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Research Paper|Volume 12, Issue 14|pp 14092—14124

Blood DNA methylation sites predict death risk in a longitudinal study of 12, 300 individuals

Elena Colicino1, Riccardo Marioni2, Cavin Ward-Caviness3,33, Rahul Gondalia4, Weihua Guan5, Brian Chen6, Pei-Chien Tsai7, Tianxiao Huan8, Gao Xu9, Agha Golareh9, Joel Schwartz10, Pantel Vokonas11, Allan Just1, John M. Starr12, Allan F. McRae13, Naomi R. Wray13, Peter M. Visscher13, Jan Bressler14, Wen Zhang15, Toshiko Tanaka6, Ann Zenobia Moore6, Luke C. Pilling16, Guosheng Zhang17, James D. Stewart4, Yun Li4, Lifang Hou18, Juan Castillo-Fernandez7, Tim Spector7, Douglas P. Kiel19, Joanne M. Murabito20, Chunyu Liu21, Mike Mendelson22, Tim Assimes23, Devin Absher24, Phil S. Tsaho25, Ake T. Lu25, Luigi Ferrucci26, Rory Wilson27, Melanie Waldenberger27, Holger Prokisch28, Stefania Bandinelli29, Jordana T. Bell7, Daniel Levy30, Ian J. Deary31, Steve Horvath25, Jim Pankow32, Annette Peters33, Eric A. Whitsel4, Andrea Baccarelli9
  • 1Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
  • 2Centre for Genomic and Experimental Medicine, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh EH4 2XU, UK
  • 3US Environmental Protection Agency, Chapel Hill, NC 27514, USA
  • 4Gillings School of Global Public Health, University of North Carolina, Chapel Hill, NC 27514, USA
  • 5Division of Biostatistics, School of Public Health, University of Minnesota, Minneapolis, MN 55455, USA
  • 6Longitudinal Study Section, Translational Gerontology Branch, National Institute of Aging, Bethesda, MD 20892, USA
  • 7Department of Twin Research and Genetic Epidemiology, King’s College London, London SE1 7EH, UK
  • 8National Heart, Lung, and Blood Institute, Bethesda, MD 20892, USA
  • 9Columbia University Mailman School of Public Health, New York, NY 10032, USA
  • 10Harvard T.H. Chan School of Public Health, Boston, MA 02115, USA
  • 11VA Boston Healthcare System and Boston University Schools of Public Health and Medicine, Boston, MA 02115, USA
  • 12Alzheimer Scotland Dementia Research Centre, University of Edinburgh, Edinburgh EH8 9JZ, UK
  • 13Institute for Molecular Bioscience, University of Queensland, Brisbane, QLD, Australia
  • 14University of Texas Health Science Center at Houston, Houston, TX 77030, USA
  • 15Department of Biostatistics and Data Science, School of Public Health, University of Texas Health Science Center at Houston, Houston, TX 77030, USA
  • 16Epidemiology and Public Health Group, University of Exeter Medical School, Exeter, UK
  • 17Department of Genetics, University of North Carolina, Chapel Hill, NC 27514, USA
  • 18Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
  • 19Hebrew SeniorLife Institute for Aging Research and Department of Medicine, Beth Israel Deaconess Medical Center and Harvard Medical School Boston, MA 02215, USA
  • 20Section General Internal Medicine, Department of Medicine, Boston University School of Medicine, Boston, MA 02215, USA
  • 21Boston University School of Public Health, Boston, MA 02215, USA
  • 22Boston University School of Medicine, Boston, MA 02215, USA
  • 23Stanford University School of Medicine, Stanford, CA 94305, USA
  • 24Hudson Alpha Institute for Biotechnology, Huntsville, AL 35806, USA
  • 25Department of Human Genetics, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA 90095, USA
  • 26National Institute of Aging, Bethesda, MD 20892, USA
  • 27Research Unit of Molecular Epidemiology, Helmholtz Zentrum Munich, German Research Center for Environmental Health, Neuherberg D-85764, Germany
  • 28Institute of Human Genetics, Helmholtz Zentrum Munich, German Research Center for Environmental Health, Neuherberg S-85764, Germany
  • 29Geriatric Unit, Azienda Sanitaria Firenze, Florence, Italy
  • 30Framingham Heart Study, Framingham, MA 01702, USA
  • 31Department of Psychology, University of Edinburgh, Edinburgh EH8 9JZ, UK
  • 32Division of Epidemiology and Community Health, School of Public Health, University of Minnesota, Minneapolis, MN 55455, USA
  • 33Institute for Epidemiology II, Helmholtz Zentrum Munich, German Research Center for Environmental Health, Neuherberg D-85764, Germany
* First authors
# Last authors
Received: February 10, 2020Accepted: May 25, 2020Published: July 22, 2020

Copyright: © 2020 Colicino et al. This is an open access article distributed under the terms of the Creative Commons Attribution License (CC BY 3.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.

Abstract

DNA methylation has fundamental roles in gene programming and aging that may help predict mortality. However, no large-scale study has investigated whether site-specific DNA methylation predicts all-cause mortality. We used the Illumina-HumanMethylation450-BeadChip to identify blood DNA methylation sites associated with all-cause mortality for 12, 300 participants in 12 Cohorts of the Heart and Aging Research in Genetic Epidemiology (CHARGE) Consortium. Over an average 10-year follow-up, there were 2,561 deaths across the cohorts. Nine sites mapping to three intergenic and six gene-specific regions were associated with mortality (P < 9.3x10-7) independently of age and other mortality predictors. Six sites (cg14866069, cg23666362, cg20045320, cg07839457, cg07677157, cg09615688)—mapping respectively to BMPR1B, MIR1973, IFITM3, NLRC5, and two intergenic regions—were associated with reduced mortality risk. The remaining three sites (cg17086398, cg12619262, cg18424841)—mapping respectively to SERINC2, CHST12, and an intergenic region—were associated with increased mortality risk. DNA methylation at each site predicted 5%–15% of all deaths. We also assessed the causal association of those sites to age-related chronic diseases by using Mendelian randomization, identifying weak causal relationship between cg18424841 and cg09615688 with coronary heart disease. Of the nine sites, three (cg20045320, cg07839457, cg07677157) were associated with lower incidence of heart disease risk and two (cg20045320, cg07839457) with smoking and inflammation in prior CHARGE analyses. Methylation of cg20045320, cg07839457, and cg17086398 was associated with decreased expression of nearby genes (IFITM3, IRF, NLRC5, MT1, MT2, MARCKSL1) linked to immune responses and cardiometabolic diseases. These sites may serve as useful clinical tools for mortality risk assessment and preventative care.