Genome-wide survey reveals predisposing diabetes type 2-related DNA methylation variations in human peripheral blood

TLDR

DNA methylation variation is hypothesized to influence individual susceptibility to type 2 diabetes, yet direct, sequence‑independent associations remain unproven. The study aimed to identify disease‑contributing methylation changes by screening the genome of 1,169 T2DM cases and controls and then focusing on the most significant loci. A pool‑based genome‑wide screen revealed differentially methylated sites overlapping known T2DM‑associated regions, followed by detailed analysis of the top‑ranking sites. Hypomethylation of a CpG in the first intron of FTO was linked to a 6.1 % increase in T2DM odds per 1 % methylation loss, was independent of local genotype, predicted future disease in a prospective cohort, and co‑localized with enhancers and methylation‑sensitive transcription factor binding sites, establishing it as an early risk marker.

Abstract

Inter-individual DNA methylation variations were frequently hypothesized to alter individual susceptibility to Type 2 Diabetes Mellitus (T2DM). Sequence-influenced methylations were described in T2DM-associated genomic regions, but evidence for direct, sequence-independent association with disease risk is missing. Here, we explore disease-contributing DNA methylation through a stepwise study design: first, a pool-based, genome-scale screen among 1169 case and control individuals revealed an excess of differentially methylated sites in genomic regions that were previously associated with T2DM through genetic studies. Next, in-depth analyses were performed at selected top-ranking regions. A CpG site in the first intron of the FTO gene showed small (3.35%) but significant (P = 0.000021) hypomethylation of cases relative to controls. The effect was independent of the sequence polymorphism in the region and persists among individuals carrying the sequence-risk alleles. The odds of belonging to the T2DM group increased by 6.1% for every 1% decrease in methylation (OR = 1.061, 95% CI: 1.032–1.090), the odds ratio for decrease of 1 standard deviation of methylation (adjusted to gender) was 1.5856 (95% CI: 1.2824–1.9606) and the sensitivity (area under the curve = 0.638, 95% CI: 0.586–0.690; males = 0.675, females = 0.609) was better than that of the strongest known sequence variant. Furthermore, a prospective study in an independent population cohort revealed significant hypomethylation of young individuals that later progressed to T2DM, relative to the individuals who stayed healthy. Further genomic analysis revealed co-localization with gene enhancers and with binding sites for methylation-sensitive transcriptional regulators. The data showed that low methylation level at the analyzed sites is an early marker of T2DM and suggests a novel mechanism by which early-onset, inter-individual methylation variation at isolated non-promoter genomic sites predisposes to T2DM.