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Gadd DA, Hillary RF, McCartney DL, Zaghlool SB, Stevenson AJ, Cheng Y, Fawns-Ritchie C, Nangle C, Campbell A, Flaig R, Harris SE, Walker RM, Shi L, Tucker-Drob EM, Gieger C, Peters A, Waldenberger M, Graumann J, McRae AF, Deary IJ, Porteous DJ, Hayward C, Visscher PM, Cox SR, Evans KL, McIntosh AM, Suhre K, Marioni RE. Epigenetic scores for the circulating proteome as tools for disease prediction. eLife 2022; 11:e71802. [PMID: 35023833 PMCID: PMC8880990 DOI: 10.7554/elife.71802] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2021] [Accepted: 01/11/2022] [Indexed: 11/13/2022] Open
Abstract
Protein biomarkers have been identified across many age-related morbidities. However, characterising epigenetic influences could further inform disease predictions. Here, we leverage epigenome-wide data to study links between the DNA methylation (DNAm) signatures of the circulating proteome and incident diseases. Using data from four cohorts, we trained and tested epigenetic scores (EpiScores) for 953 plasma proteins, identifying 109 scores that explained between 1% and 58% of the variance in protein levels after adjusting for known protein quantitative trait loci (pQTL) genetic effects. By projecting these EpiScores into an independent sample (Generation Scotland; n = 9537) and relating them to incident morbidities over a follow-up of 14 years, we uncovered 137 EpiScore-disease associations. These associations were largely independent of immune cell proportions, common lifestyle and health factors, and biological aging. Notably, we found that our diabetes-associated EpiScores highlighted previous top biomarker associations from proteome-wide assessments of diabetes. These EpiScores for protein levels can therefore be a valuable resource for disease prediction and risk stratification.
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Affiliation(s)
- Danni A Gadd
- Centre for Genomic and Experimental Medicine, Institute of Genetics and Cancer, University of EdinburghEdinburghUnited Kingdom
| | - Robert F Hillary
- Centre for Genomic and Experimental Medicine, Institute of Genetics and Cancer, University of EdinburghEdinburghUnited Kingdom
| | - Daniel L McCartney
- Centre for Genomic and Experimental Medicine, Institute of Genetics and Cancer, University of EdinburghEdinburghUnited Kingdom
| | - Shaza B Zaghlool
- Department of Physiology and Biophysics, Weill Cornell Medicine-Qatar, Education CityDohaQatar
- Computer Engineering Department, Virginia TechBlacksburgUnited States
| | - Anna J Stevenson
- Centre for Genomic and Experimental Medicine, Institute of Genetics and Cancer, University of EdinburghEdinburghUnited Kingdom
| | - Yipeng Cheng
- Centre for Genomic and Experimental Medicine, Institute of Genetics and Cancer, University of EdinburghEdinburghUnited Kingdom
| | - Chloe Fawns-Ritchie
- Centre for Genomic and Experimental Medicine, Institute of Genetics and Cancer, University of EdinburghEdinburghUnited Kingdom
- Department of Psychology, University of EdinburghEdinburghUnited Kingdom
| | - Cliff Nangle
- Centre for Genomic and Experimental Medicine, Institute of Genetics and Cancer, University of EdinburghEdinburghUnited Kingdom
| | - Archie Campbell
- Centre for Genomic and Experimental Medicine, Institute of Genetics and Cancer, University of EdinburghEdinburghUnited Kingdom
| | - Robin Flaig
- Centre for Genomic and Experimental Medicine, Institute of Genetics and Cancer, University of EdinburghEdinburghUnited Kingdom
| | - Sarah E Harris
- Department of Psychology, University of EdinburghEdinburghUnited Kingdom
- Lothian Birth Cohorts, University of EdinburghEdinburghUnited Kingdom
| | - Rosie M Walker
- Centre for Clinical Brain Sciences, Chancellor’s Building, University of EdinburghEdinburghUnited Kingdom
| | - Liu Shi
- Department of Psychiatry, University of OxfordOxfordUnited Kingdom
| | - Elliot M Tucker-Drob
- Department of Psychology, The University of Texas at AustinAustinUnited States
