Improving stem cell-derived pancreatic islets using single-cell multiome-inferred regulomes [Adult-snRNA-seq]

Pancreatic islet cells derived from human pluripotent stem cells hold great promise for modeling and treating diabetes. Differences between stem cell-derived and primary islets remain, but molecular insights to inform improvements are limited. Here, we acquire single-cell transcriptomes and accessible chromatin profiles during in vitro islet differentiation and from primary childhood and adult pancreas for comparison. We delineate major cell types, define their regulomes, and describe spatiotemporal regulatory relationships between transcription factors. CDX2 emerged as a regulator of enterochromaffin-like cells, which we show resemble a previously unrecognized, transient CDX2-expressing ß-cell-related population in fetal pancreas, arguing against a non-pancreatic origin as proposed. Furthermore, we observe insufficient activation of signal-dependent transcriptional programs during in vitro ß-cell maturation and identify sex hormones as drivers of childhood ß-cell proliferation. Altogether, our analysis provides a comprehensive understanding of cell fate acquisition in stem cell-derived islets and a framework for manipulating cell identities and maturity. Overall design: In this analysis, we used single nucleus RNA-seq (snRNA-seq) to analyze cells from adult human pancreas (ages: 20 - 31 years). We obtained transcriptomic signatures from both exocrine and endocrine cells, but focused on a-, ß-, d- and ?-cells (1,859 cells in total) for downstream analysis. We integrated these data with snATAC-seq data from adult human pancreas for gene regulatory network (GRN) analysis. Comparing this GRN from adult endocrine cells to similarly integrated datasets from human pluripotent stem cell-derived islets (SC-islets) and childhood human pancreatic endocrine cells allowed us to identify gene regulatory differences between SC-islet cell types and primary childhood and adult islet cell types.