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Tobi EW, Slagboom PE, van Dongen J, Kremer D, Stein AD, Putter H, Heijmans BT, Lumey LH. Prenatal famine and genetic variation are independently and additively associated with DNA methylation at regulatory loci within IGF2/H19. PLoS One 2012; 7:e37933. [PMID: 22666415 PMCID: PMC3364289 DOI: 10.1371/journal.pone.0037933] [Citation(s) in RCA: 125] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2012] [Accepted: 04/25/2012] [Indexed: 02/07/2023] Open
Abstract
Both the early environment and genetic variation may affect DNA methylation, which is one of the major molecular marks of the epigenome. The combined effect of these factors on a well-defined locus has not been studied to date. We evaluated the association of periconceptional exposure to the Dutch Famine of 1944-45, as an example of an early environmental exposure, and single nucleotide polymorphisms covering the genetic variation (tagging SNPs) with DNA methylation at the imprinted IGF2/H19 region, a model for an epigenetically regulated genomic region. DNA methylation was measured at five differentially methylated regions (DMRs) that regulate the imprinted status of the IGF2/H19 region. Small but consistent differences in DNA methylation were observed comparing 60 individuals with periconceptional famine exposure with unexposed same-sex siblings at all IGF2 DMRs (P(BH)<0.05 after adjustment for multiple testing), but not at the H19 DMR. IGF2 DMR0 methylation was associated with IGF2 SNP rs2239681 (P(BH) = 0.027) and INS promoter methylation with INS SNPs, including rs689, which tags the INS VNTR, suggesting a mechanism for the reported effect of the VNTR on INS expression (P(BH) = 3.4 × 10(-3)). Prenatal famine and genetic variation showed similar associations with IGF2/H19 methylation and their contributions were additive. They were small in absolute terms (<3%), but on average 0.5 standard deviations relative to the variation in the population. Our analyses suggest that environmental and genetic factors could have independent and additive similarly sized effects on DNA methylation at the same regulatory site.
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Affiliation(s)
- Elmar W. Tobi
- Molecular Epidemiology, Leiden University Medical Center, Leiden, The Netherlands
| | - P. Eline Slagboom
- Molecular Epidemiology, Leiden University Medical Center, Leiden, The Netherlands
- The Netherlands consortium for Healthy Ageing, Leiden University Medical Center, Leiden, The Netherlands
| | - Jenny van Dongen
- Molecular Epidemiology, Leiden University Medical Center, Leiden, The Netherlands
- Biological Psychology, VU University Amsterdam, Amsterdam, The Netherlands
| | - Dennis Kremer
- Molecular Epidemiology, Leiden University Medical Center, Leiden, The Netherlands
| | - Aryeh D. Stein
- Hubert Department of Global Health, Rollins School of Public Health, Emory University, Atlanta, Georgia, United States of America
| | - Hein Putter
- Medical Statistics, Leiden University Medical Center, Leiden, The Netherlands
| | - Bastiaan T. Heijmans
- Molecular Epidemiology, Leiden University Medical Center, Leiden, The Netherlands
- The Netherlands consortium for Healthy Ageing, Leiden University Medical Center, Leiden, The Netherlands
| | - L. H. Lumey
- Department of Epidemiology, Mailman School of Public Health, Columbia University, New York, New York, United States of America
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Melzer D, Perry JRB, Hernandez D, Corsi AM, Stevens K, Rafferty I, Lauretani F, Murray A, Gibbs JR, Paolisso G, Rafiq S, Simon-Sanchez J, Lango H, Scholz S, Weedon MN, Arepalli S, Rice N, Washecka N, Hurst A, Britton A, Henley W, van de Leemput J, Li R, Newman AB, Tranah G, Harris T, Panicker V, Dayan C, Bennett A, McCarthy MI, Ruokonen A, Jarvelin MR, Guralnik J, Bandinelli S, Frayling TM, Singleton A, Ferrucci L. A genome-wide association study identifies protein quantitative trait loci (pQTLs). PLoS Genet 2008; 4:e1000072. [PMID: 18464913 PMCID: PMC2362067 DOI: 10.1371/journal.pgen.1000072] [Citation(s) in RCA: 380] [Impact Index Per Article: 23.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2007] [Accepted: 04/11/2008] [Indexed: 11/18/2022] Open
Abstract
There is considerable evidence that human genetic variation influences gene expression. Genome-wide studies have revealed that mRNA levels are associated with genetic variation in or close to the gene coding for those mRNA transcripts – cis effects, and elsewhere in the genome – trans effects. The role of genetic variation in determining protein levels has not been systematically assessed. Using a genome-wide association approach we show that common genetic variation influences levels of clinically relevant proteins in human serum and plasma. We evaluated the role of 496,032 polymorphisms on levels of 42 proteins measured in 1200 fasting individuals from the population based InCHIANTI study. Proteins included insulin, several interleukins, adipokines, chemokines, and