vivian Drory,
Monica Povedano,
Carvalho Mamede de,
Susana Pinto,
Markus Weber,
Guy Rouleau,
Vincenzo Silani,
John E. Landers,
Christopher E. Shaw,
Peter M. Andersen,
Allan F. McRae,
Es Michael A. van,
R. Jeroen Pasterkamp,
Naomi R. Wray,
Russell L. McLaughlin,
Orla Hardiman,
Kevin P. Kenna,
Ellen Tsai,
Heiko Runz,
Ammar Al-Chalabi,
den Berg Leonard H. van,
Damme Philip Van,
Jonathan Mill,
Jan H. Veldink
Abstract
Amyotrophic lateral sclerosis (ALS) is a fatal neurodegenerative disease with an estimated heritability of around 50%. DNA methylation patterns can serve as biomarkers of (past) exposures and disease progression, as well as providing a potential mechanism that mediates genetic or environmental risk. Here, we present a blood-based epigenome-wide association study (EWAS) meta-analysis in 10,462 samples (7,344 ALS patients and 3,118 controls), representing the largest case-control study of DNA methylation for any disease to date. We identified a total of 45 differentially methylated positions (DMPs) annotated to 42 genes, which are enriched for pathways and traits related to metabolism, cholesterol biosynthesis, and immunity. We show that DNA-methylation-based proxies for HDL-cholesterol, BMI, white blood cell (WBC) proportions and alcohol intake were independently associated with ALS. Integration of these results with our latest GWAS showed that cholesterol biosynthesis was causally related to ALS. Finally, we found that DNA methylation levels at several DMPs and blood cell proportion estimates derived from DNA methylation data, are associated with survival rate in patients, and could represent indicators of underlying disease processes.
Meta-analysis of genome-wide DNA methylation identifies shared associations across neurodegenerative disorders
Marta F. Nabais,
Simon M. Laws,
Tian Lin,
Costanza L. Vallerga,
Nicola J. Armstrong,
Ian P. Blair,
John B. Kwok
+ 63 more
Marta F. Nabais,
Simon M. Laws,
Tian Lin,
Costanza L. Vallerga,
Nicola J. Armstrong,
Ian P. Blair,
John B. Kwok,
Karen A. Mather,
George D. Mellick,
Perminder S. Sachdev,
Leanne Wallace,
Anjali K. Henders,
Ramona A. J. Zwamborn,
Paul J. Hop,
Katie Lunnon,
Ehsan Pishva,
Janou A. Y. Roubroeks,
Hilkka Soininen,
Magda Tsolaki,
Patrizia Mecocci,
Simon Lovestone,
Iwona Kłoszewska,
Bruno Vellas,
Sarah Furlong,
Fleur C. Garton,
Robert D. Henderson,
Susan Mathers,
Pamela A. McCombe,
Merrilee Needham,
Shyuan T. Ngo,
Garth Nicholson,
Roger Pamphlett,
Dominic B. Rowe,
Frederik J. Steyn,
Kelly L. Williams,
Tim J. Anderson,
Steven R. Bentley,
John Dalrymple-Alford,
Javed Fowder,
Jacob Gratten,
Glenda Halliday,
Ian B. Hickie,
Martin Kennedy,
Simon J. G. Lewis,
Grant W. Montgomery,
John Pearson,
Toni L. Pitcher,
Peter Silburn,
Futao Zhang,
Peter M. Visscher,
Jian Yang,
Anna J. Stevenson,
Robert F. Hillary,
Riccardo E. Marioni,
Sarah E. Harris,
Ian J. Deary,
Ashley R. Jones,
Aleksey Shatunov,
Alfredo Iacoangeli,
Rheenen Wouter van,
den Berg Leonard H. van,
Pamela J. Shaw,
Cristopher E. Shaw,
Karen E. Morrison,
Ammar Al-Chalabi,
Jan H. Veldink,
Eilis Hannon,
Jonathan Mill,
Naomi R. Wray,
Allan F. McRae
BackgroundPeople with neurodegenerative disorders show diverse clinical syndromes, genetic heterogeneity, and distinct brain pathological changes, but studies report overlap between these features. DNA methylation (DNAm) provides a way to explore this overlap and heterogeneity as it is determined by the combined effects of genetic variation and the environment. In this study, we aim to identify shared blood DNAm differences between controls and people with Alzheimer’s disease, amyotrophic lateral sclerosis, and Parkinson’s disease.ResultsWe use a mixed-linear model method (MOMENT) that accounts for the effect of (un)known confounders, to test for the association of each DNAm site with each disorder. While only three probes are found to be genome-wide significant in each MOMENT association analysis of amyotrophic lateral sclerosis and Parkinson’s disease (and none with Alzheimer’s disease), a fixed-effects meta-analysis of the three disorders results in 12 genome-wide significant differentially methylated positions. Predicted immune cell-type proportions are disrupted across all neurodegenerative disorders. Protein inflammatory markers are correlated with profile sum-scores derived from disease-associated immune cell-type proportions in a healthy aging cohort. In contrast, they are not correlated with MOMENT DNAm-derived profile sum-scores, calculated using effect sizes of the 12 differentially methylated positions as weights.ConclusionsWe identify shared differentially methylated positions in whole blood between neurodegenerative disorders that point to shared pathogenic mechanisms. These shared differentially methylated positions may reflect causes or consequences of disease, but they are unlikely to reflect cell-type proportion differences.
A central role for anterior cingulate cortex in the control of pathological aggression
Heukelum Sabrina van,
Kerli Tulva,
Femke E Geers,
Dulm Sanne van,
I Hyun Ruisch,
Jonathan Mill,
Joana F Viana
+ 7 more
Heukelum Sabrina van,
Kerli Tulva,
Femke E Geers,
Dulm Sanne van,
I Hyun Ruisch,
Jonathan Mill,
Joana F Viana,
Christian F Beckmann,
Jan K Buitelaar,
Geert Poelmans,
Jeffrey C Glennon,
Brent A Vogt,
Martha N Havenith,
Arthur S C França
Controlling aggression is a crucial skill in social species like rodents and humans and has been associated with anterior cingulate cortex (ACC). Here, we directly link the failed regulation of aggression in BALB/cJ mice to ACC hypofunction. We first show that ACC in BALB/cJ mice is structurally degraded: neuron density is decreased, with pervasive neuron death and reactive astroglia. Gene-set enrichment analysis suggested that this process is driven by neuronal degeneration, which then triggers toxic astrogliosis. cFos expression across ACC indicated functional consequences: during aggressive encounters, ACC was engaged in control mice, but not BALB/cJ mice. Chemogenetically activating ACC during aggressive encounters drastically suppressed pathological aggression but left species-typical aggression intact. The network effects of our chemogenetic perturbation suggest that this behavioral rescue is mediated by suppression of amygdala and hypothalamus and activation of mediodorsal thalamus. Together, these findings highlight the central role of ACC in curbing pathological aggression.
Mitochondrial D-Loop Region Methylation and Copy Number in Peripheral Blood DNA of Parkinson’s Disease Patients
Andrea Stoccoro,
Adam R. Smith,
Filippo Baldacci,
Gamba Claudia Del,
Annalisa Lo Gerfo,
Roberto Ceravolo,
Katie Lunnon
+ 2 more
Andrea Stoccoro,
Adam R. Smith,
Filippo Baldacci,
Gamba Claudia Del,
Annalisa Lo Gerfo,
Roberto Ceravolo,
Katie Lunnon,
Lucia Migliore,
Fabio Coppedè
Altered mitochondrial DNA (mtDNA) methylation has been detected in several human pathologies, although little attention has been given to neurodegenerative diseases. Recently, altered methylation levels of the mitochondrial displacement loop (D-loop) region, which regulates mtDNA replication, were observed in peripheral blood cells of Alzheimer's disease and amyotrophic lateral sclerosis patients. However, nothing is yet known about D-loop region methylation levels in peripheral blood of Parkinson's disease (PD) patients. In the current study, we investigated D-loop methylation levels and mtDNA copy number in peripheral blood of 30 PD patients and 30 age- and sex-matched control subjects. DNA methylation analyses have been performed by means of methylation-sensitive high-resolution melting (MS-HRM) and pyrosequencing techniques, while mtDNA copy number was analyzed by quantitative PCR. MS-HRM and pyrosequencing analyses provided very similar D-loop methylation levels in PD patients and control subjects, and no differences between the two groups have been observed. Treatment with L-dopa and duration of the disease had no effect on D-loop methylation levels in PD patients. Additionally, mtDNA copy number did not differ between PD patients and control subjects. Current results suggest that D-loop methylation levels are not altered in peripheral blood of PD patients nor influenced by dopaminergic treatment.
Attenuated Induction of the Unfolded Protein Response in Adult Human Primary Astrocytes in Response to Recurrent Low Glucose
Paul G. Weightman Potter, Sam J. Washer, Aaron R. Jeffries, Janet E. Holley, Nick J. Gutowski, Emma L. Dempster, Craig Beall
Paul G. Weightman Potter,
Sam J. Washer,
Aaron R. Jeffries,
Janet E. Holley,
Nick J. Gutowski,
Emma L. Dempster,
Craig Beall
Aims/hypothesis: Recurrent hypoglycaemia (RH) is a major side-effect of intensive insulin therapy for people with diabetes. Changes in hypoglycaemia sensing by the brain contribute to the development of impaired counterregulatory responses to and awareness of hypoglycaemia. Little is known about the intrinsic changes in human astrocytes in response to acute and recurrent low glucose (RLG) exposure.
Methods: Human primary astrocytes (HPA) were exposed to zero, one, three or four bouts of low glucose (0.1 mmol/l) for three hours per day for four days to mimic RH. On the fourth day, DNA and RNA were collected. Differential gene expression and ontology analyses were performed using DESeq2 and GOseq, respectively. DNA methylation was assessed using the Infinium MethylationEPIC BeadChip platform.
Results: 24 differentially expressed genes (DEGs) were detected (after correction for multiple comparisons). One bout of low glucose exposure had the largest effect on gene expression. Pathway analyses revealed that endoplasmic-reticulum (ER) stress-related genes such as HSPA5, XBP1, and MANF, involved in the unfolded protein response (UPR), were all significantly increased following low glucose (LG) exposure, which was diminished following RLG. There was little correlation between differentially methylated positions and changes in gene expression yet the number of bouts of LG exposure produced distinct methylation signatures.
Conclusions/interpretation: These data suggest that exposure of human astrocytes to transient LG triggers activation of genes involved in the UPR linked to endoplasmic reticulum (ER) stress. Following RLG, the activation of UPR related genes was diminished, suggesting attenuated ER stress. This may be a consequence of a successful metabolic adaptation, as previously reported, that better preserves intracellular energy levels and a reduced necessity for the UPR.
Association of childhood neighborhood disadvantage with young adult DNA methylation
A. Reuben,
K. Sugden,
L. Arsenault,
D. Corcoran,
A. Danese,
H.L. Fisher,
T.E. Moffitt
+ 7 more
A. Reuben,
K. Sugden,
L. Arsenault,
D. Corcoran,
A. Danese,
H.L. Fisher,
T.E. Moffitt,
J.B. Newbury,
C. Odgers,
J. Prinz,
L.J. Rasmussen,
B. Williams,
J. Mill,
A. Caspi
Ceremonial Ayahuasca in Amazonian Retreats—Mental Health and Epigenetic Outcomes From a Six-Month Naturalistic Study
Simon G. D. Ruffell,
Nige Netzband,
WaiFung Tsang,
Merlin Davies,
Antonio Inserra,
Matthew Butler,
James J. H. Rucker
+ 4 more
Simon G. D. Ruffell,
Nige Netzband,
WaiFung Tsang,
Merlin Davies,
Antonio Inserra,
Matthew Butler,
James J. H. Rucker,
Luís Fernando Tófoli,
Emma Louise Dempster,
Allan H. Young,
Celia J. A. Morgan
Ayahuasca is a natural psychoactive brew, used in traditional ceremonies in the Amazon basin. Recent research has indicated that ayahuasca is pharmacologically safe and its use may be positively associated with improvements in psychiatric symptoms. The mechanistic effects of ayahuasca are yet to be fully established. In this prospective naturalistic study, 63 self-selected participants took part in ayahuasca ceremonies at a retreat centre in the Peruvian Amazon. Participants undertook the Beck Depression Inventory (BDI-II), State-Trait Anxiety Inventory (STAI), Self-compassion Scale (SCS), Clinical Outcomes in Routine Evaluation-Outcome Measure (CORE-OM), as well as secondary measures, pre- and post-retreat and at 6-months. Participants also provided saliva samples for pre/post epigenetic analysis. Overall, a statistically significant decrease in BDI-II (13.9 vs. 6.1, p < 0.001), STAI (44.4 vs. 34.3 p < 0.001) scores, and CORE-OM scores were observed (37.3 vs. 22.3 p < 0.001) at post-retreat, as well as a concurrent increase in SCS (3.1 vs. 3.6, p < 0.001). Psychometric improvements were sustained, and on some measures values further decreased at 6-month follow-up, suggesting a potential for lasting therapeutic effects. Changes in memory valence were linked to the observed psychometric improvements. Epigenetic findings were equivocal, but indicated that further research in candidate genes, such as sigma non-opioid intracellular receptor 1 (SIGMAR1), is warranted. This data adds to the literature supporting ayahuasca's possible positive impact on mental health when conducted in a ceremonial context. Further investigation into clinical samples, as well as greater analyses into the mechanistic action of ayahuasca is advised.
A meta-analysis of epigenome-wide association studies in Alzheimer’s disease highlights novel differentially methylated loci across cortex
Rebecca G. Smith,
Ehsan Pishva,
Gemma Shireby,
Adam R. Smith,
Janou A. Y. Roubroeks,
Eilis Hannon,
Gregory Wheildon
+ 21 more
Rebecca G. Smith,
Ehsan Pishva,
Gemma Shireby,
Adam R. Smith,
Janou A. Y. Roubroeks,
Eilis Hannon,
Gregory Wheildon,
Diego Mastroeni,
Gilles Gasparoni,
Matthias Riemenschneider,
Armin Giese,
Andrew J. Sharp,
Leonard Schalkwyk,
Vahram Haroutunian,
Wolfgang Viechtbauer,
den Hove Daniel L. A. van,
Michael Weedon,
Danielle Brokaw,
Paul T. Francis,
Alan J. Thomas,
Seth Love,
Kevin Morgan,
Jörn Walter,
Paul D. Coleman,
David A. Bennett,
Jager Philip L. De,
Jonathan Mill,
Katie Lunnon
Epigenome-wide association studies of Alzheimer’s disease have highlighted neuropathology-associated DNA methylation differences, although existing studies have been limited in sample size and utilized different brain regions. Here, we combine data from six DNA methylomic studies of Alzheimer’s disease (N = 1453 unique individuals) to identify differential methylation associated with Braak stage in different brain regions and across cortex. We identify 236 CpGs in the prefrontal cortex, 95 CpGs in the temporal gyrus and ten CpGs in the entorhinal cortex at Bonferroni significance, with none in the cerebellum. Our cross-cortex meta-analysis (N = 1408 donors) identifies 220 CpGs associated with neuropathology, annotated to 121 genes, of which 84 genes have not been previously reported at this significance threshold. We have replicated our findings using two further DNA methylomic datasets consisting of a further >600 unique donors. The meta-analysis summary statistics are available in our online data resource (www.epigenomicslab.com/ad-meta-analysis/).
Characterizing the properties of bisulfite sequencing data: maximizing power and sensitivity to identify between-group differences in DNA methylation
BackgroundThe combination of sodium bisulfite treatment with highly-parallel sequencing is a common method for quantifying DNA methylation across the genome. The power to detect between-group differences in DNA methylation using bisulfite-sequencing approaches is influenced by both experimental (e.g. read depth, missing data and sample size) and biological (e.g. mean level of DNA methylation and difference between groups) parameters. There is, however, no consensus about the optimal thresholds for filtering bisulfite sequencing data with implications for the reproducibility of findings in epigenetic epidemiology.ResultsWe used a large reduced representation bisulfite sequencing (RRBS) dataset to assess the distribution of read depth across DNA methylation sites and the extent of missing data. To investigate how various study variables influence power to identify DNA methylation differences between groups, we developed a framework for simulating bisulfite sequencing data. As expected, sequencing read depth, group size, and the magnitude of DNA methylation difference between groups all impacted upon statistical power. The influence on power was not dependent on one specific parameter, but reflected the combination of study-specific variables. As a resource to the community, we have developed a tool, POWEREDBiSeq, which utilizes our simulation framework to predict study-specific power for the identification of DNAm differences between groups, taking into account user-defined read depth filtering parameters and the minimum sample size per group.ConclusionsOur data-driven approach highlights the importance of filtering bisulfite-sequencing data by minimum read depth and illustrates how the choice of threshold is influenced by the specific study design and the expected differences between groups being compared. The POWEREDBiSeq tool, which can be applied to different types of bisulfite sequencing data (e.g. RRBS, whole genome bisulfite sequencing (WGBS), targeted bisulfite sequencing and amplicon-based bisulfite sequencing), can help users identify the level of data filtering needed to optimize power and aims to improve the reproducibility of bisulfite sequencing studies.
The association of epigenetic clocks in brain tissue with brain pathologies and common aging phenotypes
Francine Grodstein,
Bernardo Lemos,
Lei Yu,
Hans-Ulrich Klein,
Artemis Iatrou,
Aron S Buchman,
Gemma L Shireby
+ 4 more
Francine Grodstein,
Bernardo Lemos,
Lei Yu,
Hans-Ulrich Klein,
Artemis Iatrou,
Aron S Buchman,
Gemma L Shireby,
Jonathan Mill,
Julie A Schneider,
Jager Philip L De,
David A Bennett
Epigenetic clocks are calculated by combining DNA methylation states across select CpG sites to estimate biologic age, and have been noted as the most successful markers of biologic aging to date. Yet, limited research has considered epigenetic clocks calculated in brain tissue. We used DNA methylation states in dorsolateral prefrontal cortex specimens from 721 older participants of the Religious Orders Study and Rush Memory and Aging Project, to calculate DNA methylation age using four established epigenetic clocks: Hannum, Horvath, PhenoAge, GrimAge, and a new Cortical clock. The four established clocks were trained in blood samples (Hannum, PhenoAge, GrimAge) or using 51 human tissue and cell types (Horvath); the recent Cortical clock is the first trained in postmortem cortical tissue. Participants were recruited beginning in 1994 (Religious Orders Study) and 1997 (Memory and Aging Project), and followed annually with questionnaires and clinical evaluations; brain specimens were obtained for 80-90% of participants. Mean age at death was 88.0 (SD 6.7) years. We used linear regression, logistic regression, and linear mixed models, to examine relations of epigenetic clock ages to neuropathologic and clinical aging phenotypes, controlling for chronologic age, sex, education, and depressive symptomatology. Hannum, Horvath, PhenoAge and Cortical clock ages were related to pathologic diagnosis of Alzheimer's disease (AD), as well as to Aβ load (a hallmark pathology of Alzheimer's disease). However, associations were substantially stronger for the Cortical than other clocks; for example, each standard deviation (SD) increase in Hannum, Horvath, and PhenoAge clock age was related to approximately 30% greater likelihood of pathologic AD (all p < 0.05), while each SD increase in Cortical age was related to 90% greater likelihood of pathologic AD (odds ratio = 1.91, 95% confidence interval 1.38, 2.62). Moreover, Cortical age was significantly related to other AD pathology (eg, mean tau tangle density, p = 0.003), and to odds of neocortical Lewy body pathology (for each SD increase in Cortical age, odds ratio = 2.00, 95% confidence 1.27, 3.17), although no clocks were related to cerebrovascular neuropathology. Cortical age was the only epigenetic clock significantly associated with the clinical phenotypes examined, from dementia to cognitive decline (5 specific cognitive systems, and a global cognitive measure averaging 17 tasks) to Parkinsonian signs. Overall, our findings provide evidence of the critical necessity for bespoke clocks of brain aging for advancing research to understand, and eventually prevent, neurodegenerative diseases of aging.
Interaction between genetic predisposition, smoking, and dementia risk: a population-based cohort study
Na Zhang,
Janice M. Ranson,
Zhi-Jie Zheng,
Eilis Hannon,
Zhenwei Zhou,
Xuejun Kong,
David J. Llewellyn
+ 2 more
Na Zhang,
Janice M. Ranson,
Zhi-Jie Zheng,
Eilis Hannon,
Zhenwei Zhou,
Xuejun Kong,
David J. Llewellyn,
Daniel A. King,
Jie Huang
We evaluated whether the association between cigarette smoking and dementia risk is modified by genetic predisposition including apolipoprotein E (APOE) genotype and polygenic risk (excluding the APOE region). We included 193,198 UK Biobank participants aged 60–73 years without dementia at baseline. Of non-APOE-ε4 carriers, 0.89% (95% CI 0.73–1.08%) current smokers developed dementia compared with 0.49% (95% CI 0.44–0.55%) of never smokers (adjusted HR 1.78; 95% CI 1.39–2.29). In contrast, of one APOE-ε4 allele carriers, 1.69% (95% CI 1.31–2.12%) current smokers developed dementia compared with 1.40% (95% CI 1.25–1.55%) of never smokers (adjusted HR 1.06; 95% CI 0.77–1.45); of two APOE-ε4 alleles carriers, 4.90% (95% CI 2.92–7.61%) current smokers developed dementia compared with 3.87% (95% CI 3.11–4.74%) of never smokers (adjusted HR 0.94; 95% CI 0.49–1.79). Of participants with high polygenic risk, 1.77% (95% CI 1.35–2.27%) current smokers developed dementia compared with 1.05% (95% CI 0.91–1.21%) of never smokers (adjusted HR 1.63; 95% CI 1.16–2.28). A significant interaction was found between APOE genotype and smoking status (P = 0.002) while no significant interaction was identified between polygenic risk and smoking status (P = 0.25). APOE genotype but not polygenic risk modified the effect of smoking on dementia risk.
Novel epigenetic clock for fetal brain development predicts prenatal age for cellular stem cell models and derived neurons
Leonard C. Steg,
Gemma L. Shireby,
Jennifer Imm,
Jonathan P. Davies,
Alice Franklin,
Robert Flynn,
Seema C. Namboori
+ 18 more
Leonard C. Steg,
Gemma L. Shireby,
Jennifer Imm,
Jonathan P. Davies,
Alice Franklin,
Robert Flynn,
Seema C. Namboori,
Akshay Bhinge,
Aaron R. Jeffries,
Joe Burrage,
Grant W. A. Neilson,
Emma M. Walker,
Leo W. Perfect,
Jack Price,
Grainne McAlonan,
Deepak P. Srivastava,
Nicholas J. Bray,
Emma L. Cope,
Kimberley M. Jones,
Nicholas D. Allen,
Ehsan Pishva,
Emma L. Dempster,
Katie Lunnon,
Jonathan Mill,
Eilis Hannon
Induced pluripotent stem cells (iPSCs) and their differentiated neurons (iPSC-neurons) are a widely used cellular model in the research of the central nervous system. However, it is unknown how well they capture age-associated processes, particularly given that pluripotent cells are only present during the earliest stages of mammalian development. Epigenetic clocks utilize coordinated age-associated changes in DNA methylation to make predictions that correlate strongly with chronological age. It has been shown that the induction of pluripotency rejuvenates predicted epigenetic age. As existing clocks are not optimized for the study of brain development, we developed the fetal brain clock (FBC), a bespoke epigenetic clock trained in human prenatal brain samples in order to investigate more precisely the epigenetic age of iPSCs and iPSC-neurons. The FBC was tested in two independent validation cohorts across a total of 194 samples, confirming that the FBC outperforms other established epigenetic clocks in fetal brain cohorts. We applied the FBC to DNA methylation data from iPSCs and embryonic stem cells and their derived neuronal precursor cells and neurons, finding that these cell types are epigenetically characterized as having an early fetal age. Furthermore, while differentiation from iPSCs to neurons significantly increases epigenetic age, iPSC-neurons are still predicted as being fetal. Together our findings reiterate the need to better understand the limitations of existing epigenetic clocks for answering biological research questions and highlight a limitation of iPSC-neurons as a cellular model of age-related diseases.
DNA methylation-based sex classifier to predict sex and identify sex chromosome aneuploidy
Yucheng Wang,
Eilis Hannon,
Olivia A. Grant,
Tyler J. Gorrie-Stone,
Meena Kumari,
Jonathan Mill,
Xiaojun Zhai
+ 2 more
Yucheng Wang,
Eilis Hannon,
Olivia A. Grant,
Tyler J. Gorrie-Stone,
Meena Kumari,
Jonathan Mill,
Xiaojun Zhai,
Klaus D. McDonald-Maier,
Leonard C. Schalkwyk
BackgroundSex is an important covariate of epigenome-wide association studies due to its strong influence on DNA methylation patterns across numerous genomic positions. Nevertheless, many samples on the Gene Expression Omnibus (GEO) frequently lack a sex annotation or are incorrectly labelled. Considering the influence that sex imposes on DNA methylation patterns, it is necessary to ensure that methods for filtering poor samples and checking of sex assignment are accurate and widely applicable.ResultsHere we presented a novel method to predict sex using only DNA methylation beta values, which can be readily applied to almost all DNA methylation datasets of different formats (raw IDATs or text files with only signal intensities) uploaded to GEO. We identified 4345 significantly (p<0.01) sex-associated CpG sites present on both 450K and EPIC arrays, and constructed a sex classifier based on the two first principal components of the DNA methylation data of sex-associated probes mapped on sex chromosomes. The proposed method is constructed using whole blood samples and exhibits good performance across a wide range of tissues. We further demonstrated that our method can be used to identify samples with sex chromosome aneuploidy, this function is validated by five Turner syndrome cases and one Klinefelter syndrome case.ConclusionsThis proposed sex classifier not only can be used for sex predictions but also applied to identify samples with sex chromosome aneuploidy, and it is freely and easily accessible by calling the ‘estimateSex’ function from the newest wateRmelon Bioconductor package (https://github.com/schalkwyk/wateRmelon).
Characterization of DNA Methylomic Signatures in Induced Pluripotent Stem Cells During Neuronal Differentiation
Jennifer Imm,
Ehsan Pishva,
Muhammadd Ali,
Talitha L. Kerrigan,
Aaron Jeffries,
Joe Burrage,
Enrico Glaab
+ 4 more
Jennifer Imm,
Ehsan Pishva,
Muhammadd Ali,
Talitha L. Kerrigan,
Aaron Jeffries,
Joe Burrage,
Enrico Glaab,
Emma L. Cope,
Kimberley M. Jones,
Nicholas D. Allen,
Katie Lunnon
In development, differentiation from a pluripotent state results in global epigenetic changes, although the extent to which this occurs in induced pluripotent stem cell-based neuronal models has not been extensively characterized. In the present study, induced pluripotent stem cell colonies (33Qn1 line) were differentiated and collected at four time-points, with DNA methylation assessed using the Illumina Infinium Human Methylation EPIC BeadChip array. Dynamic changes in DNA methylation occurring during differentiation were investigated using a data-driven trajectory inference method. We identified a large number of Bonferroni-significant loci that showed progressive alterations in DNA methylation during neuronal differentiation. A gene-gene interaction network analysis identified 60 densely connected genes that were influential in the differentiation of neurons, with STAT3 being the gene with the highest connectivity.
A machine learning case–control classifier for schizophrenia based on DNA methylation in blood
Chathura J. Gunasekara,
Eilis Hannon,
Harry MacKay,
Cristian Coarfa,
Andrew McQuillin,
David St. Clair,
Jonathan Mill
+ 1 more
Chathura J. Gunasekara,
Eilis Hannon,
Harry MacKay,
Cristian Coarfa,
Andrew McQuillin,
David St. Clair,
Jonathan Mill,
Robert A. Waterland
Epigenetic dysregulation is thought to contribute to the etiology of schizophrenia (SZ), but the cell type-specificity of DNA methylation makes population-based epigenetic studies of SZ challenging. To train an SZ case–control classifier based on DNA methylation in blood, therefore, we focused on human genomic regions of systemic interindividual epigenetic variation (CoRSIVs), a subset of which are represented on the Illumina Human Methylation 450K (HM450) array. HM450 DNA methylation data on whole blood of 414 SZ cases and 433 non-psychiatric controls were used as training data for a classification algorithm with built-in feature selection, sparse partial least squares discriminate analysis (SPLS-DA); application of SPLS-DA to HM450 data has not been previously reported. Using the first two SPLS-DA dimensions we calculated a “risk distance” to identify individuals with the highest probability of SZ. The model was then evaluated on an independent HM450 data set on 353 SZ cases and 322 non-psychiatric controls. Our CoRSIV-based model classified 303 individuals as cases with a positive predictive value (PPV) of 80%, far surpassing the performance of a model based on polygenic risk score (PRS). Importantly, risk distance (based on CoRSIV methylation) was not associated with medication use, arguing against reverse causality. Risk distance and PRS were positively correlated (Pearson r = 0.28, P = 1.28 × 10−12), and mediational analysis suggested that genetic effects on SZ are partially mediated by altered methylation at CoRSIVs. Our results indicate two innate dimensions of SZ risk: one based on genetic, and the other on systemic epigenetic variants.
Sites of active gene regulation in the prenatal frontal cortex and their role in neuropsychiatric disorders
Manuela R. Kouakou, Darren Cameron, Eilis Hannon, Emma L. Dempster, Jonathan Mill, Matthew J. Hill, Nicholas J. Bray
Manuela R. Kouakou,
Darren Cameron,
Eilis Hannon,
Emma L. Dempster,
Jonathan Mill,
Matthew J. Hill,
Nicholas J. Bray
Abstract Common genetic variation appears to largely influence risk for neuropsychiatric disorders through effects on gene regulation. It is therefore possible to shed light on the biology of these conditions by testing for enrichment of associated genetic variation within regulatory genomic regions operating in specific tissues or cell types. Here, we have used ATAC-Seq to map open chromatin (an index of active regulatory genomic regions) in bulk tissue, NeuN+ and NeuN− nuclei from the prenatal human frontal cortex, and tested enrichment of SNP heritability for 5 neuropsychiatric disorders (autism spectrum disorder, ADHD, bipolar disorder, major depressive disorder and schizophrenia) within these regions. We observed significant enrichment of SNP heritability for ADHD, major depressive disorder and schizophrenia within open chromatin regions mapped in bulk fetal frontal cortex, and for all 5 tested neuropsychiatric conditions when we restricted these sites to those overlapping histone modifications indicative of enhancers (H3K4me1) or promoters (H3K4me3) in fetal brain. SNP heritability for neuropsychiatric disorders was significantly enriched in open chromatin regions identified in fetal frontal cortex NeuN- as well as NeuN+ nuclei overlapping fetal brain H3K4me1 or H3K4me3 sites. We additionally demonstrate the utility of our mapped open chromatin regions for prioritizing potentially functional SNPs at genome-wide significant risk loci for neuropsychiatric disorders. Our data provide evidence for an early neurodevelopmental component to a range of neuropsychiatric conditions and highlight an important role for regulatory genomic regions active within both NeuN+ and NeuN− cells of the prenatal brain.
DunedinPACE: A DNA methylation biomarker of the Pace of Aging
DW Belsky,
A Caspi,
DL Corcoran,
K Sugden,
R Poulton,
L Arseneault,
A Baccarelli
+ 13 more
DW Belsky,
A Caspi,
DL Corcoran,
K Sugden,
R Poulton,
L Arseneault,
A Baccarelli,
K Chamarti,
X Gao,
E Hannon,
HL Harrington,
R Houts,
M Kothari,
D Kwon,
J Mill,
J Schwartz,
P Vokonas,
C Wang,
B Williams,
TE Moffitt
ABSTRACT
Measures to quantify changes in the pace of biological aging in response to intervention are needed to evaluate geroprotective interventions for humans. We used data from the Dunedin Study 1972-3 birth cohort tracking within-individual decline in 19 indicators of organ-system integrity across four time points spanning two decades to model Pace of Aging. We distilled this two-decade Pace of Aging into a single-time-point DNA-methylation blood-test using elastic-net regression and a DNA-methylation dataset restricted to exclude probes with low test-retest reliability. We evaluated the resulting measure, named DunedinPACE, in five additional datasets. DunedinPACE showed high test-retest reliability, was associated with morbidity, disability, and mortality, and indicated faster aging in young adults with childhood adversity. DunedinPACE effect-sizes were similar to GrimAge Clock effect-sizes. In analysis of morbidity, disability, and mortality, DunedinPACE and added incremental prediction beyond GrimAge. DunedinPACE is a novel blood biomarker of the pace of aging for gerontology and geroscience.
Epigenomic features related to microglia are associated with attenuated effect of APOE ε4 on Alzheimer's disease risk in humans
Yiyi Ma,
Lei Yu,
Marta Olah,
Rebecca Smith,
Stephanie R. Oatman,
Mariet Allen,
Ehsan Pishva
+ 7 more
Yiyi Ma,
Lei Yu,
Marta Olah,
Rebecca Smith,
Stephanie R. Oatman,
Mariet Allen,
Ehsan Pishva,
Bin Zhang,
Vilas Menon,
Nilüfer Ertekin‐Taner,
Katie Lunnon,
David A. Bennett,
Hans‐Ulrich Klein,
Jager Philip L. De
Not all apolipoprotein E (APOE) ε4 carriers who survive to advanced age develop Alzheimer's disease (AD); factors attenuating the risk of ε4 on AD may exist. Guided by the top ε4-attenuating signals from methylome-wide association analyses (N = 572, ε4+ and ε4-) of neurofibrillary tangles and neuritic plaques, we conducted a meta-analysis for pathological AD within the ε4+ subgroups (N = 235) across four independent collections of brains. Cortical RNA-seq and microglial morphology measurements were used in functional analyses. Three out of the four significant CpG dinucleotides were captured by one principal component (PC1), which interacts with ε4 on AD, and is associated with expression of innate immune genes and activated microglia. In ε4 carriers, reduction in each unit of PC1 attenuated the odds of AD by 58% (odds ratio = 2.39, 95% confidence interval = [1.64,3.46], P = 7.08 × 10-6 ). An epigenomic factor associated with a reduced proportion of activated microglia (epigenomic factor of activated microglia, EFAM) appears to attenuate the risk of ε4 on AD.
Genomic and phenotypic insights from an atlas of genetic effects on DNA methylation
Josine L. Min,
Gibran Hemani,
Eilis Hannon,
Koen F. Dekkers,
Juan Castillo-Fernandez,
René Luijk,
Elena Carnero-Montoro
+ 149 more
Josine L. Min,
Gibran Hemani,
Eilis Hannon,
Koen F. Dekkers,
Juan Castillo-Fernandez,
René Luijk,
Elena Carnero-Montoro,
Daniel J. Lawson,
Kimberley Burrows,
Matthew Suderman,
Andrew D. Bretherick,
Tom G. Richardson,
Johanna Klughammer,
Valentina Iotchkova,
Gemma Sharp,
Ahmad Al Khleifat,
Aleksey Shatunov,
Alfredo Iacoangeli,
Wendy L. McArdle,
Karen M. Ho,
Ashish Kumar,
Cilla Söderhäll,
Carolina Soriano-Tárraga,
Eva Giralt-Steinhauer,
Nabila Kazmi,
Dan Mason,
Allan F. McRae,
David L. Corcoran,
Karen Sugden,
Silva Kasela,
Alexia Cardona,
Felix R. Day,
Giovanni Cugliari,
Clara Viberti,
Simonetta Guarrera,
Michael Lerro,
Richa Gupta,
Sailalitha Bollepalli,
Pooja Mandaviya,
Yanni Zeng,
Toni-Kim Clarke,
Rosie M. Walker,
Vanessa Schmoll,
Darina Czamara,
Carlos Ruiz-Arenas,
Faisal I. Rezwan,
Riccardo E. Marioni,
Tian Lin,
Yvonne Awaloff,
Marine Germain,
Dylan Aïssi,
Ramona Zwamborn,
Kristel van Eijk,
Annelot Dekker,
Jenny van Dongen,
Jouke-Jan Hottenga,
Gonneke Willemsen,
Cheng-Jian Xu,
Guillermo Barturen,
Francesc Català-Moll,
Martin Kerick,
Carol Wang,
Phillip Melton,
Hannah R. Elliott,
Jean Shin,
Manon Bernard,
Idil Yet,
Melissa Smart,
Tyler Gorrie-Stone,
Chris Shaw,
Ammar Al Chalabi,
Susan M. Ring,
Göran Pershagen,
Erik Melén,
Jordi Jiménez-Conde,
Jaume Roquer,
Deborah A. Lawlor,
John Wright,
Nicholas G. Martin,
Grant W. Montgomery,
Terrie E. Moffitt,
Richie Poulton,
Tõnu Esko,
Lili Milani,
Andres Metspalu,
John R. B. Perry,
Ken K. Ong,
Nicholas J. Wareham,
Giuseppe Matullo,
Carlotta Sacerdote,
Salvatore Panico,
Avshalom Caspi,
Louise Arseneault,
France Gagnon,
Miina Ollikainen,
Jaakko Kaprio,
Janine F. Felix,
Fernando Rivadeneira,
Henning Tiemeier,
Marinus H. van IJzendoorn,
André G. Uitterlinden,
Vincent W. V. Jaddoe,
Chris Haley,
Andrew M. McIntosh,
Kathryn L. Evans,
Alison Murray,
Katri Räikkönen,
Jari Lahti,
Ellen A. Nohr,
Thorkild I. A. Sørensen,
Torben Hansen,
Camilla S. Morgen,
Elisabeth B. Binder,
Susanne Lucae,
Juan Ramon Gonzalez,
Mariona Bustamante,
Jordi Sunyer,
John W. Holloway,
Wilfried Karmaus,
Hongmei Zhang,
Ian J. Deary,
Naomi R. Wray,
John M. Starr,
Marian Beekman,
Diana van Heemst,
P. Eline Slagboom,
Pierre-Emmanuel Morange,
David-Alexandre Trégouët,
Jan H. Veldink,
Gareth E. Davies,
Eco J. C. de Geus,
Dorret I. Boomsma,
Judith M. Vonk,
Bert Brunekreef,
Gerard H. Koppelman,
Marta E. Alarcón-Riquelme,
Rae-Chi Huang,
Craig E. Pennell,
Joyce van Meurs,
M. Arfan Ikram,
Alun D. Hughes,
Therese Tillin,
Nish Chaturvedi,
Zdenka Pausova,
Tomas Paus,
Timothy D. Spector,
Meena Kumari,
Leonard C. Schalkwyk,
Peter M. Visscher,
George Davey Smith,
Christoph Bock,
Tom R. Gaunt,
Jordana T. Bell,
Bastiaan T. Heijmans,
Jonathan Mill,
Caroline L. Relton
Characterizing genetic influences on DNA methylation (DNAm) provides an opportunity to understand mechanisms underpinning gene regulation and disease. In the present study, we describe results of DNAm quantitative trait locus (mQTL) analyses on 32,851 participants, identifying genetic variants associated with DNAm at 420,509 DNAm sites in blood. We present a database of >270,000 independent mQTLs, of which 8.5% comprise long-range (trans) associations. Identified mQTL associations explain 15–17% of the additive genetic variance of DNAm. We show that the genetic architecture of DNAm levels is highly polygenic. Using shared genetic control between distal DNAm sites, we constructed networks, identifying 405 discrete genomic communities enriched for genomic annotations and complex traits. Shared genetic variants are associated with both DNAm levels and complex diseases, but only in a minority of cases do these associations reflect causal relationships from DNAm to trait or vice versa, indicating a more complex genotype–phenotype map than previously anticipated.
