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Peng Q, Liu X, Li W, Jing H, Li J, Gao X, Luo Q, Breeze CE, Pan S, Zheng Q, Li G, Qian J, Yuan L, Yuan N, You C, Du S, Zheng Y, Yuan Z, Tan J, Jia P, Wang J, Zhang G, Lu X, Shi L, Guo S, Liu Y, Ni T, Wen B, Zeng C, Jin L, Teschendorff AE, Liu F, Wang S. Analysis of blood methylation quantitative trait loci in East Asians reveals ancestry-specific impacts on complex traits. Nat Genet 2024; 56:846-860. [PMID: 38641644 DOI: 10.1038/s41588-023-01494-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2021] [Accepted: 08/02/2023] [Indexed: 04/21/2024]
Abstract
Methylation quantitative trait loci (mQTLs) are essential for understanding the role of DNA methylation changes in genetic predisposition, yet they have not been fully characterized in East Asians (EAs). Here we identified mQTLs in whole blood from 3,523 Chinese individuals and replicated them in additional 1,858 Chinese individuals from two cohorts. Over 9% of mQTLs displayed specificity to EAs, facilitating the fine-mapping of EA-specific genetic associations, as shown for variants associated with height. Trans-mQTL hotspots revealed biological pathways contributing to EA-specific genetic associations, including an ERG-mediated 233 trans-mCpG network, implicated in hematopoietic cell differentiation, which likely reflects binding efficiency modulation of the ERG protein complex. More than 90% of mQTLs were shared between different blood cell lineages, with a smaller fraction of lineage-specific mQTLs displaying preferential hypomethylation in the respective lineages. Our study provides new insights into the mQTL landscape across genetic ancestries and their downstream effects on cellular processes and diseases/traits.
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Affiliation(s)
- Qianqian Peng
- CAS Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Xinxuan Liu
- CAS Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing, China
- School of Future Technology, University of Chinese Academy of Sciences, Beijing, China
| | - Wenran Li
- CAS Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Han Jing
- CAS Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Jiarui Li
- CAS Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Xingjian Gao
- CAS Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing, China
| | - Qi Luo
- CAS Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China
| | | | - Siyu Pan
- CAS Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing, China
| | - Qiwen Zheng
- CAS Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing, China
| | - Guochao Li
- CAS Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing, China
| | - Jiaqiang Qian
- CAS Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Liyun Yuan
- CAS Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Na Yuan
- CAS Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing, China
| | - Chenglong You
- CAS Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Siyuan Du
- CAS Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Yuanting Zheng
- State Key Laboratory of Genetic Engineering, Collaborative Innovation Center for Genetics and Development, and Human Phenome Institute, Fudan University, Shanghai, China
- Ministry of Education Key Laboratory of Contemporary Anthropology, Department of Anthropology and Human Genetics, School of Life Sciences, Fudan University, Shanghai, China
| | - Ziyu Yuan
- Taizhou Institute of Health Sciences, Fudan University, Taizhou, China
| | - Jingze Tan
- Ministry of Education Key Laboratory of Contemporary Anthropology, Department of Anthropology and Human Genetics, School of Life Sciences, Fudan University, Shanghai, China
| | - Peilin Jia
- CAS Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing, China
| | - Jiucun Wang
- State Key Laboratory of Genetic Engineering, Collaborative Innovation Center for Genetics and Development, and Human Phenome Institute, Fudan University, Shanghai, China
- Taizhou Institute of Health Sciences, Fudan University, Taizhou, China
- Research Unit of Dissecting the Population Genetics and Developing New Technologies for Treatment and Prevention of Skin Phenotypes and Dermatological Diseases (2019RU058), Chinese Academy of Medical Sciences, Shanghai, China
| | - Guoqing Zhang
- CAS Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China
- Taizhou Institute of Health Sciences, Fudan University, Taizhou, China
| | - Xianping Lu
- Shenzhen Chipscreen Biosciences Co. Ltd., Shenzhen, China
| | - Leming Shi
- State Key Laboratory of Genetic Engineering, Collaborative Innovation Center for Genetics and Development, and Human Phenome Institute, Fudan University, Shanghai, China
- Ministry of Education Key Laboratory of Contemporary Anthropology, Department of Anthropology and Human Genetics, School of Life Sciences, Fudan University, Shanghai, China
- Taizhou Institute of Health Sciences, Fudan University, Taizhou, China
| | - Shicheng Guo
- Department of Medical Genetics, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, WI, USA
- Center for Precision Medicine Research, Marshfield Clinic Research Institute, Marshfield, WI, USA
| | - Yun Liu
- MOE Key Laboratory of Metabolism and Molecular Medicine, Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Fudan University, Shanghai, China
| | - Ting Ni
- State Key Laboratory of Genetic Engineering, Collaborative Innovation Center of Genetics and Development, Human Phenome Institute, School of Life Sciences and Huashan Hospital, Fudan University, Shanghai, China
| | - Bo Wen
- State Key Laboratory of Genetic Engineering, Collaborative Innovation Center for Genetics and Development, and Human Phenome Institute, Fudan University, Shanghai, China
- The Fifth People's Hospital of Shanghai and Institutes of Biomedical Sciences, Fudan University, Shanghai, China
| | - Changqing Zeng
- CAS Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing, China
| | - Li Jin
- State Key Laboratory of Genetic Engineering, Collaborative Innovation Center for Genetics and Development, and Human Phenome Institute, Fudan University, Shanghai, China
- Taizhou Institute of Health Sciences, Fudan University, Taizhou, China
- Research Unit of Dissecting the Population Genetics and Developing New Technologies for Treatment and Prevention of Skin Phenotypes and Dermatological Diseases (2019RU058), Chinese Academy of Medical Sciences, Shanghai, China
| | - Andrew E Teschendorff
- CAS Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China.
| | - Fan Liu
- CAS Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing, China.
- School of Future Technology, University of Chinese Academy of Sciences, Beijing, China.
- Department of Forensic Sciences, College of Criminal Justice, Naif Arab University of Security Sciences, Riyadh, Kingdom of Saudi Arabia.
| | - Sijia Wang
- CAS Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China.
- Taizhou Institute of Health Sciences, Fudan University, Taizhou, China.
- Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming, China.
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2
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Shang L, Zhao W, Wang YZ, Li Z, Choi JJ, Kho M, Mosley TH, Kardia SLR, Smith JA, Zhou X. meQTL mapping in the GENOA study reveals genetic determinants of DNA methylation in African Americans. Nat Commun 2023; 14:2711. [PMID: 37169753 PMCID: PMC10175543 DOI: 10.1038/s41467-023-37961-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2022] [Accepted: 04/07/2023] [Indexed: 05/13/2023] Open
Abstract
Identifying genetic variants that are associated with variation in DNA methylation, an analysis commonly referred to as methylation quantitative trait locus (meQTL) mapping, is an important first step towards understanding the genetic architecture underlying epigenetic variation. Most existing meQTL mapping studies have focused on individuals of European ancestry and are underrepresented in other populations, with a particular absence of large studies in populations with African ancestry. We fill this critical knowledge gap by performing a large-scale cis-meQTL mapping study in 961 African Americans from the Genetic Epidemiology Network of Arteriopathy (GENOA) study. We identify a total of 4,565,687 cis-acting meQTLs in 320,965 meCpGs. We find that 45% of meCpGs harbor multiple independent meQTLs, suggesting potential polygenic genetic architecture underlying methylation variation. A large percentage of the cis-meQTLs also colocalize with cis-expression QTLs (eQTLs) in the same population. Importantly, the identified cis-meQTLs explain a substantial proportion (median = 24.6%) of methylation variation. In addition, the cis-meQTL associated CpG sites mediate a substantial proportion (median = 24.9%) of SNP effects underlying gene expression. Overall, our results represent an important step toward revealing the co-regulation of methylation and gene expression, facilitating the functional interpretation of epigenetic and gene regulation underlying common diseases in African Americans.
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Affiliation(s)
- Lulu Shang
- Department of Biostatistics, School of Public Health, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Wei Zhao
- Department of Epidemiology, School of Public Health, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Yi Zhe Wang
- Department of Epidemiology, School of Public Health, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Zheng Li
- Department of Biostatistics, School of Public Health, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Jerome J Choi
- Population Health Sciences, University of Wisconsin-Madison School of Medicine and Public Health, Madison, WI, 53726, USA
| | - Minjung Kho
- Department of Epidemiology, School of Public Health, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Thomas H Mosley
- Memory Impairment and Neurodegenerative Dementia (MIND) Center, University of Mississippi Medical Center, Jackson, MS, 39126, USA
| | - Sharon L R Kardia
- Department of Epidemiology, School of Public Health, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Jennifer A Smith
- Department of Epidemiology, School of Public Health, University of Michigan, Ann Arbor, MI, 48109, USA.
| | - Xiang Zhou
- Department of Biostatistics, School of Public Health, University of Michigan, Ann Arbor, MI, 48109, USA.
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Romanowska J, Nustad HE, Page CM, Denault WRP, Lee Y, Magnus MC, Haftorn KL, Gjerdevik M, Novakovic B, Saffery R, Gjessing HK, Lyle R, Magnus P, Håberg SE, Jugessur A. The X-factor in ART: does the use of assisted reproductive technologies influence DNA methylation on the X chromosome? Hum Genomics 2023; 17:35. [PMID: 37085889 PMCID: PMC10122315 DOI: 10.1186/s40246-023-00484-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2023] [Accepted: 04/10/2023] [Indexed: 04/23/2023] Open
Abstract
BACKGROUND Assisted reproductive technologies (ART) may perturb DNA methylation (DNAm) in early embryonic development. Although a handful of epigenome-wide association studies of ART have been published, none have investigated CpGs on the X chromosome. To bridge this knowledge gap, we leveraged one of the largest collections of mother-father-newborn trios of ART and non-ART (natural) conceptions to date to investigate sex-specific DNAm differences on the X chromosome. The discovery cohort consisted of 982 ART and 963 non-ART trios from the Norwegian Mother, Father, and Child Cohort Study (MoBa). To verify our results from the MoBa cohort, we used an external cohort of 149 ART and 58 non-ART neonates from the Australian 'Clinical review of the Health of adults conceived following Assisted Reproductive Technologies' (CHART) study. The Illumina EPIC array was used to measure DNAm in both datasets. In the MoBa cohort, we performed a set of X-chromosome-wide association studies ('XWASs' hereafter) to search for sex-specific DNAm differences between ART and non-ART newborns. We tested several models to investigate the influence of various confounders, including parental DNAm. We also searched for differentially methylated regions (DMRs) and regions of co-methylation flanking the most significant CpGs. Additionally, we ran an analogous model to our main model on the external CHART dataset. RESULTS In the MoBa cohort, we found more differentially methylated CpGs and DMRs in girls than boys. Most of the associations persisted after controlling for parental DNAm and other confounders. Many of the significant CpGs and DMRs were in gene-promoter regions, and several of the genes linked to these CpGs are expressed in tissues relevant for both ART and sex (testis, placenta, and fallopian tube). We found no support for parental DNAm-dependent features as an explanation for the observed associations in the newborns. The most significant CpG in the boys-only analysis was in UBE2DNL, which is expressed in testes but with unknown function. The most significant CpGs in the girls-only analysis were in EIF2S3 and AMOT. These three loci also displayed differential DNAm in the CHART cohort. CONCLUSIONS Genes that co-localized with the significant CpGs and DMRs associated with ART are implicated in several key biological processes (e.g., neurodevelopment) and disorders (e.g., intellectual disability and autism). These connections are particularly compelling in light of previous findings indicating that neurodevelopmental outcomes differ in ART-conceived children compared to those naturally conceived.
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Affiliation(s)
- Julia Romanowska
- Centre for Fertility and Health, Norwegian Institute of Public Health, Oslo, Norway.
- Department of Global Public Health and Primary Care, University of Bergen, Bergen, Norway.
| | - Haakon E Nustad
- Centre for Fertility and Health, Norwegian Institute of Public Health, Oslo, Norway
- DeepInsight, 0154, Oslo, Norway
| | - Christian M Page
- Centre for Fertility and Health, Norwegian Institute of Public Health, Oslo, Norway
- Department of Mathematics, Faculty of Mathematics and Natural Sciences, University of Oslo, Oslo, Norway
| | - William R P Denault
- Centre for Fertility and Health, Norwegian Institute of Public Health, Oslo, Norway
- Department of Human Genetics, University of Chicago, Chicago, IL, USA
| | - Yunsung Lee
- Centre for Fertility and Health, Norwegian Institute of Public Health, Oslo, Norway
| | - Maria C Magnus
- Centre for Fertility and Health, Norwegian Institute of Public Health, Oslo, Norway
| | - Kristine L Haftorn
- Centre for Fertility and Health, Norwegian Institute of Public Health, Oslo, Norway
| | - Miriam Gjerdevik
- Centre for Fertility and Health, Norwegian Institute of Public Health, Oslo, Norway
- Department of Computer Science, Electrical Engineering and Mathematical Sciences, Western Norway University of Applied Sciences, Bergen, Norway
| | - Boris Novakovic
- Murdoch Children's Research Institute, Melbourne, Australia
- Department of Paediatrics, University of Melbourne, Melbourne, Australia
| | - Richard Saffery
- Murdoch Children's Research Institute, Melbourne, Australia
- Department of Paediatrics, University of Melbourne, Melbourne, Australia
| | - Håkon K Gjessing
- Centre for Fertility and Health, Norwegian Institute of Public Health, Oslo, Norway
- Department of Global Public Health and Primary Care, University of Bergen, Bergen, Norway
| | - Robert Lyle
- Centre for Fertility and Health, Norwegian Institute of Public Health, Oslo, Norway
- Department of Medical Genetics, Oslo University Hospital and University of Oslo, Oslo, Norway
| | - Per Magnus
- Centre for Fertility and Health, Norwegian Institute of Public Health, Oslo, Norway
| | - Siri E Håberg
- Centre for Fertility and Health, Norwegian Institute of Public Health, Oslo, Norway
| | - Astanand Jugessur
- Centre for Fertility and Health, Norwegian Institute of Public Health, Oslo, Norway
- Department of Global Public Health and Primary Care, University of Bergen, Bergen, Norway
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4
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Nabais MF, Gadd DA, Hannon E, Mill J, McRae AF, Wray NR. An overview of DNA methylation-derived trait score methods and applications. Genome Biol 2023; 24:28. [PMID: 36797751 PMCID: PMC9936670 DOI: 10.1186/s13059-023-02855-7] [Citation(s) in RCA: 13] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2022] [Accepted: 01/17/2023] [Indexed: 02/18/2023] Open
Abstract
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.
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Affiliation(s)
- Marta F Nabais
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD, 4072, Australia
- University of Exeter Medical School, RILD Building, RD&E Hospital Wonford, Barrack Road, Exeter, EX2 5DW, UK
| | - Danni A Gadd
- Centre for Genomic and Experimental Medicine, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, EH4 2XU, UK
| | - Eilis Hannon
- University of Exeter Medical School, RILD Building, RD&E Hospital Wonford, Barrack Road, Exeter, EX2 5DW, UK
| | - Jonathan Mill
- University of Exeter Medical School, RILD Building, RD&E Hospital Wonford, Barrack Road, Exeter, EX2 5DW, UK
| | - Allan F McRae
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD, 4072, Australia
| | - Naomi R Wray
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD, 4072, Australia.
- Queensland Brain Institute, The University of Queensland, Brisbane, QLD, 4072, Australia.
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5
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Oliva M, Demanelis K, Lu Y, Chernoff M, Jasmine F, Ahsan H, Kibriya MG, Chen LS, Pierce BL. DNA methylation QTL mapping across diverse human tissues provides molecular links between genetic variation and complex traits. Nat Genet 2023; 55:112-122. [PMID: 36510025 PMCID: PMC10249665 DOI: 10.1038/s41588-022-01248-z] [Citation(s) in RCA: 53] [Impact Index Per Article: 53.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2021] [Accepted: 10/26/2022] [Indexed: 12/14/2022]
Abstract
Studies of DNA methylation (DNAm) in solid human tissues are relatively scarce; tissue-specific characterization of DNAm is needed to understand its role in gene regulation and its relevance to complex traits. We generated array-based DNAm profiles for 987 human samples from the Genotype-Tissue Expression (GTEx) project, representing 9 tissue types and 424 subjects. We characterized methylome and transcriptome correlations (eQTMs), genetic regulation in cis (mQTLs and eQTLs) across tissues and e/mQTLs links to complex traits. We identified mQTLs for 286,152 CpG sites, many of which (>5%) show tissue specificity, and mQTL colocalizations with 2,254 distinct GWAS hits across 83 traits. For 91% of these loci, a candidate gene link was identified by integration of functional maps, including eQTMs, and/or eQTL colocalization, but only 33% of loci involved an eQTL and mQTL present in the same tissue type. With this DNAm-focused integrative analysis, we contribute to the understanding of molecular regulatory mechanisms in human tissues and their impact on complex traits.
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Affiliation(s)
- Meritxell Oliva
- Department of Public Health Sciences, University of Chicago, Chicago, IL, USA.
| | - Kathryn Demanelis
- Department of Medicine, University of Pittsburgh, Pittsburgh, PA, USA
| | - Yihao Lu
- Department of Public Health Sciences, University of Chicago, Chicago, IL, USA
| | - Meytal Chernoff
- Department of Public Health Sciences, University of Chicago, Chicago, IL, USA
| | - Farzana Jasmine
- Department of Public Health Sciences, University of Chicago, Chicago, IL, USA
| | - Habibul Ahsan
- Department of Public Health Sciences, University of Chicago, Chicago, IL, USA
- Department of Human Genetics, University of Chicago, Chicago, IL, USA
- Comprehensive Cancer Center, University of Chicago, Chicago, IL, USA
- Department of Medicine, University of Chicago, Chicago, IL, USA
- Institute for Population and Precision Health, University of Chicago, Chicago, IL, USA
| | - Muhammad G Kibriya
- Department of Public Health Sciences, University of Chicago, Chicago, IL, USA
- Institute for Population and Precision Health, University of Chicago, Chicago, IL, USA
| | - Lin S Chen
- Department of Public Health Sciences, University of Chicago, Chicago, IL, USA.
| | - Brandon L Pierce
- Department of Public Health Sciences, University of Chicago, Chicago, IL, USA.
- Department of Human Genetics, University of Chicago, Chicago, IL, USA.
- Comprehensive Cancer Center, University of Chicago, Chicago, IL, USA.
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6
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Ferguson LB, Mayfield RD, Messing RO. RNA biomarkers for alcohol use disorder. Front Mol Neurosci 2022; 15:1032362. [PMID: 36407766 PMCID: PMC9673015 DOI: 10.3389/fnmol.2022.1032362] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2022] [Accepted: 10/17/2022] [Indexed: 11/06/2022] Open
Abstract
Alcohol use disorder (AUD) is highly prevalent and one of the leading causes of disability in the US and around the world. There are some molecular biomarkers of heavy alcohol use and liver damage which can suggest AUD, but these are lacking in sensitivity and specificity. AUD treatment involves psychosocial interventions and medications for managing alcohol withdrawal, assisting in abstinence and reduced drinking (naltrexone, acamprosate, disulfiram, and some off-label medications), and treating comorbid psychiatric conditions (e.g., depression and anxiety). It has been suggested that various patient groups within the heterogeneous AUD population would respond more favorably to specific treatment approaches. For example, there is some evidence that so-called reward-drinkers respond better to naltrexone than acamprosate. However, there are currently no objective molecular markers to separate patients into optimal treatment groups or any markers of treatment response. Objective molecular biomarkers could aid in AUD diagnosis and patient stratification, which could personalize treatment and improve outcomes through more targeted interventions. Biomarkers of treatment response could also improve AUD management and treatment development. Systems biology considers complex diseases and emergent behaviors as the outcome of interactions and crosstalk between biomolecular networks. A systems approach that uses transcriptomic (or other -omic data, e.g., methylome, proteome, metabolome) can capture genetic and environmental factors associated with AUD and potentially provide sensitive, specific, and objective biomarkers to guide patient stratification, prognosis of treatment response or relapse, and predict optimal treatments. This Review describes and highlights state-of-the-art research on employing transcriptomic data and artificial intelligence (AI) methods to serve as molecular biomarkers with the goal of improving the clinical management of AUD. Considerations about future directions are also discussed.