liver function markers that are implicated in many common diseases including metabolic, inflammatory, and infectious conditions. We identified eight Cis effects, including variants in or near the IL6R (p = 1.8×10−57), CCL4L1 (p = 3.9×10−21), IL18 (p = 6.8×10−13), LPA (p = 4.4×10−10), GGT1 (p = 1.5×10−7), SHBG (p = 3.1×10−7), CRP (p = 6.4×10−6) and IL1RN (p = 7.3×10−6) genes, all associated with their respective protein products with effect sizes ranging from 0.19 to 0.69 standard deviations per allele. Mechanisms implicated include altered rates of cleavage of bound to unbound soluble receptor (IL6R), altered secretion rates of different sized proteins (LPA), variation in gene copy number (CCL4L1) and altered transcription (GGT1). We identified one novel trans effect that was an association between ABO blood group and tumour necrosis factor alpha (TNF-alpha) levels (p = 6.8×10−40), but this finding was not present when TNF-alpha was measured using a different assay , or in a second study, suggesting an assay-specific association. Our results show that protein levels share some of the features of the genetics of gene expression. These include the presence of strong genetic effects in cis locations. The identification of protein quantitative trait loci (pQTLs) may be a powerful complementary method of improving our understanding of disease pathways. One of the central dogmas of molecular genetics is that DNA is transcribed to RNA which is translated to protein and alterations to proteins can influence human diseases. Genome-wide association studies have recently revealed many new DNA variants that influence human diseases. To complement these efforts, several genome-wide studies have established that DNA variation influences mRNA expression levels. Loci influencing mRNA levels have been termed “eQTLs”. In this study we have performed the first genome-wide association study of the third piece in this jigsaw – the role of DNA variation in relation to protein levels, or “pQTLs”. We analysed 42 proteins measured in blood fractions from the InCHIANTI study. We identified eight cis effects including common variants in or near the IL6R, CCL4, IL18, LPA, GGT1, SHBG, CRP and IL1RN genes, all associated with blood levels of their respective protein products. Mechanisms implicated included altered transcription (GGT1) but also rates of cleavage of bound to unbound soluble receptor (IL6R), altered secretion rates of different sized proteins (LPA) and variation in gene copy number (CCL4). Blood levels of many of these proteins are correlated with human diseases and the identification of “pQTLs” may in turn help our understanding of disease.
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Affiliation(s)
- David Melzer
- Department of Epidemiology and Public Health, Institute of Biomedical and Clinical Sciences, Peninsula College of Medicine and Dentistry, University of Exeter, Devon, United Kingdom
- Genetics of Complex Traits, Institute of Biomedical and Clinical Sciences, Peninsula College of Medicine and Dentistry, University of Exeter, Devon, United Kingdom
| | - John R. B. Perry
- Genetics of Complex Traits, Institute of Biomedical and Clinical Sciences, Peninsula College of Medicine and Dentistry, University of Exeter, Devon, United Kingdom
| | - Dena Hernandez
- Laboratory of Neurogenetics, National Institute of Aging, Porter Neuroscience Research Center, Bethesda, Maryland, United States of America
| | - Anna-Maria Corsi
- Tuscany Regional Health Agency, I.O.T. and Department of Medical and Surgical Critical Care, University of Florence, Florence, Italy
| | - Kara Stevens
- Department of Epidemiology and Public Health, Institute of Biomedical and Clinical Sciences, Peninsula College of Medicine and Dentistry, University of Exeter, Devon, United Kingdom
- Genetics of Complex Traits, Institute of Biomedical and Clinical Sciences, Peninsula College of Medicine and Dentistry, University of Exeter, Devon, United Kingdom
| | - Ian Rafferty
- Laboratory of Neurogenetics, National Institute of Aging, Porter Neuroscience Research Center, Bethesda, Maryland, United States of America
| | - Fulvio Lauretani
- Tuscany Regional Health Agency, I.O.T. and Department of Medical and Surgical Critical Care, University of Florence, Florence, Italy
| | - Anna Murray
- Department of Epidemiology and Public Health, Institute of Biomedical and Clinical Sciences, Peninsula College of Medicine and Dentistry, University of Exeter, Devon, United Kingdom
- Genetics of Complex Traits, Institute of Biomedical and Clinical Sciences, Peninsula College of Medicine and Dentistry, University of Exeter, Devon, United Kingdom
| | - J. Raphael Gibbs
- Laboratory of Neurogenetics, National Institute of Aging, Porter Neuroscience Research Center, Bethesda, Maryland, United States of America
| | - Giuseppe Paolisso
- Department of Geriatric Medicine and Metabolic Diseases, Second University of Naples, Naples, Italy
| | - Sajjad Rafiq
