Department of Developmental Biology and Cancer Research, Institute for Medical Research Israel-Canada, Hebrew University-Hadassah Medical School, Jerusalem 91120, Israel.
Hum Mol Genet. 2012 Jan 15;21(2):371-83. doi: 10.1093/hmg/ddr472. Epub 2011 Oct 12.
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.
个体间的 DNA 甲基化变异被频繁假设为改变个体对 2 型糖尿病（T2DM）的易感性。在与 T2DM 相关的基因组区域中描述了序列影响的甲基化，但缺乏与疾病风险直接、序列无关的关联证据。在这里，我们通过逐步研究设计来探索致病的 DNA 甲基化：首先，在 1169 例病例和对照个体的基于池的全基因组筛选中，在先前通过遗传研究与 T2DM 相关的基因组区域中发现了过多的差异甲基化位点。接下来，在选定的排名靠前的区域进行了深入分析。FTO 基因第一内含子中的一个 CpG 位点显示出病例相对于对照的微小（3.35%）但显著（P=0.000021）低甲基化。该效应独立于该区域的序列多态性，并在携带序列风险等位基因的个体中持续存在。与对照组相比，每个百分点的甲基化降低 6.1%，则患 2 型糖尿病的几率增加（OR=1.061，95%CI：1.032-1.090），甲基化降低 1 个标准差的比值（调整性别后）为 1.5856（95%CI：1.2824-1.9606），并且灵敏度（曲线下面积=0.638，95%CI：0.586-0.690；男性=0.675，女性=0.609）优于最强的已知序列变体。此外，在一个独立的人群队列中的前瞻性研究显示，与保持健康的个体相比，后来发展为 T2DM 的年轻个体的甲基化显著降低。进一步的基因组分析显示，与基因增强子以及与甲基化敏感转录调节剂结合的位点共定位。这些数据表明，在所分析的位点上的低甲基化水平是 T2DM 的早期标志物，并提出了一种新的机制，即孤立的非启动子基因组位点的早发性、个体间甲基化变异使个体易患 T2DM。
