Insulin promoter in human pancreatic β cells contacts diabetes susceptibility loci and regulates genes affecting insulin metabolism

Abstract

Both type 1 and type 2 diabetes involve a complex interplay between genetic, epigenetic, and environmental factors. Our laboratory has been interested in the physical interactions, in nuclei of human pancreatic β cells, between the insulin ( gene and other genes that are involved in insulin metabolism. We have identified, using Circularized Chromosome Conformation Capture (4C), many physical contacts in a human pancreatic β cell line between the promoter on chromosome 11 and sites on most other chromosomes. Many of these contacts are associated with type 1 or type 2 diabetes susceptibility loci. To determine whether physical contact is correlated with an ability of the locus to affect expression of these genes, we knock down expression by targeting the promoter; 259 genes are either up or down-regulated. Of these, 46 make physical contact with We analyze a subset of the contacted genes and show that all are associated with acetylation of histone H3 lysine 27, a marker of actively expressed genes. To demonstrate the usefulness of this approach in revealing regulatory pathways, we identify from among the contacted sites the previously uncharacterized gene and show that it plays an important role in controlling the effect of somatostatin-28 on insulin secretion. These results are consistent with models in which clustering of genes supports transcriptional activity. This may be a particularly important mechanism in pancreatic β cells and in other cells where a small subset of genes is expressed at high levels.

Single cell chromatin accessibility reveals pancreatic islet cell type- and state-specific regulatory programs of diabetes risk

“…(Figure 5c). Published 4C data from the EndoC-βH1 human beta cell line 77 anchored on the INS promoter supported the existence of physical interactions between this site and the INS promoter in beta cells (Supplementary Figure 12a). Interestingly, the site was more accessible in INS high beta cells compared to INS low beta cells, and rs231361 was predicted to have state-specific effects on beta cell chromatin accessibility (INS high beta FDR q=.060; INS low beta FDR q=.40).…”

“…We downloaded and re-analyzed published 4C data of the INS promoter for the beta cell line EndoC-βH1 77 with 4C-ker 111 . We first created a reduced genome using 25 bp flanking sequences of BglII cutting sites.…”

Association of common type 1 and type 2 diabetes gene variants with latent autoimmune diabetes in adults: A meta‐analysis

“…The period of insulin independence in LADA patients could be due to the slower destruction of insulin‐producing β‐cells in the pancreas. The INS gene plays a vital role in the process of insulin secretion and metabolism . Evidence suggests that polymorphism in the INS VNTR locus increases the risk of T1D or LADA by affecting the expression of INS in the thymus, thereby resulting in insulin autoimmunity .…”

“…The results obtained in the present study are in accordance with those of earlier studies showing an association of the PTPN22 rs2476601 polymorphism with T1D and LADA. 35,44,45 The period of insulin independence in LADA patients could be due to the slower destruction of insulin-producing 46,47 Evidence suggests that polymorphism in the INS VNTR locus increases the risk of T1D or LADA by affecting the expression of INS in the thymus, thereby resulting in insulin autoimmunity. 15,48 Therefore, we performed a meta-analysis of the INS rs689 polymorphism using nine studies to determine its association with LADA.…”

The supply chain of human pancreatic β cell lines

“…The EndoC-βH1 cells were also used to show that in human β cells the methyltransferases mixed-lineage leukemia 3 and 4 (MLL3/4) bind to the transcription factors MAFA and MAFB, and that the complexes formed thereby are necessary for proper glucose-induced insulin secretion (82). Another example for which the EndoC-βH1 cells were crucial is the demonstration of physical contact between the insulin promoter and diabetes susceptibility loci and the insulin promoter's involvement in the regulation of insulin transport and metabolism in human β cells (83). Peptidomic-based approaches have also used the human β cell lines to identify target epitopes processed and presented by β cells, thereby providing the first HLA-I peptidome catalog of human β cells (84).…”