Genome-wide DNA methylation analysis of human pancreatic islets from type 2 diabetic and non-diabetic donors identifies candidate genes that influence insulin secretion.
Genome-wide DNA methylation analysis of human pancreatic islets from type 2 diabetic and non-diabetic donors identifies candidate genes that influence insulin secretion.
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DOI：
10.1371/journal.pgen.1004160
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发表时间：
2014-03
期刊：
影响因子：
4.5
通讯作者：
Ling C
中科院分区：
文献类型：
--
作者：
Dayeh T;Volkov P;Salö S;Hall E;Nilsson E;Olsson AH;Kirkpatrick CL;Wollheim CB;Eliasson L;Rönn T;Bacos K;Ling C
胰岛素分泌受损是 2 型糖尿病 (T2D) 的一个标志。表观遗传学可能影响疾病易感性。为了描述胰岛中的人类甲基化组并确定 T2D 的表观遗传基础，我们分析了来自 T2D 和非糖尿病供体的胰岛中 479,927 个 CpG 位点的 DNA 甲基化和转录组。我们提供了人类胰岛、β 和 α 细胞中整体 DNA 甲基化模式的详细图谱。靠近转录起始位点的基因组区域甲基化程度较低，而远离转录起始位点的区域如基因体、3'UTR和基因间区域甲基化程度较高。虽然 CpG 岛甲基化程度较低，但周围 2 kb 海岸显示出中等程度的甲基化，而更远的区域（陆架和公海）在人类胰岛、β 细胞和 α 细胞中甲基化程度较高。经过多次测试校正后，我们在 T2D 胰岛中鉴定出 1,649 个 CpG 位点和 853 个基因，包括 TCF7L2、FTO 和 KCNQ1，这些基因具有差异 DNA 甲基化。大多数差异甲基化的 CpG 位点具有中等程度的甲基化，并且在 CpG 岛屿中代表性不足（~7%），而在公海中代表性较高（~60%）。 102个差异甲基化基因，包括CDKN1A、PDE7B、SEPT9和EXOC3L2，在T2D胰岛中差异表达。 CDKN1A 和 PDE7B 启动子的甲基化在体外抑制了它们的转录活性。功能分析表明，已确定的候选基因影响胰腺 β 和 α 细胞，因为 Exoc3l 沉默会减少胞吐作用，而 Cdkn1a、Pde7b 和 Sept9 的过度表达分别扰乱克隆 β 和 α 细胞中的胰岛素和胰高血糖素分泌。总之，我们的数据可以作为人类胰岛甲基化组的参考。我们提供了在人类 T2D 胰岛中 DNA 甲基化和表达发生改变的新靶基因，这些基因导致胰岛素和胰高血糖素分泌受到干扰。这些结果强调了表观遗传学在 T2D 发病机制中的重要性。 DNA甲基化等表观遗传修饰与人类疾病的发展有关。然而，2 型糖尿病 (T2D) 患者的全基因组表观遗传学分析仍然很少。在这项研究中，我们旨在通过分析来自 T2D 和非糖尿病供体的人胰岛中 479,927 个 CpG 位点的 DNA 甲基化来揭示 T2D 的表观遗传学基础。我们在 T2D 胰岛中鉴定出 1,649 个 CpG 位点和 853 个具有差异 DNA 甲基化（倍数变化 6-59%）的基因。其中包括已报道的糖尿病基因座，例如 TCF7L2、FTO 和 KCNQ1。此外，我们发现 102 个基因在 T2D 胰岛中显示出差异 DNA 甲基化和基因表达，包括 CDKN1A、PDE7B、SEPT9 和 EXOC3L2。最后，我们提供了功能证据，证明已确定的候选基因直接影响胰腺 β 细胞中的胰岛素分泌和胞吐作用以及 α 细胞中的胰高血糖素分泌。总体而言，这项研究提供了人类胰岛甲基化组的详细图谱，并证明人类胰岛 DNA 甲基化的改变会导致激素分泌紊乱和 T2D 的发病机制。
Impaired insulin secretion is a hallmark of type 2 diabetes (T2D). Epigenetics may affect disease susceptibility. To describe the human methylome in pancreatic islets and determine the epigenetic basis of T2D, we analyzed DNA methylation of 479,927 CpG sites and the transcriptome in pancreatic islets from T2D and non-diabetic donors. We provide a detailed map of the global DNA methylation pattern in human islets, β- and α-cells. Genomic regions close to the transcription start site showed low degrees of methylation and regions further away from the transcription start site such as the gene body, 3′UTR and intergenic regions showed a higher degree of methylation. While CpG islands were hypomethylated, the surrounding 2 kb shores showed an intermediate degree of methylation, whereas regions further away (shelves and open sea) were hypermethylated in human islets, β- and α-cells. We identified 1,649 CpG sites and 853 genes, including TCF7L2, FTO and KCNQ1, with differential DNA methylation in T2D islets after correction for multiple testing. The majority of the differentially methylated CpG sites had an intermediate degree of methylation and were underrepresented in CpG islands (∼7%) and overrepresented in the open sea (∼60%). 102 of the differentially methylated genes, including CDKN1A, PDE7B, SEPT9 and EXOC3L2, were differentially expressed in T2D islets. Methylation of CDKN1A and PDE7B promoters in vitro suppressed their transcriptional activity. Functional analyses demonstrated that identified candidate genes affect pancreatic β- and α-cells as Exoc3l silencing reduced exocytosis and overexpression of Cdkn1a, Pde7b and Sept9 perturbed insulin and glucagon secretion in clonal β- and α-cells, respectively. Together, our data can serve as a reference methylome in human islets. We provide new target genes with altered DNA methylation and expression in human T2D islets that contribute to perturbed insulin and glucagon secretion. These results highlight the importance of epigenetics in the pathogenesis of T2D. Epigenetic modifications such as DNA methylation are implicated in the development of human disease. However, genome-wide epigenetic analyses in patients with type 2 diabetes (T2D) remain scarce. In this study we aimed to unravel the epigenetic basis of T2D by analyzing DNA methylation of 479,927 CpG sites in human pancreatic islets from T2D and non-diabetic donors. We identified 1,649 CpG sites and 853 genes with differential DNA methylation (fold change 6–59%) in T2D islets. These include reported diabetes loci, such as TCF7L2, FTO and KCNQ1. Furthermore, we found 102 genes that showed both differential DNA methylation and gene expression in T2D islets, including CDKN1A, PDE7B, SEPT9 and EXOC3L2. Finally, we provide functional proof that identified candidate genes directly affect insulin secretion and exocytosis in pancreatic β-cells as well as glucagon secretion in α-cells. Overall, this study provides a detailed map of the methylome in human pancreatic islets and demonstrates that altered DNA methylation in human islets contributes to perturbed hormone secretion and the pathogenesis of T2D.
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