151
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Affiliation(s)
- Richard Saffery
- Murdoch Childrens Research Institute, Parkville, Victoria, Australia.,Department of Paediatrics, University of Melbourne, Parkville, Victoria, Australia
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152
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Edgar RD, Jones MJ, Robinson WP, Kobor MS. An empirically driven data reduction method on the human 450K methylation array to remove tissue specific non-variable CpGs. Clin Epigenetics 2017; 9:11. [PMID: 28184257 PMCID: PMC5290610 DOI: 10.1186/s13148-017-0320-z] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2016] [Accepted: 01/31/2017] [Indexed: 11/10/2022] Open
Abstract
Background Population based epigenetic association studies of disease and exposures are becoming more common with the availability of economical genome-wide technologies for interrogation of the methylome, such as the Illumina 450K Human Methylation Array (450K). Often, the expected small number of differentially methylated cytosine-guanine pairs (CpGs) in studies of the human methylome presents a statistical challenge, as the large number of CpGs measured on the 450K necessitates careful multiple test correction. While the 450K is a highly useful tool for population epigenetic studies, many of the CpGs tested are not variable and thus of limited information content in the context of the study and tissue. CpGs with observed lack of variability in the tissue under study could be removed to reduce the data dimensionality, limit the severity of multiple test correction and allow for improved detection of differential DNA methylation. Methods Here, we performed a meta-analysis of 450K data from three commonly studied human tissues, namely blood (605 samples), buccal epithelial cells (121 samples) and placenta (157 samples). We developed lists of CpGs that are non-variable in each tissue. Results These lists are surprisingly large (blood 114,204 CpGs, buccal epithelial cells 120,009 CpGs and placenta 101,367 CpGs) and thus will be valuable filters for epigenetic association studies, considerably reducing the dimensionality of the 450K and subsequently the multiple testing correction severity. Conclusions We propose this empirically derived method for data reduction to allow for more power in detecting differential DNA methylation associated with exposures in studies on the human methylome. Electronic supplementary material The online version of this article (doi:10.1186/s13148-017-0320-z) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Rachel D Edgar
- Department of Medical Genetics, BC Children's Hospital, University of British Columbia, Vancouver, Canada
| | - Meaghan J Jones
- Department of Medical Genetics, BC Children's Hospital, University of British Columbia, Vancouver, Canada
| | - Wendy P Robinson
- Department of Medical Genetics, BC Children's Hospital, University of British Columbia, Vancouver, Canada
| | - Michael S Kobor
- Department of Medical Genetics, BC Children's Hospital, University of British Columbia, Vancouver, Canada
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153
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Grimaldi V, De Pascale MR, Zullo A, Soricelli A, Infante T, Mancini FP, Napoli C. Evidence of epigenetic tags in cardiac fibrosis. J Cardiol 2017; 69:401-408. [DOI: 10.1016/j.jjcc.2016.10.004] [Citation(s) in RCA: 44] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/13/2016] [Revised: 09/17/2016] [Accepted: 10/12/2016] [Indexed: 01/18/2023]
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154
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Epigenome-wide association studies for cancer biomarker discovery in circulating cell-free DNA: technical advances and challenges. Curr Opin Genet Dev 2017; 42:48-55. [DOI: 10.1016/j.gde.2017.01.017] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2016] [Revised: 01/12/2017] [Accepted: 01/27/2017] [Indexed: 12/18/2022]
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155
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Janssen BG, Gyselaers W, Byun HM, Roels HA, Cuypers A, Baccarelli AA, Nawrot TS. Placental mitochondrial DNA and CYP1A1 gene methylation as molecular signatures for tobacco smoke exposure in pregnant women and the relevance for birth weight. J Transl Med 2017; 15:5. [PMID: 28052772 PMCID: PMC5209876 DOI: 10.1186/s12967-016-1113-4] [Citation(s) in RCA: 52] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2016] [Accepted: 12/18/2016] [Indexed: 12/18/2022] Open
Abstract
BACKGROUND Maternal smoking during pregnancy results in an increased risk of low birth weight through perturbations in the utero-placental exchange. Epigenetics and mitochondrial function in fetal tissues might be molecular signatures responsive to in utero tobacco smoke exposure. METHODS In the framework of the ENVIRONAGE birth cohort, we investigated the effect of self-reported tobacco smoke exposure during pregnancy on birth weight and the relation with placental tissue markers such as, (1) relative mitochondrial DNA (mtDNA) content as determined by real-time quantitative PCR, (2) DNA methylation of specific loci of mtDNA (D-loop and MT-RNR1), and (3) DNA methylation of the biotransformation gene CYP1A1 (the last two determined by bisulfite-pyrosequencing). The total pregnant mother sample included 255 non-smokers, 65 former-smokers who had quit smoking before pregnancy, and 62 smokers who continued smoking during pregnancy. RESULTS Smokers delivered newborns with a birth weight on average 208 g lower [95% confidence interval (CI) -318 to -99, p = 0.0002] than mothers who did not smoke during pregnancy. In the smoker group, the relative mtDNA content was lower (-21.6%, 95% CI -35.4 to -4.9%, p = 0.01) than in the non-smoker group; whereas, absolute mtDNA methylation levels of MT-RNR1 were higher (+0.62%, 95% CI 0.21 to 1.02%, p = 0.003). Lower CpG-specific methylation of CYP1A1 in placental tissue (-4.57%, 95% CI -7.15 to -1.98%, p < 0.0001) were observed in smokers compared with non-smokers. Nevertheless, no mediation of CYP1A1 methylation nor any other investigated molecular signature was observed for the association between tobacco smoke exposure and birth weight. CONCLUSIONS mtDNA content, methylation of specific loci of mtDNA, and CYP1A1 methylation in placental tissue may serve as molecular signatures for the association between gestational tobacco smoke exposure and low birth weight.
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Affiliation(s)
- Bram G Janssen
- Centre for Environmental Sciences, Hasselt University, Hasselt, Belgium
| | - Wilfried Gyselaers
- Department of Obstetrics, East-Limburg Hospital, Genk, Belgium.,Department of Physiology, Hasselt University, Diepenbeek, Belgium
| | - Hyang-Min Byun
- Laboratory of Environmental Epigenetics, Exposure Epidemiology and Risk Program, Harvard School of Public Health, Boston, MA, 02215, USA
| | - Harry A Roels
- Centre for Environmental Sciences, Hasselt University, Hasselt, Belgium.,Louvain Centre for Toxicology and Applied Pharmacology (LTAP), Université Catholique de Louvain, Brussels, Belgium
| | - Ann Cuypers
- Centre for Environmental Sciences, Hasselt University, Hasselt, Belgium
| | - Andrea A Baccarelli
- Laboratory of Environmental Epigenetics, Exposure Epidemiology and Risk Program, Harvard School of Public Health, Boston, MA, 02215, USA.,Department of Environmental Health Sciences, Mailman School of Public Health, Columbia University, New York, NY, 10032, USA
| | - Tim S Nawrot
- Centre for Environmental Sciences, Hasselt University, Hasselt, Belgium. .,Department of Public Health & Primary Care, Occupational and Environmental Medicine, Leuven University, Louvain, Belgium. .,Centre for Environmental Sciences, Hasselt University, Agoralaan Gebouw D, 3590, Diepenbeek, Belgium.
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156
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Galanter JM, Gignoux CR, Oh SS, Torgerson D, Pino-Yanes M, Thakur N, Eng C, Hu D, Huntsman S, Farber HJ, Avila PC, Brigino-Buenaventura E, LeNoir MA, Meade K, Serebrisky D, Rodríguez-Cintrón W, Kumar R, Rodríguez-Santana JR, Seibold MA, Borrell LN, Burchard EG, Zaitlen N. Differential methylation between ethnic sub-groups reflects the effect of genetic ancestry and environmental exposures. eLife 2017; 6:e20532. [PMID: 28044981 PMCID: PMC5207770 DOI: 10.7554/elife.20532] [Citation(s) in RCA: 131] [Impact Index Per Article: 18.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2016] [Accepted: 11/23/2016] [Indexed: 12/19/2022] Open
Abstract
Populations are often divided categorically into distinct racial/ethnic groups based on social rather than biological constructs. Genetic ancestry has been suggested as an alternative to this categorization. Herein, we typed over 450,000 CpG sites in whole blood of 573 individuals of diverse Hispanic origin who also had high-density genotype data. We found that both self-identified ethnicity and genetically determined ancestry were each significantly associated with methylation levels at 916 and 194 CpGs, respectively, and that shared genomic ancestry accounted for a median of 75.7% (IQR 45.8% to 92%) of the variance in methylation associated with ethnicity. There was a significant enrichment (p=4.2×10-64) of ethnicity-associated sites amongst loci previously associated environmental exposures, particularly maternal smoking during pregnancy. We conclude that differential methylation between ethnic groups is partially explained by the shared genetic ancestry but that environmental factors not captured by ancestry significantly contribute to variation in methylation.
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Affiliation(s)
- Joshua M Galanter
- Department of Medicine, University of California, San Francisco, United States
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, United States
- Department of Epidemiology and Biostatistics, University of California, San Francisco, San Francisco, United States
| | | | - Sam S Oh
- Department of Medicine, University of California, San Francisco, United States
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, United States
- Department of Epidemiology and Biostatistics, University of California, San Francisco, San Francisco, United States
| | - Dara Torgerson
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, United States
| | - Maria Pino-Yanes
- Hospital Universitario Nuestra Señora de Candelaria, Tenerife, Spain
- CIBER de Enfermedades Respiratorias, Instituto de Salud Carlos III, Madrid, Spain
| | - Neeta Thakur
- Department of Medicine, University of California, San Francisco, United States
| | - Celeste Eng
- Department of Medicine, University of California, San Francisco, United States
| | - Donglei Hu
- Department of Medicine, University of California, San Francisco, United States
| | - Scott Huntsman
- Department of Medicine, University of California, San Francisco, United States
| | - Harold J Farber
- Department of Pediatrics, Baylor College of Medicine and Texas Children’s Hospital, Houston, Texas
| | - Pedro C Avila
- Division of Allergy and Immunology, Feinberg School of Medicine, Northwestern University, Chicago, Illinois
| | | | | | - Kelly Meade
- Department of Pediatrics, Children’s Hospital and Research Center, Oakland, United States
| | | | | | - Rajesh Kumar
- Division of Allergy and Immunology, The Ann and Robert H Lurie Children’s Hospital of Chicago, Chicago, United States
| | | | - Max A Seibold
- Center for Genes, Environment, and Health, Department of Pediatrics, National Jewish Health, Denver, United States
| | - Luisa N Borrell
- Graduate School of Public Health and Health Policy, City University of New York, New York, United States
| | - Esteban G Burchard
- Department of Medicine, University of California, San Francisco, United States
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, United States
| | - Noah Zaitlen
- Department of Medicine, University of California, San Francisco, United States
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157
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Kertes DA, Kamin HS, Hughes DA, Rodney NC, Bhatt S, Mulligan CJ. Prenatal Maternal Stress Predicts Methylation of Genes Regulating the Hypothalamic-Pituitary-Adrenocortical System in Mothers and Newborns in the Democratic Republic of Congo. Child Dev 2016; 87:61-72. [PMID: 26822443 DOI: 10.1111/cdev.12487] [Citation(s) in RCA: 137] [Impact Index Per Article: 17.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Exposure to stress early in life permanently shapes activity of the hypothalamic-pituitary-adrenocortical (HPA) axis and the brain. Prenatally, glucocorticoids pass through the placenta to the fetus with postnatal impacts on brain development, birth weight (BW), and HPA axis functioning. Little is known about the biological mechanisms by which prenatal stress affects postnatal functioning. This study addresses this gap by examining the effect of chronic stress and traumatic war-related stress on epigenetic changes in four key genes regulating the HPA axis in neonatal cord blood, placenta, and maternal blood: CRH, CRHBP, NR3C1, and FKBP5. Participants were 24 mother-newborn dyads in the conflict-ridden region of the eastern Democratic Republic of Congo. BW data were collected at delivery and maternal interviews were conducted to assess culturally relevant chronic and war-related stressors. Chronic stress and war trauma had widespread effects on HPA axis gene methylation, with significant effects observed at transcription factor binding (TFB) sites in all target genes tested. Some changes in methylation were unique to chronic or war stress, whereas others were observed across both stressor types. Moreover, stress exposures impacted maternal and fetal tissues differently, supporting theoretical models that stress impacts vary according to life phase. Methylation in several NR3C1 and CRH CpG sites, all located at TFB sites, was associated with BW. These findings suggest that prenatal stress exposure impacts development via epigenetic changes in HPA axis genes.
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Affiliation(s)
| | | | - David A Hughes
- Institute of Evolutionary Biology (CSIC-Universitat Pompeu Fabra)
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158
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Paul DS, Teschendorff AE, Dang MA, Lowe R, Hawa MI, Ecker S, Beyan H, Cunningham S, Fouts AR, Ramelius A, Burden F, Farrow S, Rowlston S, Rehnstrom K, Frontini M, Downes K, Busche S, Cheung WA, Ge B, Simon MM, Bujold D, Kwan T, Bourque G, Datta A, Lowy E, Clarke L, Flicek P, Libertini E, Heath S, Gut M, Gut IG, Ouwehand WH, Pastinen T, Soranzo N, Hofer SE, Karges B, Meissner T, Boehm BO, Cilio C, Elding Larsson H, Lernmark Å, Steck AK, Rakyan VK, Beck S, Leslie RD. Increased DNA methylation variability in type 1 diabetes across three immune effector cell types. Nat Commun 2016; 7:13555. [PMID: 27898055 PMCID: PMC5141286 DOI: 10.1038/ncomms13555] [Citation(s) in RCA: 111] [Impact Index Per Article: 13.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2016] [Accepted: 10/04/2016] [Indexed: 02/06/2023] Open
Abstract
The incidence of type 1 diabetes (T1D) has substantially increased over the past decade, suggesting a role for non-genetic factors such as epigenetic mechanisms in disease development. Here we present an epigenome-wide association study across 406,365 CpGs in 52 monozygotic twin pairs discordant for T1D in three immune effector cell types. We observe a substantial enrichment of differentially variable CpG positions (DVPs) in T1D twins when compared with their healthy co-twins and when compared with healthy, unrelated individuals. These T1D-associated DVPs are found to be temporally stable and enriched at gene regulatory elements. Integration with cell type-specific gene regulatory circuits highlight pathways involved in immune cell metabolism and the cell cycle, including mTOR signalling. Evidence from cord blood of newborns who progress to overt T1D suggests that the DVPs likely emerge after birth. Our findings, based on 772 methylomes, implicate epigenetic changes that could contribute to disease pathogenesis in T1D.
