Hang, Y. | Search bioRxiv

bioRxiv2019

Single nucleus RNA sequencing maps acinar cell states in a human pancreas cell atlas

Molecular evidence of cellular heterogeneity in the human exocrine pancreas has not been established, due to the local concentration of hydrolytic enzymes that can rapidly degrade cells and RNA upon resection. Here we innovated single-nucleus RNA sequencing protocols, and profiled more than 120,000 cells from adult and neonatal human donors to create the first comprehensive atlas of human pancreas cells, including epithelial and non-epithelial constituents. Adult and neonatal pancreata shared common features, including the presence of previously undetected acinar subtypes, but also showed marked differences in the composition of the endocrine, endothelial, and immune compartments. Spatial cartography, including cell proximity mapping through in situ sequencing, revealed dynamic developmental cell topographies in the endocrine and exocrine pancreas. Our human pancreas cell atlas can be interrogated to understand pancreatic cell biology, and provides a crucial reference set for future comparisons with diseased tissue samples to map the cellular foundations of pancreatic diseases.

genomics↗

bioRxiv2019

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

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 {beta}-cells and used these to predict {beta}-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 findingsO_LIPancreas patch-seq provides a single-cell survey of function-transcriptome pairing in 1,369 islet cells from donors with and without diabetes C_LIO_LIExpression of a specific subset of genes predicts {beta}-cell electrophysiology in transcriptome-function networks. C_LIO_LICompromised {beta}-cell function in T2D correlates with altered ETV1 expression and inflammatory pathways C_LIO_LIFunctional heterogeneity in -cells maps to ER stress and islet lineage markers C_LIO_LIApplication of patch-seq to cells from rare cryopreserved islets from donors with T1D C_LI

genomics↗