GENETIC CONTROL OF DECONVOLVED BRAIN CELL-TYPES
Chloe Yap, Chongyuan Luo, Dorothea Seiler Vellame, Arjun Bhattacharya, Alice Franklin, Jonathan Mill, Michael Gandal
Chloe Yap,
Chongyuan Luo,
Dorothea Seiler Vellame,
Arjun Bhattacharya,
Alice Franklin,
Jonathan Mill,
Michael Gandal
CELL-TYPE-SPECIFIC PATTERNS OF DNA METHYLATION IN THE DEVELOPING HUMAN BRAIN
Jonathan Davies,
Alice Franklin,
Gina Commin,
Emma Walker,
Stefania Policicchio,
Aaron Jeffries,
Joe Burrage
+ 7 more
Jonathan Davies,
Alice Franklin,
Gina Commin,
Emma Walker,
Stefania Policicchio,
Aaron Jeffries,
Joe Burrage,
Barry Chioza,
Jinyue Liu,
Nick Bray,
Shyam Prabhakar,
Eilis Hannon,
Emma Dempster,
Jonathan Mill
TH44. LEVERAGING DNA METHYLATION QUANTITATIVE-TRAIT LOCI TO CHARACTERIZE THE RELATIONSHIP BETWEEN METHYLOMIC VARIATION, GENE EXPRESSION, AND PSYCHIATRIC DISEASE
Gemma Shireby,
Eilis Hannon,
Gina Commin,
Joe Burrage,
Jonathan Davies,
Stefania Policicchio,
Leo Schalkwyk
+ 2 more
Gemma Shireby,
Eilis Hannon,
Gina Commin,
Joe Burrage,
Jonathan Davies,
Stefania Policicchio,
Leo Schalkwyk,
Emma Dempster,
Jonathan Mill
Identical twins carry a persistent epigenetic signature of early genome programming
Dongen Jenny van,
Scott D. Gordon,
Allan F. McRae,
Veronika V. Odintsova,
Hamdi Mbarek,
Charles E. Breeze,
Karen Sugden
+ 29 more
Dongen Jenny van,
Scott D. Gordon,
Allan F. McRae,
Veronika V. Odintsova,
Hamdi Mbarek,
Charles E. Breeze,
Karen Sugden,
Sara Lundgren,
Juan E. Castillo-Fernandez,
Eilis Hannon,
Terrie E. Moffitt,
Fiona A. Hagenbeek,
Beijsterveldt Catharina E. M. van,
Hottenga Jouke Jan,
Pei-Chien Tsai,
Josine L. Min,
Gibran Hemani,
Erik A. Ehli,
Franziska Paul,
Claudio D. Stern,
Bastiaan T. Heijmans,
P. Eline Slagboom,
Lucia Daxinger,
der Maarel Silvère M. van,
Geus Eco J. C. de,
Gonneke Willemsen,
Grant W. Montgomery,
Bruno Reversade,
Miina Ollikainen,
Jaakko Kaprio,
Tim D. Spector,
Jordana T. Bell,
Jonathan Mill,
Avshalom Caspi,
Nicholas G. Martin,
Dorret I. Boomsma
Monozygotic (MZ) twins and higher-order multiples arise when a zygote splits during pre-implantation stages of development. The mechanisms underpinning this event have remained a mystery. Because MZ twinning rarely runs in families, the leading hypothesis is that it occurs at random. Here, we show that MZ twinning is strongly associated with a stable DNA methylation signature in adult somatic tissues. This signature spans regions near telomeres and centromeres, Polycomb-repressed regions and heterochromatin, genes involved in cell-adhesion, WNT signaling, cell fate, and putative human metastable epialleles. Our study also demonstrates a never-anticipated corollary: because identical twins keep a lifelong molecular signature, we can retrospectively diagnose if a person was conceived as monozygotic twin.
Association of birthweight and penetrance of diabetes in individuals with HNF4A-MODY: a cohort study
Jonathan M. Locke,
Petra Dusatkova,
Kevin Colclough,
Alice E. Hughes,
John M. Dennis,
Beverley Shields,
Sarah E. Flanagan
+ 6 more
Jonathan M. Locke,
Petra Dusatkova,
Kevin Colclough,
Alice E. Hughes,
John M. Dennis,
Beverley Shields,
Sarah E. Flanagan,
Maggie H. Shepherd,
Emma L. Dempster,
Andrew T. Hattersley,
Michael N. Weedon,
Stepanka Pruhova,
Kashyap A. Patel
Epigenome-wide association study of human frontal cortex identifies differential methylation in Lewy body pathology
Lasse Pihlstrøm,
Gemma Shireby,
Hanneke Geut,
Sandra Pilar Henriksen,
Annemieke J.M. Rozemüller,
Jon-Anders Tunold,
Eilis Hannon
+ 7 more
Lasse Pihlstrøm,
Gemma Shireby,
Hanneke Geut,
Sandra Pilar Henriksen,
Annemieke J.M. Rozemüller,
Jon-Anders Tunold,
Eilis Hannon,
Paul Francis,
Alan J Thomas,
Seth Love,
Netherlands Brain Bank,
Jonathan Mill,
de Berg Wilma D.J. van,
Mathias Toft
Abstract Parkinson’s disease (PD) and dementia with Lewy bodies (DLB) are closely related progressive disorders with no available causal therapy, neuropathologically characterized by intraneuronal aggregates of misfolded α-synuclein. To explore the role of DNA methylation changes in PD and DLB pathogenesis, we performed an epigenome-wide association study (EWAS) of 322 postmortem frontal cortex samples and replicated results in an independent set of 219 donors. We report novel differentially methylated replicating loci associated with Braak Lewy body stage near SFMBT2, PHYHIP, BRF1 / PACS2 and DGKG . The DGKG locus also showed evidence of DNA methylation changes in the earliest, preclinical stage of disease. Differentially methylated probes were independent of known PD genetic risk alleles. Meta-analysis provided suggestive evidence for a differentially methylated locus within the chromosomal region affected by the PD-associated 22q11.2 deletion. Our findings elucidate novel disease pathways in PD and DLB and generate hypotheses for future molecular studies of Lewy body pathology.
Sites of active gene regulation in the prenatal frontal cortex and their role in neuropsychiatric disorders
Manuela R. Kouakou, Darren Cameron, Eilis Hannon, Emma L. Dempster, Jonathan Mill, Matthew J. Hill, Nicholas J. Bray
Manuela R. Kouakou,
Darren Cameron,
Eilis Hannon,
Emma L. Dempster,
Jonathan Mill,
Matthew J. Hill,
Nicholas J. Bray
American Journal of Medical Genetics Part B Neuropsychiatric Genetics
Common genetic variation appears to largely influence risk for neuropsychiatric disorders through effects on gene regulation. It is therefore possible to shed light on the biology of these conditions by testing for enrichment of associated genetic variation within regulatory genomic regions operating in specific tissues or cell types. Here, we have used the assay for transposase-accessible chromatin with high-throughput sequencing (ATAC-Seq) to map open chromatin (an index of active regulatory genomic regions) in bulk tissue, NeuN+ and NeuN- nuclei from the prenatal human frontal cortex, and tested enrichment of single-nucleotide polymorphism (SNP) heritability for five neuropsychiatric disorders (autism spectrum disorder, attention deficit hyperactivity disorder [ADHD], bipolar disorder, major depressive disorder, and schizophrenia) within these regions. We observed significant enrichment of SNP heritability for ADHD, major depressive disorder, and schizophrenia within open chromatin regions (OCRs) mapped in bulk fetal frontal cortex, and for all five tested neuropsychiatric conditions when we restricted these sites to those overlapping histone modifications indicative of enhancers (H3K4me1) or promoters (H3K4me3) in fetal brain. SNP heritability for neuropsychiatric disorders was significantly enriched in OCRs identified in fetal frontal cortex NeuN- as well as NeuN+ nuclei overlapping fetal brain H3K4me1 or H3K4me3 sites. We additionally demonstrate the utility of our mapped OCRs for prioritizing potentially functional SNPs at genome-wide significant risk loci for neuropsychiatric disorders. Our data provide evidence for an early neurodevelopmental component to a range of neuropsychiatric conditions and highlight an important role for regulatory genomic regions active within both NeuN+ and NeuN- cells of the prenatal brain.
Full-length transcript sequencing of human and mouse cerebral cortex identifies widespread isoform diversity and alternative splicing
Szi Kay Leung,
Aaron R. Jeffries,
Isabel Castanho,
Ben T. Jordan,
Karen Moore,
Jonathan P. Davies,
Emma L. Dempster
+ 13 more
Szi Kay Leung,
Aaron R. Jeffries,
Isabel Castanho,
Ben T. Jordan,
Karen Moore,
Jonathan P. Davies,
Emma L. Dempster,
Nicholas J. Bray,
Paul O’Neill,
Elizabeth Tseng,
Zeshan Ahmed,
David A. Collier,
Erin D. Jeffery,
Shyam Prabhakar,
Leonard Schalkwyk,
Connor Jops,
Michael J. Gandal,
Gloria M. Sheynkman,
Eilis Hannon,
Jonathan Mill
Alternative splicing is a post-transcriptional regulatory mechanism producing distinct mRNA molecules from a single pre-mRNA with a prominent role in the development and function of the central nervous system. We used long-read isoform sequencing to generate full-length transcript sequences in the human and mouse cortex. We identify novel transcripts not present in existing genome annotations, including transcripts mapping to putative novel (unannotated) genes and fusion transcripts incorporating exons from multiple genes. Global patterns of transcript diversity are similar between human and mouse cortex, although certain genes are characterized by striking differences between species. We also identify developmental changes in alternative splicing, with differential transcript usage between human fetal and adult cortex. Our data confirm the importance of alternative splicing in the cortex, dramatically increasing transcriptional diversity and representing an important mechanism underpinning gene regulation in the brain. We provide transcript-level data for human and mouse cortex as a resource to the scientific community.
Common and rare variant association analyses in amyotrophic lateral sclerosis identify 15 risk loci with distinct genetic architectures and neuron-specific biology
Wouter van Rheenen,
Rick A. A. van der Spek,
Mark K. Bakker,
Joke J. F. A. van Vugt,
Paul J. Hop,
Ramona A. J. Zwamborn,
Niek de Klein
+ 185 more
Wouter van Rheenen,
Rick A. A. van der Spek,
Mark K. Bakker,
Joke J. F. A. van Vugt,
Paul J. Hop,
Ramona A. J. Zwamborn,
Niek de Klein,
Harm-Jan Westra,
Olivier B. Bakker,
Patrick Deelen,
Gemma Shireby,
Eilis Hannon,
Matthieu Moisse,
Denis Baird,
Restuadi Restuadi,
Egor Dolzhenko,
Annelot M. Dekker,
Klara Gawor,
Henk-Jan Westeneng,
Gijs H. P. Tazelaar,
Kristel R. van Eijk,
Maarten Kooyman,
Ross P. Byrne,
Mark Doherty,
Mark Heverin,
Ahmad Al Khleifat,
Alfredo Iacoangeli,
Aleksey Shatunov,
Nicola Ticozzi,
Johnathan Cooper-Knock,
Bradley N. Smith,
Marta Gromicho,
Siddharthan Chandran,
Suvankar Pal,
Karen E. Morrison,
Pamela J. Shaw,
John Hardy,
Richard W. Orrell,
Michael Sendtner,
Thomas Meyer,
Nazli Başak,
Anneke J. van der Kooi,
Antonia Ratti,
Isabella Fogh,
Cinzia Gellera,
Giuseppe Lauria,
Stefania Corti,
Cristina Cereda,
Daisy Sproviero,
Sandra D’Alfonso,
Gianni Sorarù,
Gabriele Siciliano,
Massimiliano Filosto,
Alessandro Padovani,
Adriano Chiò,
Andrea Calvo,
Cristina Moglia,
Maura Brunetti,
Antonio Canosa,
Maurizio Grassano,
Ettore Beghi,
Elisabetta Pupillo,
Giancarlo Logroscino,
Beatrice Nefussy,
Alma Osmanovic,
Angelica Nordin,
Yossef Lerner,
Michal Zabari,
Marc Gotkine,
Robert H. Baloh,
Shaughn Bell,
Patrick Vourc’h,
Philippe Corcia,
Philippe Couratier,
Stéphanie Millecamps,
Vincent Meininger,
François Salachas,
Jesus S. Mora Pardina,
Abdelilah Assialioui,
Ricardo Rojas-García,
Patrick A. Dion,
Jay P. Ross,
Albert C. Ludolph,
Jochen H. Weishaupt,
David Brenner,
Axel Freischmidt,
Gilbert Bensimon,
Alexis Brice,
Alexandra Durr,
Christine A. M. Payan,
Safa Saker-Delye,
Nicholas W. Wood,
Simon Topp,
Rosa Rademakers,
Lukas Tittmann,
Wolfgang Lieb,
Andre Franke,
Stephan Ripke,
Alice Braun,
Julia Kraft,
David C. Whiteman,
Catherine M. Olsen,
Andre G. Uitterlinden,
Albert Hofman,
Marcella Rietschel,
Sven Cichon,
Markus M. Nöthen,
Philippe Amouyel,
Bryan J. Traynor,
Andrew B. Singleton,
Miguel Mitne Neto,
Ruben J. Cauchi,
Roel A. Ophoff,
Martina Wiedau-Pazos,
Catherine Lomen-Hoerth,
Vivianna M. van Deerlin,
Julian Grosskreutz,
Annekathrin Roediger,
Nayana Gaur,
Alexander Jörk,
Tabea Barthel,
Erik Theele,
Benjamin Ilse,
Beatrice Stubendorff,
Otto W. Witte,
Robert Steinbach,
Christian A. Hübner,
Caroline Graff,
Lev Brylev,
Vera Fominykh,
Vera Demeshonok,
Anastasia Ataulina,
Boris Rogelj,
Blaž Koritnik,
Janez Zidar,
Metka Ravnik-Glavač,
Damjan Glavač,
Zorica Stević,
Vivian Drory,
Monica Povedano,
Ian P. Blair,
Matthew C. Kiernan,
Beben Benyamin,
Robert D. Henderson,
Sarah Furlong,
Susan Mathers,
Pamela A. McCombe,
Merrilee Needham,
Shyuan T. Ngo,
Garth A. Nicholson,
Roger Pamphlett,
Dominic B. Rowe,
Frederik J. Steyn,
Kelly L. Williams,
Karen A. Mather,
Perminder S. Sachdev,
Anjali K. Henders,
Leanne Wallace,
Mamede de Carvalho,
Susana Pinto,
Susanne Petri,
Markus Weber,
Guy A. Rouleau,
Vincenzo Silani,
Charles J. Curtis,
Gerome Breen,
Jonathan D. Glass,
Robert H. Brown,
John E. Landers,
Christopher E. Shaw,
Peter M. Andersen,
Ewout J. N. Groen,
Michael A. van Es,
R. Jeroen Pasterkamp,
Dongsheng Fan,
Fleur C. Garton,
Allan F. McRae,
George Davey Smith,
Tom R. Gaunt,
Michael A. Eberle,
Jonathan Mill,
Russell L. McLaughlin,
Orla Hardiman,
Kevin P. Kenna,
Naomi R. Wray,
Ellen Tsai,
Heiko Runz,
Lude Franke,
Ammar Al-Chalabi,
Philip Van Damme,
Leonard H. van den Berg,
Jan H. Veldink
Amyotrophic lateral sclerosis (ALS) is a fatal neurodegenerative disease with a lifetime risk of one in 350 people and an unmet need for disease-modifying therapies. We conducted a cross-ancestry genome-wide association study (GWAS) including 29,612 patients with ALS and 122,656 controls, which identified 15 risk loci. When combined with 8,953 individuals with whole-genome sequencing (6,538 patients, 2,415 controls) and a large cortex-derived expression quantitative trait locus (eQTL) dataset (MetaBrain), analyses revealed locus-specific genetic architectures in which we prioritized genes either through rare variants, short tandem repeats or regulatory effects. ALS-associated risk loci were shared with multiple traits within the neurodegenerative spectrum but with distinct enrichment patterns across brain regions and cell types. Of the environmental and lifestyle risk factors obtained from the literature, Mendelian randomization analyses indicated a causal role for high cholesterol levels. The combination of all ALS-associated signals reveals a role for perturbations in vesicle-mediated transport and autophagy and provides evidence for cell-autonomous disease initiation in glutamatergic neurons.
Investigating epigenetic loci implicated in Alzheimer’s disease via the CRISPR‐Cas9 system
Michael Schrauben, Adam R. Smith, Sam Washer, Emma Dempster, Katie Lunnon
Michael Schrauben,
Adam R. Smith,
Sam Washer,
Emma Dempster,
Katie Lunnon
Abstract Background Differentially methylated positions (DMPs) identified by Epigenome‐wide association studies (EWAS) of Alzheimer’s disease (AD) were modified by the CRISPR‐Cas9 system to investigate the role of epigenetic alterations in AD pathogenesis. Method Cell lines of neuronal phenotype (SH‐SY5Y) and microglial phenotype (IHM‐SV40) were used to explore the functional consequence of loci demethylation, where removal of the methyl groups was achieved by the modified CRISPR‐dCas9 system. Lentiviral delivery of the dCas9‐TET1CD demethylase tool and guide RNA (gRNA) constructs targeting the CpG sites associated with differential expression of ANK1 and BIN1 in AD was validated by fluorescence‐activated cell sorting (FACS). Bisulphite pyrosequencing was applied to confirm the DNA methylation edit. Result High transduction efficiencies were observed during FACS of SH‐SY5Y cells transduced with CRISPR‐dCas9 constructs targeting the BIN1 locus and IHM‐SV40 cells with constructs against the ANK1 locus. Methylation analysis of these target regions in the modified cell lines demonstrated a reduction in methylation when compared to the untreated control cells. This modification was maintained over a three‐week period. Conclusion Delivery and activity of our CRISPR‐dCas9 fusion constructs was demonstrated in cell line models of AD. In the future, we intend to profile the epigenome and transcriptome of these modified cell lines to identify any off‐target effects of the CRISPR‐dCas9 system and determine differences in mRNA transcript variant levels of our target genes.
DunedinPACE, a DNA methylation biomarker of the pace of aging
Daniel W Belsky,
Avshalom Caspi,
David L Corcoran,
Karen Sugden,
Richie Poulton,
Louise Arseneault,
Andrea Baccarelli
+ 13 more
Daniel W Belsky,
Avshalom Caspi,
David L Corcoran,
Karen Sugden,
Richie Poulton,
Louise Arseneault,
Andrea Baccarelli,
Kartik Chamarti,
Xu Gao,
Eilis Hannon,
Hona Lee Harrington,
Renate Houts,
Meeraj Kothari,
Dayoon Kwon,
Jonathan Mill,
Joel Schwartz,
Pantel Vokonas,
Cuicui Wang,
Benjamin S Williams,
Terrie E Moffitt
Background: Measures to quantify changes in the pace of biological aging in response to intervention are needed to evaluate geroprotective interventions for humans. Previously, we showed that quantification of the pace of biological aging from a DNA-methylation blood test was possible (Belsky et al., 2020). Here, we report a next-generation DNA-methylation biomarker of Pace of Aging, DunedinPACE (for Pace of Aging Calculated from the Epigenome).
Methods: We used data from the Dunedin Study 1972-1973 birth cohort tracking within-individual decline in 19 indicators of organ-system integrity across four time points spanning two decades to model Pace of Aging. We distilled this two-decade Pace of Aging into a single-time-point DNA-methylation blood-test using elastic-net regression and a DNA-methylation dataset restricted to exclude probes with low test-retest reliability. We evaluated the resulting measure, named DunedinPACE, in five additional datasets.
Results: DunedinPACE showed high test-retest reliability, was associated with morbidity, disability, and mortality, and indicated faster aging in young adults with childhood adversity. DunedinPACE effect-sizes were similar to GrimAge Clock effect-sizes. In analysis of incident morbidity, disability, and mortality, DunedinPACE and added incremental prediction beyond GrimAge.
Conclusions: DunedinPACE is a novel blood biomarker of the pace of aging for gerontology and geroscience.
Funding: This research was supported by US-National Institute on Aging grants AG032282, AG061378, AG066887, and UK Medical Research Council grant MR/P005918/1.
Author Correction: Common and rare variant association analyses in amyotrophic lateral sclerosis identify 15 risk loci with distinct genetic architectures and neuron-specific biology
Wouter van Rheenen,
Rick A. A. van der Spek,
Mark K. Bakker,
Joke J. F. A. van Vugt,
Paul J. Hop,
Ramona A. J. Zwamborn,
Niek de Klein
+ 185 more
Wouter van Rheenen,
Rick A. A. van der Spek,
Mark K. Bakker,
Joke J. F. A. van Vugt,
Paul J. Hop,
Ramona A. J. Zwamborn,
Niek de Klein,
Harm-Jan Westra,
Olivier B. Bakker,
Patrick Deelen,
Gemma Shireby,
Eilis Hannon,
Matthieu Moisse,
Denis Baird,
Restuadi Restuadi,
Egor Dolzhenko,
Annelot M. Dekker,
Klara Gawor,
Henk-Jan Westeneng,
Gijs H. P. Tazelaar,
Kristel R. van Eijk,
Maarten Kooyman,
Ross P. Byrne,
Mark Doherty,
Mark Heverin,
Ahmad Al Khleifat,
Alfredo Iacoangeli,
Aleksey Shatunov,
Nicola Ticozzi,
Johnathan Cooper-Knock,
Bradley N. Smith,
Marta Gromicho,
Siddharthan Chandran,
Suvankar Pal,
Karen E. Morrison,
Pamela J. Shaw,
John Hardy,
Richard W. Orrell,
Michael Sendtner,
Thomas Meyer,
Nazli Başak,
Anneke J. van der Kooi,
Antonia Ratti,
Isabella Fogh,
Cinzia Gellera,
Giuseppe Lauria,
Stefania Corti,
Cristina Cereda,
Daisy Sproviero,
Sandra D’Alfonso,
Gianni Sorarù,
Gabriele Siciliano,
Massimiliano Filosto,
Alessandro Padovani,
Adriano Chiò,
Andrea Calvo,
Cristina Moglia,
Maura Brunetti,
Antonio Canosa,
Maurizio Grassano,
Ettore Beghi,
Elisabetta Pupillo,
Giancarlo Logroscino,
Beatrice Nefussy,
Alma Osmanovic,
Angelica Nordin,
Yossef Lerner,
Michal Zabari,
Marc Gotkine,
Robert H. Baloh,
Shaughn Bell,
Patrick Vourc’h,
Philippe Corcia,
Philippe Couratier,
Stéphanie Millecamps,
Vincent Meininger,
François Salachas,
Jesus S. Mora Pardina,
Abdelilah Assialioui,
Ricardo Rojas-García,
Patrick A. Dion,
Jay P. Ross,
Albert C. Ludolph,
Jochen H. Weishaupt,
David Brenner,
Axel Freischmidt,
Gilbert Bensimon,
Alexis Brice,
Alexandra Durr,
Christine A. M. Payan,
Safa Saker-Delye,
Nicholas W. Wood,
Simon Topp,
Rosa Rademakers,
Lukas Tittmann,
Wolfgang Lieb,
Andre Franke,
Stephan Ripke,
Alice Braun,
Julia Kraft,
David C. Whiteman,
Catherine M. Olsen,
Andre G. Uitterlinden,
Albert Hofman,
Marcella Rietschel,
Sven Cichon,
Markus M. Nöthen,
Philippe Amouyel,
Bryan J. Traynor,
Andrew B. Singleton,
Miguel Mitne Neto,
Ruben J. Cauchi,
Roel A. Ophoff,
Martina Wiedau-Pazos,
Catherine Lomen-Hoerth,
Vivianna M. van Deerlin,
Julian Grosskreutz,
Annekathrin Roediger,
Nayana Gaur,
Alexander Jörk,
Tabea Barthel,
Erik Theele,
Benjamin Ilse,
Beatrice Stubendorff,
Otto W. Witte,
Robert Steinbach,
Christian A. Hübner,
Caroline Graff,
Lev Brylev,
Vera Fominykh,
Vera Demeshonok,
Anastasia Ataulina,
Boris Rogelj,
Blaž Koritnik,
Janez Zidar,
Metka Ravnik-Glavač,
Damjan Glavač,
Zorica Stević,
Vivian Drory,
Monica Povedano,
Ian P. Blair,
Matthew C. Kiernan,
Beben Benyamin,
Robert D. Henderson,
Sarah Furlong,
Susan Mathers,
Pamela A. McCombe,
Merrilee Needham,
Shyuan T. Ngo,
Garth A. Nicholson,
Roger Pamphlett,
Dominic B. Rowe,
Frederik J. Steyn,
Kelly L. Williams,
Karen A. Mather,
Perminder S. Sachdev,
Anjali K. Henders,
Leanne Wallace,
Mamede de Carvalho,
Susana Pinto,
Susanne Petri,
Markus Weber,
Guy A. Rouleau,
Vincenzo Silani,
Charles J. Curtis,
Gerome Breen,
Jonathan D. Glass,
Robert H. Brown,
John E. Landers,
Christopher E. Shaw,
Peter M. Andersen,
Ewout J. N. Groen,
Michael A. van Es,
R. Jeroen Pasterkamp,
Dongsheng Fan,
Fleur C. Garton,
Allan F. McRae,
George Davey Smith,
Tom R. Gaunt,
Michael A. Eberle,
Jonathan Mill,
Russell L. McLaughlin,
Orla Hardiman,
Kevin P. Kenna,
Naomi R. Wray,
Ellen Tsai,
Heiko Runz,
Lude Franke,
Ammar Al-Chalabi,
Philip Van Damme,
Leonard H. van den Berg,
Jan H. Veldink
In the current study we have performed an Epigenome‐Wide Association Study (EWAS) comparing bulk brain tissue in individuals with AD and non‐demented controls with or without a systemic infection, followed by targeted validation in isolated microglia. DNA methylation is being quantified from 300 post‐mortem brain samples, 75 AD cases with infection, 75 AD cases without an infection, 75 non‐demented controls with infection and 75 non‐demented controls without an infection. DNA methylation of isolated microglia is also being quantified and gene expression data collected from the same samples to allow integration of epigenetic and transcriptomic data. Statistical analyses performed using our established EWAS pipeline will identify significant differentially methylated positions. This is particularly expected to be observable in regions across genes implicated in disease pathology. Through cross‐examination of the four study groups we will identify novel patterns of methylation in those suffering from neuroinflammation not previously observed, also providing critical insight into the underlying molecular changes that arise in microglia as a result of neuroinflammation.
Investigating epigenetic loci implicated in Alzheimer’s disease via the CRISPR‐Cas9 system
Michael Schrauben, Sam Washer, Adam R. Smith, Emma Dempster, Katie Lunnon
Michael Schrauben,
Sam Washer,
Adam R. Smith,
Emma Dempster,
Katie Lunnon
Differentially methylated positions (DMPs) identified by Epigenome‐wide association studies (EWAS) of Alzheimer’s disease (AD) were modified by the CRISPR‐Cas9 system to investigate the role of epigenetic alterations in AD pathogenesis. Cell lines of neuronal phenotype (SH‐SY5Y) and microglial phenotype (IHM‐SV40) were used to explore the functional consequence of loci demethylation, where removal of the methyl groups was achieved by the modified CRISPR‐dCas9 system. Lentiviral delivery of the dCas9‐TET1CD demethylase tool and guide RNA (gRNA) constructs targeting the CpG sites associated with differential expression of ANK1 and BIN1 in AD was validated by fluorescence activated cell sorting (FACS). Bisulphite pyrosequencing was applied to confirm the DNA methylation edit and RT‐qPCR was performed to assess changes in mRNA expression. High transduction efficiencies were observed during FACS of SH‐SY5Y cells transduced with CRISPR‐dCas9 constructs targeting the BIN1 locus and IHM‐SV40 cells with constructs against the ANK1 locus. Methylation analysis of these target regions in the modified cell lines demonstrated a reduction in methylation when compared to the untreated control cells. Full‐length transcript expression levels of ANK1 and BIN1 showed no significant differences between experimental conditions. Delivery and activity of our CRISPR‐dCas9 fusion constructs was demonstrated in cell line models of AD.
A role for epigenetic mechanisms in Lewy body dementias
Jennifer L Imm,
Joshua Harvey,
Ehsan Pishva,
Byron Creese,
Leonidas Chouliaras,
Emma Dempster,
Clive Ballard
+ 4 more
Jennifer L Imm,
Joshua Harvey,
Ehsan Pishva,
Byron Creese,
Leonidas Chouliaras,
Emma Dempster,
Clive Ballard,
John T O'Brien,
Dag Aarsland,
Jonathan Mill,
Katie Lunnon
The Lewy body diseases, Dementia with Lewy bodies (DLB), Parkinson’s disease (PD) and Parkinson’s disease dementia (PDD) are all neurodegenerative diseases classified by the accumulation of alpha‐synuclein in neurons, forming Lewy bodies (LB). We hypothesise that these LBs cause epigenetic changes within neurons and surrounding cells and that these changes can be used to distinguish the different LB diseases from one another. Bulk tissue from the cingulate gyrus and prefrontal cortex will be as analysed for DNA methylation levels using the Illumina Infinium Methylation EPIC array to generate quantitative methylation data for over 850,000 CpG sites across the genome (n=∼100/disease group). Linear regression and pathway analyses will be used to identify loci that are significantly different or specific to each disease. Following this we will validate loci and determine their cellular specificity using a subset of samples (15 DLB, 15 PDD, 15 PD only, 15 controls) using fluorescence activated cell sorting (FACS). In each sample we will isolate various different cellular populations, including neurons, microglia, oligodendrocytes and astrocytes before profiling these using the EPIC array. Study groups have been sourced consisting of cases with PD, PDD and DLB based on LB deposition and clinical symptom staging. Control cases have been selected for matched age and levels of concomitant AD pathology. Cases for FACS (n=15/group) have been selected to allow where possible a high base RIN, pH and minimal post‐mortem interval. We are collating a well powered study cohort to interrogate the epigenetic basis of neuropathological progression and clinical staging of LB disease, controlling for levels of concomitant AD pathology. Follow up FACS sorting and analysis will allow for the cell specific methylation changes occurring in each of the LB diseases.
Targeted bisulfite sequencing analysis of candidate genes associated with Alzheimer’s disease
Greg Wheildon, Adam R. Smith, Rebecca G. Smith, Katie Lunnon
Greg Wheildon,
Adam R. Smith,
Rebecca G. Smith,
Katie Lunnon
The histopathological changes in Alzheimer’s disease (AD), including extensive deposits of amyloid β plaques and neurofibrillary tangles occur many years before the onset of clinical symptoms and epigenetic processes such as DNA methylation may contribute to this delay. Recent epigenome‐wide association studies (EWAS) have identified a number of loci in specific genes that show robust and reproducible alterations in DNA methylation changes in AD brain samples. However, the technologies used for these studies only assess a limited number of methylation sites in each gene and further analysis of methylation changes across the entire gene are required to determine the exact extent and pattern of methylation changes in disease. In this study we have performed targeted bisulfite sequencing and RNA sequencing in the Brains for Dementia Research (BDR) tissue sample resource, which is a highly characterised cohort containing tissue with a high degree of standardised pathological, clinical and administrative data available to allow comparative studies. Prefrontal cortex brain samples from 96 individuals were selected from the BDR cohort and grouped by Braak stage (Control 0‐II; mild cognitive impairment III‐IV; AD V‐VI). DNA and RNA was simultaneously extracted before next generation RNA‐seq was performed on all 96 samples to analyse the AD transcriptome and data extracted for 30 genomic regions of interest identified from previous EWAS. Concurrently for the DNA, Agilent Sure Select target baits captured the same 30 target genomic regions that were bisulfite sequenced for a subset of 60 samples, allowing analysis of differentially methylated positions (DMPs). The exact location of DMPs within the targeted genomic regions were identified and compared between each group. Similarly, differential expression of mRNA transcripts encoded by these genes were also identified and related to methylation levels. This study builds on previous work that identified differential methylation in several genomic regions that were associated with Braak stage. By identifying the exact positions that are subjected to differential methylation and the potential impact these changes have on gene expression this work provides further evidence that dysregulation of methylation is associated with pathological changes in AD prefrontal cortex.
Machine learning-based prediction of cognitive outcomes in de novo Parkinson's disease
Joshua Harvey,
Rick A Reijnders,
Rachel Cavill,
Annelien Duits,
Sebastian Köhler,
Lars Eijssen,
Bart PF Rutten
+ 6 more
Joshua Harvey,
Rick A Reijnders,
Rachel Cavill,
Annelien Duits,
Sebastian Köhler,
Lars Eijssen,
Bart PF Rutten,
Gemma Shireby,
Ali Torkamani,
Byron Creese,
Albert FG Leentjens,
Katie Lunnon,
Ehsan Pishva
Cognitive impairment is a debilitating symptom in Parkinson’s disease (PD). We aimed to establish an accurate multivariate machine learning (ML) model to predict cognitive outcome in newly diagnosed PD cases from the Parkinson’s Progression Markers Initiative (PPMI). Annual cognitive assessments over an eight-year time span were used to define two cognitive outcomes of i) cognitive impairment, and ii) dementia conversion. Selected baseline variables were organized into three subsets of clinical, biofluid and genetic/epigenetic measures and tested using four different ML algorithms. Irrespective of the ML algorithm used, the models consisting of the clinical variables performed best and showed better prediction of cognitive impairment outcome over dementia conversion. We observed a marginal improvement in the prediction performance when clinical, biofluid, and epigenetic/genetic variables were all included in one model. Several cerebrospinal fluid measures and an epigenetic marker showed high predictive weighting in multiple models when included alongside clinical variables.
Machine learning-based prediction of cognitive outcomes in de novo Parkinson’s disease
Joshua Harvey,
Rick A Reijnders,
Rachel Cavill,
Annelien Duits,
Sebastian Köhler,
Lars Eijssen,
Bart PF Rutten
+ 6 more
Joshua Harvey,
Rick A Reijnders,
Rachel Cavill,
Annelien Duits,
Sebastian Köhler,
Lars Eijssen,
Bart PF Rutten,
Gemma Shireby,
Ali Torkamani,
Byron Creese,
Albert FG Leentjens,
Katie Lunnon,
Ehsan Pishva
Abstract Cognitive impairment is a debilitating symptom in Parkinson’s disease (PD). We aimed to establish an accurate multivariate machine learning (ML) model to predict cognitive outcome in newly diagnosed PD cases from the Parkinson’s Progression Markers Initiative (PPMI). Annual cognitive assessments over an eight-year time span were used to define two cognitive outcomes of i) cognitive impairment, and ii) dementia conversion. Selected baseline variables were organized into three subsets of clinical, biofluid and genetic/epigenetic measures and tested using four different ML algorithms. Irrespective of the ML algorithm used, the models consisting of the clinical variables performed best and showed better prediction of cognitive impairment outcome over dementia conversion. We observed a marginal improvement in the prediction performance when clinical, biofluid, and epigenetic/genetic variables were all included in one model. Several cerebrospinal fluid measures and an epigenetic marker showed high predictive weighting in multiple models when included alongside clinical variables.
Can epigenetics shine a light on the biological pathways underlying major mental disorders?
Luis Alameda,
Giulia Trotta,
Harriet Quigley,
Victoria Rodriguez,
Romayne Gadelrab,
Daniella Dwir,
Emma Dempster
+ 2 more
Luis Alameda,
Giulia Trotta,
Harriet Quigley,
Victoria Rodriguez,
Romayne Gadelrab,
Daniella Dwir,
Emma Dempster,
Chloe C. Y. Wong,
Forti Marta Di
A significant proportion of the global burden of disease can be attributed to mental illness. Despite important advances in identifying risk factors for mental health conditions, the biological processing underlying causal pathways to disease onset remain poorly understood. This represents a limitation to implement effective prevention and the development of novel pharmacological treatments. Epigenetic mechanisms have emerged as mediators of environmental and genetic risk factors which might play a role in disease onset, including childhood adversity (CA) and cannabis use (CU). Particularly, human research exploring DNA methylation has provided new and promising insights into the role of biological pathways implicated in the aetio-pathogenesis of psychiatric conditions, including: monoaminergic (Serotonin and Dopamine), GABAergic, glutamatergic, neurogenesis, inflammatory and immune response and oxidative stress. While these epigenetic changes have been often studied as disease-specific, similarly to the investigation of environmental risk factors, they are often transdiagnostic. Therefore, we aim to review the existing literature on DNA methylation from human studies of psychiatric diseases (i) to identify epigenetic modifications mapping onto biological pathways either transdiagnostically or specifically related to psychiatric diseases such as Eating Disorders, Post-traumatic Stress Disorder, Bipolar and Psychotic Disorder, Depression, Autism Spectrum Disorder and Anxiety Disorder, and (ii) to investigate a convergence between some of these epigenetic modifications and the exposure to known risk factors for psychiatric disorders such as CA and CU, as well as to other epigenetic confounders in psychiatry research.
Genome-wide study of DNA methylation shows alterations in metabolic, inflammatory, and cholesterol pathways in ALS
Paul J. Hop,
Ramona A.J. Zwamborn,
Eilis Hannon,
Gemma L. Shireby,
Marta F. Nabais,
Emma M. Walker,
Wouter van Rheenen
+ 147 more
Paul J. Hop,
Ramona A.J. Zwamborn,
Eilis Hannon,
Gemma L. Shireby,
Marta F. Nabais,
Emma M. Walker,
Wouter van Rheenen,
Joke J.F.A. van Vugt,
Annelot M. Dekker,
Henk-Jan Westeneng,
Gijs H.P. Tazelaar,
Kristel R. van Eijk,
Matthieu Moisse,
Denis Baird,
Ahmad Al Khleifat,
Alfredo Iacoangeli,
Nicola Ticozzi,
Antonia Ratti,
Jonathan Cooper-Knock,
Karen E. Morrison,
Pamela J. Shaw,
A. Nazli Basak,
Adriano Chiò,
Andrea Calvo,
Cristina Moglia,
Antonio Canosa,
Maura Brunetti,
Maurizio Grassano,
Marc Gotkine,
Yossef Lerner,
Michal Zabari,
Patrick Vourc’h,
Philippe Corcia,
Philippe Couratier,
Jesus S. Mora Pardina,
Teresa Salas,
Patrick Dion,
Jay P. Ross,
Robert D. Henderson,
Susan Mathers,
Pamela A. McCombe,
Merrilee Needham,
Garth Nicholson,
Dominic B. Rowe,
Roger Pamphlett,
Karen A. Mather,
Perminder S. Sachdev,
Sarah Furlong,
Fleur C. Garton,
Anjali K. Henders,
Tian Lin,
Shyuan T. Ngo,
Frederik J. Steyn,
Leanne Wallace,
Kelly L. Williams,
Miguel Mitne Neto,
Ruben J. Cauchi,
Ian P. Blair,
Matthew C. Kiernan,
Vivian Drory,
Monica Povedano,
Mamede de Carvalho,
Susana Pinto,
Markus Weber,
Guy A. Rouleau,
Vincenzo Silani,
John E. Landers,
Christopher E. Shaw,
Peter M. Andersen,
Allan F. McRae,
Michael A. van Es,
R. Jeroen Pasterkamp,
Naomi R. Wray,
Russell L. McLaughlin,
Orla Hardiman,
Kevin P. Kenna,
Ellen Tsai,
Heiko Runz,
Ammar Al-Chalabi,
Leonard H. van den Berg,
Philip Van Damme,
Jonathan Mill,
Jan H. Veldink,
Bastiaan T. Heijmans,
Peter A.C. t Hoen,
Joyce van Meurs,
Rick Jansen,
Lude Franke,
Dorret I. Boomsma,
Rene Pool,
Jenny van Dongen,
Joukje J. Hottenga,
Marleen M.J. van Greevenbroek,
Coen D.A. Stehouwer,
Carla J.H. van der Kallen,
Casper G. Schalkwijk,
Cisca Wijmenga,
Lude Franke,
Sasha Zhernakova,
Ettje F. Tigchelaar,
P. Eline Slagboom,
Marian Beekman,
Joris Deelen,
Diana van Heemst,
Jan H. Veldink,
Leonard H. van den Berg,
Cornelia M. van Duijn,
Bert A. Hofman,
Aaron Isaacs,
Andre G. Uitterlinden,
Joyce van Meurs,
P. Mila Jhamai,
Michael Verbiest,
H. Eka D. Suchiman,
Marijn Verkerk,
Ruud van der Breggen,
Jeroen van Rooij,
Nico Lakenberg,
Hailiang Mei,
Maarten van Iterson,
Michiel van Galen,
Jan Bot,
Dasha V. Zhernakova,
Rick Jansen,
Peter van ‘t Hof,
Patrick Deelen,
Irene Nooren,
Peter A.C. t Hoen,
Bastiaan T. Heijmans,
Matthijs Moed,
Lude Franke,
Martijn Vermaat,
Dasha V. Zhernakova,
Rene Luijk,
Marc Jan Bonder,
Maarten van Iterson,
Patrick Deelen,
Freerk van Dijk,
Michiel van Galen,
Wibowo Arindrarto,
Szymon M. Kielbasa,
Morris A. Swertz,
Erik W. van Zwet,
Rick Jansen,
Peter A.C. t Hoen,
Bastiaan T. Heijmans,
Ammar Al-Chalabi,
Naomi R. Wray,
Gilbert Bensimon,
Orla Hardiman,
Adriano Chio,
Jan H. Veldink,
George Davey Smith,
Jonathan Mill
Amyotrophic lateral sclerosis (ALS) is a fatal neurodegenerative disease with an estimated heritability between 40 and 50%. DNA methylation patterns can serve as proxies of (past) exposures and disease progression, as well as providing a potential mechanism that mediates genetic or environmental risk. Here, we present a blood-based epigenome-wide association study meta-analysis in 9706 samples passing stringent quality control (6763 patients, 2943 controls). We identified a total of 45 differentially methylated positions (DMPs) annotated to 42 genes, which are enriched for pathways and traits related to metabolism, cholesterol biosynthesis, and immunity. We then tested 39 DNA methylation-based proxies of putative ALS risk factors and found that high-density lipoprotein cholesterol, body mass index, white blood cell proportions, and alcohol intake were independently associated with ALS. Integration of these results with our latest genome-wide association study showed that cholesterol biosynthesis was potentially causally related to ALS. Last, DNA methylation at several DMPs and blood cell proportion estimates derived from DNA methylation data were associated with survival rate in patients, suggesting that they might represent indicators of underlying disease processes potentially amenable to therapeutic interventions.
