Combinatorial BMP4 and Activin direct choice between alternate routes to endoderm during human gastrulation [scRNA-seq]

Cellular differentiation requires the proper interpretation of multiple signalling cues which vary in concentration. How exactly the combination and history of signals a cell is exposed to influences a fate decision remains poorly understood. In this study we use hESCs as a tractable model system to explore how combinations of cues guide state transitions during gastrulation. Using single-cell transcriptomics and live-cell imaging of engineered hESCs expressing endogenous cell state reporters, we reconstructed developmental lineages and obtained single-cell measurements of fate specification dynamics during gastrulation. We found that definitive endoderm, one of the three germ layers, arises from two distinct developmental trajectories: a direct route from pluripotency, and an indirect route via a mesoderm progenitor state. Furthermore, by modulating the signalling input we found that the relative concentration of Activin and BMP4 controls the choice between alternate trajectories to endoderm. These findings reveal a lineage convergence event during human gastrulation with multiple routes existing to definitive endoderm dictated by the combination of signalling cues presented. This work shows that the combination cues a cell is exposed to not only directs the final fate outcome it assumes, but the developmental route taken. Overall design: scRNA-Seq was performed on cultured hESC line H1 WT cells treated with Activin 100 ng/mL and BMP4 10 ng/mL or BMP4 50 ng/mL in a E5 basal media and switched between cues at different points in time. The aim of this work was to characterise what cell fates are aquired when hESCs are treated with these signals for different durations and orders.