Type 1 diabetes (T1D) is characterized by autoimmune destruction of insulin-producing beta cells in pancreatic islets. While studies of T1D risk mechanisms have largely focused on immune cell function, recent evidence suggests the beta cells themselves actively contribute to the disease process. Beta cells are exposed to different environmental stimuli and stressors in the course of T1D development, such as pro-inflammatory cytokines and hyperglycemia which can contribute to beta cell stress and death. However, the extent to which T1D risk variants affect the beta cell epigenome and gene regulation in response to these external signals is unknown. To gain a deeper understanding of the variants, genes, and pathways that impact beta cell function and survival in T1D pathophysiology, it is critical to map changes in beta cell gene regulation the context of T1D-relevant immune and metabolic stressors. We have generated chromatin accessibility maps from primary pancreatic islet samples exposed to T1D-relevant cytokines and identified thousands of cytokine-responsive sites and transcription factors. Integrating these data with T1D genetic fine-mapping then revealed T1D risk variants with cytokine- dependent effects on islet chromatin accessibility. The proposed project will build on these findings in combining human genetics, islet epigenomics, and genome engineering to map T1D risk variants that affect beta cell chromatin upon in vitro exposure to multiple T1D-relevant stressors and identify target genes of stress-induced T1D variant effects that impact beta cell ER stress and survival. To accomplish this, in Aim 1 we will generate comprehensive maps of changes in beta cell chromatin accessibility and transcription factor binding upon exposure to multiple T1D-relevant stressors. Using these data, we will then fine-map T1D risk variants with stress-induced effects on beta cell chromatin using QTL mapping and validate their allelic effects using reporter assays.
In Aim 2, we will identify target genes of stress-induced T1D variants by generating and analyzing changes in beta cell gene expression and 3D chromatin architecture upon exposure to the same stressors, and then validate target genes of stress-induced sites using a CRISPRi regulatory screen. Finally, in Aim 3 we will identify target genes of T1D risk variants that directly modulate beta cell ER stress and survival phenotypes using genome-wide CRISPR-mediated loss-of-function screens. The cellular phenotype of these genes will then be validated using CRISPR-mediated gene deletions in hiPSC-derived beta cells. Together our findings will provide novel insight into the intrinsic role of beta cells in T1D pathophysiology and inform therapeutic intervention through target discovery of T1D risk genes involved in beta cell stress response and survival.
An improved understanding of type 1 diabetes (T1D) risk mechanisms requires detailed studies of T1D- associated changes in beta cell gene regulation and function. To gain a deeper comprehension of the genetic variants and genes that impact beta cell function and survival in the context of disease progression, we propose to combine human genetics, islet epigenomics, and genome engineering to model changes in beta cell chromatin in response to different T1D-relevant immune and metabolic stressors. Our findings will provide novel insight into the intrinsic role of beta cells in T1D pathophysiology and inform therapeutic intervention through target discovery of T1D risk genes involved in beta cell stress response and survival.