Description

Deconstructing pancreatic islet development at single-cell resolution

H. Efsun Arda¹, Martin Enge², Jennifer Tsai¹, Philip T. Pauerstein¹, Cecil M. Benitez¹, Paul Giresi³, Lingyu Li¹, Krissie Tellez¹, William J. Greenleaf⁴, Stephen Quake^2,5, Howard Y. Chang³, Seung K. Kim^{1, 6}

¹Dept. of Developmental Biology, ²Dept. of Bioengineering, ³Dept. of Dermatology, Center for Personal Dynamic Regulomes, ⁴Dept. of Genetics, ⁵Chan Zuckerberg Biohub, San Francisco, CA, USA, ⁶Dept. of Medicine, Stanford University School of Medicine, Stanford, CA, USA

Cellular differentiation in fetal development is orchestrated by coordinated interactions between transcription factors and the cis-regulatory domains in the genome. Our ability to characterize the regulatory logic underlying organ development has been hindered by the paucity of genomic approaches that can assay limiting number of cells, such as progenitor populations. In this study, we used multi-model single-cell approaches to elucidate the molecular events that govern in vivo pancreatic endocrine cell differentiation.

In mice, islet progenitors arise from pancreatic duct cells that transiently express Neurog3, a bHLH factor. To understand the dynamics of Neurog3-dependent endocrine cell fate determination, we performed ATAC-Seq on lineage-traced cells. Our analysis revealed massive reorganization of accessible regions in progenitor cells dependent on Neurog3 activity, such as increased accessibility of hormone specific loci. To elucidate the downstream effects of the changing chromatin landscape during endocrine cell differentiation, we used single-cell gene expression assays. We found a novel intermediary cellular state subsequent to Neurog+ progenitors in which hormone lineage decisions occur. Finally, we expanded our analysis to human fetal endocrine cell development which remains largely unexplored. We provide a single-cell expression atlas of human pancreatic cells and point to the differences between human and mouse islet cell differentiation.

We anticipate our findings from these and similar efforts will reveal gene regulatory networks governing pancreatic endocrine development, and facilitate efforts toward stem cell based, regenerative therapies.