- Population Research Center, The University of Texas at AustinAustinUnited States
| | - Christian Gieger
- Research Unit Molecular Epidemiology, Helmholtz Zentrum München, German Research Center for Environmental HealthNeuherbergGermany
- Institute of Epidemiology, Helmholtz Zentrum München, German Research Center for Environmental HealthNeuherbergGermany
- German Center for Cardiovascular Research (DZHK), partner site Munich Heart AllianceMunichGermany
- German Center for Diabetes Research (DZD)NeuherbergGermany
| | - Annette Peters
- Institute of Epidemiology, Helmholtz Zentrum München, German Research Center for Environmental HealthNeuherbergGermany
- German Center for Cardiovascular Research (DZHK), partner site Munich Heart AllianceMunichGermany
- German Center for Diabetes Research (DZD)NeuherbergGermany
| | - Melanie Waldenberger
- Research Unit Molecular Epidemiology, Helmholtz Zentrum München, German Research Center for Environmental HealthNeuherbergGermany
- Institute of Epidemiology, Helmholtz Zentrum München, German Research Center for Environmental HealthNeuherbergGermany
- German Center for Cardiovascular Research (DZHK), partner site Munich Heart AllianceMunichGermany
| | - Johannes Graumann
- Scientific Service Group Biomolecular Mass Spectrometry, Max Planck Institute for Heart and Lung Research, W.G. Kerckhoff InstituteBad NauheimGermany
- German Centre for Cardiovascular Research (DZHK), Partner Site Rhine-Main, Max Planck Institute of Heart and Lung ResearchBad NauheimGermany
| | - Allan F McRae
- Institute for Molecular Bioscience, University of QueenslandBrisbaneAustralia
| | - Ian J Deary
- Department of Psychology, University of EdinburghEdinburghUnited Kingdom
- Lothian Birth Cohorts, University of EdinburghEdinburghUnited Kingdom
| | - David J Porteous
- Centre for Genomic and Experimental Medicine, Institute of Genetics and Cancer, University of EdinburghEdinburghUnited Kingdom
| | - Caroline Hayward
- Centre for Genomic and Experimental Medicine, Institute of Genetics and Cancer, University of EdinburghEdinburghUnited Kingdom
- Medical Research Council Human Genetics Unit, Institute of Genetics and Cancer, University of EdinburghEdinburghUnited Kingdom
| | - Peter M Visscher
- Institute for Molecular Bioscience, University of QueenslandBrisbaneAustralia
| | - Simon R Cox
- Department of Psychology, University of EdinburghEdinburghUnited Kingdom
- Lothian Birth Cohorts, University of EdinburghEdinburghUnited Kingdom
| | - Kathryn L Evans
- Centre for Genomic and Experimental Medicine, Institute of Genetics and Cancer, University of EdinburghEdinburghUnited Kingdom
| | - Andrew M McIntosh
- Centre for Genomic and Experimental Medicine, Institute of Genetics and Cancer, University of EdinburghEdinburghUnited Kingdom
- Division of Psychiatry, University of Edinburgh, Royal Edinburgh HospitalEdinburghUnited Kingdom
| | - Karsten Suhre
- Department of Physiology and Biophysics, Weill Cornell Medicine-Qatar, Education CityDohaQatar
| | - Riccardo E Marioni
- Centre for Genomic and Experimental Medicine, Institute of Genetics and Cancer, University of EdinburghEdinburghUnited Kingdom
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Gomez-Alonso MDC, Kretschmer A, Wilson R, Pfeiffer L, Karhunen V, Seppälä I, Zhang W, Mittelstraß K, Wahl S, Matias-Garcia PR, Prokisch H, Horn S, Meitinger T, Serrano-Garcia LR, Sebert S, Raitakari O, Loh M, Rathmann W, Müller-Nurasyid M, Herder C, Roden M, Hurme M, Jarvelin MR, Ala-Korpela M, Kooner JS, Peters A, Lehtimäki T, Chambers JC, Gieger C, Kettunen J, Waldenberger M. DNA methylation and lipid metabolism: an EWAS of 226 metabolic measures. Clin Epigenetics 2021; 13:7. [PMID: 33413638 PMCID: PMC7789600 DOI: 10.1186/s13148-020-00957-8] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2020] [Accepted: 10/22/2020] [Indexed: 02/07/2023] Open
Abstract