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Affiliation(s)
- Dirk S. Paul
- Medical Genomics, UCL Cancer Institute, University College London, London WC1E 6BT, UK
- Cardiovascular Epidemiology Unit, Department of Public Health and Primary Care, University of Cambridge, Strangeways Research Laboratory, Cambridge CB1 8RN, UK
| | - Andrew E. Teschendorff
- CAS Key Lab of Computational Biology, CAS-MPG Partner Institute for Computational Biology, Shanghai Institute for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, China
- Statistical Cancer Genomics, UCL Cancer Institute, University College London, London WC1E 6BT, UK
| | - Mary A.N. Dang
- The Blizard Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, London E1 2AT, UK
| | - Robert Lowe
- The Blizard Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, London E1 2AT, UK
| | - Mohammed I. Hawa
- The Blizard Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, London E1 2AT, UK
| | - Simone Ecker
- Medical Genomics, UCL Cancer Institute, University College London, London WC1E 6BT, UK
| | - Huriya Beyan
- The Blizard Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, London E1 2AT, UK
| | - Stephanie Cunningham
- The Blizard Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, London E1 2AT, UK
| | - Alexandra R. Fouts
- Barbara Davis Center for Childhood Diabetes, University of Colorado School of Medicine, Aurora, Colorado 80045, USA
| | - Anita Ramelius
- Department of Clinical Sciences, Lund University, Skåne University Hospital, SE-20502 Malmö, Sweden
| | - Frances Burden
- Department of Haematology, University of Cambridge, Cambridge Biomedical Campus, Cambridge CB2 0PT, UK
- National Health Service Blood and Transplant, Cambridge Biomedical Campus, Cambridge CB2 0PT, UK
| | - Samantha Farrow
- Department of Haematology, University of Cambridge, Cambridge Biomedical Campus, Cambridge CB2 0PT, UK
- National Health Service Blood and Transplant, Cambridge Biomedical Campus, Cambridge CB2 0PT, UK
| | - Sophia Rowlston
- Department of Haematology, University of Cambridge, Cambridge Biomedical Campus, Cambridge CB2 0PT, UK
- National Health Service Blood and Transplant, Cambridge Biomedical Campus, Cambridge CB2 0PT, UK
| | - Karola Rehnstrom
- Department of Haematology, University of Cambridge, Cambridge Biomedical Campus, Cambridge CB2 0PT, UK
- National Health Service Blood and Transplant, Cambridge Biomedical Campus, Cambridge CB2 0PT, UK
| | - Mattia Frontini
- Department of Haematology, University of Cambridge, Cambridge Biomedical Campus, Cambridge CB2 0PT, UK
- National Health Service Blood and Transplant, Cambridge Biomedical Campus, Cambridge CB2 0PT, UK
- British Heart Foundation Centre of Excellence, Cambridge Biomedical Campus, Cambridge CB2 0QQ, UK
| | - Kate Downes
- Department of Haematology, University of Cambridge, Cambridge Biomedical Campus, Cambridge CB2 0PT, UK
- National Health Service Blood and Transplant, Cambridge Biomedical Campus, Cambridge CB2 0PT, UK
| | - Stephan Busche
- Department of Human Genetics, McGill University, Montreal, Québec, Canada H3A 0G1
- McGill University and Genome Quebec Innovation Centre, Montreal, Québec, Canada H3A 0G1
| | - Warren A. Cheung
- Department of Human Genetics, McGill University, Montreal, Québec, Canada H3A 0G1
- McGill University and Genome Quebec Innovation Centre, Montreal, Québec, Canada H3A 0G1
| | - Bing Ge
- Department of Human Genetics, McGill University, Montreal, Québec, Canada H3A 0G1
- McGill University and Genome Quebec Innovation Centre, Montreal, Québec, Canada H3A 0G1
| | - Marie-Michelle Simon
- Department of Human Genetics, McGill University, Montreal, Québec, Canada H3A 0G1
- McGill University and Genome Quebec Innovation Centre, Montreal, Québec, Canada H3A 0G1
| | - David Bujold
- Department of Human Genetics, McGill University, Montreal, Québec, Canada H3A 0G1
- McGill University and Genome Quebec Innovation Centre, Montreal, Québec, Canada H3A 0G1
| | - Tony Kwan
- Department of Human Genetics, McGill University, Montreal, Québec, Canada H3A 0G1
- McGill University and Genome Quebec Innovation Centre, Montreal, Québec, Canada H3A 0G1
| | - Guillaume Bourque
- Department of Human Genetics, McGill University, Montreal, Québec, Canada H3A 0G1
- McGill University and Genome Quebec Innovation Centre, Montreal, Québec, Canada H3A 0G1
| | - Avik Datta
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Ernesto Lowy
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Laura Clarke
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Paul Flicek
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Emanuele Libertini
- Medical Genomics, UCL Cancer Institute, University College London, London WC1E 6BT, UK
| | - Simon Heath
- CNAG-CRG, Centre for Genomic Regulation, Barcelona Institute of Science and Technology (BIST), Baldiri Reixac 4, 08028 Barcelona, Spain
- Universitat Pompeu Fabra, Plaça de la Mercè 10, 08002 Barcelona, Spain
| | - Marta Gut
- CNAG-CRG, Centre for Genomic Regulation, Barcelona Institute of Science and Technology (BIST), Baldiri Reixac 4, 08028 Barcelona, Spain
- Universitat Pompeu Fabra, Plaça de la Mercè 10, 08002 Barcelona, Spain
| | - Ivo G Gut
- CNAG-CRG, Centre for Genomic Regulation, Barcelona Institute of Science and Technology (BIST), Baldiri Reixac 4, 08028 Barcelona, Spain
- Universitat Pompeu Fabra, Plaça de la Mercè 10, 08002 Barcelona, Spain
| | - Willem H. Ouwehand
- Department of Haematology, University of Cambridge, Cambridge Biomedical Campus, Cambridge CB2 0PT, UK
- National Health Service Blood and Transplant, Cambridge Biomedical Campus, Cambridge CB2 0PT, UK
- British Heart Foundation Centre of Excellence, Cambridge Biomedical Campus, Cambridge CB2 0QQ, UK
- Human Genetics, Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SA, UK
| | - Tomi Pastinen
- Department of Human Genetics, McGill University, Montreal, Québec, Canada H3A 0G1
- McGill University and Genome Quebec Innovation Centre, Montreal, Québec, Canada H3A 0G1
| | - Nicole Soranzo
- Department of Haematology, University of Cambridge, Cambridge Biomedical Campus, Cambridge CB2 0PT, UK
- Human Genetics, Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SA, UK
| | - Sabine E. Hofer
- Department of Pediatrics, Medical University of Innsbruck, 6020 Innsbruck, Austria
| | - Beate Karges
- Division of Endocrinology and Diabetes, RWTH Aachen University, 52074 Aachen, Germany
- German Center for Diabetes Research (DZD), 85764 Neuherberg, Germany
| | - Thomas Meissner
- German Center for Diabetes Research (DZD), 85764 Neuherberg, Germany
- Department of General Pediatrics, Neonatology and Pediatric Cardiology, University Children's Hospital, Heinrich Heine University of Düsseldorf, 40225 Düsseldorf, Germany
| | - Bernhard O. Boehm
- Division of Endocrinology, Department of Internal Medicine I, Ulm University Medical Centre, 89081 Ulm, Germany
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore 636921, Singapore
- Imperial College London, London SW7 2AZ, UK
| | - Corrado Cilio
- Department of Clinical Sciences, Lund University, Skåne University Hospital, SE-20502 Malmö, Sweden
| | - Helena Elding Larsson
- Department of Clinical Sciences, Lund University, Skåne University Hospital, SE-20502 Malmö, Sweden
| | - Åke Lernmark
- Department of Clinical Sciences, Lund University, Skåne University Hospital, SE-20502 Malmö, Sweden
| | - Andrea K. Steck
- Barbara Davis Center for Childhood Diabetes, University of Colorado School of Medicine, Aurora, Colorado 80045, USA
| | - Vardhman K. Rakyan
- The Blizard Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, London E1 2AT, UK
| | - Stephan Beck
- Medical Genomics, UCL Cancer Institute, University College London, London WC1E 6BT, UK
| | - R. David Leslie
- The Blizard Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, London E1 2AT, UK
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159
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Dirks RAM, Stunnenberg HG, Marks H. Genome-wide epigenomic profiling for biomarker discovery. Clin Epigenetics 2016; 8:122. [PMID: 27895806 PMCID: PMC5117701 DOI: 10.1186/s13148-016-0284-4] [Citation(s) in RCA: 50] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2016] [Accepted: 11/02/2016] [Indexed: 12/24/2022] Open
Abstract
A myriad of diseases is caused or characterized by alteration of epigenetic patterns, including changes in DNA methylation, post-translational histone modifications, or chromatin structure. These changes of the epigenome represent a highly interesting layer of information for disease stratification and for personalized medicine. Traditionally, epigenomic profiling required large amounts of cells, which are rarely available with clinical samples. Also, the cellular heterogeneity complicates analysis when profiling clinical samples for unbiased genome-wide biomarker discovery. Recent years saw great progress in miniaturization of genome-wide epigenomic profiling, enabling large-scale epigenetic biomarker screens for disease diagnosis, prognosis, and stratification on patient-derived samples. All main genome-wide profiling technologies have now been scaled down and/or are compatible with single-cell readout, including: (i) Bisulfite sequencing to determine DNA methylation at base-pair resolution, (ii) ChIP-Seq to identify protein binding sites on the genome, (iii) DNaseI-Seq/ATAC-Seq to profile open chromatin, and (iv) 4C-Seq and HiC-Seq to determine the spatial organization of chromosomes. In this review we provide an overview of current genome-wide epigenomic profiling technologies and main technological advances that allowed miniaturization of these assays down to single-cell level. For each of these technologies we evaluate their application for future biomarker discovery. We will focus on (i) compatibility of these technologies with methods used for clinical sample preservation, including methods used by biobanks that store large numbers of patient samples, and (ii) automation of these technologies for robust sample preparation and increased throughput.
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Affiliation(s)
- René A M Dirks
- Department of Molecular Biology, Faculty of Science, Radboud Institute for Molecular Life Sciences, Radboud University, 6500HB Nijmegen, The Netherlands
| | - Hendrik G Stunnenberg
- Department of Molecular Biology, Faculty of Science, Radboud Institute for Molecular Life Sciences, Radboud University, 6500HB Nijmegen, The Netherlands
| | - Hendrik Marks
- Department of Molecular Biology, Faculty of Science, Radboud Institute for Molecular Life Sciences, Radboud University, 6500HB Nijmegen, The Netherlands
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160
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Gallaugher M, Canty AJ, Paterson AD. Factors associated with heterogeneity in microarray gene expression in peripheral blood mononuclear cells from large pedigrees. BMC Proc 2016; 10:91-95. [PMID: 27980617 PMCID: PMC5133527 DOI: 10.1186/s12919-016-0011-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
BACKGROUND Genome-wide microarray expression is a rich source of functional genomic data. We examined evidence for differences in expression from peripheral blood mononuclear cells between individuals, examined some of factors that may be responsible and provide recommendations for analysis. METHODS A total of 643 individuals from 17 large Mexican American pedigrees had microarray gene expression data generated from peripheral blood mononuclear cells. This data has previously been used to map cis- and trans-expression quantitative trait loci using genome-wide linkage analysis. We estimated both principal components and cell proportions in these data, and tested them for association with clinical factors to provide insight into causes of variation in gene expression between individuals. RESULTS We identified that there were highly significant differences in the second principal component of gene expression between pedigrees, with 3 pedigrees being outliers. The estimated cell proportions identified 1 individual who was a gross outlier, as well as pedigrees that differed from others in their estimated proportions of helper and cytotoxic T cells. CONCLUSIONS These phenomena could be from either pedigree-specific genetic variation, technical artefacts, or clinical factors. Incorporating factors that influence gene expression into genetic analysis, and exclusion of outliers could improve the power of genetic mapping of expression traits.
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Affiliation(s)
- Michael Gallaugher
- Department of Mathematics and Statistics, McMaster University, Hamilton, ON L8S 4 K1 Canada
| | - Angelo J. Canty
- Department of Mathematics and Statistics, McMaster University, Hamilton, ON L8S 4 K1 Canada
| | - Andrew D. Paterson
- Genetics and Genome Biology Program, The Hospital for Sick Children Research Institute, Toronto, ON M5G 0A4 Canada
- Dalla Lana School of Public Health, University of Toronto, Toronto, ON M5G 0A4 Canada
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161
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Li M, Weinberger DR. RETRACTION: Illuminating the dark road from schizophrenia genetic associations to disease mechanisms. Natl Sci Rev 2016. [DOI: 10.1093/nsr/nww065] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Abstract
Recent large-scale genome-wide association studies (GWAS) have enabled the discovery of common genetic variations contributing to risk architectures of schizophrenia in human populations; however, the majority of GWAS-identified variants are located in large genomic regions spanning multiple genes, and recognizing the precise targets and mechanisms of these clinical associations is now the major challenge. Here, we review recent progress in schizophrenia genetics, functional genomics and related neuroscience research, and propose a functional pipeline to translate schizophrenia GWAS risk loci into disease biology and information for drug discovery. The pipeline includes identification of underlying molecular mechanisms using transcriptomic data in human brain, prioritization of putative functional causative variants by the integration of genetic epidemiological and bioinformatics methods as well as molecular approaches, and in vitro and in vivo experimental characterizations of the identified targeted species and causative variants to dissect the relevant disease biology. These approaches will accelerate progress from schizophrenia genetic studies to biological mechanisms and ultimately guide the development of prognostic, preventive and therapeutic measures.
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Affiliation(s)
- Ming Li
- Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences and Yunnan Province, Kunming Institute of Zoology, Kunming 650223, China
- Lieber Institute for Brain Development, Johns Hopkins Medical Campus, Baltimore, 21205, USA
| | - Daniel R Weinberger
- Lieber Institute for Brain Development, Johns Hopkins Medical Campus, Baltimore, 21205, USA
- Department of Psychiatry, Johns Hopkins University School of Medicine, Baltimore, 21205, USA
- Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, 21205, USA
- Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, 21205, USA
- McKusick Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, 21205, USA
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162
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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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163
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Liu H, Guo G. Opportunities and challenges of big data for the social sciences: The case of genomic data. SOCIAL SCIENCE RESEARCH 2016; 59:13-22. [PMID: 27480368 PMCID: PMC5480284 DOI: 10.1016/j.ssresearch.2016.04.016] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/30/2015] [Revised: 04/08/2016] [Accepted: 04/13/2016] [Indexed: 05/04/2023]
Abstract
In this paper, we draw attention to one unique and valuable source of big data, genomic data, by demonstrating the opportunities they provide to social scientists. We discuss different types of large-scale genomic data and recent advances in statistical methods and computational infrastructure used to address challenges in managing and analyzing such data. We highlight how these data and methods can be used to benefit social science research.
