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Vasu MM, Sumitha PS, Rahna P, Thanseem I, Anitha A. microRNAs in Autism Spectrum Disorders. Curr Pharm Des 2020; 25:4368-4378. [PMID: 31692427 DOI: 10.2174/1381612825666191105120901] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2019] [Accepted: 10/31/2019] [Indexed: 01/10/2023]
Abstract
BACKGROUND Efforts to unravel the extensive impact of the non-coding elements of the human genome on cell homeostasis and pathological processes have gained momentum over the last couple of decades. miRNAs refer to short, often 18-25 nucleotides long, non-coding RNA molecules which can regulate gene expression. Each miRNA can regulate several mRNAs. METHODS This article reviews the literature on the roles of miRNAs in autism. RESULTS Considering the fact that ~ 1% of the human DNA encodes different families of miRNAs, their overall impact as critical regulators of gene expression in the mammalian brain should be immense. Though the autism spectrum disorders (ASDs) are predominantly genetic in nature and several candidate genes are already identified, the highly heterogeneous and multifactorial nature of the disorder makes it difficult to identify common genetic risk factors. Several studies have suggested that the environmental factors may interact with the genetic factors to increase the risk. miRNAs could possibly be one of those factors which explain this link between genetics and the environment. CONCLUSION In the present review, we have summarized our current knowledge on miRNAs and their complex roles in ASD, and also on their therapeutic applications.
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Affiliation(s)
- Mahesh Mundalil Vasu
- Department of Neurogenetics, Institute for Communicative and Cognitive Neurosciences (ICCONS), Kavalappara, Shoranur, Palakkad - 679 523, Kerala, India
| | - Puthiripadath S Sumitha
- Department of Neurogenetics, Institute for Communicative and Cognitive Neurosciences (ICCONS), Kavalappara, Shoranur, Palakkad - 679 523, Kerala, India
| | - Parakkal Rahna
- Department of Neurogenetics, Institute for Communicative and Cognitive Neurosciences (ICCONS), Kavalappara, Shoranur, Palakkad - 679 523, Kerala, India
| | - Ismail Thanseem
- Department of Neurogenetics, Institute for Communicative and Cognitive Neurosciences (ICCONS), Kavalappara, Shoranur, Palakkad - 679 523, Kerala, India
| | - Ayyappan Anitha
- Department of Neurogenetics, Institute for Communicative and Cognitive Neurosciences (ICCONS), Kavalappara, Shoranur, Palakkad - 679 523, Kerala, India
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52
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Stathopoulos S, Gaujoux R, Lindeque Z, Mahony C, Van Der Colff R, Van Der Westhuizen F, O'Ryan C. DNA Methylation Associated with Mitochondrial Dysfunction in a South African Autism Spectrum Disorder Cohort. Autism Res 2020; 13:1079-1093. [PMID: 32490597 PMCID: PMC7496548 DOI: 10.1002/aur.2310] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2019] [Revised: 01/24/2020] [Accepted: 04/20/2020] [Indexed: 02/06/2023]
Abstract
Autism spectrum disorder (ASD) is characterized by phenotypic heterogeneity and a complex genetic architecture which includes distinctive epigenetic patterns. We report differential DNA methylation patterns associated with ASD in South African children. An exploratory whole‐epigenome methylation screen using the Illumina 450 K MethylationArray identified differentially methylated CpG sites between ASD and controls that mapped to 898 genes (P ≤ 0.05) which were enriched for nine canonical pathways converging on mitochondrial metabolism and protein ubiquitination. Targeted Next Generation Bisulfite Sequencing of 27 genes confirmed differential methylation between ASD and control in our cohort. DNA pyrosequencing of two of these genes, the mitochondrial enzyme Propionyl‐CoA Carboxylase subunit Beta (PCCB) and Protocadherin Alpha 12 (PCDHA12), revealed a wide range of methylation levels (9–49% and 0–54%, respectively) in both ASD and controls. Three CpG loci were differentially methylated in PCCB (P ≤ 0.05), while PCDHA12, previously linked to ASD, had two significantly different CpG sites (P ≤ 0.001) between ASD and control. Differentially methylated CpGs were hypomethylated in ASD. Metabolomic analysis of urinary organic acids revealed that three metabolites, 3‐hydroxy‐3‐methylglutaric acid (P = 0.008), 3‐methyglutaconic acid (P = 0.018), and ethylmalonic acid (P = 0.043) were significantly elevated in individuals with ASD. These metabolites are directly linked to mitochondrial respiratory chain disorders, with a putative link to PCCB, consistent with impaired mitochondrial function. Our data support an association between DNA methylation and mitochondrial dysfunction in the etiology of ASD. Autism Res 2020, 13: 1079‐1093. © 2020 The Authors. Autism Research published by International Society for Autism Research published by Wiley Periodicals, Inc. Lay Summary Epigenetic changes are chemical modifications of DNA which can change gene function. DNA methylation, a type of epigenetic modification, is linked to autism. We examined DNA methylation in South African children with autism and identified mitochondrial genes associated with autism. Mitochondria are power‐suppliers in cells and mitochondrial genes are essential to metabolism and energy production, which are important for brain cells during development. Our findings suggest that some individuals with ASD also have mitochondrial dysfunction.
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Affiliation(s)
- Sofia Stathopoulos
- Department of Molecular and Cell Biology, University of Cape Town, Cape Town, South Africa
| | | | - Zander Lindeque
- Human Metabolomics, North-West University, Potchefstroom, South Africa
| | - Caitlyn Mahony
- Department of Molecular and Cell Biology, University of Cape Town, Cape Town, South Africa
| | - Rachelle Van Der Colff
- Department of Molecular and Cell Biology, University of Cape Town, Cape Town, South Africa
| | | | - Colleen O'Ryan
- Department of Molecular and Cell Biology, University of Cape Town, Cape Town, South Africa
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53
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Hollander JA, Cory-Slechta DA, Jacka FN, Szabo ST, Guilarte TR, Bilbo SD, Mattingly CJ, Moy SS, Haroon E, Hornig M, Levin ED, Pletnikov MV, Zehr JL, McAllister KA, Dzierlenga AL, Garton AE, Lawler CP, Ladd-Acosta C. Beyond the looking glass: recent advances in understanding the impact of environmental exposures on neuropsychiatric disease. Neuropsychopharmacology 2020; 45:1086-1096. [PMID: 32109936 PMCID: PMC7234981 DOI: 10.1038/s41386-020-0648-5] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/09/2019] [Accepted: 02/17/2020] [Indexed: 12/22/2022]
Abstract
The etiologic pathways leading to neuropsychiatric diseases remain poorly defined. As genomic technologies have advanced over the past several decades, considerable progress has been made linking neuropsychiatric disorders to genetic underpinnings. Interest and consideration of nongenetic risk factors (e.g., lead exposure and schizophrenia) have, in contrast, lagged behind heritable frameworks of explanation. Thus, the association of neuropsychiatric illness to environmental chemical exposure, and their potential interactions with genetic susceptibility, are largely unexplored. In this review, we describe emerging approaches for considering the impact of chemical risk factors acting alone and in concert with genetic risk, and point to the potential role of epigenetics in mediating exposure effects on transcription of genes implicated in mental disorders. We highlight recent examples of research in nongenetic risk factors in psychiatric disorders that point to potential shared biological mechanisms-synaptic dysfunction, immune alterations, and gut-brain interactions. We outline new tools and resources that can be harnessed for the study of environmental factors in psychiatric disorders. These tools, combined with emerging experimental evidence, suggest that there is a need to broadly incorporate environmental exposures in psychiatric research, with the ultimate goal of identifying modifiable risk factors and informing new treatment strategies for neuropsychiatric disease.