BACKGROUND The discovery of robust and trans-ethnically replicated DNA methylation markers of metabolic phenotypes, has hinted at a potential role of epigenetic mechanisms in lipid metabolism. However, DNA methylation and the lipid compositions and lipid concentrations of lipoprotein sizes have been scarcely studied. Here, we present an epigenome-wide association study (EWAS) (N = 5414 total) of mostly lipid-related metabolic measures, including a fine profiling of lipoproteins. As lipoproteins are the main players in the different stages of lipid metabolism, examination of epigenetic markers of detailed lipoprotein features might improve the diagnosis, prognosis, and treatment of metabolic disturbances. RESULTS We conducted an EWAS of leukocyte DNA methylation and 226 metabolic measurements determined by nuclear magnetic resonance spectroscopy in the population-based KORA F4 study (N = 1662) and replicated the results in the LOLIPOP, NFBC1966, and YFS cohorts (N = 3752). Follow-up analyses in the discovery cohort included investigations into gene transcripts, metabolic-measure ratios for pathway analysis, and disease endpoints. We identified 161 associations (p value < 4.7 × 10-10), covering 16 CpG sites at 11 loci and 57 metabolic measures. Identified metabolic measures were primarily medium and small lipoproteins, and fatty acids. For apolipoprotein B-containing lipoproteins, the associations mainly involved triglyceride composition and concentrations of cholesterol esters, triglycerides, free cholesterol, and phospholipids. All associations for HDL lipoproteins involved triglyceride measures only. Associated metabolic measure ratios, proxies of enzymatic activity, highlight amino acid, glucose, and lipid pathways as being potentially epigenetically implicated. Five CpG sites in four genes were associated with differential expression of transcripts in blood or adipose tissue. CpG sites in ABCG1 and PHGDH showed associations with metabolic measures, gene transcription, and metabolic measure ratios and were additionally linked to obesity or previous myocardial infarction, extending previously reported observations. CONCLUSION Our study provides evidence of a link between DNA methylation and the lipid compositions and lipid concentrations of different lipoprotein size subclasses, thus offering in-depth insights into well-known associations of DNA methylation with total serum lipids. The results support detailed profiling of lipid metabolism to improve the molecular understanding of dyslipidemia and related disease mechanisms.
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Affiliation(s)
- Monica Del C Gomez-Alonso
- Research Unit of Molecular Epidemiology, Institute of Epidemiology, Helmholtz Zentrum München German Research Center for Environmental Health, Ingolstaedter Landstraße 1, 85764, Neuherberg, Germany
- Institute of Epidemiology, Helmholtz Zentrum München German Research Center for Environmental Health, Neuherberg, Germany
| | - Anja Kretschmer
- Research Unit of Molecular Epidemiology, Institute of Epidemiology, Helmholtz Zentrum München German Research Center for Environmental Health, Ingolstaedter Landstraße 1, 85764, Neuherberg, Germany
- Institute of Epidemiology, Helmholtz Zentrum München German Research Center for Environmental Health, Neuherberg, Germany
| | - Rory Wilson
- Research Unit of Molecular Epidemiology, Institute of Epidemiology, Helmholtz Zentrum München German Research Center for Environmental Health, Ingolstaedter Landstraße 1, 85764, Neuherberg, Germany
- Institute of Epidemiology, Helmholtz Zentrum München German Research Center for Environmental Health, Neuherberg, Germany
| | - Liliane Pfeiffer
- Research Unit of Molecular Epidemiology, Institute of Epidemiology, Helmholtz Zentrum München German Research Center for Environmental Health, Ingolstaedter Landstraße 1, 85764, Neuherberg, Germany
- Institute of Epidemiology, Helmholtz Zentrum München German Research Center for Environmental Health, Neuherberg, Germany
| | - Ville Karhunen
- Department of Epidemiology and Biostatistics, Imperial College London, London, UK
- Center for Life Course Health Research, University of Oulu, Oulu University Hospital, Oulu, Finland