Evaluation of nanopore sequencing for epigenetic epidemiology: a comparison with DNA methylation microarrays
Robert Flynn,
Sam Washer,
Aaron R Jeffries,
Alexandria Andrayas,
Gemma Shireby,
Meena Kumari,
Leonard C Schalkwyk
+ 2 more
Robert Flynn,
Sam Washer,
Aaron R Jeffries,
Alexandria Andrayas,
Gemma Shireby,
Meena Kumari,
Leonard C Schalkwyk,
Jonathan Mill,
Eilis Hannon
Abstract
Most epigenetic epidemiology to date has utilized microarrays to identify positions in the genome where variation in DNA methylation is associated with environmental exposures or disease. However, these profile less than 3% of DNA methylation sites in the human genome, potentially missing affected loci and preventing the discovery of disrupted biological pathways. Third generation sequencing technologies, including Nanopore sequencing, have the potential to revolutionise the generation of epigenetic data, not only by providing genuine genome-wide coverage but profiling epigenetic modifications direct from native DNA. Here we assess the viability of using Nanopore sequencing for epidemiology by performing a comparison with DNA methylation quantified using the most comprehensive microarray available, the Illumina EPIC array. We implemented a CRISPR-Cas9 targeted sequencing approach in concert with Nanopore sequencing to profile DNA methylation in three genomic regions to attempt to rediscover genomic positions that existing technologies have shown are differentially methylated in tobacco smokers. Using Nanopore sequencing reads, DNA methylation was quantified at 1,779 CpGs across three regions, providing a finer resolution of DNA methylation patterns compared to the EPIC array. The correlation of estimated levels of DNA methylation between platforms was high. Furthermore, we identified 12 CpGs where hypomethylation was significantly associated with smoking status, including 10 within the AHRR gene. In summary, Nanopore sequencing is a valid option for identifying genomic loci where large differences in DNAm are associated with a phenotype and has the potential to advance our understanding of the role differential methylation plays in the aetiology of complex disease.
DNA methylation signatures of Alzheimer’s disease neuropathology in the cortex are primarily driven by variation in non-neuronal cell-types
Gemma Shireby,
Emma Dempster,
Stefania Policicchio,
Rebecca G Smith,
Ehsan Pishva,
Barry Chioza,
Jonathan P Davies
+ 10 more
Gemma Shireby,
Emma Dempster,
Stefania Policicchio,
Rebecca G Smith,
Ehsan Pishva,
Barry Chioza,
Jonathan P Davies,
Joe Burrage,
Katie Lunnon,
Dorothea Seiler-Vellame,
Seth Love,
Alan Thomas,
Keeley Brookes,
Kevin Morgan,
Paul Francis,
Eilis Hannon,
Jonathan Mill
ABSTRACT
Alzheimer’s disease (AD) is a chronic neurodegenerative disease characterized by the progressive accumulation of amyloid-beta and neurofibrillary tangles of tau in the neocortex. Utilizing extensive neuropathology data from the Brains for Dementia Research (BDR) cohort we performed the most systematic epigenome-wide association study (EWAS) of multiple measures of AD neuropathology yet undertaken, profiling DNA methylation in two cortical regions from 631 donors. We meta-analyzed our results with those from previous studies of DNA methylation in AD cortex (total n = 2,013 donors), identifying 334 cortical differentially methylated positions (DMPs) associated with AD pathology including methylomic variation at novel loci not previously implicated in dementia. We subsequently characterized DNA methylation in purified nuclei populations - enriched for neurons, oligodendrocytes and microglia - exploring the extent to which cortex AD-associated DMPs reflect differences manifest in specific cell populations. We find that the majority of DMPs identified in ‘bulk’ cortex tissue actually reflect DNA methylation differences occurring in non-neuronal cells, with dramatically increased effect sizes observed in microglia-enriched nuclei populations. Our study highlights the power of utilizing multiple measures of neuropathology to identify epigenetic signatures of AD and the importance of characterizing disease-associated variation in purified neural cell-types.
A comparison of blood and brain‐derived ageing and inflammation‐related DNA methylation signatures and their association with microglial burdens
Anna J. Stevenson,
Daniel L. McCartney,
Danni A. Gadd,
Gemma Shireby,
Robert F. Hillary,
Declan King,
Makis Tzioras
+ 15 more
Anna J. Stevenson,
Daniel L. McCartney,
Danni A. Gadd,
Gemma Shireby,
Robert F. Hillary,
Declan King,
Makis Tzioras,
Nicola Wrobel,
Sarah McCafferty,
Lee Murphy,
Barry W. McColl,
Paul Redmond,
Adele M. Taylor,
Sarah E. Harris,
Tom C. Russ,
Andrew M. McIntosh,
Jonathan Mill,
Colin Smith,
Ian J. Deary,
Simon R. Cox,
Riccardo E. Marioni,
Tara L. Spires‐Jones
Inflammation and ageing-related DNA methylation patterns in the blood have been linked to a variety of morbidities, including cognitive decline and neurodegenerative disease. However, it is unclear how these blood-based patterns relate to patterns within the brain and how each associates with central cellular profiles. In this study, we profiled DNA methylation in both the blood and in five post mortem brain regions (BA17, BA20/21, BA24, BA46 and hippocampus) in 14 individuals from the Lothian Birth Cohort 1936. Microglial burdens were additionally quantified in the same brain regions. DNA methylation signatures of five epigenetic ageing biomarkers ('epigenetic clocks'), and two inflammatory biomarkers (methylation proxies for C-reactive protein and interleukin-6) were compared across tissues and regions. Divergent associations between the inflammation and ageing signatures in the blood and brain were identified, depending on region assessed. Four out of the five assessed epigenetic age acceleration measures were found to be highest in the hippocampus (β range = 0.83-1.14, p ≤ 0.02). The inflammation-related DNA methylation signatures showed no clear variation across brain regions. Reactive microglial burdens were found to be highest in the hippocampus (β = 1.32, p = 5 × 10-4 ); however, the only association identified between the blood- and brain-based methylation signatures and microglia was a significant positive association with acceleration of one epigenetic clock (termed DNAm PhenoAge) averaged over all five brain regions (β = 0.40, p = 0.002). This work highlights a potential vulnerability of the hippocampus to epigenetic ageing and provides preliminary evidence of a relationship between DNA methylation signatures in the brain and differences in microglial burdens.
A comparison of feature selection methodologies and learning algorithms in the development of a DNA methylation-based telomere length estimator
Trevor Doherty,
Emma Dempster,
Eilis Hannon,
Jonathan Mill,
Richie Poulton,
David Corcoran,
Karen Sugden
+ 5 more
Trevor Doherty,
Emma Dempster,
Eilis Hannon,
Jonathan Mill,
Richie Poulton,
David Corcoran,
Karen Sugden,
Ben Williams,
Avshalom Caspi,
Terrie E Moffitt,
Sarah Jane Delany,
Therese M. Murphy
Abstract The field of epigenomics holds great promise in understanding and treating disease with advances in machine learning (ML) and artificial intelligence being vitally important in this pursuit. Increasingly, research now utilises DNA methylation measures at cytosine-guanine dinucleotides (CpG) to detect disease and estimate biological traits such as aging. Given the high dimensionality of DNA methylation data, feature-selection techniques are commonly employed to reduce dimensionality and identify the most important subset of features. In this study, we test and compare a range of feature-selection methods and ML algorithms in the development of a novel DNA methylation-based telomere length (TL) estimator. We found that principal component analysis in advance of elastic net regression led to the overall best performing estimator when evaluated using a nested cross-validation analysis and two independent test cohorts. In contrast, the baseline model of elastic net regression with no prior feature reduction stage performed worst - suggesting a prior feature-selection stage may have important utility. The variance in performance across tested approaches shows that estimators are sensitive to data set heterogeneity and the development of an optimal DNA methylation-based estimator should benefit from the robust methodological approach used in this study. Additionally, we observed that different DNA methylation-based TL estimators, which have few common CpGs, are associated with many of the same biological entities. Moreover, our methodology which utilises a range of feature-selection approaches and ML algorithms could be applied to other biological markers and disease phenotypes, to examine their relationship with DNA methylation and predictive value.
Methylome analysis of ALS patients and presymptomatic mutation carriers in blood cells
Wolfgang P Ruf,
Eilis Hannon,
Axel Freischmidt,
Veselin Grozdanov,
David Brenner,
Kathrin Müller,
Antje Knehr
+ 7 more
Wolfgang P Ruf,
Eilis Hannon,
Axel Freischmidt,
Veselin Grozdanov,
David Brenner,
Kathrin Müller,
Antje Knehr,
Kornelia Günther,
Johannes Dorst,
Ole Ammerpohl,
Karin M Danzer,
Jonathan Mill,
Albert C Ludolph,
Jochen H Weishaupt
Amyotrophic lateral sclerosis (ALS) is a fatal motoneuron disease with a monogenic cause in approximately 10% of cases. However, familial clustering of disease without inheritance in a Mendelian manner and the broad range of phenotypes suggest the presence of epigenetic mechanisms. Hence, we performed an epigenome-wide association study on sporadic, symptomatic and presymptomatic familial ALS cases with mutations in C9ORF72 and FUS and healthy controls studying DNA methylation in blood cells. We found differentially methylated DNA positions (DMPs) and regions embedding DMPs associated with either disease status, C9ORF72 or FUS mutation status. One DMP reached methylome-wide significance and is attributed to a region encoding a long non-coding RNA (LOC389247). Furthermore, we could demonstrate co-localization of DMPs with an ALS-associated GWAS region near the SCN7A/SCN9A and XIRP2 genes. Finally, a classifier model that predicts disease status (ALS, healthy) classified all but one presymptomatic mutation carrier as healthy, suggesting that the presence of ALS symptoms rather than the presence of ALS-associated genetic mutations is associated with blood cell DNA methylation.
Developmental disruption to the cortical transcriptome and synaptosome in a model of SETD1A loss-of-function
Nicholas E Clifton,
Matthew L Bosworth,
Niels Haan,
Elliott Rees,
Peter A Holmans,
Lawrence S Wilkinson,
Anthony R Isles
+ 2 more
Nicholas E Clifton,
Matthew L Bosworth,
Niels Haan,
Elliott Rees,
Peter A Holmans,
Lawrence S Wilkinson,
Anthony R Isles,
Mark O Collins,
Jeremy Hall
Large-scale genomic studies of schizophrenia implicate genes involved in the epigenetic regulation of transcription by histone methylation and genes encoding components of the synapse. However, the interactions between these pathways in conferring risk to psychiatric illness are unknown. Loss-of-function (LoF) mutations in the gene encoding histone methyltransferase, SETD1A, confer substantial risk to schizophrenia. Among several roles, SETD1A is thought to be involved in the development and function of neuronal circuits. Here, we employed a multi-omics approach to study the effects of heterozygous Setd1a LoF on gene expression and synaptic composition in mouse cortex across five developmental timepoints from embryonic day 14 to postnatal day 70. Using RNA sequencing, we observed that Setd1a LoF resulted in the consistent downregulation of genes enriched for mitochondrial pathways. This effect extended to the synaptosome, in which we found age-specific disruption to both mitochondrial and synaptic proteins. Using large-scale patient genomics data, we observed no enrichment for genetic association with schizophrenia within differentially expressed transcripts or proteins, suggesting they derive from a distinct mechanism of risk from that implicated by genomic studies. This study highlights biological pathways through which SETD1A LOF may confer risk to schizophrenia. Further work is required to determine whether the effects observed in this model reflect human pathology.
Evaluation of nanopore sequencing for epigenetic epidemiology: a comparison with DNA methylation microarrays
Robert Flynn,
Sam Washer,
Aaron R Jeffries,
Alexandria Andrayas,
Gemma Shireby,
Meena Kumari,
Leonard C Schalkwyk
+ 2 more
Robert Flynn,
Sam Washer,
Aaron R Jeffries,
Alexandria Andrayas,
Gemma Shireby,
Meena Kumari,
Leonard C Schalkwyk,
Jonathan Mill,
Eilis Hannon
Most epigenetic epidemiology to date has utilized microarrays to identify positions in the genome where variation in DNA methylation is associated with environmental exposures or disease. However, these profile less than 3% of DNA methylation sites in the human genome, potentially missing affected loci and preventing the discovery of disrupted biological pathways. Third generation sequencing technologies, including Nanopore sequencing, have the potential to revolutionize the generation of epigenetic data, not only by providing genuine genome-wide coverage but profiling epigenetic modifications direct from native DNA. Here we assess the viability of using Nanopore sequencing for epidemiology by performing a comparison with DNA methylation quantified using the most comprehensive microarray available, the Illumina EPIC array. We implemented a CRISPR-Cas9 targeted sequencing approach in concert with Nanopore sequencing to profile DNA methylation in three genomic regions to attempt to rediscover genomic positions that existing technologies have shown are differentially methylated in tobacco smokers. Using Nanopore sequencing reads, DNA methylation was quantified at 1779 CpGs across three regions, providing a finer resolution of DNA methylation patterns compared to the EPIC array. The correlation of estimated levels of DNA methylation between platforms was high. Furthermore, we identified 12 CpGs where hypomethylation was significantly associated with smoking status, including 10 within the AHRR gene. In summary, Nanopore sequencing is a valid option for identifying genomic loci where large differences in DNAm are associated with a phenotype and has the potential to advance our understanding of the role differential methylation plays in the etiology of complex disease.
Uncertainty quantification of reference based cellular deconvolution algorithms
Dorothea Seiler Vellame,
Gemma Shireby,
Ailsa MacCalman,
Emma L Dempster,
Joe Burrage,
Tyler Gorrie-Stone,
Leonard S Schalkwyk
+ 2 more
Dorothea Seiler Vellame,
Gemma Shireby,
Ailsa MacCalman,
Emma L Dempster,
Joe Burrage,
Tyler Gorrie-Stone,
Leonard S Schalkwyk,
Jonathan Mill,
Eilis Hannon
Abstract
The majority of epigenetic epidemiology studies to date have generated genome-wide profiles from bulk tissues (e.g. whole blood) however these are vulnerable to confounding from variation in cellular composition. Proxies for cellular composition can be mathematically derived from the bulk tissue profiles using a deconvolution algorithm however, there is no method to assess the validity of these estimates for a dataset where the true cellular proportions are unknown. In this study, we describe, validate and characterise a sample level accuracy metric for derived cellular heterogeneity variables. The CETYGO score captures the deviation between a sample’s DNAm profile and its expected profile given the estimated cellular proportions and cell type reference profiles.We demonstrate that the CETYGO score consistently distinguishes inaccurate and incomplete deconvolutions when applied to reconstructed whole blood profiles. By applying our novel metric to > 6,300 empirical whole blood profiles, we find that estimating accurate cellular composition is influenced by both technical and biological variation. In particular, we show that when using the standard reference panel for whole blood, less accurate estimates are generated for females, neonates, older individuals and smokers. Our results highlight the utility of a metric to assess the accuracy of cellular deconvolution, and describe how it can enhance studies of DNA methylation that are reliant on statistical proxies for cellular heterogeneity. To facilitate incorporating our methodology into existing pipelines, we have made it freely available as an R package (
https://github.com/ds420/CETYGO
).
Functional characterization of the schizophrenia associated gene AS3MT identifies a role in neuronal development
Sam J. Washer,
Robert Flynn,
Asami Oguro‐Ando,
Eilis Hannon,
Joe Burrage,
Aaron Jeffries,
Jonathan Mill
+ 1 more
Sam J. Washer,
Robert Flynn,
Asami Oguro‐Ando,
Eilis Hannon,
Joe Burrage,
Aaron Jeffries,
Jonathan Mill,
Emma L. Dempster
American Journal of Medical Genetics Part B Neuropsychiatric Genetics
Genome-wide association studies (GWAS) have identified multiple genomic regions associated with schizophrenia, although many variants reside in noncoding regions characterized by high linkage disequilibrium (LD) making the elucidation of molecular mechanisms challenging. A genomic region on chromosome 10q24 has been consistently associated with schizophrenia with risk attributed to the AS3MT gene. Although AS3MT is hypothesized to play a role in neuronal development and differentiation, work to fully understand the function of this gene has been limited. In this study we explored the function of AS3MT using a neuronal cell line (SH-SY5Y). We confirm previous findings of isoform specific expression of AS3MT during SH-SY5Y differentiation toward neuronal fates. Using CRISPR-Cas9 gene editing we generated AS3MT knockout SH-SY5Y cell lines and used RNA-seq to identify significant changes in gene expression in pathways associated with neuronal development, inflammation, extracellular matrix formation, and RNA processing, including dysregulation of other genes strongly implicated in schizophrenia. We did not observe any morphological changes in cell size and neurite length following neuronal differentiation and MAP2 immunocytochemistry. These results provide novel insights into the potential role of AS3MT in brain development and identify pathways through which genetic variation in this region may confer risk for schizophrenia.
Association of Pace of Aging Measured by Blood-Based DNA Methylation With Age-Related Cognitive Impairment and Dementia
Karen Sugden,
Avshalom Caspi,
Maxwell L. Elliott,
Kyle J. Bourassa,
Kartik Chamarti,
David L. Corcoran,
Ahmad R. Hariri
+ 9 more
Karen Sugden,
Avshalom Caspi,
Maxwell L. Elliott,
Kyle J. Bourassa,
Kartik Chamarti,
David L. Corcoran,
Ahmad R. Hariri,
Renate M. Houts,
Meeraj Kothari,
Stephen Kritchevsky,
George A. Kuchel,
Jonathan S. Mill,
Benjamin S. Williams,
Daniel W. Belsky,
Terrie E. Moffitt,
for the Alzheimer's Disease Neuroimaging Initiative*
BACKGROUND AND OBJECTIVES: DNA methylation algorithms are increasingly used to estimate biological aging; however, how these proposed measures of whole-organism biological aging relate to aging in the brain is not known. We used data from the Alzheimer's Disease Neuroimaging Initiative (ADNI) and the Framingham Heart Study (FHS) Offspring Cohort to test the association between blood-based DNA methylation measures of biological aging and cognitive impairment and dementia in older adults.
METHODS: We tested 3 "generations" of DNA methylation age algorithms (first generation: Horvath and Hannum clocks; second generation: PhenoAge and GrimAge; and third generation: DunedinPACE, Dunedin Pace of Aging Calculated from the Epigenome) against the following measures of cognitive impairment in ADNI: clinical diagnosis of dementia and mild cognitive impairment, scores on Alzheimer disease (AD) / Alzheimer disease and related dementias (ADRD) screening tests (Alzheimer's Disease Assessment Scale, Mini-Mental State Examination, and Montreal Cognitive Assessment), and scores on cognitive tests (Rey Auditory Verbal Learning Test, Logical Memory test, and Trail Making Test). In an independent replication in the FHS Offspring Cohort, we further tested the longitudinal association between the DNA methylation algorithms and the risk of developing dementia.
RESULTS: In ADNI (N = 649 individuals), the first-generation (Horvath and Hannum DNA methylation age clocks) and the second-generation (PhenoAge and GrimAge) DNA methylation measures of aging were not consistently associated with measures of cognitive impairment in older adults. By contrast, a third-generation measure of biological aging, DunedinPACE, was associated with clinical diagnosis of Alzheimer disease (beta [95% CI] = 0.28 [0.08-0.47]), poorer scores on Alzheimer disease/ADRD screening tests (beta [Robust SE] = -0.10 [0.04] to 0.08[0.04]), and cognitive tests (beta [Robust SE] = -0.12 [0.04] to 0.10 [0.03]). The association between faster pace of aging, as measured by DunedinPACE, and risk of developing dementia was confirmed in a longitudinal analysis of the FHS Offspring Cohort (N = 2,264 individuals, hazard ratio [95% CI] = 1.27 [1.07-1.49]).
DISCUSSION: Third-generation blood-based DNA methylation measures of aging could prove valuable for measuring differences between individuals in the rate at which they age and in their risk for cognitive decline, and for evaluating interventions to slow aging.
Epigenetic age acceleration is associated with oligodendrocyte proportions in MSA and control brain tissue
Megha Murthy,
Gemma Shireby,
Yasuo Miki,
Emmanuelle Viré,
Tammaryn Lashley,
Thomas T. Warner,
Jonathan Mill
+ 1 more
Megha Murthy,
Gemma Shireby,
Yasuo Miki,
Emmanuelle Viré,
Tammaryn Lashley,
Thomas T. Warner,
Jonathan Mill,
Conceição Bettencourt
Abstract Aims Epigenetic clocks are widely applied as surrogates for biological age in different tissues and/or diseases, including several neurodegenerative diseases. Despite white matter (WM) changes often being observed in neurodegenerative diseases, no study has investigated epigenetic ageing in white matter. Methods We analysed the performances of two DNA methylation-based clocks, DNAmClock Multi and DNAmClock Cortical , in post-mortem WM tissue from multiple subcortical regions and the cerebellum, and in oligodendrocyte-enriched nuclei. We also examined epigenetic ageing in control and multiple system atrophy (MSA) (WM and mixed WM and grey matter), as MSA is a neurodegenerative disease comprising pronounced WM changes and α-synuclein aggregates in oligodendrocytes. Results Estimated DNA methylation (DNAm) ages showed strong correlations with chronological ages, even in WM (e.g., DNAmClock Cortical , r = [0.80-0.97], p<0.05). However, performances and DNAm age estimates differed between clocks and brain regions. DNAmClock Multi significantly underestimated ages in all cohorts except in the MSA prefrontal cortex mixed tissue, whereas DNAmClock Cortica tended towards age overestimations. Pronounced age overestimations in the oligodendrocyte-enriched cohorts (e.g., oligodendrocyte-enriched nuclei, p=6.1×10 -5 ) suggested that this cell-type ages faster. Indeed, significant positive correlations were observed between estimated oligodendrocyte proportions and DNAm age acceleration estimated by DNAmClock Cortica (r>0.31, p<0.05), and similar trends with DNAmClock Multi . Although increased age acceleration was observed in MSA compared to controls, no significant differences were observed upon adjustment for possible confounders (e.g., cell-type proportions). Conclusions Our findings show that oligodendrocyte proportions positively influence epigenetic age acceleration across brain regions and highlight the need to further investigate this in ageing and neurodegeneration.
Epigenome-wide association study of human frontal cortex identifies differential methylation in Lewy body pathology
Lasse Pihlstrøm,
Gemma Shireby,
Hanneke Geut,
Sandra Pilar Henriksen,
Annemieke J. M. Rozemuller,
Jon-Anders Tunold,
Eilis Hannon
+ 6 more
Lasse Pihlstrøm,
Gemma Shireby,
Hanneke Geut,
Sandra Pilar Henriksen,
Annemieke J. M. Rozemuller,
Jon-Anders Tunold,
Eilis Hannon,
Paul Francis,
Alan J. Thomas,
Seth Love,
Jonathan Mill,
de Berg Wilma D. J. van,
Mathias Toft
Parkinson’s disease (PD) and dementia with Lewy bodies (DLB) are closely related progressive disorders with no available disease-modifying therapy, neuropathologically characterized by intraneuronal aggregates of misfolded α-synuclein. To explore the role of DNA methylation changes in PD and DLB pathogenesis, we performed an epigenome-wide association study (EWAS) of 322 postmortem frontal cortex samples and replicated results in an independent set of 200 donors. We report novel differentially methylated replicating loci associated with Braak Lewy body stage near TMCC2, SFMBT2, AKAP6 and PHYHIP. Differentially methylated probes were independent of known PD genetic risk alleles. Meta-analysis provided suggestive evidence for a differentially methylated locus within the chromosomal region affected by the PD-associated 22q11.2 deletion. Our findings elucidate novel disease pathways in PD and DLB and generate hypotheses for future molecular studies of Lewy body pathology.
Neuropsychiatric symptoms in AD: the search for mechanisms
New work building on the results of genome-wide association studies in Alzheimer disease has identified molecular mechanisms that are shared with some psychiatric disorders. The study leveraged ‘omics data and has the realistic potential to elucidate unknown disease mechanisms; however, a lack of information about neuropsychiatric symptoms in the participants with Alzheimer disease limits the conclusions.
LONG READ TRANSCRIPTOME SEQUENCING REVEALS ISOFORM DIVERSITY ACROSS HUMAN NEURODEVELOPMENT
Rosemary Bamford,
Aaron R. Jeffries,
Emma Walker,
Szi Kay Leung,
Gina Commin,
Jonathan P. Davies,
Emma Dempster
+ 2 more
Rosemary Bamford,
Aaron R. Jeffries,
Emma Walker,
Szi Kay Leung,
Gina Commin,
Jonathan P. Davies,
Emma Dempster,
Eilis Hannon,
Jonathan Mill
DEVELOPMENTAL TRAJECTORIES OF DNA METHYLATION IN NEURAL CELL POPULATIONS IN HUMAN CORTEX AND LINKS TO NEURODEVELOPMENTAL DISORDERS
Jonathan Davies,
Alice Franklin,
Emma Walker,
Nick Owens,
Nick Bray,
Rosemary A. Bamford,
Gina Commin
+ 5 more
Jonathan Davies,
Alice Franklin,
Emma Walker,
Nick Owens,
Nick Bray,
Rosemary A. Bamford,
Gina Commin,
Barry Chioza,
Joe Burrage,
Emma Dempster,
Eilis Hannon,
Jonathan Mill
IDENTIFYING CELL-TYPE-SPECIFIC EPIGENETIC VARIATION IN THE CORTEX ASSOCIATED WITH SCHIZOPHRENIA
Eilis Hannon,
Jonathan Davies,
Barry Chioza,
Stefania Policicchio,
Joe Burrage,
Gina Commin,
Aaron R. Jeffries
+ 3 more
Eilis Hannon,
Jonathan Davies,
Barry Chioza,
Stefania Policicchio,
Joe Burrage,
Gina Commin,
Aaron R. Jeffries,
Leo Schalkwyk,
Emma Dempster,
Jonathan Mill
DNA methylation signatures of Alzheimer’s disease neuropathology in the cortex are primarily driven by variation in non-neuronal cell-types
Gemma Shireby,
Emma L. Dempster,
Stefania Policicchio,
Rebecca G. Smith,
Ehsan Pishva,
Barry Chioza,
Jonathan P. Davies
+ 10 more
Gemma Shireby,
Emma L. Dempster,
Stefania Policicchio,
Rebecca G. Smith,
Ehsan Pishva,
Barry Chioza,
Jonathan P. Davies,
Joe Burrage,
Katie Lunnon,
Vellame Dorothea Seiler,
Seth Love,
Alan Thomas,
Keeley Brookes,
Kevin Morgan,
Paul Francis,
Eilis Hannon,
Jonathan Mill
Alzheimer’s disease (AD) is a chronic neurodegenerative disease characterized by the progressive accumulation of amyloid-beta and neurofibrillary tangles of tau in the neocortex. We profiled DNA methylation in two regions of the cortex from 631 donors, performing an epigenome-wide association study of multiple measures of AD neuropathology. We meta-analyzed our results with those from previous studies of DNA methylation in AD cortex (total n = 2013 donors), identifying 334 cortical differentially methylated positions (DMPs) associated with AD pathology including methylomic variation at loci not previously implicated in dementia. We subsequently profiled DNA methylation in NeuN+ (neuronal-enriched), SOX10+ (oligodendrocyte-enriched) and NeuN–/SOX10– (microglia- and astrocyte-enriched) nuclei, finding that the majority of DMPs identified in ‘bulk’ cortex tissue reflect DNA methylation differences occurring in non-neuronal cells. Our study highlights the power of utilizing multiple measures of neuropathology to identify epigenetic signatures of AD and the importance of characterizing disease-associated variation in purified cell-types.
Study of the associations between short telomeres, sex hormones and pulmonary fibrosis
Anna Duckworth,
Katherine S. Ruth,
Julia K. Prague,
Anne-Marie Russell,
Howard Almond,
John Conway,
Robin N Beaumont
+ 8 more
Anna Duckworth,
Katherine S. Ruth,
Julia K. Prague,
Anne-Marie Russell,
Howard Almond,
John Conway,
Robin N Beaumont,
Andrew R Wood,
Susan Martin,
Katie Lunnon,
Mark A. Lindsay,
Anna Murray,
Michael A. Gibbons,
Jess Tyrrell,
Chris J. Scotton
Abstract Background Pulmonary fibrosis (PF) is an incurable fibrotic lung disease with limited treatment options and a high mortality. Evidence is growing that short telomeres cause both heritable and idiopathic pulmonary fibrosis (IPF). Based on survival data, we hypothesised that sex hormones are protective against premature telomere attrition and could influence PF disease onset and/or progression. Methods Associations between IPF, sex hormone concentrations and measured leukocyte telomere length (LTL) were examined for unrelated UK Biobank participants of European ancestry with a diagnosis of IPF (415 females, 718 males) against controls (204,321 females, 174,254 males). Polygenic risk scores were used to explore causality between sex hormone indices, LTL and disease. Findings Strong associations were found between IPF and LTL. For females, higher odds of having IPF was associated with early menopause and premature ovarian failure. Menopause age correlated positively with both age of IPF diagnosis and age of death. For males, IPF prevalence and stages of disease were associated with serum bioavailable testosterone concentrations. For both sexes, evidence of lower concentrations of sex hormones was associated with shorter LTL. Genetic analysis also inferred bi-directional causal links between sex hormone binding globulin concentration, which impacts free testosterone concentration, and LTL in males. Interpretation Our findings suggest that higher sex hormone concentrations protect against IPF onset and progression, possibly by slowing telomere shortening. Hormonal supplementation may delay or prevent disease onset for those with telomere-associated PF risk and improve disease prognosis. This warrants further exploration in a randomised controlled trial. Funding Medical Research Council.
O101 / #272 TRANSCRIPTOMICS STUDY ON THE EFFECT OF TONIC AND BURST EXTRACELLULAR STIMULATION ON GENE EXPRESSION IN HUMAN NEURON-LIKE CELL CULTURES TRACK 1: MECHANISMS OF ACTION, MAPPING AND SPINAL CORD STIMULATION
Juan Graterol, Emma Dempster
Juan Graterol,
Emma Dempster
Neuromodulation Technology at the Neural Interface
Designing genetic studies for people with intellectual disabilities: Practical lessons from a pilot study
Adrian Sellers,
Sharon Hudson,
Joanna Ledger,
Charlotte Moorehouse,
Charlotte Young,
Ian Groeber,
Bridget Knight
+ 3 more
Adrian Sellers,
Sharon Hudson,
Joanna Ledger,
Charlotte Moorehouse,
Charlotte Young,
Ian Groeber,
Bridget Knight,
Jonathan Mill,
Jon Allard,
Rohit Shankar
Journal of Policy and Practice in Intellectual Disabilities
Abstract Genetic variations are overrepresented in people with intellectual disability (PwID), particularly those with physical and mental health co‐morbidities, but remain significantly under‐diagnosed. Lack of suitable research studies, a natural extension of the complexities posed of consenting and recruitment is considered culpable. There is a resultant dearth of evidence on establishing bespoke genetic studies for adult PwID. This report outlines the challenges faced in the implementation and administration of a pilot genetic study for adult PwID hoping to better inform future genetic study designs for PwID. Adult participants with a diagnosis of ID (ICD10 F70‐F73) and epilepsy (ICD10 G40) were recruited to The P en i nsula study e x ploring genomic stratification in i ntell e ctual disability and epilepsy via the ethically approved Royal Devon and Exeter Tissue Bank (RDETB) (16/SC/016). Managed within the National Institute for Health Research (NIHR) Exeter Clinical Research Framework, the RDETB was set up to proactively collect and store ‘spare’ tissue from routine clinical procedures such as venepunctures for routine good practice biochemistry monitoring. Participants who satisfied the criteria for the need for routine bloods to monitor their general health were identified to be invited for participation. From October 2017 to March 2020 from a total caseload of 375 PwID and epilepsy, 291 were screened (77.6%), 116 (39.9%) identified as potentially eligible and sent study information and genetic samples obtained from 30 (8%). Analysis showed 75% of PwID had some biochemical abnormalities requiring further medical attention. The recruitment was influenced by the clinical care set up in implementing the sanctioned ethics. However, where bloods were achieved it proved to be beneficial in identifying hitherto undiagnosed medical problems. While the challenges to gain consent, are considerable, the reasonable adjustments needed to facilitate participation and the immediate clinical benefits where engagement was successful are significant.
Uncovering the genetic architecture of broad antisocial behavior through a genome-wide association study meta-analysis
Jorim J. Tielbeek,
Emil Uffelmann,
Benjamin S. Williams,
Lucía Colodro-Conde,
Éloi Gagnon,
Travis T. Mallard,
Brandt E. Levitt
+ 76 more
Jorim J. Tielbeek,
Emil Uffelmann,
Benjamin S. Williams,
Lucía Colodro-Conde,
Éloi Gagnon,
Travis T. Mallard,
Brandt E. Levitt,
Philip R. Jansen,
Ada Johansson,
Hannah M. Sallis,
Giorgio Pistis,
Gretchen R. B. Saunders,
Andrea G. Allegrini,
Kaili Rimfeld,
Bettina Konte,
Marieke Klein,
Annette M. Hartmann,
Jessica E. Salvatore,
Ilja M. Nolte,
Ditte Demontis,
Anni L. K. Malmberg,
S. Alexandra Burt,
Jeanne E. Savage,
Karen Sugden,
Richie Poulton,
Kathleen Mullan Harris,
Scott Vrieze,
Matt McGue,
William G. Iacono,
Nina Roth Mota,
Jonathan Mill,
Joana F. Viana,
Brittany L. Mitchell,
Jose J. Morosoli,
Till F. M. Andlauer,
Isabelle Ouellet-Morin,
Richard E. Tremblay,
Sylvana M. Côté,
Jean-Philippe Gouin,
Mara R. Brendgen,
Ginette Dionne,
Frank Vitaro,
Michelle K. Lupton,
Nicholas G. Martin,
Enrique Castelao,
Katri Räikkönen,
Johan G. Eriksson,
Jari Lahti,
Catharina A. Hartman,
Albertine J. Oldehinkel,
Harold Snieder,
Hexuan Liu,
Martin Preisig,
Alyce Whipp,
Eero Vuoksimaa,
Yi Lu,
Patrick Jern,
Dan Rujescu,
Ina Giegling,
Teemu Palviainen,
Jaakko Kaprio,
Kathryn Paige Harden,
Marcus R. Munafò,
Geneviève Morneau-Vaillancourt,
Robert Plomin,
Essi Viding,
Brian B. Boutwell,
Fazil Aliev,
Danielle M. Dick,
Arne Popma,
Stephen V. Faraone,
Anders D. Børglum,
Sarah E. Medland,
Barbara Franke,
Michel Boivin,
Jean-Baptiste Pingault,
Jeffrey C. Glennon,
J. C. Barnes,
Simon E. Fisher,
Terrie E. Moffitt,
Avshalom Caspi,
Tinca J. C. Polderman,
Danielle Posthuma
Despite the substantial heritability of antisocial behavior (ASB), specific genetic variants robustly associated with the trait have not been identified. The present study by the Broad Antisocial Behavior Consortium (BroadABC) meta-analyzed data from 28 discovery samples (N = 85,359) and five independent replication samples (N = 8058) with genotypic data and broad measures of ASB. We identified the first significant genetic associations with broad ASB, involving common intronic variants in the forkhead box protein P2 (FOXP2) gene (lead SNP rs12536335, p = 6.32 × 10−10). Furthermore, we observed intronic variation in Foxp2 and one of its targets (Cntnap2) distinguishing a mouse model of pathological aggression (BALB/cJ strain) from controls (BALB/cByJ strain). Polygenic risk score (PRS) analyses in independent samples revealed that the genetic risk for ASB was associated with several antisocial outcomes across the lifespan, including diagnosis of conduct disorder, official criminal convictions, and trajectories of antisocial development. We found substantial genetic correlations of ASB with mental health (depression rg = 0.63, insomnia rg = 0.47), physical health (overweight rg = 0.19, waist-to-hip ratio rg = 0.32), smoking (rg = 0.54), cognitive ability (intelligence rg = −0.40), educational attainment (years of schooling rg = −0.46) and reproductive traits (age at first birth rg = −0.58, father’s age at death rg = −0.54). Our findings provide a starting point toward identifying critical biosocial risk mechanisms for the development of ASB.
Brain DNA methylomic analysis of frontotemporal lobar degeneration reveals OTUD4 in shared dysregulated signatures across pathological subtypes
Katherine Fodder,
Megha Murthy,
Patrizia Rizzu,
Christina E. Toomey,
Rahat Hasan,
Jack Humphrey,
Towfique Raj
+ 5 more
Katherine Fodder,
Megha Murthy,
Patrizia Rizzu,
Christina E. Toomey,
Rahat Hasan,
Jack Humphrey,
Towfique Raj,
Katie Lunnon,
Jonathan Mill,
Peter Heutink,
Tammaryn Lashley,
Conceição Bettencourt
ABSTRACT Frontotemporal lobar degeneration (FTLD) is an umbrella term describing the neuropathology of a clinically, genetically and pathologically heterogeneous group of diseases, including frontotemporal dementia (FTD) and progressive supranuclear palsy (PSP). Among the major FTLD pathological subgroups, FTLD with TDP-43 positive inclusions (FTLD-TDP) and FTLD with tau positive inclusions (FTLD-tau) are the most common, representing about 90% of the cases. Although alterations in DNA methylation have been consistently associated with neurodegenerative diseases, including Alzheimer’s disease and Parkinson’s disease, little is known for FTLD and its heterogeneous subgroups and subtypes. The main goal of this study was to investigate DNA methylation variation in FTLD-TDP and FTLD-tau. We used frontal cortex genome-wide DNA methylation profiles from three FTLD cohorts (234 individuals), generated using the Illumina 450K or EPIC microarray. We performed epigenome-wide association studies (EWAS) for each cohort followed by meta-analysis to identify shared differential methylated loci across FTLD subgroups/subtypes. Additionally, we used weighted gene correlation network analysis to identify co-methylation signatures associated with FTLD and other disease-related traits. Wherever possible, we also incorporated relevant gene/protein expression data. After accounting for a conservative Bonferroni multiple testing correction, the EWAS meta-analysis revealed two differentially methylated loci in FTLD, one annotated to OTUD4 (5’UTR-shore) and the other to NFATC1 (gene body-island). Of these loci, OTUD4 showed consistent upregulation of mRNA and protein expression in FTLD. Additionally, in the three independent co-methylation networks, OTUD4 -containing modules were enriched for EWAS meta-analysis top loci and were strongly associated with the FTLD status. These co-methylation modules were enriched for genes implicated in the ubiquitin system, RNA/stress granule formation and glutamatergic synaptic signalling. Altogether, our findings identified novel FTLD-associated loci, and support a role for DNA methylation as a mechanism involved in the dysregulation of biological processes relevant to FTLD, highlighting novel potential avenues for therapeutic development.
Exploring the mediation of DNA methylation across the epigenome between childhood adversity and First Episode of Psychosis – findings from the EU-GEI study
Luis Alameda,
Zhonghua Liu,
Pak Sham,
AAS Monica,
Trotta Giulia,
Rodriguez Victoria,
Marta di Forti
+ 35 more
Luis Alameda,
Zhonghua Liu,
Pak Sham,
AAS Monica,
Trotta Giulia,
Rodriguez Victoria,
Marta di Forti,
Stilo Simona,
Kandaswamy Radhika,
Celso Arango,
Manuel Arrojo,
Miquel Bernardo,
Julio Bobes,
Haan Lieuwe de,
Cristina Del-Ben,
Charlotte Gayer-Anderson,
Sideli Lucia,
Peter Jones,
Hannah Jongsma,
James Kirkbride,
Caterina La Cascia,
Antonio Lasalvia,
Sarah Tosato,
Pierre Michel Llorca,
Paulo Menezes,
Jim van Os,
Quattrone Diego,
Bart Rutten,
José Santos,
Julio Sanjuan,
Jean-Paul Selten,
Andrei Szöke,
Ilaria Tarricone,
Andrea Tortelli,
Eva Velthorst,
Craig Morgan,
Emma Dempster,
Eilis Hannon,
Joe Burrage,
Jonathan Mill,
Robin Murray,
Chloe Wong
Studies conducted in psychotic disorders have shown that DNA-methylation (DNAm) is sensitive to the impact of Childhood Adversity (CA). However, whether it mediates the association between CA and psychosis is yet to be explored. Epigenome-wide association studies (EWAS) using the Illumina Infinium-Methylation EPIC array in peripheral blood tissue from 366 First-episode of psychosis and 517 healthy controls was performed. Polyvictimization scores were created for abuse, neglect, and composite adversity with the Childhood Trauma Questionnaire (CTQ). Regressions examining (I) CTQ scores with psychosis; (II) with DNAm EWAS level and (III), then between DNAm and caseness, adjusted for a variety of confounders were conducted. Divide-Aggregate Composite-null Test for the composite null hypothesis of no mediation effect was conducted. Enrichment analyses were conducted with missMethyl package and the KEGG database. Our results show that CA was associated with psychosis (Composite: OR = 3.09; p = <0.001; abuse: OR = 2.95; p<0.001; neglect: OR = 3.25; p=<0.001). None of the CpG sites significantly mediated the adversity-psychosis association after Bonferroni correction (p<8.1x10-8). However, 28, 34 and 29 differentially methylated probes associated with 21, 27, 20 genes passed a less stringent discovery threshold (p<5x10-5) for composite, abuse, and neglect respectively, with a lack of overlap between abuse and neglect. These included genes previously associated with psychosis in EWAS studies, such as PANK1, SPEG TBKBP1, TSNARE1 or H2R. Downstream gene ontology analyses did not reveal any biological pathways that survived false discovery rate correction. Although at a non-significant level, DNAm changes in genes previously associated with schizophrenia in EWAS studies may mediate the CA-psychosis association. These results and associated involved processes such as mitochondrial or histaminergic dysfunction, immunity or neural signaling require replication in well-powered samples. Mediating genes were not associated with abuse and neglect, tentatively suggest differential biological trajectories linking CA subtypes and psychosis.