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Affiliation(s)
- Jonathan A Hollander
- Genes, Environment and Health Branch, National Institute of Environmental Health Sciences, NIH, Research Triangle Park, NC, USA.
| | - Deborah A Cory-Slechta
- Department of Environmental Medicine, Box EHSC, University of Rochester Medical Center, Rochester, NY, USA
| | - Felice N Jacka
- Food & Mood Centre, IMPACT SRC, School of Medicine, Deakin University, Geelong, VIC, Australia
- iMPACT (the Institute for Mental and Physical Health and Clinical Translation), Food & Mood Centre, Deakin University, Geelong, VIC, Australia
- Centre for Adolescent Health, Murdoch Children's Research Institute, Melbourne, VIC, Australia
- Black Dog Institute, Sydney, NSW, Australia
- James Cook University, Townsville, QLD, Australia
| | - Steven T Szabo
- Duke University Medical Center, Durham, NC, USA
- Durham Veterans Affairs Medical Center, Durham, NC, USA
| | - Tomás R Guilarte
- Department of Environmental Health Sciences Robert Stempel College of Public Health and Social Work, Florida International University, Miami, FL, USA
| | - Staci D Bilbo
- Department of Psychology & Neuroscience, Duke University, Durham, NC, USA
| | - Carolyn J Mattingly
- Department of Biological Sciences, Center for Human Health and the Environment, North Carolina State University, Raleigh, NC, USA
| | - Sheryl S Moy
- Department of Psychiatry and Carolina Institute for Developmental Disabilities, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Ebrahim Haroon
- Department of Psychiatry and Behavioral Sciences, Emory University School of Medicine, Atlanta, GA, USA
| | - Mady Hornig
- Department of Epidemiology, Mailman School of Public Health, Columbia University, New York, NY, USA
| | - Edward D Levin
- Department of Psychiatry and Behavioral Sciences, Duke University, Durham, NC, USA
| | - Mikhail V Pletnikov
- Departments of Psychiatry, Neuroscience, Molecular and Comparative Pathobiology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Julia L Zehr
- Developmental Mechanisms and Trajectories of Psychopathology Branch, National Institute of Mental Health, NIH, Rockville, MD, USA
| | - Kimberly A McAllister
- Genes, Environment and Health Branch, National Institute of Environmental Health Sciences, NIH, Research Triangle Park, NC, USA
| | - Anika L Dzierlenga
- Genes, Environment and Health Branch, National Institute of Environmental Health Sciences, NIH, Research Triangle Park, NC, USA
| | - Amanda E Garton
- Genes, Environment and Health Branch, National Institute of Environmental Health Sciences, NIH, Research Triangle Park, NC, USA
| | - Cindy P Lawler
- Genes, Environment and Health Branch, National Institute of Environmental Health Sciences, NIH, Research Triangle Park, NC, USA
| | - Christine Ladd-Acosta
- Department of Epidemiology and Wendy Klag Center for Autism and Developmental Disabilities, Johns Hopkins University, Baltimore, MD, USA
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54
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Wendt FR, Pathak GA, Tylee DS, Goswami A, Polimanti R. Heterogeneity and Polygenicity in Psychiatric Disorders: A Genome-Wide Perspective. ACTA ACUST UNITED AC 2020; 4:2470547020924844. [PMID: 32518889 PMCID: PMC7254587 DOI: 10.1177/2470547020924844] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2020] [Accepted: 04/17/2020] [Indexed: 12/15/2022]
Abstract
Genome-wide association studies (GWAS) have been performed for many psychiatric disorders and revealed a complex polygenic architecture linking mental and physical health phenotypes. Psychiatric diagnoses are often heterogeneous, and several layers of trait heterogeneity may contribute to detection of genetic risks per disorder or across multiple disorders. In this review, we discuss these heterogeneities and their consequences on the discovery of risk loci using large-scale genetic data. We primarily highlight the ways in which sex and diagnostic complexity contribute to risk locus discovery in schizophrenia, bipolar disorder, attention deficit hyperactivity disorder, autism spectrum disorder, posttraumatic stress disorder, major depressive disorder, obsessive-compulsive disorder, Tourette’s syndrome and chronic tic disorder, anxiety disorders, suicidality, feeding and eating disorders, and substance use disorders. Genetic data also have facilitated discovery of clinically relevant subphenotypes also described here. Collectively, GWAS of psychiatric disorders revealed that the understanding of heterogeneity, polygenicity, and pleiotropy is critical to translate genetic findings into treatment strategies.
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Affiliation(s)
- Frank R Wendt
- Department of Psychiatry, Yale School of Medicine and VA CT Healthcare Center, West Haven, CT, USA
| | - Gita A Pathak
- Department of Psychiatry, Yale School of Medicine and VA CT Healthcare Center, West Haven, CT, USA
| | - Daniel S Tylee
- Department of Psychiatry, Yale School of Medicine and VA CT Healthcare Center, West Haven, CT, USA
| | - Aranyak Goswami
- Department of Psychiatry, Yale School of Medicine and VA CT Healthcare Center, West Haven, CT, USA
| | - Renato Polimanti
- Department of Psychiatry, Yale School of Medicine and VA CT Healthcare Center, West Haven, CT, USA
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55
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Li M, Zou D, Li Z, Gao R, Sang J, Zhang Y, Li R, Xia L, Zhang T, Niu G, Bao Y, Zhang Z. EWAS Atlas: a curated knowledgebase of epigenome-wide association studies. Nucleic Acids Res 2020; 47:D983-D988. [PMID: 30364969 PMCID: PMC6324068 DOI: 10.1093/nar/gky1027] [Citation(s) in RCA: 159] [Impact Index Per Article: 39.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2018] [Accepted: 10/17/2018] [Indexed: 12/20/2022] Open
Abstract
Epigenome-Wide Association Study (EWAS) has become increasingly significant in identifying the associations between epigenetic variations and different biological traits. In this study, we develop EWAS Atlas (http://bigd.big.ac.cn/ewas), a curated knowledgebase of EWAS that provides a comprehensive collection of EWAS knowledge. Unlike extant data-oriented epigenetic resources, EWAS Atlas features manual curation of EWAS knowledge from extensive publications. In the current implementation, EWAS Atlas focuses on DNA methylation—one of the key epigenetic marks; it integrates a large number of 329 172 high-quality EWAS associations, involving 112 tissues/cell lines and covering 305 traits, 1830 cohorts and 390 ontology entities, which are completely based on manual curation from 649 studies reported in 401 publications. In addition, it is equipped with a powerful trait enrichment analysis tool, which is capable of profiling trait-trait and trait-epigenome relationships. Future developments include regular curation of recent EWAS publications, incorporation of more epigenetic marks and possible integration of EWAS with GWAS. Collectively, EWAS Atlas is dedicated to the curation, integration and standardization of EWAS knowledge and has the great potential to help researchers dissect molecular mechanisms of epigenetic modifications associated with biological traits.
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Affiliation(s)
- Mengwei Li
- BIG Data Center, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China.,CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China.,College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Dong Zou
- BIG Data Center, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China.,CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China
| | - Zhaohua Li
- BIG Data Center, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China.,CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China.,School of Future Technology, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Ran Gao
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China.,CAS Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China
| | - Jian Sang
- BIG Data Center, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China.,CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China.,College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yuansheng Zhang
- BIG Data Center, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China.,CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China.,College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Rujiao Li
- BIG Data Center, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China.,CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China
| | - Lin Xia
- BIG Data Center, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China.,CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China.,College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Tao Zhang
- BIG Data Center, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China.,CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China.,College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Guangyi Niu
- BIG Data Center, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China.,CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China.,College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yiming Bao
- BIG Data Center, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China.,CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China.,College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China.,School of Future Technology, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Zhang Zhang
- BIG Data Center, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China.,CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China.,College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China.,CAS Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China
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56
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High polygenic burden is associated with blood DNA methylation changes in individuals with suicidal behavior. J Psychiatr Res 2020; 123:62-71. [PMID: 32036075 DOI: 10.1016/j.jpsychires.2020.01.008] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/23/2019] [Revised: 01/06/2020] [Accepted: 01/24/2020] [Indexed: 12/27/2022]
Abstract
Suicidal behavior is result of the interaction of several contributors, including genetic and environmental factors. The integration of approaches considering the polygenic component of suicidal behavior, such as polygenic risk scores (PRS) and DNA methylation is promising for improving our understanding of the complex interplay between genetic and environmental factors in this behavior. The aim of this study was the evaluation of DNA methylation differences between individuals with high and low genetic burden for suicidality. The present study was divided into two phases. In the first phase, genotyping with the Psycharray chip was performed in a discovery sample of 568 Mexican individuals, of which 149 had suicidal behavior (64 individuals with suicidal ideation, 50 with suicide attempt and 35 with completed suicide). Then, a PRS analysis based on summary statistics from the Psychiatric Genomic Consortium was performed in the discovery sample. In a second phase, we evaluated DNA methylation differences between individuals with high and low genetic burden for suicidality in a sub-sample of the discovery sample (target sample) of 94 subjects. We identified 153 differentially methylated sites between individuals with low and high-PRS. Among genes mapped to differentially methylated sites, we found genes involved in neurodevelopment (CHD7, RFX4, KCNA1, PLCB1, PITX1, NUMBL) and ATP binding (KIF7, NUBP2, KIF6, ATP8B1, ATP11A, CLCN7, MYLK, MAP2K5). Our results suggest that genetic variants might increase the predisposition to epigenetic variations in genes involved in neurodevelopment. This study highlights the possible implication of polygenic burden in the alteration of epigenetic changes in suicidal behavior.