| | - Ilkka Seppälä
- Department of Clinical Chemistry, Pirkanmaa Hospital District, Fimlab Laboratories, and Finnish Cardiovascular Research Center, Tampere, Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
| | - Weihua Zhang
- Department of Epidemiology and Biostatistics, Imperial College London, London, UK
- Department of Cardiology, Ealing Hospital, London North West University Healthcare NHS Trust, London, Middlesex, UK
| | - Kirstin Mittelstraß
- Research Unit of Molecular Epidemiology, Institute of Epidemiology, Helmholtz Zentrum München German Research Center for Environmental Health, Ingolstaedter Landstraße 1, 85764, Neuherberg, Germany
- Institute of Epidemiology, Helmholtz Zentrum München German Research Center for Environmental Health, Neuherberg, Germany
| | - Simone Wahl
- Research Unit of Molecular Epidemiology, Institute of Epidemiology, Helmholtz Zentrum München German Research Center for Environmental Health, Ingolstaedter Landstraße 1, 85764, Neuherberg, Germany
- Institute of Epidemiology, Helmholtz Zentrum München German Research Center for Environmental Health, Neuherberg, Germany
| | - Pamela R Matias-Garcia
- Research Unit of Molecular Epidemiology, Institute of Epidemiology, Helmholtz Zentrum München German Research Center for Environmental Health, Ingolstaedter Landstraße 1, 85764, Neuherberg, Germany
- Institute of Epidemiology, Helmholtz Zentrum München German Research Center for Environmental Health, Neuherberg, Germany
| | - Holger Prokisch
- Institute of Human Genetics, Helmholtz Zentrum München German Research Center for Environmental Health, Neuherberg, Germany
- Institute of Human Genetics, School of Medicine, Technical University Munich, Munich, Germany
| | - Sacha Horn
- Research Unit of Molecular Epidemiology, Institute of Epidemiology, Helmholtz Zentrum München German Research Center for Environmental Health, Ingolstaedter Landstraße 1, 85764, Neuherberg, Germany
- Institute of Epidemiology, Helmholtz Zentrum München German Research Center for Environmental Health, Neuherberg, Germany
| | - Thomas Meitinger
- Institute of Human Genetics, Helmholtz Zentrum München German Research Center for Environmental Health, Neuherberg, Germany
- Institute of Human Genetics, School of Medicine, Technical University Munich, Munich, Germany
- German Center for Cardiovascular Research (DZHK), Partner Site Munich Heart Alliance, Munich, Germany
| | - Luis R Serrano-Garcia
- Research Unit of Molecular Epidemiology, Institute of Epidemiology, Helmholtz Zentrum München German Research Center for Environmental Health, Ingolstaedter Landstraße 1, 85764, Neuherberg, Germany
- Institute of Epidemiology, Helmholtz Zentrum München German Research Center for Environmental Health, Neuherberg, Germany
- Chair of Microbiology, Technical University of Munich, Freising, Germany
| | - Sylvain Sebert
- Center for Life Course Health Research, University of Oulu, Oulu University Hospital, Oulu, Finland
| | - Olli Raitakari
- Centre for Population Health Research, University of Turku, Turku University Hospital, Turku, Finland
- Research Centre of Applied and Preventive Cardiovascular Medicine, University of Turku, Turku, Finland
- Department of Clinical Physiology and Nuclear Medicine, University of Turku, Turku University Hospital, Turku, Finland
| | - Marie Loh
- Department of Epidemiology and Biostatistics, Imperial College London, London, UK
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore, Singapore
| | - Wolfgang Rathmann
- Institute for Biometrics and Epidemiology, German Diabetes Center, Leibniz Center for Diabetes Research at Heinrich Heine University Düsseldorf, Düsseldorf, Germany
- German Center for Diabetes Research (DZD), Munich-Neuherberg, Germany
| | - Martina Müller-Nurasyid
- Chair of Genetic Epidemiology, IBE, Faculty of Medicine, LMU Munich, Munich, Germany
- Institute of Genetic Epidemiology, Helmholtz Zentrum München German Research Center for Environmental Health, Neuherberg, Germany