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Affiliation(s)
- Laura B. Ferguson
- Waggoner Center for Alcohol and Addiction Research, University of Texas at Austin, Austin, TX, United States,Department of Neurology, Dell Medical School, University of Texas at Austin, Austin, TX, United States,Department of Neuroscience, University of Texas at Austin, Austin, TX, United States,*Correspondence: Laura B. Ferguson,
| | - R. Dayne Mayfield
- Waggoner Center for Alcohol and Addiction Research, University of Texas at Austin, Austin, TX, United States,Department of Neuroscience, University of Texas at Austin, Austin, TX, United States
| | - Robert O. Messing
- Waggoner Center for Alcohol and Addiction Research, University of Texas at Austin, Austin, TX, United States,Department of Neurology, Dell Medical School, University of Texas at Austin, Austin, TX, United States,Department of Neuroscience, University of Texas at Austin, Austin, TX, United States
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7
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Migliore L, Coppedè F. Gene-environment interactions in Alzheimer disease: the emerging role of epigenetics. Nat Rev Neurol 2022; 18:643-660. [PMID: 36180553 DOI: 10.1038/s41582-022-00714-w] [Citation(s) in RCA: 60] [Impact Index Per Article: 30.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/18/2022] [Indexed: 12/15/2022]
Abstract
With the exception of a few monogenic forms, Alzheimer disease (AD) has a complex aetiology that is likely to involve multiple susceptibility genes and environmental factors. The role of environmental factors is difficult to determine and, until a few years ago, the molecular mechanisms underlying gene-environment (G × E) interactions in AD were largely unknown. Here, we review evidence that has emerged over the past two decades to explain how environmental factors, such as diet, lifestyle, alcohol, smoking and pollutants, might interact with the human genome. In particular, we discuss how various environmental AD risk factors can induce epigenetic modifications of key AD-related genes and pathways and consider how epigenetic mechanisms could contribute to the effects of oxidative stress on AD onset. Studies on early-life exposures are helping to uncover critical time windows of sensitivity to epigenetic influences from environmental factors, thereby laying the foundations for future primary preventative approaches. We conclude that epigenetic modifications need to be considered when assessing G × E interactions in AD.
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Affiliation(s)
- Lucia Migliore
- Department of Translational Research and of New Surgical and Medical Technologies, University of Pisa, Pisa, Italy. .,Department of Laboratory Medicine, Pisa University Hospital, Pisa, Italy.
| | - Fabio Coppedè
- Department of Translational Research and of New Surgical and Medical Technologies, University of Pisa, Pisa, Italy
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8
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Massi MC, Dominoni L, Ieva F, Fiorito G. A Deep Survival EWAS approach estimating risk profile based on pre-diagnostic DNA methylation: An application to breast cancer time to diagnosis. PLoS Comput Biol 2022; 18:e1009959. [PMID: 36155971 PMCID: PMC9536632 DOI: 10.1371/journal.pcbi.1009959] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2022] [Revised: 10/06/2022] [Accepted: 09/10/2022] [Indexed: 11/19/2022] Open
Abstract
Previous studies for cancer biomarker discovery based on pre-diagnostic blood DNA methylation (DNAm) profiles, either ignore the explicit modeling of the Time To Diagnosis (TTD), or provide inconsistent results. This lack of consistency is likely due to the limitations of standard EWAS approaches, that model the effect of DNAm at CpG sites on TTD independently. In this work, we aim to identify blood DNAm profiles associated with TTD, with the aim to improve the reliability of the results, as well as their biological meaningfulness. We argue that a global approach to estimate CpG sites effect profile should capture the complex (potentially non-linear) relationships interplaying between sites. To prove our concept, we develop a new Deep Learning-based approach assessing the relevance of individual CpG Islands (i.e., assigning a weight to each site) in determining TTD while modeling their combined effect in a survival analysis scenario. The algorithm combines a tailored sampling procedure with DNAm sites agglomeration, deep non-linear survival modeling and SHapley Additive exPlanations (SHAP) values estimation to aid robustness of the derived effects profile. The proposed approach deals with the common complexities arising from epidemiological studies, such as small sample size, noise, and low signal-to-noise ratio of blood-derived DNAm. We apply our approach to a prospective case-control study on breast cancer nested in the EPIC Italy cohort and we perform weighted gene-set enrichment analyses to demonstrate the biological meaningfulness of the obtained results. We compared the results of Deep Survival EWAS with those of a traditional EWAS approach, demonstrating that our method performs better than the standard approach in identifying biologically relevant pathways. Blood-derived DNAm profiles could be exploited as new biomarkers for cancer risk stratification and possibly, early detection. This is of particular interest since blood is a convenient tissue to assay for constitutional methylation and its collection is non-invasive. Exploiting pre-diagnostic blood DNAm data opens the further opportunity to investigate the association of DNAm at baseline on cancer risk, modeling the relationship between sites’ methylation and the Time to Diagnosis. Previous studies mostly provide inconsistent results likely due to the limitations of standard EWAS approaches, that model the effect of DNAm at CpG sites on TTD independently. In this work we argue that an approach to estimate single CpG sites’ effect while modeling their combined effect on the survival outcome is needed, and we claim that such approach should capture the complex (potentially non-linear) relationships interplaying between sites. We prove this concept by developing a novel approach to analyze a prospective case-control study on breast cancer nested in the EPIC Italy cohort. A weighted gene set enrichment analysis confirms that our approach outperforms standard EWAS in identifying biologically meaningful pathways.
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Affiliation(s)
- Michela Carlotta Massi
- Health Data Science Centre, Human Technopole Foundation, Milan, Italy
- MOX Laboratory for Modeling and Scientific Computing, Dept. of Mathematics, Politecnico di Milano, Milan, Italy
- * E-mail:
| | - Lorenzo Dominoni
- MOX Laboratory for Modeling and Scientific Computing, Dept. of Mathematics, Politecnico di Milano, Milan, Italy
| | - Francesca Ieva
- Health Data Science Centre, Human Technopole Foundation, Milan, Italy
- MOX Laboratory for Modeling and Scientific Computing, Dept. of Mathematics, Politecnico di Milano, Milan, Italy
| | - Giovanni Fiorito
- Laboratory of Biostatistics, Dept. of Biomedical Sciences, University of Sassari, Sassari, Italy
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9
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Nustad HE, Steinsland I, Ollikainen M, Cazaly E, Kaprio J, Benjamini Y, Gervin K, Lyle R. Modeling dependency structures in 450k DNA methylation data. Bioinformatics 2022; 38:885-891. [PMID: 34788815 PMCID: PMC8796368 DOI: 10.1093/bioinformatics/btab774] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2021] [Revised: 11/01/2021] [Accepted: 11/09/2021] [Indexed: 02/04/2023] Open
Abstract
MOTIVATION DNA methylation has been shown to be spatially dependent across chromosomes. Previous studies have focused on the influence of genomic context on the dependency structure, while not considering differences in dependency structure between individuals. RESULTS We modeled spatial dependency with a flexible framework to quantify the dependency structure, focusing on inter-individual differences by exploring the association between dependency parameters and technical and biological variables. The model was applied to a subset of the Finnish Twin Cohort study (N = 1611 individuals). The estimates of the dependency parameters varied considerably across individuals, but were generally consistent across chromosomes within individuals. The variation in dependency parameters was associated with bisulfite conversion plate, zygosity, sex and age. The age differences presumably reflect accumulated environmental exposures and/or accumulated small methylation differences caused by stochastic mitotic events, establishing recognizable, individual patterns more strongly seen in older individuals. AVAILABILITY AND IMPLEMENTATION The twin dataset used in the current study are located in the Biobank of the National Institute for Health and Welfare, Finland. All the biobanked data are publicly available for use by qualified researchers following a standardized application procedure (https://thl.fi/en/web/thl-biobank/for-researchers). A R-script for fitting the dependency structure to publicly available DNA methylation data with the software used in this article is provided in supplementary data. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Haakon E Nustad
- Department of Medical Genetics and Norwegian Sequencing Centre, Oslo University Hospital, 0450 Oslo, Norway
- Institute of Clinical Medicine, Faculty of Medicine, University of Oslo, 0372 Oslo, Norway
- Department of Pharmacy, PharmaTox Strategic Research Initiative, University of Oslo, 0371 Oslo, Norway
- Centre for Fertility and Health, Norwegian Institute of Public Health, 0213 Oslo, Norway
| | - Ingelin Steinsland
- Department of Mathematical Sciences, Norwegian University of Science and Technology, 7034 Trondheim, Norway
| | - Miina Ollikainen
- Institute for Molecular Medicine Finland FIMM, Helsinki Institute of Life Science, University of Helsinki, FI-00014 Helsinki, Finland
| | - Emma Cazaly
- Institute for Molecular Medicine Finland FIMM, Helsinki Institute of Life Science, University of Helsinki, FI-00014 Helsinki, Finland
| | - Jaakko Kaprio
- Institute for Molecular Medicine Finland FIMM, Helsinki Institute of Life Science, University of Helsinki, FI-00014 Helsinki, Finland
| | - Yuval Benjamini
- Department of Statistics and Data Science, The Hebrew University, Mount Scopus, Jerusalem 9190501, Israel
| | - Kristina Gervin
- Department of Pharmacy, PharmaTox Strategic Research Initiative, University of Oslo, 0371 Oslo, Norway
- Division of Clinical Neuroscience, Department of Research and Innovation, Oslo University Hospital, 0450 Oslo, Norway
- Pharmacoepidemiology and Drug Safety Research Group, Department of Pharmacy, Faculty of Mathematics and Natural Sciences, University of Oslo, 0363 Oslo, Norway
| | - Robert Lyle
- Department of Medical Genetics and Norwegian Sequencing Centre, Oslo University Hospital, 0450 Oslo, Norway
- Centre for Fertility and Health, Norwegian Institute of Public Health, 0213 Oslo, Norway
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10
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Genotype-dependent epigenetic regulation of DLGAP2 in alcohol use and dependence. Mol Psychiatry 2021; 26:4367-4382. [PMID: 31745236 DOI: 10.1038/s41380-019-0588-9] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/10/2019] [Revised: 10/22/2019] [Accepted: 10/30/2019] [Indexed: 12/13/2022]
Abstract
Alcohol misuse is a major public health problem originating from genetic and environmental risk factors. Alterations in the brain epigenome may orchestrate changes in gene expression that lead to alcohol misuse and dependence. Through epigenome-wide association analysis of DNA methylation from human brain tissues, we identified a differentially methylated region, DMR-DLGAP2, associated with alcohol dependence. Methylation within DMR-DLGAP2 was found to be genotype-dependent, allele-specific and associated with reward processing in brain. Methylation at the DMR-DLGAP2 regulated expression of DLGAP2 in vitro, and Dlgap2-deficient mice showed reduced alcohol consumption compared with wild-type controls. These results suggest that DLGAP2 may be an interface for genetic and epigenetic factors controlling alcohol use and dependence.
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11
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Nosova O, Bazov I, Karpyak V, Hallberg M, Bakalkin G. Epigenetic and Transcriptional Control of the Opioid Prodynorphine Gene: In-Depth Analysis in the Human Brain. Molecules 2021; 26:molecules26113458. [PMID: 34200173 PMCID: PMC8201134 DOI: 10.3390/molecules26113458] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2021] [Revised: 05/26/2021] [Accepted: 06/01/2021] [Indexed: 12/19/2022] Open
Abstract
Neuropeptides serve as neurohormones and local paracrine regulators that control neural networks regulating behavior, endocrine system and sensorimotor functions. Their expression is characterized by exceptionally restricted profiles. Circuit-specific and adaptive expression of neuropeptide genes may be defined by transcriptional and epigenetic mechanisms controlled by cell type and subtype sequence-specific transcription factors, insulators and silencers. The opioid peptide dynorphins play a critical role in neurological and psychiatric disorders, pain processing and stress, while their mutations cause profound neurodegeneration in the human brain. In this review, we focus on the prodynorphin gene as a model for the in-depth epigenetic and transcriptional analysis of expression of the neuropeptide genes. Prodynorphin studies may provide a framework for analysis of mechanisms relevant for regulation of neuropeptide genes in normal and pathological human brain.
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Affiliation(s)
- Olga Nosova
- Department of Pharmaceutical Biosciences, Uppsala University, 75124 Uppsala, Sweden; (I.B.); (M.H.)
- Correspondence: (O.N.); (G.B.)
| | - Igor Bazov
- Department of Pharmaceutical Biosciences, Uppsala University, 75124 Uppsala, Sweden; (I.B.); (M.H.)
| | | | - Mathias Hallberg
- Department of Pharmaceutical Biosciences, Uppsala University, 75124 Uppsala, Sweden; (I.B.); (M.H.)
| | - Georgy Bakalkin
- Department of Pharmaceutical Biosciences, Uppsala University, 75124 Uppsala, Sweden; (I.B.); (M.H.)
- Correspondence: (O.N.); (G.B.)
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12
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Chi C, Ye Y, Chen B, Huang H. Bipartite graph-based approach for clustering of cell lines by gene expression-drug response associations. Bioinformatics 2021; 37:2617-2626. [PMID: 33682877 PMCID: PMC8428606 DOI: 10.1093/bioinformatics/btab143] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2020] [Revised: 02/16/2021] [Accepted: 03/01/2021] [Indexed: 01/29/2023] Open
Abstract
MOTIVATION In pharmacogenomic studies, the biological context of cell lines influences the predictive ability of drug-response models and the discovery of biomarkers. Thus, similar cell lines are often studied together based on prior knowledge of biological annotations. However, this selection approach is not scalable with the number of annotations, and the relationship between gene-drug association patterns and biological context may not be obvious. RESULTS We present a procedure to compare cell lines based on their gene-drug association patterns. Starting with a grouping of cell lines from biological annotation, we model gene-drug association patterns for each group as a bipartite graph between genes and drugs. This is accomplished by applying sparse canonical correlation analysis (SCCA) to extract the gene-drug associations, and using the canonical vectors to construct the edge weights. Then, we introduce a nuclear norm-based dissimilarity measure to compare the bipartite graphs. Accompanying our procedure is a permutation test to evaluate the significance of similarity of cell line groups in terms of gene-drug associations. In the pharmacogenomics datasets CTRP2, GDSC2, and CCLE, hierarchical clustering of carcinoma groups based on this dissimilarity measure uniquely reveals clustering patterns driven by carcinoma subtype rather than primary site. Next, we show that the top associated drugs or genes from SCCA can be used to characterize the clustering patterns of haematopoietic and lymphoid malignancies. Finally, we confirm by simulation that when drug responses are linearly-dependent on expression, our approach is the only one that can effectively infer the true hierarchy compared to existing approaches. AVAILABILITY Bipartite graph-based hierarchical clustering is implemented in R and can be obtained from CRAN: https://CRAN.R-project.org/package=hierBipartite. The source code is available at https://github.com/CalvinTChi/hierBipartite. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Calvin Chi
- Center for Computational Biology, University of California, Berkeley, CA 94720, USA
| | - Yuting Ye
- Division of Biostatistics, University of California, Berkeley, CA 94720, USA
| | - Bin Chen
- Department of Pediatrics and Human Development, Michigan State University, Grand Rapids, MI 48912, USA.,Department of Pharmacology and Toxicology, Michigan State University, Grand Rapids, MI 48824, USA
| | - Haiyan Huang
- Center for Computational Biology, University of California, Berkeley, CA 94720, USA.,Department of Statistics, University of California, Berkeley, CA 94720, USA
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13
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Yu X, Yang Q, Wang D, Li Z, Chen N, Kong DX. Predicting lung adenocarcinoma disease progression using methylation-correlated blocks and ensemble machine learning classifiers. PeerJ 2021; 9:e10884. [PMID: 33628643 PMCID: PMC7894106 DOI: 10.7717/peerj.10884] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2020] [Accepted: 01/12/2021] [Indexed: 01/20/2023] Open
Abstract
Applying the knowledge that methyltransferases and demethylases can modify adjacent cytosine-phosphorothioate-guanine (CpG) sites in the same DNA strand, we found that combining multiple CpGs into a single block may improve cancer diagnosis. However, survival prediction remains a challenge. In this study, we developed a pipeline named "stacked ensemble of machine learning models for methylation-correlated blocks" (EnMCB) that combined Cox regression, support vector regression (SVR), and elastic-net models to construct signatures based on DNA methylation-correlated blocks for lung adenocarcinoma (LUAD) survival prediction. We used methylation profiles from the Cancer Genome Atlas (TCGA) as the training set, and profiles from the Gene Expression Omnibus (GEO) as validation and testing sets. First, we partitioned the genome into blocks of tightly co-methylated CpG sites, which we termed methylation-correlated blocks (MCBs). After partitioning and feature selection, we observed different diagnostic capacities for predicting patient survival across the models. We combined the multiple models into a single stacking ensemble model. The stacking ensemble model based on the top-ranked block had the area under the receiver operating characteristic curve of 0.622 in the TCGA training set, 0.773 in the validation set, and 0.698 in the testing set. When stratified by clinicopathological risk factors, the risk score predicted by the top-ranked MCB was an independent prognostic factor. Our results showed that our pipeline was a reliable tool that may facilitate MCB selection and survival prediction.