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57
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Wallace C. Eliciting priors and relaxing the single causal variant assumption in colocalisation analyses. PLoS Genet 2020; 16:e1008720. [PMID: 32310995 PMCID: PMC7192519 DOI: 10.1371/journal.pgen.1008720] [Citation(s) in RCA: 142] [Impact Index Per Article: 35.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2019] [Revised: 04/30/2020] [Accepted: 03/17/2020] [Indexed: 01/03/2023] Open
Abstract
Horizontal integration of summary statistics from different GWAS traits can be used to evaluate evidence for their shared genetic causality. One popular method to do this is a Bayesian method, coloc, which is attractive in requiring only GWAS summary statistics and no linkage disequilibrium estimates and is now being used routinely to perform thousands of comparisons between traits. Here we show that while most users do not adjust default software values, misspecification of prior parameters can substantially alter posterior inference. We suggest data driven methods to derive sensible prior values, and demonstrate how sensitivity analysis can be used to assess robustness of posterior inference. The flexibility of coloc comes at the expense of an unrealistic assumption of a single causal variant per trait. This assumption can be relaxed by stepwise conditioning, but this requires external software and an LD matrix aligned to study alleles. We have now implemented conditioning within coloc, and propose a new alternative method, masking, that does not require LD and approximates conditioning when causal variants are independent. Importantly, masking can be used in combination with conditioning where allelically aligned LD estimates are available for only a single trait. We have implemented these developments in a new version of coloc which we hope will enable more informed choice of priors and overcome the restriction of the single causal variant assumptions in coloc analysis.
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Affiliation(s)
- Chris Wallace
- Cambridge Institute for Therapeutic Immunology & Infectious Disease, and MRC Biostatistics Unit, University of Cambridge, Cambridge, United Kingdom
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58
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Hannon E, Schendel D, Ladd-Acosta C, Grove J, Hansen CS, Hougaard DM, Bresnahan M, Mors O, Hollegaard MV, Bækvad-Hansen M, Hornig M, Mortensen PB, Børglum AD, Werge T, Pedersen MG, Nordentoft M, Buxbaum JD, Daniele Fallin M, Bybjerg-Grauholm J, Reichenberg A, Mill J. Variable DNA methylation in neonates mediates the association between prenatal smoking and birth weight. Philos Trans R Soc Lond B Biol Sci 2020; 374:20180120. [PMID: 30966880 DOI: 10.1098/rstb.2018.0120] [Citation(s) in RCA: 39] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Abstract
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'.
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Affiliation(s)
- Eilis Hannon
- 1 University of Exeter Medical School, University of Exeter , Exeter , UK
| | - Diana Schendel
- 2 Department of Public Health, Aarhus University , Aarhus , Denmark.,3 National Centre for Register-Based Research, Aarhus University , Aarhus , Denmark.,8 The Lundbeck Foundation Initiative for Integrative Psychiatric Research, iPSYCH , Aarhus , Denmark
| | - Christine Ladd-Acosta
- 9 Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health , Baltimore, MD , USA.,10 Wendy Klag Center for Autism and Developmental Disabilities, Johns Hopkins Bloomberg School of Public Health , Baltimore, MD , USA
| | - Jakob Grove
- 4 Centre for Integrative Sequencing, iSEQ, Aarhus University , Aarhus , Denmark.,5 Department of Biomedicine - Human Genetics, Aarhus University , Aarhus , Denmark.,6 Bioinformatics Research Centre, Aarhus University , Aarhus , Denmark.,8 The Lundbeck Foundation Initiative for Integrative Psychiatric Research, iPSYCH , Aarhus , Denmark.,12 Centre for Genomics and Personalized Medicine , Aarhus , Denmark
| | - Christine Søholm Hansen
- 8 The Lundbeck Foundation Initiative for Integrative Psychiatric Research, iPSYCH , Aarhus , Denmark.,13 Center for Neonatal Screening, Department for Congenital Disorders, Statens Serum Institut , Copenhagen , Denmark.,14 Institute of Biological Psychiatry, MHC Sct. Hans, Mental Health Services , Copenhagen , Denmark
| | - David Michael Hougaard
- 8 The Lundbeck Foundation Initiative for Integrative Psychiatric Research, iPSYCH , Aarhus , Denmark.,13 Center for Neonatal Screening, Department for Congenital Disorders, Statens Serum Institut , Copenhagen , Denmark
| | - Michaeline Bresnahan
- 15 Center for Infection and Immunity, Columbia University Mailman School of Public Health , New York, NY , USA
| | - Ole Mors
- 8 The Lundbeck Foundation Initiative for Integrative Psychiatric Research, iPSYCH , Aarhus , Denmark.,17 Psychosis Research Unit, Aarhus University Hospital , Risskov , Denmark
| | - Mads Vilhelm Hollegaard
- 8 The Lundbeck Foundation Initiative for Integrative Psychiatric Research, iPSYCH , Aarhus , Denmark.,13 Center for Neonatal Screening, Department for Congenital Disorders, Statens Serum Institut , Copenhagen , Denmark
| | - Marie Bækvad-Hansen
- 8 The Lundbeck Foundation Initiative for Integrative Psychiatric Research, iPSYCH , Aarhus , Denmark.,13 Center for Neonatal Screening, Department for Congenital Disorders, Statens Serum Institut , Copenhagen , Denmark
| | - Mady Hornig
- 15 Center for Infection and Immunity, Columbia University Mailman School of Public Health , New York, NY , USA.,16 Department of Epidemiology, Columbia University Mailman School of Public Health , New York, NY , USA
| | - Preben Bo Mortensen
- 3 National Centre for Register-Based Research, Aarhus University , Aarhus , Denmark.,7 Centre for Integrated Register-based Research, Aarhus University , Aarhus , Denmark.,8 The Lundbeck Foundation Initiative for Integrative Psychiatric Research, iPSYCH , Aarhus , Denmark
| | - Anders D Børglum
- 4 Centre for Integrative Sequencing, iSEQ, Aarhus University , Aarhus , Denmark.,5 Department of Biomedicine - Human Genetics, Aarhus University , Aarhus , Denmark.,8 The Lundbeck Foundation Initiative for Integrative Psychiatric Research, iPSYCH , Aarhus , Denmark.,12 Centre for Genomics and Personalized Medicine , Aarhus , Denmark
| | - Thomas Werge
- 8 The Lundbeck Foundation Initiative for Integrative Psychiatric Research, iPSYCH , Aarhus , Denmark.,14 Institute of Biological Psychiatry, MHC Sct. Hans, Mental Health Services , Copenhagen , Denmark.,18 Department of Clinical Medicine, Mental Health Center Copenhagen, University of Copenhagen , Copenhagen , Denmark
| | - Marianne Giørtz Pedersen
- 3 National Centre for Register-Based Research, Aarhus University , Aarhus , Denmark.,7 Centre for Integrated Register-based Research, Aarhus University , Aarhus , Denmark.,8 The Lundbeck Foundation Initiative for Integrative Psychiatric Research, iPSYCH , Aarhus , Denmark
| | - Merete Nordentoft
- 8 The Lundbeck Foundation Initiative for Integrative Psychiatric Research, iPSYCH , Aarhus , Denmark.,19 Mental Health Services in the Capital Region of Denmark, Mental Health Center Copenhagen, University of Copenhagen , Copenhagen , Denmark
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- 8 The Lundbeck Foundation Initiative for Integrative Psychiatric Research, iPSYCH , Aarhus , Denmark
| | - Joseph D Buxbaum
- 20 Seaver Autism Center for Research and Treatment, Department of Psychiatry, Icahn School of Medicine at Mount Sinai , New York, NY , USA
| | - M Daniele Fallin
- 10 Wendy Klag Center for Autism and Developmental Disabilities, Johns Hopkins Bloomberg School of Public Health , Baltimore, MD , USA.,11 Department of Mental Health, Johns Hopkins Bloomberg School of Public Health , Baltimore, MD , USA
| | - Jonas Bybjerg-Grauholm
- 8 The Lundbeck Foundation Initiative for Integrative Psychiatric Research, iPSYCH , Aarhus , Denmark.,13 Center for Neonatal Screening, Department for Congenital Disorders, Statens Serum Institut , Copenhagen , Denmark
| | - Abraham Reichenberg
- 20 Seaver Autism Center for Research and Treatment, Department of Psychiatry, Icahn School of Medicine at Mount Sinai , New York, NY , USA
| | - Jonathan Mill
- 1 University of Exeter Medical School, University of Exeter , Exeter , UK
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59
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Mooney MA, Ryabinin P, Wilmot B, Bhatt P, Mill J, Nigg JT. Large epigenome-wide association study of childhood ADHD identifies peripheral DNA methylation associated with disease and polygenic risk burden. Transl Psychiatry 2020; 10:8. [PMID: 32066674 PMCID: PMC7026179 DOI: 10.1038/s41398-020-0710-4] [Citation(s) in RCA: 39] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/03/2019] [Revised: 12/09/2019] [Accepted: 12/20/2019] [Indexed: 12/17/2022] Open
Abstract
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.