Machine learning-based prediction of cognitive outcomes in de novo Parkinson’s disease
Joshua Harvey,
Rick A. Reijnders,
Rachel Cavill,
Annelien Duits,
Sebastian Köhler,
Lars Eijssen,
Bart P. F. Rutten
+ 6 more
Joshua Harvey,
Rick A. Reijnders,
Rachel Cavill,
Annelien Duits,
Sebastian Köhler,
Lars Eijssen,
Bart P. F. Rutten,
Gemma Shireby,
Ali Torkamani,
Byron Creese,
Albert F. G. Leentjens,
Katie Lunnon,
Ehsan Pishva
Cognitive impairment is a debilitating symptom in Parkinson’s disease (PD). We aimed to establish an accurate multivariate machine learning (ML) model to predict cognitive outcome in newly diagnosed PD cases from the Parkinson’s Progression Markers Initiative (PPMI). Annual cognitive assessments over an 8-year time span were used to define two cognitive outcomes of (i) cognitive impairment, and (ii) dementia conversion. Selected baseline variables were organized into three subsets of clinical, biofluid and genetic/epigenetic measures and tested using four different ML algorithms. Irrespective of the ML algorithm used, the models consisting of the clinical variables performed best and showed better prediction of cognitive impairment outcome over dementia conversion. We observed a marginal improvement in the prediction performance when clinical, biofluid, and epigenetic/genetic variables were all included in one model. Several cerebrospinal fluid measures and an epigenetic marker showed high predictive weighting in multiple models when included alongside clinical variables.
A Role for Epigenetic Mechanisms in the Lewy Body Dementias
Jennifer L Imm,
Joshua Harvey,
Byron Creese,
Leonidas Chouliaras,
Emma Dempster,
Clive G Ballard,
John T O'Brien
+ 4 more
Jennifer L Imm,
Joshua Harvey,
Byron Creese,
Leonidas Chouliaras,
Emma Dempster,
Clive G Ballard,
John T O'Brien,
Dag Aarsland,
Jonathan Mill,
Ehsan Pishva,
Katie Lunnon
Abstract Background The Lewy body diseases, Dementia with Lewy bodies (DLB), Parkinson’s disease (PD) and Parkinson’s disease dementia (PDD) are all neurodegenerative diseases classified by the accumulation of alpha‐synuclein in neurons, forming Lewy bodies (LB). We hypothesise that these LBs cause epigenetic changes within neurons and surrounding cells and that these changes can be used to distinguish the different diseases from one another. Method Bulk tissue from the cingulate gyrus and prefrontal cortex was analyzed on the Illumina Infinium Methylation EPIC array generating a quantitative measure of DNA methylation for over 850,000 CpG sites (n=∼100/disease group). Linear regression and pathway analyses were then used to identify loci that are significantly different or specific to each disease. Result Study groups have been sourced consisting of cases with PD, PDD and DLB based on LB deposition and clinical symptom staging. Age‐matched control cases have been selected that have similar levels of concomitant AD pathology to the disease groups. We have identified significant changes in methylation associated with both phenotype and neuropathology alongside the cellular pathways these changes correspond with. Conclusion We have collated a well powered study cohort to interrogate the epigenetic basis of neuropathological progression and clinical staging of LB disease, controlling for levels of concomitant AD pathology. We have completed DNA methylation analysis for two disease relevant brain regions and identified both phenotype neuropathology associated changes within these regions. Processing of samples for fluorescence activated nuclei sorting (FANS) and laser capture microdissection (LCM) has begun (n=15/group) to assess the cell type specificity of the methylation changes and the effect of Lewy bodies on neuronal methylation respectively.
An Epigenome‐wide association study of psychosis in Alzheimer's disease dorsolateral prefrontal cortex
Luke Stephen Weymouth,
Morteza P Kouhsar,
Byron Creese,
Sverre Bergh,
Yehani Wedatilake,
Ali Torkamani,
Adam R. Smith
+ 7 more
Luke Stephen Weymouth,
Morteza P Kouhsar,
Byron Creese,
Sverre Bergh,
Yehani Wedatilake,
Ali Torkamani,
Adam R. Smith,
Geir Selbaek,
Robert Sweet,
Clive G Ballard,
Jonathan Mill,
Julia Kofler,
Ehsan Pishva,
Katie Lunnon
Abstract Background Psychosis is a debilitating syndrome occurring in 40‐60% of people with Alzheimer’s disease (AD) and corresponds with a more severe disease course. Evidence suggests that psychosis in AD (AD+P) is associated with a distinct profile of neurobiological changes, but little is known about the molecular processes driving etiology. In this study we performed an epigenome‐wide association study (EWAS) to investigate DNA methylation associated with AD+P in the dorsolateral prefrontal cortex of 192 post‐mortem brain samples. Method Brain samples with corresponding in life neuropsychiatric assessments were obtained from the University of Pittsburgh Alzheimer’s disease Research Center (PITT‐ADRC). AD pathology was assessed and classified using CERAD neuritic plaque density score, Braak neurofibrillary tangle stages and NIA‐RI criteria. The presence or absence of delusions and hallucinations was scored on the CERAD Behavioral Rating Scale. DNA was extracted, bisulfite treated and then profiled on the Illumina Methylation EPIC Array. Result After data processing and quality control we used linear regression models to compare 152 AD+P samples to 40 AD samples without psychosis (AD‐P). A regional analysis of spatially correlated p‐values highlighted four differentially methylated regions (DMRs) associated with psychosis, which are being replicated in other data sets and validated for cell specificity using fluorescence activated nuclei sorting (FANS). Conclusion The development of effective therapies for AD+P is an urgent priority. To address this we have collated a well powered study cohort to interrogate the epigenetic basis of AD+P, finding significant methylomic variation. This variation provides an insight into potential mechanisms and biomarkers which will help to identify drug targets and enable better treatment with existing medications.
Telomere Length Variation in the Lewy Body Diseases and its Relationship to Epigenetic Age
Jennifer L Imm, Joshua Harvey, Adam R. Smith, Ehsan Pishva, Katie Lunnon
Jennifer L Imm,
Joshua Harvey,
Adam R. Smith,
Ehsan Pishva,
Katie Lunnon
Abstract Background The Lewy body diseases (LBDs), Dementia with Lewy bodies (DLB), Parkinson’s disease (PD) and Parkinson’s disease dementia (PDD) are all neurodegenerative diseases classified by the accumulation of alpha‐synuclein in neurons, forming Lewy bodies (LBs). As both the LBDs and the shortening of telomeres are well established with aging it is reasonable to hypothesise some involvement of telomere shortening in the LBDs. There are few studies addressing telomere length changes in the LBDs and as these studies are often conflicting, we aim to rectify this disparity and establish whether there is a relationship between disease diagnosis, LB Braak staging and epigenetic age. Method Bulk cingulate gyrus and prefrontal cortex tissue was used to determine absolute telomere length using quantitative real‐time PCR. Alongside sample DNA, standards for either telomeric repeats or a housekeeping gene, ribosomal phosphoprotein P0 (36B4), for which the copy number was known were run. Calculation of absolute telomere length was achieved by dividing the telomere copies per reaction by the corresponding 36B4 copies per reaction. This value was then further divided by 92 to give the length per individual telomere. Linear regression was used to determine significance within each brain region controlling for age, gender and cellular composition. DNA methylation was assessed using the Illumina EPIC array and epigenetic age was derived using the Horvath skin and blood clock. Result We have used 136 PD, 307 PDD, 178 DLB and 302 control samples in two different brain regions in order to determine the relationship between telomere length, epigenetic age, neuropathology and clinical diagnosis. Conclusion We have studied how telomere length varies not only in relation to epigenetic age in post‐mortem brain samples but also how it relates to clinical diagnosis and neuropathology in the LBDs.
An epigenome wide association study of sub‐phenotypes in Parkinson’s disease.
Joshua Harvey,
Adam R. Smith,
Luke Stephen Weymouth,
Rebecca G. Smith,
Leon Hubbard,
Kate Bresner,
Ehsan Pishva
+ 3 more
Joshua Harvey,
Adam R. Smith,
Luke Stephen Weymouth,
Rebecca G. Smith,
Leon Hubbard,
Kate Bresner,
Ehsan Pishva,
Nigel Williams,
Katie Lunnon,
Byron Creese
Abstract Background Parkinson’s disease (PD) is a highly heterogeneous disorder, encompassing a complex spectrum of clinical presentation including motor, sleep, cognitive and neuropsychiatric symptoms. Together the cumulative effects of these symptoms have huge impacts on individual quality of life. Here we aim to investigate genome wide DNA‐methylation in post‐mortem PD brain samples and test for region specific association with common secondary symptoms of sleep disorder, visual hallucinations and dementia. Method DNA methylation data was generated on the Illumina 450K microarray for a cohort of 142 individual post mortem brain samples from the Frontal Cortex (FC), Caudate Putamen (CP) and Substantia Nigra (SN). Data was quality controlled following standardized, previously published pipelines. Clinical records for each case were assessed for binary status of sleep disorder, visual hallucinations and dementia. Linear models were used to identify differentially methylated positions (DMPs) for each of these outcomes, controlling for age, sex, post‐mortem interval and inferred cell‐type proportions as covariates. Result Thus far, results been only been generated for the dementia phenotype, with one genome wide significant loci passing multiple testing correction in the frontal cortex (p = 5.25e‐8). This DMP, found in the gene FAM175A / ABRAXAS‐1 (cg14699004), is hypomethylated in PD patients with preserved cognition, with comparable higher measures in PD‐Dementia and control samples. This effect appeared to be FC specific, with no DMPs passing genome wide significance in other brain regions tested. Conclusion Preliminary evidence indicates potential sub‐phenotype associated DMPs, with methylation at one site specifically associated with dementia within the FC. Current analysis is focussing on generating reference results across each of the phenotypes and brain regions assessed. Future work will look at Weighted Gene Correlation Network Analysis to identify networks associated with these individual phenotypes.
Investigating the molecular consequences of co‐morbidites in Alzheimer’s disease
Lachlan Ford MacBean, Adam R. Smith, Rebecca G. Smith, Katie Lunnon
Lachlan Ford MacBean,
Adam R. Smith,
Rebecca G. Smith,
Katie Lunnon
Abstract Background Due to the transient and highly sensitive nature of DNA methylation, it is important that Epigenome‐Wide Association Studies (EWAS) account for numerous variables that may influence the methylome as it is becoming increasingly clear that other diseases can influence the onset and severity of Alzheimer’s disease (AD). Method DNA was extracted from both AD (n = 119) and cognitively normal (n = 76) post‐mortem middle‐temporal gyrus brain tissue and DNA methylation quantified using Illumina methylation arrays. Combining the methylation beta values with detailed phenotypic data collected for each patient, including data on diabetes mellitus and TDP.43 proteinopathy, Principal Component Analysis was performed to determine co‐morbidities of AD that had a confounding effect on DNA methylation across the genome. Linear regression models were then designed to compare the methylomic consequences of TDP.43 proteinopathy in AD when co‐morbidities, such as DLB, are corrected for. Additionally, Analysis of Variance was used to conduct an EWAS evidencing the additional methylomic consequences of diabetes on AD‐diagnosed patients. Results An EWAS of AD and diabetes mellitus showed significant differential methylation at several sites across the genome, in particular within the gene BACE2 , suppression of which promotes β‐cell survival. Further linear regression analysis of methylation data that had been corrected for co‐morbidities, including DLB, shows that much of the methylation changes seen in EWAS may be accounted for by these confounding diseases, while changes in genes associated with the pathology of interest retain their significance. In the study of TDP.43 proteinopathy and AD this can be observed at probes in the genes HAX1 , CUX1 , and CCDC88C . Conclusion The next step for this project is to obtain more samples with clinical information on common co‐morbidities of AD. EWAS focussed on the effects of TDP.43 proteinopathy and diabetes mellitus can then be performed with greater power and the specific pathways identified. Nonetheless, this pilot data emphasises the need for comprehensive clinical data when performing studies on methylomic data.
Machine learning‐based prediction of cognitive outcomes in de novo Parkinson's disease
Joshua Harvey,
Rick A Reijnders,
Rachel Cavill,
Annelien Duits,
Sebastian Köhler,
Lars M.T. Eijssen,
Bart P.F. Rutten
+ 6 more
Joshua Harvey,
Rick A Reijnders,
Rachel Cavill,
Annelien Duits,
Sebastian Köhler,
Lars M.T. Eijssen,
Bart P.F. Rutten,
Gemma Shireby,
Ali Torkamani,
Byron Creese,
Albert F.G. Leentjens,
Katie Lunnon,
Ehsan Pishva
Abstract Background Cognitive impairment is a debilitating symptom in Parkinson’s disease (PD), with high variability in onset and course of progression. This present study aimed to establish an accurate multivariate machine learning model to predict cognitive outcome in newly diagnosed PD. Method Using baseline measures from the Parkinson’s Progression Markers Initiative (PPMI) cohort we subset clinical, biofluid and genetic/epigenetic variables. Annual cognitive assessments over an eight‐year time span were used to define two outcomes of i) dementia conversion, and ii) cognitive impairment. Outcomes and variable subsets were tested using multiple machine learning (ML) algorithms (random forest, elasticnet, SVM‐linear and cforest) to predict prognosis of individual cognitive decline in PD. Prediction was assessed using multiple measures including Area under the Curve (AUC) and Mathews Correlation Coefficient (MCC). Result For both cognitive outcomes, irrespective of the of ML algorithm, models consisting of clinical variables alone performed best, with high specificity and the largest AUC's (0.88 ‐ 0.92) and MCC's (0.57‐0.80). Notably, cognitive impairment outcome showed better sensitivity than dementia conversion outcome (0.72 – 0.81 vs 0.29 – 0.64, respectively). Addition of biological and genetic variables did not largely improve the model performance. However, a number of cerebrospinal fluid (CSF) proteins and epigenetic markers showed high predictive weighting in multiple models, when included alongside clinical variables. Conclusion Machine learning algorithms can accurately predict cognitive impairment development in PD. Within the generated models, clinical predictors appear to play a more prominent role than biological predictors. We further present additional future study data, expanding epigenetic research into PD dementia.
Characterisation of D409V/WT mice as a novel dementia model
Millie Sander, Jonathan T Brown, Clive G Ballard, Katie Lunnon
Millie Sander,
Jonathan T Brown,
Clive G Ballard,
Katie Lunnon
Abstract Background Alzheimer’s disease (AD) and dementia with Lewy bodies (DLB) share various pathological and symptomatic traits. Such overlap complicates diagnosis, ultimately impacting the level of care and treatment options available to patients. The development of novel models to further understand DLB is therefore imperative. Recent research indicates mice with heterozygous mutations (D409V/WT) in the GBA gene to be a viable option, presenting DLB‐associated characteristics such as age‐related cognitive decline, an increase in monomeric α‐synuclein deposition and cholinergic dysfunction (Clarke et al. , 2019). Methods To further characterise D409V/WT mice, we looked at measures of brain atrophy, patterns of neuronal firing, and transcriptomic changes. Global brain atrophy was assessed using six different measures surrounding cortical thickness and ventricle size from cresyl violet stained coronal sections. Neuronal activity in the medial septum was recorded through a series of multi‐electrode array (MEA) studies, and RNA was extracted from the same region in order to investigate transcriptional changes. All studies used WT littermates as controls. Results At 12 months of age, D409V/WT mice exhibited both ventricle enlargement and cortical thinning when compared with WT controls. All six measures used were significant at the p < 0.05 level. Neuronal firing appeared to be disrupted among D409V/WT mice compared to WT controls, but this was not found to be significant. Further analysis is currently being undertaken to determine the effects of both cell and slice variation upon these results. We anticipate all further MEA analysis, and transcriptomic analysis to be complete by 31 st May 2022. Conclusions These findings support D409V/WT mice to be a candidate model for DLB. Following further characterisation, we suggest this model may be useful in better understanding DLB and developing novel diagnostic tools.
An integrated systems‐level analysis of the molecular changes resulting from systemic inflammation and amyloid‐beta immunisation in Alzheimer’s disease
Lachlan Ford MacBean, Adam R. Smith, Rebecca G. Smith, Delphine Boche, Katie Lunnon
Lachlan Ford MacBean,
Adam R. Smith,
Rebecca G. Smith,
Delphine Boche,
Katie Lunnon
Abstract Background Post‐mortem histological examination of active amyloid‐beta immunisation participant brains revealed changes to Alzheimer’s neuropathology, including high levels of plaque removal and increased microglia phagocytic activity. We hypothesise that there are neuroinflammation‐associated changes to DNA methylation in the post‐mortem brain tissue of the study participants. This study was run in parallel with a study investigating the molecular consequences of systemic infections in AD. As systemic infections are linked to the development and onset of AD; we hypothesise that epigenetic and transcriptomic changes arise in microglia because of systemic inflammation and may drive the progression of AD. Method PFC and cerebellum tissue was acquired from 16 patients who had received varying doses of the AN‐1792 vaccine or a placebo. PFC tissue was also collected from AD patients who were diagnosed with a systemic infection at time of death (n = 65), AD patients not diagnosed with an infection (n = 70), cognitively normal patients diagnosed with an infection (n = 48). Tissue from cognitively normal patients with no systemic infection diagnosis (n = 66) was also collected, from which age‐matched controls were used for the immunisation study. DNA was extracted from all cases and Infinium methylation EPIC array employed for quantitative interrogation of methylation sites across the genome. Using linear regression analysis, regions of significant differential methylation were identified and annotated to disease relevant genes. Result Epigenomic analyses have documented differential methylation dynamics in genes previously associated with AD both globally and in glial cells. This study also shows differences in DNA methylation in key genes in systemic infection cases, both in AD and cognitively normal patients, and immunised brain tissue. Conclusion Discovery of disease‐related methylation dynamics in immunised AD brains indicate a specific regulatory response to amyloid‐beta immunisation. Likewise, differential methylation in immunised and systemic infection cases proposes a role for DNA methylation as a key player in regulating microglial phagocytic activity and suggests key biomarkers as potential therapeutic targets.
Targeted bisulfite sequencing analysis of candidate genes associated with Alzheimer’s disease.
Greg Wheildon,
Adam R. Smith,
Darren Soanes,
Rebecca G. Smith,
Karen Moore,
Paul O'Neill,
Kevin Morgan
+ 6 more
Greg Wheildon,
Adam R. Smith,
Darren Soanes,
Rebecca G. Smith,
Karen Moore,
Paul O'Neill,
Kevin Morgan,
Alan J Thomas,
Paul T Francis,
Seth Love,
Jonathan Mill,
Ehsan Pishva,
Katie Lunnon
Abstract Background Recent epigenome‐wide association studies (EWAS) have identified a number of loci in specific genes that show robust and reproducible alterations in DNA methylation in Alzheimer’s disease brain samples. The standard method to assess methylation in EWAS is via microarrays, however, these only target a limited number of methylation sites in each gene. Therefore, further analysis of methylation changes across the entire gene are required to determine the exact extent and pattern of methylation changes in disease. In this study we have performed targeted bisulfite sequencing for candidate genes in the Brains for Dementia Research (BDR) tissue sample resource, which is a highly characterized cohort containing tissue with a high degree of standardized pathological, clinical and administrative data available to allow comparative studies. Method Prefrontal cortex brain samples from 60 individuals were selected from the BDR cohort and grouped by Braak stage (Control 0‐II; mild cognitive impairment III‐IV; AD V‐VI). The DNA was extracted, before 30 genomic regions of interest, identified from previous AD EWAS, were captured using Agilent Sure Select target baits. The DNA was next‐generation bisulfite sequenced, before the sequence reads were aligned and the methylation status of cytosine residues were called using the Bismark Bisulfite Mapper program. Differentially methylated positions (DMPs) were then analyzed across the three groups. Result The degree and extent of methylation within the targeted genomic regions were identified and quantified for each group before being analyzed using linear regression models. Conclusion This study builds on previous work that identified differential methylation in several genomic regions that were associated with Braak stage. By identifying the exact positions that are subjected to differential methylation this work provides further evidence that dysregulation of methylation is associated with pathological changes in AD prefrontal cortex.
Polygenic risk score association with cognitive decline in Parkinson’s Disease
Joshua Harvey,
Rick A Reijnders,
Gemma Shireby,
Annelien Duits,
Sebastian Köhler,
Byron Creese,
Katie Lunnon
+ 1 more
Joshua Harvey,
Rick A Reijnders,
Gemma Shireby,
Annelien Duits,
Sebastian Köhler,
Byron Creese,
Katie Lunnon,
Ehsan Pishva
Abstract Background Cognitive impairment is a common and debilitating symptom in Parkinson’s disease (PD) with high variability in individual trajectory of decline. We sought to explore heterogeneity in the trajectory of individual cognitive change in a cohort of early stage PD patients and test association to cumulative genetic risk identified in large scale Genome Wide Association Studies (GWAS). Method Using longitudinal measures of the Montreal Cognitive Assessment (MoCA) we employed latent class mixed modelling (LCMM) to identify and investigate unknown populations in the Parkinson’s Progression Markers Inititative (PPMI) de‐novo PD cohort. Tranformed MoCA scores were modelled as a quadratic function of years from baseline, controlling for age, gender and motor symptom severity. Optimal group number was identified and determined using standardly advised model fit metrics. Polygenic risk scores (PRS) for five GWAS were calculated using PRSice‐2 applied to genotyping array data. Association of PRS with cognitive groups was tested using linear models and ANOVA tests. Result LCMM showed optimal fit statistics for three classes (lowest BIC, high entropy) and these groups were retained for further analysis The largest identified class (n = 240) on average, presented at baseline with higher MoCA scores and remained stable over time. The second class (n = 132) presented with lower MoCA scores and showed a slow declining trajectory whilst the smallest class (n = 13) presented with lower MoCA scores but declined at a rapid rate. Educational attainment and Alzheimer’s disease (AD) GWAS derived PRS were significantly associated with cognitive class and explained the highest amount of phenotypic variance. For PD case‐control status, only the PD PRS was significantly associated with Parkinson’s status and explained a similar level of phenotypic variation. Conclusion Latent class analysis may provide utility in subsetting longitudinal cognitive outcome groups for use in groupwise comparisons. Using this method we show evidence for association of educational attainment and AD cumulative genetic risk and worse cognitive outcomes in early PD.
DNA methylation profiling across brain regions in Huntington’s disease.
Greg Wheildon, Luke Stephen Weymouth, Adam R. Smith, Rebecca G. Smith, Claire Troakes, Safa Al‐Sarraj, Katie Lunnon
Greg Wheildon,
Luke Stephen Weymouth,
Adam R. Smith,
Rebecca G. Smith,
Claire Troakes,
Safa Al‐Sarraj,
Katie Lunnon
Abstract Background Huntington’s disease (HD) is an autosomal dominant condition that occurs due to the expansion of a CAG trinucleotide repeat in the Huntingtin (HTT) gene. The translated HTT protein has an expanded polyglutamine sequence thought to cause deleterious effects. These effects cause severe neurodegeneration in the striatum. In HD there is also clear atrophy in the cerebellum and a reduction in cortical thickness, including in the entorhinal cortex (EC). Epigenome wide association studies (EWAS) of DNA methylation differences in HD have thus far been limited to the cerebral cortex and use older technologies such as the Illumina 450K array. In this study, we performed an EWAS of HD in the striatum, EC and cerebellum, using the Illumina EPIC methylation array to profile 850, 000 sites across the genome. Method 120 striatum, EC and cerebellum DNA samples from 22 control and 20 HD subjects were selected and matched for sex, age and post‐mortem interval. The samples were chosen to be as free from co‐existing pathologies as possible. The majority of subjects were represented in each brain region. The DNA was bisulfite converted, randomized and profiled using the EPIC array. The methylation intensities for each sample were subjected to quality control (QC). Following QC, the samples were analyzed in R for differences in methylation between HD and control samples within each brain region, before being subjected to cross‐regional analysis. Result We have used linear regression models to identify differentially methylated positions (DMPs) in specific brain regions in HD. We have used regional analyses to identify differentially methylated regions (DMRs) consisting of multiple adjacent DMPs. Finally, downstream analyses have highlighted epigenetically altered pathways in disease. Conclusion This study builds a clearer picture of DNA methylation profiles in HD in disease relevant brain regions. Future studies should integrate this with other levels of genomic regulation.
DNA methylation of mitochondrial DNA shows variation in human brain.
Greg Wheildon,
Adam R. Smith,
Darren Soanes,
Francesca Southern,
Mathew Devall,
Karen Moore,
Paul O'Neill
+ 2 more
Greg Wheildon,
Adam R. Smith,
Darren Soanes,
Francesca Southern,
Mathew Devall,
Karen Moore,
Paul O'Neill,
Claire Troakes,
Katie Lunnon
Abstract Background There is growing evidence for the role of DNA methylation in regulating the transcription of mitochondrial genes, particularly in neurodegenerative disorders characterized by mitochondrial dysfunction including Alzheimer’s disease (AD). However, to date, a cross‐comparative analysis of the mitochondrial DNA methylome in neurodegenerative disorders has yet to be undertaken. Method Here, we present an interrogation of the mitochondrial DNA methylome at single base resolution, using pyrosequencing, across different types of neurodegenerative disorders. We performed a targeted study design to investigate the D‐Loop methylation of the mtDNA in the entorhinal cortex (EC) for a pilot cohort of 26 AD, 22 Dementia with Lewy bodies (DLB) and 26 control samples, matched as closely as possible for age and sex. This research forms the basis of a larger study which will compare D‐Loop methylation in several brain regions including the EC, superior temporal gyrus and cerebellum in AD, DLB, Vascular dementia, Huntington’s (HD) and Parkinson’s disease (PD) samples. The striatum and substantia nigra, will also be analyzed in the HD and PD samples respectively. Result We have identified DNA methylation differences at the D‐Loop in different neurodegenerative diseases. In particular, we have found two statistically significant sites that show a decrease in percentage methylation of approximately 4% and 3% in the EC of the DLB brain samples compared to controls. Conclusion We have discovered differences in DNA methylation across the mitochondrial genome between different types of neurodegenerative disorders in human brain samples using pyrosequencing. Moving forward we will take this approach and expand into the larger cohort to further investigate the role of mitochondrial epigenetic mechanisms in neurodegenerative disorders.
An integrated systems‐level analysis of the molecular changes resulting from systemic infections in Alzheimer’s disease
Lachlan Ford MacBean, Adam R. Smith, Rebecca G. Smith, Katie Lunnon
Lachlan Ford MacBean,
Adam R. Smith,
Rebecca G. Smith,
Katie Lunnon
Abstract Background To fully understand the molecular consequences of neuroinflammation and systemic infection in Alzheimer’s disease (AD), it is important to scrutinise molecular changes occurring in the brain in individuals with AD after they have had a systemic infection. Recently, several epigenome‐wide association studies (EWAS) have identified robust and reproducible alterations in AD brain samples compared to controls. In the current study we have performed an EWAS comparing bulk brain tissue in individuals with AD and non‐demented controls with or without a systemic infection. Method DNA methylation arrays were employed for quantification of DNA methylation in extracted DNA from 276 prefrontal cortex brain tissue samples (controls, n = 72; AD‐diagnosed, n = 86; cognitively normal with infection, n = 48; AD‐diagnosed with infection, n = 70). Methylation values were quality checked and normalised before Analysis of Variance was performed to identify sites of significant differential methylation across all groups. Probes that were significant to AD‐only patients and infection‐only patients, when compared to controls, were removed, leaving only probes that were specifically differentially methylated in infection‐AD cases. Results Overall, more significant changes in methylation across the genome can be observed in AD patients who also suffered from systemic infection compared to AD‐only patients and infection‐only patients. By removing probes that are significantly associated with either systemic infections or AD, the remaining significant probes are therefore more likely to be associated with the consequences of infections, specifically within AD patients. Identified genes include AUTS2 , a gene implicated in developmental disorders, and ADAR , a protein‐coding gene involved in the control of the innate immune response and controlling the function of certain neurotransmitters. Conclusion The exact pathways affected by systemic infection are yet to be scrutinised, however this initial data provides evidence that unique changes to the methylome occur in AD‐diagnosed patients who additionally suffer from a systemic infection. The next steps of this project include isolating microglia to observe methylation changes specific to these cells, as well as incorporating more sample data sets to improve power.
Characterizing the relationship between telomere length and DNA methylation age in induced pluripotent stem cells during neuronal differentiation
Jennifer L Imm, Emma L Cope, Kimberly M Jones, Joe Burrage, Nicholas D Allen, Katie Lunnon
Jennifer L Imm,
Emma L Cope,
Kimberly M Jones,
Joe Burrage,
Nicholas D Allen,
Katie Lunnon
Abstract Background Induced pluripotent stem cells (iPSCs) and their resultant neurons are popular models for studying diseases of aging, such as Alzheimer’s disease (AD). One hallmark of aging is the decreasing length of telomeres, the repetitive, protective DNA sequences at the end of each chromosome. We have previously demonstrated that whilst epigenetic age does increase with differentiation, iPSC‐derived neurons still have a fetal DNA methylation profile. It has also been shown by others that telomere length in iPSC‐derived neurons is shorter than the that of the stem cells from which they are derived. However, to our knowledge no one has looked at both epigenetic age and telomere length in the same samples. Therefore, we have collected DNA from different stages of the differentiation of iPSCs into neurons in order to look at the relationship between epigenetic age and telomere length. Method Human fibroblast cells were reprogrammed using lentiviral transfection. The resulting iPSC colonies were expanded, differentiated and collected at four different time points: day0 (iPSCs), day16 (neuronal progenitor cells), day37 and day58 (mature neurons). DNA methylation was assessed using the Illumina EPIC array and epigenetic age was derived using both the Horvath skin and blood clock and the Steg fetal brain clock. Absolute telomere length was determined using quantitative real‐time PCR. Result This study has identified the telomere dynamics of iPSCs as they undergo differentiation into cortical neurons. Not only this, but by also calculating the epigenetic age in the same samples we have been able to look at the relationship between telomere length and epigenetic age using two differentiation DNA methylation age calculators. Conclusion We have outlined the relationship between telomere length and DNA methylation age of iPSCs as they differentiate into cortical neurons. This information is important to consider when using iPSCs to model age‐related diseases such as AD.
Uncertainty quantification of reference-based cellular deconvolution algorithms
Dorothea Seiler Vellame,
Gemma Shireby,
Ailsa MacCalman,
Emma L Dempster,
Joe Burrage,
Tyler Gorrie-Stone,
Leonard S Schalkwyk
+ 2 more
Dorothea Seiler Vellame,
Gemma Shireby,
Ailsa MacCalman,
Emma L Dempster,
Joe Burrage,
Tyler Gorrie-Stone,
Leonard S Schalkwyk,
Jonathan Mill,
Eilis Hannon
The majority of epigenetic epidemiology studies to date have generated genome-wide profiles from bulk tissues (e.g., whole blood) however these are vulnerable to confounding from variation in cellular composition. Proxies for cellular composition can be mathematically derived from the bulk tissue profiles using a deconvolution algorithm; however, there is no method to assess the validity of these estimates for a dataset where the true cellular proportions are unknown. In this study, we describe, validate and characterize a sample level accuracy metric for derived cellular heterogeneity variables. The CETYGO score captures the deviation between a sample's DNA methylation profile and its expected profile given the estimated cellular proportions and cell type reference profiles. We demonstrate that the CETYGO score consistently distinguishes inaccurate and incomplete deconvolutions when applied to reconstructed whole blood profiles. By applying our novel metric to >6,300 empirical whole blood profiles, we find that estimating accurate cellular composition is influenced by both technical and biological variation. In particular, we show that when using a common reference panel for whole blood, less accurate estimates are generated for females, neonates, older individuals and smokers. Our results highlight the utility of a metric to assess the accuracy of cellular deconvolution, and describe how it can enhance studies of DNA methylation that are reliant on statistical proxies for cellular heterogeneity. To facilitate incorporating our methodology into existing pipelines, we have made it freely available as an R package (https://github.com/ds420/CETYGO).
Epigenetic age acceleration is associated with oligodendrocyte proportions in MSA and control brain tissue
Megha Murthy,
Gemma Shireby,
Yasuo Miki,
Emmanuelle Viré,
Tammaryn Lashley,
Thomas T. Warner,
Jonathan Mill
+ 1 more
Megha Murthy,
Gemma Shireby,
Yasuo Miki,
Emmanuelle Viré,
Tammaryn Lashley,
Thomas T. Warner,
Jonathan Mill,
Conceição Bettencourt
AIMS: Epigenetic clocks are widely applied as surrogates for biological age in different tissues and/or diseases, including several neurodegenerative diseases. Despite white matter (WM) changes often being observed in neurodegenerative diseases, no study has investigated epigenetic ageing in white matter.
METHODS: We analysed the performances of two DNA methylation-based clocks, DNAmClockMulti and DNAmClockCortical , in post-mortem WM tissue from multiple subcortical regions and the cerebellum, and in oligodendrocyte-enriched nuclei. We also examined epigenetic ageing in control and multiple system atrophy (MSA) (WM and mixed WM and grey matter), as MSA is a neurodegenerative disease comprising pronounced WM changes and α-synuclein aggregates in oligodendrocytes.
RESULTS: Estimated DNA methylation (DNAm) ages showed strong correlations with chronological ages, even in WM (e.g., DNAmClockCortical , r = [0.80-0.97], p < 0.05). However, performances and DNAm age estimates differed between clocks and brain regions. DNAmClockMulti significantly underestimated ages in all cohorts except in the MSA prefrontal cortex mixed tissue, whereas DNAmClockCortical tended towards age overestimations. Pronounced age overestimations in the oligodendrocyte-enriched cohorts (e.g., oligodendrocyte-enriched nuclei, p = 6.1 × 10-5 ) suggested that this cell type ages faster. Indeed, significant positive correlations were observed between estimated oligodendrocyte proportions and DNAm age acceleration estimated by DNAmClockCortical (r > 0.31, p < 0.05), and similar trends were obtained with DNAmClockMulti . Although increased age acceleration was observed in MSA compared with controls, no significant differences were detected upon adjustment for possible confounders (e.g., cell-type proportions).
CONCLUSIONS: Our findings show that oligodendrocyte proportions positively influence epigenetic age acceleration across brain regions and highlight the need to further investigate this in ageing and neurodegeneration.
Social mobility across the lifecourse and DNA methylation age acceleration in adults in the UK
Yanchun Bao,
Tyler Gorrie-Stone,
Eilis Hannon,
Amanda Hughes,
Alexandria Andrayas,
Grant Neilson,
Joe Burrage
+ 3 more
Yanchun Bao,
Tyler Gorrie-Stone,
Eilis Hannon,
Amanda Hughes,
Alexandria Andrayas,
Grant Neilson,
Joe Burrage,
Jonathon Mill,
Leonard Schalkwyk,
Meena Kumari
Disadvantaged socio-economic position (SEP) is associated with greater biological age, relative to chronological age, measured by DNA methylation (positive ‘age acceleration’, AA). Social mobility has been proposed to ameliorate health inequalities. This study aimed to understand the association of social mobility with positive AA. Diagonal reference modelling and ordinary least square regression techniques were applied to explore social mobility and four measures of age acceleration (first-generation: ‘Horvath’, ‘Hannum’ and second-generation: ‘Phenoage’, DunedinPoAm) in n = 3140 participants of the UK Household Longitudinal Study. Disadvantaged SEP in early life is associated with positive AA for three (Hannum, Phenoage and DunedinPoAm) of the four measures examined while the second generation biomarkers are associated with SEP in adulthood (p < 0.01). Social mobility was associated with AA measured with Hannum only such that compared to no mobility, upward mobility was associated with greater age independently of origin and destination SEP. Compared to continuously advantaged groups, downward mobility was associated with positive Phenoage (1.06y [− 0.03, 2.14]) and DunedinPoAm assessed AA (0.96y [0.24, 1.68]). For these two measures, upward mobility was associated with negative AA (Phenoage, − 0.65y [− 1.30, − 0.002]; DunedinPoAm, − 0.96y [− 1.47, − 0.46]) compared to continually disadvantaged groups. While we find some support for three models of lifecourse epidemiology with early life as a sensitive period, SEP across the lifecourse and social mobility for age acceleration measured with DNA methylation, our findings suggest that disadvantaged SEP across the lifecourse is most consistently associated with positive AA.
Assessing the burden of rare DNA methylation deviations in schizophrenia
Christine Søholm Hansen, Andrew McQuillin, Claire David St, Jonathan Mill, Eilis Hannon, Andrew J. Sharp, Magdalena Janecka
Christine Søholm Hansen,
Andrew McQuillin,
Claire David St,
Jonathan Mill,
Eilis Hannon,
Andrew J. Sharp,
Magdalena Janecka
Abstract
Along with case-control group differences in DNA methylation (DNAm) identified in epigenomewide association studies (EWAS), multiple rare DNAm outliers may exist in subsets of cases, underlying the etiological heterogeneity of some disorders. This creates an impetus for novel approaches focused on detecting rare/private outliers in the individual methylomes. Here, we present a novel, data-driven method - Outlier Methylation Analysis (OMA) – which through optimization detects genomic regions with strongly deviating DNAm levels, which we call outlier methylation regions (OMRs).
Focusing on schizophrenia (SCZ) - a neuropsychiatric disorder with a heterogeneous etiology – we applied the OMA method in two independent, publicly available SCZ case-control samples with DNAm array information. We found SCZ cases had an increased burden of OMRs compared to controls (IRR=1.22, p=1.8×10
-8
), and case OMRs were enriched in regions relevant to cellular differentiation and development (i.e. polycomb repressed elements in the Gm12878 differentiated cell line, p=1.9×10
-5
, and poised promoters in the H1hesc stem cell line, p=5.4×10
-4
). Furthermore, SCZ cases were ~2.5-fold enriched (p=1.1×10
-3
) for OMRs overlapping genesets associated with developmental processes. The OMR burden was reduced in clozapine-treated, compared to untreated, SCZ cases (IRR=0.88, p=9.5×10
-3
), and also associated with increased chronological age (IRR=1.01, p= 2.7×10
-16
).
Our findings demonstrate an elevated burden of OMRs in SCZ, implying methylomic dysregulation in SCZ which could correspond to the etiological heterogeneity among cases. These results remain to be causally examined and replicated in other cohorts and tissues. For this, and applications in other traits, we offer the OMA method to the scientific community.