- Institute of Medical Biostatistics, Epidemiology and Informatics (IMBEI), University Medical Center, Johannes Gutenberg University, 55101, Mainz, Germany
| | - Christian Herder
- German Center for Diabetes Research (DZD), Munich-Neuherberg, Germany
- Institute for Clinical Diabetology, German Diabetes Center, Leibniz Center for Diabetes Research at Heinrich Heine University Düsseldorf, Düsseldorf, Germany
- Division of Endocrinology and Diabetology, Medical Faculty, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Michael Roden
- German Center for Diabetes Research (DZD), Munich-Neuherberg, Germany
- Institute for Clinical Diabetology, German Diabetes Center, Leibniz Center for Diabetes Research at Heinrich Heine University Düsseldorf, Düsseldorf, Germany
- Division of Endocrinology and Diabetology, Medical Faculty, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Mikko Hurme
- Department of Microbiology and Immunology, Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
| | - Marjo-Riitta Jarvelin
- Department of Epidemiology and Biostatistics, Imperial College London, London, UK
- Center for Life Course Health Research, University of Oulu, Oulu University Hospital, Oulu, Finland
- UKMRC-PHE Centre for Environment and Health, School of Public Health, Imperial College London, London, UK
- Department of Life Sciences, College of Health and Life Sciences, Brunel University London, London, UK
| | - Mika Ala-Korpela
- Center for Life Course Health Research, University of Oulu, Oulu University Hospital, Oulu, Finland
- NMR Metabolomics Laboratory, School of Pharmacy, University of Eastern Finland, Kuopio, Finland
- Computational Medicine, Faculty of Medicine, University of Oulu, Oulu, Finland
- Biocenter Oulu, University of Oulu, Oulu, Finland
| | - Jaspal S Kooner
- Department of Cardiology, Ealing Hospital, London North West University Healthcare NHS Trust, London, Middlesex, UK
- National Heart and Lung Institute, Imperial College London, London, UK
- Imperial College Healthcare NHS Trust, London, UK
- MRC-PHE Centre for Environment and Health, Imperial College London, London, UK
| | - Annette Peters
- Institute of Epidemiology, Helmholtz Zentrum München German Research Center for Environmental Health, Neuherberg, Germany
| | - Terho Lehtimäki
- Department of Clinical Chemistry, Pirkanmaa Hospital District, Fimlab Laboratories, and Finnish Cardiovascular Research Center, Tampere, Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
| | - John C Chambers
- Department of Epidemiology and Biostatistics, Imperial College London, London, UK
- Department of Cardiology, Ealing Hospital, London North West University Healthcare NHS Trust, London, Middlesex, UK
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore, Singapore
- Imperial College Healthcare NHS Trust, London, UK
- MRC-PHE Centre for Environment and Health, Imperial College London, London, UK
| | - Christian Gieger
- Research Unit of Molecular Epidemiology, Institute of Epidemiology, Helmholtz Zentrum München German Research Center for Environmental Health, Ingolstaedter Landstraße 1, 85764, Neuherberg, Germany
- Institute of Epidemiology, Helmholtz Zentrum München German Research Center for Environmental Health, Neuherberg, Germany
| | - Johannes Kettunen
- Center for Life Course Health Research, University of Oulu, Oulu University Hospital, Oulu, Finland
- Computational Medicine, Faculty of Medicine, University of Oulu, Oulu, Finland
- Biocenter Oulu, University of Oulu, Oulu, Finland
| | - Melanie Waldenberger
- Research Unit of Molecular Epidemiology, Institute of Epidemiology, Helmholtz Zentrum München German Research Center for Environmental Health, Ingolstaedter Landstraße 1, 85764, Neuherberg, Germany.
- Institute of Epidemiology, Helmholtz Zentrum München German Research Center for Environmental Health, Neuherberg, Germany.
- German Center for Cardiovascular Research (DZHK), Partner Site Munich Heart Alliance, Munich, Germany.
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