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Fraszczyk E, Spijkerman AMW, Zhang Y, Brandmaier S, Day FR, Zhou L, Wackers P, Dollé MET, Bloks VW, Gào X, Gieger C, Kooner J, Kriebel J, Picavet HSJ, Rathmann W, Schöttker B, Loh M, Verschuren WMM, van Vliet-Ostaptchouk JV, Wareham NJ, Chambers JC, Ong KK, Grallert H, Brenner H, Luijten M, Snieder H. Epigenome-wide association study of incident type 2 diabetes: a meta-analysis of five prospective European cohorts. Diabetologia 2022; 65:763-776. [PMID: 35169870 PMCID: PMC8960572 DOI: 10.1007/s00125-022-05652-2] [Citation(s) in RCA: 22] [Impact Index Per Article: 11.0] [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] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/14/2020] [Accepted: 11/15/2021] [Indexed: 02/02/2023]
Abstract
AIMS/HYPOTHESIS Type 2 diabetes is a complex metabolic disease with increasing prevalence worldwide. Improving the prediction of incident type 2 diabetes using epigenetic markers could help tailor prevention efforts to those at the highest risk. The aim of this study was to identify predictive methylation markers for incident type 2 diabetes by combining epigenome-wide association study (EWAS) results from five prospective European cohorts. METHODS We conducted a meta-analysis of EWASs in blood collected 7-10 years prior to type 2 diabetes diagnosis. DNA methylation was measured with Illumina Infinium Methylation arrays. A total of 1250 cases and 1950 controls from five longitudinal cohorts were included: Doetinchem, ESTHER, KORA1, KORA2 and EPIC-Norfolk. Associations between DNA methylation and incident type 2 diabetes were examined using robust linear regression with adjustment for potential confounders. Inverse-variance fixed-effects meta-analysis of cohort-level individual CpG EWAS estimates was performed using METAL. The methylGSA R package was used for gene set enrichment analysis. Confirmation of genome-wide significant CpG sites was performed in a cohort of Indian Asians (LOLIPOP, UK). RESULTS The meta-analysis identified 76 CpG sites that were differentially methylated in individuals with incident type 2 diabetes compared with control individuals (p values <1.1 × 10-7). Sixty-four out of 76 (84.2%) CpG sites were confirmed by directionally consistent effects and p values <0.05 in an independent cohort of Indian Asians. However, on adjustment for baseline BMI only four CpG sites remained genome-wide significant, and addition of the 76 CpG methylation risk score to a prediction model including established predictors of type 2 diabetes (age, sex, BMI and HbA1c) showed no improvement (AUC 0.757 vs 0.753). Gene set enrichment analysis of the full epigenome-wide results clearly showed enrichment of processes linked to insulin signalling, lipid homeostasis and inflammation. CONCLUSIONS/INTERPRETATION By combining results from five European cohorts, and thus significantly increasing study sample size, we identified 76 CpG sites associated with incident type 2 diabetes. Replication of 64 CpGs in an independent cohort of Indian Asians suggests that the association between DNA methylation levels and incident type 2 diabetes is robust and independent of ethnicity. Our data also indicate that BMI partly explains the association between DNA methylation and incident type 2 diabetes. Further studies are required to elucidate the underlying biological mechanisms and to determine potential causal roles of the differentially methylated CpG sites in type 2 diabetes development.