From methylation to myelination: epigenomic and transcriptomic profiling of chronic inactive demyelinated multiple sclerosis lesions
Assia Tiane,
Melissa Schepers,
Rick A. Reijnders,
Veggel Lieve van,
Sarah Chenine,
Ben Rombaut,
Emma Dempster
+ 8 more
Assia Tiane,
Melissa Schepers,
Rick A. Reijnders,
Veggel Lieve van,
Sarah Chenine,
Ben Rombaut,
Emma Dempster,
Catherine Verfaillie,
Kobi Wasner,
Anne Grünewald,
Jos Prickaerts,
Ehsan Pishva,
Niels Hellings,
den Hove Daniel van,
Tim Vanmierlo
Abstract Introduction In the progressive phase of multiple sclerosis (MS), the hampered differentiation capacity of oligodendrocyte precursor cells (OPCs) eventually results in remyelination failure. We have previously shown that DNA methylation of Id2/Id4 is highly involved in OPC differentiation and remyelination. In this study, we took an unbiased approach by determining genome-wide DNA methylation patterns within chronically demyelinated MS lesions and investigated how certain epigenetic signatures relate to OPC differentiation capacity. Methods We compared genome-wide DNA methylation and transcriptional profiles between chronically demyelinated MS lesions and matched normal-appearing white matter (NAWM), making use of post-mortem brain tissue (n=9/group). DNA methylation differences that inversely correlated with mRNA expression of their corresponding genes were validated for their cell-type specificity in laser-captured OPCs using pyrosequencing. The CRISPR-dCas9-DNMT3a/TET1 system was used to epigenetically edit human-iPSC-derived oligodendrocytes to assess the effect on cellular differentiation. Results Our data show hypermethylation of CpGs within genes that cluster in gene ontologies related to myelination and axon ensheathment. Cell type-specific validation indicates a region-dependent hypermethylation of MBP , encoding for myelin basic protein, in OPCs obtained from white matter lesions compared to NAWM-derived OPCs. By altering the DNA methylation state of specific CpGs within the promotor region of MBP , using epigenetic editing, we show that cellular differentiation can be bidirectionally manipulated using the CRISPR-dCas9-DNMT3a/TET1 system in vitro . Conclusion Our data indicate that OPCs within chronically demyelinated MS lesions acquire an inhibitory phenotype, which translates into hypermethylation of crucial myelination related genes. Altering the epigenetic status of MBP can restore the differentiation capacity of OPCs and possibly boost (re)myelination.
Genome-wide characterization of mitochondrial DNA methylation in human brain
Matthew Devall,
Darren M. Soanes,
Adam R. Smith,
Emma L. Dempster,
Rebecca G. Smith,
Joe Burrage,
Artemis Iatrou
+ 9 more
Matthew Devall,
Darren M. Soanes,
Adam R. Smith,
Emma L. Dempster,
Rebecca G. Smith,
Joe Burrage,
Artemis Iatrou,
Eilis Hannon,
Claire Troakes,
Karen Moore,
Paul O’Neill,
Safa Al-Sarraj,
Leonard Schalkwyk,
Jonathan Mill,
Michael Weedon,
Katie Lunnon
Background: There is growing interest in the role of DNA methylation in regulating the transcription of mitochondrial genes, particularly in brain disorders characterized by mitochondrial dysfunction. Here, we present a novel approach to interrogate the mitochondrial DNA methylome at single base resolution using targeted bisulfite sequencing. We applied this method to investigate mitochondrial DNA methylation patterns in post-mortem superior temporal gyrus and cerebellum brain tissue from seven human donors.
Results: We show that mitochondrial DNA methylation patterns are relatively low but conserved, with peaks in DNA methylation at several sites, such as within the D-LOOP and the genes MT-ND2, MT-ATP6, MT-ND4, MT-ND5 and MT-ND6, predominantly in a non-CpG context. The elevated DNA methylation we observe in the D-LOOP we validate using pyrosequencing. We identify loci that show differential DNA methylation patterns associated with age, sex and brain region. Finally, we replicate previously reported differentially methylated regions between brain regions from a methylated DNA immunoprecipitation sequencing study.
Conclusions: We have annotated patterns of DNA methylation at single base resolution across the mitochondrial genome in human brain samples. Looking to the future this approach could be utilized to investigate the role of mitochondrial epigenetic mechanisms in disorders that display mitochondrial dysfunction.
The relationship between case–control differential gene expression from brain tissue and genetic associations in schizophrenia
Nicholas E. Clifton, Anton Schulmann, Schizophrenia Working Group of the Psychiatric Genomics Consortium, Peter A. Holmans, Michael C. O'Donovan, P. Vawter
Nicholas E. Clifton,
Anton Schulmann,
Schizophrenia Working Group of the Psychiatric Genomics Consortium,
Peter A. Holmans,
Michael C. O'Donovan,
P. Vawter
American Journal of Medical Genetics Part B Neuropsychiatric Genetics
Large numbers of genetic loci have been identified that are known to contain common risk alleles for schizophrenia, but linking associated alleles to specific risk genes remains challenging. Given that most alleles that influence liability to schizophrenia are thought to do so by altered gene expression, intuitively, case-control differential gene expression studies should highlight genes with a higher probability of being associated with schizophrenia and could help identify the most likely causal genes within associated loci. Here, we test this hypothesis by comparing transcriptome analysis of the dorsolateral prefrontal cortex from 563 schizophrenia cases and 802 controls with genome-wide association study (GWAS) data from the third wave study of the Psychiatric Genomics Consortium. Genes differentially expressed in schizophrenia were not enriched for common allelic association statistics compared with other brain-expressed genes, nor were they enriched for genes within associated loci previously reported to be prioritized by genetic fine-mapping. Genes prioritized by Summary-based Mendelian Randomization were underexpressed in cases compared to other genes in the same GWAS loci. However, the overall strength and direction of expression change predicted by SMR were not related to that observed in the differential expression data. Overall, this study does not support the hypothesis that genes identified as differentially expressed from RNA sequencing of bulk brain tissue are enriched for those that show evidence for genetic associations. Such data have limited utility for prioritizing genes in currently associated loci in schizophrenia.
DOP88 Understanding the molecular mechanisms of anti-TNF treatment failure: Whole blood DNA methylation changes associated with primary non-response to anti-TNF treatment in patients with Crohn’s disease
S Lin,
E Hannon,
J F Waring,
M Reppell,
N Smaoui,
V L Pivorunas,
H Guay
+ 7 more
S Lin,
E Hannon,
J F Waring,
M Reppell,
N Smaoui,
V L Pivorunas,
H Guay,
N Chanchlani,
C Bewshea,
B Y H Bai,
N A Kennedy,
J R Goodhand,
J Mill,
T Ahmad
Abstract Background Anti-TNF treatment failure in patients with IBD is common and frequently related to low drug concentrations. DNA methylation sites from whole blood have been identified as effective biomarkers predicting treatment response to methotrexate and etanercept in patients with rheumatoid arthritis. We sought to define differences in DNA methylation associated with primary non-response (PNR) to anti-TNF treatment in patients with Crohn’s disease. Methods The Personalised Anti-TNF Therapy in Crohn’s disease (PANTS) study is a prospective UK-wide study investigating anti-TNF treatment failure in patients with active luminal Crohn’s disease. DNA methylation from whole blood was assessed using the Illumina EPIC Beadchip at baseline, weeks 14, 30 and 52. We compared DNA methylation profiles in a subset of adalimumab- and infliximab-treated patients who experienced PNR at week 14 and were not in remission at week 54 (infliximab = 99, adalimumab = 94) with patients who responded at week 14 and were in remission at week 54 (infliximab = 99, adalimumab = 93). Low anti-TNF drug concentration was defined as an infliximab level <3mg/L and adalimumab level <5mg/L. Epigenome-wide association (EWAS) analysis was performed using linear mixed models, where p values < 9 x 10-8 were considered significant. Because we observed significant changes in CD4 and CD8 T cells, B cells, NK cells, monocytes and granulocytes following anti-TNF treatment we adjusted our models for derived cell proportions (Figure 1). Results Overall, between baseline and week 14, we observed 4999 differentially methylated probes (DMPs) annotated to 2376 genes. Pathway analysis identified 108 significant gene ontology terms enriched in biological processes related to immune system processes and responses (Figure 2). EWAS analysis at baseline identified 48 DMPs annotated to 36 genes associated with PNR (Figure 3). The majority of DMPs (40/48) were hypermethylated (p < 0.001): of those annotated to genes, 25 were located in the gene body, 5 in the 5’ untranslated regions (UTR), 4 in transcription start sites and the remaining in 3’UTR. When EWAS analysis at baseline was stratified by anti-TNF drug concentration, 27 DMPs annotated to 17 genes were associated with PNR and low drug concentration. Of these, 11 DMPs were independently associated with low anti-TNF drug concentration at week 14 (Figure 4). We did not identify any DMPs associated with PNR with adequate drug concentration. Conclusion Our data suggests that baseline DNA methylation profiles may be used as a predictor for anti-TNF drug concentration at week 14.
DNA Methylation of α-Synuclein Intron 1 Is Significantly Decreased in the Frontal Cortex of Parkinson’s Individuals with GBA1 Mutations
Adam R. Smith, David M. Richards, Katie Lunnon, Anthony H. V. Schapira, Anna Migdalska-Richards
Adam R. Smith,
David M. Richards,
Katie Lunnon,
Anthony H. V. Schapira,
Anna Migdalska-Richards
Parkinson's disease (PD) is a common movement disorder, estimated to affect 4% of individuals by the age of 80. Mutations in the glucocerebrosidase 1 (GBA1) gene represent the most common genetic risk factor for PD, with at least 7-10% of non-Ashkenazi PD individuals carrying a GBA1 mutation (PD-GBA1). Although similar to idiopathic PD, the clinical presentation of PD-GBA1 includes a slightly younger age of onset, a higher incidence of neuropsychiatric symptoms, and a tendency to earlier, more prevalent and more significant cognitive impairment. The pathophysiological mechanisms underlying PD-GBA1 are incompletely understood, but, as in idiopathic PD, α-synuclein accumulation is thought to play a key role. It has been hypothesized that this overexpression of α-synuclein is caused by epigenetic modifications. In this paper, we analyze DNA methylation levels at 17 CpG sites located within intron 1 and the promoter of the α-synuclein (SNCA) gene in three different brain regions (frontal cortex, putamen and substantia nigra) in idiopathic PD, PD-GBA1 and elderly non-PD controls. In all three brain regions we find a tendency towards a decrease in DNA methylation within an eight CpG region of intron 1 in both idiopathic PD and PD-GBA1. The trend towards a reduction in DNA methylation was more pronounced in PD-GBA1, with a significant decrease in the frontal cortex. This suggests that PD-GBA1 and idiopathic PD have distinct epigenetic profiles, and highlights the importance of separating idiopathic PD and PD-GBA1 cases. This work also provides initial evidence that different genetic subtypes might exist within PD, each characterized by its own pathological mechanism. This may have important implications for how PD is diagnosed and treated.
An overview of DNA methylation-derived trait score methods and applications
Marta F. Nabais, Danni A. Gadd, Eilis Hannon, Jonathan Mill, Allan F. McRae, Naomi R. Wray
Marta F. Nabais,
Danni A. Gadd,
Eilis Hannon,
Jonathan Mill,
Allan F. McRae,
Naomi R. Wray
Microarray technology has been used to measure genome-wide DNA methylation in thousands of individuals. These studies typically test the associations between individual DNA methylation sites (“probes”) and complex traits or diseases. The results can be used to generate methylation profile scores (MPS) to predict outcomes in independent data sets. Although there are many parallels between MPS and polygenic (risk) scores (PGS), there are key differences. Here, we review motivations, methods, and applications of DNA methylation-based trait prediction, with a focus on common diseases. We contrast MPS with PGS, highlighting where assumptions made in genetic modeling may not hold in epigenetic data.
Wnt-7a-positive dendritic cytonemes induce synaptogenesis in cortical neurons
Thomas M. Piers, Seema C. Namboori, Akshay Bhinge, Richard Killick, Steffen Scholpp
Thomas M. Piers,
Seema C. Namboori,
Akshay Bhinge,
Richard Killick,
Steffen Scholpp
Summary
Neuronal circuits evolve as a precisely patterned network. In this context, a growing neuron must locate the appropriate target area on a neurite of a neighbouring cell with which to connect. Controlled target selection involves dendritic filopodial contacts and requires the exact apposition of synaptic components. Calcium signalling has been postulated to trigger the transformation from dendritic filopodia into functional synapses. However, calcium is a rather unspecific signalling system, and it needs to be clarified how the exact development of synaptic connections is controlled. Similarly, Wnt/β-catenin signalling promotes synapse formation; however, how secreted Wnts induce and maintain synapses on neuronal dendrites is not well understood. Here, we show that Wnt-7a is tethered to the tips of dynamic dendritic filopodia during spine formation in human cortical neurons. These filopodia can activate Wnt signalling precisely at the contact sites on the dendrites of an adjacent neuron. Subsequently, local calcium transients can be observed at these Wnt-positive contact sites. Depleting either the filopodial-loaded Wnt or the extracellular calcium pool blocks the clustering of pre- and post-synaptic markers, hence the establishment of stable connections. Therefore, we postulate that local Wnt-7a signalling from the tip of the dendritic filopodia, verified by simultaneous calcium signalling, provides an elegant mechanism for orchestrating focal synapse maturation.
Novel CYP1B1-RMDN2 Alzheimer’s disease locus identified by genome-wide association analysis of cerebral tau deposition on PET
Kwangsik Nho,
Shannon L. Risacher,
Liana Apostolova,
Paula J. Bice,
Jared Brosch,
Rachael Deardorff,
Kelley Faber
+ 55 more
Kwangsik Nho,
Shannon L. Risacher,
Liana Apostolova,
Paula J. Bice,
Jared Brosch,
Rachael Deardorff,
Kelley Faber,
Martin R. Farlow,
Tatiana Foroud,
Sujuan Gao,
Thea Rosewood,
Jun Pyo Kim,
Kelly Nudelman,
Meichen Yu,
Paul Aisen,
Reisa Sperling,
Basavaraj Hooli,
Sergey Shcherbinin,
Diana Svaldi,
Clifford R. Jack,
William J. Jagust,
Susan Landau,
Aparna Vasanthakumar,
Jeffrey F. Waring,
Vincent Doré,
Simon M. Laws,
Colin L. Masters,
Tenielle Porter,
Christopher C. Rowe,
Victor L Villemagne,
Logan Dumitrescu,
Timothy J. Hohman,
Julia B. Libby,
Elizabeth Mormino,
Rachel F. Buckley,
Keith Johnson,
Hyun-Sik Yang,
Ronald C. Petersen,
Vijay K. Ramanan,
Prashanthi Vemuri,
Ann D. Cohen,
Kang-Hsien Fan,
M. Ilyas Kamboh,
Oscar L. Lopez,
David A. Bennett,
Muhammad Ali,
Tammie Benzinger,
Carlos Cruchaga,
Diana Hobbs,
Jager Philip L. De,
Masashi Fujita,
Vaishnavi Jadhav,
Bruce T. Lamb,
Andy P. Tsai,
Isabel Castanho,
Jonathan Mill,
Michael W. Weiner,
Alzheimer’s Disease Neuroimaging Initiative,
of Defense the Alzheimer’s Disease Neuroimaging Initiative – Department,
the Anti-Amyloid Treatment in Asymptomatic Alzheimer’s Study,
Biomarker & Lifestyle Study Australian Imaging,
Andrew J. Saykin
Determining the genetic architecture of Alzheimer's disease (AD) pathologies can enhance mechanistic understanding and inform precision medicine strategies. Here, we performed a genome-wide association study of cortical tau quantified by positron emission tomography in 3,136 participants from 12 independent studies. The CYP1B1-RMDN2 locus was associated with tau deposition. The most significant signal was at rs2113389, which explained 4.3% of the variation in cortical tau, while APOE4 rs429358 accounted for 3.6%. rs2113389 was associated with higher tau and faster cognitive decline. Additive effects, but no interactions, were observed between rs2113389 and diagnosis, APOE4 , and Aβ positivity. CYP1B1 expression was upregulated in AD. rs2113389 was associated with higher CYP1B1 expression and methylation levels. Mouse model studies provided additional functional evidence for a relationship between CYP1B1 and tau deposition but not Aβ. These results may provide insight into the genetic basis of cerebral tau and novel pathways for therapeutic development in AD.
Genome‐wide DNA methylation analysis of aggressive behaviour: a longitudinal population‐based study
Ehsan Pishva,
den Hove Daniel L. A. van,
Valentin Laroche,
Aneth Lvovs,
Arunima Roy,
Gabriela Ortega,
Joe Burrage
+ 5 more
Ehsan Pishva,
den Hove Daniel L. A. van,
Valentin Laroche,
Aneth Lvovs,
Arunima Roy,
Gabriela Ortega,
Joe Burrage,
Toomas Veidebaum,
Margus Kanarik,
Jonathan Mill,
Klaus‐Peter Lesch,
Jaanus Harro
BACKGROUND: Human aggression is influenced by an interplay between genetic predisposition and experience across the life span. This interaction is thought to occur through epigenetic mechanisms, inducing differential gene expression, thereby moderating neuronal cell and circuit function, and thus shaping aggressive behaviour.
METHODS: Genome-wide DNA methylation (DNAm) levels were measured in peripheral blood obtained from 95 individuals participating in the Estonian Children Personality Behaviours and Health Study (ECPBHS) at 15 and 25 years of age. We examined the association between aggressive behaviour, as measured by Life History of Aggression (LHA) total score and DNAm levels both assessed at age 25. We further examined the pleiotropic effect of genetic variants regulating LHA-associated differentially methylated positions (DMPs) and multiple traits related to aggressive behaviours. Lastly, we tested whether the DNA methylomic loci identified in association with LHA at age 25 were also present at age 15.
RESULTS: We found one differentially methylated position (DMP) (cg17815886; p = 1.12 × 10-8 ) and five differentially methylated regions (DMRs) associated with LHA after multiple testing adjustments. The DMP annotated to the PDLIM5 gene, and DMRs resided in the vicinity of four protein-encoding genes (TRIM10, GTF2H4, SLC45A4, B3GALT4) and a long intergenic non-coding RNA (LINC02068). We observed evidence for the colocalization of genetic variants associated with top DMPs and general cognitive function, educational attainment and cholesterol levels. Notably, a subset of the DMPs associated with LHA at age 25 also displayed altered DNAm patterns at age 15 with high accuracy in predicting aggression.
CONCLUSIONS: Our findings highlight the potential role of DNAm in the development of aggressive behaviours. We observed pleiotropic genetic variants associated with identified DMPs, and various traits previously established to be relevant in shaping aggression in humans. The concordance of DNAm signatures in adolescents and young adults may have predictive value for inappropriate and maladaptive aggression later in life.
Whole blood DNA methylation changes are associated with anti-TNF drug concentration in patients with Crohn’s disease
Simeng Lin,
Eilis Hannon,
Mark Reppell,
Jeffrey F. Waring,
Nizar Smaoui,
Valerie Pivorunas,
Heath Guay
+ 8 more
Simeng Lin,
Eilis Hannon,
Mark Reppell,
Jeffrey F. Waring,
Nizar Smaoui,
Valerie Pivorunas,
Heath Guay,
Neil Chanchlani,
Claire Bewshea,
Benjamin Y H Bai,
Nicholas A Kennedy,
James R Goodhand,
Jonathan Mill,
Tariq Ahmad,
PANTS Consortium
Abstract Background and Aims Anti-TNF treatment failure in patients with inflammatory bowel disease (IBD) is common and frequently related to low drug concentrations. In order to identify patients who may benefit from dose optimisation at the outset of anti-TNF therapy, we sought to define epigenetic biomarkers in whole blood at baseline associated with anti-TNF drug concentrations at week 14. Methods DNA methylation from 1,104 whole blood samples from the Personalised Anti-TNF Therapy in Crohn’s disease (PANTS) study were assessed using the Illumina EPIC Beadchip at baseline, weeks 14, 30 and 54. We compared DNA methylation profiles in anti-TNF-treated patients who experienced primary non-response at week 14 and were not in remission at week 30 or 54 (infliximab n = 99, adalimumab n = 94) with patients who responded at week 14 and were in remission at week 30 or 54 (infliximab n = 99, adalimumab n = 93). Results Overall, between baseline and week 14, we observed 4,999 differentially methylated probes (DMPs) annotated to 2376 genes following anti-TNF treatment. Pathway analysis identified 108 significant gene ontology terms enriched in biological processes related to immune system processes and responses. Epigenome-wide association (EWAS) analysis identified 323 DMPs annotated to 210 genes at baseline associated with higher anti-TNF drug concentrations at week 14. Of these, 125 DMPs demonstrated shared associations with other common traits (proportion of shared CpGs compared to DMPs) including body mass index (23.2%), followed by CRP (11.5%), smoking (7.4%), alcohol consumption per day (7.1%) and IBD type (6.8%). EWAS of primary non-response to anti-TNF identified 20 DMPs that were associated with both anti-TNF drug concentration and primary non-response to anti-TNF with a strong correlation of the coefficients (Spearman’s rho = −0.94, p < 0.001). Conclusion Baseline DNA methylation profiles may be used as a predictor for anti-TNF drug concentration at week 14 to identify patients who may benefit from dose optimisation at the outset of anti-TNF therapy.
Genetic impacts on DNA methylation help elucidate regulatory genomic processes
Sergio Villicaña,
Juan Castillo-Fernandez,
Eilis Hannon,
Colette Christiansen,
Pei-Chien Tsai,
Jane Maddock,
Diana Kuh
+ 9 more
Sergio Villicaña,
Juan Castillo-Fernandez,
Eilis Hannon,
Colette Christiansen,
Pei-Chien Tsai,
Jane Maddock,
Diana Kuh,
Matthew Suderman,
Christine Power,
Caroline Relton,
George Ploubidis,
Andrew Wong,
Rebecca Hardy,
Alissa Goodman,
Ken K. Ong,
Jordana T. Bell
Abstract Pinpointing genetic impacts on DNA methylation can improve our understanding of pathways that underlie gene regulation and disease risk. We report heritability and methylation quantitative trait locus (meQTL) analysis at 724,499 CpGs profiled with the Illumina Infinium MethylationEPIC array in 2,358 blood samples from three UK cohorts, with replication. Methylation levels at 34.2% of CpGs were affected by SNPs, and 98% of effects were cis -acting or within 1 Mbp of the tested CpG. Our results are consistent with meQTL analyses based on the former Illumina Infinium HumanMethylation450 array. Both meQTL SNPs and CpGs with meQTLs were overrepresented in enhancers, which have improved coverage on this platform compared to previous approaches. Co-localisation analyses across genetic effects on DNA methylation and 56 human traits identified 1,520 co-localisations across 1,325 unique CpGs and 34 phenotypes, including in disease-relevant genes, such ICOSLG (inflammatory bowel disease), and USP1 and DOCK7 (total cholesterol levels). Enrichment analysis of meQTLs and integration with expression QTLs gave insights into mechanisms underlying cis -meQTLs, for example through disruption of transcription factor binding sites for CTCF and SMC3, and trans -meQTLs, for example through regulating the expression of ACD and SENP7 which can modulate DNA methylation at distal sites. Our findings improve the characterisation of the mechanisms underlying DNA methylation variability and are informative for prioritisation of GWAS variants for functional follow-ups. A results database and viewer are available online.
Cross-National and Cross-Generational Evidence That Educational Attainment May Slow the Pace of Aging in European-Descent Individuals.
Karen Sugden,
Terrie E Moffitt,
Thalida Em Arpawong,
Louise Arseneault,
Daniel W Belsky,
David L Corcoran,
Eileen M Crimmins
+ 8 more
Karen Sugden,
Terrie E Moffitt,
Thalida Em Arpawong,
Louise Arseneault,
Daniel W Belsky,
David L Corcoran,
Eileen M Crimmins,
Eilis Hannon,
Renate Houts,
Jonathan S Mill,
Richie Poulton,
Sandhya Ramrakha,
Jasmin Wertz,
Benjamin S Williams,
Avshalom Caspi
OBJECTIVES: Individuals with more education are at lower risk of developing multiple, different age-related diseases than their less-educated peers. A reason for this might be that individuals with more education age slower. There are 2 complications in testing this hypothesis. First, there exists no definitive measure of biological aging. Second, shared genetic factors contribute toward both lower educational attainment and the development of age-related diseases. Here, we tested whether the protective effect of educational attainment was associated with the pace of aging after accounting for genetic factors.
METHODS: We examined data from 5 studies together totaling almost 17,000 individuals with European ancestry born in different countries during different historical periods, ranging in age from 16 to 98 years old. To assess the pace of aging, we used DunedinPACE, a DNA methylation algorithm that reflects an individual's rate of aging and predicts age-related decline and Alzheimer's disease and related disorders. To assess genetic factors related to education, we created a polygenic score based on the results of a genome-wide association study of educational attainment.
RESULTS: Across the 5 studies, and across the life span, higher educational attainment was associated with a slower pace of aging even after accounting for genetic factors (meta-analysis effect size = -0.20; 95% confidence interval [CI]: -0.30 to -0.10; p = .006). Further, this effect persisted after taking into account tobacco smoking (meta-analysis effect size = -0.13; 95% CI: -0.21 to -0.05; p = .01).
DISCUSSION: These results indicate that higher levels of education have positive effects on the pace of aging, and that the benefits can be realized irrespective of individuals' genetics.
Exploring the mediation of DNA methylation across the epigenome between childhood adversity and First Episode of Psychosis—findings from the EU-GEI study
Luis Alameda,
Zhonghua Liu,
Pak C. Sham,
Monica Aas,
Giulia Trotta,
Victoria Rodriguez,
Forti Marta Di
+ 37 more
Luis Alameda,
Zhonghua Liu,
Pak C. Sham,
Monica Aas,
Giulia Trotta,
Victoria Rodriguez,
Forti Marta Di,
Simona A. Stilo,
Radhika Kandaswamy,
Celso Arango,
Manuel Arrojo,
Miguel Bernardo,
Julio Bobes,
Haan Lieuwe de,
Cristina Marta Del-Ben,
Charlotte Gayer-Anderson,
Lucia Sideli,
Peter B. Jones,
Hannah E. Jongsma,
James B. Kirkbride,
Cascia Caterina La,
Antonio Lasalvia,
Sarah Tosato,
Pierre-Michel Llorca,
Paulo Rossi Menezes,
Os Jim van,
Diego Quattrone,
Bart P. Rutten,
Jose Luis Santos,
Julio Sanjuán,
Jean-Paul Selten,
Andrei Szöke,
Ilaria Tarricone,
Andrea Tortelli,
Eva Velthorst,
Craig Morgan,
Emma Dempster,
Eilis Hannon,
Joe Burrage,
Daniella Dwir,
Atheeshaan Arumuham,
Jonathan Mill,
Robin M. Murray,
Chloe C. Y. Wong
AbtractStudies conducted in psychotic disorders have shown that DNA-methylation (DNAm) is sensitive to the impact of Childhood Adversity (CA). However, whether it mediates the association between CA and psychosis is yet to be explored. Epigenome wide association studies (EWAS) using the Illumina Infinium-Methylation EPIC array in peripheral blood tissue from 366 First-episode of psychosis and 517 healthy controls was performed. Adversity scores were created for abuse, neglect and composite adversity with the Childhood Trauma Questionnaire (CTQ). Regressions examining (I) CTQ scores with psychosis; (II) with DNAm EWAS level and (III) between DNAm and caseness, adjusted for a variety of confounders were conducted. Divide-Aggregate Composite-null Test for the composite null-hypothesis of no mediation effect was conducted. Enrichment analyses were conducted with missMethyl package and the KEGG database. Our results show that CA was associated with psychosis (Composite: OR = 1.68; p = <0.001; abuse: OR = 2.16; p < 0.001; neglect: OR = 2.27; p = <0.001). None of the CpG sites significantly mediated the adversity-psychosis association after Bonferroni correction (p < 8.1 × 10−8). However, 28, 34 and 29 differentially methylated probes associated with 21, 27, 20 genes passed a less stringent discovery threshold (p < 5 × 10−5) for composite, abuse and neglect respectively, with a lack of overlap between abuse and neglect. These included genes previously associated to psychosis in EWAS studies, such as PANK1, SPEG TBKBP1, TSNARE1 or H2R. Downstream gene ontology analyses did not reveal any biological pathways that survived false discovery rate correction. Although at a non-significant level, DNAm changes in genes previously associated with schizophrenia in EWAS studies may mediate the CA-psychosis association. These results and associated involved processes such as mitochondrial or histaminergic disfunction, immunity or neural signalling requires replication in well powered samples. The lack of overlap between mediating genes associated with abuse and neglect suggests differential biological trajectories linking CA subtypes and psychosis.
A comparison of feature selection methodologies and learning algorithms in the development of a DNA methylation-based telomere length estimator
Trevor Doherty,
Emma Dempster,
Eilis Hannon,
Jonathan Mill,
Richie Poulton,
David Corcoran,
Karen Sugden
+ 5 more
Trevor Doherty,
Emma Dempster,
Eilis Hannon,
Jonathan Mill,
Richie Poulton,
David Corcoran,
Karen Sugden,
Ben Williams,
Avshalom Caspi,
Terrie E. Moffitt,
Sarah Jane Delany,
Therese M. Murphy
BackgroundThe field of epigenomics holds great promise in understanding and treating disease with advances in machine learning (ML) and artificial intelligence being vitally important in this pursuit. Increasingly, research now utilises DNA methylation measures at cytosine–guanine dinucleotides (CpG) to detect disease and estimate biological traits such as aging. Given the challenge of high dimensionality of DNA methylation data, feature-selection techniques are commonly employed to reduce dimensionality and identify the most important subset of features. In this study, our aim was to test and compare a range of feature-selection methods and ML algorithms in the development of a novel DNA methylation-based telomere length (TL) estimator. We utilised both nested cross-validation and two independent test sets for the comparisons.ResultsWe found that principal component analysis in advance of elastic net regression led to the overall best performing estimator when evaluated using a nested cross-validation analysis and two independent test cohorts. This approach achieved a correlation between estimated and actual TL of 0.295 (83.4% CI [0.201, 0.384]) on the EXTEND test data set. Contrastingly, the baseline model of elastic net regression with no prior feature reduction stage performed less well in general—suggesting a prior feature-selection stage may have important utility. A previously developed TL estimator, DNAmTL, achieved a correlation of 0.216 (83.4% CI [0.118, 0.310]) on the EXTEND data. Additionally, we observed that different DNA methylation-based TL estimators, which have few common CpGs, are associated with many of the same biological entities.ConclusionsThe variance in performance across tested approaches shows that estimators are sensitive to data set heterogeneity and the development of an optimal DNA methylation-based estimator should benefit from the robust methodological approach used in this study. Moreover, our methodology which utilises a range of feature-selection approaches and ML algorithms could be applied to other biological markers and disease phenotypes, to examine their relationship with DNA methylation and predictive value.
Brain DNA methylomic analysis of frontotemporal lobar degeneration reveals OTUD4 in shared dysregulated signatures across pathological subtypes
Katherine Fodder,
Megha Murthy,
Patrizia Rizzu,
Christina E. Toomey,
Rahat Hasan,
Jack Humphrey,
Towfique Raj
+ 5 more
Katherine Fodder,
Megha Murthy,
Patrizia Rizzu,
Christina E. Toomey,
Rahat Hasan,
Jack Humphrey,
Towfique Raj,
Katie Lunnon,
Jonathan Mill,
Peter Heutink,
Tammaryn Lashley,
Conceição Bettencourt
Frontotemporal lobar degeneration (FTLD) is an umbrella term describing the neuropathology of a clinically, genetically and pathologically heterogeneous group of diseases, including frontotemporal dementia (FTD) and progressive supranuclear palsy (PSP). Among the major FTLD pathological subgroups, FTLD with TDP-43 positive inclusions (FTLD-TDP) and FTLD with tau-positive inclusions (FTLD-tau) are the most common, representing about 90% of the cases. Although alterations in DNA methylation have been consistently associated with neurodegenerative diseases, including Alzheimer’s disease and Parkinson’s disease, little is known for FTLD and its heterogeneous subgroups and subtypes. The main goal of this study was to investigate DNA methylation variation in FTLD-TDP and FTLD-tau. We used frontal cortex genome-wide DNA methylation profiles from three FTLD cohorts (142 FTLD cases and 92 controls), generated using the Illumina 450K or EPIC microarrays. We performed epigenome-wide association studies (EWAS) for each cohort followed by meta-analysis to identify shared differentially methylated loci across FTLD subgroups/subtypes. In addition, we used weighted gene correlation network analysis to identify co-methylation signatures associated with FTLD and other disease-related traits. Wherever possible, we also incorporated relevant gene/protein expression data. After accounting for a conservative Bonferroni multiple testing correction, the EWAS meta-analysis revealed two differentially methylated loci in FTLD, one annotated to OTUD4 (5’UTR-shore) and the other to NFATC1 (gene body-island). Of these loci, OTUD4 showed consistent upregulation of mRNA and protein expression in FTLD. In addition, in the three independent co-methylation networks, OTUD4-containing modules were enriched for EWAS meta-analysis top loci and were strongly associated with the FTLD status. These co-methylation modules were enriched for genes implicated in the ubiquitin system, RNA/stress granule formation and glutamatergic synaptic signalling. Altogether, our findings identified novel FTLD-associated loci, and support a role for DNA methylation as a mechanism involved in the dysregulation of biological processes relevant to FTLD, highlighting novel potential avenues for therapeutic development.
Epigenetic age acceleration in frontotemporal lobar degeneration: a comprehensive analysis in the blood and brain
Megha Murthy, Patrizia Rizzu, Peter Heutink, Jonathan Mill, Tammaryn Lashley, Conceição Bettencourt
Megha Murthy,
Patrizia Rizzu,
Peter Heutink,
Jonathan Mill,
Tammaryn Lashley,
Conceição Bettencourt
Abstract Frontotemporal lobar degeneration (FTLD) includes a heterogeneous group of disorders pathologically characterized by the degeneration of the frontal and temporal lobes. In addition to major genetic contributors of FTLD such as mutations in MAPT, GRN , and C9orf72 , recent work has identified several epigenetic modifications including significant differential DNA methylation in DLX1 , and OTUD4 loci. As aging remains to be one of the major risk factors for FTLD, we investigated the presence of accelerated epigenetic aging in FTLD compared to controls. We calculated epigenetic age in both peripheral blood and brain tissues of multiple FTLD subtypes using several DNA methylation clocks, i.e., DNAmClock Multi , DNAmClock Hannum , DNAmClock Cortical , GrimAge and PhenoAge, and determined age acceleration and its association with different cellular proportions and clinical traits. Significant epigenetic age acceleration was observed in the peripheral blood of both frontotemporal dementia (FTD) and progressive supranuclear palsy (PSP) patients compared to controls with DNAmClock Hannum , even after accounting for confounding factors. A similar trend was observed with both DNAmClock Multi and DNAmClock Cortical in post-mortem frontal cortex tissue of PSP patients and in FTLD cases harboring GRN mutations. Our findings support that increased epigenetic age acceleration in the peripheral blood could be an indicator for PSP and to a smaller extent, FTD.
From methylation to myelination: epigenomic and transcriptomic profiling of chronic inactive demyelinated multiple sclerosis lesions
Assia Tiane,
Melissa Schepers,
Rick A. Reijnders,
Veggel Lieve van,
Sarah Chenine,
Ben Rombaut,
Emma Dempster
+ 8 more
Assia Tiane,
Melissa Schepers,
Rick A. Reijnders,
Veggel Lieve van,
Sarah Chenine,
Ben Rombaut,
Emma Dempster,
Catherine Verfaillie,
Kobi Wasner,
Anne Grünewald,
Jos Prickaerts,
Ehsan Pishva,
Niels Hellings,
den Hove Daniel van,
Tim Vanmierlo
In the progressive phase of multiple sclerosis (MS), the hampered differentiation capacity of oligodendrocyte precursor cells (OPCs) eventually results in remyelination failure. We have previously shown that DNA methylation of Id2/Id4 is highly involved in OPC differentiation and remyelination. In this study, we took an unbiased approach by determining genome-wide DNA methylation patterns within chronically demyelinated MS lesions and investigated how certain epigenetic signatures relate to OPC differentiation capacity. We compared genome-wide DNA methylation and transcriptional profiles between chronically demyelinated MS lesions and matched normal-appearing white matter (NAWM), making use of post-mortem brain tissue (n = 9/group). DNA methylation differences that inversely correlated with mRNA expression of their corresponding genes were validated for their cell-type specificity in laser-captured OPCs using pyrosequencing. The CRISPR–dCas9-DNMT3a/TET1 system was used to epigenetically edit human-iPSC-derived oligodendrocytes to assess the effect on cellular differentiation. Our data show hypermethylation of CpGs within genes that cluster in gene ontologies related to myelination and axon ensheathment. Cell type-specific validation indicates a region-dependent hypermethylation of MBP, encoding for myelin basic protein, in OPCs obtained from white matter lesions compared to NAWM-derived OPCs. By altering the DNA methylation state of specific CpGs within the promotor region of MBP, using epigenetic editing, we show that cellular differentiation and myelination can be bidirectionally manipulated using the CRISPR–dCas9-DNMT3a/TET1 system in vitro. Our data indicate that OPCs within chronically demyelinated MS lesions acquire an inhibitory phenotype, which translates into hypermethylation of crucial myelination-related genes. Altering the epigenetic status of MBP can restore the differentiation capacity of OPCs and possibly boost (re)myelination.
Transcription‐based drug repurposing in Alzheimer disease psychosis
Morteza P Kouhsar,
Byron Creese,
Luke Stephen Weymouth,
Adam R. Smith,
Sverre Bergh,
Yehani Wedatilake,
Geir Selbæk
+ 7 more
Morteza P Kouhsar,
Byron Creese,
Luke Stephen Weymouth,
Adam R. Smith,
Sverre Bergh,
Yehani Wedatilake,
Geir Selbæk,
Ali Torkamani,
Jonathan Mill,
Clive G Ballard,
Robert Sweet,
Julia Kofler,
Ehsan Pishva,
Katie Lunnon
Abstract Background There are at least 50 million people with Alzheimer’s Disease (AD) or other dementias worldwide. About 50% of people with AD may develop psychotic symptoms (delusions and hallucinations). However, there is no effective pharmacological therapy for psychosis in AD and all current treatments are based on antipsychotics originally designed for other disorders like schizophrenia. In this study, we identify the molecular signature of psychosis in AD in post‐mortem brain samples and then use the connectivity map (CMAP) and library of network‐based cellular signatures (LINC) to predict candidate drugs based on the disease transcriptional signature. Method We generated RNA‐Seq data (Illumina Stranded mRNA Prep) and compared the gene expression levels across 4 groups: Control, AD with no psychosis (AD), AD with Delusions (ADD), and AD with both Delusions and Hallucinations (ADDH). The final identified differentially expressed up and down‐regulated genes (DEGs) were used as query signatures in the CMAP and LINC databases to identify drugs that could potentially reverse the gene expression signatures in disease samples. To investigate the disease mechanisms and the effect of repurposed drugs on it, a drug‐target interaction network was reconstructed and combined with the human interactome. Enrichment analysis of this network identifies AD and psychosis‐related pathways and the potential effect the nominated drugs have on them. Result After filtering out the common DEGs, 357, 171, and 66 unique genes remained in the AD, ADD, and ADDH signature sets, respectively. The signatureSearch package was used to search transcriptome signatures against CMAP and LINC. The top ranked drugs, based on negative connectivity scores, were selected as final results. Gene set enrichment analysis of the drug target genes presented some key pathways and activities related to psychiatric disorders. For example, serotonin receptor signalling pathway is one of the most over‐represented pathway of target genes in both ADD and ADDH groups. Conclusion This study can improve our understanding of the molecular mechanisms underlying AD psychosis. The candidate drugs we have identified could be repurposed for clinical trials of psychosis in AD and provide valuable knowledge for future pharmacological research.
Quantifying the proportion of different cell types in the human cortex using DNA methylation profiles
Eilis Hannon,
Emma L Dempster,
Barry Chioza,
Jonathan P Davies,
Georgina ET Blake,
Joe Burrage,
Stefania Policicchio
+ 5 more
Eilis Hannon,
Emma L Dempster,
Barry Chioza,
Jonathan P Davies,
Georgina ET Blake,
Joe Burrage,
Stefania Policicchio,
Alice Franklin,
Emma M Walker,
Rosemary A Bamford,
Leonard C Schalkwyk,
Jonathan Mill
Abstract Background Due to inter-individual variation in the cellular composition of the human cortex, it is essential that covariates that capture these differences are included in epigenome-wide association studies using bulk tissue. As experimentally derived cell counts are often unavailable, computational solutions have been adopted to estimate the proportion of different cell-types using DNA methylation data. Here, we validate and profile the use of an expanded reference DNA methylation dataset incorporating two neuronal- and three glial-cell subtypes for quantifying the cellular composition of the human cortex. Results We tested eight reference panels containing different combinations of neuronal- and glial-cell types and characterized their performance in deconvoluting cell proportions from computationally reconstructed or empirically-derived human cortex DNA methylation data. Our analyses demonstrate that these novel brain deconvolution models produce accurate estimates of cellular proportions from profiles generated on postnatal human cortex samples, they are not appropriate for the use in prenatal cortex or cerebellum tissue samples. Applying our models to an extensive collection of empirical datasets, we show that glial cells are twice as abundant as neuronal cells in the human cortex and identify significant associations between increased Alzheimer’s disease neuropathology and the proportion of specific cell types including a decrease in NeuNNeg/SOX10Neg nuclei and an increase of NeuNNeg/SOX10Pos nuclei. Conclusions Our novel deconvolution models produce accurate estimates for cell proportions in the human cortex. These models are available as a resource to the community enabling the control of cellular heterogeneity in epigenetic studies of brain disorders performed on bulk cortex tissue.
