Dissecting cell-type specific pathophysiological changes in human type-2 diabetic pancreatic islets using single-cell transcriptomic data

Pancreatic islet (dys)function is central to glucose homeostasis and type 2 diabetes (patho)physiology. Human islets consist of multiple endocrine (alpha, beta, delta, gamma), endothelial, and resident/inflitrating immune cells whose coordinated functions modulate glucose mobilization or disposal. Single cell transcriptome profiling (scRNA-seq) studies have been applied to dissect human islet cellular heterogeneity, identify islet cell (sub)populations, and define their molecular repertoire. However, precise understanding of cell type-specific alterations in type 2 diabetic vs. non-diabetic individuals is lacking, due in part to the limited number of individuals or single cell transcriptomes per individual profiled for comparison. Here, we create a comprehensive single cell transcriptome atlas of 245,878 human islet cells from 48 individuals spanning non-diabetic (ND), pre-diabetic (PD), and type 2 diabetic (T2D) states and matched for sex, age, and ancestry and define marker gene sets that are robustly expressed across disease states for each of the 14 cell types identified. We observe significant decreases in the number of beta cells sampled from T2D vs. ND or PD donors. Two of eight putative beta cell subpopulations, with ‘high functioning’ and ‘senescent’ cell gene signatures, increase and decrease in T2D donor islets, respectively. Importantly, we identify 511 differentially expressed genes in beta cells from T2D vs. ND donors. This includes monogenic and type 2 diabetes effector genes, such as HNF1A, DGKB, ST6GAL1, and FXYD2, for which genetic and environmental effects on their expression is concordant.  Human beta cell and islet knockdown of selected newly-identified down-regulated genes impairs beta cell viability or function. Together, this study provides new and robust, cell type-resolved insights on the cellular and molecular changes in healthy vs. diabetic human islets and represents a valuable resource to the islet biology and type 2 diabetes communities. Pancreatic islets from 17 type 2 diabetic (T2D), 17 non-diabetic (ND) and 14 prediabetic (PD) cadaveric organ donors were dissociated to single cell suspension and captured/profiled using 10x Genomics single-cell RNA-seq platform ND: Islet29, Islet34, Islet37, Islet38, Islet42, Islet45, Islet47, Islet54, Islet57, Islet59, Islet61, Islet68, Islet73, Islet80, Islet104, Islet107, Islet123 PD: Islet40, Islet50, Islet53, Islet55, Islet56, Islet58, Islet62, Islet63, Islet70, Islet85, Islet89, Islet101, Islet118, Islet127 T2D: Islet28, Islet30, Islet31, Islet32, Islet33, Islet39, Islet41, Islet44, Islet48, Islet52, Islet60, Islet71, Islet84, Islet91, Islet126, Islet119, Islet128