Expression and functional assessment of candidate type 2 diabetes susceptibility genes identify four new genes contributing to human insulin secretion

Abstract

ObjectivesGenome-wide association studies (GWAS) have identified >100 loci independently contributing to type 2 diabetes (T2D) risk. However, translational implications for precision medicine and for the development of novel treatments have been disappointing, due to poor knowledge of how these loci impact T2D pathophysiology. Here, we aimed to measure the expression of genes located nearby T2D associated signals and to assess their effect on insulin secretion from pancreatic beta cells.MethodsThe expression of 104 candidate T2D susceptibility genes was measured in a human multi-tissue panel, through PCR-free expression assay. The effects of the knockdown of beta-cell enriched genes were next investigated on insulin secretion from the human EndoC-βH1 beta-cell line. Finally, we performed RNA-sequencing (RNA-seq) so as to assess the pathways affected by the knockdown of the new genes impacting insulin secretion from EndoC-βH1, and we analyzed the expression of the new genes in mouse models with altered pancreatic beta-cell function.ResultsWe found that the candidate T2D susceptibility genes' expression is significantly enriched in pancreatic beta cells obtained by laser capture microdissection or sorted by flow cytometry and in EndoC-βH1 cells, but not in insulin sensitive tissues. Furthermore, the knockdown of seven T2D-susceptibility genes (CDKN2A, GCK, HNF4A, KCNK16, SLC30A8, TBC1D4, and TCF19) with already known expression and/or function in beta cells changed insulin secretion, supporting our functional approach. We showed first evidence for a role in insulin secretion of four candidate T2D-susceptibility genes (PRC1, SRR, ZFAND3, and ZFAND6) with no previous knowledge of presence and function in beta cells. RNA-seq in EndoC-βH1 cells with decreased expression of PRC1, SRR, ZFAND6, or ZFAND3 identified specific gene networks related to T2D pathophysiology. Finally, a positive correlation between the expression of Ins2 and the expression of Prc1, Srr, Zfand6, and Zfand3 was found in mouse pancreatic islets with altered beta-cell function.ConclusionsThis study showed the ability of post-GWAS functional studies to identify new genes and pathways involved in human pancreatic beta-cell function and in T2D pathophysiology.

Genetic Drivers of Pancreatic Islet Function

“…5). Genetic variation in the MODY genes has also been shown to play a role in type 2 diabetes (NDIAYE et al 2017). …”

Effects of variants of 50 genes on diabetes risk among the Chinese population born in the early 1960s

“…Diabetes is caused by a progressive loss of β‐cell insulin secretion frequently against a background of insulin resistance, or autoimmune β‐cell destruction, usually leading to absolute insulin deficiency . Among the 50 SNPs included in this study, most loci exerted their primary effects on disease risk through deficient insulin secretion, some loci were related to insulin resistance or insulin sensibility, and some loci may be the adapter or receptor that can indirectly affect insulin sensitivity or increase diabetes susceptibility …”

“…22,23 Among the 50 SNPs included in this study, most loci exerted their primary effects on disease risk through deficient insulin secretion, some loci were related to insulin resistance or insulin sensibility, and some loci may be the adapter or receptor that can indirectly affect insulin sensitivity or increase diabetes susceptibility. 8,10,28,32,[36][37][38][39][40][41][42][43][44] Among the susceptibility loci examined herein, we confirmed significant evidence for an association with diabetes risk for 10 loci in the Chinese population in the following genes: cyclindependentkinase 5 regulatory subunit associated protein 1 (CDKAL1) (rs10946398), adaptorrelated protein complex 3 subunit sigma 2 (AP3S2) (rs2028299), SREBF chaperone (SCAP) (rs4858889), RAS guanyl releasing protein 1 (RASGRP1) (rs7403531), Gprotein-coupled receptor kinase 5 (GRK5) (rs10886471), diacylglycerol kinase beta/transmembrane protein 195 (DGKB/TMEM195) (rs2191349), zinc finger AN1-type containing 3 (ZFAND3) (rs9470794), kelchdomain containing 5 (KLHDC5) (rs10842994), melatonin receptor 1B (MTNR1B) (rs10830963), and ankyrin1 (ANK1) (rs516946). Previous studies have identified an association between diabetes risk and SNPs for CDKAL1 in European Americans, African Americans, UK samples, Indians, Korean, and Chinese, 33,[45][46][47][48][49] making CDKAL1 one of the most highly replicated genes identified.…”

“…To date, more than 100 single nucleotide polymorphisms (SNPs) have been identified as diabetes risk loci in different ethnic populations by genome‐wide association studies (GWAS) . However, few studies have investigated many loci in a representative Chinese population.…”

“…[3][4][5][6][7] To date, more than 100 single nucleotide polymorphisms (SNPs) have been identified as diabetes risk loci in different ethnic populations by genome-wide association studies (GWAS). 8 However, few studies have investigated many loci in a representative Chinese population. So, in this study we used data from the China National Nutrition and Health Survey (CNNHS) 2010 to 2012 to evaluate genetic susceptibility by combining the 61 SNPs identified from recent GWAS.…”