2000-LB: Multiome Profiling of Human Islets Nominates Beta-Cell–Specific Cytokine Response Profiles Underlying Type 1 Diabetes

Inflammation in the islet may be an early trigger of beta cell stress which can lead to islet autoimmunity and type 1 diabetes (T1D). We exposed human islets (N=8 donors) to proinflammatory cytokines (IL-1-beta and TNF-alpha) and used single nucleus multiomic sequencing to jointly profile RNA expression and chromatin accessibility (10X Genomics Multiome). We pooled cytokine-treated and untreated islets for single nucleus experiments using a randomized block design, which reduced sample-to-sample variability and eliminated batch confounding of treatment effects. We included 37,170 high quality nuclei in downstream analysis and identified transcriptional response to cytokines in three major islet cell types (887 genes in alpha cells, 2,998 genes in beta cells, 547 genes in ductal cells), including upregulation of MHC class I in all three cell types. Beta cells showed significant downregulation in marker gene expression (INS fold change = 0.55, p = 3 x 10-5), but marker gene expression did not change in alpha (GCG fold change in alpha cells = 0.68, p = 0.07) or ductal cells (KRT19 fold change in ductal cells = 0.82, p = 0.60). Pathway analyses indicated upregulation of proinflammatory pathways in all three cell types and downregulation of a hallmark beta cell pathway in beta cells only (p = 0.005). Finally, pathway analysis of cell type-specific gene expression changes, using residualized treatment effect sizes per cell type, indicated enhanced upregulation of the TGF-beta signaling pathway in beta cells as compared to alpha or ductal cells. In conclusion, using single nucleus profiling with a randomized study design, we found beta cell-specific responses to proinflammatory cytokines which may contribute to beta cell demise underlying type 1 diabetes. Analyses of cytokine effects on chromatin accessibility to nominate upstream transcriptional regulators are underway. C. Robertson: None. X. Wang: None. P. Orchard: None. J. Meng: None. V. Dolgachev: None. N. Manickam: Employee; 10x Genomics. N. Narisu: None. M. Erdos: None. F.S. Collins: None. S. Chen: None. S.C. Parker: Research Support; Pfizer Inc. NIH NIDDK (DK127777); NIH NIDDK (DK007245)