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Affiliation(s)
- Michael A. Mooney
- grid.5288.70000 0000 9758 5690Division of Bioinformatics & Computational Biology, Department of Medical Informatics & Clinical Epidemiology, Oregon Health & Science University, Portland, OR USA ,grid.5288.70000 0000 9758 5690OHSU Knight Cancer Institute, Portland, OR USA
| | - Peter Ryabinin
- grid.5288.70000 0000 9758 5690Oregon Clinical and Translational Research Institute, Portland, OR USA
| | - Beth Wilmot
- grid.5288.70000 0000 9758 5690Division of Bioinformatics & Computational Biology, Department of Medical Informatics & Clinical Epidemiology, Oregon Health & Science University, Portland, OR USA ,grid.5288.70000 0000 9758 5690Oregon Clinical and Translational Research Institute, Portland, OR USA
| | - Priya Bhatt
- grid.5288.70000 0000 9758 5690Division of Psychology, Department of Psychiatry, Oregon Health & Science University, Portland, OR USA
| | - Jonathan Mill
- grid.8391.30000 0004 1936 8024University of Exeter Medical School, Exeter University, Exeter, UK
| | - Joel T. Nigg
- grid.5288.70000 0000 9758 5690Division of Psychology, Department of Psychiatry, Oregon Health & Science University, Portland, OR USA ,grid.5288.70000 0000 9758 5690Department of Behavioral Neuroscience, Oregon Health & Science University, Portland, OR USA
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60
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Abstract
The prevalence of autism spectrum disorder (ASD) has been increasing steadily over the last 20 years; however, the molecular basis for the majority of ASD cases remains unknown. Recent advances in next-generation sequencing and detection of DNA modifications have made methylation-dependent regulation of transcription an attractive hypothesis for being a causative factor in ASD etiology. Evidence for abnormal DNA methylation in ASD can be seen on multiple levels, from genetic mutations in epigenetic machinery to loci-specific and genome-wide changes in DNA methylation. Epimutations in DNA methylation can be acquired throughout life, as global DNA methylation reprogramming is dynamic during embryonic development and the early postnatal period that corresponds to the peak time of synaptogenesis. However, technical advances and causative evidence still need to be established before abnormal DNA methylation and ASD can be confidently associated.
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Affiliation(s)
- Martine W Tremblay
- Program in Genetics and Genomics, Duke University, Durham, North Carolina 27710, USA
| | - Yong-Hui Jiang
- Program in Genetics and Genomics, Duke University, Durham, North Carolina 27710, USA.,Departments of Pediatrics and Neurobiology, Duke University School of Medicine, Durham, North Carolina 27710, USA;
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61
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Kalkbrenner AE, Meier SM, Madley-Dowd P, Ladd-Acosta C, Fallin MD, Parner E, Schendel D. Familial confounding of the association between maternal smoking in pregnancy and autism spectrum disorder in offspring. Autism Res 2019; 13:134-144. [PMID: 31464107 DOI: 10.1002/aur.2196] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2018] [Accepted: 08/06/2019] [Indexed: 12/20/2022]
Abstract
Evidence supports no link between maternal smoking in pregnancy and autism spectrum disorder (autism) overall. To address remaining questions about the unexplained heterogeneity between study results and the possibility of risk for specific autism sub-phenotypes, we conducted a whole-population cohort study in Denmark. We followed births 1991-2011 (1,294,906 persons, including 993,301 siblings in 728,271 families), from 1 year of age until an autism diagnosis (13,547), death, emigration, or December 31, 2012. Autism, with and without attention deficit hyperactivity disorder (ADHD) and with and without intellectual disability (ID) were based on ICD-8 and ICD-10 codes from Danish national health registers, including 3,319 autism + ADHD, 10,228 autism - no ADHD, 2,205 autism + ID, and 11,342 autism - no ID. We estimated hazard ratios (HRs) and 95% confidence intervals (95% CIs) between any maternal smoking (from birth records) and autism (or sub-phenotypes) using survival models with robust standard errors, stratifying by birth year and adjusting for child sex, parity, and parental age, education, income, and psychiatric history. To additionally address confounding using family designs, we constructed a maternal cluster model (adjusting for the smoking proportion within the family), and a stratified sibling model. Associations with maternal smoking and autism were elevated in conventional adjusted analyses (HR of 1.17 [1.13-1.22]) but attenuated in the maternal cluster (0.98 [0.88-1.09]) and sibling (0.86 [0.64-1.15]) models. Similarly, risks of autism sub-phenotypes with maternal smoking were attenuated in the family-based models. Together these results support that smoking in pregnancy is not linked with autism or select autism comorbid sub-phenotypes after accounting for familial confounding. Autism Res 2020, 13: 134-144. © 2019 International Society for Autism Research, Wiley Periodicals, Inc. LAY SUMMARY: Smoking during pregnancy has many harmful impacts, which may include harming the baby's developing brain. However, in a study of thousands of families in Denmark, it does not appear that smoking in pregnancy leads to autism or autism in combination with intellectual problems or attention deficits, once you account for the way smoking patterns and developmental disabilities run in families.
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Affiliation(s)
- Amy E Kalkbrenner
- Joseph J. Zilber School of Public Health, University of Wisconsin-Milwaukee, Milwaukee, Wisconsin
| | - Sandra M Meier
- Child and Adolescent Mental Health Centre-Mental Health Services Capital Region, Copenhagen Region, Denmark.,Psychosis Research Unit, Aarhus University Hospital, Risskov, Denmark.,The Lundbeck Foundation Initiative for Integrative Psychiatric Research, iPSYCH, Aarhus, Denmark
| | - Paul Madley-Dowd
- Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK
| | - Christine Ladd-Acosta
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland.,Wendy Klag Center for Autism and Developmental Disabilities, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland
| | - Margaret Daniele Fallin
- Wendy Klag Center for Autism and Developmental Disabilities, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland.,Department of Mental Health, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland
| | - Erik Parner
- Department of Public Health, Section for Biostatistics, Aarhus University, Aarhus, Denmark
| | - Diana Schendel
- Lundbeck Foundation Initiative for Integrative Psychiatric Research, iPSYCH, National Centre for Register-based Research, Aarhus University, Aarhus, Denmark.,Department of Economics and Business, National Centre for Register-based Research, Aarhus University, Aarhus, Denmark.,Department of Public Health, Section for Epidemiology, Aarhus University, Aarhus, Denmark
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62
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Gervin K, Salas LA, Bakulski KM, van Zelm MC, Koestler DC, Wiencke JK, Duijts L, Moll HA, Kelsey KT, Kobor MS, Lyle R, Christensen BC, Felix JF, Jones MJ. Systematic evaluation and validation of reference and library selection methods for deconvolution of cord blood DNA methylation data. Clin Epigenetics 2019; 11:125. [PMID: 31455416 PMCID: PMC6712867 DOI: 10.1186/s13148-019-0717-y] [Citation(s) in RCA: 103] [Impact Index Per Article: 20.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2019] [Accepted: 07/29/2019] [Indexed: 12/20/2022] Open
Abstract
BACKGROUND Umbilical cord blood (UCB) is commonly used in epigenome-wide association studies of prenatal exposures. Accounting for cell type composition is critical in such studies as it reduces confounding due to the cell specificity of DNA methylation (DNAm). In the absence of cell sorting information, statistical methods can be applied to deconvolve heterogeneous cell mixtures. Among these methods, reference-based approaches leverage age-appropriate cell-specific DNAm profiles to estimate cellular composition. In UCB, four reference datasets comprising DNAm signatures profiled in purified cell populations have been published using the Illumina 450 K and EPIC arrays. These datasets are biologically and technically different, and currently, there is no consensus on how to best apply them. Here, we systematically evaluate and compare these datasets and provide recommendations for reference-based UCB deconvolution. RESULTS We first evaluated the four reference datasets to ascertain both the purity of the samples and the potential cell cross-contamination. We filtered samples and combined datasets to obtain a joint UCB reference. We selected deconvolution libraries using two different approaches: automatic selection using the top differentially methylated probes from the function pickCompProbes in minfi and a standardized library selected using the IDOL (Identifying Optimal Libraries) iterative algorithm. We compared the performance of each reference separately and in combination, using the two approaches for reference library selection, and validated the results in an independent cohort (Generation R Study, n = 191) with matched Fluorescence-Activated Cell Sorting measured cell counts. Strict filtering and combination of the references significantly improved the accuracy and efficiency of cell type estimates. Ultimately, the IDOL library outperformed the library from the automatic selection method implemented in pickCompProbes. CONCLUSION These results have important implications for epigenetic studies in UCB as implementing this method will optimally reduce confounding due to cellular heterogeneity. This work provides guidelines for future reference-based UCB deconvolution and establishes a framework for combining reference datasets in other tissues.