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Affiliation(s)
- Xin Yu
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, Hubei, China
- Agricultural Bioinformatics Key Laboratory of Hubei Province, College of Informatics, Huazhong Agricultural University, Wuhan, Hubei, China
| | - Qian Yang
- Agricultural Bioinformatics Key Laboratory of Hubei Province, College of Informatics, Huazhong Agricultural University, Wuhan, Hubei, China
| | - Dong Wang
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, Hubei, China
- Agricultural Bioinformatics Key Laboratory of Hubei Province, College of Informatics, Huazhong Agricultural University, Wuhan, Hubei, China
| | - Zhaoyang Li
- Agricultural Bioinformatics Key Laboratory of Hubei Province, College of Informatics, Huazhong Agricultural University, Wuhan, Hubei, China
| | - Nianhang Chen
- Agricultural Bioinformatics Key Laboratory of Hubei Province, College of Informatics, Huazhong Agricultural University, Wuhan, Hubei, China
| | - De-Xin Kong
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, Hubei, China
- Agricultural Bioinformatics Key Laboratory of Hubei Province, College of Informatics, Huazhong Agricultural University, Wuhan, Hubei, China
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14
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An introduction to EpiPol (Epigenetic affecting Polymorphism) concept with an in silico identification of CpG-affecting SNPs in the upstream regulatory sequences of human AHR gene. Meta Gene 2020. [DOI: 10.1016/j.mgene.2020.100805] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
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15
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Yu F, Xu C, Deng HW, Shen H. A novel computational strategy for DNA methylation imputation using mixture regression model (MRM). BMC Bioinformatics 2020; 21:552. [PMID: 33261550 PMCID: PMC7708217 DOI: 10.1186/s12859-020-03865-z] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2020] [Accepted: 11/09/2020] [Indexed: 12/19/2022] Open
Abstract
BACKGROUND DNA methylation is an important heritable epigenetic mark that plays a crucial role in transcriptional regulation and the pathogenesis of various human disorders. The commonly used DNA methylation measurement approaches, e.g., Illumina Infinium HumanMethylation-27 and -450 BeadChip arrays (27 K and 450 K arrays) and reduced representation bisulfite sequencing (RRBS), only cover a small proportion of the total CpG sites in the human genome, which considerably limited the scope of the DNA methylation analysis in those studies. RESULTS We proposed a new computational strategy to impute the methylation value at the unmeasured CpG sites using the mixture of regression model (MRM) of radial basis functions, integrating information of neighboring CpGs and the similarities in local methylation patterns across subjects and across multiple genomic regions. Our method achieved a better imputation accuracy over a set of competing methods on both simulated and empirical data, particularly when the missing rate is high. By applying MRM to an RRBS dataset from subjects with low versus high bone mineral density (BMD), we recovered methylation values of ~ 300 K CpGs in the promoter regions of chromosome 17 and identified some novel differentially methylated CpGs that are significantly associated with BMD. CONCLUSIONS Our method is well applicable to the numerous methylation studies. By expanding the coverage of the methylation dataset to unmeasured sites, it can significantly enhance the discovery of novel differential methylation signals and thus reveal the mechanisms underlying various human disorders/traits.
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Affiliation(s)
- Fangtang Yu
- Center for Bioinformatics and Genomics, Department of Biostatistics and Data Science, School of Public Health and Tropical Medicine, Tulane University, New Orleans, LA, 70112, USA
| | - Chao Xu
- Center for Bioinformatics and Genomics, Department of Biostatistics and Data Science, School of Public Health and Tropical Medicine, Tulane University, New Orleans, LA, 70112, USA
| | - Hong-Wen Deng
- Center for Bioinformatics and Genomics, Department of Biostatistics and Data Science, School of Public Health and Tropical Medicine, Tulane University, New Orleans, LA, 70112, USA
| | - Hui Shen
- Center for Bioinformatics and Genomics, Department of Biostatistics and Data Science, School of Public Health and Tropical Medicine, Tulane University, New Orleans, LA, 70112, USA.
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16
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Abante J, Fang Y, Feinberg AP, Goutsias J. Detection of haplotype-dependent allele-specific DNA methylation in WGBS data. Nat Commun 2020; 11:5238. [PMID: 33067439 PMCID: PMC7567826 DOI: 10.1038/s41467-020-19077-1] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2019] [Accepted: 09/22/2020] [Indexed: 12/19/2022] Open
Abstract
In heterozygous genomes, allele-specific measurements can reveal biologically significant differences in DNA methylation between homologous alleles associated with local changes in genetic sequence. Current approaches for detecting such events from whole-genome bisulfite sequencing (WGBS) data perform statistically independent marginal analysis at individual cytosine-phosphate-guanine (CpG) sites, thus ignoring correlations in the methylation state, or carry-out a joint statistical analysis of methylation patterns at four CpG sites producing unreliable statistical evidence. Here, we employ the one-dimensional Ising model of statistical physics and develop a method for detecting allele-specific methylation (ASM) events within segments of DNA containing clusters of linked single-nucleotide polymorphisms (SNPs), called haplotypes. Comparisons with existing approaches using simulated and real WGBS data show that our method provides an improved fit to data, especially when considering large haplotypes. Importantly, the method employs robust hypothesis testing for detecting statistically significant imbalances in mean methylation level and methylation entropy, as well as for identifying haplotypes for which the genetic variant carries significant information about the methylation state. As such, our ASM analysis approach can potentially lead to biological discoveries with important implications for the genetics of complex human diseases.
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Affiliation(s)
- J Abante
- Whitaker Biomedical Engineering Institute, Johns Hopkins University, Baltimore, MD, 21218, USA.
- Department of Electrical & Computer Engineering, Johns Hopkins University, Baltimore, MD, 21218, USA.
| | - Y Fang
- Center for Epigenetics, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD, 21205, USA
| | - A P Feinberg
- Center for Epigenetics, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD, 21205, USA
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA
| | - J Goutsias
- Whitaker Biomedical Engineering Institute, Johns Hopkins University, Baltimore, MD, 21218, USA.
- Department of Electrical & Computer Engineering, Johns Hopkins University, Baltimore, MD, 21218, USA.
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17
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Lin N, Liu J, Castle J, Wan J, Shendre A, Liu Y, Wang C, He C. Genome-wide DNA methylation profiling in human breast tissue by Illumina TruSeq methyl capture EPIC sequencing and infinium methylationEPIC beadchip microarray. Epigenetics 2020; 16:754-769. [PMID: 33048617 PMCID: PMC8216193 DOI: 10.1080/15592294.2020.1827703] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
A newly-developed platform, the Illumina TruSeq Methyl Capture EPIC library prep (TruSeq EPIC), builds on the content of the Infinium MethylationEPIC Beadchip Microarray (EPIC-array) and leverages the power of next-generation sequencing for targeted bisulphite sequencing. We empirically examined the performance of TruSeq EPIC and EPIC-array in assessing genome-wide DNA methylation in breast tissue samples. TruSeq EPIC provided data with a much higher density in the regions when compared to EPIC-array (~2.74 million CpGs with at least 10X coverage vs ~752 K CpGs, respectively). Approximately 398 K CpGs were common and measured across the two platforms in every sample. Overall, there was high concordance in methylation levels between the two platforms (Pearson correlation r = 0.98, P < 0.0001). However, we observed that TruSeq EPIC measurements provided a wider dynamic range and likely a higher quantitative sensitivity for CpGs that were either hypo- or hyper-methylated (β close to 0 or 1, respectively). In addition, when comparing different breast tissue types TruSeq EPIC identified more differentially methylated CpGs than EPIC-array, not only out of additional sites interrogated by TruSeq EPIC alone, but also out of common sites interrogated by both platforms. Our results suggest that both platforms show high reproducibility and reliability in genome-wide DNA methylation profiling, while TruSeq EPIC had a significant improvement over EPIC-array regarding genomic resolution and coverage. The wider dynamic range and likely higher precision of the estimates by the TruSeq EPIC may lead to the identification of novel differentially methylated markers that are associated with disease risk.
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Affiliation(s)
- Nan Lin
- The Cancer Prevention and Control Research Program, University of Kentucky Markey Cancer Center, Lexington, KY, USA
| | - Jinpeng Liu
- The Cancer Prevention and Control Research Program, University of Kentucky Markey Cancer Center, Lexington, KY, USA
| | - James Castle
- The Cancer Prevention and Control Research Program, University of Kentucky Markey Cancer Center, Lexington, KY, USA
| | - Jun Wan
- Department of Medical & Molecular Genetics, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Aditi Shendre
- Department of Biomedical Informatics, The Ohio State University, Columbus, OH, USA
| | - Yunlong Liu
- Department of Medical & Molecular Genetics, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Chi Wang
- The Cancer Prevention and Control Research Program, University of Kentucky Markey Cancer Center, Lexington, KY, USA
| | - Chunyan He
- The Cancer Prevention and Control Research Program, University of Kentucky Markey Cancer Center, Lexington, KY, USA.,Department of Internal Medicine, Division of Medical Oncology, College of Medicine, University of Kentucky, Lexington, KY, USA
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18
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Gatev E, Gladish N, Mostafavi S, Kobor MS. CoMeBack: DNA methylation array data analysis for co-methylated regions. Bioinformatics 2020; 36:2675-2683. [DOI: 10.1093/bioinformatics/btaa049] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2019] [Revised: 12/23/2019] [Accepted: 01/20/2020] [Indexed: 01/06/2023] Open
Abstract
Abstract
Motivation
High-dimensional DNA methylation (DNAm) array coverage, while sparse in the context of the entire DNA methylome, still constitutes a very large number of CpG probes. The ensuing multiple-test corrections affect the statistical power to detect associations, likely contributing to prevalent limited reproducibility. Array probes measuring proximal CpG sites often have correlated levels of DNAm that may not only be biologically meaningful but also imply statistical dependence and redundancy. New methods that account for such correlations between adjacent probes may enable improved specificity, discovery and interpretation of statistical associations in DNAm array data.
Results
We developed a method named Co-Methylation with genomic CpG Background (CoMeBack) that estimates DNA co-methylation, defined as proximal CpG probes with correlated DNAm across individuals. CoMeBack outputs co-methylated regions (CMRs), spanning sets of array probes constructed based on all genomic CpG sites, including those not measured on the array, and without any phenotypic variable inputs. This approach can reduce the multiple-test correction burden, while enhancing the discovery and specificity of statistical associations. We constructed and validated CMRs in whole blood, using publicly available Illumina Infinium 450 K array data from over 5000 individuals. These CMRs were enriched for enhancer chromatin states, and binding site motifs for several transcription factors involved in blood physiology. We illustrated how CMR-based epigenome-wide association studies can improve discovery and reduce false positives for associations with chronological age.
Availability and implementation
https://bitbucket.org/flopflip/comeback.
Supplementary information
Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Evan Gatev
- Graduate Program in Bioinformatics, University of British Columbia, Vancouver, BC V5T 4S6, Canada
- Department of Finance, Beedie School of Business, Simon Fraser University, Burnaby, BC V5A 1S6, Canada
- BC Children’s Hospital Research Institute, Vancouver, BC V5Z 4H4, Canada
- Centre for Molecular Medicine and Therapeutics, Vancouver, BC V5Z 4H4, Canada
| | - Nicole Gladish
- BC Children’s Hospital Research Institute, Vancouver, BC V5Z 4H4, Canada
- Centre for Molecular Medicine and Therapeutics, Vancouver, BC V5Z 4H4, Canada
- Department of Medical Genetics
| | - Sara Mostafavi
- BC Children’s Hospital Research Institute, Vancouver, BC V5Z 4H4, Canada
- Centre for Molecular Medicine and Therapeutics, Vancouver, BC V5Z 4H4, Canada
- Department of Medical Genetics
- Department of Statistics, University of British Columbia, Vancouver, BC V6T 1Z4, Canada
| | - Michael S Kobor
- BC Children’s Hospital Research Institute, Vancouver, BC V5Z 4H4, Canada
- Centre for Molecular Medicine and Therapeutics, Vancouver, BC V5Z 4H4, Canada
- Department of Medical Genetics
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19
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Bazov I, Sarkisyan D, Kononenko O, Watanabe H, Taqi MM, Stålhandske L, Verbeek DS, Mulder J, Rajkowska G, Sheedy D, Kril J, Sun X, Syvänen AC, Yakovleva T, Bakalkin G. Neuronal Expression of Opioid Gene is Controlled by Dual Epigenetic and Transcriptional Mechanism in Human Brain. Cereb Cortex 2019; 28:3129-3142. [PMID: 28968778 DOI: 10.1093/cercor/bhx181] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2017] [Indexed: 12/13/2022] Open
Abstract
Molecular mechanisms that define patterns of neuropeptide expression are essential for the formation and rewiring of neural circuits. The prodynorphin gene (PDYN) gives rise to dynorphin opioid peptides mediating depression and substance dependence. We here demonstrated that PDYN is expressed in neurons in human dorsolateral prefrontal cortex (dlPFC), and identified neuronal differentially methylated region in PDYN locus framed by CCCTC-binding factor binding sites. A short, nucleosome size human-specific promoter CpG island (CGI), a core of this region may serve as a regulatory module, which is hypomethylated in neurons, enriched in 5-hydroxymethylcytosine, and targeted by USF2, a methylation-sensitive E-box transcription factor (TF). USF2 activates PDYN transcription in model systems, and binds to nonmethylated CGI in dlPFC. USF2 and PDYN expression is correlated, and USF2 and PDYN proteins are co-localized in dlPFC. Segregation of activatory TF and repressive CGI methylation may ensure contrasting PDYN expression in neurons and glia in human brain.
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Affiliation(s)
- Igor Bazov
- Division of Biological Research on Drug Dependence, Department of Pharmaceutical Biosciences, Uppsala University, Uppsala, Sweden
| | - Daniil Sarkisyan
- Division of Biological Research on Drug Dependence, Department of Pharmaceutical Biosciences, Uppsala University, Uppsala, Sweden
| | - Olga Kononenko
- Division of Biological Research on Drug Dependence, Department of Pharmaceutical Biosciences, Uppsala University, Uppsala, Sweden
| | - Hiroyuki Watanabe
- Division of Biological Research on Drug Dependence, Department of Pharmaceutical Biosciences, Uppsala University, Uppsala, Sweden
| | - Mumtaz Malik Taqi
- Division of Biological Research on Drug Dependence, Department of Pharmaceutical Biosciences, Uppsala University, Uppsala, Sweden.,Faculty of Medicine, NORMENT, University of Oslo, Oslo, Norway
| | - Lada Stålhandske
- Division of Biological Research on Drug Dependence, Department of Pharmaceutical Biosciences, Uppsala University, Uppsala, Sweden
| | - Dineke S Verbeek
- Department of Genetics, University Medical Center Groningen, University of Groningen, 9700 RB Groningen, The Netherlands
| | - Jan Mulder
- Department of Neuroscience, Science for Life Laboratory, Karolinska Institute, Stockholm, Sweden
| | - Grazyna Rajkowska
- Department of Psychiatry and Human Behavior, University of Mississippi Medical Center, Jackson, MS, USA
| | - Donna Sheedy
- Discipline of Pathology, Sydney Medical School, University of Sydney, Sydney NSW, Australia
| | - Jillian Kril
- Discipline of Pathology, Sydney Medical School, University of Sydney, Sydney NSW, Australia
| | - Xueguang Sun
- Zymo Research Corporation, 17062 Murphy Avenue, Irvine, CA, USA.,Division of Human Genetics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
| | - Ann-Christine Syvänen
- Department of Medical Sciences, Molecular Medicine and Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Tatiana Yakovleva
- Division of Biological Research on Drug Dependence, Department of Pharmaceutical Biosciences, Uppsala University, Uppsala, Sweden
| | - Georgy Bakalkin
- Division of Biological Research on Drug Dependence, Department of Pharmaceutical Biosciences, Uppsala University, Uppsala, Sweden
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20
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Gunasekara CJ, Scott CA, Laritsky E, Baker MS, MacKay H, Duryea JD, Kessler NJ, Hellenthal G, Wood AC, Hodges KR, Gandhi M, Hair AB, Silver MJ, Moore SE, Prentice AM, Li Y, Chen R, Coarfa C, Waterland RA. A genomic atlas of systemic interindividual epigenetic variation in humans. Genome Biol 2019; 20:105. [PMID: 31155008 PMCID: PMC6545702 DOI: 10.1186/s13059-019-1708-1] [Citation(s) in RCA: 53] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2019] [Accepted: 05/06/2019] [Indexed: 01/05/2023] Open
Abstract
BACKGROUND DNA methylation is thought to be an important determinant of human phenotypic variation, but its inherent cell type specificity has impeded progress on this question. At exceptional genomic regions, interindividual variation in DNA methylation occurs systemically. Like genetic variants, systemic interindividual epigenetic variants are stable, can influence phenotype, and can be assessed in any easily biopsiable DNA sample. We describe an unbiased screen for human genomic regions at which interindividual variation in DNA methylation is not tissue-specific. RESULTS For each of 10 donors from the NIH Genotype-Tissue Expression (GTEx) program, CpG methylation is measured by deep whole-genome bisulfite sequencing of genomic DNA from tissues representing the three germ layer lineages: thyroid (endoderm), heart (mesoderm), and brain (ectoderm). We develop a computational algorithm to identify genomic regions at which interindividual variation in DNA methylation is consistent across all three lineages. This approach identifies 9926 correlated regions of systemic interindividual variation (CoRSIVs). These regions, comprising just 0.1% of the human genome, are inter-correlated over long genomic distances, associated with transposable elements and subtelomeric regions, conserved across diverse human ethnic groups, sensitive to periconceptional environment, and associated with genes implicated in a broad range of human disorders and phenotypes. CoRSIV methylation in one tissue can predict expression of associated genes in other tissues. CONCLUSIONS In addition to charting a previously unexplored molecular level of human individuality, this atlas of human CoRSIVs provides a resource for future population-based investigations into how interindividual epigenetic variation modulates risk of disease.
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Affiliation(s)
- Chathura J Gunasekara
- USDA/ARS Children's Nutrition Research Center, Department of Pediatrics, Baylor College of Medicine, Houston, TX, USA
| | - C Anthony Scott
- USDA/ARS Children's Nutrition Research Center, Department of Pediatrics, Baylor College of Medicine, Houston, TX, USA
| | - Eleonora Laritsky
- USDA/ARS Children's Nutrition Research Center, Department of Pediatrics, Baylor College of Medicine, Houston, TX, USA
| | - Maria S Baker
- USDA/ARS Children's Nutrition Research Center, Department of Pediatrics, Baylor College of Medicine, Houston, TX, USA
| | - Harry MacKay
- USDA/ARS Children's Nutrition Research Center, Department of Pediatrics, Baylor College of Medicine, Houston, TX, USA
| | - Jack D Duryea
- USDA/ARS Children's Nutrition Research Center, Department of Pediatrics, Baylor College of Medicine, Houston, TX, USA
| | - Noah J Kessler
- MRC Unit The Gambia at London School of Hygiene and Tropical Medicine, Keneba, The Gambia
- Department of Women and Children's Health, King's College London, London, UK
| | - Garrett Hellenthal
- Department of Genetics, Evolution and Environment, UCL Genetics Institute, University College London, London, WC1E 6BT, UK
| | - Alexis C Wood
- USDA/ARS Children's Nutrition Research Center, Department of Pediatrics, Baylor College of Medicine, Houston, TX, USA
| | - Kelly R Hodges
- Department of Obstetrics and Gynecology, Baylor College of Medicine, Houston, TX, USA
| | - Manisha Gandhi
- Department of Obstetrics and Gynecology, Baylor College of Medicine, Houston, TX, USA
| | - Amy B Hair
- Department of Pediatrics - Neonatology, Baylor College of Medicine, Houston, TX, USA
| | - Matt J Silver
- MRC Unit The Gambia at London School of Hygiene and Tropical Medicine, Keneba, The Gambia
| | - Sophie E Moore
- MRC Unit The Gambia at London School of Hygiene and Tropical Medicine, Keneba, The Gambia
- Department of Women and Children's Health, King's College London, London, UK
| | - Andrew M Prentice
- MRC Unit The Gambia at London School of Hygiene and Tropical Medicine, Keneba, The Gambia
| | - Yumei Li
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Rui Chen
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Cristian Coarfa
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX, USA.
| | - Robert A Waterland
- USDA/ARS Children's Nutrition Research Center, Department of Pediatrics, Baylor College of Medicine, Houston, TX, USA.
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA.
