Coordination between endoderm progression and gastruloid elongation controls endodermal morphotype choice

Embryos mostly follow a single morphogenetic trajectory, where variability is largely quantitative with no qualitative differences. This robustness stands in contrast to in-vitro embryo-like models, which, like most organoids, display a high degree of variability. What makes embryonic morphogenesis so robust is unclear. We use the gastruloid model to study the morphogenetic progression of definitive endoderm (DE) and its divergence. We first catalog the different morphologies and characterize their statistics. We then learn predictive models for the lineage morphotype based on earlier expression and morphology measurements. Finally, we analyze these models to identify key drivers of morphotype variability, and devise personalized (gastruloid-specific) as well as global interventions that will lower this variability and steer morphotype choice. In the process we identify two types of coordination that are lacking in the in-vitro model but are required for robust gut tube formation. We expect the insights obtained here will improve the quality and usability of 3D embryo-like models, chart a methodology extendable to other organoids for controlling variability, and will also shed light on the factors that provide the embryo its morphogenetic robustness.