RNA-seq at different stages of human pancreatic β cell differentiation reveals proliferation dynamics and SMAD9 in directing β cell fate.

Human pluripotent stem cells (hPSCs), such as human embryonic stem cells (hESCs) and human induced pluripotent stem cells (hiPSCs), have been successfully differentiated into pancreatic β-like cells for disease modeling and intended cell replacement therapy. These differentiating human pancreatic cells provide important insights into human pancreas development, given the difficulty in accessing human fetal pancreatic tissue. Although in-depth transcriptomic analyses, such as RNA-sequencing (RNA-Seq), have been conducted, insights into pancreatic developmental dynamics and the discovery of new pancreatic gene functions remain limited. Here, we analyzed the developmental dynamics of differentiating β-like cells and identified transcription factor signatures involved in the transition from pancreatic progenitors to endocrine progenitors, and then to β-like cells. We identified and demonstrated multiple cell cycle genes to be downregulated during late-state pancreatic β cell differentiation, accounting for their decreased proliferation during maturation. We further identified and characterized the role of yet-unreported SMAD9 in contributing toward human β cell identity and insulin secretion function. Overall, we report a rich resource of transcription factor signatures uniquely up- or downregulated during human pancreatic β cell differentiation that can be further tapped into for pancreatic biology and gene discovery.