Single nucleus-resolved chromatin accessibility profiles of pancreatic islet cells

Michelle Lee (University of Pennsylvania)

Michelle Lee, Jonathan Schug, Elisabetta Manduchi, Eric Waite, Erin Duffy, Danielle Jaffe, Ali Naji, Mark Atkinson, Alvin Powers, Klaus Kaestner.

Deep molecular profiling of pancreatic islet cells via single-cell RNA-sequencing (scRNA-seq) has revealed cell type specific transcriptome profiles. However, scRNA-seq suffers from ‘dropout’, or missing signals, for genes expressed at low levels, such as those encoding transcription factors or signaling molecules. In addition, there is significant of cross-contamination of ambient RNA from lysed cells in each cell, complicating the detection of rare and/or transitional cell types or states. Therefore, additional molecular profiles are required to strengthen our understanding of cell type identity and reveal potential subpopulations of cells. Single nucleus Assay for Transposase-Accessible Chromatin sequencing (snATAC-seq) reveals regulatory element sequence and key transcription factor motifs that function in a cell type specific manner, complementing gene expression. Therefore, we employed snATAC-seq to advance our understanding of cell type identity for key human pancreatic cell types.

We performed snATAC-seq on pancreatic islets obtained from 33 deceased organ donors that were non-diabetic, auto-antibody positive but normoglycemic, type 1 diabetic, or type 2 diabetic, and performed computational analyses.

Summary of Results
By unsupervised clustering, we found that chromatin accessibility profiles alone can identify the major pancreatic cell types, including five endocrine cell populations. Furthermore, the accessible chromatin regions of the various cell types showed enrichment for specific transcription factor binding motifs. Moreover, we observed a population of cells displaying a transitional phenotype related to but distinct from alpha cells. Cells of this population showed accessibility at the glucagon promoter, the defining marker of alpha cells, but also displayed multiple open chromatin regions enriched for the binding motifs of developmental transcription factors, raising the possibility that even adult human islets contain a subset of transitional and possibly progenitor type cells.

We demonstrate that chromatin accessibility captures important characteristics of cell type identity in the human pancreas. Moreover, snATAC-seq discovered a subpopulation of cells that show a progenitor-like phenotype. Thus, snATAC-seq reveal novel information and putative transitional cell types that complement gene expression analysis by scRNA-seq. Future integration of these data promises to further our understanding of cell type identity and function of human pancreatic cells.