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Affiliation(s)
- Hexuan Liu
- Department of Sociology, The University of North Carolina at Chapel Hill, USA; Carolina Population Center, The University of North Carolina at Chapel Hill, USA; School of Criminal Justice, The University of Cincinnati, USA.
| | - Guang Guo
- Department of Sociology, The University of North Carolina at Chapel Hill, USA; Carolina Center for Genome Sciences, The University of North Carolina at Chapel Hill, USA; Carolina Population Center, The University of North Carolina at Chapel Hill, USA
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164
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Kim S, Eliot M, Koestler DC, Houseman EA, Wetmur JG, Wiencke JK, Kelsey KT. Enlarged leukocyte referent libraries can explain additional variance in blood-based epigenome-wide association studies. Epigenomics 2016; 8:1185-92. [PMID: 27529193 DOI: 10.2217/epi-2016-0037] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
AIM We examined whether variation in blood-based epigenome-wide association studies could be more completely explained by augmenting existing reference DNA methylation libraries. MATERIALS & METHODS We compared existing and enhanced libraries in predicting variability in three publicly available 450K methylation datasets that collected whole-blood samples. Models were fit separately to each CpG site and used to estimate the additional variability when adjustments for cell composition were made with each library. RESULTS Calculation of the mean difference in the CpG-specific residual sums of squares error between models for an arthritis, aging and metabolic syndrome dataset, indicated that an enhanced library explained significantly more variation across all three datasets (p < 10(-3)). CONCLUSION Pathologically important immune cell subtypes can explain important variability in epigenome-wide association studies done in blood.
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Affiliation(s)
- Stephanie Kim
- Department of Epidemiology, Brown University School of Public Health, Providence, RI 02912, USA.,Department of Environmental Health, Boston University School of Public Health, Boston, MA 02118, USA
| | - Melissa Eliot
- Department of Epidemiology, Brown University School of Public Health, Providence, RI 02912, USA
| | - Devin C Koestler
- Department of Biostatistics, University of Kansas Medical Center, Kansas City, KA 66160, USA
| | - Eugene A Houseman
- Oregon State University College of Public Health & Human Sciences, Corvallis, OR 97331, USA
| | - James G Wetmur
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - John K Wiencke
- Department of Neurological Surgery, University of California San Francisco, San Francisco, CA 94158, USA
| | - Karl T Kelsey
- Department of Epidemiology, Brown University School of Public Health, Providence, RI 02912, USA.,Department of Laboratory Medicine & Pathology, Brown University, Providence, RI 02912, USA
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165
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Williams L, Seki Y, Delahaye F, Cheng A, Fuloria M, Hughes Einstein F, Charron MJ. DNA hypermethylation of CD3(+) T cells from cord blood of infants exposed to intrauterine growth restriction. Diabetologia 2016; 59:1714-23. [PMID: 27185256 DOI: 10.1007/s00125-016-3983-7] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/22/2016] [Accepted: 04/19/2016] [Indexed: 12/18/2022]
Abstract
AIMS/HYPOTHESIS Intrauterine growth restriction (IUGR) is associated with increased susceptibility to obesity, metabolic syndrome and type 2 diabetes. Although the mechanisms underlying the developmental origins of metabolic disease are poorly understood, evidence suggests that epigenomic alterations play a critical role. We sought to identify changes in DNA methylation patterns that are associated with IUGR in CD3(+) T cells purified from umbilical cord blood obtained from male newborns who were appropriate for gestational age (AGA) or who had been exposed to IUGR. METHODS CD3(+) T cells were isolated from cord blood obtained from IUGR and AGA infants. The genome-wide methylation profile in eight AGA and seven IUGR samples was determined using the HELP tagging assay. Validation analysis using targeted bisulfite sequencing and bisulfite massARRAY was performed on the original cohort as well as biological replicates consisting of two AGA and four IUGR infants. The Segway algorithm was used to identify methylation changes within regulatory regions of the genome. RESULTS A global shift towards hypermethylation in IUGR was seen compared with AGA (89.8% of 4,425 differentially methylated loci), targeted to regulatory regions of the genome, specifically promoters and enhancers. Pathway analysis identified dysregulation of pathways involved in metabolic disease (type 2 diabetes mellitus, insulin signalling, mitogen-activated protein kinase signalling) and T cell development, regulation and activation (T cell receptor signalling), as well as transcription factors (TCF3, LEF1 and NFATC) that regulate T cells. Furthermore, bump-hunting analysis revealed differentially methylated regions in PRDM16 and HLA-DPB1, genes important for adipose tissue differentiation, stem cell maintenance and function and T cell activation. CONCLUSIONS/INTERPRETATION Our findings suggest that the alterations in methylation patterns observed in IUGR CD3(+) T cells may have functional consequences in targeted genes, regulatory regions and transcription factors. These may serve as biomarkers to identify those at 'high risk' for diminished attainment of full health potential who can benefit from early interventions. ACCESS TO RESEARCH MATERIALS HELP tagging data: Gene Expression Omnibus database (GSE77268), scheduled to be released on 25 January 2019.
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Affiliation(s)
- Lyda Williams
- Department of Biochemistry, Albert Einstein College of Medicine, 1300 Morris Park Avenue, Rm F312, Bronx, NY, 10461, USA
| | - Yoshinori Seki
- Department of Biochemistry, Albert Einstein College of Medicine, 1300 Morris Park Avenue, Rm F312, Bronx, NY, 10461, USA
| | - Fabien Delahaye
- Department of Obstetrics and Gynecology and Women's Health, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Alex Cheng
- Department of Biochemistry, Albert Einstein College of Medicine, 1300 Morris Park Avenue, Rm F312, Bronx, NY, 10461, USA
| | - Mamta Fuloria
- Department of Pediatrics, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Francine Hughes Einstein
- Department of Obstetrics and Gynecology and Women's Health, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Maureen J Charron
- Department of Biochemistry, Albert Einstein College of Medicine, 1300 Morris Park Avenue, Rm F312, Bronx, NY, 10461, USA.
- Department of Obstetrics and Gynecology and Women's Health, Albert Einstein College of Medicine, Bronx, NY, USA.
- Department of Medicine, Division of Endocrinology, Albert Einstein College of Medicine, Bronx, NY, USA.
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166
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Lin X, Barton S, Holbrook JD. How to make DNA methylome wide association studies more powerful. Epigenomics 2016; 8:1117-29. [PMID: 27052998 PMCID: PMC5066141 DOI: 10.2217/epi-2016-0017] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2016] [Accepted: 03/23/2016] [Indexed: 02/06/2023] Open
Abstract
Genome-wide association studies had a troublesome adolescence, while researchers increased statistical power, in part by increasing subject numbers. Interrogating the interaction of genetic and environmental influences raised new challenges of statistical power, which were not easily bested by the addition of subjects. Screening the DNA methylome offers an attractive alternative as methylation can be thought of as a proxy for the combined influences of genetics and environment. There are statistical challenges unique to DNA methylome data and also multiple features, which can be exploited to increase power. We anticipate the development of DNA methylome association study designs and new analytical methods, together with integration of data from other molecular species and other studies, which will boost statistical power and tackle causality. In this way, the molecular trajectories that underlie disease development will be uncovered.
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Affiliation(s)
- Xinyi Lin
- Singapore Institute for Clinical Sciences (SICS), Agency for Science & Technology Research (A*STAR), Brenner Centre for Molecular Medicine, 30 Medical Drive, 117609, Singapore
| | - Sheila Barton
- MRC Lifecourse Epidemiology Unit, Faculty of Medicine, University of Southampton, Southampton, SO16 6YD, UK
| | - Joanna D Holbrook
- Singapore Institute for Clinical Sciences (SICS), Agency for Science & Technology Research (A*STAR), Brenner Centre for Molecular Medicine, 30 Medical Drive, 117609, Singapore
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167
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Townsend MK, Aschard H, De Vivo I, Michels KB, Kraft P. Genomics, Telomere Length, Epigenetics, and Metabolomics in the Nurses' Health Studies. Am J Public Health 2016; 106:1663-8. [PMID: 27459442 DOI: 10.2105/ajph.2016.303344] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
OBJECTIVES To review the contribution of the Nurses' Health Study (NHS) and NHS II to genomics, epigenetics, and metabolomics research. METHODS We performed a narrative review of the publications of the NHS and NHS II between 1990 and 2016 based on biospecimens, including blood and tumor tissue, collected from participants. RESULTS The NHS has contributed to the discovery of genetic loci influencing more than 45 complex human phenotypes, including cancers, diabetes, cardiovascular disease, reproductive characteristics, and anthropometric traits. The combination of genomewide genotype data with extensive exposure and lifestyle data has enabled the evaluation of gene-environment interactions. Furthermore, data suggest that longer telomere length increases risk of cancers not related to smoking, and that modifiable factors (e.g., diet) may have an impact on telomere length. "Omics" research in the NHS continues to expand, with epigenetics and metabolomics becoming greater areas of focus. CONCLUSIONS The combination of prospective biomarker data and broad exposure information has enabled the NHS to participate in a variety of "omics" research, contributing to understanding of the epidemiology and biology of multiple complex diseases.
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Affiliation(s)
- Mary K Townsend
- Mary K. Townsend is with the Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA. Hugues Aschard and Peter Kraft are with the Department of Epidemiology at the Harvard T. H. Chan School of Public Health, Boston. Immaculata De Vivo is with the Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School and the Department of Epidemiology at the Harvard T. H. Chan School of Public Health. Karin B. Michels is with the Channing Division of Network Medicine in the Department of Medicine and the Obstetrics and Gynecology Epidemiology Center in the Department of Obstetrics, Gynecology, and Reproductive Biology at Brigham and Women's Hospital and Harvard Medical School, and the Department of Epidemiology at the Harvard T. H. Chan School of Public Health
| | - Hugues Aschard
- Mary K. Townsend is with the Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA. Hugues Aschard and Peter Kraft are with the Department of Epidemiology at the Harvard T. H. Chan School of Public Health, Boston. Immaculata De Vivo is with the Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School and the Department of Epidemiology at the Harvard T. H. Chan School of Public Health. Karin B. Michels is with the Channing Division of Network Medicine in the Department of Medicine and the Obstetrics and Gynecology Epidemiology Center in the Department of Obstetrics, Gynecology, and Reproductive Biology at Brigham and Women's Hospital and Harvard Medical School, and the Department of Epidemiology at the Harvard T. H. Chan School of Public Health
| | - Immaculata De Vivo
- Mary K. Townsend is with the Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA. Hugues Aschard and Peter Kraft are with the Department of Epidemiology at the Harvard T. H. Chan School of Public Health, Boston. Immaculata De Vivo is with the Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School and the Department of Epidemiology at the Harvard T. H. Chan School of Public Health. Karin B. Michels is with the Channing Division of Network Medicine in the Department of Medicine and the Obstetrics and Gynecology Epidemiology Center in the Department of Obstetrics, Gynecology, and Reproductive Biology at Brigham and Women's Hospital and Harvard Medical School, and the Department of Epidemiology at the Harvard T. H. Chan School of Public Health
| | - Karin B Michels
- Mary K. Townsend is with the Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA. Hugues Aschard and Peter Kraft are with the Department of Epidemiology at the Harvard T. H. Chan School of Public Health, Boston. Immaculata De Vivo is with the Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School and the Department of Epidemiology at the Harvard T. H. Chan School of Public Health. Karin B. Michels is with the Channing Division of Network Medicine in the Department of Medicine and the Obstetrics and Gynecology Epidemiology Center in the Department of Obstetrics, Gynecology, and Reproductive Biology at Brigham and Women's Hospital and Harvard Medical School, and the Department of Epidemiology at the Harvard T. H. Chan School of Public Health
| | - Peter Kraft
- Mary K. Townsend is with the Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA. Hugues Aschard and Peter Kraft are with the Department of Epidemiology at the Harvard T. H. Chan School of Public Health, Boston. Immaculata De Vivo is with the Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School and the Department of Epidemiology at the Harvard T. H. Chan School of Public Health. Karin B. Michels is with the Channing Division of Network Medicine in the Department of Medicine and the Obstetrics and Gynecology Epidemiology Center in the Department of Obstetrics, Gynecology, and Reproductive Biology at Brigham and Women's Hospital and Harvard Medical School, and the Department of Epidemiology at the Harvard T. H. Chan School of Public Health
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168
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Klein HU, De Jager PL. Uncovering the Role of the Methylome in Dementia and Neurodegeneration. Trends Mol Med 2016; 22:687-700. [PMID: 27423266 DOI: 10.1016/j.molmed.2016.06.008] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2016] [Revised: 06/13/2016] [Accepted: 06/15/2016] [Indexed: 12/14/2022]
Abstract
Our understanding of the epigenome has advanced dramatically over the past decade, particularly in terms of DNA methylation, a modification found throughout the genome. Studies of the brain and neurons have outlined an increasingly complex architecture involving not just CG dinucleotide methylation but also methylation of other dinucleotides, and modifications of methylated bases such as 5-hydroxymethylcytosine. Different modifications may play an important role in brain development, function and decline; recent descriptions of the effects of aging and neurodegenerative processes such as Alzheimer disease on methylation profiles have ushered in an era of DNA methylome-wide association studies. Rapidly improving technologies and study designs are returning robust results, and investigations of the human brain's epigenome are increasingly feasible, complementing insights gained from genetic studies.
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Affiliation(s)
- Hans-Ulrich Klein
- Program in Translational Neuropsychiatric Genomics and Partners Multiple Sclerosis Center, Ann Romney Center for Neurologic Diseases, Department of Neurology, Brigham and Women's Hospital, Boston, MA, USA; Harvard Medical School, Boston, MA, USA; Program in Medical and Population Genetics, Broad Institute, Cambridge, MA, USA
| | - Philip L De Jager
- Program in Translational Neuropsychiatric Genomics and Partners Multiple Sclerosis Center, Ann Romney Center for Neurologic Diseases, Department of Neurology, Brigham and Women's Hospital, Boston, MA, USA; Harvard Medical School, Boston, MA, USA; Program in Medical and Population Genetics, Broad Institute, Cambridge, MA, USA.
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169
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Lappalainen T. Functional genomics bridges the gap between quantitative genetics and molecular biology. Genome Res 2016; 25:1427-31. [PMID: 26430152 PMCID: PMC4579327 DOI: 10.1101/gr.190983.115] [Citation(s) in RCA: 53] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Deep characterization of molecular function of genetic variants in the human genome is becoming increasingly important for understanding genetic associations to disease and for learning to read the regulatory code of the genome. In this paper, I discuss how recent advances in both quantitative genetics and molecular biology have contributed to understanding functional effects of genetic variants, lessons learned from eQTL studies, and future challenges in this field.
