Genome-Wide DNA Methylation Analysis of Human Pancreatic Islets from Type 2 Diabetic and Non-Diabetic Donors Identifies Candidate Genes That Influence Insulin Secretion

Abstract

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.

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“…of adjustment for cell composition in placenta/cord blood (24), the influence of maternal genetics on placental gene expression, the potential underrepresentation of differential methylation in CpG islands (25), and the inability to obtain-for ethical reasons-target tissues for the assessment of tissue-specific DNA methylation/expression. The strengths include the strict inclusion criteria (leading to distinct AGA and SGA populations and avoiding perinatal confounders) and the parallel assessments of placenta/cord blood pairs.…”

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“…DNA methylation is a significant candidate for biomarker development, because the methylated CpG sites present high stability compared with high mutation variability in any given type of cancer [228]. DNA hyper-methylation can silence genes that are profoundly involved in the secretion of insulin and glucagon [229]. Patients with type 2 diabetes express altered GDM in skeletal muscles, adipose tissue, and pancreatic islets [230].…”

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“…Histone modification and DNA methylation causing altered gene expression and impaired insulin secretion in animal studies suggest presence of epigenetic factors in T2DM development. 57,58 Differential DNA methylation of CpG sites within TCF7L2 gene loci and its effect on insulin secretion in T2DM, 59 may be of interest in CFRD as well.…”