Comparative and integrative single cell analysis reveals new insights into the transcriptional immaturity of stem cell-derived ß cells.

Diabetes cell replacement therapy has the potential to be transformed by human pluripotent stem cell-derived ß cells (SC-ß cells). However, the precise identity of SC-ß cells in relationship to primary fetal and adult ß-cells remains unclear. Here, we used single-cell sequencing datasets to characterize the transcriptional identity of islets from in vitro differentiation, fetal islets, and adult islets. Our analysis revealed that SC-ß cells share a core ß-cell transcriptional identity with human adult and fetal ß-cells, however SC-ß cells possess a unique transcriptional profile characterized by the persistent expression and activation of progenitor and neural-biased gene networks. These networks are present in SC-ß cells, irrespective of the derivation protocol used. Notably, fetal ß-cells also exhibit this neural signature at the transcriptional level. Our findings offer insights into the transcriptional identity of SC-ß cells and underscore the need for further investigation of the role of neural transcriptional networks in their development.

Single-nucleus multi-omics of human stem cell-derived islets identifies deficiencies in lineage specification.

Insulin-producing ß 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 ß 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.