Charting in vitro beta cell differentiation by single cell RNA sequencing

In vitro differentiation of human stem cells can produce pancreatic beta cells, the insulin-secreting cell type whose loss underlies Type 1 Diabetes. As a step towards mastery of this process, we report on transcriptional profiling of >100,000 individual cells sampled during in vitro beta cell differentiation and describe the cells that emerge. We resolve populations corresponding to beta cells, alpha-like poly-hormonal cells, non-endocrine cells that resemble pancreatic exocrine cells and a previously unreported population resembling enterochromaffin cells. We show that the beta and alpha-like cells are stable for weeks in culture without exogenous growth factors and that gene expression changes associated with in vivo beta cell maturation are recapitulated in vitro. We demonstrate that stem-cell derived enterochromaffin cells can synthesize and secrete serotonin in vitro. To remove exocrine cells, we characterize a scalable re-aggregation technique that efficiently selects endocrine cells. Finally, we use a high-resolution sequencing time course to characterize gene expression dynamics during human pancreatic endocrine induction from which we develop a lineage model of in vitro beta cell differentiation. This study provides a deeper perspective on the current state of human stem cell differentiation and is a jumping-off point for future endeavors in in vitro differentiation of pancreatic islet cells and their application in regenerative medicine. Single-cell mRNA sequencing of pluripotent stem cells differentiating in vitro towards pancreatic beta cells. The data & metadata match the initial submission of the manuscript, not the final version.