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21
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Shimada M, Miyagawa T, Toyoda H, Tokunaga K, Honda M. Epigenome-wide association study of DNA methylation in narcolepsy: an integrated genetic and epigenetic approach. Sleep 2019; 41:4841708. [PMID: 29425374 DOI: 10.1093/sleep/zsy019] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Narcolepsy with cataplexy, which is a hypersomnia characterized by excessive daytime sleepiness and cataplexy, is a multifactorial disease caused by both genetic and environmental factors. Several genetic factors including HLA-DQB1*06:02 have been identified; however, the disease etiology is still unclear. Epigenetic modifications, such as DNA methylation, have been suggested to play an important role in the pathogenesis of complex diseases. Here, we examined DNA methylation profiles of blood samples from narcolepsy and healthy control individuals and performed an epigenome-wide association study (EWAS) to investigate methylation loci associated with narcolepsy. Moreover, data from the EWAS and a previously performed narcolepsy genome-wide association study were integrated to search for methylation loci with causal links to the disease. We found that (1) genes annotated to the top-ranked differentially methylated positions (DMPs) in narcolepsy were associated with pathways of hormone secretion and monocarboxylic acid metabolism. (2) Top-ranked narcolepsy-associated DMPs were significantly more abundant in non-CpG island regions and more than 95 per cent of such sites were hypomethylated in narcolepsy patients. (3) The integrative analysis identified the CCR3 region where both a single methylation site and multiple single-nucleotide polymorphisms were found to be associated with the disease as a candidate region responsible for narcolepsy. The findings of this study suggest the importance of future replication studies, using methylation technologies with wider genome coverage and/or larger number of samples, to confirm and expand on these results.
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Affiliation(s)
- Mihoko Shimada
- Sleep Disorders Project, Department of Psychiatry and Behavioral Sciences, Tokyo Metropolitan Institute of Medical Science, Tokyo, Japan.,Department of Human Genetics, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Taku Miyagawa
- Sleep Disorders Project, Department of Psychiatry and Behavioral Sciences, Tokyo Metropolitan Institute of Medical Science, Tokyo, Japan.,Department of Human Genetics, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Hiromi Toyoda
- Sleep Disorders Project, Department of Psychiatry and Behavioral Sciences, Tokyo Metropolitan Institute of Medical Science, Tokyo, Japan
| | - Katsushi Tokunaga
- Department of Human Genetics, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Makoto Honda
- Sleep Disorders Project, Department of Psychiatry and Behavioral Sciences, Tokyo Metropolitan Institute of Medical Science, Tokyo, Japan.,Seiwa Hospital, Neuropsychiatric Research Institute, Tokyo, Japan
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22
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Ewing E, Kular L, Fernandes SJ, Karathanasis N, Lagani V, Ruhrmann S, Tsamardinos I, Tegner J, Piehl F, Gomez-Cabrero D, Jagodic M. Combining evidence from four immune cell types identifies DNA methylation patterns that implicate functionally distinct pathways during Multiple Sclerosis progression. EBioMedicine 2019; 43:411-423. [PMID: 31053557 PMCID: PMC6558224 DOI: 10.1016/j.ebiom.2019.04.042] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2019] [Revised: 04/15/2019] [Accepted: 04/23/2019] [Indexed: 12/22/2022] Open
Abstract
Background Multiple Sclerosis (MS) is a chronic inflammatory disease and a leading cause of progressive neurological disability among young adults. DNA methylation, which intersects genes and environment to control cellular functions on a molecular level, may provide insights into MS pathogenesis. Methods We measured DNA methylation in CD4+ T cells (n = 31), CD8+ T cells (n = 28), CD14+ monocytes (n = 35) and CD19+ B cells (n = 27) from relapsing-remitting (RRMS), secondary progressive (SPMS) patients and healthy controls (HC) using Infinium HumanMethylation450 arrays. Monocyte (n = 25) and whole blood (n = 275) cohorts were used for validations. Findings B cells from MS patients displayed most significant differentially methylated positions (DMPs), followed by monocytes, while only few DMPs were detected in T cells. We implemented a non-parametric combination framework (omicsNPC) to increase discovery power by combining evidence from all four cell types. Identified shared DMPs co-localized at MS risk loci and clustered into distinct groups. Functional exploration of changes discriminating RRMS and SPMS from HC implicated lymphocyte signaling, T cell activation and migration. SPMS-specific changes, on the other hand, implicated myeloid cell functions and metabolism. Interestingly, neuronal and neurodegenerative genes and pathways were also specifically enriched in the SPMS cluster. Interpretation We utilized a statistical framework (omicsNPC) that combines multiple layers of evidence to identify DNA methylation changes that provide new insights into MS pathogenesis in general, and disease progression, in particular. Fund This work was supported by the Swedish Research Council, Stockholm County Council, AstraZeneca, European Research Council, Karolinska Institutet and Margaretha af Ugglas Foundation.
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Affiliation(s)
- Ewoud Ewing
- Department of Clinical Neuroscience, Center for Molecular Medicine, Karolinska Institutet, Stockholm 17177, Sweden
| | - Lara Kular
- Department of Clinical Neuroscience, Center for Molecular Medicine, Karolinska Institutet, Stockholm 17177, Sweden
| | - Sunjay J Fernandes
- Unit of Computational Medicine, Department of Medicine, Solna, Center for Molecular Medicine, Karolinska Institutet, Stockholm, 17177, Sweden; Science for Life Laboratory, Solna, Sweden
| | - Nestoras Karathanasis
- Institute of Computer Science, Foundation for Research and Technology-Hellas, Heraklion, Greece; Computational Medicine Center, Thomas Jefferson University, 1020 Locust Street, Philadelphia, PA 19107, USA
| | - Vincenzo Lagani
- Institute of Chemical Biology, Ilia State University, Tbilisi, Georgia; Gnosis Data Analysis PC, Heraklion, Greece
| | - Sabrina Ruhrmann
- Department of Clinical Neuroscience, Center for Molecular Medicine, Karolinska Institutet, Stockholm 17177, Sweden
| | - Ioannis Tsamardinos
- Gnosis Data Analysis PC, Heraklion, Greece; Department of Computer Science, University of Crete, Heraklion, Greece
| | - Jesper Tegner
- Unit of Computational Medicine, Department of Medicine, Solna, Center for Molecular Medicine, Karolinska Institutet, Stockholm, 17177, Sweden; Biological and Environmental Sciences and Engineering Division, Computer, Electrical and Mathematical Sciences and Engineering Division, King Abdullah University of Science and Technology, Saudi Arabia; Science for Life Laboratory, Solna, Sweden
| | - Fredrik Piehl
- Department of Clinical Neuroscience, Center for Molecular Medicine, Karolinska Institutet, Stockholm 17177, Sweden; Center for Neurology, Academic Specialist Clinic, Stockholm Health Services, Stockholm, Sweden
| | - David Gomez-Cabrero
- Unit of Computational Medicine, Department of Medicine, Solna, Center for Molecular Medicine, Karolinska Institutet, Stockholm, 17177, Sweden; Translational Bioinformatics Unit, Navarrabiomed, Complejo Hospitalario de Navarra (CHN), Universidad Pública de Navarra (UPNA), IdiSNA, Pamplona, Spain; Centre for Host Microbiome Interactions, Faculty of Dentistry, Oral & Craniofacial Sciences, King's College London, UK
| | - Maja Jagodic
- Department of Clinical Neuroscience, Center for Molecular Medicine, Karolinska Institutet, Stockholm 17177, Sweden.
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23
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Karlsson L, Barbaro M, Ewing E, Gomez-Cabrero D, Lajic S. Epigenetic Alterations Associated With Early Prenatal Dexamethasone Treatment. J Endocr Soc 2019; 3:250-263. [PMID: 30623163 PMCID: PMC6320242 DOI: 10.1210/js.2018-00377] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/19/2018] [Accepted: 12/07/2018] [Indexed: 11/19/2022] Open
Abstract
Prenatal treatment with dexamethasone (DEX) reduces virilization in girls with congenital adrenal hyperplasia (CAH). It has potential short- and long-term risks and has been shown to affect cognitive functions. Here, we investigate whether epigenetic modification of DNA during early developmental stages may be a key mediating mechanism by which prenatal DEX treatment could result in poor outcomes in the offspring. We analyzed genome-wide CD4+ T cell DNA methylation, assessed using the Infinium HumanMethylation450 BeadChip array in 29 individuals (mean age = 16.4 ± 5.9 years) at risk for CAH and treated with DEX during the first trimester and 37 population controls (mean age = 17.0 years, SD = 6.1 years). We identified 9672 differentially methylated probes (DMPs) associated with DEX treatment and 7393 DMPs associated with a DEX × sex interaction. DMPs were enriched in intergenic regions located near epigenetic markers for active enhancers. Functional enrichment of DMPs was mostly associated with immune functioning and inflammation but also with nonimmune-related functions. DEX-associated DMPs enriched near single nucleotide polymorphisms (SNPs) associated with inflammatory bowel disease, and DEX × sex-associated DMPs enriched near SNPs associated with asthma. DMPs in genes involved in the regulation and maintenance of methylation and steroidogenesis were identified as well. Methylation in the BDNF, FKBP5, and NR3C1 genes were associated with the performance on several Wechsler Adult Intelligence Scale-Fourth Edition subscales. In conclusion, this study indicates that DNA methylation is altered after prenatal DEX treatment. This finding may have implications for the future health of the exposed individual.
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Affiliation(s)
- Leif Karlsson
- Department of Women’s and Children’s Health, Karolinska Institutet, Paediatric Endocrinology Unit (Q2:08), Karolinska University Hospital, Stockholm, Sweden
| | - Michela Barbaro
- Department of Molecular Medicine and Surgery, Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden
- Center for Inherited Metabolic Diseases (CMMS L7:05), Karolinska University Hospital, Stockholm, Sweden
| | - Ewoud Ewing
- Department of Clinical Neuroscience, Centre for Molecular Medicine, Karolinska Institutet (L8:05), Karolinska University Hospital, Stockholm, Sweden
| | - David Gomez-Cabrero
- Unit for Computational Medicine, Karolinska Institutet (L8:05), Karolinska University Hospital, Stockholm, Sweden
- Mucosal and Salivary Biology Division, King’s College, London Dental Institute, London, United Kingdom
- Translational Bioinformatics Unit, NavarraBiomed, Complejo Hospitalario de Navarra (CHN), Universidad Pública de Navarra (UPNA), IdiSNA, Pamplona, Navarra, Spain
| | - Svetlana Lajic
- Department of Women’s and Children’s Health, Karolinska Institutet, Paediatric Endocrinology Unit (Q2:08), Karolinska University Hospital, Stockholm, Sweden
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24
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Parmar P, Lowry E, Cugliari G, Suderman M, Wilson R, Karhunen V, Andrew T, Wiklund P, Wielscher M, Guarrera S, Teumer A, Lehne B, Milani L, de Klein N, Mishra PP, Melton PE, Mandaviya PR, Kasela S, Nano J, Zhang W, Zhang Y, Uitterlinden AG, Peters A, Schöttker B, Gieger C, Anderson D, Boomsma DI, Grabe HJ, Panico S, Veldink JH, van Meurs JBJ, van den Berg L, Beilin LJ, Franke L, Loh M, van Greevenbroek MMJ, Nauck M, Kähönen M, Hurme MA, Raitakari OT, Franco OH, Slagboom PE, van der Harst P, Kunze S, Felix SB, Zhang T, Chen W, Mori TA, Bonnefond A, Heijmans BT, Muka T, Kooner JS, Fischer K, Waldenberger M, Froguel P, Huang RC, Lehtimäki T, Rathmann W, Relton CL, Matullo G, Brenner H, Verweij N, Li S, Chambers JC, Järvelin MR, Sebert S. Association of maternal prenatal smoking GFI1-locus and cardio-metabolic phenotypes in 18,212 adults. EBioMedicine 2018; 38:206-216. [PMID: 30442561 PMCID: PMC6306313 DOI: 10.1016/j.ebiom.2018.10.066] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2018] [Revised: 10/26/2018] [Accepted: 10/26/2018] [Indexed: 01/06/2023] Open
Abstract
BACKGROUND DNA methylation at the GFI1-locus has been repeatedly associated with exposure to smoking from the foetal period onwards. We explored whether DNA methylation may be a mechanism that links exposure to maternal prenatal smoking with offspring's adult cardio-metabolic health. METHODS We meta-analysed the association between DNA methylation at GFI1-locus with maternal prenatal smoking, adult own smoking, and cardio-metabolic phenotypes in 22 population-based studies from Europe, Australia, and USA (n = 18,212). DNA methylation at the GFI1-locus was measured in whole-blood. Multivariable regression models were fitted to examine its association with exposure to prenatal and own adult smoking. DNA methylation levels were analysed in relation to body mass index (BMI), waist circumference (WC), fasting glucose (FG), high-density lipoprotein cholesterol (HDL-C), triglycerides (TG), diastolic, and systolic blood pressure (BP). FINDINGS Lower DNA methylation at three out of eight GFI1-CpGs was associated with exposure to maternal prenatal smoking, whereas, all eight CpGs were associated with adult own smoking. Lower DNA methylation at cg14179389, the strongest maternal prenatal smoking locus, was associated with increased WC and BP when adjusted for sex, age, and adult smoking with Bonferroni-corrected P < 0·012. In contrast, lower DNA methylation at cg09935388, the strongest adult own smoking locus, was associated with decreased BMI, WC, and BP (adjusted 1 × 10-7 < P < 0.01). Similarly, lower DNA methylation at cg12876356, cg18316974, cg09662411, and cg18146737 was associated with decreased BMI and WC (5 × 10-8 < P < 0.001). Lower DNA methylation at all the CpGs was consistently associated with higher TG levels. INTERPRETATION Epigenetic changes at the GFI1 were linked to smoking exposure in-utero/in-adulthood and robustly associated with cardio-metabolic risk factors. FUND: European Union's Horizon 2020 research and innovation programme under grant agreement no. 633595 DynaHEALTH.
