Type 1 diabetes risk genes mediate pancreatic beta cell survival in response to proinflammatory cytokines

Beta cells intrinsically contribute to the pathogenesis of type 1 diabetes (T1D), but the genes and molecular processes that mediate beta cell survival in T1D remain largely unknown. We combined high throughput functional genomics and human genetics to identify T1D risk loci regulating genes affecting beta cell survival in response to the proinflammatory cytokines IL-1b, IFNg, and TNFa. We mapped cytokine-responsive candidate cis­­-regulatory elements (cCREs) active in beta cells using ATAC-seq and single nuclear ATAC-seq (snATAC-seq), and linked cytokine-responsive beta cell cCREs to putative target genes using single cell co-accessibility and HiChIP. We performed a genome-wide pooled CRISPR loss-of-function screen in EndoC-βH1 cells, which identified hundreds of genes affecting cytokine-induced beta cell loss. We identified thousands of variants in cytokine-responsive beta cell cCREs altering transcription factor (TF) binding using high-throughput SNP-SELEX. Together our findings reveal processes and genes acting in beta cells during cytokine exposure that intrinsically modulate risk of T1D. Primary human islets from 12 donors were cultured in vitro with pro-inflammatory cytokines (IL-1b, IFNg, and TNFa) at multiple doses and durations. ATAC-seq, snATAC-Seq (10x Genomics) and RNA-seq were performed in treated and untreated matched samples to map islet and beta cells regulatory programs in response to cytokine stimulation. The cell line EndoC-βH1, a model for human beta cells, was profiled with HiChIP in untreated and cytokine-treated conditions, to identify long range chromatin interaction, and was used to perform a CRIPSR-KO screen to identify genes affecting cytokine-induced beta cell loss. SELEX-Seq was used to determine the in-vitro binding of hundreds of transcription factors at genetic variants located within islet regulatory elements.