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Affiliation(s)
- Tuuli Lappalainen
- New York Genome Center, New York, New York 10013, USA; Department of Systems Biology, Columbia University, New York, New York 10032, USA
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170
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Muka T, Nano J, Voortman T, Braun KVE, Ligthart S, Stranges S, Bramer WM, Troup J, Chowdhury R, Dehghan A, Franco OH. The role of global and regional DNA methylation and histone modifications in glycemic traits and type 2 diabetes: A systematic review. Nutr Metab Cardiovasc Dis 2016; 26:553-566. [PMID: 27146363 DOI: 10.1016/j.numecd.2016.04.002] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/09/2015] [Revised: 04/04/2016] [Accepted: 04/04/2016] [Indexed: 02/08/2023]
Abstract
BACKGROUND New evidence suggests the potential involvement of epigenetic mechanisms in type 2 diabetes (T2D) as a crucial interface between the effects of genetic predisposition and environmental influences. AIM To systematically review studies investigating the association between epigenetic marks (DNA methylation and histone modifications) with T2D and glycemic traits (glucose and insulin levels, insulin resistance measured by HOMA-IR). METHOD AND RESULTS Six bibliographic databases (Embase.com, Medline (Ovid), Web-of-Science, PubMed, Cochrane Central and Google Scholar) were screened until 28th August 2015. We included randomized controlled trials, cohort, case-control and cross-sectional studies in humans that examined the association between epigenetic marks (global, candidate or genome-wide methylation of DNA and histone modifications) with T2D, glucose and insulin levels and insulin metabolism. Of the initially identified 3879 references, 53 articles, based on 47 unique studies met our inclusion criteria. Overall, data were available on 10,823 participants, with a total of 3358 T2D cases. There was no consistent evidence for an association between global DNA-methylation with T2D, glucose, insulin and insulin resistance. The studies reported epigenetic regulation of several candidate genes for diabetes susceptibility in blood cells, muscle, adipose tissue and placenta to be related with T2D without any general overlap between them. Histone modifications in relation to T2D were reported only in 3 observational studies. CONCLUSIONS AND RELEVANCE Current evidence supports an association between epigenetic marks and T2D. However, overall evidence is limited, highlighting the need for further larger-scale and prospective investigations to establish whether epigenetic marks may influence the risk of developing T2D.
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Affiliation(s)
- T Muka
- Department of Epidemiology, Erasmus MC, University Medical Center, Rotterdam, The Netherlands; Department of Nutrition, Harvard T.H. Chan School of Public Health, Boston, MA, USA.
| | - J Nano
- Department of Epidemiology, Erasmus MC, University Medical Center, Rotterdam, The Netherlands
| | - T Voortman
- Department of Epidemiology, Erasmus MC, University Medical Center, Rotterdam, The Netherlands; Department of Nutrition, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - K V E Braun
- Department of Epidemiology, Erasmus MC, University Medical Center, Rotterdam, The Netherlands
| | - S Ligthart
- Department of Epidemiology, Erasmus MC, University Medical Center, Rotterdam, The Netherlands
| | - S Stranges
- Department of Population Health, Luxembourg Institute of Health, Luxembourg
| | - W M Bramer
- Medical Library, Erasmus MC, University Medical Center, Rotterdam, The Netherlands
| | - J Troup
- Research and Development, Metagenics, Inc, USA
| | - R Chowdhury
- Department of Public Health & Primary Care, Cardiovascular Epidemiology Unit, University of Cambridge, Cambridge, CB1 8RN, United Kingdom
| | - A Dehghan
- Department of Epidemiology, Erasmus MC, University Medical Center, Rotterdam, The Netherlands
| | - O H Franco
- Department of Epidemiology, Erasmus MC, University Medical Center, Rotterdam, The Netherlands
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171
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Quantitative comparison of DNA methylation assays for biomarker development and clinical applications. Nat Biotechnol 2016; 34:726-37. [PMID: 27347756 DOI: 10.1038/nbt.3605] [Citation(s) in RCA: 223] [Impact Index Per Article: 27.9] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2015] [Accepted: 05/10/2016] [Indexed: 02/08/2023]
Abstract
DNA methylation patterns are altered in numerous diseases and often correlate with clinically relevant information such as disease subtypes, prognosis and drug response. With suitable assays and after validation in large cohorts, such associations can be exploited for clinical diagnostics and personalized treatment decisions. Here we describe the results of a community-wide benchmarking study comparing the performance of all widely used methods for DNA methylation analysis that are compatible with routine clinical use. We shipped 32 reference samples to 18 laboratories in seven different countries. Researchers in those laboratories collectively contributed 21 locus-specific assays for an average of 27 predefined genomic regions, as well as six global assays. We evaluated assay sensitivity on low-input samples and assessed the assays' ability to discriminate between cell types. Good agreement was observed across all tested methods, with amplicon bisulfite sequencing and bisulfite pyrosequencing showing the best all-round performance. Our technology comparison can inform the selection, optimization and use of DNA methylation assays in large-scale validation studies, biomarker development and clinical diagnostics.
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172
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Abstract
Epigenome-wide association studies represent one means of applying genome-wide assays to identify molecular events that could be associated with human phenotypes. The epigenome is especially intriguing as a target for study, as epigenetic regulatory processes are, by definition, heritable from parent to daughter cells and are found to have transcriptional regulatory properties. As such, the epigenome is an attractive candidate for mediating long-term responses to cellular stimuli, such as environmental effects modifying disease risk. Such epigenomic studies represent a broader category of disease -omics, which suffer from multiple problems in design and execution that severely limit their interpretability. Here we define many of the problems with current epigenomic studies and propose solutions that can be applied to allow this and other disease -omics studies to achieve their potential for generating valuable insights.
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Affiliation(s)
- Ewan Birney
- European Bioinformatics Institute (EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge, United Kingdom
| | - George Davey Smith
- University of Bristol, School of Social and Community Medicine, Oakfield House, Oakfield Grove, United Kingdom
| | - John M. Greally
- Department of Genetics, Albert Einstein College of Medicine, Bronx, New York, United States of America
- * E-mail:
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173
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Suzuki M, Maekawa R, Patterson NE, Reynolds DM, Calder BR, Reznik SE, Heo HJ, Einstein FH, Greally JM. Amnion as a surrogate tissue reporter of the effects of maternal preeclampsia on the fetus. Clin Epigenetics 2016; 8:67. [PMID: 27293492 PMCID: PMC4902972 DOI: 10.1186/s13148-016-0234-1] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2016] [Accepted: 06/02/2016] [Indexed: 01/17/2023] Open
Abstract
BACKGROUND Preeclampsia, traditionally characterized by high blood pressure and proteinuria, is a common pregnancy complication, which affects 2-8 % of all pregnancies. Although children born to women with preeclampsia have a higher risk of hypertension in later life, the mechanism of this increased risk is unknown. DNA methylation is an epigenetic modification that has been studied as a mediator of cellular memory of adverse exposures in utero. Since each cell type in the body has a unique DNA profile, cell subtype composition is a major confounding factor in studies of tissues with heterogeneous cell types. The best way to avoid this confounding effect is by using purified cell types. However, using purified cell types in large cohort translational studies is difficult. The amnion, the inner layer of the fetal membranes of the placenta, is derived from the epiblast and consists of two cell types, which are easy to isolate from the delivered placenta. In this study, we demonstrate the value of using amnion samples for DNA methylation studies, revealing distinctive patterns between fetuses exposed to proteinuria or hypertension and fetuses from normal pregnancies. RESULTS We performed a genome-wide DNA methylation analysis, HpaII tiny fragment Enrichment by Ligation-mediated PCR (HELP)-tagging, on 62 amnion samples from the placentas of uncomplicated, normal pregnancies and from those with complications of preeclampsia or hypertension. Using a regression model approach, we found 123, 85, and 99 loci with high-confidence hypertension-associated, proteinuria-associated, and hypertension- and proteinuria-associated DNA methylation changes, respectively. A gene ontology analysis showed DNA methylation changes to be selecting genes with different biological processes in exposure status. We also found that these differentially methylated regions overlap loci previously reported as differentially methylated regions in preeclampsia. CONCLUSIONS Our findings support prior observations that preeclampsia is associated with changes of DNA methylation near genes that have previously been found to be dysregulated in preeclampsia. We propose that amniotic membranes represent a valuable surrogate fetal tissue on which to perform epigenome-wide association studies of adverse intrauterine conditions.
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Affiliation(s)
- Masako Suzuki
- />Center for Epigenomics, Department of Genetics, Albert Einstein College of Medicine, 1301 Morris Park Avenue, Bronx, NY 10461 USA
| | - Ryo Maekawa
- />Center for Epigenomics, Department of Genetics, Albert Einstein College of Medicine, 1301 Morris Park Avenue, Bronx, NY 10461 USA
- />Department of Obstetrics and Gynecology, Yamaguchi University Graduate School of Medicine, Minamikogushi 1-1-1, Ube, 755-8505 Japan
| | - Nicole E. Patterson
- />Center for Epigenomics, Department of Genetics, Albert Einstein College of Medicine, 1301 Morris Park Avenue, Bronx, NY 10461 USA
| | - David M. Reynolds
- />Center for Epigenomics, Department of Genetics, Albert Einstein College of Medicine, 1301 Morris Park Avenue, Bronx, NY 10461 USA
| | - Brent R. Calder
- />Center for Epigenomics, Department of Genetics, Albert Einstein College of Medicine, 1301 Morris Park Avenue, Bronx, NY 10461 USA
| | - Sandra E. Reznik
- />Department of Pharmaceutical Sciences, College of Pharmacy and Health Sciences, St. John’s University, Jamaica, NY 11439 USA
- />Department of Pathology, Albert Einstein College of Medicine, Bronx, NY 10461 USA
- />Department of Obstetrics and Gynecology and Women’s Health, Albert Einstein College of Medicine, 1301 Morris Park Avenue, Price 322, Bronx, NY 10461 USA
| | - Hye J. Heo
- />Department of Obstetrics and Gynecology and Women’s Health, Albert Einstein College of Medicine, 1301 Morris Park Avenue, Price 322, Bronx, NY 10461 USA
| | - Francine Hughes Einstein
- />Department of Obstetrics and Gynecology and Women’s Health, Albert Einstein College of Medicine, 1301 Morris Park Avenue, Price 322, Bronx, NY 10461 USA
| | - John M. Greally
- />Center for Epigenomics, Department of Genetics, Albert Einstein College of Medicine, 1301 Morris Park Avenue, Bronx, NY 10461 USA
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174
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Ryu D, Xu H, George V, Su S, Wang X, Shi H, Podolsky RH. Differential methylation tests of regulatory regions. Stat Appl Genet Mol Biol 2016; 15:237-51. [PMID: 26982617 DOI: 10.1515/sagmb-2015-0037] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
Differential methylation of regulatory elements is critical in epigenetic researches and can be statistically tested. We developed a new statistical test, the generalized integrated functional test (GIFT), that tests for regional differences in methylation based on the methylation percent at each CpG site within a genomic region. The GIFT uses estimated subject-specific profiles with smoothing methods, specifically wavelet smoothing, and calculates an ANOVA-like test to compare the average profile of groups. In this way, possibly correlated CpG sites within the regulatory region are compared all together. Simulations and analyses of data obtained from patients with chronic lymphocytic leukemia indicate that GIFT has good statistical properties and is able to identify promising genomic regions. Further, GIFT is likely to work with multiple different types of experiments since different smoothing methods can be used to estimate the profiles of data without noise. Matlab code for GIFT and sample data are available at http://www.augusta.edu/mcg/biostatepi/people/software/gift.html.
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175
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Next-generation sequencing identifies major DNA methylation changes during progression of Ph+ chronic myeloid leukemia. Leukemia 2016; 30:1861-8. [PMID: 27211271 PMCID: PMC5240019 DOI: 10.1038/leu.2016.143] [Citation(s) in RCA: 44] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2015] [Revised: 05/11/2016] [Accepted: 05/16/2016] [Indexed: 12/13/2022]
Abstract
Little is known about the impact of DNA methylation on the evolution/progression of Ph+ chronic myeloid leukemia (CML). We investigated the methylome of CML patients in chronic phase (CP-CML), accelerated phase (AP-CML) and blast crisis (BC-CML) as well as in controls by reduced representation bisulfite sequencing. Although only ~600 differentially methylated CpG sites were identified in samples obtained from CP-CML patients compared with controls, ~6500 differentially methylated CpG sites were found in samples from BC-CML patients. In the majority of affected CpG sites, methylation was increased. In CP-CML patients who progressed to AP-CML/BC-CML, we identified up to 897 genes that were methylated at the time of progression but not at the time of diagnosis. Using RNA-sequencing, we observed downregulated expression of many of these genes in BC-CML compared with CP-CML samples. Several of them are well-known tumor-suppressor genes or regulators of cell proliferation, and gene re-expression was observed by the use of epigenetic active drugs. Together, our results demonstrate that CpG site methylation clearly increases during CML progression and that it may provide a useful basis for revealing new targets of therapy in advanced CML.
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176
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Ponsonby AL, Symeonides C, Vuillermin P, Mueller J, Sly PD, Saffery R. Epigenetic regulation of neurodevelopmental genes in response to in utero exposure to phthalate plastic chemicals: How can we delineate causal effects? Neurotoxicology 2016; 55:92-101. [PMID: 27208563 DOI: 10.1016/j.neuro.2016.05.011] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2016] [Revised: 05/03/2016] [Accepted: 05/17/2016] [Indexed: 01/27/2023]
Abstract
Accumulating evidence, from animal models and human observational studies, implicates the in utero (and early postnatal) environment in the 'programming' of risk for a variety of adverse outcomes and health trajectories. The modern environment is replete with man-made compounds such as plastic product chemicals (PPC), including phenols and phthalates. Evidence from several human cohorts implicates exposure to these chemicals in adverse offspring neurodevelopment, though a direct causal relationship has not been firmly established. In this review we consider a potential causal pathway that encompasses epigenetic human variation, and how we might test this mechanistic hypothesis in human studies. In the first part of this report we outline how PPCs induce epigenetic change, focusing on the brain derived neurotrophic factor (BDNF) gene, a key regulator of neurodevelopment. Further, we discuss the role of the epigenetics of BDNF and other genes in neurodevelopment and the emerging human evidence of an association between phthalate exposure and adverse offspring neurodevelopment. We discuss aspects of epidemiological and molecular study design and analysis that could be employed to strengthen the level of human evidence to infer causality. We undertake this using an exemplar recent research example: maternal prenatal smoking, linked to methylation change at the aryl hydrocarbon receptor repressor (AHRR) gene at birth, now shown to mediate some of the effects of maternal smoking on birth weight. Characterizing the relationship between the modern environment and the human molecular pathways underpinning its impact on early development is paramount to understanding the public health significance of modern day chemical exposures.