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Affiliation(s)
- Kristina Gervin
- Pharmacoepidemiology and Drug Safety Research Group, Department of Pharmacy, School of Pharmacy, University of Oslo, Oslo, Norway
- PharmaTox Strategic Research Initiative, Faculty of Mathematics and Natural Sciences, University of Oslo, Oslo, Norway
| | - Lucas A Salas
- Department of Epidemiology, Geisel School of Medicine, Dartmouth College, Lebanon, USA
| | - Kelly M Bakulski
- Department of Epidemiology, University of Michigan School of Public Health, Ann Arbor, MI, USA
| | - Menno C van Zelm
- Department of Immunology and Pathology, Central Clinical School, Monash University and The Alfred Hospital, Melbourne, Australia
- Department of Immunology, Erasmus MC, University Medical Center Rotterdam, Rotterdam, the Netherlands
| | - Devin C Koestler
- Department of Biostatistics, University of Kansas Medical Center, Kansas, KS, USA
| | - John K Wiencke
- Department of Neurological Surgery, University of California San Francisco, San Francisco, CA, USA
| | - Liesbeth Duijts
- The Generation R Study Group, Erasmus MC, University Medical Center Rotterdam, Rotterdam, the Netherlands
- Department of Pediatrics, Division of Respiratory Medicine and Allergology, Erasmus MC-Sophia Children's Hospital, University Medical Center Rotterdam, Rotterdam, the Netherlands
- Department of Pediatrics, Division of Neonatology, Erasmus MC-Sophia Children's Hospital, University Medical Center Rotterdam, Rotterdam, the Netherlands
| | - Henriëtte A Moll
- Department of Pediatrics, Erasmus MC-Sophia Children's Hospital, University Medical Center Rotterdam, Rotterdam, the Netherlands
| | - Karl T Kelsey
- Department of Pathology and Laboratory Medicine, Brown University, Providence, RI, USA
- Department of Epidemiology, Brown University, Providence, RI, USA
| | - Michael S Kobor
- Department of Medical Genetics, University of British Columbia, and BC Children's Hospital Research Institute, Vancouver, Canada
| | - Robert Lyle
- PharmaTox Strategic Research Initiative, Faculty of Mathematics and Natural Sciences, University of Oslo, Oslo, Norway
- Department of Medical Genetics, Oslo University Hospital, Oslo, Norway
| | - Brock C Christensen
- Department of Epidemiology, Geisel School of Medicine, Dartmouth College, Lebanon, USA
- Department of Molecular and Systems Biology, and Community and Family Medicine, Geisel School of Medicine, Dartmouth College, Lebanon, USA
- Department of Community and Family Medicine, Geisel School of Medicine, Dartmouth College, Lebanon, USA
| | - Janine F Felix
- The Generation R Study Group, Erasmus MC, University Medical Center Rotterdam, Rotterdam, the Netherlands
- Department of Pediatrics, Erasmus MC-Sophia Children's Hospital, University Medical Center Rotterdam, Rotterdam, the Netherlands
- Department of Epidemiology, Erasmus MC, University Medical Center Rotterdam, Rotterdam, the Netherlands
| | - Meaghan J Jones
- Department of Biochemistry and Medical Genetics, University of Manitoba, and Children's Hospital Research Institute of Manitoba, Winnipeg, Canada.
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63
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Pain O, Pocklington AJ, Holmans PA, Bray NJ, O’Brien HE, Hall LS, Pardiñas AF, O’Donovan MC, Owen MJ, Anney R. Novel Insight Into the Etiology of Autism Spectrum Disorder Gained by Integrating Expression Data With Genome-wide Association Statistics. Biol Psychiatry 2019; 86:265-273. [PMID: 31230729 PMCID: PMC6664597 DOI: 10.1016/j.biopsych.2019.04.034] [Citation(s) in RCA: 46] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/28/2018] [Revised: 04/24/2019] [Accepted: 04/25/2019] [Indexed: 12/14/2022]
Abstract
BACKGROUND A recent genome-wide association study (GWAS) of autism spectrum disorder (ASD) (ncases = 18,381, ncontrols = 27,969) has provided novel opportunities for investigating the etiology of ASD. Here, we integrate the ASD GWAS summary statistics with summary-level gene expression data to infer differential gene expression in ASD, an approach called transcriptome-wide association study (TWAS). METHODS Using FUSION software, ASD GWAS summary statistics were integrated with predictors of gene expression from 16 human datasets, including adult and fetal brains. A novel adaptation of established statistical methods was then used to test for enrichment within candidate pathways and specific tissues and at different stages of brain development. The proportion of ASD heritability explained by predicted expression of genes in the TWAS was estimated using stratified linkage disequilibrium score regression. RESULTS This study identified 14 genes as significantly differentially expressed in ASD, 13 of which were outside of known genome-wide significant loci (±500 kb). XRN2, a gene proximal to an ASD GWAS locus, was inferred to be significantly upregulated in ASD, providing insight into the functional consequence of this associated locus. One novel transcriptome-wide significant association from this study is the downregulation of PDIA6, which showed minimal evidence of association in the GWAS, and in gene-based analysis using MAGMA. Predicted gene expression in this study accounted for 13.0% of the total ASD single nucleotide polymorphism heritability. CONCLUSIONS This study has implicated several genes as significantly up/downregulated in ASD, providing novel and useful information for subsequent functional studies. This study also explores the utility of TWAS-based enrichment analysis and compares TWAS results with a functionally agnostic approach.
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Affiliation(s)
- Oliver Pain
- Medical Research Council Centre for Neuropsychiatric Genetics and Genomics, Division of Psychological Medicine and Clinical Neurosciences, School of Medicine, Cardiff University, Cardiff, United Kingdom,Social, Genetic and Developmental Psychiatry Centre, Institute of Psychiatry, Psychology and Neuroscience, King's College London, London, United Kingdom
| | - Andrew J. Pocklington
- Medical Research Council Centre for Neuropsychiatric Genetics and Genomics, Division of Psychological Medicine and Clinical Neurosciences, School of Medicine, Cardiff University, Cardiff, United Kingdom
| | - Peter A. Holmans
- Medical Research Council Centre for Neuropsychiatric Genetics and Genomics, Division of Psychological Medicine and Clinical Neurosciences, School of Medicine, Cardiff University, Cardiff, United Kingdom
| | - Nicholas J. Bray
- Medical Research Council Centre for Neuropsychiatric Genetics and Genomics, Division of Psychological Medicine and Clinical Neurosciences, School of Medicine, Cardiff University, Cardiff, United Kingdom
| | - Heath E. O’Brien
- Medical Research Council Centre for Neuropsychiatric Genetics and Genomics, Division of Psychological Medicine and Clinical Neurosciences, School of Medicine, Cardiff University, Cardiff, United Kingdom
| | - Lynsey S. Hall
- Medical Research Council Centre for Neuropsychiatric Genetics and Genomics, Division of Psychological Medicine and Clinical Neurosciences, School of Medicine, Cardiff University, Cardiff, United Kingdom
| | - Antonio F. Pardiñas
- Medical Research Council Centre for Neuropsychiatric Genetics and Genomics, Division of Psychological Medicine and Clinical Neurosciences, School of Medicine, Cardiff University, Cardiff, United Kingdom
| | - Michael C. O’Donovan
- Medical Research Council Centre for Neuropsychiatric Genetics and Genomics, Division of Psychological Medicine and Clinical Neurosciences, School of Medicine, Cardiff University, Cardiff, United Kingdom
| | - Michael J. Owen
- Medical Research Council Centre for Neuropsychiatric Genetics and Genomics, Division of Psychological Medicine and Clinical Neurosciences, School of Medicine, Cardiff University, Cardiff, United Kingdom
| | - Richard Anney
- Medical Research Council Centre for Neuropsychiatric Genetics and Genomics, Division of Psychological Medicine and Clinical Neurosciences, School of Medicine, Cardiff University, Cardiff, United Kingdom.
