UC San Diego

In response to external signaling factors, human pluripotent stem cells (hPSCs) can be induced to differentiate into diverse cell types. This unique property establishes hPSCs as a valuable model system to study human developmental processes. Furthermore, mature cell types generated through in vitro differentiation protocols can be studied in place of primary cells in circumstances where primary cells are difficult to obtain or exist in small numbers.Here we used established protocols to differentiate hPSCs towards the pancreatic beta cell fate. Using genomic assays, we characterized changes in the epigenome that accompany the commitment of differentiating cells to the pancreatic organ lineage. Focusing on distal regulatory elements, we investigated the function of FOXA pioneer transcription factors in the activation of pancreatic enhancers. We find that these factors are necessary for pancreatic lineage commitment and show that differential DNA sequence specifies distinct temporal patterns of FOXA recruitment to pancreatic enhancers, with profound effects on gene expression. Using models of liver and lung development, we show relevance of our findings across endodermal lineages. We next identified a group of pancreatic enhancers that are activated in response to retinoic acid signaling and whose subsequent deactivation is dependent on the enzyme LSD1. We demonstrate a critical role for LSD1 in limiting the duration of signal-dependent enhancer activation during pancreatic lineage commitment. We then integrated epigenomic analyses with data from genome-wide association studies to identify type 2 diabetes (T2D) risk variants within pancreatic enhancers. Using gene editing in hPSCs, we assigned target genes to variant-containing pancreatic enhancers and performed knockdown experiments in zebrafish to determine the developmental roles of these target genes. These experiments identify a developmental contribution to risk of T2D pathogenesis. Finally, we established a co-culture system between mature beta-like cells derived from induced pluripotent stem cells of donors with type 1 diabetes (T1D) and autoreactive T cell clones. This system is currently being used to identify a potential contribution of direct antigen presentation by beta cells to T1D pathogenesis. Altogether, our work demonstrates the utility of in vitro hPSC differentiation systems in modeling pancreatic development, disease risk, and disease pathogenesis.