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Affiliation(s)
- Anne-Louise Ponsonby
- Murdoch Childrens Research Institute, Royal Children's Hospital, University of Melbourne, Parkville, Victoria, Australia.
| | - Christos Symeonides
- Murdoch Childrens Research Institute, Royal Children's Hospital, University of Melbourne, Parkville, Victoria, Australia
| | - Peter Vuillermin
- Murdoch Childrens Research Institute, Royal Children's Hospital, University of Melbourne, Parkville, Victoria, Australia; Deakin University, Geelong, Victoria, Australia; Child Health Research Unit, Barwon Health, Geelong, Victoria, Australia
| | - Jochen Mueller
- National Research Centre for Environmental Toxicology, University of Queensland, Brisbane, Australia
| | - Peter D Sly
- Child Health Research Centre, University of Queensland, Brisbane, Australia
| | - Richard Saffery
- Murdoch Childrens Research Institute, Royal Children's Hospital, University of Melbourne, Parkville, Victoria, Australia
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177
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Oliver VF, Jaffe AE, Song J, Wang G, Zhang P, Branham KE, Swaroop A, Eberhart CG, Zack DJ, Qian J, Merbs SL. Differential DNA methylation identified in the blood and retina of AMD patients. Epigenetics 2016; 10:698-707. [PMID: 26067391 DOI: 10.1080/15592294.2015.1060388] [Citation(s) in RCA: 53] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023] Open
Abstract
Age-related macular degeneration (AMD) is a major cause of blindness in the western world. While genetic studies have linked both common and rare variants in genes involved in regulation of the complement system to increased risk of development of AMD, environmental factors, such as smoking and nutrition, can also significantly affect the risk of developing the disease and the rate of disease progression. Since epigenetics has been implicated in mediating, in part, the disease risk associated with some environmental factors, we investigated a possible epigenetic contribution to AMD. We performed genome-wide DNA methylation profiling of blood from AMD patients and controls. No differential methylation site reached genome-wide significance; however, when epigenetic changes in and around known GWAS-defined AMD risk loci were explored, we found small but significant DNA methylation differences in the blood of neovascular AMD patients near age-related maculopathy susceptibility 2 (ARMS2), a top-ranked GWAS locus preferentially associated with neovascular AMD. The methylation level of one of the CpG sites significantly correlated with the genotype of the risk SNP rs10490924, suggesting a possible epigenetic mechanism of risk. Integrating genome-wide DNA methylation analysis of retina samples with and without AMD together with blood samples, we further identified a consistent, replicable change in DNA methylation in the promoter region of protease serine 50 (PRSS50). These methylation changes may identify sites in novel genes that are susceptible to non-genetic factors known to contribute to AMD development and progression.
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Key Words
- AMD, Age-related macular degeneration
- AMD-MMAP, Michigan, Mayo
- AREDS, Age-Related Eye Disease Study
- AREDS, and Pennsylvania
- DNA methylation
- DNAm, DNA methylation
- GA, geographic atrophy
- GWAS, genome-wide association study
- KEC, Kellogg Eye Center
- LCLs, lymphoblastoid cell lines
- NV, choroidal neovascularization
- RPE, retinal pigment epithelium
- age-related macular degeneration
- genome-wide methylation
- meQTL, methylation quantitative trait loci
- methyl-QTL
- peripheral blood leukocytes
- retina
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Affiliation(s)
- Verity F Oliver
- a Department of Ophthalmology; Johns Hopkins University; School of Medicine ; Baltimore , MD USA
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178
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Taudt A, Colomé-Tatché M, Johannes F. Genetic sources of population epigenomic variation. Nat Rev Genet 2016; 17:319-32. [DOI: 10.1038/nrg.2016.45] [Citation(s) in RCA: 118] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
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179
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Do C, Lang C, Lin J, Darbary H, Krupska I, Gaba A, Petukhova L, Vonsattel JP, Gallagher M, Goland R, Clynes R, Dwork A, Kral J, Monk C, Christiano A, Tycko B. Mechanisms and Disease Associations of Haplotype-Dependent Allele-Specific DNA Methylation. Am J Hum Genet 2016; 98:934-955. [PMID: 27153397 DOI: 10.1016/j.ajhg.2016.03.027] [Citation(s) in RCA: 78] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2015] [Accepted: 03/25/2016] [Indexed: 10/21/2022] Open
Abstract
Haplotype-dependent allele-specific methylation (hap-ASM) can impact disease susceptibility, but maps of this phenomenon using stringent criteria in disease-relevant tissues remain sparse. Here we apply array-based and Methyl-Seq approaches to multiple human tissues and cell types, including brain, purified neurons and glia, T lymphocytes, and placenta, and identify 795 hap-ASM differentially methylated regions (DMRs) and 3,082 strong methylation quantitative trait loci (mQTLs), most not previously reported. More than half of these DMRs have cell type-restricted ASM, and among them are 188 hap-ASM DMRs and 933 mQTLs located near GWAS signals for immune and neurological disorders. Targeted bis-seq confirmed hap-ASM in 12/13 loci tested, including CCDC155, CD69, FRMD1, IRF1, KBTBD11, and S100A(∗)-ILF2, associated with immune phenotypes, MYT1L, PTPRN2, CMTM8 and CELF2, associated with neurological disorders, NGFR and HLA-DRB6, associated with both immunological and brain disorders, and ZFP57, a trans-acting regulator of genomic imprinting. Polymorphic CTCF and transcription factor (TF) binding sites were over-represented among hap-ASM DMRs and mQTLs, and analysis of the human data, supplemented by cross-species comparisons to macaques, indicated that CTCF and TF binding likelihood predicts the strength and direction of the allelic methylation asymmetry. These results show that hap-ASM is highly tissue specific; an important trans-acting regulator of genomic imprinting is regulated by this phenomenon; and variation in CTCF and TF binding sites is an underlying mechanism, and maps of hap-ASM and mQTLs reveal regulatory sequences underlying supra- and sub-threshold GWAS peaks in immunological and neurological disorders.
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180
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How to interpret epigenetic association studies: a guide for clinicians. BONEKEY REPORTS 2016; 5:797. [PMID: 27195108 DOI: 10.1038/bonekey.2016.24] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/03/2015] [Accepted: 03/15/2016] [Indexed: 01/23/2023]
Abstract
Epigenetic mechanisms are able to alter gene expression, without altering DNA sequence, in a stable manner through cell divisions. They include, among others, the methylation of DNA cytosines and microRNAs and allow the cells to adapt to changing environmental conditions. In recent years, epigenetic association studies are providing new insights into the pathogenesis of complex disorders including prevalent skeletal disorders. Unlike the genome, the epigenome is cell and tissue specific and may change with age and a number of acquired factors. This poses particular difficulties for the design and interpretation of epigenetic studies, particularly those exploring the association of genome-wide epigenetic marks with disease phenotypes. In this report, we propose a framework to help in the critical appraisal of epigenetic association studies. In line with previous suggestions, we focus on the questions critical to appraise the validity of the study, to interpret the results and to assess the generalizability and relevance of the information.
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181
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McGregor K, Bernatsky S, Colmegna I, Hudson M, Pastinen T, Labbe A, Greenwood CM. An evaluation of methods correcting for cell-type heterogeneity in DNA methylation studies. Genome Biol 2016; 17:84. [PMID: 27142380 PMCID: PMC4855979 DOI: 10.1186/s13059-016-0935-y] [Citation(s) in RCA: 102] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2016] [Accepted: 04/05/2016] [Indexed: 01/01/2023] Open
Abstract
BACKGROUND Many different methods exist to adjust for variability in cell-type mixture proportions when analyzing DNA methylation studies. Here we present the result of an extensive simulation study, built on cell-separated DNA methylation profiles from Illumina Infinium 450K methylation data, to compare the performance of eight methods including the most commonly used approaches. RESULTS We designed a rich multi-layered simulation containing a set of probes with true associations with either binary or continuous phenotypes, confounding by cell type, variability in means and standard deviations for population parameters, additional variability at the level of an individual cell-type-specific sample, and variability in the mixture proportions across samples. Performance varied quite substantially across methods and simulations. In particular, the number of false positives was sometimes unrealistically high, indicating limited ability to discriminate the true signals from those appearing significant through confounding. Methods that filtered probes had consequently poor power. QQ plots of p values across all tested probes showed that adjustments did not always improve the distribution. The same methods were used to examine associations between smoking and methylation data from a case-control study of colorectal cancer, and we also explored the effect of cell-type adjustments on associations between rheumatoid arthritis cases and controls. CONCLUSIONS We recommend surrogate variable analysis for cell-type mixture adjustment since performance was stable under all our simulated scenarios.
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Affiliation(s)
- Kevin McGregor
- />McGill University, Department of Epidemiology, Biostatistics, and Occupational Health, 1020 Pine Ave. West, Montréal, H3A 1A2 QC Canada
- />Lady Davis Research Institute, Jewish General Hospital, 3755 Chemin de la Côte Sainte Catherine, Montréal, H3T 1E2 QC Canada
| | - Sasha Bernatsky
- />Lady Davis Research Institute, Jewish General Hospital, 3755 Chemin de la Côte Sainte Catherine, Montréal, H3T 1E2 QC Canada
| | - Ines Colmegna
- />The Research Institute of the McGill University Health Centre, Montréal, QC Canada
| | - Marie Hudson
- />Lady Davis Research Institute, Jewish General Hospital, 3755 Chemin de la Côte Sainte Catherine, Montréal, H3T 1E2 QC Canada
- />Division of Rheumatology, Jewish General Hospital, Montréal, QC Canada
- />Department of Medicine, McGill University, Montréal, QC Canada
| | - Tomi Pastinen
- />McGill University and Genome Quebec Innovation Centre, McGill University, Montréal, QC Canada
- />Department of Human Genetics, McGill University, Montréal, QC Canada
| | - Aurélie Labbe
- />McGill University, Department of Epidemiology, Biostatistics, and Occupational Health, 1020 Pine Ave. West, Montréal, H3A 1A2 QC Canada
- />Department of Psychiatry, McGill University, Montréal, QC Canada
- />The Douglas Mental Health University Institute, Verdun, QC Canada
| | - Celia M.T. Greenwood
- />Lady Davis Research Institute, Jewish General Hospital, 3755 Chemin de la Côte Sainte Catherine, Montréal, H3T 1E2 QC Canada
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182
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Wright ML, Dozmorov MG, Wolen AR, Jackson-Cook C, Starkweather AR, Lyon DE, York TP. Establishing an analytic pipeline for genome-wide DNA methylation. Clin Epigenetics 2016; 8:45. [PMID: 27127542 PMCID: PMC4848848 DOI: 10.1186/s13148-016-0212-7] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2016] [Accepted: 04/18/2016] [Indexed: 01/01/2023] Open
Abstract
The need for research investigating DNA methylation (DNAm) in clinical studies has increased, leading to the evolution of new analytic methods to improve accuracy and reproducibility of the interpretation of results from these studies. The purpose of this article is to provide clinical researchers with a summary of the major data processing steps routinely applied in clinical studies investigating genome-wide DNAm using the Illumina HumanMethylation 450K BeadChip. In most studies, the primary goal of employing DNAm analysis is to identify differential methylation at CpG sites among phenotypic groups. Experimental design considerations are crucial at the onset to minimize bias from factors related to sample processing and avoid confounding experimental variables with non-biological batch effects. Although there are currently no de facto standard methods for analyzing these data, we review the major steps in processing DNAm data recommended by several research studies. We describe several variations available for clinical researchers to process, analyze, and interpret DNAm data. These insights are applicable to most types of genome-wide DNAm array platforms and will be applicable for the next generation of DNAm array technologies (e.g., the 850K array). Selection of the DNAm analytic pipeline followed by investigators should be guided by the research question and supported by recently published methods.
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Affiliation(s)
| | - Mikhail G. Dozmorov
- />Department of Biostatistics, Virginia Commonwealth University, Richmond, VA USA
| | - Aaron R. Wolen
- />Center for Clinical and Translational Research, Virginia Commonwealth University, Richmond, VA USA
| | - Colleen Jackson-Cook
- />Departments of Pathology and Human and Molecular Genetics, Virginia Commonwealth University, Richmond, VA USA
| | | | - Debra E. Lyon
- />College of Nursing, University of Florida, Gainesville, FL USA
| | - Timothy P. York
- />Department of Human and Molecular Genetics, Virginia Commonwealth University, Richmond, VA USA
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183
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Chen YC, Chen TW, Su MC, Chen CJ, Chen KD, Liou CW, Tang P, Wang TY, Chang JC, Wang CC, Lin HC, Chin CH, Huang KT, Lin MC, Hsiao CC. Whole Genome DNA Methylation Analysis of Obstructive Sleep Apnea: IL1R2, NPR2, AR, SP140 Methylation and Clinical Phenotype. Sleep 2016; 39:743-55. [PMID: 26888452 DOI: 10.5665/sleep.5620] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2015] [Accepted: 11/03/2015] [Indexed: 12/14/2022] Open
Abstract
STUDY OBJECTIVES We hypothesized that DNA methylation patterns may contribute to disease severity or the development of hypertension and excessive daytime sleepiness (EDS) in patients with obstructive sleep apnea (OSA). METHODS Illumina's (San Diego, CA, USA) DNA methylation 27-K assay was used to identify differentially methylated loci (DML). DNA methylation levels were validated by pyrosequencing. A discovery cohort of 15 patients with OSA and 6 healthy subjects, and a validation cohort of 72 patients with sleep disordered breathing (SDB). RESULTS Microarray analysis identified 636 DMLs in patients with OSA versus healthy subjects, and 327 DMLs in patients with OSA and hypertension versus those without hypertension. In the validation cohort, no significant difference in DNA methylation levels of six selected genes was found between the primary snoring subjects and OSA patients (primary outcome). However, a secondary outcome analysis showed that interleukin-1 receptor 2 (IL1R2) promoter methylation (-114 cytosine followed by guanine dinucleotide sequence [CpG] site) was decreased and IL1R2 protein levels were increased in the patients with SDB with an oxygen desaturation index > 30. Androgen receptor (AR) promoter methylation (-531 CpG site) and AR protein levels were both increased in the patients with SDB with an oxygen desaturation index > 30. Natriuretic peptide receptor 2 (NPR2) promoter methylation (-608/-618 CpG sites) were decreased, whereas levels of both NPR2 and serum C type natriuretic peptide protein were increased in the SDB patients with EDS. Speckled protein 140 (SP140) promoter methylation (-194 CpG site) was increased, and SP140 protein levels were decreased in the patients with SDB and EDS. CONCLUSIONS IL1R2 hypomethylation and AR hypermethylation may constitute an important determinant of disease severity, whereas NPR2 hypomethylation and SP140 hypermethylation may provide a biomarker for vulnerability to EDS in OSA. COMMENTARY A commentary on this article appears in this issue on page 723.