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Affiliation(s)
- Priyanka Parmar
- Center for Life Course Health Research, University of Oulu, Oulu, Finland; Biocenter Oulu, University of Oulu, Oulu, Finland
| | - Estelle Lowry
- Center for Life Course Health Research, University of Oulu, Oulu, Finland; Biocenter Oulu, University of Oulu, Oulu, Finland
| | - Giovanni Cugliari
- Department of Medical Sciences, University of Turin, Turin, Italy; Italian Institute for Genomic Medicine, IIGM, Turin, Italy
| | - Matthew Suderman
- MRC Integrative Epidemiology Unit, Population Health Sciences, Bristol Medical School, University of Bristol, UK
| | - Rory Wilson
- Research Unit of Molecular Epidemiology, Helmholtz Zentrum München, German Research Centre for Environmental Health, Neuherberg, Bavaria, Germany; Helmholtz Zentrum München, German Research Centre for Environmental Health, Institute of Epidemiology, Neuherberg, Bavaria, Germany
| | - Ville Karhunen
- Department of Epidemiology and Biostatistics, MRC-PHE Centre for Environment and Health, School of Public Health, Imperial College London, London
| | - Toby Andrew
- Genomics of Common Disease, Department of Medicine, Imperial College London, London, UK
| | - Petri Wiklund
- Center for Life Course Health Research, University of Oulu, Oulu, Finland; Department of Epidemiology and Biostatistics, MRC-PHE Centre for Environment and Health, School of Public Health, Imperial College London, London; Department of Health Sciences, University of Jyväskylä, Jyväskylä, Finland
| | - Matthias Wielscher
- Department of Epidemiology and Biostatistics, MRC-PHE Centre for Environment and Health, School of Public Health, Imperial College London, London
| | - Simonetta Guarrera
- Department of Medical Sciences, University of Turin, Turin, Italy; Italian Institute for Genomic Medicine, IIGM, Turin, Italy
| | - Alexander Teumer
- Department of Internal Medicine B, University Medicine Greifswald, Greifswald, Germany; Partner Site Greifswald, DZHK (German Centre for Cardiovascular Research), Greifswald, Germany
| | - Benjamin Lehne
- Department of Epidemiology and Biostatistics, MRC-PHE Centre for Environment and Health, School of Public Health, Imperial College London, London
| | - Lili Milani
- Estonian Genome Centre, Institute of Genomics, University of Tartu, Tartu, Estonia; Science for Life Laboratory, Department of Medical Sciences, Uppsala University, Sweden
| | - Niek de Klein
- Department of Genetics, University Medical Centre Groningen, University of Groningen, Groningen, The Netherlands
| | - Pashupati P Mishra
- Department of Clinical Chemistry, Fimlab Laboratories, Tampere, Finland; Department of Clinical Chemistry, Finnish Cardiovascular Research Centre - Tampere, Faculty of Medicine and Life Sciences, University of Tampere, Tampere, Finland
| | - Phillip E Melton
- School of Pharmacy and Biomedical Sciences, Curtin University, Bentley, Australia; Curtin UWA Centre for Genetic Origins of Health and Disease, School of Biomedical Sciences, The University of Western Australia, Crawley, Australia
| | - Pooja R Mandaviya
- Department of Internal Medicine, Erasmus University Medical Centre, Rotterdam, The Netherlands
| | - Silva Kasela
- Estonian Genome Centre, Institute of Genomics, University of Tartu, Tartu, Estonia
| | - Jana Nano
- Helmholtz Zentrum München, German Research Centre for Environmental Health, Institute of Epidemiology, Neuherberg, Bavaria, Germany; Department of Epidemiology, Erasmus University Medical Centre, Rotterdam, The Netherlands
| | - Weihua Zhang
- Department of Epidemiology and Biostatistics, MRC-PHE Centre for Environment and Health, School of Public Health, Imperial College London, London; Department of Cardiology, Ealing Hospital, North West Healthcare NHS Trust, London, UK
| | - Yan Zhang
- Division of Clinical Epidemiology and Aging Research, German Cancer Research Centre (DKFZ), Im Neuenheimer Feld, Heidelberg, Germany
| | - Andre G Uitterlinden
- Department of Internal Medicine, Erasmus University Medical Centre, Rotterdam, The Netherlands; Department of Epidemiology, Erasmus University Medical Centre, Rotterdam, The Netherlands
| | - Annette Peters
- Research Unit of Molecular Epidemiology, Helmholtz Zentrum München, German Research Centre for Environmental Health, Neuherberg, Bavaria, Germany; Helmholtz Zentrum München, German Research Centre for Environmental Health, Institute of Epidemiology, Neuherberg, Bavaria, Germany; German Centre for Cardiovascular Research (DZHK), Partner Site Munich Heart Alliance, Munich, Germany
| | - Ben Schöttker
- Division of Clinical Epidemiology and Aging Research, German Cancer Research Centre (DKFZ), Im Neuenheimer Feld, Heidelberg, Germany; Network Aging Research, University of Heidelberg, Bergheimer Straße, Heidelberg, Germany
| | - Christian Gieger
- Research Unit of Molecular Epidemiology, Helmholtz Zentrum München, German Research Centre for Environmental Health, Neuherberg, Bavaria, Germany; Helmholtz Zentrum München, German Research Centre for Environmental Health, Institute of Epidemiology, Neuherberg, Bavaria, Germany; German Centre for Cardiovascular Research (DZHK), Partner Site Munich Heart Alliance, Munich, Germany
| | - Denise Anderson
- Telethon Kids Institute, University of Western Australia, Perth, Australia
| | - Dorret I Boomsma
- Department of Biological Psychology, School of Public Health, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
| | - Hans J Grabe
- Department of Psychiatry and Psychotherapy, University Medicine Greifswald, Greifswald, Germany; German Centre for Neurodegenerative Diseases DZNE, Site Rostock/Greifswald, Greifswald, Germany
| | - Salvatore Panico
- Department of Clinical Medicine and Surgery, Federico II University, Naples, Italy
| | - Jan H Veldink
- Department of Neurology, Brain Centre Rudolf Magnus, University Medical Centre Utrecht, Utrecht, The Netherlands
| | - Joyce B J van Meurs
- Department of Internal Medicine, Erasmus University Medical Centre, Rotterdam, The Netherlands
| | - Leonard van den Berg
- Department of Neurology, Brain Centre Rudolf Magnus, University Medical Centre Utrecht, Utrecht, The Netherlands
| | | | - Lude Franke
- Department of Genetics, University Medical Centre Groningen, University of Groningen, Groningen, The Netherlands
| | - Marie Loh
- Department of Epidemiology and Biostatistics, MRC-PHE Centre for Environment and Health, School of Public Health, Imperial College London, London; Translational Laboratory in Genetic Medicine (TLGM), Agency for Science, Technology and Research (A*STAR), 8A Biomedical Grove, Immunos, Level 5, Singapore, Singapore; Institute of Health Sciences, University of Oulu, Finland
| | - Marleen M J van Greevenbroek
- Department of Internal Medicine and School for Cardiovascular Diseases (CARIM), Maastricht University Medical Centre, Maastricht, The Netherlands
| | - Matthias Nauck
- Partner Site Greifswald, DZHK (German Centre for Cardiovascular Research), Greifswald, Germany; Institute of Clinical Chemistry and Laboratory Medicine, University Medicine Greifswald, Greifswald, Germany
| | - Mika Kähönen
- Department of Clinical Physiology, Tampere University Hospital, Tampere, Finland; Department of Clinical Physiology, Finnish Cardiovascular Research Centre - Tampere, Faculty of Medicine and Life Sciences, University of Tampere, Tampere, Finland
| | - Mikko A Hurme
- Department of Microbiology and Immunology, Faculty of Medicine and Life Sciences, University of Tampere, Tampere, Finland
| | - Olli T Raitakari
- Department of Clinical Physiology and Nuclear Medicine, Turku University Hospital, Turku, Finland; Research Centre of Applied and Preventive Cardiovascular Medicine, University of Turku, Turku, Finland
| | - Oscar H Franco
- Department of Epidemiology, Erasmus University Medical Centre, Rotterdam, The Netherlands
| | - P Eline Slagboom
- Molecular Epidemiology, Department of Biomedical Data Sciences, Leiden University Medical Centre, Leiden, The Netherlands
| | - Pim van der Harst
- Department of Genetics, University Medical Centre Groningen, University of Groningen, Groningen, The Netherlands; Department of Cardiology, University Medical Centre Groningen, University of Groningen, Groningen, The Netherlands; Durrer Centre for Cardiogenetic Research, ICIN - Netherlands Heart Institute, Utrecht, The Netherlands
| | - Sonja Kunze
- Research Unit of Molecular Epidemiology, Helmholtz Zentrum München, German Research Centre for Environmental Health, Neuherberg, Bavaria, Germany; Helmholtz Zentrum München, German Research Centre for Environmental Health, Institute of Epidemiology, Neuherberg, Bavaria, Germany
| | - Stephan B Felix
- Partner Site Greifswald, DZHK (German Centre for Cardiovascular Research), Greifswald, Germany
| | - Tao Zhang
- Department of Epidemiology, School of Public Health and Tropical Medicine, Tulane University, New Orleans, USA; Department of Biostatistics, School of Public Health, Shandong University, Jinan, China
| | - Wei Chen
- Department of Epidemiology, School of Public Health and Tropical Medicine, Tulane University, New Orleans, USA
| | - Trevor A Mori
- Medical School, University of Western Australia, Perth, Australia
| | - Amelie Bonnefond
- Genomics of Common Disease, Department of Medicine, Imperial College London, London, UK; European Genomic Institute for Diabetes (EGID), Institut Pasteur de Lille, University of Lille, CNRS UMR 8199, Lille, France
| | - Bastiaan T Heijmans
- Molecular Epidemiology, Department of Biomedical Data Sciences, Leiden University Medical Centre, Leiden, The Netherlands
| | - Taulant Muka
- Department of Epidemiology, Erasmus University Medical Centre, Rotterdam, The Netherlands
| | - Jaspal S Kooner
- Department of Cardiology, Ealing Hospital, North West Healthcare NHS Trust, London, UK; Imperial College Healthcare NHS Trust, London, UK; Department of Epidemiology and Biostatistics, MRC-PHE Centre for Environment and Health, School of Public Health, Imperial College London, London; Imperial College London, National Heart and Lung Institute, London, UK
| | - Krista Fischer
- Estonian Genome Centre, Institute of Genomics, University of Tartu, Tartu, Estonia
| | - Melanie Waldenberger
- Research Unit of Molecular Epidemiology, Helmholtz Zentrum München, German Research Centre for Environmental Health, Neuherberg, Bavaria, Germany; Helmholtz Zentrum München, German Research Centre for Environmental Health, Institute of Epidemiology, Neuherberg, Bavaria, Germany; German Centre for Cardiovascular Research (DZHK), Partner Site Munich Heart Alliance, Munich, Germany
| | - Philippe Froguel
- Genomics of Common Disease, Department of Medicine, Imperial College London, London, UK; European Genomic Institute for Diabetes (EGID), Institut Pasteur de Lille, University of Lille, CNRS UMR 8199, Lille, France
| | - Rae-Chi Huang
- Telethon Kids Institute, University of Western Australia, Perth, Australia
| | - Terho Lehtimäki
- Department of Clinical Chemistry, Fimlab Laboratories, Tampere, Finland; Department of Clinical Chemistry, Finnish Cardiovascular Research Centre - Tampere, Faculty of Medicine and Life Sciences, University of Tampere, Tampere, Finland
| | - Wolfgang Rathmann
- Institute for Biometrics and Epidemiology, German Diabetes Centre, Leibniz Centre for Diabetes Research at Heinrich, Heine University, Düsseldorf, Germany
| | - Caroline L Relton
- MRC Integrative Epidemiology Unit, Population Health Sciences, Bristol Medical School, University of Bristol, UK
| | - Giuseppe Matullo
- Department of Medical Sciences, University of Turin, Turin, Italy; Italian Institute for Genomic Medicine, IIGM, Turin, Italy
| | - Hermann Brenner
- Division of Clinical Epidemiology and Aging Research, German Cancer Research Centre (DKFZ), Im Neuenheimer Feld, Heidelberg, Germany; Network Aging Research, University of Heidelberg, Bergheimer Straße, Heidelberg, Germany
| | - Niek Verweij
- Department of Cardiology, University Medical Centre Groningen, University of Groningen, Groningen, The Netherlands
| | - Shengxu Li
- Children's Hospitals and Clinics of Minnesota, Children's Minnesota Research Institute, Minneapolis, MN 55404, USA
| | - John C Chambers
- Department of Epidemiology and Biostatistics, MRC-PHE Centre for Environment and Health, School of Public Health, Imperial College London, London; Department of Cardiology, Ealing Hospital, North West Healthcare NHS Trust, London, UK; Imperial College Healthcare NHS Trust, London, UK; Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore, Singapore
| | - Marjo-Riitta Järvelin
- Center for Life Course Health Research, University of Oulu, Oulu, Finland; Biocenter Oulu, University of Oulu, Oulu, Finland; Department of Epidemiology and Biostatistics, MRC-PHE Centre for Environment and Health, School of Public Health, Imperial College London, London; Department of Life Sciences, College of Health and Life Sciences, Brunel University London, Uxbridge, UK.
| | - Sylvain Sebert
- Center for Life Course Health Research, University of Oulu, Oulu, Finland; Biocenter Oulu, University of Oulu, Oulu, Finland; Medical Research Centre (MRC) Oulu, Oulu University Hospital, University of Oulu, Oulu, Finland.
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25
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Hannon E, Gorrie-Stone TJ, Smart MC, Burrage J, Hughes A, Bao Y, Kumari M, Schalkwyk LC, Mill J. Leveraging DNA-Methylation Quantitative-Trait Loci to Characterize the Relationship between Methylomic Variation, Gene Expression, and Complex Traits. Am J Hum Genet 2018; 103:654-665. [PMID: 30401456 PMCID: PMC6217758 DOI: 10.1016/j.ajhg.2018.09.007] [Citation(s) in RCA: 101] [Impact Index Per Article: 16.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2018] [Accepted: 09/14/2018] [Indexed: 11/23/2022] Open
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. 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.
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Affiliation(s)
- Eilis Hannon
- University of Exeter Medical School, University of Exeter, Exeter EX2 5DW, United Kingdom
| | - Tyler J Gorrie-Stone
- School of Biological Sciences, University of Essex, Colchester, CO4 3SQ, United Kingdom
| | - Melissa C Smart
- Institute for Social and Economic Research, University of Essex, Colchester CO3 3LG, United Kingdom
| | - Joe Burrage
- University of Exeter Medical School, University of Exeter, Exeter EX2 5DW, United Kingdom
| | - Amanda Hughes
- Institute for Social and Economic Research, University of Essex, Colchester CO3 3LG, United Kingdom
| | - Yanchun Bao
- Institute for Social and Economic Research, University of Essex, Colchester CO3 3LG, United Kingdom
| | - Meena Kumari
- Institute for Social and Economic Research, University of Essex, Colchester CO3 3LG, United Kingdom
| | - Leonard C Schalkwyk
- School of Biological Sciences, University of Essex, Colchester, CO4 3SQ, United Kingdom
| | - Jonathan Mill
- University of Exeter Medical School, University of Exeter, Exeter EX2 5DW, United Kingdom.
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Zhao L, Liu D, Xu J, Wang Z, Chen Y, Lei C, Li Y, Liu G, Jiang Y. The framework for population epigenetic study. Brief Bioinform 2018; 19:89-100. [PMID: 27760738 DOI: 10.1093/bib/bbw098] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2016] [Indexed: 12/15/2022] Open
Abstract
At present, understanding of DNA methylation at the population level is still limited. Here, we first extended the classical framework of population genetics, such as single nucleotide polymorphism allele frequency, linkage disequilibrium (LD), LD block and haplotype, to epigenetics. Then, as an example, we compared the DNA methylation disequilibrium (MD) maps between HapMap CEU (Caucasian residents of European ancestry from Utah) population and YRI (Yoruba people from Ibadan) population (lymphoblastoid cell lines). We analyzed the differences and similarities between CEU and YRI from the following aspects: SMP (single methylation polymorphism) allele frequency, SMP allele association, MD, MD block and methylation haplotype (meplotype) frequency. The results showed that CEU and YRI had similar distribution of SMP allele frequency, and shared many MD block region. We believe that the framework of population genetics can be used in the population epigenetics. The population epigenetic framework also has potential prospects in the study of complex diseases, such as epigenome-wide association study.
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27
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Bomsztyk K, Denisenko O, Wang Y. DNA methylation yields epigenetic clues into the diabetic nephropathy of Pima Indians. Kidney Int 2018; 93:1272-1275. [PMID: 29792271 DOI: 10.1016/j.kint.2018.02.015] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2018] [Accepted: 02/16/2018] [Indexed: 12/22/2022]
Abstract
Environmental factors drive epigenetic programming. DNA methylation is the best studied modification transmitting epigenetic information. A study by Qiu et al. examined potential epigenetic roots for the decline of renal function in Pima Indians. A genomewide survey of blood leukocytes uncovered differentially methylated DNA sites in regulatory regions of genes associated with chronic kidney disease. This longitudinal study provides the first clues on epigenetic links between environmental factors and a high prevalence of diabetic kidney disease in Pima Indians.
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Affiliation(s)
- Karol Bomsztyk
- UW Medicine Lake Union, University of Washington, Seattle, Washington 98109, USA.
| | - Oleg Denisenko
- UW Medicine Lake Union, University of Washington, Seattle, Washington 98109, USA
| | - Yuliang Wang
- UW Medicine Lake Union, University of Washington, Seattle, Washington 98109, USA; Paul G. Allen School of Computer Science & Engineering, University of Washington, Washington, 98195, USA
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28
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DNA methylation as a mediator of HLA-DRB1*15:01 and a protective variant in multiple sclerosis. Nat Commun 2018; 9:2397. [PMID: 29921915 PMCID: PMC6008330 DOI: 10.1038/s41467-018-04732-5] [Citation(s) in RCA: 111] [Impact Index Per Article: 18.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2018] [Accepted: 05/17/2018] [Indexed: 01/28/2023] Open
Abstract
The human leukocyte antigen (HLA) haplotype DRB1*15:01 is the major risk factor for multiple sclerosis (MS). Here, we find that DRB1*15:01 is hypomethylated and predominantly expressed in monocytes among carriers of DRB1*15:01. A differentially methylated region (DMR) encompassing HLA-DRB1 exon 2 is particularly affected and displays methylation-sensitive regulatory properties in vitro. Causal inference and Mendelian randomization provide evidence that HLA variants mediate risk for MS via changes in the HLA-DRB1 DMR that modify HLA-DRB1 expression. Meta-analysis of 14,259 cases and 171,347 controls confirms that these variants confer risk from DRB1*15:01 and also identifies a protective variant (rs9267649, p < 3.32 × 10-8, odds ratio = 0.86) after conditioning for all MS-associated variants in the region. rs9267649 is associated with increased DNA methylation at the HLA-DRB1 DMR and reduced expression of HLA-DRB1, suggesting a modulation of the DRB1*15:01 effect. Our integrative approach provides insights into the molecular mechanisms of MS susceptibility and suggests putative therapeutic strategies targeting a methylation-mediated regulation of the major risk gene.
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29
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Affiliation(s)
- Andrew P Feinberg
- From the Department of Medicine, Johns Hopkins University School of Medicine, the Department of Biomedical Engineering, Whiting School of Engineering, and the Department of Mental Health, Johns Hopkins Bloomberg School of Public Health - all in Baltimore
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30
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Kular L, Kular S. Epigenetics applied to psychiatry: Clinical opportunities and future challenges. Psychiatry Clin Neurosci 2018; 72:195-211. [PMID: 29292553 DOI: 10.1111/pcn.12634] [Citation(s) in RCA: 39] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/02/2017] [Revised: 12/12/2017] [Accepted: 12/26/2017] [Indexed: 12/11/2022]
Abstract
Psychiatric disorders are clinically heterogeneous and debilitating chronic diseases resulting from a complex interplay between gene variants and environmental factors. Epigenetic processes, such as DNA methylation and histone posttranslational modifications, instruct the cell/tissue to correctly interpret external signals and adjust its functions accordingly. Given that epigenetic modifications are sensitive to environment, stable, and reversible, epigenetic studies in psychiatry could represent a promising approach to better understanding and treating disease. In the present review, we aim to discuss the clinical opportunities and challenges arising from the epigenetic research in psychiatry. Using selected examples, we first recapitulate key findings supporting the role of adverse life events, alone or in combination with genetic risk, in epigenetic programming of neuropsychiatric systems. Epigenetic studies further report encouraging findings about the use of methylation changes as diagnostic markers of disease phenotype and predictive tools of progression and response to treatment. Then we discuss the potential of using targeted epigenetic pharmacotherapy, combined with psychosocial interventions, for future personalized medicine for patients. Finally, we review the methodological limitations that could hinder interpretation of epigenetic data in psychiatry. They mainly arise from heterogeneity at the individual and tissue level and require future strategies in order to reinforce the biological relevance of epigenetic data and its translational use in psychiatry. Overall, we suggest that epigenetics could provide new insights into a more comprehensive interpretation of mental illness and might eventually improve the nosology, treatment, and prevention of psychiatric disorders.
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Affiliation(s)
- Lara Kular
- Department of Clinical Neuroscience, Center for Molecular Medicine, Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden
| | - Sonia Kular
- Adult Psychiatry Unit of Laval Secteur Est, Laval, France
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31
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Jenkinson G, Abante J, Feinberg AP, Goutsias J. An information-theoretic approach to the modeling and analysis of whole-genome bisulfite sequencing data. BMC Bioinformatics 2018. [PMID: 29514626 PMCID: PMC5842653 DOI: 10.1186/s12859-018-2086-5] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
BACKGROUND DNA methylation is a stable form of epigenetic memory used by cells to control gene expression. Whole genome bisulfite sequencing (WGBS) has emerged as a gold-standard experimental technique for studying DNA methylation by producing high resolution genome-wide methylation profiles. Statistical modeling and analysis is employed to computationally extract and quantify information from these profiles in an effort to identify regions of the genome that demonstrate crucial or aberrant epigenetic behavior. However, the performance of most currently available methods for methylation analysis is hampered by their inability to directly account for statistical dependencies between neighboring methylation sites, thus ignoring significant information available in WGBS reads. RESULTS We present a powerful information-theoretic approach for genome-wide modeling and analysis of WGBS data based on the 1D Ising model of statistical physics. This approach takes into account correlations in methylation by utilizing a joint probability model that encapsulates all information available in WGBS methylation reads and produces accurate results even when applied on single WGBS samples with low coverage. Using the Shannon entropy, our approach provides a rigorous quantification of methylation stochasticity in individual WGBS samples genome-wide. Furthermore, it utilizes the Jensen-Shannon distance to evaluate differences in methylation distributions between a test and a reference sample. Differential performance assessment using simulated and real human lung normal/cancer data demonstrate a clear superiority of our approach over DSS, a recently proposed method for WGBS data analysis. Critically, these results demonstrate that marginal methods become statistically invalid when correlations are present in the data. CONCLUSIONS This contribution demonstrates clear benefits and the necessity of modeling joint probability distributions of methylation using the 1D Ising model of statistical physics and of quantifying methylation stochasticity using concepts from information theory. By employing this methodology, substantial improvement of DNA methylation analysis can be achieved by effectively taking into account the massive amount of statistical information available in WGBS data, which is largely ignored by existing methods.
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Affiliation(s)
- Garrett Jenkinson
- Whitaker Biomedical Engineering Institute, Johns Hopkins University, Baltimore, MD, USA.,Center for Epigenetics, Johns Hopkins School of Medicine, Baltimore, MD, USA
| | - Jordi Abante
- Whitaker Biomedical Engineering Institute, Johns Hopkins University, Baltimore, MD, USA
| | - Andrew P Feinberg
- Center for Epigenetics, Johns Hopkins School of Medicine, Baltimore, MD, USA.,Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD, USA.,Department of Medicine, Johns Hopkins School of Medicine, Baltimore, MD, USA
| | - John Goutsias
- Whitaker Biomedical Engineering Institute, Johns Hopkins University, Baltimore, MD, USA.
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Pierce BL, Tong L, Argos M, Demanelis K, Jasmine F, Rakibuz-Zaman M, Sarwar G, Islam MT, Shahriar H, Islam T, Rahman M, Yunus M, Kibriya MG, Chen LS, Ahsan H. Co-occurring expression and methylation QTLs allow detection of common causal variants and shared biological mechanisms. Nat Commun 2018; 9:804. [PMID: 29476079 PMCID: PMC5824840 DOI: 10.1038/s41467-018-03209-9] [Citation(s) in RCA: 49] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2016] [Accepted: 01/26/2018] [Indexed: 12/21/2022] Open
Abstract
Inherited genetic variation affects local gene expression and DNA methylation in humans. Most expression quantitative trait loci (cis-eQTLs) occur at the same genomic location as a methylation QTL (cis-meQTL), suggesting a common causal variant and shared mechanism. Using DNA and RNA from peripheral blood of Bangladeshi individuals, here we use co-localization methods to identify eQTL-meQTL pairs likely to share a causal variant. We use partial correlation and mediation analyses to identify >400 of these pairs showing evidence of a causal relationship between expression and methylation (i.e., shared mechanism) with many additional pairs we are underpowered to detect. These co-localized pairs are enriched for SNPs showing opposite associations with expression and methylation, although many SNPs affect multiple CpGs in opposite directions. This work demonstrates the pervasiveness of co-regulated expression and methylation in the human genome. Applying this approach to other types of molecular QTLs can enhance our understanding of regulatory mechanisms.
