Insulin-producing β cells created from human pluripotent stem cells have potential as a therapy for insulin-dependent diabetes, but human pluripotent stem cell-derived islets (SC-islets) still differ from their in vivo counterparts. To better understand the state of cell types within SC-islets and identify lineage specification deficiencies, we used single-nucleus multi-omic sequencing to analyse chromatin accessibility and transcriptional profiles of SC-islets and primary human islets. Here we provide an analysis that enabled the derivation of gene lists and activity for identifying each SC-islet cell type compared with primary islets. Within SC-islets, we found that the difference between β cells and awry enterochromaffin-like cells is a gradient of cell states rather than a stark difference in identity. Furthermore, transplantation of SC-islets in vivo improved cellular identities overtime, while long-term in vitro culture did not. Collectively, our results highlight the importance of chromatin and transcriptional landscapes during islet cell specification and maturation.
Insulin-secreting β-cells within the pancreatic islets of Langerhans are lost in patients with type 1 diabetes1. Islets can be generated in vitro by differentiation of human pluripotent stem cells2-5, but understanding of the molecular events governing this process is limited. Here, we use single-cell multiomics to measure chromatin accessibility and transcriptional profiles of 120,064 cells to characterize and delineate maturation of islets from in vitro differentiation. We find distinguishing chromatin accessibility and gene expression signatures as well as dynamic profiles for each major islet cell type produced from in vitro differentiation. Furthermore, based on chromatin accessibility, β, α, and δ cells from in vitro differentiation are more ambiguous in their cellular identity than from isolated primary islets. However, extended time in vitro or with transplantation into mice drives more distinct states of chromatin accessibility for each cell type. Modulation of CTCF expression redirects cell fate from pancreatic islet endocrine to an intestinal enteroendocrine-like cell type. Additionally, knockdown of ARID1B enhances β-cell maturation transcriptionally and by chromatin accessibility. These results provide a comprehensive atlas and insights into cell fate identity and maturation of stem cell-derived islets, which will inform on their utility for therapy and disease modeling6-8.
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