Epigenetic insights into neuropsychiatric and cognitive symptoms in Parkinson’s disease: A DNA co-methylation network analysis
Joshua Harvey,
Adam R. Smith,
Luke S. Weymouth,
Rebecca G. Smith,
Isabel Castanho,
Leon Hubbard,
Byron Creese
+ 4 more
Joshua Harvey,
Adam R. Smith,
Luke S. Weymouth,
Rebecca G. Smith,
Isabel Castanho,
Leon Hubbard,
Byron Creese,
Kate Bresner,
Nigel Williams,
Ehsan Pishva,
Katie Lunnon
Abstract Parkinson’s disease is a highly heterogeneous disorder, encompassing a complex spectrum of clinical presentation including motor, sleep, cognitive and neuropsychiatric symptoms. We aimed to investigate genome-wide DNA methylation networks in post-mortem Parkinson’s disease brain samples and test for region-specific association with common neuropsychiatric and cognitive symptoms. Of traits tested, we identify a co-methylation module in the substantia nigra with significant correlation to depressive symptoms and with ontological enrichment for terms relevant to neuronal and synaptic processes. Notably, expression of the genes annotated to the methylation loci present within this module are found to be significantly enriched in neuronal subtypes within the substantia nigra. These findings highlight the potential involvement of neuronal-specific changes within the substantia nigra with regard to depressive symptoms in Parkinson’s disease.
Epigenetic Age Acceleration in Frontotemporal Lobar Degeneration: A Comprehensive Analysis in the Blood and Brain
Megha Murthy, Patrizia Rizzu, Peter Heutink, Jonathan Mill, Tammaryn Lashley, Conceição Bettencourt
Megha Murthy,
Patrizia Rizzu,
Peter Heutink,
Jonathan Mill,
Tammaryn Lashley,
Conceição Bettencourt
Frontotemporal lobar degeneration (FTLD) includes a heterogeneous group of disorders pathologically characterized by the degeneration of the frontal and temporal lobes. In addition to major genetic contributors of FTLD such as mutations in MAPT, GRN, and C9orf72, recent work has identified several epigenetic modifications including significant differential DNA methylation in DLX1, and OTUD4 loci. As aging remains one of the major risk factors for FTLD, we investigated the presence of accelerated epigenetic aging in FTLD compared to controls. We calculated epigenetic age in both peripheral blood and brain tissues of multiple FTLD subtypes using several DNA methylation clocks, i.e., DNAmClockMulti, DNAmClockHannum, DNAmClockCortical, GrimAge, and PhenoAge, and determined age acceleration and its association with different cellular proportions and clinical traits. Significant epigenetic age acceleration was observed in the peripheral blood of both frontotemporal dementia (FTD) and progressive supranuclear palsy (PSP) patients compared to controls with DNAmClockHannum, even after accounting for confounding factors. A similar trend was observed with both DNAmClockMulti and DNAmClockCortical in post-mortem frontal cortex tissue of PSP patients and in FTLD cases harboring GRN mutations. Our findings support that increased epigenetic age acceleration in the peripheral blood could be an indicator for PSP and to a smaller extent, FTD.
Genetic impacts on DNA methylation help elucidate regulatory genomic processes
Sergio Villicaña,
Juan Castillo-Fernandez,
Eilis Hannon,
Colette Christiansen,
Pei-Chien Tsai,
Jane Maddock,
Diana Kuh
+ 9 more
Sergio Villicaña,
Juan Castillo-Fernandez,
Eilis Hannon,
Colette Christiansen,
Pei-Chien Tsai,
Jane Maddock,
Diana Kuh,
Matthew Suderman,
Christine Power,
Caroline Relton,
George Ploubidis,
Andrew Wong,
Rebecca Hardy,
Alissa Goodman,
Ken K. Ong,
Jordana T. Bell
BackgroundPinpointing genetic impacts on DNA methylation can improve our understanding of pathways that underlie gene regulation and disease risk.ResultsWe report heritability and methylation quantitative trait locus (meQTL) analysis at 724,499 CpGs profiled with the Illumina Infinium MethylationEPIC array in 2358 blood samples from three UK cohorts. Methylation levels at 34.2% of CpGs are affected by SNPs, and 98% of effects are cis-acting or within 1 Mbp of the tested CpG. Our results are consistent with meQTL analyses based on the former Illumina Infinium HumanMethylation450 array. Both SNPs and CpGs with meQTLs are overrepresented in enhancers, which have improved coverage on this platform compared to previous approaches. Co-localisation analyses across genetic effects on DNA methylation and 56 human traits identify 1520 co-localisations across 1325 unique CpGs and 34 phenotypes, including in disease-relevant genes, such as USP1 and DOCK7 (total cholesterol levels), and ICOSLG (inflammatory bowel disease). Enrichment analysis of meQTLs and integration with expression QTLs give insights into mechanisms underlying cis-meQTLs (e.g. through disruption of transcription factor binding sites for CTCF and SMC3) and trans-meQTLs (e.g. through regulating the expression of ACD and SENP7 which can modulate DNA methylation at distal sites).ConclusionsOur findings improve the characterisation of the mechanisms underlying DNA methylation variability and are informative for prioritisation of GWAS variants for functional follow-ups. The MeQTL EPIC Database and viewer are available online at https://epicmeqtl.kcl.ac.uk.
Whole Blood DNA Methylation Changes Are Associated with Anti-TNF Drug Concentration in Patients with Crohn’s Disease
Simeng Lin,
Eilis Hannon,
Mark Reppell,
Jeffrey F Waring,
Nizar Smaoui,
Valerie Pivorunas,
Heath Guay
+ 7 more
Simeng Lin,
Eilis Hannon,
Mark Reppell,
Jeffrey F Waring,
Nizar Smaoui,
Valerie Pivorunas,
Heath Guay,
Neil Chanchlani,
Claire Bewshea,
Benjamin Y H Bai,
Nicholas A Kennedy,
James R Goodhand,
Jonathan Mill,
Tariq Ahmad
BACKGROUND AND AIMS: Anti-tumour necrosis factor [TNF] treatment failure in patients with inflammatory bowel disease [IBD] is common and frequently related to low drug concentrations. In order to identify patients who may benefit from dose optimisation at the outset of anti-TNF therapy, we sought to define epigenetic biomarkers in whole blood at baseline associated with anti-TNF drug concentrations at week 14.
METHODS: DNA methylation from 1104 whole blood samples from 385 patients in the Personalised Anti-TNF Therapy in Crohn's disease [PANTS] study were assessed using the Illumina EPIC Beadchip [v1.0] at baseline and weeks 14, 30, and 54. We compared DNA methylation profiles in anti-TNF-treated patients who experienced primary non-response at week 14 if they were assessed at subsequent time points and were not in remission at week 30 or 54 [infliximab n = 99, adalimumab n = 94], with patients who responded at week 14 and when assessed at subsequent time points were in remission at week 30 or 54 [infliximab n = 99, adalimumab n = 93].
RESULTS: Overall, between baseline and week 14, we observed 4999 differentially methylated positions [DMPs] annotated to 2376 genes following anti-TNF treatment. Pathway analysis identified 108 significant gene ontology terms enriched in biological processes related to immune system processes and responses. Epigenome-wide association [EWAS] analysis identified 323 DMPs annotated to 210 genes at baseline associated with higher anti-TNF drug concentrations at Week 14. Of these, 125 DMPs demonstrated shared associations with other common traits [proportion of shared CpGs compared with DMPs] including body mass index [23.2%], followed by C-reactive protein [CRP] [11.5%], smoking [7.4%], alcohol consumption per day [7.1%], and IBD type [6.8%]. EWAS of primary non-response to anti-TNF identified 20 DMPs that were associated with both anti-TNF drug concentration and primary non-response to anti-TNF with a strong correlation of the coefficients [Spearman's rho = -0.94, p <0.001].
CONCLUSION: Baseline DNA methylation profiles may be used as a predictor for anti-TNF drug concentration at week 14 to identify patients who may benefit from dose optimisation at the outset of anti-TNF therapy.
Epigenome-wide profiling in the dorsal raphe nucleus highlights cell-type-specific changes in TNXB in Alzheimer’s disease
RJM Riemens,
E Pishva,
A Iatrou,
J Roubroeks,
J Nolz,
R Lardenoije,
M Ali
+ 14 more
RJM Riemens,
E Pishva,
A Iatrou,
J Roubroeks,
J Nolz,
R Lardenoije,
M Ali,
Sol A Del,
R Delgado-Morales,
M Esteller,
G Kenis,
BPF Rutten,
KP Lesch,
SD Ginsberg,
P Coleman,
J Mill,
D Mastroeni,
A Ramirez,
T Haaf,
K Lunnon,
den Hove DLA van
Abstract Recent studies have demonstrated that the dorsal raphe nucleus (DRN) is among the first brain regions affected in Alzheimer’s disease. Hence, in this study we conducted the first comprehensive epigenetic analysis of the DRN in AD, targeting both bulk tissue and single isolated cells. The Illumina Infinium MethylationEPIC BeadChip array was used to analyze the bulk tissue, assessing differentially modified positions (DMoPs) and regions (DMoRs) associated with Braak stage. The strongest Braak stage-associated DMoR in TNXB was targeted in a second patient cohort utilizing single laser-capture microdissected serotonin-positive (5-HT+) and -negative (5-HT-) cells isolated from the DRN. Our study revealed previously identified epigenetic loci, including TNXB and PGLYRP1 , and novel loci, including RBMXL2 , CAST , GNAT1 , MALAT1 , and DNAJB13 . Strikingly, we found that the methylation profile of TNXB depends both on disease phenotype and cell type analyzed, emphasizing the significance of single cell(-type) neuroepigenetic studies in AD.
Methylomic signature of current cannabis use in two first-episode psychosis cohorts
Emma Dempster,
Chloe Wong,
Joe Burrage,
Eilis Hannon,
Diego Quattrone,
Trotta Giulia,
Victoria Rodriguez
+ 45 more
Emma Dempster,
Chloe Wong,
Joe Burrage,
Eilis Hannon,
Diego Quattrone,
Trotta Giulia,
Victoria Rodriguez,
Edoardo Spinazzola,
Giada Tripoli,
Isabelle Austin-Zimmerman,
Z Li,
Charlotte Gayer-Anderson,
Tom Freeman,
Emma Johnson,
Hannah Jongsma,
Stilo Simona,
Caterina La Cascia,
Laura Ferraro,
Daniele La Barbera,
Antonio Lasalvia,
Sarah Tosato,
Ilaria Tarricone,
Giuseppe D’Andrea,
Michela Galatolo,
Andrea Tortelli,
Celso Arango,
Peter Jones,
Maurizio Pompili,
Jean-Paul Selten,
Haan Lieuwe de,
Paulo Menezes,
Cristina Marta Del-Ben,
José Santos,
Manuel Arrojo,
Julio Bobes,
Julio Sanjuan,
Miquel Bernardo,
Gerome Breen,
Valeria Mondelli,
Paola Dazzan,
Conrad Iyegbe,
Evangelos Vassos,
Craig Morgan,
Diptendu Mukherjee,
Jim van Os,
Bart Rutten,
Michael O'Donovan,
Pak Sham,
Jonathan Mill,
Robin Murray,
Marta di Forti,
Luis Alameda
The rising prevalence and legalization of cannabis worldwide have underscored the need for a comprehensive understanding of its biological impact, particularly on mental health. Epigenetic mechanisms, specifically DNA methylation, have gained increasing recognition as vital factors in the interplay between risk factors and mental health. This study aimed to explore the effects of current cannabis use and potency on DNA methylation in two independent cohorts of individuals experiencing first-episode psychosis (FEP) compared to control subjects. The combined sample consisted of 682 participants (cannabis users (n = 188) and never users (n = 494)). DNA methylation profiles were generated on blood-derived DNA samples using the Illumina DNA methylation array platform. Each cohort was analysed individually and then meta-analysed. We identified one CpG site (cg11669285) in the CAVIN1 gene that showed differential methylation with current cannabis use, surpassing the array-wide significance threshold, and independent of the tobacco-related epigenetic signature. Furthermore, a CpG site localized in the MCU gene (cg11669285) achieved array-wide significance in the analysis of high-potency cannabis use. Pathway and regional analyses identified cannabis-related epigenetic deviations in genes linked to immune and mitochondrial function, both of which are known to be influenced by cannabinoids. Notably, the analyses focused on first-onset psychoses identified differential methylation at nominal significance in a CpG site situated in the TRPV2 gene, which is known to be activated by cannabinoids. Overall, these findings contribute to our understanding of the epigenetic consequences of current cannabis use in the general population and in first-episode psychosis and highlight potential molecular pathways affected by cannabis exposure.
Epigenetic insights into neuropsychiatric and cognitive symptoms in Parkinson's disease: A DNA co-methylation network analysis
Joshua Harvey,
Adam R Smith,
Luke S Weymouth,
Rebecca G Smith,
Isabel Castanho,
Leon Hubbard,
Byron Creese
+ 4 more
Joshua Harvey,
Adam R Smith,
Luke S Weymouth,
Rebecca G Smith,
Isabel Castanho,
Leon Hubbard,
Byron Creese,
Kate Bresner,
Nigel Williams,
Ehsan Pishva,
Katie Lunnon
Parkinson's disease is a highly heterogeneous disorder, encompassing a complex spectrum of clinical presentation including motor, sleep, cognitive and neuropsychiatric symptoms. We aimed to investigate genome-wide DNA methylation networks in post-mortem Parkinson's disease brain samples and test for region-specific association with common neuropsychiatric and cognitive symptoms. Of traits tested, we identify a co-methylation module in the substantia nigra with significant correlation to depressive symptoms and with ontological enrichment for terms relevant to neuronal and synaptic processes. Notably, expression of the genes annotated to the methylation loci present within this module are found to be significantly enriched in neuronal subtypes within the substantia nigra. These findings highlight the potential involvement of neuronal-specific changes within the substantia nigra with regard to depressive symptoms in Parkinson's disease.
Long-read transcript sequencing identifies differential isoform expression in the entorhinal cortex in a transgenic model of tau pathology
Szi Kay Leung,
Aaron R Jeffries,
Isabel Castanho,
Rosemary A Bamford,
Karen Moore,
Emma L Dempster,
Jonathan T Brown
+ 4 more
Szi Kay Leung,
Aaron R Jeffries,
Isabel Castanho,
Rosemary A Bamford,
Karen Moore,
Emma L Dempster,
Jonathan T Brown,
Zeshan Ahmed,
Paul O’Neill,
Eilis Hannon,
Jonathan Mill
Abstract Increasing evidence suggests that alternative splicing plays an important role in Alzheimer’s disease (AD), a devastating neurodegenerative disorder involving the intracellular aggregation of hyperphosphorylated tau. We used long-read cDNA sequencing to profile transcript diversity in the entorhinal cortex of wild-type (WT) and transgenic (TG) mice harboring a mutant form of human tau. Whole transcriptome profiling showed that previously reported gene-level expression differences between WT and TG mice reflect changes in the abundance of specific transcripts. Ultradeep targeted long-read cDNA sequencing of genes implicated in AD revealed hundreds of novel isoforms and identified specific transcripts associated with the development of tau pathology. Our results highlight the importance of differential transcript usage, even in the absence of gene-level expression alterations, as a mechanism underpinning gene regulation in the development of neuropathology. Our transcript annotations and a novel informatics pipeline for the analysis of long-read transcript sequencing data are provided as a resource to the community.
Blood-based multivariate methylation risk score for cognitive impairment and dementia
Jarno Koetsier,
Rachel Cavill,
Rick Reijnders,
Joshua Harvey,
Kay Deckers,
Sebastian Köhler,
Lars Eijssen
+ 44 more
Jarno Koetsier,
Rachel Cavill,
Rick Reijnders,
Joshua Harvey,
Kay Deckers,
Sebastian Köhler,
Lars Eijssen,
Rebecca G. Smith,
Adam R. Smith,
Joe Burrage,
Emma M. Walker,
Gemma Shireby,
Eilis Hannon,
Emma Dempster,
Tim Frayling,
Jonathan Mill,
Valerija Dobricic,
Yasmine Sommerer,
Peter Johannsen,
Michael Wittig,
Andre Franke,
Rik Vandenberghe,
Jolien Schaeverbeke,
Yvonne Freund-Levi,
Lutz Frölich,
Philip Scheltens,
Charlotte Teunissen,
Giovanni Frisoni,
Olivier Blin,
Jill Richardson,
Régis Bordet,
Sebastiaan Engelborghs,
Roeck Ellen de,
Pablo Martinez-Lage,
Mikel Tainta,
Alberto Lleó,
Isabel Sala,
Julius Popp,
Gwedoline Peyratout,
Frans Verhey,
Magda Tsolaki,
Ulf Andreasson,
Kaj Blennow,
Henrik Zetterberg,
Johannes Streffer,
Stephanie J. B. Vos,
Simon Lovestone,
Pieter-Jelle Visser,
Lars Bertram,
Katie Lunnon,
Ehsan Pishva
ABSTRACT INTRODUCTION Given the established association between DNA methylation and the pathophysiology of dementia and its plausible role as a molecular mediator of lifestyle and environment, blood-derived DNA methylation data could enable early detection of dementia risk. METHODS In conjunction with an extensive array of machine learning techniques, we employed whole blood genome-wide DNA methylation data as a surrogate for 14 modifiable and non-modifiable factors in the assessment of dementia risk in two independent cohorts of Alzheimer’s disease (AD) and Parkinson’s disease (PD). RESULTS We established a multivariate methylation risk score (MMRS) to identify the status of mild cognitive impairment (MCI) cross-sectionally, independent of age and sex. We further demonstrated significant predictive capability of this score for the prospective onset of cognitive decline in AD and PD. DISCUSSION Our work shows the potential of employing blood-derived DNA methylation data in the assessment of dementia risk.
W76. CELL-SPECIFIC METHYLOMIC VARIATION IN NEURODEVELOPMENT AND SCHIZOPHRENIA
Jonathan Mill,
Eilis Hannon,
Emma Dempster,
Alice Franklin,
Joe Burrage,
Jonathan Davies,
Barry Chioza
+ 4 more
Jonathan Mill,
Eilis Hannon,
Emma Dempster,
Alice Franklin,
Joe Burrage,
Jonathan Davies,
Barry Chioza,
Gina Commin,
Aaron R. Jeffries,
Rosemary A. Bamford,
Leo Schalkwyk
Background There is mounting evidence to support a role for developmentally regulated epigenetic variation in the molecular etiology of schizophrenia. Previous analyses of epigenetic variation in the human brain have been limited to the study of bulk tissue, which is a heterogeneous mix of different cell types. We sought to characterize cell-type-specific epigenetic signatures across human cortex development and relate this to differences identified in schizophrenia. Methods To obtain purified populations of neural cell types from post-mortem prefrontal cortex tissue, we used fluorescence-activated nuclei sorting (FANS) to gate and select NeuN+/SATB2+ (neuronal), SOX10+ (oligodendrocytes) and IRF8+ (microglial) immunolabeled nuclei populations derived from prefrontal cortex tissue from 150 schizophrenia cases and 150 controls, profiling DNA methylation using the Illumina EPIC BeadArray. In parallel we characterized cell-type-specific DNA methylation profiles in 150 fetal cortex samples spanning 6 weeks post-conception (wpc) to 23 wpc. After processing these data though a standardised quality control pipeline, that validates cell identity, we performed a cell-type-specific association analysis of schizophrenia status using a mixed effect models. Results We identified > 100 positions across the genome with significant epigenetic differences associated with schizophrenia. Many of these associations were specific to a single cell type, although some were associated with consistent differences across all neural cell types tested. We identified dramatic cell-type-specific shifts in DNA methylation across human cortex development, with enrichment of neurodevelopmentally-dynamic sites amongst genomic regions implicated in schizophrenia. Discussion Our data support the hypothesis that schizophrenia has an important early neurodevelopmental component, and confirm that epigenetic mechanisms may mediate these effects. Our results advance previous epigenetic analyses of schizophrenia by determining the relevant neural cell-type underlying epigenetic dysregulation in disease.
ULTRA-DEEP LONG READ TRANSCRIPTOME SEQUENCING REVEALS DRAMATIC ISOFORM DIVERSITY ACROSS HUMAN CORTEX DEVELOPMENT: RELEVANCE FOR GENETIC STUDIES OF PSYCHIATRIC DISORDERS
Rosemary A. Bamford,
Szi Kay Leung,
Aaron R. Jeffries,
Alice Franklin,
Gina Commin,
Jonathan Davies,
Emma Dempster
+ 2 more
Rosemary A. Bamford,
Szi Kay Leung,
Aaron R. Jeffries,
Alice Franklin,
Gina Commin,
Jonathan Davies,
Emma Dempster,
Eilis Hannon,
Jonathan Mill
Background Alternative splicing (AS) is a post-transcriptional regulatory mechanism producing distinct mRNA molecules from a single pre-mRNA with a prominent role in the development and function of the central nervous system. Because alternatively spliced transcripts from a single gene can produce proteins with different functions, there is increasing interest in their role in human disease. AS is particularly important and prevalent in the central nervous system, where it impacts neurodevelopment, aging and key neural functions. AS is a common feature of many neuropsychiatric diseases, with recent studies highlighting splicing differences associated with autism and schizophrenia. Novel long read sequencing approaches provide a novel opportunity to generate full-length transcript sequences and fully characterise isoform diversity. Methods We used Oxford Nanopore Technology (ONT) whole transcriptome sequencing to profile isoform diversity across human cortex development and postnatal aging (n = 49 donors aged 8 weeks post-conception to 95 years). In parallel we undertook ultradeep targeted transcript sequencing across a panel of >300 genes implicated in schizophrenia, autism, intellectual disability and developmental delay, profiling a larger set of >100 cortex samples spanning the lifecourse. cDNA was sequenced using the ONT PromethION system and data processed using a novel analysis pipeline developed by our group for isoform visualisation and quantification. Transcript annotations were integrated with cell-type-specific DNA methylation data generated on the same samples. Results We identify widespread transcript diversity in the developing cortex with the detection of thousands of novel transcripts not previously described in existing genomic annotations, including for genes associated with neuropsychiatric disease. We identify developmental changes in alternative splicing, with dramatic shifts in transcript usage between fetal and adult cortex. We also identify sex-differences in isoform use across human cortex development, including for many autosomal genes. Finally, we highlight many examples of alternative splicing colocalizing with developmentally-dynamic regions of differential DNA methylation. Discussion Our data confirm the importance of alternative splicing in the human cortex, dramatically increasing transcriptional diversity and representing an important mechanism underpinning gene regulation in the developing brain. Our transcript annotations and sequencing data are available as a resource to the research community via browsable tracks and a searchable transcript visualization database.
T86. PREDICTING PSYCHOSIS: EXPLORING THE ADDITIVE AND INTERACTION EFFECTS OF GENETIC AND EPIGENETIC RISK SCORES
Leticia Spindola,
Anne-Kristin Stavrum,
Kevin O'Connell,
Eilis Hannon,
Jonathan Mill,
Srdjan Djurovic,
Ingrid Melle
+ 2 more
Leticia Spindola,
Anne-Kristin Stavrum,
Kevin O'Connell,
Eilis Hannon,
Jonathan Mill,
Srdjan Djurovic,
Ingrid Melle,
Ole Andreassen,
Hellard Stephanie Le
Background Previous studies have explored polygenic risk scores (PRS) for predicting complex traits, but few have investigated combining DNA methylation (DNAm) with PRS to improve phenotype prediction. A recent study examined whether DNAm risk scores (MRS) could independently or in addition to PRS predict body mass index (BMI) and height. BMI and height have different contributions from genetics and the environment. The study found that MRS predict BMI independently of PRS and in an additive manner, while having minimal impact on height, which aligns with the evidence that genetic factors play a larger role in height variability. These findings suggest that integrating genetic and DNAm information could be valuable for predicting complex traits with significant environmental influence, like psychiatric traits. In our study, we aimed to determine how schizophrenia-derived PRS (SCZ-PRS) and MRS (SCZ-MRS) explain inter-individual variability in psychosis and whether their effects on the phenotype are additive or interactive. Methods We analyzed a dataset consisting of 921 individuals with psychosis and 774 controls from the Thematically Organised Psychosis (TOP) cohort. SCZ-PRS were derived from the largest SCZ GWAS to date. SCZ-MRS were obtained using the pruning and thresholding (P+T) CoMeBack approach, and SCZ methylation probe effects were estimated from a random-effect meta-analysis of five cohorts obtained from the largest SCZ EWAS to date. Both SCZ-PRS and SCZ-MRS were adjusted for technical and biological variables. Logistic regression was used to assess the variance in psychosis explained by SCZ-MRS and SCZ-PRS individually and combined (Nagelkerke R2). We also examined evidence of interaction between SCZ-MRS and SCZ-PRS. An ANOVA was used to compare the variation in psychosis explained by the interaction versus the additive model. Results In our preliminary results, both SCZ-PRS and SCZ-MRS were individually associated with psychosis in the anticipated direction (PRS: OR=1.291, 95%CI 1.173-1.424; MRS: OR=1.010, 95%CI 1.006-1.014). SCZ-PRS explained more variance in psychosis compared to SCZ-MRS (Nagelkerke R2 PRS=0.021, MRS=0.019). When we included both SCZ-PRS and SCZ-MRS in an additive model for psychosis, each score maintained its independent association with the phenotype. The additive model explained 3.8% of the variance (Nagelkerke R2=0.038), suggesting a mainly additive effect of the two scores on psychosis. There was no significant interaction between SCZ-PRS and SCZ-MRS for psychosis, and the interaction model (Nagelkerke R2=0.038) did not explained a larger proportion of variance than did the additive model (ANOVA p-value=0.316). Discussion We found that SCZ-MRS improved prediction of psychosis independent of and in addition to SCZ-PRS. Due to the larger sample size in the latest SCZ GWAS compared to the SCZ EWAS, MRS was expected to explain less phenotype variance than PRS. The two scores exhibited an additive effect, indicating that SCZ-MRS capture information that is independent of the genetic determinants of SCZ. These results align with the findings for BMI, providing further evidence that combining genetic and DNAm information enhances the prediction of complex traits. Nonetheless, these results are preliminary, and further studies are necessary to better understand the predictive power achieved by combining methylation and genetic risk scores for complex traits.
Corrigendum: Ceremonial ayahuasca in amazonian retreats—mental health and epigenetic outcomes from a six-month naturalistic study
Simon G. D. Ruffell,
Nige Netzband,
WaiFung Tsang,
Merlin Davies,
Antonio Inserra,
Matthew Butler,
James J. H. Rucker
+ 4 more
Simon G. D. Ruffell,
Nige Netzband,
WaiFung Tsang,
Merlin Davies,
Antonio Inserra,
Matthew Butler,
James J. H. Rucker,
Luís Fernando Tófoli,
Emma Louise Dempster,
Allan H. Young,
Celia J. A. Morgan
Abstract Background Genes encoding synaptic proteins or mRNA targets of the RNA binding protein, Fragile X mental retardation protein (FMRP), have been linked to schizophrenia and autism spectrum disorder (ASD) through the enrichment of genetic variants conferring risk to these disorders. FMRP binds many transcripts with synaptic functions and is thought to be a key regulator of their local translation, a process which enables rapid and compartmentalized protein synthesis required for development and plasticity. Methods Here, we used summary statistics from large-scale genome-wide association studies to test the hypothesis that the subset of synaptic genes encoding localized transcripts is more strongly associated with schizophrenia and ASD than non-localized transcripts. We also postulated that this subset of synaptic genes is responsible for associations attributed to FMRP targets. Results We show that schizophrenia associations were enriched in genes encoding localized synaptic transcripts compared to the remaining synaptic genes, or to the remaining localized transcripts; this also applied to ASD associations, although only for transcripts observed after stimulation by fear conditioning. The genetic associations with either disorder captured by these gene sets were independent of those derived from FMRP targets. Furthermore, we found that schizophrenia association was related to FMRP interactions with mRNAs in somata, but not in dendrites, whilst ASD association was related to FMRP binding in either compartment. Conclusions Our data suggest that synaptic transcripts capable of rapid and compartmentalized local translation are particularly relevant to the pathogenesis of schizophrenia and ASD, but do not characterize the associations attributed to current sets of FMRP targets.
Developmentally dynamic changes in DNA methylation in the human pancreas
Ailsa MacCalman,
Franco Elisa De,
Alice Franklin,
Christine S. Flaxman,
Sarah J. Richardson,
Kathryn Murrall,
Joe Burrage
+ 9 more
Ailsa MacCalman,
Franco Elisa De,
Alice Franklin,
Christine S. Flaxman,
Sarah J. Richardson,
Kathryn Murrall,
Joe Burrage,
Barts Pancreas Tissue Bank,
Emma M Walker,
Noel G. Morgan,
Andrew T. Hattersley,
Emma L. Dempster,
Eilis J. Hannon,
Aaron R. Jeffries,
Nick D. L. Owens,
Jonathan Mill
ABSTRACT Development of the human pancreas requires the precise temporal control of gene expression via epigenetic mechanisms and the binding of key transcription factors. We quantified genome-wide patterns of DNA methylation in human fetal pancreatic samples from donors aged 6 to 21 post-conception weeks. We found dramatic changes in DNA methylation across pancreas development, with >21% of sites characterized as developmental differentially methylated positions (dDMPs) including many annotated to genes associated with monogenic diabetes. An analysis of DNA methylation in postnatal pancreas tissue showed that the dramatic temporal changes in DNA methylation occurring in the developing pancreas are largely limited to the prenatal period. Significant differences in DNA methylation were observed between males and females at a number of autosomal sites, with a small proportion of sites showing sex-specific DNA methylation trajectories across pancreas development. Pancreas dDMPs were not distributed equally across the genome, and were depleted in regulatory domains characterized by open chromatin and the binding of known pancreatic development transcription factors. Finally, we compared our pancreas dDMPs to previous findings from the human brain, identifying evidence for tissue-specific developmental changes in DNA methylation. To our knowledge, this represents the most extensive exploration of DNA methylation patterns during human fetal pancreas development, confirming the prenatal period as a time of major epigenomic plasticity.
Rapid and Inducible Mislocalization of Endogenous TDP43 in a Novel Human Model of Amyotrophic Lateral Sclerosis
Johanna Ganssauge, Sophie Hawkins, Seema Namboori, Szi-Kay Leung, Jonathan Mill, Akshay Bhinge
Johanna Ganssauge,
Sophie Hawkins,
Seema Namboori,
Szi-Kay Leung,
Jonathan Mill,
Akshay Bhinge
Abstract Transactive response DNA binding protein 43 kDa (TDP43) proteinopathy, characterized by the mislocalization and aggregation of TDP43, is a hallmark of several neurodegenerative diseases including Amyotrophic Lateral Sclerosis (ALS). In this study, we describe the development of a new model of TDP43 proteinopathy using human induced pluripotent stem cell (iPSC)-derived neurons. Utilizing a genome engineering approach, we induced the mislocalization of endogenous TDP43 from the nucleus to the cytoplasm without mutating the TDP43 gene or using chemical stressors. Our model successfully recapitulates key early and late pathological features of TDP43 proteinopathy, including neuronal loss, reduced neurite complexity, and cytoplasmic accumulation and aggregation of TDP43. Concurrently, the loss of nuclear TDP43 leads to splicing defects, while its cytoplasmic gain adversely affects microRNA expression. Strikingly, our observations suggest that TDP43 is capable of sustaining its own mislocalization, thereby perpetuating and further aggravating the proteinopathy. This innovative model provides a valuable tool for the in-depth investigation of the consequences of TDP43 proteinopathy. It offers a clinically relevant platform that will accelerate identification of potential therapeutic targets for the treatment of TDP43-associated neurodegenerative diseases including sporadic ALS.
A methylome-wide association study of major depression with out-of-sample case-control classification and trans-ancestry comparison
Xueyi Shen,
Miruna Barbu,
Doretta Caramaschi,
Ryan Arathimos,
Darina Czamara,
Friederike S. David,
Anna Dearman
+ 75 more
Xueyi Shen,
Miruna Barbu,
Doretta Caramaschi,
Ryan Arathimos,
Darina Czamara,
Friederike S. David,
Anna Dearman,
Evelyn Dilkes,
Marisol Herrera-Rivero,
Floris Huider,
Luise Kühn,
Kuan-Chen Lu,
Teemu Palviainen,
Alicia Marie Schowe,
Gemma Shireby,
Antoine Weihs,
Chloe C. Y. Wong,
Eleanor Davyson,
Hannah Casey,
Mark J Adams,
Antje-Kathrin Allgaier,
Michael Barber,
Joe Burrage,
Avshalom Caspi,
Ricardo Costeira,
Erin C. Dunn,
Lisa Feldmann,
Josef Frank,
Franz Joseph Freisleder,
Danni A. Gadd,
Ellen Greimel,
Eilis Hannon,
Sarah E Harris,
Georg Homuth,
David M. Howard,
Stella Iurato,
Tellervo Korhonen,
Tzu-Pin Lu,
Nicholas G Martin,
Jade Martins,
Edel McDermott,
Susanne Meinert,
Pau Navarro,
Miina Ollikainen,
Verena Pehl,
Charlotte Piechaczek,
Aline D. Scherff,
Frederike Stein,
Fabian Streit,
Alexander Teumer,
Henry Völzke,
Dongen Jenny van,
Rosie M. Walker,
Natan Yusupov,
Louise Arseneault,
Jordana T. Bell,
Klaus Berger,
Elisabeth Binder,
Dorret I. Boomsma,
Simon R Cox,
Udo Dannlowski,
Kathryn L. Evans,
Helen L. Fisher,
Andreas J. Forstner,
Hans J. Grabe,
Jaakko Kaprio,
Tilo Kircher,
Johannes Kopf-Beck,
Meena Kumari,
Po-Hsiu Kuo,
Qingqin S Li,
Terrie E. Moffitt,
Hugh Mulcahy,
Therese M. Murphy,
Gerd Schulte-Körne,
Jonathan Mill,
Cathryn M. Lewis,
BeCOME Working Group,
OPTIMA Working Group,
PGC MDD Working Group,
Naomi R Wray,
Andrew M McIntosh
Abstract Major Depression (MD) is a leading cause of global disease burden, and both experimental and population-based studies suggest that differences in DNA methylation (DNAm) may be associated with the condition. However, previous DNAm studies have not so far been widely replicated, suggesting a need for larger meta-analysis studies. In the present study, the Psychiatric Genomics Consortium Major Depressive Disorder working group conducted a meta-analysis of methylome-wide association analysis (MWAS) for life-time MD across 18 studies of 24,754 European-ancestry participants (5,443 MD cases) and an East Asian sample (243 cases, 1846 controls). We identified fifteen CpG sites associated with lifetime MD with methylome-wide significance (p < 6.42×10 - 8 ). Top CpG effect sizes in European ancestries were positively correlated with those from an independent East Asian MWAS (r = 0.482 and p = 0.068 for significant CpG sites, r = 0.261 and p = 0.009 for the top 100 CpG sites). Methylation score (MS) created using the MWAS summary statistics was significantly associated with MD status in an out-of-sample classification analysis (β = 0.122, p = 0.005, AUC = 0.53). MS was also associated with five inflammatory markers, with the strongest association found with Tumor Necrosis Factor Beta (β=-0.154, p=1.5×10 - 5 ). Mendelian randomisation (MR) analysis demonstrated that 23 CpG sites were potentially causally associated with MD and six of those were replicated in an independent mQTL dataset (Wald’s ratio test, absolute β ranged from 0.056 to 0.932, p ranged from 7×10 - 3 to 4.58×10 - 6 ). CpG sites located in the Major Histocompatibility complex (MHC) region showed the strongest evidence from MR analysis of being associated with MD. Our study provides evidence that variations in DNA methylation are associated with MD, and further evidence supporting involvement of the immune system. Larger sample sizes in diverse ancestries are likely to reveal replicable associations to improve mechanistic inferences with the potential to inform molecular target identification.
Elucidating distinct molecular signatures of Lewy body dementias
Dementia with Lewy bodies and Parkinson's disease dementia are common neurodegenerative diseases that share similar neuropathological profiles and spectra of clinical symptoms but are primarily differentiated by the order in which symptoms manifest. The question of whether a distinct molecular pathological profile could distinguish these disorders is yet to be answered. However, in recent years, studies have begun to investigate genomic, epigenomic, transcriptomic and proteomic differences that may differentiate these disorders, providing novel insights in to disease etiology. In this review, we present an overview of the clinical and pathological hallmarks of Lewy body dementias before summarizing relevant research into genetic, epigenetic, transcriptional and protein signatures in these diseases, with a particular interest in those resolving "omic" level changes. We conclude by suggesting future research directions to address current gaps and questions present within the field.
Accelerated Pace of Aging in Schizophrenia: Five Case-Control Studies
Avshalom Caspi, Gemma Shireby, Jonathan Mill, Terrie E Moffitt, Karen Sugden, Eilis Hannon
Avshalom Caspi,
Gemma Shireby,
Jonathan Mill,
Terrie E Moffitt,
Karen Sugden,
Eilis Hannon
BACKGROUND: Schizophrenia is associated with increased risk of developing multiple aging-related diseases, including metabolic, respiratory, and cardiovascular diseases, and Alzheimer's and related dementias, leading to the hypothesis that schizophrenia is accompanied by accelerated biological aging. This has been difficult to test because there is no widely accepted measure of biological aging. Epigenetic clocks are promising algorithms that are used to calculate biological age on the basis of information from combined cytosine-phosphate-guanine sites (CpGs) across the genome, but they have yielded inconsistent and often negative results about the association between schizophrenia and accelerated aging. Here, we tested the schizophrenia-aging hypothesis using a DNA methylation measure that is uniquely designed to predict an individual's rate of aging.
METHODS: We brought together 5 case-control datasets to calculate DunedinPACE (Pace of Aging Calculated from the Epigenome), a new measure trained on longitudinal data to detect differences between people in their pace of aging over time. Data were available from 1812 psychosis cases (schizophrenia or first-episode psychosis) and 1753 controls. Mean chronological age was 38.9 (SD = 13.6) years.
RESULTS: We observed consistent associations across datasets between schizophrenia and accelerated aging as measured by DunedinPACE. These associations were not attributable to tobacco smoking or clozapine medication.
CONCLUSIONS: Schizophrenia is accompanied by accelerated biological aging by midlife. This may explain the wide-ranging risk among people with schizophrenia for developing multiple different age-related physical diseases, including metabolic, respiratory, and cardiovascular diseases, and dementia. Measures of biological aging could prove valuable for assessing patients' risk for physical and cognitive decline and for evaluating intervention effectiveness.
Longitudinal changes in DNA methylation associated with clozapine use in treatment-resistant schizophrenia from two international cohorts
Amy L. Gillespie,
Emma M. Walker,
Eilis Hannon,
Grant McQueen,
Kyra-Verena Sendt,
Alessia Avila,
John Lally
+ 12 more
Amy L. Gillespie,
Emma M. Walker,
Eilis Hannon,
Grant McQueen,
Kyra-Verena Sendt,
Alessia Avila,
John Lally,
Cynthia Okhuijsen-Pfeifer,
der Horst Marte van,
Alkomiet Hasan,
Emma L. Dempster,
Joe Burrage,
Jan Bogers,
Dan Cohen,
Marco P. Boks,
Alice Egerton,
Jurjen J. Luykx,
Jonathan Mill,
James H. MacCabe
Abstract The second-generation antipsychotic clozapine is used as a medication for treatment-resistant schizophrenia. It has previously been associated with epigenetic changes in pre-clinical rodent models and cross-sectional studies of treatment-resistant schizophrenia. Cross-sectional studies are susceptible to confounding, however, and cannot disentangle the effects of diagnosis and medication. We therefore profiled DNA methylation in sequential blood samples (n=126) from two independent cohorts of patients (n=38) with treatment-resistant schizophrenia spectrum disorders who commenced clozapine after study enrolment and were followed up for up to six months. We identified significant non-linear changes in cell-type proportion estimates derived from DNA methylation data - specifically B-cells - associated with time on clozapine. Mixed effects regression models were used to identify changes in DNA methylation at specific sites associated with time on clozapine, identifying 37 differentially methylated positions (DMPs) (p < 5×10 −5 ) in a linear model and 90 DMPs in a non-linear quadratic model. We compared these results to data from our previous epigenome-wide association study (EWAS) meta-analysis of psychosis, finding evidence that many previously identified DMPs associated with schizophrenia and treatment-resistant schizophrenia might reflect exposure to clozapine. In conclusion, our results indicate that clozapine exposure is associated with changes in DNA methylation and cellular composition. Our study shows that medication effects might confound many case-control studies of neuropsychiatric disorders performed in blood.