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Affiliation(s)
- Yung-Che Chen
- Division of Pulmonary and Critical Care Medicine, Kaohsiung Chang Gung Memorial Hospital and Chang Gung University College of Medicine, Kaohsiung, Taiwan.,Sleep Center, Kaohsiung Chang Gung Memorial Hospital and Chang Gung University College of Medicine, Kaohsiung, Taiwan.,Graduate Institute of Clinical Medical Sciences, Chang Gung University, Taiwan
| | - Ting-Wen Chen
- Molecular Medicine Research Center, Chang Gung University, Taiwan.,Bioinformatics Center, Chang Gung University, Taiwan
| | - Mao-Chang Su
- Division of Pulmonary and Critical Care Medicine, Kaohsiung Chang Gung Memorial Hospital and Chang Gung University College of Medicine, Kaohsiung, Taiwan.,Sleep Center, Kaohsiung Chang Gung Memorial Hospital and Chang Gung University College of Medicine, Kaohsiung, Taiwan.,Chang Gung University of Science and Technology, Chia-yi, Taiwan
| | - Chung-Jen Chen
- Division of Rheumatology, Kaohsiung Chang Gung Memorial Hospital and Chang Gung University College of Medicine, Kaohsiung, Taiwan
| | - Kuang-Den Chen
- Center of Translational Research in Biomedical Sciences, Kaohsiung Chang Gung Memorial Hospital and Chang Gung University College of Medicine, Kaohsiung, Taiwan
| | - Chia-Wei Liou
- Department of Neurology, Kaohsiung Chang Gung Memorial Hospital and Chang Gung University College of Medicine, Kaohsiung, Taiwan
| | - Petrus Tang
- Molecular Medicine Research Center, Chang Gung University, Taiwan.,Bioinformatics Center, Chang Gung University, Taiwan
| | - Ting-Ya Wang
- Division of Pulmonary and Critical Care Medicine, Kaohsiung Chang Gung Memorial Hospital and Chang Gung University College of Medicine, Kaohsiung, Taiwan
| | - Jen-Chieh Chang
- Graduate Institute of Clinical Medical Sciences, Chang Gung University, Taiwan
| | - Chin-Chou Wang
- Division of Pulmonary and Critical Care Medicine, Kaohsiung Chang Gung Memorial Hospital and Chang Gung University College of Medicine, Kaohsiung, Taiwan.,Sleep Center, Kaohsiung Chang Gung Memorial Hospital and Chang Gung University College of Medicine, Kaohsiung, Taiwan.,Chang Gung University of Science and Technology, Chia-yi, Taiwan
| | - Hsin-Ching Lin
- Sleep Center, Kaohsiung Chang Gung Memorial Hospital and Chang Gung University College of Medicine, Kaohsiung, Taiwan.,Department of Otolaryngology, Kaohsiung Chang Gung Memorial Hospital and Chang Gung University College of Medicine, Kaohsiung, Taiwan
| | - Chien-Hung Chin
- Division of Pulmonary and Critical Care Medicine, Kaohsiung Chang Gung Memorial Hospital and Chang Gung University College of Medicine, Kaohsiung, Taiwan.,Sleep Center, Kaohsiung Chang Gung Memorial Hospital and Chang Gung University College of Medicine, Kaohsiung, Taiwan
| | - Kuo-Tung Huang
- Division of Pulmonary and Critical Care Medicine, Kaohsiung Chang Gung Memorial Hospital and Chang Gung University College of Medicine, Kaohsiung, Taiwan.,Sleep Center, Kaohsiung Chang Gung Memorial Hospital and Chang Gung University College of Medicine, Kaohsiung, Taiwan
| | - Meng-Chih Lin
- Division of Pulmonary and Critical Care Medicine, Kaohsiung Chang Gung Memorial Hospital and Chang Gung University College of Medicine, Kaohsiung, Taiwan.,Sleep Center, Kaohsiung Chang Gung Memorial Hospital and Chang Gung University College of Medicine, Kaohsiung, Taiwan.,Graduate Institute of Clinical Medical Sciences, Chang Gung University, Taiwan
| | - Chang-Chun Hsiao
- Graduate Institute of Clinical Medical Sciences, Chang Gung University, Taiwan
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184
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Koestler DC, Jones MJ, Usset J, Christensen BC, Butler RA, Kobor MS, Wiencke JK, Kelsey KT. Improving cell mixture deconvolution by identifying optimal DNA methylation libraries (IDOL). BMC Bioinformatics 2016; 17:120. [PMID: 26956433 PMCID: PMC4782368 DOI: 10.1186/s12859-016-0943-7] [Citation(s) in RCA: 117] [Impact Index Per Article: 14.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2015] [Accepted: 02/09/2016] [Indexed: 12/16/2022] Open
Abstract
Background Confounding due to cellular heterogeneity represents one of the foremost challenges currently facing Epigenome-Wide Association Studies (EWAS). Statistical methods leveraging the tissue-specificity of DNA methylation for deconvoluting the cellular mixture of heterogenous biospecimens offer a promising solution, however the performance of such methods depends entirely on the library of methylation markers being used for deconvolution. Here, we introduce a novel algorithm for Identifying Optimal Libraries (IDOL) that dynamically scans a candidate set of cell-specific methylation markers to find libraries that optimize the accuracy of cell fraction estimates obtained from cell mixture deconvolution. Results Application of IDOL to training set consisting of samples with both whole-blood DNA methylation data (Illumina HumanMethylation450 BeadArray (HM450)) and flow cytometry measurements of cell composition revealed an optimized library comprised of 300 CpG sites. When compared existing libraries, the library identified by IDOL demonstrated significantly better overall discrimination of the entire immune cell landscape (p = 0.038), and resulted in improved discrimination of 14 out of the 15 pairs of leukocyte subtypes. Estimates of cell composition across the samples in the training set using the IDOL library were highly correlated with their respective flow cytometry measurements, with all cell-specific R2>0.99 and root mean square errors (RMSEs) ranging from [0.97 % to 1.33 %] across leukocyte subtypes. Independent validation of the optimized IDOL library using two additional HM450 data sets showed similarly strong prediction performance, with all cell-specific R2>0.90 and RMSE<4.00 %. In simulation studies, adjustments for cell composition using the IDOL library resulted in uniformly lower false positive rates compared to competing libraries, while also demonstrating an improved capacity to explain epigenome-wide variation in DNA methylation within two large publicly available HM450 data sets. Conclusions Despite consisting of half as many CpGs compared to existing libraries for whole blood mixture deconvolution, the optimized IDOL library identified herein resulted in outstanding prediction performance across all considered data sets and demonstrated potential to improve the operating characteristics of EWAS involving adjustments for cell distribution. In addition to providing the EWAS community with an optimized library for whole blood mixture deconvolution, our work establishes a systematic and generalizable framework for the assembly of libraries that improve the accuracy of cell mixture deconvolution. Electronic supplementary material The online version of this article (doi:10.1186/s12859-016-0943-7) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Devin C Koestler
- Department of Biostatistics, University of Kansas Medical Center, 3901 Rainbow Blvd., Kansas City, 66160, KS, USA.
| | - Meaghan J Jones
- Centre for Molecular Medicine and Therapeutics, Child and Family Research Institute, Department of Medical Genetics, The University of British Columbia, 950 West 28th Ave., Vancouver, V5Z 4H4, BC, Canada.
| | - Joseph Usset
- Department of Biostatistics, University of Kansas Medical Center, 3901 Rainbow Blvd., Kansas City, 66160, KS, USA.
| | - Brock C Christensen
- Department of Epidemiology, Geisel School of Medicine, Dartmouth College, 1 Medical Center Dr., Lebanon, 03756, NH, USA. .,Department of Pharmacology and Toxicology, Dartmouth College, 1 Rope Ferry Rd., Hanover, 03755, NH, USA. .,Department of Community and Family Medicine, Geisel School of Medicine, Dartmouth College, 1 Medical Center Dr., Lebanon, 03756, NH, USA.
| | - Rondi A Butler
- Department of Pathology and Laboratory Medicine, Brown University, 70 Ship St., Providence, 02912, RI, USA.
| | - Michael S Kobor
- Centre for Molecular Medicine and Therapeutics, Child and Family Research Institute, Department of Medical Genetics, The University of British Columbia, 950 West 28th Ave., Vancouver, V5Z 4H4, BC, Canada.
| | - John K Wiencke
- Department of Neurological Surgery, University of California San Francisco, 505 Parnassus Ave., San Francisco, 94143, CA, USA.
| | - Karl T Kelsey
- Department of Pathology and Laboratory Medicine, Brown University, 70 Ship St., Providence, 02912, RI, USA. .,Department of Epidemiology, Brown University, 121 South Main St., Providence, 02912, RI, USA.
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185
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Price EM, Peñaherrera MS, Portales-Casamar E, Pavlidis P, Van Allen MI, McFadden DE, Robinson WP. Profiling placental and fetal DNA methylation in human neural tube defects. Epigenetics Chromatin 2016; 9:6. [PMID: 26889207 PMCID: PMC4756451 DOI: 10.1186/s13072-016-0054-8] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2015] [Accepted: 01/25/2016] [Indexed: 12/16/2022] Open
Abstract
Background The incidence of neural tube defects (NTDs) declined by about 40 % in Canada with the introduction of a national folic acid (FA) fortification program. Despite the fact that few Canadians currently exhibit folate deficiency, NTDs are still the second most common congenital abnormality. FA fortification may have aided in reducing the incidence of NTDs by overcoming abnormal one carbon metabolism cycling, the process which provides one carbon units for methylation of DNA. We considered that NTDs persisting in a folate-replete population may also occur in the context of FA-independent compromised one carbon metabolism, and that this might manifest as abnormal DNA methylation (DNAm). Second trimester human placental chorionic villi, kidney, spinal cord, brain, and muscle were collected from 19 control, 22 spina bifida, and 15 anencephalic fetuses in British Columbia, Canada. DNA was extracted, assessed for methylenetetrahydrofolate reductase (MTHFR) genotype and for genome-wide DNAm using repetitive elements, in addition to the Illumina Infinium HumanMethylation450 (450k) array. Results No difference in repetitive element DNAm was noted between NTD status groups. Using a false discovery rate <0.05 and average group difference in DNAm ≥0.05, differentially methylated array sites were identified only in (1) the comparison of anencephaly to controls in chorionic villi (n = 4 sites) and (2) the comparison of spina bifida to controls in kidney (n = 3342 sites). Conclusions We suggest that the distinctive DNAm of spina bifida kidneys may be consequent to the neural tube defect or reflective of a common etiology for abnormal neural tube and renal development. Though there were some small shifts in DNAm in the other tested tissues, our data do not support the long-standing hypothesis of generalized altered genome-wide DNAm in NTDs. This finding may be related to the fact that most Canadians are not folate deficient, but it importantly opens the field to the investigation of other epigenetic and non-epigenetic mechanisms in the etiology of NTDs. Electronic supplementary material The online version of this article (doi:10.1186/s13072-016-0054-8) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- E Magda Price
- Child and Family Research Institute, 950 W 28th Ave, Vancouver, BC V5Z 4H4 UK ; Dept of Medical Genetics, University of British Columbia, C201-4500 Oak St, Vancouver, BC V6H 3N1 UK ; Dept of Obstetrics and Gynaecology, University of British Columbia, C420-4500 Oak St, Vancouver, BC V6H 3N1 UK
| | - Maria S Peñaherrera
- Child and Family Research Institute, 950 W 28th Ave, Vancouver, BC V5Z 4H4 UK ; Dept of Medical Genetics, University of British Columbia, C201-4500 Oak St, Vancouver, BC V6H 3N1 UK
| | | | - Paul Pavlidis
- Centre for High-Throughput Biology, University of British Columbia, 2185 East Mall, Vancouver, V6T 1Z4 UK ; Dept of Psychiatry, University of British Columbia, 2255 Wesbrook Mall, Vancouver, BC V6T 2A1 UK
| | - Margot I Van Allen
- Dept of Medical Genetics, University of British Columbia, C201-4500 Oak St, Vancouver, BC V6H 3N1 UK
| | - Deborah E McFadden
- Dept of Medical Genetics, University of British Columbia, C201-4500 Oak St, Vancouver, BC V6H 3N1 UK ; Dept of Pathology and Laboratory Medicine, Rm G227-2211, Wesbrook Mall, Vancouver, BC V6T 2B5 UK
| | - Wendy P Robinson
- Child and Family Research Institute, 950 W 28th Ave, Vancouver, BC V5Z 4H4 UK ; Dept of Medical Genetics, University of British Columbia, C201-4500 Oak St, Vancouver, BC V6H 3N1 UK
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186
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Vilahur N, Vahter M, Broberg K. The Epigenetic Effects of Prenatal Cadmium Exposure. Curr Environ Health Rep 2016; 2:195-203. [PMID: 25960943 PMCID: PMC4417128 DOI: 10.1007/s40572-015-0049-9] [Citation(s) in RCA: 55] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Prenatal exposure to the highly toxic and common pollutant cadmium has been associated with adverse effects on child health and development. However, the underlying biological mechanisms of cadmium toxicity remain partially unsolved. Epigenetic disruption due to early cadmium exposure has gained attention as a plausible mode of action, since epigenetic signatures respond to environmental stimuli and the fetus undergoes drastic epigenomic rearrangements during embryogenesis. In the current review, we provide a critical examination of the literature addressing prenatal cadmium exposure and epigenetic effects in human, animal, and in vitro studies. We conducted a PubMed search and obtained eight recent studies addressing this topic, focusing almost exclusively on DNA methylation. These studies provide evidence that cadmium alters epigenetic signatures in the DNA of the placenta and of the newborns, and some studies indicated marked sexual differences for cadmium-related DNA methylation changes. Associations between early cadmium exposure and DNA methylation might reflect interference with de novo DNA methyltransferases. More studies, especially those including environmentally relevant doses, are needed to confirm the toxicoepigenomic effects of prenatal cadmium exposure and how that relates to the observed health effects of cadmium in childhood and later life.
