Genetic variation can modulate gene expression, and thereby phenotypic variation and susceptibility to complex diseases such as type 2 diabetes (T2D). Here we harnessed the potential of DNA and RNA sequencing in human pancreatic islets from 89 deceased donors to identify genes of potential importance in the pathogenesis of T2D. We present a catalog of genetic variants regulating gene expression (eQTL) and exon use (sQTL), including many long noncoding RNAs, which are enriched in known T2D-associated loci. Of 35 eQTL genes, whose expression differed between normoglycemic and hyperglycemic individuals, siRNA of tetraspanin 33 (TSPAN33), 5′-nucleotidase, ecto (NT5E), transmembrane emp24 protein transport domain containing 6 (TMED6), and p21 protein activated kinase 7 (PAK7) in INS1 cells resulted in reduced glucose-stimulated insulin secretion. In addition, we provide a genome-wide catalog of allelic expression imbalance, which is also enriched in known T2D-associated loci. Notably, allelic imbalance in paternally expressed gene 3 (PEG3) was associated with its promoter methylation and T2D status. Finally, RNA editing events were less common in islets than previously suggested in other tissues. Taken together, this study provides new insights into the complexity of gene regulation in human pancreatic islets and better understanding of how genetic variation can influence glucose metabolism.T ype 2 diabetes (T2D) is an increasing global health problem (1). Although genome-wide association studies (GWAS) have yielded more than 70 loci associated with T2D or related traits (2, 3), they have not provided the expected breakthrough in our understanding of the pathogenesis of the disease. They have nonetheless pointed at a central role of the pancreatic islets and β-cell dysfunction in the development of the disease (4, 5). It therefore seems pertinent to focus on human pancreatic islets to obtain insights into the molecular mechanisms causing the disease (6, 7). Given that most SNPs associated with T2D lie in noncoding regions, the majority of causal variants are likely to regulate gene expression rather than protein function per se. Therefore, combination of DNA and RNA sequencing in the same individuals may help to disentangle the role these SNPs play in the pathogenesis of the disease (8). Although the human pancreatic islet transcriptome has been previously described (6, 9-18), using microarrays or RNA sequencing of a limited number of nondiabetic individuals, this has not allowed a more global analysis of the complexity of the islet transcriptome in T2D. Here we combined genotypic imputation, expression microarrays, and exome and RNA sequencing (ExomeSeq and RNA-Seq) in a large number of human pancreatic islets from deceased donors with and without T2D. This study identified a number of novel genes, including long intergenic noncoding RNAs (lincRNAs), whose expression and/or splicing influences insulin secretion and is associated with glycemia. In addition, we provide a catalog of RNA editing and allele-specific expr...
Glucose-stimulated insulin secretion is biphasic, with a rapid first phase and a slowly developing sustained second phase; both are disturbed in type 2 diabetes (T2D). Biphasic secretion results from vastly different release probabilities of individual insulin granules, but the morphological and molecular basis for this is unclear. Here, we show that human insulin secretion and exocytosis critically depend on the availability of membrane-docked granules and that T2D is associated with a strong reduction in granule docking. Glucose accelerated granule docking, and this effect was absent in T2D. Newly docked granules only slowly acquired release competence; this was regulated by major signaling pathways, but not glucose. Gene expression analysis indicated that key proteins involved in granule docking are downregulated in T2D, and overexpression of these proteins increased granule docking. The findings establish granule docking as an important glucose-dependent step in human insulin secretion that is dysregulated in T2D.
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