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Affiliation(s)
- Brandon L Pierce
- Department of Public Health Sciences, The University of Chicago, Chicago, IL, 60637, USA.
- Department of Human Genetics, The University of Chicago, Chicago, IL, 60637, USA.
- Comprehensive Cancer Center, The University of Chicago, Chicago, IL, 60637, USA.
| | - Lin Tong
- Department of Public Health Sciences, The University of Chicago, Chicago, IL, 60637, USA
| | - Maria Argos
- Division of Epidemiology and Biostatistics, University of Illinois at Chicago, Chicago, IL, 60612, USA
| | - Kathryn Demanelis
- Department of Public Health Sciences, The University of Chicago, Chicago, IL, 60637, USA
| | - Farzana Jasmine
- Department of Public Health Sciences, The University of Chicago, Chicago, IL, 60637, USA
| | | | - Golam Sarwar
- UChicago Research Bangladesh, Mohakhali, Dhaka, 1230, Bangladesh
| | - Md Tariqul Islam
- UChicago Research Bangladesh, Mohakhali, Dhaka, 1230, Bangladesh
| | - Hasan Shahriar
- UChicago Research Bangladesh, Mohakhali, Dhaka, 1230, Bangladesh
| | - Tariqul Islam
- UChicago Research Bangladesh, Mohakhali, Dhaka, 1230, Bangladesh
| | - Mahfuzar Rahman
- UChicago Research Bangladesh, Mohakhali, Dhaka, 1230, Bangladesh
- Research and Evaluation Division, BRAC, Dhaka, 1212, Bangladesh
| | - Md Yunus
- International Centre for Diarrhoeal Disease Research Bangladesh, Dhaka, 1000, Bangladesh
| | - Muhammad G Kibriya
- Department of Public Health Sciences, The University of Chicago, Chicago, IL, 60637, USA
| | - Lin S Chen
- Department of Public Health Sciences, The University of Chicago, Chicago, IL, 60637, USA
| | - Habibul Ahsan
- Department of Public Health Sciences, The University of Chicago, Chicago, IL, 60637, USA.
- Department of Human Genetics, The University of Chicago, Chicago, IL, 60637, USA.
- Comprehensive Cancer Center, The University of Chicago, Chicago, IL, 60637, USA.
- Department of Medicine, The University of Chicago, Chicago, IL, 60637, USA.
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33
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A DNA methylation biomarker of alcohol consumption. Mol Psychiatry 2018; 23:422-433. [PMID: 27843151 PMCID: PMC5575985 DOI: 10.1038/mp.2016.192] [Citation(s) in RCA: 233] [Impact Index Per Article: 38.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/11/2016] [Revised: 09/05/2016] [Accepted: 09/14/2016] [Indexed: 12/11/2022]
Abstract
The lack of reliable measures of alcohol intake is a major obstacle to the diagnosis and treatment of alcohol-related diseases. Epigenetic modifications such as DNA methylation may provide novel biomarkers of alcohol use. To examine this possibility, we performed an epigenome-wide association study of methylation of cytosine-phosphate-guanine dinucleotide (CpG) sites in relation to alcohol intake in 13 population-based cohorts (ntotal=13 317; 54% women; mean age across cohorts 42-76 years) using whole blood (9643 European and 2423 African ancestries) or monocyte-derived DNA (588 European, 263 African and 400 Hispanic ancestry) samples. We performed meta-analysis and variable selection in whole-blood samples of people of European ancestry (n=6926) and identified 144 CpGs that provided substantial discrimination (area under the curve=0.90-0.99) for current heavy alcohol intake (⩾42 g per day in men and ⩾28 g per day in women) in four replication cohorts. The ancestry-stratified meta-analysis in whole blood identified 328 (9643 European ancestry samples) and 165 (2423 African ancestry samples) alcohol-related CpGs at Bonferroni-adjusted P<1 × 10-7. Analysis of the monocyte-derived DNA (n=1251) identified 62 alcohol-related CpGs at P<1 × 10-7. In whole-blood samples of people of European ancestry, we detected differential methylation in two neurotransmitter receptor genes, the γ-Aminobutyric acid-A receptor delta and γ-aminobutyric acid B receptor subunit 1; their differential methylation was associated with expression levels of a number of genes involved in immune function. In conclusion, we have identified a robust alcohol-related DNA methylation signature and shown the potential utility of DNA methylation as a clinically useful diagnostic test to detect current heavy alcohol consumption.
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Saffari A, Silver MJ, Zavattari P, Moi L, Columbano A, Meaburn EL, Dudbridge F. Estimation of a significance threshold for epigenome-wide association studies. Genet Epidemiol 2018; 42:20-33. [PMID: 29034560 PMCID: PMC5813244 DOI: 10.1002/gepi.22086] [Citation(s) in RCA: 103] [Impact Index Per Article: 17.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2016] [Revised: 05/30/2017] [Accepted: 07/24/2017] [Indexed: 12/17/2022]
Abstract
Epigenome-wide association studies (EWAS) are designed to characterise population-level epigenetic differences across the genome and link them to disease. Most commonly, they assess DNA-methylation status at cytosine-guanine dinucleotide (CpG) sites, using platforms such as the Illumina 450k array that profile a subset of CpGs genome wide. An important challenge in the context of EWAS is determining a significance threshold for declaring a CpG site as differentially methylated, taking multiple testing into account. We used a permutation method to estimate a significance threshold specifically for the 450k array and a simulation extrapolation approach to estimate a genome-wide threshold. These methods were applied to five different EWAS datasets derived from a variety of populations and tissue types. We obtained an estimate of α=2.4×10-7 for the 450k array, and a genome-wide estimate of α=3.6×10-8. We further demonstrate the importance of these results by showing that previously recommended sample sizes for EWAS should be adjusted upwards, requiring samples between ∼10% and ∼20% larger in order to maintain type-1 errors at the desired level.
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Affiliation(s)
- Ayden Saffari
- Department of Non‐Communicable Disease EpidemiologyLondon School of Hygiene and Tropical MedicineLondonUnited Kingdom
- MRC Unit, The Gambia and MRC International Nutrition GroupLondon School of Hygiene and Tropical MedicineLondonUnited Kingdom
- Department of Psychological Sciences, BirkbeckUniversity of LondonLondonUnited Kingdom
| | - Matt J. Silver
- MRC Unit, The Gambia and MRC International Nutrition GroupLondon School of Hygiene and Tropical MedicineLondonUnited Kingdom
| | - Patrizia Zavattari
- Department of Biomedical SciencesUniversity of CagliariCagliariSardiniaItaly
| | - Loredana Moi
- Department of Biomedical SciencesUniversity of CagliariCagliariSardiniaItaly
| | - Amedeo Columbano
- Department of Biomedical SciencesUniversity of CagliariCagliariSardiniaItaly
| | - Emma L. Meaburn
- Department of Psychological Sciences, BirkbeckUniversity of LondonLondonUnited Kingdom
| | - Frank Dudbridge
- Department of Non‐Communicable Disease EpidemiologyLondon School of Hygiene and Tropical MedicineLondonUnited Kingdom
- Department of Health SciencesUniversity of LeicesterLeicesterUnited Kingdom
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Zhu Z, Meng W, Liu P, Zhu X, Liu Y, Zou H. DNA hypomethylation of a transcription factor binding site within the promoter of a gout risk gene NRBP1 upregulates its expression by inhibition of TFAP2A binding. Clin Epigenetics 2017; 9:99. [PMID: 28932319 PMCID: PMC5603049 DOI: 10.1186/s13148-017-0401-z] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2017] [Accepted: 09/05/2017] [Indexed: 01/20/2023] Open
Abstract
BACKGROUND Genome-wide association studies (GWASs) have identified dozens of loci associated with gout, but for most cases, the risk genes and the underlying molecular mechanisms contributing to these associations are unknown. This study sought to understand the molecular mechanism of a common genetic variant, rs780093, in the development of gout, both in vitro and in vivo. RESULTS Nuclear receptor binding protein 1 (NRBP1), as a gout risk gene, and its regulatory region, 72 bp upstream of the transcription start site, designated as B1, were identified through integrative analyses of genome-wide genotype and DNA methylation data. We observed elevated NRBP1 expression in human peripheral blood mononuclear cells (PBMCs) from gout patients. In vitro luciferase reporter and protein pulldown assay results showed that DNA methylation could increase the binding of the transcription factor TFAP2A to B1, leading to suppressed gene expression. There results were further confirmed by in vivo bisulfite pyrosequencing showing that hypomethylation on B1 is associated with increased NRBP1 expression in gout patients. CONCLUSIONS Hypomethylation at the promoter region of NRBP1 reduces the binding of TFAP2A and thus leads to elevated NRBP1 expression, which might contribute to the development of gout.
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Affiliation(s)
- Zaihua Zhu
- Division of Rheumatology and Immunology, Huashan Hospital, Fudan University, Shanghai, China
- Institute of Rheumatology, Immunology and Allergy, Fudan University, Shanghai, China
| | - Weida Meng
- The Ministry of Education Key Laboratory of Metabolism and Molecular Medicine, Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Fudan University, Shanghai, China
| | - Peiru Liu
- The Ministry of Education Key Laboratory of Metabolism and Molecular Medicine, Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Fudan University, Shanghai, China
| | - Xiaoxia Zhu
- Division of Rheumatology and Immunology, Huashan Hospital, Fudan University, Shanghai, China
- Institute of Rheumatology, Immunology and Allergy, Fudan University, Shanghai, China
| | - Yun Liu
- The Ministry of Education Key Laboratory of Metabolism and Molecular Medicine, Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Fudan University, Shanghai, China
| | - Hejian Zou
- Division of Rheumatology and Immunology, Huashan Hospital, Fudan University, Shanghai, China
- Institute of Rheumatology, Immunology and Allergy, Fudan University, Shanghai, China
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36
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Bell CG. The Epigenomic Analysis of Human Obesity. Obesity (Silver Spring) 2017; 25:1471-1481. [PMID: 28845613 DOI: 10.1002/oby.21909] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/28/2017] [Revised: 05/09/2017] [Accepted: 05/11/2017] [Indexed: 12/31/2022]
Abstract
OBJECTIVE Analysis of the epigenome-the chemical modifications and packaging of the genome that can influence or indicate its activity-enables molecular insight into cell type-specific machinery. It can, therefore, reveal the pathophysiological mechanisms at work in disease. Detected changes can also represent physiological responses to adverse environmental exposures, thus enabling the epigenetic mark of DNA methylation to act as an epidemiological biomarker, even in surrogate tissue. This makes epigenomic analysis an attractive prospect to further understand the pathobiology and epidemiological aspects of obesity. Furthermore, integrating epigenomic data with known obesity-associated common genetic variation can aid in deciphering their molecular mechanisms. METHODS AND CONCLUSIONS This review primarily examines epidemiological or population-based studies of epigenetic modifications in relation to adiposity traits, as opposed to animal or cell models. It discusses recent work exploring the epigenome with respect to human obesity, which to date has predominately consisted of array-based studies of DNA methylation in peripheral blood. It is of note that highly replicated BMI DNA methylation associations are not causal, but strongly driven by coassociations for more precisely measured intertwined outcomes and factors, such as hyperlipidemia, hyperglycemia, and inflammation. Finally, the potential for the future exploration of the epigenome in obesity and related disorders is considered.
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Affiliation(s)
- Christopher G Bell
- MRC Lifecourse Epidemiology Unit, University of Southampton, Southampton, UK
- Epigenomic Medicine, Biological Sciences, Faculty of Environmental and Natural Sciences, University of Southampton, Southampton, UK
- Human Development and Health Academic Unit, Institute of Developmental Sciences, University of Southampton, Southampton, UK
- Department of Twin Research and Genetic Epidemiology, King's College London, London, UK
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37
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Bunning BJ, DeKruyff RH, Nadeau KC. Epigenetic Changes During Food-Specific Immunotherapy. Curr Allergy Asthma Rep 2017; 16:87. [PMID: 27943047 DOI: 10.1007/s11882-016-0665-y] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
PURPOSE OF REVIEW The prevalence and severity of IgE-mediated food allergy has increased dramatically over the last 15 years and is becoming a global health problem. Multiple lines of evidence suggest that epigenetic modifications of the genome resulting from gene-environment interactions have a key role in the increased prevalence of atopic disease. In this review, we describe the recent evidence suggesting how epigenetic changes mediate susceptibility to food allergies, and discuss how immunotherapy (IT) may reverse these effects. We discuss the areas of the epigenome as yet unexplored in terms of food allergy and IT such as histone modification and chromatin accessibility, and new techniques that may be utilized in future studies. RECENT FINDINGS Recent findings provide strong evidence that DNA methylation of certain promoter regions such as Forkhead box protein 3 is associated with clinical reactivity, and further, can be changed during IT treatment. Reports on other epigenetic changes are limited but also show evidence of significant change based on both disease status and treatment. In comparison to epigenetic studies focusing on asthma and allergic rhinitis, food allergy remains understudied. However, within the next decade, it is likely that epigenetic modifications may be used as biomarkers to aid in diagnosis and treatment of food-allergic patients. DNA methylation at specific loci has shown associations between food challenge outcomes, successful desensitization treatment, and overall phenotype compared to healthy controls.
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Affiliation(s)
- Bryan J Bunning
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Stanford University, Stanford, CA, USA.,Sean N. Parker Center for Allergy and Asthma Research, Stanford University School of Medicine, Stanford, CA, USA
| | - Rosemarie H DeKruyff
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Stanford University, Stanford, CA, USA.,Sean N. Parker Center for Allergy and Asthma Research, Stanford University School of Medicine, Stanford, CA, USA
| | - Kari C Nadeau
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Stanford University, Stanford, CA, USA. .,Sean N. Parker Center for Allergy and Asthma Research, Stanford University School of Medicine, Stanford, CA, USA. .,Sean N. Parker Center for Allergy and Asthma Research, Division of Pulmonary and Critical Care Medicine, Department of Medicine, Stanford University, Stanford University School of Medicine, 269 Campus Drive, CCSR 3215, MC 5366, Stanford, CA, 94305-5101, USA.
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38
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Zheleznyakova GY, Piket E, Marabita F, Pahlevan Kakhki M, Ewing E, Ruhrmann S, Needhamsen M, Jagodic M, Kular L. Epigenetic research in multiple sclerosis: progress, challenges, and opportunities. Physiol Genomics 2017; 49:447-461. [PMID: 28754822 DOI: 10.1152/physiolgenomics.00060.2017] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Revised: 07/24/2017] [Indexed: 01/02/2023] Open
Abstract
Multiple sclerosis (MS) is a chronic inflammatory and demyelinating disease of the central nervous system. MS likely results from a complex interplay between predisposing causal gene variants (the strongest influence coming from HLA class II locus) and environmental risk factors such as smoking, infectious mononucleosis, and lack of sun exposure/vitamin D. However, little is known about the mechanisms underlying MS development and progression. Moreover, the clinical heterogeneity and variable response to treatment represent additional challenges to a comprehensive understanding and efficient treatment of disease. Epigenetic processes, such as DNA methylation and histone posttranslational modifications, integrate influences from the genes and the environment to regulate gene expression accordingly. Studying epigenetic modifications, which are stable and reversible, may provide an alternative approach to better understand and manage disease. We here aim to review findings from epigenetic studies in MS and further discuss the challenges and clinical opportunities arising from epigenetic research, many of which apply to other diseases with similar complex etiology. A growing body of evidence supports a role of epigenetic processes in the mechanisms underlying immune pathogenesis and nervous system dysfunction in MS. However, disparities between studies shed light on the need to consider possible confounders and methodological limitations for a better interpretation of the data. Nevertheless, translational use of epigenetics might offer new opportunities in epigenetic-based diagnostics and therapeutic tools for a personalized care of MS patients.
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Affiliation(s)
- Galina Y Zheleznyakova
- Department of Clinical Neuroscience, Center for Molecular Medicine, Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden
| | - Eliane Piket
- Department of Clinical Neuroscience, Center for Molecular Medicine, Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden
| | - Francesco Marabita
- Department of Clinical Neuroscience, Center for Molecular Medicine, Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden
| | - Majid Pahlevan Kakhki
- Department of Clinical Neuroscience, Center for Molecular Medicine, Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden
| | - Ewoud Ewing
- Department of Clinical Neuroscience, Center for Molecular Medicine, Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden
| | - Sabrina Ruhrmann
- Department of Clinical Neuroscience, Center for Molecular Medicine, Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden
| | - Maria Needhamsen
- Department of Clinical Neuroscience, Center for Molecular Medicine, Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden
| | - Maja Jagodic
- Department of Clinical Neuroscience, Center for Molecular Medicine, Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden
| | - Lara Kular
- Department of Clinical Neuroscience, Center for Molecular Medicine, Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden
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Solomon O, Yousefi P, Huen K, Gunier RB, Escudero-Fung M, Barcellos LF, Eskenazi B, Holland N. Prenatal phthalate exposure and altered patterns of DNA methylation in cord blood. ENVIRONMENTAL AND MOLECULAR MUTAGENESIS 2017; 58:398-410. [PMID: 28556291 PMCID: PMC6488305 DOI: 10.1002/em.22095] [Citation(s) in RCA: 46] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/22/2016] [Revised: 04/11/2017] [Accepted: 04/12/2017] [Indexed: 05/18/2023]
Abstract
Epigenetic changes such as DNA methylation may be a molecular mechanism through which environmental exposures affect health. Phthalates are known endocrine disruptors with ubiquitous exposures in the general population including pregnant women, and they have been linked with a number of adverse health outcomes. We examined the association between in utero phthalate exposure and altered patterns of cord blood DNA methylation in 336 Mexican-American newborns. Concentrations of 11 phthalate metabolites were analyzed in maternal urine samples collected at 13 and 26 weeks gestation as a measure of fetal exposure. DNA methylation was assessed using the Infinium HumanMethylation 450K BeadChip adjusting for cord blood cell composition. To identify differentially methylated regions (DMRs) that may be more informative than individual CpG sites, we used two different approaches, DMRcate and comb-p. Regional assessment by both methods identified 27 distinct DMRs, the majority of which were in relation to multiple phthalate metabolites. Most of the significant DMRs (67%) were observed for later pregnancy (26 weeks gestation). Further, 51% of the significant DMRs were associated with the di-(2-ethylhexyl) phthalate metabolites. Five individual CpG sites were associated with phthalate metabolite concentrations after multiple comparisons adjustment (FDR), all showing hypermethylation. Genes with DMRs were involved in inflammatory response (IRAK4 and ESM1), cancer (BRCA1 and LASP1), endocrine function (CNPY1), and male fertility (IFT140, TESC, and PRDM8). These results on differential DNA methylation in newborns with prenatal phthalate exposure provide new insights and targets to explore mechanism of adverse effects of phthalates on human health. Environ. Mol. Mutagen. 58:398-410, 2017. © 2017 Wiley Periodicals, Inc.