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Affiliation(s)
- Nadia Vilahur
- Institute of Environmental Medicine, Unit of Metals and Health, Karolinska Institutet, Nobels väg 13, Box 210, SE-171 77 Stockholm, Sweden
| | - Marie Vahter
- Institute of Environmental Medicine, Unit of Metals and Health, Karolinska Institutet, Nobels väg 13, Box 210, SE-171 77 Stockholm, Sweden
| | - Karin Broberg
- Institute of Environmental Medicine, Unit of Metals and Health, Karolinska Institutet, Nobels väg 13, Box 210, SE-171 77 Stockholm, Sweden
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187
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Sun YV, Hu YJ. Integrative Analysis of Multi-omics Data for Discovery and Functional Studies of Complex Human Diseases. ADVANCES IN GENETICS 2016; 93:147-90. [PMID: 26915271 DOI: 10.1016/bs.adgen.2015.11.004] [Citation(s) in RCA: 235] [Impact Index Per Article: 29.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Complex and dynamic networks of molecules are involved in human diseases. High-throughput technologies enable omics studies interrogating thousands to millions of makers with similar biochemical properties (eg, transcriptomics for RNA transcripts). However, a single layer of "omics" can only provide limited insights into the biological mechanisms of a disease. In the case of genome-wide association studies, although thousands of single nucleotide polymorphisms have been identified for complex diseases and traits, the functional implications and mechanisms of the associated loci are largely unknown. Additionally, the genomic variants alone are not able to explain the changing disease risk across the life span. DNA, RNA, protein, and metabolite often have complementary roles to jointly perform a certain biological function. Such complementary effects and synergistic interactions between omic layers in the life course can only be captured by integrative study of multiple molecular layers. Building upon the success in single-omics discovery research, population studies started adopting the multi-omics approach to better understanding the molecular function and disease etiology. Multi-omics approaches integrate data obtained from different omic levels to understand their interrelation and combined influence on the disease processes. Here, we summarize major omics approaches available in population research, and review integrative approaches and methodologies interrogating multiple omic layers, which enhance the gene discovery and functional analysis of human diseases. We seek to provide analytical recommendations for different types of multi-omics data and study designs to guide the emerging multi-omic research, and to suggest improvement of the existing analytical methods.
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Affiliation(s)
- Yan V Sun
- Department of Epidemiology, Rollins School of Public Health, Atlanta, GA, United States; Department of Biomedical Informatics, School of Medicine, Atlanta, GA, United States
| | - Yi-Juan Hu
- Department of Biostatistics and Bioinformatics, Rollins School of Public Health, Emory University, Atlanta, GA, United States
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188
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Yan H, Tian S, Slager SL, Sun Z, Ordog T. Genome-Wide Epigenetic Studies in Human Disease: A Primer on -Omic Technologies. Am J Epidemiol 2016; 183:96-109. [PMID: 26721890 DOI: 10.1093/aje/kwv187] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2015] [Accepted: 07/09/2015] [Indexed: 12/12/2022] Open
Abstract
Epigenetic information encoded in covalent modifications of DNA and histone proteins regulates fundamental biological processes through the action of chromatin regulators, transcription factors, and noncoding RNA species. Epigenetic plasticity enables an organism to respond to developmental and environmental signals without genetic changes. However, aberrant epigenetic control plays a key role in pathogenesis of disease. Normal epigenetic states could be disrupted by detrimental mutations and expression alteration of chromatin regulators or by environmental factors. In this primer, we briefly review the epigenetic basis of human disease and discuss how recent discoveries in this field could be translated into clinical diagnosis, prevention, and treatment. We introduce platforms for mapping genome-wide chromatin accessibility, nucleosome occupancy, DNA-binding proteins, and DNA methylation, primarily focusing on the integration of DNA methylation and chromatin immunoprecipitation-sequencing technologies into disease association studies. We highlight practical considerations in applying high-throughput epigenetic assays and formulating analytical strategies. Finally, we summarize current challenges in sample acquisition, experimental procedures, data analysis, and interpretation and make recommendations on further refinement in these areas. Incorporating epigenomic testing into the clinical research arsenal will greatly facilitate our understanding of the epigenetic basis of disease and help identify novel therapeutic targets.
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189
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Zhong J, Agha G, Baccarelli AA. The Role of DNA Methylation in Cardiovascular Risk and Disease: Methodological Aspects, Study Design, and Data Analysis for Epidemiological Studies. Circ Res 2016; 118:119-131. [PMID: 26837743 DOI: 10.1161/circresaha.115.305206] [Citation(s) in RCA: 147] [Impact Index Per Article: 18.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/30/2015] [Accepted: 10/01/2015] [Indexed: 01/14/2023]
Abstract
Epidemiological studies have demonstrated that genetic, environmental, behavioral, and clinical factors contribute to cardiovascular disease development. How these risk factors interact at the cellular level to cause cardiovascular disease is not well known. Epigenetic epidemiology enables researchers to explore critical links between genomic coding, modifiable exposures, and manifestation of disease phenotype. One epigenetic link, DNA methylation, is potentially an important mechanism underlying these associations. In the past decade, there has been a significant increase in the number of epidemiological studies investigating cardiovascular risk factors and outcomes in relation to DNA methylation, but many gaps remain in our understanding of the underlying cause and biological implications. In this review, we provide a brief overview of the biology and mechanisms of DNA methylation and its role in cardiovascular disease. In addition, we summarize the current evidence base in epigenetic epidemiology studies relevant to cardiovascular health and disease and discuss the limitations, challenges, and future directions of the field. Finally, we provide guidelines for well-designed epigenetic epidemiology studies, with particular focus on methodological aspects, study design, and analytical challenges.
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Affiliation(s)
- Jia Zhong
- Department of Environmental Health, Harvard T.H. Chan School of Public Health, Boston, Massachusetts, USA
| | - Golareh Agha
- Department of Environmental Health, Harvard T.H. Chan School of Public Health, Boston, Massachusetts, USA
| | - Andrea A Baccarelli
- Department of Environmental Health, Harvard T.H. Chan School of Public Health, Boston, Massachusetts, USA
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190
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Mitchell C, Schneper LM, Notterman DA. DNA methylation, early life environment, and health outcomes. Pediatr Res 2016; 79:212-9. [PMID: 26466079 PMCID: PMC4798238 DOI: 10.1038/pr.2015.193] [Citation(s) in RCA: 76] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/09/2015] [Accepted: 07/27/2015] [Indexed: 11/09/2022]
Abstract
Epigenetics, and especially DNA methylation, have recently become provocative biological explanations for early-life environmental effects on later health. Despite the large increase in papers on the topic over the last few years, many questions remain with regards to the biological feasibility of this mechanism and the strength of the evidence to date. In this review, we examine the literature on early-life effects on epigenetic patterns, with special emphasis on social environmental influences. First, we review the basic biology of epigenetic modification of DNA and debate the role of early-life stressful, protective, and positive environments on gene-specific, system-specific, and whole-genome epigenetic patterns later in life. Second, we compare the epigenetic literatures of both humans and other animals and review the research linking epigenetic patterns to health in order to complete the mechanistic pathway. Third, we discuss physical environmental and social environmental effects, which have to date, generally not been jointly considered. Finally, we close with a discussion of the current state of the area's research, its future direction, and its potential use in pediatric health.
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Affiliation(s)
- Colter Mitchell
- Survey Research Center and Population Studies Center, University of Michigan, Ann Arbor, Michigan
| | - Lisa M. Schneper
- Department of Molecular Biology, Princeton University, Princeton, New Jersey
| | - Daniel A. Notterman
- Department of Molecular Biology, Princeton University, Princeton, New Jersey
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191
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Ancey PB, Testoni B, Gruffaz M, Cros MP, Durand G, Le Calvez-Kelm F, Durantel D, Herceg Z, Hernandez-Vargas H. Genomic responses to hepatitis B virus (HBV) infection in primary human hepatocytes. Oncotarget 2015; 6:44877-91. [PMID: 26565721 PMCID: PMC4792598 DOI: 10.18632/oncotarget.6270] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2015] [Accepted: 10/14/2015] [Indexed: 01/04/2023] Open
Abstract
Viral infections are able to modify the host's cellular programs, with DNA methylation being a biological intermediate in this process. The extent to which viral infections deregulate gene expression and DNA methylation is not fully understood. In the case of Hepatitis B virus (HBV), there is evidence for an interaction between viral proteins and the host DNA methylation machinery. We studied the ability of HBV to modify the host transcriptome and methylome, using naturally infected primary human hepatocytes to better mimic the clinical setting.Gene expression was especially sensitive to culture conditions, independently of HBV infection. However, we identified non-random changes in gene expression and DNA methylation occurring specifically upon HBV infection. There was little correlation between expression and methylation changes, with transcriptome being a more sensitive marker of time-dependent changes induced by HBV. In contrast, a set of differentially methylated sites appeared early and were stable across the time course experiment. Finally, HBV-induced DNA methylation changes were defined by a specific chromatin context characterized by CpG-poor regions outside of gene promoters.These data support the ability of HBV to modulate host cell expression and methylation programs. In addition, it may serve as a reference for studies addressing the genome-wide consequences of HBV infection in human hepatocytes.
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Affiliation(s)
- Pierre-Benoit Ancey
- Epigenetics Group, International Agency for Research on Cancer (IARC), Lyon, France
| | - Barbara Testoni
- INSERM U1052, Molecular Physiopathology and New Treatments of Viral Hepatitis, Centre de Recherche en Cancérologie (CRCL), Lyon, France
| | - Marion Gruffaz
- INSERM U1052, Molecular Physiopathology and New Treatments of Viral Hepatitis, Centre de Recherche en Cancérologie (CRCL), Lyon, France
| | - Marie-Pierre Cros
- Epigenetics Group, International Agency for Research on Cancer (IARC), Lyon, France
| | - Geoffroy Durand
- Genetic Cancer Susceptibility Group, International Agency for Research on Cancer (IARC), Lyon, France
| | - Florence Le Calvez-Kelm
- Genetic Cancer Susceptibility Group, International Agency for Research on Cancer (IARC), Lyon, France
| | - David Durantel
- INSERM U1052, Molecular Physiopathology and New Treatments of Viral Hepatitis, Centre de Recherche en Cancérologie (CRCL), Lyon, France
| | - Zdenko Herceg
- Epigenetics Group, International Agency for Research on Cancer (IARC), Lyon, France
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192
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Klughammer J, Datlinger P, Printz D, Sheffield NC, Farlik M, Hadler J, Fritsch G, Bock C. Differential DNA Methylation Analysis without a Reference Genome. Cell Rep 2015; 13:2621-2633. [PMID: 26673328 PMCID: PMC4695333 DOI: 10.1016/j.celrep.2015.11.024] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2015] [Revised: 10/12/2015] [Accepted: 11/04/2015] [Indexed: 01/22/2023] Open
Abstract
Genome-wide DNA methylation mapping uncovers epigenetic changes associated with animal development, environmental adaptation, and species evolution. To address the lack of high-throughput methods for DNA methylation analysis in non-model organisms, we developed an integrated approach for studying DNA methylation differences independent of a reference genome. Experimentally, our method relies on an optimized 96-well protocol for reduced representation bisulfite sequencing (RRBS), which we have validated in nine species (human, mouse, rat, cow, dog, chicken, carp, sea bass, and zebrafish). Bioinformatically, we developed the RefFreeDMA software to deduce ad hoc genomes directly from RRBS reads and to pinpoint differentially methylated regions between samples or groups of individuals (http://RefFreeDMA.computational-epigenetics.org). The identified regions are interpreted using motif enrichment analysis and/or cross-mapping to annotated genomes. We validated our method by reference-free analysis of cell-type-specific DNA methylation in the blood of human, cow, and carp. In summary, we present a cost-effective method for epigenome analysis in ecology and evolution, which enables epigenome-wide association studies in natural populations and species without a reference genome.
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Affiliation(s)
- Johanna Klughammer
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, 1090 Vienna, Austria
| | - Paul Datlinger
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, 1090 Vienna, Austria
| | - Dieter Printz
- Children's Cancer Research Institute, St. Anna Kinderkrebsforschung, 1090 Vienna, Austria
| | - Nathan C Sheffield
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, 1090 Vienna, Austria
| | - Matthias Farlik
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, 1090 Vienna, Austria
| | - Johanna Hadler
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, 1090 Vienna, Austria
| | - Gerhard Fritsch
- Children's Cancer Research Institute, St. Anna Kinderkrebsforschung, 1090 Vienna, Austria
| | - Christoph Bock
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, 1090 Vienna, Austria; Department of Laboratory Medicine, Medical University of Vienna, 1090 Vienna, Austria; Max Planck Institute for Informatics, 66123 Saarbrücken, Germany.
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193
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194
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Shridhar K, Walia GK, Aggarwal A, Gulati S, Geetha AV, Prabhakaran D, Dhillon PK, Rajaraman P. DNA methylation markers for oral pre-cancer progression: A critical review. Oral Oncol 2015; 53:1-9. [PMID: 26690652 PMCID: PMC4788701 DOI: 10.1016/j.oraloncology.2015.11.012] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2015] [Revised: 11/10/2015] [Accepted: 11/14/2015] [Indexed: 02/07/2023]
Abstract
Although oral cancers are generally preceded by a well-established pre-cancerous stage, there is a lack of well-defined clinical and morphological criteria to detect and signal progression from pre-cancer to malignant tumours. We conducted a critical review to summarize the evidence regarding aberrant DNA methylation patterns as a potential diagnostic biomarker predicting progression. We identified all relevant human studies published in English prior to 30th April 2015 that examined DNA methylation (%) in oral pre-cancer by searching PubMed, Web-of-Science and Embase databases using combined key-searches. Twenty-one studies (18-cross-sectional; 3-longitudinal) were eligible for inclusion in the review, with sample sizes ranging from 4 to 156 affected cases. Eligible studies examined promoter region hyper-methylation of tumour suppressor genes in pathways including cell-cycle-control (n=15), DNA-repair (n=7), cell-cycle-signalling (n=4) and apoptosis (n=3). Hyper-methylated loci reported in three or more studies included p16, p14, MGMT and DAPK. Two longitudinal studies reported greater p16 hyper-methylation in pre-cancerous lesions transformed to malignancy compared to lesions that regressed (57-63.6% versus 8-32.1%; p<0.01). The one study that explored epigenome-wide methylation patterns reported three novel hyper-methylated loci (TRHDE; ZNF454; KCNAB3). The majority of reviewed studies were small, cross-sectional studies with poorly defined control groups and lacking validation. Whilst limitations in sample size and study design preclude definitive conclusions, current evidence suggests a potential utility of DNA methylation patterns as a diagnostic biomarker for oral pre-cancer progression. Robust studies such as large epigenome-wide methylation explorations of oral pre-cancer with longitudinal tracking are needed to validate the currently reported signals and identify new risk-loci and the biological pathways of disease progression.