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64
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Massrali A, Brunel H, Hannon E, Wong C, Baron-Cohen S, Warrier V. Integrated genetic and methylomic analyses identify shared biology between autism and autistic traits. Mol Autism 2019; 10:31. [PMID: 31346403 PMCID: PMC6637466 DOI: 10.1186/s13229-019-0279-z] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2019] [Accepted: 05/29/2019] [Indexed: 02/07/2023] Open
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). 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.
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Affiliation(s)
- Aicha Massrali
- Autism Research Centre, University of Cambridge, Cambridge, UK
| | - Helena Brunel
- Autism Research Centre, University of Cambridge, Cambridge, UK
| | - Eilis Hannon
- University of Exeter Medical School, University of Exeter, RILD Building, Level 4, Barrack Rd, Exeter, UK
| | - Chloe Wong
- King’s College London, Institute of Psychiatry, Psychology and Neuroscience, De Crespigny Park, London, UK
| | - iPSYCH-MINERvA Epigenetics Group
- Autism Research Centre, University of Cambridge, Cambridge, UK
- University of Exeter Medical School, University of Exeter, RILD Building, Level 4, Barrack Rd, Exeter, UK
- King’s College London, Institute of Psychiatry, Psychology and Neuroscience, De Crespigny Park, London, UK
- Cambridgeshire and Peterborough National Health Service Foundation Trust, Cambridge, UK
| | - Simon Baron-Cohen
- Autism Research Centre, University of Cambridge, Cambridge, UK
- Cambridgeshire and Peterborough National Health Service Foundation Trust, Cambridge, UK
| | - Varun Warrier
- Autism Research Centre, University of Cambridge, Cambridge, UK
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65
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Wong CCY, Smith RG, Hannon E, Ramaswami G, Parikshak NN, Assary E, Troakes C, Poschmann J, Schalkwyk LC, Sun W, Prabhakar S, Geschwind DH, Mill J. Genome-wide DNA methylation profiling identifies convergent molecular signatures associated with idiopathic and syndromic autism in post-mortem human brain tissue. Hum Mol Genet 2019; 28:2201-2211. [PMID: 31220268 PMCID: PMC6602383 DOI: 10.1093/hmg/ddz052] [Citation(s) in RCA: 54] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2019] [Revised: 03/04/2019] [Accepted: 03/04/2019] [Indexed: 12/13/2022] Open
Abstract
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.
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Affiliation(s)
- Chloe C Y Wong
- King’s College London, Institute of Psychiatry, Psychology and Neuroscience, De Crespigny Park, London, UK
| | - Rebecca G Smith
- University of Exeter Medical School, University of Exeter, Exeter, UK
| | - Eilis Hannon
- University of Exeter Medical School, University of Exeter, Exeter, UK
| | - Gokul Ramaswami
- Center for Autism Research and Treatment, and Program in Neurobehavioral Genetics, Semel Institute for Neuroscience and Human Behavior, David Geffen School of Medicine, University of California, Los Angeles, CA, USA
| | - Neelroop N Parikshak
- Center for Autism Research and Treatment, and Program in Neurobehavioral Genetics, Semel Institute for Neuroscience and Human Behavior, David Geffen School of Medicine, University of California, Los Angeles, CA, USA
| | - Elham Assary
- Department of Biological and Experimental Psychology, School of Biological and Chemical Sciences, Queen Mary University of London, London, UK
| | - Claire Troakes
- King’s College London, Institute of Psychiatry, Psychology and Neuroscience, De Crespigny Park, London, UK
| | - Jeremie Poschmann
- Centre de Recherche en Transplantation et Immunologie, Institut de Transplantation Urologie Néphrologie (ITUN), CHU Nantes, Inserm, Université de Nantes, Nantes, France
| | | | - Wenjie Sun
- Computational and Systems Biology, Genome Institute of Singapore, Singapore
| | - Shyam Prabhakar
- Computational and Systems Biology, Genome Institute of Singapore, Singapore
| | - Daniel H Geschwind
- Center for Autism Research and Treatment, and Program in Neurobehavioral Genetics, Semel Institute for Neuroscience and Human Behavior, David Geffen School of Medicine, University of California, Los Angeles, CA, USA
- Department of Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, USA
- Program in Neurogenetics, Department of Neurology, David Geffen School of Medicine, University of California, Los Angeles, CA, USA
| | - Jonathan Mill
- University of Exeter Medical School, University of Exeter, Exeter, UK
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66
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Garg P, Sharp AJ. Screening for rare epigenetic variations in autism and schizophrenia. Hum Mutat 2019; 40:952-961. [PMID: 30900359 PMCID: PMC6801017 DOI: 10.1002/humu.23740] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2018] [Revised: 02/19/2019] [Accepted: 03/06/2019] [Indexed: 01/28/2023]
Abstract
While many studies have led to the identification of rare sequence variants linked with susceptibility to autism and schizophrenia, the contribution of rare epigenetic variations (epivariations) in these disorders remains largely unexplored. Previously we presented evidence that epivariations occur relatively frequently in the human genome, and likely contribute to a subset of congenital and neurodevelopmental disorders through the disruption of dosage-sensitive genes. Here we extend this approach, studying methylation profiles from 297 samples with autism and 767 cases with schizophrenia, identifying 84 and 268 rare epivariations in these two cohorts, respectively, that were absent from 4,860 population controls. We observed multiple features associated with these epivariations that support their pathogenic relevance, including (a) a significant enrichment for epivariations in schizophrenic individuals at genes previously linked with schizophrenia, (b) increased brain expression of genes associated with epivariations found in autism cases compared with controls, (c) in autism families, a significant excess of epivariations found specifically in affected versus unaffected sibs, (d) Gene Ontology terms linked with epivariations found in autism, including "D1 dopamine receptor binding." Our study provides additional evidence that rare epivariations likely contribute to the mutational spectra underlying neurodevelopmental disorders.
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Affiliation(s)
- Paras Garg
- Department of Genetics and Genomic Sciences, Mount Sinai School of Medicine, Hess Center for Science and Medicine, New York, New York
| | - Andrew J. Sharp
- Department of Genetics and Genomic Sciences, Mount Sinai School of Medicine, Hess Center for Science and Medicine, New York, New York
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67
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Zar Kyaw T, Yamaguchi S, Imai C, Uematsu M, Sato N. The utility of post-test newborn blood spot screening cards for epigenetic association analyses: association between HIF3A methylation and birth weight-for-gestational age. J Hum Genet 2019; 64:795-801. [PMID: 31138846 PMCID: PMC6760750 DOI: 10.1038/s10038-019-0621-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2019] [Revised: 04/22/2019] [Accepted: 05/16/2019] [Indexed: 12/31/2022]
Abstract
Identification of disease-associated epigenetic markers in early life might be useful for pre-emptive intervention to prevent diseases. Epigenome-wide association analyses using newborn blood spot screening cards are an anticipated field of research in Japan. Here, in this study, post-test dried blood spot (DBS) samples were anonymized, with only three attributes of gender, gestational age, and birth weight identified. We isolated DNA from DBS (n = 300) archived for more than 3 years. The median DNA yield (ng) per individual was 429 (interquartile range 300–565). In a model epigenetic analysis, we conducted a confirmative study on the known association between birth weight and hypoxia-inducible factor 3A (HIF3A) gene methylation. DNA methylation levels and cis-acting SNP genotypes (rs8102595 and rs3826795) were measured using EpiTYPER and Taqman assays, respectively. HIF3A methylation was positively associated with birth weight-for-gestational age centile (p = 0.021). While HIF3A methylation was associated with cis-genotypes (rs8102595, p = 2.08E−13; rs3826795, p = 3.63E−09), the association with birth weight centile was retained after adjusting for cis-genotypes (p = 0.029). Thus, we successfully reproduced the results reported previously by others, and demonstrated the usefulness of archived DBS in secondary use for epigenetic association analyses.