Human naïve stem cell models reveal the role of FGF in hypoblast specification in the human embryo
Anish Dattani,
Elena Corujo-Simon,
Arthur Radley,
Tiam Heydari,
Yasaman Taheriabkenar,
Francesca Carlisle,
Simeng Lin
+ 4 more
Anish Dattani,
Elena Corujo-Simon,
Arthur Radley,
Tiam Heydari,
Yasaman Taheriabkenar,
Francesca Carlisle,
Simeng Lin,
Jonathan Mill,
Peter Zandstra,
Jennifer Nichols,
Ge Guo
SUMMARY The hypoblast is an essential extra-embryonic tissue set aside within the inner cell mass early in mammalian embryo development, in the blastocyst. Research with human embryos is challenging. Thus, stem cell models that reproduce hypoblast differentiation provide valuable alternatives. We show here that human naïve PSC to hypoblast differentiation proceeds via reversion to a transitional ICM-like state, from which hypoblast emerges in concordance with the trajectory in human blastocysts. We identified a window when fibroblast growth factor (FGF) signalling is critical for hypoblast specification. Revisiting FGF signalling in human embryos revealed that inhibition in the early blastocyst suppresses hypoblast formation. In vitro , the induction of hypoblast is synergistically enhanced by limiting trophectoderm and epiblast fates. This finding revises previous reports and establishes a conservation in lineage specification between mouse and human. Overall, this study demonstrates the utility of human naïve PSC-based models in elucidating mechanistic features of early human embryogenesis.
Enrichment of the Local Synaptic Translatome for Genetic Risk Associated With Schizophrenia and Autism Spectrum Disorder
Nicholas E Clifton, Julie Qiaojin Lin, Christine E Holt, Michael C O'Donovan, Jonathan Mill
Nicholas E Clifton,
Julie Qiaojin Lin,
Christine E Holt,
Michael C O'Donovan,
Jonathan Mill
BACKGROUND: Genes that encode synaptic proteins or messenger RNA targets of the RNA-binding protein FMRP (fragile X messenger ribonucleoprotein) have been linked to schizophrenia and autism spectrum disorder (ASD) through the enrichment of genetic variants that confer risk for these disorders. FMRP binds many transcripts with synaptic functions and is thought to regulate their local translation, a process that enables rapid and compartmentalized protein synthesis required for development and plasticity.
METHODS: We used summary statistics from large-scale genome-wide association studies of schizophrenia (74,776 cases, 101,023 controls) and ASD (18,381 cases, 27,969 controls) to test the hypothesis that the subset of synaptic genes that encode localized transcripts is more strongly associated with each disorder than nonlocalized transcripts. We also postulated that this subset of synaptic genes is responsible for associations attributed to FMRP targets.
RESULTS: Schizophrenia associations were enriched in genes encoding localized synaptic transcripts compared to the remaining synaptic genes or to the remaining localized transcripts; this also applied to ASD associations, although only for transcripts observed after stimulation by fear conditioning. The genetic associations with either disorder captured by these gene sets were independent of those derived from FMRP targets. Schizophrenia association was related to FMRP interactions with messenger RNAs in somata, but not in dendrites, while ASD association was related to FMRP binding in either compartment.
CONCLUSIONS: Our data suggest that synaptic transcripts capable of local translation are particularly relevant to the pathogenesis of schizophrenia and ASD, but they do not characterize the associations attributed to current sets of FMRP targets.
Using spatial transcriptomics to investigate region‐specific gene expression in J20 mice
Millie Sander, Jonathan T Brown, Katie Lunnon, Clive G Ballard
Millie Sander,
Jonathan T Brown,
Katie Lunnon,
Clive G Ballard
Abstract Background Alzheimer’s disease (AD) and dementia with Lewy bodies (DLB) share various pathological and symptomatic traits. As such, providing an accurate diagnosis of DLB can be difficult, ultimately impacting patient support and care. It is therefore imperative to establish biomarkers which reliably differentiate between disease states. Plasma‐derived exosomes appear to be promising in this regard. Exosomes are extracellular vesicles, containing cargos from the cell from which they originate. Increased concentrations of exosomal disease‐associated proteins, such as p‐T181‐tau and Aβ‐42, have previously been associated with cognitive decline and disease progression among AD patients (Winston et al. , 2016; Kapogiannis et al. , 2019). Method We aim to quantify exosome‐associated proteins from AD patients, DLB patients and healthy controls in order to establish exosomal signatures to differentiate between disease states. Exosomes are being isolated using differential ultracentrifugation. Nanoparticle track analysis (NTA) and western blots are being used to verify isolation, and ELISA assays against p‐T181‐tau, Aβ‐42 and α‐synuclein will be used to quantify proteins of interest. Plasma samples are being collected at baseline and after a 6 month follow‐up period in order to monitor the stability of these potential biomarkers. Result To date, full ethics approval has been granted for this study, and the differential ultracentrifugation protocol has been established. Successful isolation of particles in the size range of exosomes (30 – 100nm) has been confirmed using NTA. ELISA assays will be undertaken in the up‐coming months, with the aim of collecting and analysing baseline results by May 2023. Conclusion Exosomes already appear to be a reliable, and relatively non‐invasive biomarker for assessing disease state and progression among dementia patients. Our preliminary findings have shown successful isolation, and we believe the findings could be invaluable with regards to improved diagnosis options for DLB. References: Kapogiannis, D. et al. (2019) ‘Association of Extracellular Vesicle Biomarkers With Alzheimer Disease in the Baltimore Longitudinal Study of Aging’, JAMA Neurology . https://doi.org/10.1001/jamaneurol.2019.2462 Winston, C. N. et al. (2016) ‘Prediction of conversion from mild cognitive impairment to dementia with neuronally derived blood exosome protein profile’, Alzheimer’s and Dementia: Diagnosis, Assessment and Disease Monitoring . Elsevier Inc., 3, pp. 63‐72. https://doi.org/10.1016/j.dadm.2016.04.001.
A multi‐omic approach to elucidate novel disease mechanisms and biomarkers for psychosis in Alzheimer’s disease
Ehsan Pishva,
Morteza P Kouhsar,
Luke Stephen Weymouth,
Adam R. Smith,
Yehani Wedatilake,
Ali Torkamani,
Robert Sweet
+ 7 more
Ehsan Pishva,
Morteza P Kouhsar,
Luke Stephen Weymouth,
Adam R. Smith,
Yehani Wedatilake,
Ali Torkamani,
Robert Sweet,
Clive G Ballard,
Jonathan Mill,
Julia Kofler,
Sverre Bergh,
Geir Selbæk,
Katie Lunnon,
Byron Creese
Abstract Background Psychosis is a debilitating syndrome occurring in 40‐60% of people with Alzheimer’s disease (AD) and corresponds with a more severe disease course. Evidence suggests that psychosis in AD is associated with a distinct profile of microbiological changes, but little is known about the molecular processes driving etiology. Method Genome‐wide DNA methylation, small non‐coding (nc) RNAs (microRNA, transfer RNA, piwiRNA) and long coding and ncRNAs (mRNA, lincRNA, cicular RNAs) were quantified from 248 whole blood samples obtained from the Norwegian registry of persons assessed for cognitive symptoms (NorCog) cohort. Multi‐omics profiles of AD patients with psychosis (AD+P) were compared to the patients without psychosis (AD‐P). Result There were significant differences in DNA methylation, small ncRNAs, and long coding and ncRNAs between AD+P and AD‐P patients. Further analysis revealed specific genomic regions and molecular pathways that were differentially methylated or expressed in AD+P patients compared to AD‐P patients. Conclusion Our findings suggest that there may be distinct molecular signatures associated with AD psychosis, and that these differences may potentially be used as biomarkers for the early detection and diagnosis of AD psychosis.
Blood DNA methylomic signatures associated with CSF biomarkers of Alzheimer’s disease in the EMIF‐AD Multimodal Biomarker Discovery study
Rebecca G. Smith,
Jennifer L Imm,
Valerija Dobricic,
Yasmine Sommerer,
Isabelle Bos,
Stephanie J. B. Vos,
Frans R.J. Verhey
+ 24 more
Rebecca G. Smith,
Jennifer L Imm,
Valerija Dobricic,
Yasmine Sommerer,
Isabelle Bos,
Stephanie J. B. Vos,
Frans R.J. Verhey,
Philip Scheltens,
Sebastiaan Engelborgs,
Giovanni B Frisoni,
Olivier Blin,
Jill C Richardson,
Régis Bordet,
Magda Tsolaki,
Julius Popp,
Pablo Martinez‐Lage,
Alberto Lleo,
Peter Johannsen,
Yvonne Freund‐Levi,
Frölich Lutz,
Rik Vandenberghe,
Michael Wittig,
Andre Frank,
Simon Lovestone,
Johannes Streffer,
Ulf Andreasson,
Kaj Blennow,
Pieter Jelle Visser,
Henrik Zetterberg,
Lars Bertram,
Katie Lunnon
Abstract Background The aim of this study was to identify DNA methylation signatures that were associated with 15 CSF biomarker measures of Alzheimer’s disease (AD) or neurodegeneration. Method We profiled DNA methylation in 886 blood samples from the EMIF‐AD study using the Illumina EPIC array, identifying differentially methylated loci, and regions consisting of multiple adjacent differentially methylated sites. Results We identified Bonferroni‐significant differences in DNA methylation with respect to CSF t‐tau Z‐score (five loci), Aβ42 levels (one loci), YKL‐40 levels (six loci) and NFL (seven loci). Significant differentially methylated regions were identified in 13 of the 15 analyses, with overlapping regions featuring in multiple CSF measures( MX2, RHOH, ANKMY1, ZFP57 ) analyses, which was unsurprising given the high correlation between measures. Interestingly, we identified several regions that overlapped between the tau and amyloid ( ZBTB22 ), tau and NFL ( S100A13 ), NFL and neurogranin ( SORD ), and neurogranin and amyloid ( STRA6 ) regional analyses. Conclusion In this blood‐based epigenome‐wide association study of AD‐relevant CSF biomarkers we identified several interesting genomic loci and regions.
Multiomics‐based prediction of trajectories of global cognitive functioning in the ADNI cohort
Valentin Laroche,
Rick A Reijnders,
Joshua Harvey,
Willemijn J. Jansen,
Lars M.T. Eijssen,
Rachel Cavill,
Katie Lunnon
+ 2 more
Valentin Laroche,
Rick A Reijnders,
Joshua Harvey,
Willemijn J. Jansen,
Lars M.T. Eijssen,
Rachel Cavill,
Katie Lunnon,
den Hove Daniel L.A. van,
Ehsan Pishva
Abstract Background Cognitive impairment is the first manifestation of dementia. However, the rate of changes in cognitive function varies between individuals and unraveling heterogeneity in the trajectory of cognitive decline and dementia is crucial for adopting a suitable treatment. In this study, first, we aimed at identifying distinct trajectories of cognitive function, and next we used extensive machine learning approaches on multi‐trait ploygenic scores,CSF proteomics, plasma lipidomics and metabolomics data for classification of the trajectories identified in the initial analysis. Method Three‐year trajectories of global cognitive functioning were defined using six longitudinal measurements of the Mini‐Mental State Examination (MMSE) on 640 individuals in the Alzheimer’s disease Neuroimaging Initiative (ADNI) cohort. To compute the trajectories of cognitive function, we applied Latent Class Mixed Modeling adjusted for age, sex, and education. We used multiple machine learning algorithms, including Random Forest, Conditional Random Forest, Generalized Linear Models, and (sparse) Partial Least Square Discriminant Analysis. The best performing models were selected based on a set of prediction performance metrics. Result We identified three distinct trajectories of global cognitive function: Stable, Slow decline (SD) and Fast Decline (FD). The Random Forest algorithm performed best in prediction of the Stable versus Decliners (SD + FD), using the combined omics data. (AUC: 0.83 and a Matthews Correlation Coefficient (MCC): 0.59). The model is based on seven molecular features, among which we found lipids belonging to the ceramide pathway which has already been implicated in cognitive impairment and AD. Conclusion Defining trajectories of individuals with distinct patterns of cognitive changes over time, paired with omics‐based data, will allow the identification of new biomarkers for early detection of dementia. Additionally, they might unveil novel subtype‐specific molecular pathways which can contribute to more precise drug discovery processes.
Exploring the role of brain DNA methylomic signatures on gene expression dynamics of frontotemporal lobar degeneration
Katerine Fodder,
Megha Murthy,
Patrizia Rizzu,
Christina E. Toomey,
Rahat Hasan,
Jack Humphrey,
Towfique Raj
+ 5 more
Katerine Fodder,
Megha Murthy,
Patrizia Rizzu,
Christina E. Toomey,
Rahat Hasan,
Jack Humphrey,
Towfique Raj,
Katie Lunnon,
Jonathan Mill,
Peter Heutink,
Tammaryn Lashley,
Conceição Bettencourt
Abstract Background Frontotemporal lobar degeneration (FTLD) is an umbrella term describing the neuropathology of a clinically, genetically and pathologically heterogeneous group of diseases, which includes frontotemporal dementia and progressive supranuclear palsy. About 90% of the FTLD cases show either TDP‐43 or tau pathology (FTLD‐TDP or FTLD‐tau, respectively). Though aberrant brain DNA methylation has consistently been associated with Alzheimer’s disease and other neurodegenerative diseases, studies on FTLD are scarce. The main goal of this study was to investigate DNA methylation variation in FTLD bulk brain tissue and brain‐derived nuclei. Methods We used bulk frontal cortex genome‐wide DNA methylation profiles (Illumina 450K or EPIC microarrays) from three FTLD cohorts (N = 228). To identify unique and shared differentially methylated loci across FTLD subgroups/subtypes, we performed cohort‐specific epigenome‐wide association studies (EWAS) followed by a meta‐analysis. Additionally, we used weighted gene correlation network analysis to identify co‐methylation signatures associated with FTLD, FTLD pathological subtypes, and other disease‐related traits. To identify disturbed cell‐types and biological processes within disease associated signatures, we then carried out cell‐type and functional enrichment analyses. We also generated and have ongoing analysis of DNA methylation profiles (EPIC microarrays) of neuronal (NeuN+) and glial nuclei (NeuN‐) from FTLD‐TDP cases and controls (N = 40). Wherever possible, we also integrated additional DNA methylation, and gene and protein expression datasets. Results In bulk tissue, the EWAS meta‐analysis identified four shared differentially methylated loci in FTLD, including hypomethylation in OTUD4, a gene we found to be upregulated (mRNA and protein) in FTLD. Two of the four meta‐analysis hits (mapping to OTUD4 and CEBPZ), were found to be co‐methylated within signatures strongly associated with FTLD. Disease‐associated signatures implicate transcription regulation, the ubiquitin system, RNA/stress granule formation and glutamatergic synaptic signalling, and specific brain cell‐types, including pyramidal neurons and oligodendrocytes, in FTLD. Preliminary analysis of the neuronal and glial datasets also revealed FTLD‐associated DNA methylation signatures, which will further inform on cell‐type‐specific changes in FTLD. Conclusions Our findings identified novel FTLD‐associated loci, including OTUD4, and point to DNA methylation as an important mechanism in the dysregulation of biological processes relevant to the FTLD pathogenesis, such as RNA/stress granule formation.
Isoform characterisation & splicing signatures of AD‐risk genes using long‐read sequencing
Szi Kay Leung,
Isabel Castanho,
Aaron Jeffries,
Karen Moore,
Emma Dempster,
Jonathan T Brown,
Rosemary Bamford
+ 2 more
Szi Kay Leung,
Isabel Castanho,
Aaron Jeffries,
Karen Moore,
Emma Dempster,
Jonathan T Brown,
Rosemary Bamford,
Eilis Hannon,
Jonathan Mill
Abstract Background An increasing number of studies implicate a role for alternative splicing in development and neuropathology of Alzheimer’s disease (AD). However, it has been historically challenging to characterise splicing events, due to the inherent limitations of traditional RNA‐sequencing (RNA‐Seq) to capture full‐length transcripts critical for transcriptome assembly. In this study, we use two complementary targeted long‐read sequencing approaches, Pacific Biosciences (PacBio) isoform sequencing (Iso‐Seq) and Oxford Nanopore Technologies (ONT) nanopore cDNA sequencing, to profile the cortex of a mouse model of tau pathology (rTg4510) with ultra‐deep sequencing of a panel of 20 genes robustly implicated in AD. Method Targeted PacBio Iso‐Seq and targeted ONT profiling were performed on RNA isolated from 24 female rTg4510 transgenic and wild‐type mice, aged 2, 4, 6 and 8 months. Following successful enrichment for target genes using custom‐designed probes (IDT), library preparation were performed for subsequent sequencing on Sequel and MinION. The panel of genes selected for enrichment included genes (i.e. App, Mapt, Snca) and dementia risk genes identified from GWAS analyses. Raw sequence data was processed using a customised bioinformatics, and full‐length reads were merged and annotated with our developed custom scripts (FICLE). Result We identify thousands of novel transcripts across the panel of 20 AD‐ and dementia‐associated genes. We reveal unprecedented diversity of alternatively‐spliced isoforms with widespread usage of alternative novel 5’ and 3’ splice sites. We further robust transcriptional and splicing differences in these AD‐risk genes associated with the development of tau pathology. Among these changes, we observed global up‐regulation of Trem2‐associated isoforms and isoform switches in Bin1, further supporting a role for the dysregulation of the immune response in the development of AD pathology. Conclusion This represents the first study to comprehensively assess variable AS associated with the development of tau pathology using both PacBio Iso‐Seq and ONT nanopore sequencing. Our analyses confirm the importance of alternative RNA splicing in AD and identify evidence of differential transcript usage, even in the absence of gene‐level expression alterations. Further work will be undertaken to validate and functionally characterise these novel isoforms, and to extend these analyses to human post‐mortem AD brain samples.
New mitochondrial DNA methylation profiling method confirms epigenetic marker in the brain
Adam R. Smith, Darren Soanes, Karen Moore, Aaron Jeffries, Katie Lunnon
Adam R. Smith,
Darren Soanes,
Karen Moore,
Aaron Jeffries,
Katie Lunnon
Abstract Background There is growing evidence for the role of DNA methylation in regulating the transcription of mitochondrial genes. This is particularly important in neurodegenerative disorders characterised by mitochondrial dysfunction, including Alzheimer’s disease. However, current methods to create genome‐wide, high‐resolution analysis of the mitochondrial DNA methylome are challenging and lack control standards. Method Here, we present a new methodological approach to interrogate the mitochondrial DNA methylome at single base resolution using Oxford Nanopore technology and the creation of independent controls. Firstly, we isolate enriched mtDNA from SH‐SY5Y cell lines and post‐mortem brain tissue and use long‐range PCR (LR‐PCR) to generate 0%, 50% and 100% methylation controls. These controls were then validated using pyrosequencing and then run on the Oxford Nanopore (OXNP) long read sequencer. Finally, we used data generated by our controls to train existing methylation calling packages to better call mtDNA methylation in a post‐mortem human brain sample. Result We present a new and effective method of profiling mtDNA methylation on native DNA. Using this approach, we show that mitochondrial DNA methylation is relatively low but conserved, with peaks in DNA methylation >5% at several sites. Conclusion We have annotated patterns of DNA methylation at single base resolution across the mitochondrial genome in human brain, using our new laboratory pipeline and Oxford Nanopore technology to profile native DNA. Looking to the future this method could be utilized to further investigate the role of mitochondrial epigenetic mechanisms in neurodegenerative disorders, such as Alzheimer’s disease.
A transcriptome‐wide analysis of Alzheimer’s disease brain during systemic inflammation
Giulia Pegoraro, Rebecca G. Smith, Lachlan Ford MacBean, Adam R. Smith, Delphine Boche, Ehsan Pishva, Katie Lunnon
Giulia Pegoraro,
Rebecca G. Smith,
Lachlan Ford MacBean,
Adam R. Smith,
Delphine Boche,
Ehsan Pishva,
Katie Lunnon
Abstract Background The onset and progression of Alzheimer’s disease (AD) has been widely linked with inflammation both in the periphery and within the brain. Indeed, many AD sufferers ultimately die with a systemic infection, and infections during life can increase the risk of developing dementia and the rate of cognitive decline in AD patients. One of the aims of this study is to investigate the molecular mechanisms involved in the CNS response to systemic infections in AD through the analysis of gene expression changes. Method The cohort of patients selected for the study is composed of 238 post‐mortem prefrontal cortex brain samples. The cohort is divided as follows: 68 samples affected by AD and 55 controls, all of whom died with an infection, and 62 AD patients and 53 controls who did not have an infection at the time of the death. The infections included in the analysis consists of respiratory infections (i.e. pneumonia), urinary and chest infections. Following RNA sequencing, a weighted gene correlation network analysis (WGCNA) and pathway enrichment analysis were performed. Result The results from WGCNA show a module of particular interest with a correlation with both AD and respiratory infections, which represent most of the cases of infection. The pathway enrichment analysis performed on the genes composing this module identified several relevant biological pathways. Among the ten most significant pathways, part of them is involved in immune responses, such as “leukocyte activation involved in immune response” and “cell activation involved in immune response”. Conclusion This analysis laid the foundations for further investigations into gene expression changes associated with AD and infection. Future work will include repeating the analysis focusing on respiratory infections only, to examine if this source of heterogeneity is limiting our findings. Ultimately this data will be combined with miRNA sequencing and DNA methylation data from the same individuals, the work for which is ongoing.
Methylomic‐based molecular subtyping of late onset Alzheimer’s Disease
Valentin Laroche,
Rick A Reijnders,
Adam R. Smith,
Lars M.T. Eijssen,
Rachel Cavill,
Daniel L.A. Hove,
Katie Lunnon
+ 1 more
Valentin Laroche,
Rick A Reijnders,
Adam R. Smith,
Lars M.T. Eijssen,
Rachel Cavill,
Daniel L.A. Hove,
Katie Lunnon,
Ehsan Pishva
Abstract Background Accumulating evidence shows that the heterogeneity and temporal complexity of Alzheimer’s Disease contribute to the treatment failure. Advances in omics technologies along with development of efficient integrative analytical pipelines, provide a unique opportunity to investigate the drivers of heterogeneity at multiple molecular levels. Method We used genome‐wide DNA methylation data generated in postmortem prefrontal cortex samples from two independent biobanks of Brain for Dementia Research (BDR; n = 382) and the UK Brain Bank Network (UKBBN; n = 250). Multiple unsupervised clustering methods including network‐based, Bayesian and Ensemble approaches were applied on DNA methylation data quantified by the Illumina EPIC arrays in the discovery cohort (BDR). Following each clustering methods, distinct features related to the identified subtypes were captured using classification models such as sparse partial least square discriminant analysis and random forest. The most accurate models comprising the distinct features were used to classify the samples in the UKBBN cohort into the appropriate subtypes. Clinical and pathological evaluation of the identified subtypes have been performed for both discovery and replication cohorts Result We identified well‐defined cluster of samples in the BDR cohort. We achieved acceptable prediction values in the test data to classify the subgroups using the distinct methylation features related to the identified subtypes (AUC: 0.86 – 0.96). The best performing classification model was applied on the other independent cohort and similarly labelled samples across different cohorts were extensively characterized using relevant clinical and pathological information. Conclusion We used state‐of the‐art methods to undertake the first systematic, DNA methylomic‐based subtyping of AD. this is a vital step to unravel the heterogeneity of the disease
Establishing the contribution of genetic risk loci in the Lewy dody diseases
Jennifer L Imm,
Joshua Harvey,
Byron Creese,
Leonidas Chouliaras,
Emma Dempster,
Clive G Ballard,
John T O'Brien
+ 4 more
Jennifer L Imm,
Joshua Harvey,
Byron Creese,
Leonidas Chouliaras,
Emma Dempster,
Clive G Ballard,
John T O'Brien,
Dag Aarsland,
Jonathan Mill,
Ehsan Pishva,
Katie Lunnon
Abstract Background Dementia with Lewy bodies (DLB), Parkinson’s disease (PD) and Parkinson’s disease dementia (PDD) are termed Lewy body diseases (LBDs). These neurodegenerative diseases are classified by the accumulation of alpha‐synuclein in neurons, forming Lewy bodies (LB). Whilst pathologically similar, symptomatic staging is different. Previous genome wide association studies (GWAS) have identified classic Alzheimer’s disease (AD) and PD loci as risk loci in DLB. Therefore, we have used polygenic risk score (PRS) analysis to investigate the contribution of AD and PD variants in the LBDs. Method DNA was extracted from bulk brain tissue from 481 individuals (162 controls, 95 DLB, 156 PDD and 68 PD) and genotyped on the Illumina global screening array. After a strict quality control and imputation pipeline, PRSs for multiple relevant traits using reference GWAS summary statistics were calculated using PRSice2. Result Study groups have been sourced consisting of cases with PD, PDD and DLB based on LB deposition and clinical symptom staging. All groups, including controls are stratified for age and concomitant AD pathology. Assessing multiple PRSs for association with pathological development and clinical outcomes we have identified the contribution of genetic risk from related neurodegenerative and neuropsychiatric disorders in our cohort of PD, PDD and DLB samples. Conclusion We have collated a well powered study cohort to interrogate the genetic basis of the Lewy body dementias and the relative contribution of AD and PD risk loci in the LBDs. We are currently generating methylation quantitative trait loci (mQTLs) for this dataset using previously generated matched DNA methylation data in the brain.
Amyloid‐beta immunotherapy induces novel methylomic changes in Alzheimer’s disease brain
Lachlan Ford MacBean, Adam R. Smith, Delphine Boche, Katie Lunnon
Lachlan Ford MacBean,
Adam R. Smith,
Delphine Boche,
Katie Lunnon
Abstract Background Post‐mortem neuropathological examinations following the first active immunotherapy strategy (AN‐1792, Elan Pharmaceuticals, 2000) for Alzheimer’s disease (AD) have evidenced amyloid‐β (Aβ) plaque clearance and increased microglial phagocytic activity in immunised individuals. This study characterises the epigenetic profiles of individuals who underwent Aβ immunotherapy with the aim of discovering novel therapeutic targets and biomarkers. Method DNA was isolated from post‐mortem prefrontal cortex tissue of 16 immunised AD cases who received varying doses (ug) and number of doses during the trial period, including placebos. DNA methylation was quantified using methylation arrays and the raw intensity values processed and normalised for subsequent statistical analysis to identify differentially methylated positions (DMPs) across the genome associated with Aβ immunotherapy. Additional analyses included regions of enrichment analysis for identification of differentially methylated regions (DMRs) and weighted gene co‐expression network analysis to identify gene clusters with highly correlated methylation levels. Result After correcting for known (age, sex, cell type composition) and unknown variables, a DMP located within Chromosome 19 Open Reading Frame 12 (C19Orf12) at the genome‐wide significance level (P < 9.00E−08) was associated with Aβ immunisation. 10 DMRs were further associated with immunisation, with three regions consisting of ≥ 3 CpG sites and having a Sidak‐corrected P < 0.05. These regions were located within the CRISP2 (chr6; 49681178:49681391 [8 probes], Sidak‐corrected P = 8.29E‐05), CTTNA1 (chr5; 138210906:138211184 [8 probes], Sidak‐corrected P = 5.96E‐06), and RNF39 (chr6; 30038859:30039025 [12 probes], Sidak‐Corrected P = 2.60E‐05) genes. Conclusion Indicating better inflammatory markers can help inform of effective preventative care strategies for elders. This study provides evidence for altered epigenetic processes in the pathophysiology of AD and identifies novel processes specific to Aβ immunotherapy. The next step for this project includes analysing RNA sequencing data, to determine if observed methylomic changes correlate with gene expression, and genotyping array data.
Characterising the D409V/WT mouse as a novel model of Lewy body dementia
Millie Sander, Jonathan T Brown, Katie Lunnon, Clive G Ballard
Millie Sander,
Jonathan T Brown,
Katie Lunnon,
Clive G Ballard
Abstract Background The overlap in both pathological and symptomatic traits observed among Alzheimer’s disease (AD) and dementia with Lewy bodies (DLB) patients make accurate diagnosis difficult. Novel models to further study DLB are therefore imperative, and previous research suggests mice with heterozygous mutations in the GBA gene (D409V/WT) to be a viable option. These mice display age‐related cognitive decline and α‐synuclein deposition in the brain (Clarke et al., 2019), and our prior work found there to be significant atrophy in the brain by 12 months of age. Method We aimed to further characterise disease‐associated pathology exhibited by these mice. Cortical thickness and vesicle size was measured among mice of 3, 6, 9, 12, and 18 months of age in order to assess atrophy progression with age. Neuronal firing in the medial septum was measured at both baseline and following application of NMDA – a drug used to elicit neuronal activity. Firing rate and latency to reach peak NMDA response were used to assess neuronal dysfunction. Finally, differential expression and weighted gene co‐expression network analysis (WGCNA) was conducted to assess transcriptomic changes in the medial septum. All studies used wild‐type littermates as controls. Result Age‐associated cortical thinning and ventricle enlargement were observed, with all six measures reaching statistical significance by 12 months of age. Although latency to reach peak neuronal firing showed no difference between groups, firing rate was significantly reduced in D409V/WT mice across all conditions. Differential expression analysis found significant downregulated genes in the medial septum of the D409V/WT mice compared to the WT controls, and WGCNA analysis found various clusters of genes to be associated with both genotype and sex. Conclusion These results present examples of DLB‐associated pathology exhibited by the D409V/WT mice, supporting their potential as a novel model of disease. However, further characterisation is needed in order for these mice to be considered a reliable model, and to be employed in wide‐scale research. References: Clarke, E. et al. (2019) ‘Age‐related neurochemical and behavioural changes in D409V/WT GBA1 mouse: Relevance to lewy body dementia’, Neurochemistry International, 129. https://doi.org/10.1016/j.neuint.2019.104502 .
A study of DNA methylation in the prefrontal cortex of heterozygous GBA1 mutant mice
Luke Stephen Weymouth, Jennifer L Imm, Millie Sander, Jonathan T Brown, Katie Lunnon, Adam R. Smith
Luke Stephen Weymouth,
Jennifer L Imm,
Millie Sander,
Jonathan T Brown,
Katie Lunnon,
Adam R. Smith
Abstract Background Epigenome‐wide association studies (EWAS) of DNA methylation are being undertaken in Parkinson’s disease (PD) and Dementia with Lewy bodies (DLB) post‐mortem brain to identify novel disease mechanisms. However, there is considerable heterogeneity in clinical and neuropathological manifestation, as well as the contribution of post‐mortem factors, which can confound smaller studies. The heterozygous GBA1 (D409V/WT) mouse model of DLB presents α‐synuclein deposition, cognitive decline and cholinergic dysfunction. We have undertaken the first systematic investigation of DNA methylation in these mice to identify changes related to α‐synuclein deposition. We have also explored the effect of varying post‐mortem interval (PMI) on DNA methylation patterns, to allow us to better interpret human studies. Method In total we profiled DNA methylation using the Illumina Infinium Mouse Methylation BeadChip array in 58 mice, corresponding to 28 GBA1 D409V/WT and 30 WT mice aged 8‐23 months. Within each age group we divided mice into 5 further groups to also explore the effect of PMI: +0hrs, +24hrs, +48hrs, +72hrs & +96 hrs respectively. The mice were culled and those in the +0hrs group were immediately dissected with the prefrontal cortex being flash frozen and stored in the freezer. Mice assigned to other PMI groups were culled and stored at 4 degrees for the relevant PMI before dissection and flash freezing. DNA was extracted, bisulfite treated and then profiled for DNA methylation. Result Of the 58 mice that were sourced it was ensured that D409V/WT mice and WT mice were balanced between the 5 PMI groups. We have investigated the effect of phenotype, neuropathology and PMI on DNA methylation levels using linear regression models. Conclusion Teasing apart the effect varying PMI has on DNA methylation in post mortem brain samples will be a great aid when analysing such data going forward in large human EWASs. We have collated an in vivo study cohort to investigate DNA methylation patterns in the heterozygous D409V/WT mouse compared to WT, and interrogated the effect PMI has on the quality of methylation data. More broadly our study of PMI will have relevance to interpreting the results of human EWAS of DLB and other dementias.
Targeted bisulfite sequencing analysis of Alzheimer’s disease candidate genes reveals differential methylation across neurofibrillary tangle burden in the prefrontal cortex.
Greg Wheildon,
Adam R. Smith,
Darren Soanes,
Rebecca G. Smith,
Karen Moore,
Paul O'Neill,
Kevin Morgan
+ 6 more
Greg Wheildon,
Adam R. Smith,
Darren Soanes,
Rebecca G. Smith,
Karen Moore,
Paul O'Neill,
Kevin Morgan,
Alan J Thomas,
Seth Love,
Paul T Francis,
Jonathan Mill,
Ehsan Pishva,
Katie Lunnon
Abstract Background Recent epigenome‐wide association studies (EWAS) identified several loci in specific genes showing robust and reproducible alterations in DNA methylation in Alzheimer’s disease (AD) brain samples. Standardly, assessing methylation in EWAS is done using microarrays, which target a limited number of sites in each gene. Here, we performed targeted bisulfite sequencing of candidate genes associated with AD to determine the exact extent of methylation changes across neurofibrillary tangle burden (NFT) within these loci. Method Prefrontal cortex brain samples from 58 individuals were grouped by Braak stage (control 0‐II; intermediate III‐IV; AD V‐VI). Following DNA extraction, 30 genomic regions were captured using Agilent SureSelect target baits. After next‐generation bisulfite sequencing, reads were aligned and the methylation status of cytosine residues called using the Bismark program. Differentially methylated positions (DMPs) were analyzed across the three groups. Furthermore, the presence of differentially methylated regions (DMRs), made up of several DMPs was assessed. Methylation levels in genomic features, such as promoters and gene bodies, of the target regions were also compared. Result Methylation levels were quantified for each group. Linear regression controlled for co‐variation before differences were examined using a one‐way ANOVA, with Tukey’s post‐hoc test. Sites in several genes showed stepwise increases in DNA methylation across the groups. Interestingly, amongst the most robust sites, differences in methylation in the intermediate group when compared to the control and AD samples were observed. DMRs were observed in the groups, as were methylation differences between promotors and gene bodies in several targeted regions. Conclusion This work provides further evidence that dysregulation of methylation is associated with pathological changes in AD prefrontal cortex. Differential methylation with intermediate NFT pathology, at sites showing no difference between control and AD samples, potentially indicates early pathological changes. As DNA methylation is reversible, this could present potential targets for pharmacological intervention.
An Epigenome‐wide association study of psychosis in Alzheimer’s disease dorsolateral prefrontal cortex
Morteza P Kouhsar,
Luke Stephen Weymouth,
Byron Creese,
Sverre Bergh,
Yehani Wedatilake,
Ali Torkamani,
Adam R. Smith
+ 7 more
Morteza P Kouhsar,
Luke Stephen Weymouth,
Byron Creese,
Sverre Bergh,
Yehani Wedatilake,
Ali Torkamani,
Adam R. Smith,
Geir Selbæk,
Robert Sweet,
Clive G Ballard,
Jonathan Mill,
Julia Kofler,
Ehsan Pishva,
Katie Lunnon
Abstract Background Psychosis is a debilitating syndrome occurring in 40‐60% of people with Alzheimer’s disease (AD) and corresponds with a more severe disease course. Evidence suggests that psychosis in AD (AD+P) is associated with a distinct profile of neurobiological changes, but little is known about the molecular processes driving aetiology. In this study, we performed an epigenome‐wide association study (EWAS) to investigate DNA methylation associated with AD+P in the dorsolateral prefrontal cortex of post‐mortem brain samples. Method Brain samples were obtained from the University of Pittsburgh Alzheimer’s disease Research Centre (PITT‐ADRC). AD pathology was assessed and classified using CERAD neurotic plaque density score, Braak neurofibrillary tangle stages and NIA‐RI criteria. We used the presence or absence of delusions and hallucinations, Mini‐Mental State Exam (MMSE) and Clinical Dementia Rating (CDR) to categorise our samples into AD with Psychosis (AD+P) and AD without Psychosis (AD‐P) groups. DNA was extracted, bisulfite‐treated and profiled on the Illumina Methylation EPIC Array and genotyping was carried out on the Illumina Global Screening Array (GSA). Result After data quality control, 153 samples (40 AD‐P, 113 AD+P) remained for further analysis. The normalized beta values and the effect estimate values were used to extract Differentially Methylated positions (DMP) and differentially methylated regions (DMRs), respectively. To identify methylation quantitative trait loci (mQTLs) in both cis and trans, SNP‐CpG pairs with a p‐value threshold of <1e‐5 were calculated. We performed a colocalization analysis for the most significant DMPs and mQTLs, using publicly available summary statistics of relevant genome‐wide association studies (GWAS). Conclusion The development of effective therapies for AD+P is an urgent priority and requires a better understanding of the molecular mechanisms underlying this syndrome. To address this, we have collated a well‐powered study cohort to interrogate the epigenetic basis of AD+P in the brain and have identified several loci of interest that require further study.
DNA methylation patterns in the frontal lobe white matter of multiple system atrophy, Parkinson’s disease, and progressive supranuclear palsy: A cross-comparative investigation
Megha Murthy,
Katherine Fodder,
Yasuo Miki,
Naiomi Rambarack,
Pablo Fernandez Eduardo De,
Jonathan Mill,
Thomas T Warner
+ 2 more
Megha Murthy,
Katherine Fodder,
Yasuo Miki,
Naiomi Rambarack,
Pablo Fernandez Eduardo De,
Jonathan Mill,
Thomas T Warner,
Tammaryn Lashley,
Conceição Bettencourt
Abstract Multiple system atrophy (MSA) is a rare neurodegenerative disease characterized by neuronal loss and gliosis, with oligodendroglial cytoplasmic inclusions (GCI’s) containing α-synuclein being the primary pathological hallmark. Clinical presentations of MSA overlap with other parkinsonian disorders such as Parkinson’s disease (PD), dementia with Lewy bodies (DLB), and progressive supranuclear palsy (PSP), posing challenges in early diagnosis. Numerous studies have reported perturbations in DNA methylation in neurodegenerative diseases, with candidate loci being identified in various parkinsonian disorders including MSA, PD, and PSP. Although MSA and PSP present with substantial white matter pathology, alterations in white matter have also been reported in PD. However, studies comparing the DNA methylation architectures of white matter in these diseases are lacking. We therefore aimed to investigate three parkinsonian diseases, MSA, PD, and PSP, to identify shared and disease-specific DNA methylation alterations in white matter. Genome-wide DNA methylation profiling of frontal lobe white matter of individuals with MSA (n=17), PD (n=17), and PSP (n=16) and controls (n=15), using the Illumina EPIC array, revealed substantial commonalities in DNA methylation perturbations in MSA, PD, and PSP. We further used weighted gene correlation network analysis to identify disease-associated co-methylation signatures and identified dysregulation in processes relating to Wnt signalling, signal transduction, endoplasmic reticulum stress, mitochondrial processes, RNA interference, and endosomal transport. Our results highlight several shared DNA methylation perturbations and pathways indicative of converging molecular mechanisms contributing towards neurodegeneration in the white matter of all three parkinsonian diseases.
The Association of Hippocampal Long-Term Potentiation-Induced Gene Expression with Genetic Risk for Psychosis
Natalie L. Wellard, Nicholas E. Clifton, Elliott Rees, Kerrie L. Thomas, Jeremy Hall
Natalie L. Wellard,
Nicholas E. Clifton,
Elliott Rees,
Kerrie L. Thomas,
Jeremy Hall
Genomic studies focusing on the contribution of common and rare genetic variants of schizophrenia and bipolar disorder support the view that substantial risk is conferred through molecular pathways involved in synaptic plasticity in the neurons of cortical and subcortical brain regions, including the hippocampus. Synaptic long-term potentiation (LTP) is central to associative learning and memory and depends on a pattern of gene expression in response to neuronal stimulation. Genes related to the induction of LTP have been associated with psychiatric genetic risk, but the specific cell types and timepoints responsible for the association are unknown. Using published genomic and transcriptomic datasets, we studied the relationship between temporally defined gene expression in hippocampal pyramidal neurons following LTP and enrichment for common genetic risk for schizophrenia and bipolar disorder, and for copy number variants (CNVs) and de novo coding variants associated with schizophrenia. We observed that upregulated genes in hippocampal pyramidal neurons at 60 and 120 min following LTP induction were enriched for common variant association with schizophrenia and bipolar disorder subtype I. At 60 min, LTP-induced genes were enriched in duplications from patients with schizophrenia, but this association was not specific to pyramidal neurons, perhaps reflecting the combined effects of CNVs in excitatory and inhibitory neuron subtypes. Gene expression following LTP was not related to enrichment for de novo coding variants from schizophrenia cases. Our findings refine our understanding of the role LTP-related gene sets play in conferring risk to conditions causing psychosis and provide a focus for future studies looking to dissect the molecular mechanisms associated with this risk.