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Affiliation(s)
- Krithiga Shridhar
- Centre for Chronic Conditions and Injuries, Public Health Foundation of India, Gurgaon, Haryana, India.
| | - Gagandeep Kaur Walia
- Centre for Chronic Conditions and Injuries, Public Health Foundation of India, Gurgaon, Haryana, India
| | - Aastha Aggarwal
- Centre for Chronic Conditions and Injuries, Public Health Foundation of India, Gurgaon, Haryana, India
| | - Smriti Gulati
- Centre for Chronic Conditions and Injuries, Public Health Foundation of India, Gurgaon, Haryana, India
| | - A V Geetha
- Centre for Chronic Conditions and Injuries, Public Health Foundation of India, Gurgaon, Haryana, India
| | - Dorairaj Prabhakaran
- Centre for Chronic Conditions and Injuries, Public Health Foundation of India, Gurgaon, Haryana, India; Centre for Chronic Disease Control, Gurgaon, Haryana, India; London School of Hygiene and Tropical Medicine, London, United Kingdom
| | - Preet K Dhillon
- Centre for Chronic Conditions and Injuries, Public Health Foundation of India, Gurgaon, Haryana, India
| | - Preetha Rajaraman
- Center for Global Health, National Cancer Institute, NIH, DHHS, Bethesda, Maryland, USA
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195
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Jaffe AE. Postmortem human brain genomics in neuropsychiatric disorders--how far can we go? Curr Opin Neurobiol 2015; 36:107-11. [PMID: 26685806 DOI: 10.1016/j.conb.2015.11.002] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2015] [Revised: 11/17/2015] [Accepted: 11/20/2015] [Indexed: 12/24/2022]
Abstract
Large-scale collection of postmortem human brain tissue and subsequent genomic data generation has become a useful approach for better identifying etiological factors contributing to neuropsychiatric disorders. In particular, studying genetic risk variants in non-psychiatric controls can identify biological mechanisms of risk free from confounding factors related to epiphenomena of illness. While the field has begun moving towards cell type-specific analyses, homogenate brain tissue with accompanying cellular profiles, can still identify useful hypotheses for more focused experiments, particularly when the dysregulated cell types are unknown. Technological advances, larger sample sizes, and focused research questions can continue to further leverage postmortem human brain research to better identify and understand the molecular etiology of neuropsychiatric disorders.
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Affiliation(s)
- Andrew E Jaffe
- Lieber Institute for Brain Development, Johns Hopkins Medical Campus, Baltimore, MD 21205, United States; Department of Mental Health, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD 21205, United States; Department of Biostatistics, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD 21205, United States.
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196
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Langevin SM, Eliot M, Butler RA, Cheong A, Zhang X, McClean MD, Koestler DC, Kelsey KT. CpG island methylation profile in non-invasive oral rinse samples is predictive of oral and pharyngeal carcinoma. Clin Epigenetics 2015; 7:125. [PMID: 26635906 PMCID: PMC4668652 DOI: 10.1186/s13148-015-0160-7] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2015] [Accepted: 12/01/2015] [Indexed: 01/17/2023] Open
Abstract
BACKGROUND There are currently no screening tests in routine use for oral and pharyngeal cancer beyond visual inspection and palpation, which are provided on an opportunistic basis, indicating a need for development of novel methods for early detection, particularly in high-risk populations. We sought to address this need through comprehensive interrogation of CpG island methylation in oral rinse samples. METHODS We used the Infinium HumanMethylation450 BeadArray to interrogate DNA methylation in oral rinse samples collected from 154 patients with incident oral or pharyngeal carcinoma prior to treatment and 72 cancer-free control subjects. Subjects were randomly allocated to either a training or a testing set. For each subject, average methylation was calculated for each CpG island represented on the array. We applied a semi-supervised recursively partitioned mixture model to the CpG island methylation data to identify a classifier for prediction of case status in the training set. We then applied the resultant classifier to the testing set for validation and to assess the predictive accuracy. RESULTS We identified a methylation classifier comprised of 22 CpG islands, which predicted oral and pharyngeal carcinoma with a high degree of accuracy (AUC = 0.92, 95 % CI 0.86, 0.98). CONCLUSIONS This novel methylation panel is a strong predictor of oral and pharyngeal carcinoma case status in oral rinse samples and may have utility in early detection and post-treatment follow-up.
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Affiliation(s)
- Scott M Langevin
- Department of Environmental Health, University of Cincinnati College of Medicine, 160 Panzeca Way, ML0056, Cincinnati, OH 45267 USA
| | - Melissa Eliot
- Department of Epidemiology, Brown University, Providence, RI USA
| | - Rondi A Butler
- Department of Epidemiology, Brown University, Providence, RI USA
| | - Agnes Cheong
- Department of Veterinary and Animal Sciences, University of Massachusetts Amherst, Amherst, MA USA
| | - Xiang Zhang
- Department of Environmental Health, University of Cincinnati College of Medicine, 160 Panzeca Way, ML0056, Cincinnati, OH 45267 USA
| | - Michael D McClean
- Department of Environmental Health, Boston University School of Public Health, Boston, MA USA
| | - Devin C Koestler
- Department of Biostatistics, University of Kansas Medical Center, Kansas City, KA USA
| | - Karl T Kelsey
- Department of Epidemiology, Brown University, Providence, RI USA ; Department of Pathology and Laboratory Medicine, Brown University, 70 Ship Street, Box G-E3, Providence, RI 02912 USA
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197
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Preussner J, Bayer J, Kuenne C, Looso M. ADMIRE: analysis and visualization of differential methylation in genomic regions using the Infinium HumanMethylation450 Assay. Epigenetics Chromatin 2015; 8:51. [PMID: 26628921 PMCID: PMC4666223 DOI: 10.1186/s13072-015-0045-1] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2015] [Accepted: 11/17/2015] [Indexed: 12/18/2022] Open
Abstract
Background DNA methylation at cytosine nucleotides constitutes epigenetic gene regulation impacting cellular development and a wide range of diseases. Cytosine bases of the DNA are converted to 5-methylcytosine by the methyltransferase enzyme, acting as a reversible regulator of gene expression. Due to its outstanding importance in the epigenetic field, a number of lab techniques were developed to interrogate DNA methylation on a global range. Besides whole-genome bisulfite sequencing, the Infinium HumanMethylation450 Assay represents a versatile and cost-effective tool to investigate genome-wide changes of methylation patterns. Results Analysis of DNA Methylation In genomic REgions (ADMIRE) is an open source, semi-automatic analysis pipeline and visualization tool for Infinium HumanMethylation450 Assays with a special focus on ease of use. It features flexible experimental settings, quality control, automatic filtering, normalization, multiple testing, and differential analyses on arbitrary genomic regions. Publication-ready graphics, genome browser tracks, and table outputs include summary data and statistics, permitting instant comparison of methylation profiles between sample groups and the exploration of methylation patterns along the whole genome. ADMIREs statistical approach permits simultaneous large-scale analyses of hundreds of assays with little impact on algorithm runtimes. Conclusions The web-based version of ADMIRE provides a simple interface to researchers with limited programming skills, whereas the offline version is suitable for integration into custom pipelines. ADMIRE may be used via our freely available web service at https://bioinformatics.mpi-bn.mpg.de without any limitations concerning the size of a project. An offline version for local execution is available from our website or GitHub (https://github.molgen.mpg.de/loosolab/admire). Electronic supplementary material The online version of this article (doi:10.1186/s13072-015-0045-1) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Jens Preussner
- Bioinformatics Group, Max Planck Institute for Heart and Lung Research, Ludwigstrasse 43, 61231 Bad Nauheim, Germany
| | - Julia Bayer
- Bioinformatics Group, Max Planck Institute for Heart and Lung Research, Ludwigstrasse 43, 61231 Bad Nauheim, Germany
| | - Carsten Kuenne
- Bioinformatics Group, Max Planck Institute for Heart and Lung Research, Ludwigstrasse 43, 61231 Bad Nauheim, Germany
| | - Mario Looso
- Bioinformatics Group, Max Planck Institute for Heart and Lung Research, Ludwigstrasse 43, 61231 Bad Nauheim, Germany
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Riancho JA. Epigenetics of Osteoporosis: Critical Analysis of Epigenetic Epidemiology Studies. Curr Genomics 2015; 16:405-10. [PMID: 27019615 PMCID: PMC4765527 DOI: 10.2174/1389202916666150817213250] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2015] [Revised: 06/15/2015] [Accepted: 06/15/2015] [Indexed: 11/22/2022] Open
Abstract
Osteoarthritis (OA) is an age-related disease with poorly understood pathogenesis. Recent studies have demonstrated that miRNA might play a key role in OA initiation and development. We reviewed recent publications and elucidated the connection between miRNA and OA cartilage anabolic and catabolic signals, including four signaling pathways: TGF-β/Smads and BMPs signaling, associated with cartilage anabolism; and MAPK and NF-KB signaling, associated with cartilage catabolism. We also explored the relationships with MMP, ADAMTS and NOS (NitricOxide Synthases) families, as well as with the catabolic cytokines IL-1 and TNF-α. The potential role of miRNAs in biological processes such as cartilage degeneration, chondrocyte proliferation, and differentiation is discussed. Collective evidence indicates that miRNAs play a critical role in cartilage degeneration. These findings will aid in understanding the molecular network that governs articular cartilage homeostasis and in to elucidate the role of miRNA in the pathogenesis of OA.
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Affiliation(s)
- José A. Riancho
- Service of Internal Medicine, Hospital U.M. Valdecilla, and Department of Medicine, University of Cantabria. IDIVAL, RETICEF. Santander, Spain
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199
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Yousefi P, Huen K, Quach H, Motwani G, Hubbard A, Eskenazi B, Holland N. Estimation of blood cellular heterogeneity in newborns and children for epigenome-wide association studies. ENVIRONMENTAL AND MOLECULAR MUTAGENESIS 2015; 56:751-8. [PMID: 26332589 PMCID: PMC4636959 DOI: 10.1002/em.21966] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/02/2015] [Revised: 07/01/2015] [Accepted: 07/03/2015] [Indexed: 05/16/2023]
Abstract
Confounding by cellular heterogeneity has become a major concern for epigenome-wide association studies (EWAS) in peripheral blood samples from population and clinical studies. Adjusting for white blood cell percentage estimates produced by the minfi implementation of the Houseman algorithm (minfi) during statistical analysis is now an established method to account for this bias in adults. However, minfi has not been benchmarked against white blood cell counts in children that may differ substantially from the reference dataset used in its estimation. We compared estimates of white blood cell type percentages produced by two methods, minfi and differential cell count (DCC), in a birth cohort at two time points (birth and 12 years of age). We found that both minfi and DCC had similar trends as children aged, and neither count method differed by sex among newborns (P > 0.10). However, minfi estimates did not correlate well with DCC in samples from newborns (ρ = -0.05 for granulocytes; ρ = -0.03 for lymphocytes). In older children, correlation improved substantially (ρ = 0.77 for granulocytes; ρ = 0.75 for lymphocytes), likely due to increasing similarity with minfi's adult reference data as children aged. Our findings suggest that the minfi method may provide suitable estimates of white blood cell composition for samples from adults and older children, but may not currently be appropriate for EWAS involving newborns or young children.
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Affiliation(s)
- Paul Yousefi
- School of Public Health, University of California, Berkeley, CA, USA
| | - Karen Huen
- School of Public Health, University of California, Berkeley, CA, USA
| | - Hong Quach
- School of Public Health, University of California, Berkeley, CA, USA
| | - Girish Motwani
- School of Public Health, University of California, Berkeley, CA, USA
| | - Alan Hubbard
- School of Public Health, University of California, Berkeley, CA, USA
| | - Brenda Eskenazi
- School of Public Health, University of California, Berkeley, CA, USA
| | - Nina Holland
- School of Public Health, University of California, Berkeley, CA, USA
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200
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Gomez D, Swiatlowska P, Owens GK. Epigenetic Control of Smooth Muscle Cell Identity and Lineage Memory. Arterioscler Thromb Vasc Biol 2015; 35:2508-16. [PMID: 26449751 PMCID: PMC4662608 DOI: 10.1161/atvbaha.115.305044] [Citation(s) in RCA: 69] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2015] [Accepted: 09/23/2015] [Indexed: 12/31/2022]
Abstract
Vascular smooth muscle cells (SMCs), like all cells, acquire a cell-specific epigenetic signature during development that includes acquisition of a unique repertoire of histone and DNA modifications. These changes are postulated to induce an open chromatin state (referred to as euchromatin) on the repertoire of genes that are expressed in differentiated SMC, including SMC-selective marker genes like Acta2 and Myh11, as well as housekeeping genes expressed by most cell types. In contrast, genes that are silenced in differentiated SMC acquire modifications associated with a closed chromatin state (ie, heterochromatin) and transcriptional silencing. Herein, we review mechanisms that regulate epigenetic control of the differentiated state of SMC. In addition, we identify some of the major limitations in the field and future challenges, including development of innovative new tools and approaches, for performing single-cell epigenetic assays and locus-selective editing of the epigenome that will allow direct studies of the functional role of specific epigenetic controls during development, injury repair, and disease, including major cardiovascular diseases, such as atherosclerosis, hypertension, and microvascular disease, associated with diabetes mellitus.
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MESH Headings
- Animals
- Cardiovascular Diseases/genetics
- Cardiovascular Diseases/metabolism
- Cardiovascular Diseases/pathology
- Cardiovascular Diseases/physiopathology
- Cell Differentiation/genetics
- Cell Lineage/drug effects
- Chromatin Assembly and Disassembly
- Embryonic Stem Cells/metabolism
- Embryonic Stem Cells/pathology
- Epigenesis, Genetic
- Epigenomics/methods
- Gene Expression Regulation, Developmental
- Genetic Markers
- Humans
- Muscle Development/genetics
- Muscle, Smooth, Vascular/metabolism
- Muscle, Smooth, Vascular/pathology
- Muscle, Smooth, Vascular/physiopathology
- Myocytes, Smooth Muscle/metabolism
- Myocytes, Smooth Muscle/pathology
- Phenotype
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Affiliation(s)
- Delphine Gomez
- From the Department of Molecular Physiology and Biological Physics (D.G., G.K.O.), and Robert M. Berne Cardiovascular Research Center (P.S.), University of Virginia School of Medicine, Charlottesville
| | - Pamela Swiatlowska
- From the Department of Molecular Physiology and Biological Physics (D.G., G.K.O.), and Robert M. Berne Cardiovascular Research Center (P.S.), University of Virginia School of Medicine, Charlottesville
| | - Gary K Owens
- From the Department of Molecular Physiology and Biological Physics (D.G., G.K.O.), and Robert M. Berne Cardiovascular Research Center (P.S.), University of Virginia School of Medicine, Charlottesville.
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