- Department of Epidemiology and Public Health, Institute of Biomedical and Clinical Sciences, Peninsula College of Medicine and Dentistry, University of Exeter, Devon, United Kingdom
- Genetics of Complex Traits, Institute of Biomedical and Clinical Sciences, Peninsula College of Medicine and Dentistry, University of Exeter, Devon, United Kingdom
| | - Javier Simon-Sanchez
- Laboratory of Neurogenetics, National Institute of Aging, Porter Neuroscience Research Center, Bethesda, Maryland, United States of America
| | - Hana Lango
- Genetics of Complex Traits, Institute of Biomedical and Clinical Sciences, Peninsula College of Medicine and Dentistry, University of Exeter, Devon, United Kingdom
| | - Sonja Scholz
- Laboratory of Neurogenetics, National Institute of Aging, Porter Neuroscience Research Center, Bethesda, Maryland, United States of America
| | - Michael N. Weedon
- Genetics of Complex Traits, Institute of Biomedical and Clinical Sciences, Peninsula College of Medicine and Dentistry, University of Exeter, Devon, United Kingdom
| | - Sampath Arepalli
- Laboratory of Neurogenetics, National Institute of Aging, Porter Neuroscience Research Center, Bethesda, Maryland, United States of America
| | - Neil Rice
- Department of Epidemiology and Public Health, Institute of Biomedical and Clinical Sciences, Peninsula College of Medicine and Dentistry, University of Exeter, Devon, United Kingdom
- Genetics of Complex Traits, Institute of Biomedical and Clinical Sciences, Peninsula College of Medicine and Dentistry, University of Exeter, Devon, United Kingdom
| | - Nicole Washecka
- Laboratory of Neurogenetics, National Institute of Aging, Porter Neuroscience Research Center, Bethesda, Maryland, United States of America
| | - Alison Hurst
- Department of Epidemiology and Public Health, Institute of Biomedical and Clinical Sciences, Peninsula College of Medicine and Dentistry, University of Exeter, Devon, United Kingdom
- Genetics of Complex Traits, Institute of Biomedical and Clinical Sciences, Peninsula College of Medicine and Dentistry, University of Exeter, Devon, United Kingdom
| | - Angela Britton
- Laboratory of Neurogenetics, National Institute of Aging, Porter Neuroscience Research Center, Bethesda, Maryland, United States of America
| | - William Henley
- School of Mathematics and Statistics, University of Plymouth, Plymouth, United Kingdom
| | - Joyce van de Leemput
- Laboratory of Neurogenetics, National Institute of Aging, Porter Neuroscience Research Center, Bethesda, Maryland, United States of America
| | - Rongling Li
- Department of Preventive Medicine and Center for Genomics and Bioinformatics, College of Medicine, University of Tennessee Health Science Center, Memphis, Tennessee, United States of America
| | - Anne B. Newman
- University of Pittsburgh, Graduate School of Public Health, Departments of Epidemiology and Medicine, Pittsburgh, Pennsylvania, United States of America
| | - Greg Tranah
- San Francisco Coordinating Center, California Pacific Medical Center Research Institute, San Francisco, California, United States of America
| | - Tamara Harris
- Laboratory of Epidemiology, Demography and Biometry, National Institute on Aging, Bethesda, Maryland, United States of America
| | - Vijay Panicker
- Genetics of Complex Traits, Institute of Biomedical and Clinical Sciences, Peninsula College of Medicine and Dentistry, University of Exeter, Devon, United Kingdom
- Henry Wellcome Laboratories for Integrative Neurosciences and Endocrinology, University of Bristol, Bristol, United Kingdom
| | - Colin Dayan
- Henry Wellcome Laboratories for Integrative Neurosciences and Endocrinology, University of Bristol, Bristol, United Kingdom
| | - Amanda Bennett
- Oxford Centre for Diabetes, Endocrinology and Metabolism, Headington, Oxford, United Kingdom
| | - Mark I. McCarthy
- Oxford Centre for Diabetes, Endocrinology and Metabolism, Headington, Oxford, United Kingdom
- The Wellcome Trust Centre for Human Genetics, Roosevelt Drive, Oxford, United Kingdom
| | - Aimo Ruokonen
- Department of Clinical Chemistry, University of Oulu, Oulu, Finland
| | - Marjo-Riitta Jarvelin
- Department of Public Health, Science, and General Practice, University of Oulu, Oulu, Finland
- Department of Epidemiology and Public Health, Imperial College London, London, United Kingdom
| | - Jack Guralnik
- Laboratory of Epidemiology, Demography and Biometry, National Institute on Aging, Bethesda, Maryland, United States of America
| | | | - Timothy M. Frayling
- Genetics of Complex Traits, Institute of Biomedical and Clinical Sciences, Peninsula College of Medicine and Dentistry, University of Exeter, Devon, United Kingdom
- * E-mail:
| | - Andrew Singleton
- Laboratory of Neurogenetics, National Institute of Aging, Porter Neuroscience Research Center, Bethesda, Maryland, United States of America
| | - Luigi Ferrucci
- Longitudinal Studies Section, Clinical Research Branch, Gerontology Research Center, National Institute on Aging, Baltimore, Maryland, United States of America
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