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Affiliation(s)
- Eliza Fraszczyk
- Department of Epidemiology, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
- Centre for Health Protection, National Institute for Public Health and the Environment (RIVM), Bilthoven, the Netherlands
| | - Annemieke M W Spijkerman
- Centre for Nutrition, Prevention and Health services, National Institute for Public Health and the Environment (RIVM), Bilthoven, the Netherlands
| | - Yan Zhang
- Division of Clinical Epidemiology and Aging Research, German Cancer Research Center, Heidelberg, Germany
| | - Stefan Brandmaier
- Research Unit of Molecular Epidemiology, Institute of Epidemiology, Helmholtz Zentrum München, Neuherberg, Germany
- German Center for Diabetes Research (DZD), Neuherberg, Germany
| | - Felix R Day
- MRC Epidemiology Unit, Institute of Metabolic Science, University of Cambridge School of Clinical Medicine, Cambridge, UK
| | - Li Zhou
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore, Singapore
| | - Paul Wackers
- Centre for Health Protection, National Institute for Public Health and the Environment (RIVM), Bilthoven, the Netherlands
| | - Martijn E T Dollé
- Centre for Health Protection, National Institute for Public Health and the Environment (RIVM), Bilthoven, the Netherlands
| | - Vincent W Bloks
- Department of Pediatrics, Section of Molecular Metabolism and Nutrition, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Xīn Gào
- Division of Clinical Epidemiology and Aging Research, German Cancer Research Center, Heidelberg, Germany
| | - Christian Gieger
- Research Unit of Molecular Epidemiology, Institute of Epidemiology, Helmholtz Zentrum München, Neuherberg, Germany
- German Center for Diabetes Research (DZD), Neuherberg, Germany
| | - Jaspal Kooner
- Department of Cardiology, Ealing Hospital, Ealing, UK
- Imperial College Healthcare NHS Trust, London, UK
- MRC-PHE Centre for Environment and Health, Imperial College London, London, UK
- National Heart and Lung Institute, Imperial College London, London, UK
| | - Jennifer Kriebel
- Research Unit of Molecular Epidemiology, Institute of Epidemiology, Helmholtz Zentrum München, Neuherberg, Germany
- German Center for Diabetes Research (DZD), Neuherberg, Germany
| | - H Susan J Picavet
- Centre for Nutrition, Prevention and Health services, National Institute for Public Health and the Environment (RIVM), Bilthoven, the Netherlands
| | - Wolfgang Rathmann
- German Center for Diabetes Research (DZD), Neuherberg, Germany
- Institute for Biometrics and Epidemiology, German Diabetes Center, Auf'm Hennekamp, Duesseldorf, Germany
| | - Ben Schöttker
- Division of Clinical Epidemiology and Aging Research, German Cancer Research Center, Heidelberg, Germany
- Network Aging Research, University of Heidelberg, Heidelberg, Germany
| | - Marie Loh
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore, Singapore
| | - W M Monique Verschuren
- Centre for Nutrition, Prevention and Health services, National Institute for Public Health and the Environment (RIVM), Bilthoven, the Netherlands
- Julius Center for Health Sciences and Primary Care, University Medical Center Utrecht, Utrecht University, Utrecht, the Netherlands
| | - Jana V van Vliet-Ostaptchouk
- Genomics Coordination Center, Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Nicholas J Wareham
- MRC Epidemiology Unit, Institute of Metabolic Science, University of Cambridge School of Clinical Medicine, Cambridge, UK
| | - John C Chambers
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore, Singapore
- Department of Epidemiology and Biostatistics, Imperial College London, London, UK
| | - Ken K Ong
- MRC Epidemiology Unit, Institute of Metabolic Science, University of Cambridge School of Clinical Medicine, Cambridge, UK
- Department of Paediatrics, University of Cambridge School of Clinical Medicine, Cambridge, UK
| | - Harald Grallert
- Research Unit of Molecular Epidemiology, Institute of Epidemiology, Helmholtz Zentrum München, Neuherberg, Germany
- German Center for Diabetes Research (DZD), Neuherberg, Germany
| | - Hermann Brenner
- Division of Clinical Epidemiology and Aging Research, German Cancer Research Center, Heidelberg, Germany
- Network Aging Research, University of Heidelberg, Heidelberg, Germany
| | - Mirjam Luijten
- Centre for Health Protection, National Institute for Public Health and the Environment (RIVM), Bilthoven, the Netherlands.
| | - Harold Snieder
- Department of Epidemiology, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands.
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