Pancreas patch-seq links physiologic dysfunction in diabetes to single-cell transcriptomic phenotypes

Summary Pancreatic islet cells regulate glucose homeostasis through insulin and glucagon secretion; dysfunction of these cells leads to severe diseases like diabetes. Prior single-cell transcriptome studies have shown heterogeneous gene expression in major islet cell-types; however it remains challenging to reconcile this transcriptomic heterogeneity with observed islet cell functional variation. Here we achieved electrophysiological profiling and single-cell RNA sequencing in the same islet cell (pancreas patch-seq) thereby linking transcriptomic phenotypes to physiologic properties. We collected 1,369 cells from the pancreas of donors with or without diabetes and assessed function-gene expression networks. We identified a set of genes and pathways that drive functional heterogeneity in β-cells and used these to predict β-cell electrophysiology. We also report specific transcriptional programs that correlate with dysfunction in type 2 diabetes (T2D) and extend this approach to cryopreserved cells from donors with type 1 diabetes (T1D), generating a valuable resource for understanding islet cell heterogeneity in health and disease. Key findings Pancreas patch-seq provides a single-cell survey of function-transcriptome pairing in 1,369 islet cells from donors with and without diabetes Expression of a specific subset of genes predicts β-cell electrophysiology in transcriptome-function networks. Compromised β-cell function in T2D correlates with altered ETV1 expression and inflammatory pathways Functional heterogeneity in α-cells maps to ER stress and islet lineage markers Application of patch-seq to cells from rare cryopreserved islets from donors with T1D