Type 2 Diabetes–Associated Genetic Variants Regulate Chromatin Accessibility in Human Islets

Abstract

Type 2 diabetes (T2D) is a complex disorder in which both genetic and environmental risk factors contribute to islet dysfunction and failure. Genome-wide association studies (GWAS) have linked single nucleotide polymorphisms (SNPs), most of which are noncoding, in >200 loci to islet dysfunction and T2D. Identification of the putative causal variants and their target genes and whether they lead to gain or loss of function remains challenging. Here, we profiled chromatin accessibility in pancreatic islet samples from 19 genotyped individuals and identified 2,949 SNPs associated with in vivo -regulatory element use (i.e., chromatin accessibility quantitative trait loci [caQTL]). Among the caQTLs tested ( = 13) using luciferase reporter assays in MIN6 β-cells, more than half exhibited effects on enhancer activity that were consistent with in vivo chromatin accessibility changes. Importantly, islet caQTL analysis nominated putative causal SNPs in 13 T2D-associated GWAS loci, linking 7 and 6 T2D risk alleles, respectively, to gain or loss of in vivo chromatin accessibility. By investigating the effect of genetic variants on chromatin accessibility in islets, this study is an important step forward in translating T2D-associated GWAS SNP into functional molecular consequences.

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

“…To confirm library quality, we first analyzed the data as ensemble ATAC-seq by aggregating all high-quality mapped reads irrespective of barcode. Ensemble snATAC-seq from all three samples showed the expected insert size distribution (Supplementary Figure 1a), strong enrichment of signal at transcription start sites (TSS) (Supplementary Figure 1b), and high concordance of signal with published islet ATAC-seq data 14,27–29 (Supplementary Figure 1c).…”

Functional characterization of thousands of type 2 diabetes-associated and chromatin-modulating variants under steady state and endoplasmic reticulum stress

“…To test putative islet β cell regulatory sequences for their ability to enhance transcription from a minimal promoter and to identify SNPs that alter regulatory activity, we generated an MPRA library containing: i) 1,910 SNPs significantly associated with changes in human islet chromatin accessibility (caQTLs) 11 ; ii) 2,218 control SNPs overlapping human islet ATAC-seq peaks, which were reported to have no correlation with changes in human islet chromatin accessibility 11 ; and iii) 2,500 index and genetically linked (r 2 >0.8) SNPs/indels corresponding to 259 T2D association signals in the NHGRI/EBI GWAS Catalogue (Figure 1a, Table S2, and Methods). In total, 13,628 two-hundred base pair (bp) sequences from the human genome were included in this MPRA library.…”

“…SNPs associated with chromatin accessibility changes in islets (caQTLs) were significantly closer to the ATAC-seq peak summits than control SNPs, which are SNPs that reside in ATAC-seq peaks 11 but were not associated with chromatin accessibility changes in islets (Figure 4a). Consequently, caQTL SNPs were more likely to be MPRA active than were control SNPs (Figure 4b).…”

“…Studies designed to identify chromatin accessibility quantitative trait loci (caQTL) are being increasingly applied to nominate SNPs altering CRE activity 9, 10 . Previously, we identified 2,949 caQTLs in human islets 11 , which were significantly enriched for type 2 diabetes (T2D)-associated SNPs, highlighting the utility of this approach to nominate putative disease-associated SNPs affecting CRE activity in relevant cell types. However, caQTLs are correlative associations, and high throughput assays to directly test variant effects are needed to experimentally establish causality.…”

“…Although studies over the past several years implicate altered islet CRE function in T2D genetic risk and progression, they have colocalized only ∼1/4 of T2D-associated loci to altered chromatin accessibility and/or gene expression levels in islets 11, 17–20 . We hypothesize that this is partially because previous studies measured chromatin accessibility (caQTLs) and gene expression (eQTL) in islets cultured under steady state conditions 11, 21 , consequently missing important gene-environment interactions characteristic of a complex disorder like T2D. For example, endoplasmic reticulum (ER) stress, which is elicited by the high demands of insulin production and secretion on protein folding capacity in β cells, leads to (patho)physiologic adaptations.…”