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Affiliation(s)
- Tay Zar Kyaw
- Department of Epigenetic Epidemiology/Molecular Epidemiology, Medical Research Institute, Tokyo Medical and Dental University, 1-5-45, Yushima, Bunkyo-ku, Tokyo, 113-8510, Japan
| | - Seiji Yamaguchi
- Department of Pediatrics, Shimane University School of Medicine, Izumo, Shimane, 693-8501, Japan
| | - Chihiro Imai
- Department of Epigenetic Epidemiology/Molecular Epidemiology, Medical Research Institute, Tokyo Medical and Dental University, 1-5-45, Yushima, Bunkyo-ku, Tokyo, 113-8510, Japan
| | - Marina Uematsu
- Department of Epigenetic Epidemiology/Molecular Epidemiology, Medical Research Institute, Tokyo Medical and Dental University, 1-5-45, Yushima, Bunkyo-ku, Tokyo, 113-8510, Japan
| | - Noriko Sato
- Department of Epigenetic Epidemiology/Molecular Epidemiology, Medical Research Institute, Tokyo Medical and Dental University, 1-5-45, Yushima, Bunkyo-ku, Tokyo, 113-8510, Japan.
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Mansell G, Gorrie-Stone TJ, Bao Y, Kumari M, Schalkwyk LS, Mill J, Hannon E. Guidance for DNA methylation studies: statistical insights from the Illumina EPIC array. BMC Genomics 2019; 20:366. [PMID: 31088362 PMCID: PMC6518823 DOI: 10.1186/s12864-019-5761-7] [Citation(s) in RCA: 171] [Impact Index Per Article: 34.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2018] [Accepted: 05/02/2019] [Indexed: 12/12/2022] Open
Abstract
Background There 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. Results We 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. Conclusion We 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. Electronic supplementary material The online version of this article (10.1186/s12864-019-5761-7) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Georgina Mansell
- University of Exeter Medical School, University of Exeter, RD&E Hospital, Barrack Road, Exeter, Devon, EX2 5DW, UK
| | - Tyler J Gorrie-Stone
- School of Biological Sciences, University of Essex, Colchester, Essex, CO4 3SQ, UK
| | - Yanchun Bao
- Institute for Social and Economic Research, University of Essex, Colchester, Essex, CO3 3LG, UK
| | - Meena Kumari
- Institute for Social and Economic Research, University of Essex, Colchester, Essex, CO3 3LG, UK
| | - Leonard S Schalkwyk
- School of Biological Sciences, University of Essex, Colchester, Essex, CO4 3SQ, UK
| | - Jonathan Mill
- University of Exeter Medical School, University of Exeter, RD&E Hospital, Barrack Road, Exeter, Devon, EX2 5DW, UK
| | - Eilis Hannon
- University of Exeter Medical School, University of Exeter, RD&E Hospital, Barrack Road, Exeter, Devon, EX2 5DW, UK.
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69
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Walton E, Relton CL, Caramaschi D. Using Openly Accessible Resources to Strengthen Causal Inference in Epigenetic Epidemiology of Neurodevelopment and Mental Health. Genes (Basel) 2019; 10:E193. [PMID: 30832291 PMCID: PMC6470715 DOI: 10.3390/genes10030193] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2018] [Accepted: 01/25/2019] [Indexed: 12/18/2022] Open
Abstract
The recent focus on the role of epigenetic mechanisms in mental health has led to several studies examining the association of epigenetic processes with psychiatric conditions and neurodevelopmental traits. Some studies suggest that epigenetic changes might be causal in the development of the psychiatric condition under investigation. However, other scenarios are possible, e.g., statistical confounding or reverse causation, making it particularly challenging to derive conclusions on causality. In the present review, we examine the evidence from human population studies for a possible role of epigenetic mechanisms in neurodevelopment and mental health and discuss methodological approaches on how to strengthen causal inference, including the need for replication, (quasi-)experimental approaches and Mendelian randomization. We signpost openly accessible resources (e.g., "MR-Base" "EWAS catalog" as well as tissue-specific methylation and gene expression databases) to aid the application of these approaches.
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Affiliation(s)
- Esther Walton
- Medical Research Council Integrative Epidemiology Unit, University of Bristol, BS8 2BN Bristol, UK.
- Population Health Sciences, Bristol Medical School, University of Bristol, BS8 2BN Bristol, UK.
- Department of Psychology, University of Bath, BA2 7AY Bath, UK.
| | - Caroline L Relton
- Medical Research Council Integrative Epidemiology Unit, University of Bristol, BS8 2BN Bristol, UK.
- Population Health Sciences, Bristol Medical School, University of Bristol, BS8 2BN Bristol, UK.
| | - Doretta Caramaschi
- Medical Research Council Integrative Epidemiology Unit, University of Bristol, BS8 2BN Bristol, UK.
- Population Health Sciences, Bristol Medical School, University of Bristol, BS8 2BN Bristol, UK.
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70
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Abstract
Purpose of review This review demonstrates the growing body of evidence connecting DNA methylation to prior exposure. It highlights the potential to use DNA methylation patterns as a feasible, stable, and accurate biomarker of past exposure, opening new opportunities for environmental and gene-environment interaction studies among existing banked samples. Recent findings We present the evidence for association between past exposure, including prenatal exposures, and DNA methylation measured at a later time in the life course. We demonstrate the potential utility of DNA methylation-based biomarkers of past exposure using results from multiple studies of smoking as an example. Multiple studies show the ability to accurately predict prenatal smoking exposure based on DNA methylation measured at birth, in childhood, and even adulthood. Separate sets of DNA methylation loci have been used to predict past personal smoking exposure (postnatal) as well. Further, it appears that these two types of exposures, prenatal and previous personal exposure, can be isolated from each other. There is also a suggestion that quantitative methylation scores may be useful for estimating dose. We highlight the remaining needs for rigor in methylation biomarker development including analytic challenges as well as the need for development across multiple developmental windows, multiple tissue types, and multiple ancestries. Summary If fully developed, DNA methylation-based biomarkers can dramatically shift our ability to carry out environmental and genetic-environmental epidemiology using existing biobanks, opening up unprecedented opportunities for environmental health.
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71
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Liu A, Zhou W, Qu L, He F, Wang H, Wang Y, Cai C, Li X, Zhou W, Wang M. Altered Urinary Amino Acids in Children With Autism Spectrum Disorders. Front Cell Neurosci 2019; 13:7. [PMID: 30733669 PMCID: PMC6354128 DOI: 10.3389/fncel.2019.00007] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2018] [Accepted: 01/10/2019] [Indexed: 12/19/2022] Open
Abstract
Autism spectrum disorders (ASD) affect 1% of children. Although there is no cure, early diagnosis and behavioral intervention can relieve the symptoms. The clinical heterogeneity of ASD has created a need for improved sensitive and specific laboratory diagnostic methods. Liquid chromatography-tandem mass spectrometry (LC-MS/MS)-based analysis of the metabolome has shown great potential to uncover biomarkers for complex diseases such as ASD. Here, we used a two-step discovery–validation approach to identify potential novel metabolic biomarkers for ASD. Urine samples from 57 children with ASD and 81 matched children with typical development (TD) were analyzed by LS-MS/MS to assess differences in urinary amino acids and their metabolites (referred to as UAA indicators). A total of 63 UAA indicators were identified, of which 21 were present at significantly different levels in the urine of ASD children compared with TD children. Of these 21, the concentrations of 19 and 10 were higher and lower, respectively, in the urine of ASD children compared with TD children. Using support vector machine modeling and receiver operating characteristic curve analysis, we identified a panel of 7 UAA indicators that discriminated between the samples from ASD and TD children (lysine, 2-aminoisobutyric acid, 5-hydroxytryptamine, proline, aspartate, arginine/ornithine, and 4-hydroxyproline). Among the significantly changed pathways in ASD children were the ornithine/urea cycle (decreased levels of the excitatory amino acid aspartate [p = 2.15 × 10-10] and increased arginine/ornithine [p = 5.21 × 10-9]), tryptophan metabolism (increased levels of inhibitory 5-hydroxytryptamine p = 3.62 × 10-9), the methionine cycle (increased methionine sulfoxide [p = 1.46 × 10-10] and decreased homocysteine [p = 2.73 × 10-7]), and lysine metabolism (reduced lysine [p = 7.8 × 10-9], α-aminoadipic acid [p = 1.16 × 10-9], and 5-aminovaleric acid [p = 1.05 × 10-5]). Collectively, the data presented here identify a possible imbalance between excitatory and inhibitory amino acid metabolism in ASD children. The significantly altered UAA indicators could therefore be potential diagnostic biomarkers for ASD.
