Epigenome-wide association of DNA methylation markers in peripheral blood from Indian Asians and Europeans with incident type 2 diabetes: a nested case-control study

Summary

Background

Indian Asians, who make up a quarter of the world's population, are at high risk of developing type 2 diabetes. We investigated whether DNA methylation is associated with future type 2 diabetes incidence in Indian Asians and whether differences in methylation patterns between Indian Asians and Europeans are associated with, and could be used to predict, differences in the magnitude of risk of developing type 2 diabetes.

Methods

We did a nested case-control study of DNA methylation in Indian Asians and Europeans with incident type 2 diabetes who were identified from the 8-year follow-up of 25 372 participants in the London Life Sciences Prospective Population (LOLIPOP) study. Patients were recruited between May 1, 2002, and Sept 12, 2008. We did epigenome-wide association analysis using samples from Indian Asians with incident type 2 diabetes and age-matched and sex-matched Indian Asian controls, followed by replication testing of top-ranking signals in Europeans. For both discovery and replication, DNA methylation was measured in the baseline blood sample, which was collected before the onset of type 2 diabetes. Epigenome-wide significance was set at p<1 × 10⁻⁷. We compared methylation levels between Indian Asian and European controls without type 2 diabetes at baseline to estimate the potential contribution of DNA methylation to increased risk of future type 2 diabetes incidence among Indian Asians.

Findings

1608 (11·9%) of 13 535 Indian Asians and 306 (4·3%) of 7066 Europeans developed type 2 diabetes over a mean of 8·5 years (SD 1·8) of follow-up. The age-adjusted and sex-adjusted incidence of type 2 diabetes was 3·1 times (95% CI 2·8–3·6; p<0·0001) higher among Indian Asians than among Europeans, and remained 2·5 times (2·1–2·9; p<0·0001) higher after adjustment for adiposity, physical activity, family history of type 2 diabetes, and baseline glycaemic measures. The mean absolute difference in methylation level between type 2 diabetes cases and controls ranged from 0·5% (SD 0·1) to 1·1% (0·2). Methylation markers at five loci were associated with future type 2 diabetes incidence; the relative risk per 1% increase in methylation was 1·09 (95% CI 1·07–1·11; p=1·3 × 10⁻¹⁷) for ABCG1, 0·94 (0·92–0·95; p=4·2 × 10⁻¹¹) for PHOSPHO1, 0·94 (0·92–0·96; p=1·4 × 10⁻⁹) for SOCS3, 1·07 (1·04–1·09; p=2·1 × 10⁻¹⁰) for SREBF1, and 0·92 (0·90–0·94; p=1·2 × 10⁻¹⁷) for TXNIP. A methylation score combining results for the five loci was associated with future type 2 diabetes incidence (relative risk quartile 4 vs quartile 1 3·51, 95% CI 2·79–4·42; p=1·3 × 10⁻²⁶), and was independent of established risk factors. Methylation score was higher among Indian Asians than Europeans (p=1 × 10⁻³⁴).

Interpretation

DNA methylation might provide new insights into the pathways underlying type 2 diabetes and offer new opportunities for risk stratification and prevention of type 2 diabetes among Indian Asians.

Funding

The European Union, the UK National Institute for Health Research, the Wellcome Trust, the UK Medical Research Council, Action on Hearing Loss, the UK Biotechnology and Biological Sciences Research Council, the Oak Foundation, the Economic and Social Research Council, Helmholtz Zentrum Munchen, the German Research Center for Environmental Health, the German Federal Ministry of Education and Research, the German Center for Diabetes Research, the Munich Center for Health Sciences, the Ministry of Science and Research of the State of North Rhine-Westphalia, and the German Federal Ministry of Health.

Introduction

Type 2 diabetes is a major public health problem worldwide, particularly in rapidly urbanising countries such as India.1, 2 Indian Asians (ie, people originating from India, Pakistan, Bangladesh, or Sri Lanka), who comprise a quarter of the world's population, are at higher risk of type 2 diabetes than are North Americans and Europeans.2, 3, 4 Type 2 diabetes is estimated to affect more than 100 million people in India alone by 2030.¹

Diet, obesity, and physical inactivity are major risk factors for type 2 diabetes in Indian Asians, as they are in other populations, but differences in the prevalence of these behaviours between Indian Asians and Europeans do not seem to account for their increased risk of type 2 diabetes.5, 6 Genome-wide association studies among Indian Asians and Europeans have identified common genetic variants at about 80 genetic loci that affect the risk of type 2 diabetes,4, 7, 8, 9, 10 although these only explain about 5% of type 2 diabetes risk in both populations.11, 12 Improved understanding of the mechanisms underlying the high incidence of type 2 diabetes among Indian Asians is needed to help reverse the epidemic of type 2 diabetes in this population.

DNA methylation at cytosine–guanine nucleotide pair (CpG) sites affects gene expression, cellular differentiation, and molecular response to environmental stressors.13, 14, 15, 16 Methylation at the FTO locus and other loci containing genetic variants linked to type 2 diabetes is associated with prevalent type 2 diabetes in Ashkenazi Jews, and baseline methylation of FTO was used as a marker to predict the likelihood of progressing from normal to impaired glucose metabolism in a follow-up study.¹⁷ Additionally, disturbances in methylation at the PPARG, KCNQ1, TCF7L2, and IRS1 loci have been reported in adipose and pancreatic tissue from people with prevalent type 2 diabetes.18, 19, 20 These findings raise the possibility that alterations in DNA methylation might be involved in the biological pathways underlying development of type 2 diabetes.

Therefore, in this study, we aimed to investigate whether variations in DNA methylation are associated with future type 2 diabetes among Indian Asians, and whether differences in methylation patterns between Indian Asians and Europeans are associated with, and could be used to predict, differences in the magnitude of risk of developing type 2 diabetes.