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Affiliation(s)
- Olivia Solomon
- School of Public Health, Center for Environmental Research and Children’s Health (CERCH), University
of California, Berkeley, Berkeley, CA 94720, USA
| | - Paul Yousefi
- School of Public Health, Center for Environmental Research and Children’s Health (CERCH), University
of California, Berkeley, Berkeley, CA 94720, USA
| | - Karen Huen
- School of Public Health, Center for Environmental Research and Children’s Health (CERCH), University
of California, Berkeley, Berkeley, CA 94720, USA
| | - Robert B. Gunier
- School of Public Health, Center for Environmental Research and Children’s Health (CERCH), University
of California, Berkeley, Berkeley, CA 94720, USA
| | - Maria Escudero-Fung
- School of Public Health, Center for Environmental Research and Children’s Health (CERCH), University
of California, Berkeley, Berkeley, CA 94720, USA
| | - Lisa F. Barcellos
- School of Public Health, Center for Environmental Research and Children’s Health (CERCH), University
of California, Berkeley, Berkeley, CA 94720, USA
| | - Brenda Eskenazi
- School of Public Health, Center for Environmental Research and Children’s Health (CERCH), University
of California, Berkeley, Berkeley, CA 94720, USA
| | - Nina Holland
- School of Public Health, Center for Environmental Research and Children’s Health (CERCH), University
of California, Berkeley, Berkeley, CA 94720, USA
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40
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Traylor M, Malik R, Nalls MA, Cotlarciuc I, Radmanesh F, Thorleifsson G, Hanscombe KB, Langefeld C, Saleheen D, Rost NS, Yet I, Spector TD, Bell JT, Hannon E, Mill J, Chauhan G, Debette S, Bis JC, Longstreth WT, Ikram MA, Launer LJ, Seshadri S, Hamilton-Bruce MA, Jimenez-Conde J, Cole JW, Schmidt R, Słowik A, Lemmens R, Lindgren A, Melander O, Grewal RP, Sacco RL, Rundek T, Rexrode K, Arnett DK, Johnson JA, Benavente OR, Wasssertheil-Smoller S, Lee JM, Pulit SL, Wong Q, Rich SS, de Bakker PIW, McArdle PF, Woo D, Anderson CD, Xu H, Heitsch L, Fornage M, Jern C, Stefansson K, Thorsteinsdottir U, Gretarsdottir S, Lewis CM, Sharma P, Sudlow CLM, Rothwell PM, Boncoraglio GB, Thijs V, Levi C, Meschia JF, Rosand J, Kittner SJ, Mitchell BD, Dichgans M, Worrall BB, Markus HS. Genetic variation at 16q24.2 is associated with small vessel stroke. Ann Neurol 2017; 81:383-394. [PMID: 27997041 PMCID: PMC5366092 DOI: 10.1002/ana.24840] [Citation(s) in RCA: 67] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2016] [Revised: 12/02/2016] [Accepted: 12/03/2016] [Indexed: 02/03/2023]
Abstract
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
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Affiliation(s)
- Matthew Traylor
- Department of Medical and Molecular Genetics, King's College London, London, United Kingdom
| | - Rainer Malik
- Institute for Stroke and Dementia Research, Klinikum der Universität München, Ludwig-Maximilians University, Munich, Germany
| | - Mike A Nalls
- Laboratory of Neurogenetics, National Institute on Aging, Bethesda, MD
| | - Ioana Cotlarciuc
- Institute of Cardiovascular Research Royal Holloway University of London (ICR2UL), London, United Kingdom
| | - Farid Radmanesh
- Division of Neurocritical Care and Emergency Neurology, Massachusetts General Hospital, Boston, MA.,J. Philip Kistler Stroke Research Center, Department of Neurology, Massachusetts General Hospital, Boston, MA.,Center for Human Genetic Research, Massachusetts General Hospital, Boston, MA
| | | | - Ken B Hanscombe
- Department of Medical and Molecular Genetics, King's College London, London, United Kingdom
| | - Carl Langefeld
- Center for Public Health Genomics and Department of Biostatistical Sciences, Wake Forest School of Medicine, Winston-Salem, NC
| | - Danish Saleheen
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA
| | - Natalia S Rost
- J. Philip Kistler Stroke Research Center, Department of Neurology, Massachusetts General Hospital, Boston, MA
| | - Idil Yet
- Department of Twin Research & Genetic Epidemiology, King's College London, London, United Kingdom
| | - Tim D Spector
- Department of Twin Research & Genetic Epidemiology, King's College London, London, United Kingdom
| | - Jordana T Bell
- Department of Twin Research & Genetic Epidemiology, King's College London, London, United Kingdom
| | - Eilis Hannon
- University of Exeter Medical School, University of Exeter, Exeter, United Kingdom
| | - Jonathan Mill
- University of Exeter Medical School, University of Exeter, Exeter, United Kingdom.,Social, Genetic and Developmental Psychiatry Center, Institute of Psychiatry, Psychology and Neuroscience, King's College London, London, United Kingdom
| | - Ganesh Chauhan
- Inserm Research Center for Epidemiology and Biostatistics (U897)-Team Neuroepidemiology, Bordeaux, France.,University of Bordeaux, Bordeaux, France
| | - Stephanie Debette
- Inserm Research Center for Epidemiology and Biostatistics (U897)-Team Neuroepidemiology, Bordeaux, France.,University of Bordeaux, Bordeaux, France
| | - Joshua C Bis
- Cardiovascular Health Research Unit, Department of Medicine, University of Washington, Seattle, WA
| | - W T Longstreth
- Departments of Neurology and Epidemiology, University of Washington, Seattle, WA
| | - M Arfan Ikram
- Department of Neurology, Epidemiology and Radiology, Erasmus MC University Medical Center, Rotterdam, The Netherlands
| | - Lenore J Launer
- Laboratory of Epidemiology and Population Sciences, National Institute on Aging, Bethesda, MD
| | - Sudha Seshadri
- Boston University School of Medicine, Boston, MA.,Framingham Heart Study, Framingham, MA
| | | | | | - Jordi Jimenez-Conde
- Neurovascular Research Group (NEUVAS), Neurology Department, Institut Hospital del Mar d'Investigació Mèdica, Barcelona, Spain
| | - John W Cole
- Department of Neurology, University of Maryland School of Medicine and Baltimore VAMC, Baltimore, MD
| | - Reinhold Schmidt
- Department of Neurology, Clinical Division of Neurogeriatrics, Medical University Graz, Graz, Austria
| | - Agnieszka Słowik
- Department of Neurology, Jagiellonian University, Krakow, Poland
| | - Robin Lemmens
- KU Leuven-University of Leuven, Department of Neurosciences, Experimental Neurology and Leuven Research Institute for Neuroscience and Disease (LIND), Leuven, Belgium.,VIB, Vesalius Research Center, Laboratory of Neurobiology, Department of Neurology, Leuven, Belgium.,University Hospitals Leuven, Department of Neurology, Leuven, Belgium
| | - Arne Lindgren
- Department of Clinical Sciences Lund, Neurology, Lund University, Lund, Sweden.,Department of Neurology and Rehabilitation Medicine, Skåne University Hospital, Lund, Sweden
| | - Olle Melander
- Department of Clinical Sciences, Lund University, Malmö, Sweden
| | - Raji P Grewal
- Neuroscience Institute, Saint Francis Medical Center, School of Health and Medical Sciences, Seton Hall University, South Orange, NJ
| | - Ralph L Sacco
- Department of Neurology, Miller School of Medicine, University of Miami, Miami, FL
| | - Tatjana Rundek
- Department of Neurology, Miller School of Medicine, University of Miami, Miami, FL
| | - Kathryn Rexrode
- Harvard Medical School, Boston, MA, Center for Faculty Development and Diversity, Brigham and Women's Hospital, Boston, MA
| | - Donna K Arnett
- College of Public Health, University of Kentucky, Lexington, KY
| | - Julie A Johnson
- Department of Pharmacotherapy and Translational Research and Center for Pharmacogenomics, University of Florida, College of Pharmacy, Gainesville, FL.,Division of Cardiovascular Medicine, College of Medicine, University of Florida, Gainesville, FL
| | - Oscar R Benavente
- Department of Neurology, University of British Columbia, Vancouver, British Columbia, Canada
| | | | - Jin-Moo Lee
- Stroke Center, Department of Neurology, Washington University School of Medicine, Seattle, WA
| | - Sara L Pulit
- Department of Medical Genetics, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Quenna Wong
- Department of Biostatistics, University of Washington, Seattle, WA
| | - Stephen S Rich
- Center for Public Health Genomics, University of Virginia School of Medicine, Charlottesville, VA
| | - Paul I W de Bakker
- Julius Center for Health Sciences and Primary Care, University Medical Center Utrecht, Utrecht, The Netherlands.,Department of Medical Genetics, Center for Molecular Medicine, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Patrick F McArdle
- Department of Medicine, University of Maryland School of Medicine, MD
| | - Daniel Woo
- University of Cincinnati College of Medicine, Cincinnati, OH
| | - Christopher D Anderson
- Division of Neurocritical Care and Emergency Neurology, Massachusetts General Hospital, Boston, MA.,J. Philip Kistler Stroke Research Center, Department of Neurology, Massachusetts General Hospital, Boston, MA.,Center for Human Genetic Research, Massachusetts General Hospital, Boston, MA.,Program in Medical and Population Genetics, Broad Institute, Boston, MA
| | - Huichun Xu
- Division of Endocrinology, Diabetes and Nutrition, University of Maryland School of Medicine, Baltimore, MD
| | - Laura Heitsch
- Division of Emergency Medicine, Washington University School of Medicine, St Louis, MO
| | - Myriam Fornage
- The University of Texas Health Science Center at Houston, Houston, TX
| | - Christina Jern
- Institute of Biomedicine, the Sahlgrenska Academy at University of Gothenburg, Gothenburg, Sweden
| | - Kari Stefansson
- deCODE genetics/AMGEN, Reykjavik, Iceland.,Faculty of Medicine, University of Iceland, Reykjavik, Iceland
| | - Unnur Thorsteinsdottir
- deCODE genetics/AMGEN, Reykjavik, Iceland.,Faculty of Medicine, University of Iceland, Reykjavik, Iceland
| | - Solveig Gretarsdottir
- Center for Public Health Genomics and Department of Biostatistical Sciences, Wake Forest School of Medicine, Winston-Salem, NC
| | - Cathryn M Lewis
- Department of Medical and Molecular Genetics, King's College London, London, United Kingdom.,Social, Genetic and Developmental Psychiatry Center, Institute of Psychiatry, Psychology and Neuroscience, King's College London, London, United Kingdom
| | - Pankaj Sharma
- Institute of Cardiovascular Research Royal Holloway University of London (ICR2UL), London, United Kingdom
| | - Cathie L M Sudlow
- Center for Clinical Brain Sciences & Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, United Kingdom
| | - Peter M Rothwell
- Nuffield Department of Clinical Neurosciences, University of Oxford, Oxford, United Kingdom
| | - Giorgio B Boncoraglio
- Department of Cerebrovascular Diseases, Fondazione IRCCS Istituto Neurologico "Carlo Besta", Milano, Italy
| | - Vincent Thijs
- Framingham Heart Study, Framingham, MA.,Department of Neurology, Royal Adelaide Hospital, Adelaide, South Australia, Australia.,Department of Neurology, Austin Health and Florey Institute of Neuroscience and Mental Health, Heidelberg, Australia
| | - Chris Levi
- John Hunter Hospital, Hunter Medical Research Institute and University of Newcastle, Newcastle, NSW, Australia
| | - James F Meschia
- Department of Neurology, Mayo Clinic Jacksonville, Jacksonville, FL
| | - Jonathan Rosand
- Division of Neurocritical Care and Emergency Neurology, Massachusetts General Hospital, Boston, MA.,J. Philip Kistler Stroke Research Center, Department of Neurology, Massachusetts General Hospital, Boston, MA.,Center for Human Genetic Research, Massachusetts General Hospital, Boston, MA.,University of Cincinnati College of Medicine, Cincinnati, OH
| | - Steven J Kittner
- Department of Neurology, University of Maryland School of Medicine and Baltimore VAMC, Baltimore, MD
| | - Braxton D Mitchell
- Department of Medicine, University of Maryland School of Medicine, Baltimore, MD.,Geriatrics Research and Education Clinical Center, Baltimore Veterans Administration Medical Center, Baltimore, MD
| | - Martin Dichgans
- Institute for Stroke and Dementia Research, Klinikum der Universität München, Ludwig-Maximilians University, Munich, Germany.,Munich Cluster of Systems Neurology, SyNergy, Munich, Germany
| | - Bradford B Worrall
- Departments of Neurology and Public Health Sciences, University of Virginia School of Medicine, Charlottesville, VA
| | - Hugh S Markus
- Stroke Research Group, Division of Clinical Neurosciences, University of Cambridge, Cambridge, United Kingdom
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Lyall K, Croen L, Daniels J, Fallin MD, Ladd-Acosta C, Lee BK, Park BY, Snyder NW, Schendel D, Volk H, Windham GC, Newschaffer C. The Changing Epidemiology of Autism Spectrum Disorders. Annu Rev Public Health 2017; 38:81-102. [PMID: 28068486 PMCID: PMC6566093 DOI: 10.1146/annurev-publhealth-031816-044318] [Citation(s) in RCA: 550] [Impact Index Per Article: 78.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Autism spectrum disorder (ASD) is a complex neurodevelopmental condition with lifelong impacts. Genetic and environmental factors contribute to ASD etiology, which remains incompletely understood. Research on ASD epidemiology has made significant advances in the past decade. Current prevalence is estimated to be at least 1.5% in developed countries, with recent increases primarily among those without comorbid intellectual disability. Genetic studies have identified a number of rare de novo mutations and gained footing in the areas of polygenic risk, epigenetics, and gene-by-environment interaction. Epidemiologic investigations focused on nongenetic factors have established advanced parental age and preterm birth as ASD risk factors, indicated that prenatal exposure to air pollution and short interpregnancy interval are potential risk factors, and suggested the need for further exploration of certain prenatal nutrients, metabolic conditions, and exposure to endocrine-disrupting chemicals. We discuss future challenges and goals for ASD epidemiology as well as public health implications.
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Affiliation(s)
- Kristen Lyall
- A.J. Drexel Autism Institute, Philadelphia, Pennsylvania 19104;
| | - Lisa Croen
- Kaiser Permanente Division of Research, Oakland, California 94612
| | - Julie Daniels
- Department of Epidemiology, University of North Carolina Gillings School of Public Health, Chapel Hill, North Carolina 27599
| | - M Daniele Fallin
- Wendy Klag Center for Autism and Developmental Disabilities, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland 21205
- Department of Mental Health, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland 21205
| | - Christine Ladd-Acosta
- Wendy Klag Center for Autism and Developmental Disabilities, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland 21205
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland 21205
| | - Brian K Lee
- Department of Epidemiology and Biostatistics, Drexel University School of Public Health, Philadelphia, Pennsylvania 19104
- Department of Medical Epidemiology and Biostatistics and Department of Public Health Sciences, Karolinska Institute, SE 171-77 Stockholm, Sweden
| | - Bo Y Park
- Wendy Klag Center for Autism and Developmental Disabilities, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland 21205
- Department of Mental Health, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland 21205
| | | | - Diana Schendel
- Department of Economics and Business, National Centre for Register-Based Research, Aarhus University, DK-8210 Aarhus, Denmark
- Department of Public Health, Section for Epidemiology, Aarhus University, DK-8000 Aarhus, Denmark
- Lundbeck Foundation Initiative for Integrative Psychiatric Research, Aarhus, Denmark
| | - Heather Volk
- Wendy Klag Center for Autism and Developmental Disabilities, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland 21205
- Department of Mental Health, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland 21205
| | - Gayle C Windham
- California Department of Public Health, Division of Environmental and Occupational Disease Control, Richmond, California 94805
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Schenkel LC, Rodenhiser D, Siu V, McCready E, Ainsworth P, Sadikovic B. Constitutional Epi/Genetic Conditions: Genetic, Epigenetic, and Environmental Factors. J Pediatr Genet 2017; 6:30-41. [PMID: 28180025 PMCID: PMC5288004 DOI: 10.1055/s-0036-1593849] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2015] [Accepted: 04/14/2016] [Indexed: 12/12/2022]
Abstract
There are more than 4,000 phenotypes for which the molecular basis is at least partly known. Though defects in primary DNA structure constitute a major cause of these disorders, epigenetic disruption is emerging as an important alternative mechanism in the etiology of a broad range of congenital and developmental conditions. These include epigenetic defects caused by either localized (in cis) genetic alterations or more distant (in trans) genetic events but can also include environmental effects. Emerging evidence suggests interplay between genetic and environmental factors in the epigenetic etiology of several constitutional "epi/genetic" conditions. This review summarizes our broadening understanding of how epigenetics contributes to pediatric disease by exploring different classes of epigenomic disorders. It further challenges the simplistic dogma of "DNA encodes RNA encodes protein" to best understand the spectrum of factors that can influence genetic traits in a pediatric population.
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Affiliation(s)
- Laila C. Schenkel
- Department of Pathology and Laboratory Medicine, Western University, London, Ontario, Canada
- Children's Health Research Institute, London, Ontario, Canada
| | - David Rodenhiser
- Children's Health Research Institute, London, Ontario, Canada
- Department of Biochemistry, Western University, London, Ontario, Canada
- Department of Pediatrics, Western University, London, Ontario, Canada
- London Regional Cancer Program, London Health Sciences Centre, London, Ontario, Canada
- Department of Oncology, Western University, London, Ontario, Canada
| | - Victoria Siu
- Children's Health Research Institute, London, Ontario, Canada
- Department of Pediatrics, Western University, London, Ontario, Canada
- London Regional Cancer Program, London Health Sciences Centre, London, Ontario, Canada
| | - Elizabeth McCready
- Department of Pathology and Molecular Medicine, McMaster University, Hamilton, Ontario, Canada
| | - Peter Ainsworth
- Department of Pathology and Laboratory Medicine, Western University, London, Ontario, Canada
- Children's Health Research Institute, London, Ontario, Canada
- Department of Biochemistry, Western University, London, Ontario, Canada
- Department of Pediatrics, Western University, London, Ontario, Canada
- London Regional Cancer Program, London Health Sciences Centre, London, Ontario, Canada
- Department of Oncology, Western University, London, Ontario, Canada
| | - Bekim Sadikovic
- Department of Pathology and Laboratory Medicine, Western University, London, Ontario, Canada
- Children's Health Research Institute, London, Ontario, Canada
- London Regional Cancer Program, London Health Sciences Centre, London, Ontario, Canada
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Volberg V, Yousefi P, Huen K, Harley K, Eskenazi B, Holland N. CpG Methylation across the adipogenic PPARγ gene and its relationship with birthweight and child BMI at 9 years. BMC MEDICAL GENETICS 2017; 18:7. [PMID: 28122515 PMCID: PMC5267417 DOI: 10.1186/s12881-016-0365-4] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/19/2016] [Accepted: 12/26/2016] [Indexed: 01/05/2023]
Abstract
Background To examine methylation of the peroxisome proliferator-activated receptor γ (PPARγ) gene and its relationship with child weight status, at birth and 9 years. Methods We measured PPARγ methylation across 23 CpG sites using the Infinium Illumina 450 k array for children from the Center for the Health Assessment of Mothers and Children of Salinas (CHAMACOS) cohort at birth (N = 373) and 9 years (N = 245). Results Methylation level correlation patterns across the 23 PPARγ CpG sites were conserved between birth and 9-year ages. We found high inter-CpG correlations between sites 1–3 (methylation block 1) and also between sites 18–23 (methylation block 2) for both time points, although these patterns were less pronounced at 9 years. Additionally, sites 1–3 (north shore) had the highest intra-CpG correlations over time (r = 0.24, 0.42, and 0.3; P = 0.002, P < 0.001, P < 0.001, respectively). PPARγ methylation levels tended to increase with age, and the largest differences were observed for north shore sites (7.4%). Adjusting for sex, both site 1 and site 20 (gene body) methylation at birth was significantly and inversely associated with birth weight (β = −0.13, P = 0.033; β = −0.09, P = 0.025, respectively). Similarly, we found that site 1 and site 20 methylation at 9 years was significantly and inversely associated with 9-year BMI z-score (β = −0.41, P = 0.015; β = −0.23, P = 0.045, respectively). Conclusion Our results indicate that PPARγ methylation is highly organized and conserved over time, and highlight the potential functional importance of north shore sites, adding to a better understanding of regional human methylome patterns. Overall, our results suggest that PPARγ methylation may be associated with child body size. Electronic supplementary material The online version of this article (doi:10.1186/s12881-016-0365-4) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Vitaly Volberg
- Center for Environmental Research and Children's Health (CERCH), School of Public Health, University of California, 733 University Hall, Berkeley, CA, 94720-7360, USA
| | - Paul Yousefi
- Center for Environmental Research and Children's Health (CERCH), School of Public Health, University of California, 733 University Hall, Berkeley, CA, 94720-7360, USA
| | - Karen Huen
- Center for Environmental Research and Children's Health (CERCH), School of Public Health, University of California, 733 University Hall, Berkeley, CA, 94720-7360, USA
| | - Kim Harley
- Center for Environmental Research and Children's Health (CERCH), School of Public Health, University of California, 733 University Hall, Berkeley, CA, 94720-7360, USA
| | - Brenda Eskenazi
- Center for Environmental Research and Children's Health (CERCH), School of Public Health, University of California, 733 University Hall, Berkeley, CA, 94720-7360, USA
| | - Nina Holland
- Center for Environmental Research and Children's Health (CERCH), School of Public Health, University of California, 733 University Hall, Berkeley, CA, 94720-7360, USA.
