Epigenome-wide association study of fasting measures of glucose, insulin, and HOMA-IR in the Genetics of Lipid Lowering Drugs and Diet Network study

Abstract

Known genetic susceptibility loci for type 2 diabetes (T2D) explain only a small proportion of heritable T2D risk. We hypothesize that DNA methylation patterns may contribute to variation in diabetes-related risk factors, and this epigenetic variation across the genome can contribute to the missing heritability in T2D and related metabolic traits. We conducted an epigenome-wide association study for fasting glucose, insulin, and homeostasis model assessment of insulin resistance (HOMA-IR) among 837 nondiabetic participants in the Genetics of Lipid Lowering Drugs and Diet Network study, divided into discovery (N = 544) and replication (N = 293) stages. Cytosine guanine dinucleotide (CpG) methylation at ∼470,000 CpG sites was assayed in CD4(+) T cells using the Illumina Infinium HumanMethylation 450 Beadchip. We fit a mixed model with the methylation status of each CpG as the dependent variable, adjusting for age, sex, study site, and T-cell purity as fixed-effects and family structure as a random-effect. A Bonferroni corrected P value of 1.1 × 10(-7) was considered significant in the discovery stage. Significant associations were tested in the replication stage using identical models. Methylation of a CpG site in ABCG1 on chromosome 21 was significantly associated with insulin (P = 1.83 × 10(-7)) and HOMA-IR (P = 1.60 × 10(-9)). Another site in the same gene was significant for HOMA-IR and of borderline significance for insulin (P = 1.29 × 10(-7) and P = 3.36 × 10(-6), respectively). Associations with the top two signals replicated for insulin and HOMA-IR (P = 5.75 × 10(-3) and P = 3.35 × 10(-2), respectively). Our findings suggest that methylation of a CpG site within ABCG1 is associated with fasting insulin and merits further evaluation as a novel disease risk marker.

Figure 1

Manhattan plot of epigenome-wide results testing for association between and the methylation status of fasting insulin. The x-axis displays the chromosome on which the CpG is located, and the y-axis displays −log₁₀(P value). (A high-quality color representation of this figure is available in the online issue.)

Figure 2

Manhattan plot of epigenome-wide results testing for association between and the methylation status of HOMA-IR. The x-axis displays the chromosome on which the CpG is located, and the y-axis displays −log₁₀(P value). (A high-quality color representation of this figure is available in the online issue.)

Figure 3

Integrated regional overlap of EWAS, cis-meQTL, and GWAS signals. The x-axis displays the cis-meQTL and GWAS signals, 20 kb upstream and downstream from the EWAS signal of interest (CpG06500161); and the y-axis displays −log₁₀(P value).

Figure 4

ENCODE plot with fasting insulin EWAS signal CpG06500161. (A high-quality color representation of this figure is available in the online issue.)