Quantifying the proportion of different cell types in the human cortex using DNA methylation profiles
Eilis Hannon,
Emma L. Dempster,
Jonathan P. Davies,
Barry Chioza,
Georgina E. T. Blake,
Joe Burrage,
Stefania Policicchio
+ 5 more
Eilis Hannon,
Emma L. Dempster,
Jonathan P. Davies,
Barry Chioza,
Georgina E. T. Blake,
Joe Burrage,
Stefania Policicchio,
Alice Franklin,
Emma M. Walker,
Rosemary A. Bamford,
Leonard C. Schalkwyk,
Jonathan Mill
BackgroundDue to interindividual variation in the cellular composition of the human cortex, it is essential that covariates that capture these differences are included in epigenome-wide association studies using bulk tissue. As experimentally derived cell counts are often unavailable, computational solutions have been adopted to estimate the proportion of different cell types using DNA methylation data. Here, we validate and profile the use of an expanded reference DNA methylation dataset incorporating two neuronal and three glial cell subtypes for quantifying the cellular composition of the human cortex.ResultsWe tested eight reference panels containing different combinations of neuronal- and glial cell types and characterised their performance in deconvoluting cell proportions from computationally reconstructed or empirically derived human cortex DNA methylation data. Our analyses demonstrate that while these novel brain deconvolution models produce accurate estimates of cellular proportions from profiles generated on postnatal human cortex samples, they are not appropriate for the use in prenatal cortex or cerebellum tissue samples. Applying our models to an extensive collection of empirical datasets, we show that glial cells are twice as abundant as neuronal cells in the human cortex and identify significant associations between increased Alzheimer’s disease neuropathology and the proportion of specific cell types including a decrease in NeuNNeg/SOX10Neg nuclei and an increase of NeuNNeg/SOX10Pos nuclei.ConclusionsOur novel deconvolution models produce accurate estimates for cell proportions in the human cortex. These models are available as a resource to the community enabling the control of cellular heterogeneity in epigenetic studies of brain disorders performed on bulk cortex tissue.
Mitochondrial D-loop Methylation Levels Inversely Correlate with Disease Duration in Amyotrophic Lateral Sclerosis
Andrea Stoccoro,
Adam R Smith,
Lorena Mosca,
Alessandro Marocchi,
Francesca Gerardi,
Christian Lunetta,
Katie Lunnon
+ 2 more
Andrea Stoccoro,
Adam R Smith,
Lorena Mosca,
Alessandro Marocchi,
Francesca Gerardi,
Christian Lunetta,
Katie Lunnon,
Lucia Migliore,
Fabio Coppedè
Aim: To correlate mitochondrial D-loop region methylation levels and mtDNA copy number with disease duration in familial amyotrophic lateral sclerosis (ALS) patients. Patients & methods: The study population included 12 ALS patients with a mutation in SOD1 and 13 ALS patients with the C9orf72 hexanucleotide repeat expansion. Methylation levels of the D-loop region and mtDNA copy number were quantified using pyrosequencing and quantitative PCR, respectively. Results: We observed that D-loop methylation levels inversely correlated while mtDNA copy number positively correlated with disease duration. Conclusion: Considering the central role played by mitochondria in ALS, this preliminary study provides new knowledge for future studies aimed at identifying biomarkers of disease progression and new targets for therapeutic interventions.
Meta-analysis of epigenetic aging in schizophrenia reveals multifaceted relationships with age, sex, illness duration, and polygenic risk
Anil P. S. Ori,
Loohuis Loes M. Olde,
Jerry Guintivano,
Eilis Hannon,
Emma Dempster,
Clair David St.,
Nick J. Bass
+ 6 more
Anil P. S. Ori,
Loohuis Loes M. Olde,
Jerry Guintivano,
Eilis Hannon,
Emma Dempster,
Clair David St.,
Nick J. Bass,
Andrew McQuillin,
Jonathan Mill,
Patrick F. Sullivan,
Rene S. Kahn,
Steve Horvath,
Roel A. Ophoff
BackgroundThe study of biological age acceleration may help identify at-risk individuals and reduce the rising global burden of age-related diseases. Using DNA methylation (DNAm) clocks, we investigated biological aging in schizophrenia (SCZ), a mental illness that is associated with an increased prevalence of age-related disabilities and morbidities. In a whole blood DNAm sample of 1090 SCZ cases and 1206 controls across four European cohorts, we performed a meta-analysis of differential aging using three DNAm clocks (i.e., Hannum, Horvath, and Levine). To dissect how DNAm aging contributes to SCZ, we integrated information on duration of illness and SCZ polygenic risk, as well as stratified our analyses by chronological age and biological sex.ResultsWe found that blood-based DNAm aging is significantly altered in SCZ independent from duration of the illness since onset. We observed sex-specific and nonlinear age effects that differed between clocks and point to possible distinct age windows of altered aging in SCZ. Most notably, intrinsic cellular age (Horvath clock) is decelerated in SCZ cases in young adulthood, while phenotypic age (Levine clock) is accelerated in later adulthood compared to controls. Accelerated phenotypic aging was most pronounced in women with SCZ carrying a high polygenic burden with an age acceleration of + 3.82 years (CI 2.02–5.61, P = 1.1E−03). Phenotypic aging and SCZ polygenic risk contributed additively to the illness and together explained up to 14.38% of the variance in disease status.ConclusionsOur study contributes to the growing body of evidence of altered DNAm aging in SCZ and points to intrinsic age deceleration in younger adulthood and phenotypic age acceleration in later adulthood in SCZ. Since increased phenotypic age is associated with increased risk of all-cause mortality, our findings indicate that specific and identifiable patient groups are at increased mortality risk as measured by the Levine clock. Our study did not find that DNAm aging could be explained by the duration of illness of patients, but we did observe age- and sex-specific effects that warrant further investigation. Finally, our results show that combining genetic and epigenetic predictors can improve predictions of disease outcomes and may help with disease management in schizophrenia.
Integrating human endogenous retroviruses into transcriptome-wide association studies highlights novel risk factors for major psychiatric conditions
Rodrigo R. R. Duarte,
Oliver Pain,
Matthew L. Bendall,
Mulder Rougvie Miguel de,
Jez L. Marston,
Sashika Selvackadunco,
Claire Troakes
+ 7 more
Rodrigo R. R. Duarte,
Oliver Pain,
Matthew L. Bendall,
Mulder Rougvie Miguel de,
Jez L. Marston,
Sashika Selvackadunco,
Claire Troakes,
Szi Kay Leung,
Rosemary A. Bamford,
Jonathan Mill,
Paul F. O’Reilly,
Deepak P. Srivastava,
Douglas F. Nixon,
Timothy R. Powell
Human endogenous retroviruses (HERVs) are repetitive elements previously implicated in major psychiatric conditions, but their role in aetiology remains unclear. Here, we perform specialised transcriptome-wide association studies that consider HERV expression quantified to precise genomic locations, using RNA sequencing and genetic data from 792 post-mortem brain samples. In Europeans, we identify 1238 HERVs with expression regulated in cis, of which 26 represent expression signals associated with psychiatric disorders, with ten being conditionally independent from neighbouring expression signals. Of these, five are additionally significant in fine-mapping analyses and thus are considered high confidence risk HERVs. These include two HERV expression signatures specific to schizophrenia risk, one shared between schizophrenia and bipolar disorder, and one specific to major depressive disorder. No robust signatures are identified for autism spectrum conditions or attention deficit hyperactivity disorder in Europeans, or for any psychiatric trait in other ancestries, although this is likely a result of relatively limited statistical power. Ultimately, our study highlights extensive HERV expression and regulation in the adult cortex, including in association with psychiatric disorder risk, therefore providing a rationale for exploring neurological HERV expression in complex neuropsychiatric traits.
Brain cell-type shifts in Alzheimer’s disease, autism, and schizophrenia interrogated using methylomics and genetics
Chloe X Yap,
Daniel D Vo,
Matthew G Heffel,
Arjun Bhattacharya,
Cindy Wen,
Yuanhao Yang,
Kathryn E Kemper
+ 15 more
Chloe X Yap,
Daniel D Vo,
Matthew G Heffel,
Arjun Bhattacharya,
Cindy Wen,
Yuanhao Yang,
Kathryn E Kemper,
Jian Zeng,
Zhili Zheng,
Zhihong Zhu,
Eilis Hannon,
Dorothea Seiler Vellame,
Alice Franklin,
Christa Caggiano,
Brie Wamsley,
Daniel H Geschwind,
Noah Zaitlen,
Alexander Gusev,
Bogdan Pasaniuc,
Jonathan Mill,
Chongyuan Luo,
Michael J Gandal
Few neuropsychiatric disorders have replicable biomarkers, prompting high-resolution and large-scale molecular studies. However, we still lack consensus on a more foundational question: whether quantitative shifts in cell types-the functional unit of life-contribute to neuropsychiatric disorders. Leveraging advances in human brain single-cell methylomics, we deconvolve seven major cell types using bulk DNA methylation profiling across 1270 postmortem brains, including from individuals diagnosed with Alzheimer's disease, schizophrenia, and autism. We observe and replicate cell-type compositional shifts for Alzheimer's disease (endothelial cell loss), autism (increased microglia), and schizophrenia (decreased oligodendrocytes), and find age- and sex-related changes. Multiple layers of evidence indicate that endothelial cell loss contributes to Alzheimer's disease, with comparable effect size to APOE genotype among older people. Genome-wide association identified five genetic loci related to cell-type composition, involving plausible genes for the neurovascular unit (P2RX5 and TRPV3) and excitatory neurons (DPY30 and MEMO1). These results implicate specific cell-type shifts in the pathophysiology of neuropsychiatric disorders.
An atlas of expressed transcripts in the prenatal and postnatal human cortex
Rosemary A. Bamford,
Szi Kay Leung,
V. Kartik Chundru,
Aaron R. Jeffries,
Jonathan P. Davies,
Alice Franklin,
Xinmu Chen
+ 10 more
Rosemary A. Bamford,
Szi Kay Leung,
V. Kartik Chundru,
Aaron R. Jeffries,
Jonathan P. Davies,
Alice Franklin,
Xinmu Chen,
Andrew McQuillin,
Nicholas Bass,
APEX consortium,
Emma Walker,
Paul O’Neill,
Ehsan Pishva,
Emma L. Dempster,
Eilis Hannon,
Caroline F. Wright,
Jonathan Mill
ABSTRACT Alternative splicing is a post-transcriptional mechanism that increases the diversity of expressed transcripts and plays an important role in regulating gene expression in the developing central nervous system. We used long-read transcriptome sequencing to characterise the structure and abundance of full-length transcripts in the human cortex from donors aged 6 weeks post-conception to 83 years old. We identified thousands of novel transcripts, with dramatic differences in the diversity of expressed transcripts between prenatal and postnatal cortex. A large proportion of these previously uncharacterised transcripts have high coding potential, with corresponding peptides detected in proteomic data. Novel putative coding sequences are highly conserved and overlap de novo mutations in genes linked with neurodevelopmental disorders in individuals with relevant clinical phenotypes. Our findings underscore the potential of novel coding sequences to harbor clinically relevant variants, offering new insights into the genetic architecture of human disease. Our cortical transcript annotations are available as a resource to the research community via an online database.
Deficiency of the histone lysine demethylase KDM5B causes autism-like phenotypes via increased NMDAR signalling
Leticia Pérez-Sisqués,
Shail U. Bhatt,
Angela Caruso,
Mohi U. Ahmed,
Talia E. Gileadi,
Shoshana Spring,
Eleanor Hendy
+ 10 more
Leticia Pérez-Sisqués,
Shail U. Bhatt,
Angela Caruso,
Mohi U. Ahmed,
Talia E. Gileadi,
Shoshana Spring,
Eleanor Hendy,
Joyce Taylor-Papadimitriou,
Diana Cash,
Nicholas Clifton,
Jacob Ellegood,
Laura C. Andreae,
Jason P. Lerch,
Maria Luisa Scattoni,
K. Peter Giese,
Cathy Fernandes,
M. Albert Basson
Abstract Loss-of-function mutations in genes encoding lysine methyltransferases (KMTs) and demethylases (KDMs) responsible for regulating the trimethylation of histone 3 on lysine 4 (H3K4me3) are associated with neurodevelopmental conditions, including autism spectrum disorder and intellectual disability. To study the specific role of H3K4me3 demethylation, we investigated neurodevelopmental phenotypes in mice without KDM5B demethylase activity. These mice exhibited autism-like behaviours and increased brain size. H3K4me3 levels and the expression of neurodevelopmental genes were increased in the developing Kdm5b mutant neocortex. These included elevated expression of Grin2d . The Grin2d gene product NMDAR2D was increased in synaptosomes isolated from the Kdm5b -deficient neocortex and treating mice with the NMDAR antagonist memantine rescued deficits in ultrasonic vocalisations and reduced repetitive digging behaviours. These findings suggest that increased H3K4me3 levels and associated Grin2d gene upregulation disrupt brain development and function, leading to socio-communication deficits and repetitive behaviours, and identify a potential therapeutic target for neurodevelopmental disorders associated with KDM5B deficiency.
Anish Dattani,
Elena Corujo-Simon,
Arthur Radley,
Tiam Heydari,
Yasaman Taheriabkenar,
Francesca Carlisle,
Simeng Lin
+ 5 more
Anish Dattani,
Elena Corujo-Simon,
Arthur Radley,
Tiam Heydari,
Yasaman Taheriabkenar,
Francesca Carlisle,
Simeng Lin,
Corin Liddle,
Jonathan Mill,
Peter W Zandstra,
Jennifer Nichols,
Ge Guo
The hypoblast is an essential extraembryonic tissue set aside within the inner cell mass in the blastocyst. Research with human embryos is challenging. Thus, stem cell models that reproduce hypoblast differentiation provide valuable alternatives. We show here that human naive pluripotent stem cell (PSC) to hypoblast differentiation proceeds via reversion to a transitional ICM-like state from which the hypoblast emerges in concordance with the trajectory in human blastocysts. We identified a window when fibroblast growth factor (FGF) signaling is critical for hypoblast specification. Revisiting FGF signaling in human embryos revealed that inhibition in the early blastocyst suppresses hypoblast formation. In vitro, the induction of hypoblast is synergistically enhanced by limiting trophectoderm and epiblast fates. This finding revises previous reports and establishes a conservation in lineage specification between mice and humans. Overall, this study demonstrates the utility of human naive PSC-based models in elucidating the mechanistic features of early human embryogenesis.
Developmentally dynamic changes in DNA methylation in the human pancreas
Ailsa MacCalman,
Franco Elisa De,
Alice Franklin,
Christine S. Flaxman,
Sarah J. Richardson,
Kathryn Murrall,
Joe Burrage
+ 8 more
Ailsa MacCalman,
Franco Elisa De,
Alice Franklin,
Christine S. Flaxman,
Sarah J. Richardson,
Kathryn Murrall,
Joe Burrage,
Emma M. Walker,
Noel G. Morgan,
Andrew T. Hattersley,
Emma L. Dempster,
Eilis Hannon,
Aaron R. Jeffries,
Nick D. L. Owens,
Jonathan Mill
Development of the human pancreas requires the precise temporal control of gene expression via epigenetic mechanisms and the binding of key transcription factors. We quantified genome-wide patterns of DNA methylation in human fetal pancreatic samples from donors aged 6 to 21 post-conception weeks. We found dramatic changes in DNA methylation across pancreas development, with > 21% of sites characterized as developmental differentially methylated positions (dDMPs) including many annotated to genes associated with monogenic diabetes. An analysis of DNA methylation in postnatal pancreas tissue showed that the dramatic temporal changes in DNA methylation occurring in the developing pancreas are largely limited to the prenatal period. Significant differences in DNA methylation were observed between males and females at a number of autosomal sites, with a small proportion of sites showing sex-specific DNA methylation trajectories across pancreas development. Pancreas dDMPs were not distributed equally across the genome and were depleted in regulatory domains characterized by open chromatin and the binding of known pancreatic development transcription factors. Finally, we compared our pancreas dDMPs to previous findings from the human brain, identifying evidence for tissue-specific developmental changes in DNA methylation. This study represents the first systematic exploration of DNA methylation patterns during human fetal pancreas development and confirms the prenatal period as a time of major epigenomic plasticity.
Leveraging epigenetic signatures to determine the cell-type of origin from long read sequencing data
Abstract DNA methylation differs across tissue- and cell-types with important implications for the analysis of disease-associated differences in tissues such as blood. To uncover the biological processes affected by epigenetic dysregulation, it is essential for epigenetic studies to generate data from the appropriate cell-types. Here we propose a framework to do this computationally from long-read sequencing data, bypassing the need to isolate subtypes of cells experimentally. Using reference data for six common blood cell-types, we evaluate the potential of this approach for attributing reads to specific cells using sequencing data generated from whole blood. Our analyses show that cell-type can be accurately classified using small regions of the genome comparable in size to those generated by long-read sequencing platforms, although the accuracy of classification varies across different regions of the genome and between cell-types. We found that for approximately one third of the genome it is possible to accurately discriminate reads originating from lymphocytes and myeloid cells with the prediction of more specialised subtypes of blood cell-types also encouraging. Our approach provides an alternative computational method for generating cell-specific DNA methylation profiles for epigenetic epidemiology, accelerating our ability to reveal critical insights of the role of the epigenome in health and disease.
Using Organoids to Model Sex Differences in the Human Brain
Adam Pavlinek,
Dwaipayan Adhya,
Alex Tsompanidis,
Varun Warrier,
APEX Consortium,
Simon Baron-Cohen,
Carrie Allison
+ 33 more
Adam Pavlinek,
Dwaipayan Adhya,
Alex Tsompanidis,
Varun Warrier,
APEX Consortium,
Simon Baron-Cohen,
Carrie Allison,
Varun Warrier,
Alex Tsompanidis,
Dwaipayan Adhya,
Rosie Holt,
Paula Smith,
Tracey Parsons,
Joanna Davis,
Matthew Hassall,
Daniel H. Geschwind,
Alexander EP. Heazell,
Jonathan Mill,
Alice Franklin,
Rosie Bamford,
Jonathan Davies,
Matthew E. Hurles,
Hilary C. Martin,
Mahmoud Mousa,
David H. Rowitch,
Kathy K. Niakan,
Graham J. Burton,
Fateneh Ghafari,
Deepak P. Srivastava,
Lucia Dutan-Polit,
Adam Pavlinek,
Madeline A. Lancaster,
Ilaria Chiaradia,
Tal Biron-Shental,
Lidia V. Gabis,
Anthony C. Vernon,
Madeline Lancaster,
Jonathan Mill,
Deepak P. Srivastava,
Simon Baron-Cohen
Sex differences are widespread during neurodevelopment and play a role in neuropsychiatric conditions such as autism, which is more prevalent in males than females. In humans, males have been shown to have larger brain volumes than females with development of the hippocampus and amygdala showing prominent sex differences. Mechanistically, sex steroids and sex chromosomes drive these differences in brain development, which seem to peak during prenatal and pubertal stages. Animal models have played a crucial role in understanding sex differences, but the study of human sex differences requires an experimental model that can recapitulate complex genetic traits. To fill this gap, human induced pluripotent stem cell-derived brain organoids are now being used to study how complex genetic traits influence prenatal brain development. For example, brain organoids from individuals with autism and individuals with X chromosome-linked Rett syndrome and fragile X syndrome have revealed prenatal differences in cell proliferation, a measure of brain volume differences, and excitatory-inhibitory imbalances. Brain organoids have also revealed increased neurogenesis of excitatory neurons due to androgens. However, despite growing interest in using brain organoids, several key challenges remain that affect its validity as a model system. In this review, we discuss how sex steroids and the sex chromosomes each contribute to sex differences in brain development. Then, we examine the role of X chromosome inactivation as a factor that drives sex differences. Finally, we discuss the combined challenges of modeling X chromosome inactivation and limitations of brain organoids that need to be taken into consideration when studying sex differences.
DNA methylation patterns in the frontal lobe white matter of multiple system atrophy, Parkinson’s disease, and progressive supranuclear palsy: a cross-comparative investigation
Megha Murthy,
Katherine Fodder,
Yasuo Miki,
Naiomi Rambarack,
Pablo Fernandez Eduardo De,
Lasse Pihlstrøm,
Jonathan Mill
+ 3 more
Megha Murthy,
Katherine Fodder,
Yasuo Miki,
Naiomi Rambarack,
Pablo Fernandez Eduardo De,
Lasse Pihlstrøm,
Jonathan Mill,
Thomas T. Warner,
Tammaryn Lashley,
Conceição Bettencourt
Multiple system atrophy (MSA) is a rare neurodegenerative disease characterized by neuronal loss and gliosis, with oligodendroglial cytoplasmic inclusions (GCIs) containing α-synuclein being the primary pathological hallmark. Clinical presentations of MSA overlap with other parkinsonian disorders, such as Parkinson’s disease (PD), dementia with Lewy bodies (DLB), and progressive supranuclear palsy (PSP), posing challenges in early diagnosis. Numerous studies have reported alterations in DNA methylation in neurodegenerative diseases, with candidate loci being identified in various parkinsonian disorders including MSA, PD, and PSP. Although MSA and PSP present with substantial white matter pathology, alterations in white matter have also been reported in PD. However, studies comparing the DNA methylation architectures of white matter in these diseases are lacking. We therefore aimed to investigate genome-wide DNA methylation patterns in the frontal lobe white matter of individuals with MSA (n = 17), PD (n = 17), and PSP (n = 16) along with controls (n = 15) using the Illumina EPIC array, to identify shared and disease-specific DNA methylation alterations. Genome-wide DNA methylation profiling of frontal lobe white matter in the three parkinsonian disorders revealed substantial commonalities in DNA methylation alterations in MSA, PD, and PSP. We further used weighted gene correlation network analysis to identify disease-associated co-methylation signatures and identified dysregulation in processes relating to Wnt signaling, signal transduction, endoplasmic reticulum stress, mitochondrial processes, RNA interference, and endosomal transport to be shared between these parkinsonian disorders. Our overall analysis points toward more similarities in DNA methylation patterns between MSA and PD, both synucleinopathies, compared to that between MSA and PD with PSP, which is a tauopathy. Our results also highlight several shared DNA methylation changes and pathways indicative of converging molecular mechanisms in the white matter contributing toward neurodegeneration in all three parkinsonian disorders.
Biventricular responses to exercise and their relation to cardiorespiratory fitness in pediatric pulmonary hypertension
Guido E Pieles,
Dan-Mihai Dorobantu,
Jessica E Caterini,
Barbara Cifra,
Janette Reyes,
Ramos Sara Roldan,
Eilis Hannon
+ 5 more
Guido E Pieles,
Dan-Mihai Dorobantu,
Jessica E Caterini,
Barbara Cifra,
Janette Reyes,
Ramos Sara Roldan,
Eilis Hannon,
Craig A Williams,
Tilman Humpl,
Luc Mertens,
Greg D Wells,
Mark K Friedberg
Despite exercise intolerance being predictive of outcomes in pulmonary arterial hypertension (PAH), its underlying cardiac mechanisms are not well described. The aim of the study was to explore the biventricular response to exercise and its associations with cardiorespiratory fitness in children with PAH. Participants underwent incremental cardiopulmonary exercise testing and simultaneous exercise echocardiography on a recumbent cycle ergometer. Linear mixed models were used to assess cardiac function variance and associations between cardiac and metabolic parameters during exercise. Eleven participants were included with a mean age of 13.4 ± 2.9 yr old. Right ventricle (RV) systolic pressure (RVsp) increased from a mean of 59 ± 25 mmHg at rest to 130 ± 40 mmHg at peak exercise (P < 0.001), whereas RV fractional area change (RV-FAC) and RV-free wall longitudinal strain (RVFW-Sl) worsened (35.2 vs. 27%, P = 0.09 and -16.6 vs. -14.6%, P = 0.1, respectively). At low- and moderate-intensity exercise, RVsp was positively associated with stroke volume and O2 pulse (P < 0.1). At high-intensity exercise, RV-FAC, RVFW-Sl, and left ventricular longitudinal strain were positively associated with oxygen uptake and O2 pulse (P < 0.1), whereas stroke volume decreased toward peak (P = 0.04). In children with PAH, the increase of pulmonary pressure alone does not limit peak exercise, but rather the concomitant reduced RV functional reserve, resulting in RV to pulmonary artery (RV-PA) uncoupling, worsening of interventricular interaction and LV dysfunction. A better mechanistic understanding of PAH exercise physiopathology can inform stress testing and cardiac rehabilitation in this population.NEW & NOTEWORTHY In children with pulmonary arterial hypertension, there is a marked increase in pulmonary artery pressure during physical activity, but this is not the underlying mechanism that limits exercise. Instead, right ventricle-to-pulmonary artery uncoupling occurs at the transition from moderate to high-intensity exercise and correlates with lower peak oxygen uptake. This highlights the more complex underlying pathological responses and the need for multiparametric assessment of cardiac function reserve in these patients when feasible.
Congenital Hyperinsulinism and Novel KDM6A Duplications -Resolving Pathogenicity With Genome and Epigenetic Analyses
Jonna M E Männistö,
Jasmin J Hopkins,
Thomas I Hewat,
Fatima Nasser,
Joseph Burrage,
Antonia Dastamani,
Alice Mirante
+ 12 more
Jonna M E Männistö,
Jasmin J Hopkins,
Thomas I Hewat,
Fatima Nasser,
Joseph Burrage,
Antonia Dastamani,
Alice Mirante,
Nuala Murphy,
Jessica Rzasa,
Jennifer Kerkhof,
Raissa Relator,
Matthew B Johnson,
Thomas W Laver,
Luke Weymouth,
Jayne A L Houghton,
Matthew N Wakeling,
Bekim Sadikovic,
Emma L Dempster,
Sarah E Flanagan
The Journal of Clinical Endocrinology & Metabolism
CONTEXT: Hyperinsulinemic hypoglycemia (HI) can be the presenting feature of Kabuki syndrome (KS), which is caused by loss-of-function variants in KMT2D or KDM6A. As these genes play a critical role in maintaining methylation status in chromatin, individuals with pathogenic variants have a disease-specific epigenomic profile -an episignature.
OBJECTIVE: We evaluated the pathogenicity of three novel partial KDM6A duplications identified in three individuals presenting with neonatal-onset HI without typical features of KS at the time of genetic testing.
METHODS: Three different partial KDM6A duplications were identified by routine targeted next generation sequencing for HI and initially classified as variants of uncertain significance (VUS) as their location, and hence their impact on the gene, was not known. Whole genome sequencing (WGS) was undertaken to map the breakpoints of the duplications with DNA methylation profiling performed in two individuals to investigate the presence of a KS-specific episignature.
RESULTS: WGS confirmed the duplication in proband 1 as pathogenic as it caused a frameshift in the normal copy of the gene leading to a premature termination codon. The duplications identified in probands 2 and 3 did not alter the reading frame and therefore their significance remained uncertain after WGS. Subsequent DNA methylation profiling identified a KS-specific episignature in proband 2 but not in proband 3.
CONCLUSIONS: Our findings confirm a role for KDM6A partial gene duplications in the etiology of KS and highlight the importance of performing in-depth molecular genetic analysis to properly assess the clinical significance of VUS's in the KDM6A gene.
Long-read transcript sequencing identifies differential isoform expression in the entorhinal cortex in a transgenic model of tau pathology
Szi Kay Leung,
Rosemary A. Bamford,
Aaron R. Jeffries,
Isabel Castanho,
Barry Chioza,
Christine S. Flaxman,
Karen Moore
+ 8 more
Szi Kay Leung,
Rosemary A. Bamford,
Aaron R. Jeffries,
Isabel Castanho,
Barry Chioza,
Christine S. Flaxman,
Karen Moore,
Emma L. Dempster,
Joshua Harvey,
Jonathan T. Brown,
Zeshan Ahmed,
Paul O’Neill,
Sarah J. Richardson,
Eilis Hannon,
Jonathan Mill
Increasing evidence suggests that alternative splicing plays an important role in Alzheimer’s disease (AD) pathology. We used long-read sequencing in combination with a novel bioinformatics tool (FICLE) to profile transcript diversity in the entorhinal cortex of female transgenic (TG) mice harboring a mutant form of human tau. Our analyses revealed hundreds of novel isoforms and identified differentially expressed transcripts – including specific isoforms of Apoe, App, Cd33, Clu, Fyn and Trem2 – associated with the development of tau pathology in TG mice. Subsequent profiling of the human cortex from AD individuals and controls revealed similar patterns of transcript diversity, including the upregulation of the dominant TREM2 isoform in AD paralleling the increased expression of the homologous transcript in TG mice. Our results highlight the importance of differential transcript usage, even in the absence of gene-level expression alterations, as a mechanism underpinning gene regulation in the development of AD neuropathology.
Genetic architecture of epigenetic cortical clock age in brain tissue from older individuals: alterations in CD46 and other loci
Francine Grodstein,
Bernardo Lemos,
Jingyun Yang,
Paiva Lopes Katia de,
Ricardo A. Vialle,
Nicholas Seyfried,
Yanling Wang
+ 7 more
Francine Grodstein,
Bernardo Lemos,
Jingyun Yang,
Paiva Lopes Katia de,
Ricardo A. Vialle,
Nicholas Seyfried,
Yanling Wang,
Gemma Shireby,
Eilis Hannon,
Alan Thomas,
Keeley Brookes,
Jonathan Mill,
Jager Philip L. De,
David A. Bennett
The cortical epigenetic clock was developed in brain tissue as a biomarker of brain aging. As one way to identify mechanisms underlying aging, we conducted a GWAS of cortical age. We leveraged postmortem cortex tissue and genotyping array data from 694 participants of the Rush Memory and Aging Project and Religious Orders Study (ROSMAP; 11000,000 SNPs), and meta-analysed ROSMAP with 522 participants of Brains for Dementia Research (5,000,000 overlapping SNPs). We confirmed results using eQTL (cortical bulk and single nucleus gene expression), cortical protein levels (ROSMAP), and phenome-wide association studies (clinical/neuropathologic phenotypes, ROSMAP). In the meta-analysis, the strongest association was rs4244620 (p = 1.29 × 10-7), which also exhibited FDR-significant cis-eQTL effects for CD46 in bulk and single nucleus (microglia, astrocyte, oligodendrocyte, neuron) cortical gene expression. Additionally, rs4244620 was nominally associated with lower cognition, faster slopes of cognitive decline, and greater Parkinsonian signs (n ~ 1700 ROSMAP with SNP/phenotypic data; all p ≤ 0.04). In ROSMAP alone, the top SNP was rs4721030 (p = 8.64 × 10-8) annotated to TMEM106B and THSD7A. Further, in ROSMAP (n = 849), TMEM106B and THSD7A protein levels in cortex were related to many phenotypes, including greater AD pathology and lower cognition (all p ≤ 0.0007). Overall, we identified converging evidence of CD46 and possibly TMEM106B/THSD7A for potential roles in cortical epigenetic clock age.
Blood DNA methylomic signatures associated with CSF biomarkers of Alzheimer's disease in the EMIF‐AD study
Rebecca G. Smith,
Ehsan Pishva,
Morteza Kouhsar,
Jennifer Imm,
Valerija Dobricic,
Peter Johannsen,
Michael Wittig
+ 33 more
Rebecca G. Smith,
Ehsan Pishva,
Morteza Kouhsar,
Jennifer Imm,
Valerija Dobricic,
Peter Johannsen,
Michael Wittig,
Andre Franke,
Rik Vandenberghe,
Jolien Schaeverbeke,
Yvonne Freund‐Levi,
Lutz Frölich,
Philip Scheltens,
Charlotte E. Teunissen,
Giovanni Frisoni,
Olivier Blin,
Jill C. Richardson,
Régis Bordet,
Sebastiaan Engelborghs,
Roeck Ellen de,
Pablo Martinez‐Lage,
Miren Altuna,
Mikel Tainta,
Alberto Lleó,
Isabel Sala,
Julius Popp,
Gwendoline Peyratout,
Laura Winchester,
Alejo Nevado‐Holgado,
Frans Verhey,
Magda Tsolaki,
Ulf Andreasson,
Kaj Blennow,
Henrik Zetterberg,
Johannes Streffer,
Stephanie J. B. Vos,
Simon Lovestone,
Pieter Jelle Visser,
Lars Bertram,
Katie Lunnon
INTRODUCTION: We investigated blood DNA methylation patterns associated with 15 well-established cerebrospinal fluid (CSF) biomarkers of Alzheimer's disease (AD) pathophysiology, neuroinflammation, and neurodegeneration.
METHODS: We assessed DNA methylation in 885 blood samples from the European Medical Information Framework for Alzheimer's Disease (EMIF-AD) study using the EPIC array.
RESULTS: We identified Bonferroni-significant differential methylation associated with CSF YKL-40 (five loci) and neurofilament light chain (NfL; seven loci) levels, with two of the loci associated with CSF YKL-40 levels correlating with plasma YKL-40 levels. A co-localization analysis showed shared genetic variants underlying YKL-40 DNA methylation and CSF protein levels, with evidence that DNA methylation mediates the association between genotype and protein levels. Weighted gene correlation network analysis identified two modules of co-methylated loci correlated with several amyloid measures and enriched in pathways associated with lipoproteins and development.
DISCUSSION: We conducted the most comprehensive epigenome-wide association study (EWAS) of AD-relevant CSF biomarkers to date. Future work should explore the relationship between YKL-40 genotype, DNA methylation, and protein levels in the brain.
HIGHLIGHTS: Blood DNA methylation was assessed in the EMIF-AD MBD study. Epigenome-wide association studies (EWASs) were performed for 15 Alzheimer's disease (AD)-relevant cerebrospinal fluid (CSF) biomarker measures. Five Bonferroni-significant loci were associated with YKL-40 levels and seven with neurofilament light chain (NfL). DNA methylation in YKL-40 co-localized with previously reported genetic variation. DNA methylation potentially mediates the effect of single-nucleotide polymorphisms (SNPs) in YKL-40 on CSF protein levels.
Blood‐based multivariate methylation risk score for cognitive impairment and dementia
Jarno Koetsier,
Rachel Cavill,
Rick Reijnders,
Joshua Harvey,
Jan Homann,
Morteza Kouhsar,
Kay Deckers
+ 50 more
Jarno Koetsier,
Rachel Cavill,
Rick Reijnders,
Joshua Harvey,
Jan Homann,
Morteza Kouhsar,
Kay Deckers,
Sebastian Köhler,
Lars M. T. Eijssen,
den Hove Daniel L. A. van,
Ilja Demuth,
Sandra Düzel,
for the Alzheimer's Disease Neuroimaging Initiative,
Rebecca G. Smith,
Adam R. Smith,
Joe Burrage,
Emma M. Walker,
Gemma Shireby,
Eilis Hannon,
Emma Dempster,
Tim Frayling,
Jonathan Mill,
Valerija Dobricic,
Peter Johannsen,
Michael Wittig,
Andre Franke,
Rik Vandenberghe,
Jolien Schaeverbeke,
Yvonne Freund‐Levi,
Lutz Frölich,
Philip Scheltens,
Charlotte E. Teunissen,
Giovanni Frisoni,
Olivier Blin,
Jill C. Richardson,
Régis Bordet,
Sebastiaan Engelborghs,
Roeck Ellen de,
Pablo Martinez‐Lage,
Mikel Tainta,
Alberto Lleó,
Isabel Sala,
Julius Popp,
Gwendoline Peyratout,
Frans Verhey,
Magda Tsolaki,
Ulf Andreasson,
Kaj Blennow,
Henrik Zetterberg,
Johannes Streffer,
Stephanie J. B. Vos,
Simon Lovestone,
Pieter‐Jelle Visser,
Christina M. Lill,
Lars Bertram,
Katie Lunnon,
Ehsan Pishva
INTRODUCTION: The established link between DNA methylation and pathophysiology of dementia, along with its potential role as a molecular mediator of lifestyle and environmental influences, positions blood-derived DNA methylation as a promising tool for early dementia risk detection.
METHODS: In conjunction with an extensive array of machine learning techniques, we employed whole blood genome-wide DNA methylation data as a surrogate for 14 modifiable and non-modifiable factors in the assessment of dementia risk in independent dementia cohorts.
RESULTS: We established a multivariate methylation risk score (MMRS) for identifying mild cognitive impairment cross-sectionally, independent of age and sex (P = 2.0 × 10-3). This score significantly predicted the prospective development of cognitive impairments in independent studies of Alzheimer's disease (hazard ratio for Rey's Auditory Verbal Learning Test (RAVLT)-Learning = 2.47) and Parkinson's disease (hazard ratio for MCI/dementia = 2.59).
DISCUSSION: Our work shows the potential of employing blood-derived DNA methylation data in the assessment of dementia risk.
HIGHLIGHTS: We used whole blood DNA methylation as a surrogate for 14 dementia risk factors. Created a multivariate methylation risk score for predicting cognitive impairment. Emphasized the role of machine learning and omics data in predicting dementia. The score predicts cognitive impairment development at the population level.
Imputed DNA methylation outperforms measured loci associations with smoking and chronological age
Anne Richmond,
Jure Mur,
Sarah E Harris,
Janie Corley,
Hannah R Elliott,
Christopher N Foley,
Eilis Hannon
+ 11 more
Anne Richmond,
Jure Mur,
Sarah E Harris,
Janie Corley,
Hannah R Elliott,
Christopher N Foley,
Eilis Hannon,
Zhana Kuncheva,
Josine L Min,
Moqri,
Magatte Ndiaye,
Benjamin B Sun,
Catalina A Vallejos,
Kejun Ying,
Vadim N Gladyshev,
Simon R Cox,
Daniel L McCartney,
Riccardo E Marioni
Abstract Multi-locus signatures of blood-based DNA methylation are well-established biomarkers for lifestyle and health outcomes. Here, we focus on two CpGs that are strongly associated with age and smoking behaviour. Imputing these loci via epigenome-wide CpGs results in stronger associations with outcomes in external datasets compared to directly measured CpGs. If extended epigenome-wide, CpG imputation could augment historic arrays and recently-released, inexpensive but lower-content arrays, thereby yielding better-powered association studies.
CYP1B1-RMDN2 Alzheimer’s disease endophenotype locus identified for cerebral tau PET
Kwangsik Nho,
Shannon L. Risacher,
Liana G. Apostolova,
Paula J. Bice,
Jared R. Brosch,
Rachael Deardorff,
Kelley Faber
+ 52 more
Kwangsik Nho,
Shannon L. Risacher,
Liana G. Apostolova,
Paula J. Bice,
Jared R. Brosch,
Rachael Deardorff,
Kelley Faber,
Martin R. Farlow,
Tatiana Foroud,
Sujuan Gao,
Thea Rosewood,
Jun Pyo Kim,
Kelly Nudelman,
Meichen Yu,
Paul Aisen,
Reisa Sperling,
Basavaraj Hooli,
Sergey Shcherbinin,
Diana Svaldi,
Clifford R. Jack,
William J. Jagust,
Susan Landau,
Aparna Vasanthakumar,
Jeffrey F. Waring,
Vincent Doré,
Simon M. Laws,
Colin L. Masters,
Tenielle Porter,
Christopher C. Rowe,
Victor L. Villemagne,
Logan Dumitrescu,
Timothy J. Hohman,
Julia B. Libby,
Elizabeth Mormino,
Rachel F. Buckley,
Keith Johnson,
Hyun-Sik Yang,
Ronald C. Petersen,
Vijay K. Ramanan,
Nilüfer Ertekin-Taner,
Prashanthi Vemuri,
Ann D. Cohen,
Kang-Hsien Fan,
M. Ilyas Kamboh,
Oscar L. Lopez,
David A. Bennett,
Muhammad Ali,
Tammie Benzinger,
Carlos Cruchaga,
Diana Hobbs,
Jager Philip L. De,
Masashi Fujita,
Vaishnavi Jadhav,
Bruce T. Lamb,
Andy P. Tsai,
Isabel Castanho,
Jonathan Mill,
Michael W. Weiner,
Andrew J. Saykin
Determining the genetic architecture of Alzheimer’s disease pathologies can enhance mechanistic understanding and inform precision medicine strategies. Here, we perform a genome-wide association study of cortical tau quantified by positron emission tomography in 3046 participants from 12 independent studies. The CYP1B1-RMDN2 locus is associated with tau deposition. The most significant signal is at rs2113389, explaining 4.3% of the variation in cortical tau, while APOE4 rs429358 accounts for 3.6%. rs2113389 is associated with higher tau and faster cognitive decline. Additive effects, but no interactions, are observed between rs2113389 and diagnosis, APOE4, and amyloid beta positivity. CYP1B1 expression is upregulated in AD. rs2113389 is associated with higher CYP1B1 expression and methylation levels. Mouse model studies provide additional functional evidence for a relationship between CYP1B1 and tau deposition but not amyloid beta. These results provide insight into the genetic basis of cerebral tau deposition and support novel pathways for therapeutic development in AD.