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Affiliation(s)
- Aiping Liu
- Shiyan Prevention and Health Care Center of Shenzhen, Shenzhen, China
| | - Wei Zhou
- Division of Neonatology, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou, China
| | - Liuhong Qu
- Division of Neonatology, The Maternal and Child Health Care Hospital of Huadu District, Huadu Affiliated Hospital of Guangdong Medical University, Guangzhou, China
| | | | - Hui Wang
- Xiamen Branch of Children's Hospital of Fudan University (Xiamen Children's Hospital), Xiamen, China
| | - Yan Wang
- Division of Neonatology, The Maternal and Child Health Care Hospital of Huadu District, Huadu Affiliated Hospital of Guangdong Medical University, Guangzhou, China
| | - Chunquan Cai
- Division of Neurosurgery, Tianjin Children's Hospital, Tianjin, China
| | - Xiaoge Li
- Tianjin Jinnan Xiaozhan Hospital, Tianjin, China
| | - Wenhao Zhou
- Shanghai Key Laboratory of Birth Defects, Division of Neonatology, Children's Hospital of Fudan University, National Center for Children's Health, Shanghai, China
| | - Mingbang Wang
- Shanghai Key Laboratory of Birth Defects, Division of Neonatology, Xiamen Branch of Children's Hospital of Fudan University (Xiamen Children's Hospital), Children's Hospital of Fudan University, National Center for Children's Health, Shanghai, China
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Emberti Gialloreti L, Curatolo P. Autism Spectrum Disorder: Why Do We Know So Little? Front Neurol 2018; 9:670. [PMID: 30174643 PMCID: PMC6107753 DOI: 10.3389/fneur.2018.00670] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2018] [Accepted: 07/26/2018] [Indexed: 11/13/2022] Open
Affiliation(s)
| | - Paolo Curatolo
- Child Neurology and Psychiatry Unit, Systems Medicine Department, Tor Vergata University of Rome, Rome, Italy
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Andrews SV, Sheppard B, Windham GC, Schieve LA, Schendel DE, Croen LA, Chopra P, Alisch RS, Newschaffer CJ, Warren ST, Feinberg AP, Fallin MD, Ladd-Acosta C. Case-control meta-analysis of blood DNA methylation and autism spectrum disorder. Mol Autism 2018; 9:40. [PMID: 29988321 PMCID: PMC6022498 DOI: 10.1186/s13229-018-0224-6] [Citation(s) in RCA: 65] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2018] [Accepted: 06/21/2018] [Indexed: 11/10/2022] Open
Abstract
Background Several reports have suggested a role for epigenetic mechanisms in ASD etiology. Epigenome-wide association studies (EWAS) in autism spectrum disorder (ASD) may shed light on particular biological mechanisms. However, studies of ASD cases versus controls have been limited by post-mortem timing and severely small sample sizes. Reports from in-life sampling of blood or saliva have also been very limited in sample size and/or genomic coverage. We present the largest case-control EWAS for ASD to date, combining data from population-based case-control and case-sibling pair studies. Methods DNA from 968 blood samples from children in the Study to Explore Early Development (SEED 1) was used to generate epigenome-wide array DNA methylation (DNAm) data at 485,512 CpG sites for 453 cases and 515 controls, using the Illumina 450K Beadchip. The Simons Simplex Collection (SSC) provided 450K array DNAm data on an additional 343 cases and their unaffected siblings. We performed EWAS meta-analysis across results from the two data sets, with adjustment for sex and surrogate variables that reflect major sources of biological variation and technical confounding such as cell type, batch, and ancestry. We compared top EWAS results to those from a previous brain-based analysis. We also tested for enrichment of ASD EWAS CpGs for being targets of meQTL associations using available SNP genotype data in the SEED sample. Findings In this meta-analysis of blood-based DNA from 796 cases and 858 controls, no single CpG met a Bonferroni discovery threshold of p < 1.12 × 10− 7. Seven CpGs showed differences at p < 1 × 10− 5 and 48 at 1 × 10− 4. Of the top 7, 5 showed brain-based ASD associations as well, often with larger effect sizes, and the top 48 overall showed modest concordance (r = 0.31) in direction of effect with cerebellum samples. Finally, we observed suggestive evidence for enrichment of CpG sites controlled by SNPs (meQTL targets) among the EWAS CpG hits, which was consistent across EWAS and meQTL discovery p value thresholds. Conclusions No single CpG site showed a large enough DNAm difference between cases and controls to achieve epigenome-wide significance in this sample size. However, our results suggest the potential to observe disease associations from blood-based samples. Among the seven sites achieving suggestive statistical significance, we observed consistent, and stronger, effects at the same sites among brain samples. Discovery-oriented EWAS for ASD using blood samples will likely need even larger samples and unified genetic data to further understand DNAm differences in ASD. Electronic supplementary material The online version of this article (10.1186/s13229-018-0224-6) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Shan V Andrews
- 1Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, 615 N. Wolfe Street, Baltimore, MD 21205 USA.,2Wendy Klag Center for Autism and Developmental Disabilities, Johns Hopkins Bloomberg School of Public Health, 615 N. Wolfe Street, W6509, Baltimore, MD 21205 USA
| | - Brooke Sheppard
- 1Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, 615 N. Wolfe Street, Baltimore, MD 21205 USA.,2Wendy Klag Center for Autism and Developmental Disabilities, Johns Hopkins Bloomberg School of Public Health, 615 N. Wolfe Street, W6509, Baltimore, MD 21205 USA
| | - Gayle C Windham
- 3California Department of Public Health, Environmental Health Investigations Branch, 850 Marina Bay Parkway, Richmond, CA 94804 USA
| | - Laura A Schieve
- 4National Center on Birth Defects and Developmental Disabilities, Centers for Disease Control and Prevention, MS E-86, 1600 Clifton Road, Atlanta, GA 30333 USA
| | - Diana E Schendel
- 5Deparment of Public Health, Section of Epidemiology, Aarhus University, Aarhus, Denmark.,6Department of Economics and Business, National Centre for Register-based Research, Aarhus University, Aarhus, Denmark.,7Lundbeck Foundation Initiative for Integrative Psychiatric Research, iPSYCH, Aarhus, Denmark
| | - Lisa A Croen
- 8Kaiser Permanente Division of Research, 2000 Broadway, Oakland, CA 94612 USA
| | - Pankaj Chopra
- 9Department of Human Genetics, Emory University School of Medicine, 615 Michael Street, Atlanta, GA 30322 USA
| | - Reid S Alisch
- 10Department of Psychiatry, University of Wisconsin-Madison, 6001 Research Park Blvd, Madison, WI 53719 USA
| | - Craig J Newschaffer
- 11Department of Epidemiology and Biostatistics, Drexel University School of Public Health, 3215 Market Street, Philadelphia, PA 19104 USA.,A.J. Drexel Autism Institute, 3020 Market Street Suite 560, Philadelphia, PA 19104 USA
| | - Stephen T Warren
- 9Department of Human Genetics, Emory University School of Medicine, 615 Michael Street, Atlanta, GA 30322 USA.,13Department of Biochemistry, Emory University School of Medicine, 615 Michael Street, Atlanta, GA 30322 USA.,14Department of Pediatrics, Emory University School of Medicine, 615 Michael Street, Atlanta, GA 30322 USA
| | - Andrew P Feinberg
- 15Center for Epigenetics, Johns Hopkins School of Medicine, 855 N. Wolfe Street, Baltimore, MD 21205 USA.,16Department of Medicine, Johns Hopkins School of Medicine, 855 N. Wolfe Street, Baltimore, MD 21205 USA
| | - M Daniele Fallin
- 2Wendy Klag Center for Autism and Developmental Disabilities, Johns Hopkins Bloomberg School of Public Health, 615 N. Wolfe Street, W6509, Baltimore, MD 21205 USA.,15Center for Epigenetics, Johns Hopkins School of Medicine, 855 N. Wolfe Street, Baltimore, MD 21205 USA.,17Department of Mental Health, Johns Hopkins Bloomberg School of Public Health, 624 N. Broadway, HH850, Baltimore, MD 21205 USA
| | - Christine Ladd-Acosta
- 1Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, 615 N. Wolfe Street, Baltimore, MD 21205 USA.,2Wendy Klag Center for Autism and Developmental Disabilities, Johns Hopkins Bloomberg School of Public Health, 615 N. Wolfe Street, W6509, Baltimore, MD 21205 USA
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