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44
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Interactions between genetic, lifestyle and environmental risk factors for multiple sclerosis. Nat Rev Neurol 2016; 13:25-36. [PMID: 27934854 DOI: 10.1038/nrneurol.2016.187] [Citation(s) in RCA: 651] [Impact Index Per Article: 81.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Genetic predisposition to multiple sclerosis (MS) only explains a fraction of the disease risk; lifestyle and environmental factors are key contributors to the risk of MS. Importantly, these nongenetic factors can influence pathogenetic pathways, and some of them can be modified. Besides established MS-associated risk factors - high latitude, female sex, smoking, low vitamin D levels caused by insufficient sun exposure and/or dietary intake, and Epstein-Barr virus (EBV) infection - strong evidence now supports obesity during adolescence as a factor increasing MS risk. Organic solvents and shift work have also been reported to confer increased risk of the disease, whereas factors such as use of nicotine or alcohol, cytomegalovirus infection and a high coffee consumption are associated with a reduced risk. Certain factors - smoking, EBV infection and obesity - interact with HLA risk genes, pointing at a pathogenetic pathway involving adaptive immunity. All of the described risk factors for MS can influence adaptive and/or innate immunity, which is thought to be the main pathway modulated by MS risk alleles. Unlike genetic risk factors, many environmental and lifestyle factors can be modified, with potential for prevention, particularly for people at the greatest risk, such as relatives of individuals with MS. Here, we review recent data on environmental and lifestyle factors, with a focus on gene-environment interactions.
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EWAS: epigenome-wide association studies software 1.0 - identifying the association between combinations of methylation levels and diseases. Sci Rep 2016; 6:37951. [PMID: 27892496 PMCID: PMC5125000 DOI: 10.1038/srep37951] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2016] [Accepted: 11/02/2016] [Indexed: 11/22/2022] Open
Abstract
Similar to the SNP (single nucleotide polymorphism) data, there is non-random association of the DNA methylation level (we call it methylation disequilibrium, MD) between neighboring methylation loci. For the case-control study of complex diseases, it is important to identify the association between methylation levels combination types (we call it methylecomtype) and diseases/phenotypes. We extended the classical framework of SNP haplotype-based association study in population genetics to DNA methylation level data, and developed a software EWAS to identify the disease-related methylecomtypes. EWAS can provide the following basic functions: (1) calculating the DNA methylation disequilibrium coefficient between two CpG loci; (2) identifying the MD blocks across the whole genome; (3) carrying out case-control association study of methylecomtypes and identifying the disease-related methylecomtypes. For a DNA methylation level data set including 689 samples (354 cases and 335 controls) and 473864 CpG loci, it takes only about 25 min to complete the full scan. EWAS v1.0 can rapidly identify the association between combinations of methylation levels (methylecomtypes) and diseases. EWAS v1.0 is freely available at: http://www.ewas.org.cn or http://www.bioapp.org/ewas.
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Peter CJ, Fischer LK, Kundakovic M, Garg P, Jakovcevski M, Dincer A, Amaral AC, Ginns EI, Galdzicka M, Bryce CP, Ratner C, Waber DP, Mokler D, Medford G, Champagne FA, Rosene DL, McGaughy JA, Sharp AJ, Galler JR, Akbarian S. DNA Methylation Signatures of Early Childhood Malnutrition Associated With Impairments in Attention and Cognition. Biol Psychiatry 2016; 80:765-774. [PMID: 27184921 PMCID: PMC5036982 DOI: 10.1016/j.biopsych.2016.03.2100] [Citation(s) in RCA: 95] [Impact Index Per Article: 11.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/19/2015] [Revised: 03/10/2016] [Accepted: 03/12/2016] [Indexed: 12/11/2022]
Abstract
BACKGROUND Early childhood malnutrition affects 113 million children worldwide, impacting health and increasing vulnerability for cognitive and behavioral disorders later in life. Molecular signatures after childhood malnutrition, including the potential for intergenerational transmission, remain unexplored. METHODS We surveyed blood DNA methylomes (~483,000 individual CpG sites) in 168 subjects across two generations, including 50 generation 1 individuals hospitalized during the first year of life for moderate to severe protein-energy malnutrition, then followed up to 48 years in the Barbados Nutrition Study. Attention deficits and cognitive performance were evaluated with the Connors Adult Attention Rating Scale and Wechsler Abbreviated Scale of Intelligence. Expression of nutrition-sensitive genes was explored by quantitative reverse transcriptase polymerase chain reaction in rat prefrontal cortex. RESULTS We identified 134 nutrition-sensitive, differentially methylated genomic regions, with most (87%) specific for generation 1. Multiple neuropsychiatric risk genes, including COMT, IFNG, MIR200B, SYNGAP1, and VIPR2 showed associations of specific methyl-CpGs with attention and IQ. IFNG expression was decreased in prefrontal cortex of rats showing attention deficits after developmental malnutrition. CONCLUSIONS Early childhood malnutrition entails long-lasting epigenetic signatures associated with liability for attention and cognition, and limited potential for intergenerational transmission.
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Affiliation(s)
- Cyril J. Peter
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY 10029
| | - Laura K. Fischer
- The Chester M. Pierce, MD Division of Global Psychiatry, Massachusetts General Hospital, Harvard Medical School, Charlestown MA 02129
| | - Marija Kundakovic
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY 10029
| | - Paras Garg
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029
| | - Mira Jakovcevski
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY 10029,Max-Planck Institute for Psychiatry, D-Munich 80804
| | - Aslihan Dincer
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY 10029,Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029
| | - Ana C. Amaral
- Department of Neurology, Massachusetts General Hospital, Charlestown, MA 02129
| | - Edward I Ginns
- Departments of Psychiatry, Neurology, and Clinical Pathology, University of Massachusetts Medical School, Shrewsbury, MA 01545
| | - Marzena Galdzicka
- Department of Pathology, University of Massachusetts Medical School, Shrewsbury, MA 01545
| | | | - Chana Ratner
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY 10029
| | - Deborah P Waber
- Boston Children’s Hospital and Harvard Medical School, Boston, MA 02115
| | - David Mokler
- Department of Biomedical Sciences, College of Osteopathic Medicine, University of New England, Biddeford, ME
| | | | | | - Douglas L. Rosene
- Department of Anatomy & Neurobiology, Boston University School of Medicine, Boston MA 02118
| | - Jill A. McGaughy
- Department of Psychology, University of New Hampshire, Durham, NH 03077
| | - Andrew J. Sharp
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029
| | - Janina R. Galler
- The Chester M. Pierce, MD Division of Global Psychiatry, Massachusetts General Hospital, Harvard Medical School, Charlestown MA 02129
| | - Schahram Akbarian
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, New York.
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Qiu W, Wan E, Morrow J, Cho MH, Crapo JD, Silverman EK, DeMeo DL. The impact of genetic variation and cigarette smoke on DNA methylation in current and former smokers from the COPDGene study. Epigenetics 2016; 10:1064-73. [PMID: 26646902 DOI: 10.1080/15592294.2015.1106672] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023] Open
Abstract
DNA methylation can be affected by systemic exposures, such as cigarette smoking and genetic sequence variation; however, the relative impact of each on the epigenome is unknown. We aimed to assess if cigarette smoking and genetic variation are associated with overlapping or distinct sets of DNA methylation marks and pathways. We selected 85 Caucasian current and former smokers with genome-wide single nucleotide polymorphism (SNP) genotyping available from the COPDGene study. Genome-wide methylation was obtained on DNA from whole blood using the Illumina HumanMethylation27 platform. To determine the impact of local sequence variation on DNA methylation (mQTL), we examined the association between methylation and SNPs within 50 kb of each CpG site. To examine the impact of cigarette smoking on DNA methylation, we examined the differences in methylation by current cigarette smoking status. We detected 770 CpG sites annotated to 708 genes associated at an FDR < 0.05 in the cis-mQTL analysis and 1,287 CpG sites annotated to 1,242 genes, which were nominally associated in the smoking-CpG association analysis (P(unadjusted) < 0.05). Forty-three CpG sites annotated to 40 genes were associated with both SNP variation and current smoking; this overlap was not greater than that expected by chance. Our results suggest that cigarette smoking and genetic variants impact distinct sets of DNA methylation marks, the further elucidation of which may partially explain the variable susceptibility to the health effects of cigarette smoking. Ascertaining how genetic variation and systemic exposures differentially impact the human epigenome has relevance for both biomarker identification and therapeutic target development for smoking-related diseases.
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Affiliation(s)
- Weiliang Qiu
- a Channing Division of Network Medicine; Brigham and Women's Hospital/Harvard Medical School ; Boston , MA USA
| | - Emily Wan
- a Channing Division of Network Medicine; Brigham and Women's Hospital/Harvard Medical School ; Boston , MA USA.,b Division of Pulmonary/Critical Care; Brigham and Women's Hospital/Harvard Medical School ; Boston , MA USA
| | - Jarrett Morrow
- a Channing Division of Network Medicine; Brigham and Women's Hospital/Harvard Medical School ; Boston , MA USA
| | - Michael H Cho
- a Channing Division of Network Medicine; Brigham and Women's Hospital/Harvard Medical School ; Boston , MA USA.,b Division of Pulmonary/Critical Care; Brigham and Women's Hospital/Harvard Medical School ; Boston , MA USA
| | | | - Edwin K Silverman
- a Channing Division of Network Medicine; Brigham and Women's Hospital/Harvard Medical School ; Boston , MA USA.,b Division of Pulmonary/Critical Care; Brigham and Women's Hospital/Harvard Medical School ; Boston , MA USA
| | - Dawn L DeMeo
- a Channing Division of Network Medicine; Brigham and Women's Hospital/Harvard Medical School ; Boston , MA USA.,b Division of Pulmonary/Critical Care; Brigham and Women's Hospital/Harvard Medical School ; Boston , MA USA
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Zhou D, Li Z, Yu D, Wan L, Zhu Y, Lai M, Zhang D. Polymorphisms involving gain or loss of CpG sites are significantly enriched in trait-associated SNPs. Oncotarget 2016; 6:39995-40004. [PMID: 26503467 PMCID: PMC4741875 DOI: 10.18632/oncotarget.5650] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2015] [Accepted: 10/02/2015] [Indexed: 12/30/2022] Open
Abstract
Some single nucleotide polymorphisms (SNPs) influence the existence of CpG sites, the basis of DNA modification such as methylation and hydroxymethylation. These polymorphisms can lead to gain or loss of CpG sites and were defined as CpG site related SNPs (cgSNPs) in this study. The cgSNPs change DNA sequence and might potentially affect DNA modification such as methylation. However, the functional consequence of cgSNPs is poorly understood. We observed that a considerable proportion (23.0%) of common variants were cgSNPs in human genome. Mutations involving loss of CpG sites were associated with reduced levels of methylation (~20.2%) using The Cancer Genome Atlas (TCGA) data. Using public databases (SCAN and seeQTL) of expression quantitative trait loci (eQTLs), we found that the cgSNPs were significantly enriched in eQTLs via logistic regression and simulation test. Furthermore, we observed that cgSNPs were more likely to be trait-associated loci especially cancers using a catalog of published genome-wide association studies (GWAS) recorded by National Human Genome Research Institute (NHGRI). Our results indicated that cgSNP might be meaningful as annotation either in SNP functional prediction or in screening for trait-associated SNPs.
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Affiliation(s)
- Dan Zhou
- Department of Pathology, Zhejiang University School of Medicine, Hangzhou, Zhejiang, 310058, China.,Key Laboratory of Disease Proteomics of Zhejiang Province, Hangzhou, Zhejiang, 310058, China.,Department of Epidemiology & Biostatistics, Zhejiang University School of Public Health, Hangzhou, Zhejiang, 310058, China
| | - Zhenli Li
- Department of Pathology, Zhejiang University School of Medicine, Hangzhou, Zhejiang, 310058, China.,Key Laboratory of Disease Proteomics of Zhejiang Province, Hangzhou, Zhejiang, 310058, China
| | - Dan Yu
- Department of Pathology, Zhejiang University School of Medicine, Hangzhou, Zhejiang, 310058, China.,Key Laboratory of Disease Proteomics of Zhejiang Province, Hangzhou, Zhejiang, 310058, China
| | - Ledong Wan
- Department of Pathology, Zhejiang University School of Medicine, Hangzhou, Zhejiang, 310058, China.,Key Laboratory of Disease Proteomics of Zhejiang Province, Hangzhou, Zhejiang, 310058, China
| | - Yimin Zhu
- Department of Epidemiology & Biostatistics, Zhejiang University School of Public Health, Hangzhou, Zhejiang, 310058, China
| | - Maode Lai
- Department of Pathology, Zhejiang University School of Medicine, Hangzhou, Zhejiang, 310058, China.,Key Laboratory of Disease Proteomics of Zhejiang Province, Hangzhou, Zhejiang, 310058, China
| | - Dandan Zhang
- Department of Pathology, Zhejiang University School of Medicine, Hangzhou, Zhejiang, 310058, China.,Key Laboratory of Disease Proteomics of Zhejiang Province, Hangzhou, Zhejiang, 310058, China
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DNA methylation: conducting the orchestra from exposure to phenotype? Clin Epigenetics 2016; 8:92. [PMID: 27602172 PMCID: PMC5012062 DOI: 10.1186/s13148-016-0256-8] [Citation(s) in RCA: 126] [Impact Index Per Article: 15.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2016] [Accepted: 08/22/2016] [Indexed: 01/02/2023] Open
Abstract
DNA methylation, through 5-methyl- and 5-hydroxymethylcytosine (5mC and 5hmC), is considered to be one of the principal interfaces between the genome and our environment, and it helps explain phenotypic variations in human populations. Initial reports of large differences in methylation level in genomic regulatory regions, coupled with clear gene expression data in both imprinted genes and malignant diseases, provided easily dissected molecular mechanisms for switching genes on or off. However, a more subtle process is becoming evident, where small (<10 %) changes to intermediate methylation levels are associated with complex disease phenotypes. This has resulted in two clear methylation paradigms. The latter “subtle change” paradigm is rapidly becoming the epigenetic hallmark of complex disease phenotypes, although we are currently hampered by a lack of data addressing the true biological significance and meaning of these small differences. Our initial expectation of rapidly identifying mechanisms linking environmental exposure to a disease phenotype led to numerous observational/association studies being performed. Although this expectation remains unmet, there is now a growing body of literature on specific genes, suggesting wide ranging transcriptional and translational consequences of such subtle methylation changes. Data from the glucocorticoid receptor (NR3C1) has shown that a complex interplay between DNA methylation, extensive 5′UTR splicing, and microvariability gives rise to the overall level and relative distribution of total and N-terminal protein isoforms generated. Additionally, the presence of multiple AUG translation initiation codons throughout the complete, processed mRNA enables translation variability, hereby enhancing the translational isoforms and the resulting protein isoform diversity, providing a clear link between small changes in DNA methylation and significant changes in protein isoforms and cellular locations. Methylation changes in the NR3C1 CpG island alters the NR3C1 transcription and eventually protein isoforms in the tissues, resulting in subtle but visible physiological variability. This review addresses the current pathophysiological and clinical associations of such characteristically small DNA methylation changes, the ever-growing roles of DNA methylation and the evidence available, particularly from the glucocorticoid receptor of the cascade of events initiated by such subtle methylation changes, as well as addressing the underlying question as to what represents a genuine biologically significant difference in methylation.
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Bønnelykke K, Ober C. Leveraging gene-environment interactions and endotypes for asthma gene discovery. J Allergy Clin Immunol 2016; 137:667-79. [PMID: 26947980 DOI: 10.1016/j.jaci.2016.01.006] [Citation(s) in RCA: 80] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2015] [Revised: 12/30/2015] [Accepted: 01/08/2016] [Indexed: 12/20/2022]
Abstract
Asthma is a heterogeneous clinical syndrome that includes subtypes of disease with different underlying causes and disease mechanisms. Asthma is caused by a complex interaction between genes and environmental exposures; early-life exposures in particular play an important role. Asthma is also heritable, and a number of susceptibility variants have been discovered in genome-wide association studies, although the known risk alleles explain only a small proportion of the heritability. In this review, we present evidence supporting the hypothesis that focusing on more specific asthma phenotypes, such as childhood asthma with severe exacerbations, and on relevant exposures that are involved in gene-environment interactions (GEIs), such as rhinovirus infections, will improve detection of asthma genes and our understanding of the underlying mechanisms. We will discuss the challenges of considering GEIs and the advantages of studying responses to asthma-associated exposures in clinical birth cohorts, as well as in cell models of GEIs, to dissect the context-specific nature of genotypic risks, to prioritize variants in genome-wide association studies, and to identify pathways involved in pathogenesis in subgroups of patients. We propose that such approaches, in spite of their many challenges, present great opportunities for better understanding of asthma pathogenesis and heterogeneity and, ultimately, for improving prevention and treatment of disease.
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Affiliation(s)
- Klaus Bønnelykke
- COPSAC (Copenhagen Prospective Studies on Asthma in Childhood), Herlev and Gentofte Hospital, University of Copenhagen, Copenhagen, Denmark.
| | - Carole Ober
- Department of Human Genetics, University of Chicago, Chicago, Ill.
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