Multimodal characterization of murine gastruloid development

Gastruloids are highly scalable, three-dimensional assemblies generated from pluripotent stem cells that recapitulate fundamental principles of embryonic pattern formation in vitro. Using single cell RNA and multiome sequencing we provide a comprehensive resource mapping cellular states and cell types found during gastruloid development and compare them to the in vivo embryo. We further develop a high throughput gastruloid handling and imaging pipeline to spatially monitor cell type emergence and unfolding of symmetry breaking during gastruloid development. We report spatial variability of pluripotency states in early gastruloids that determines a binary cell response to Wnt activation. While cells situated in the core of the gastruloid revert to an ectopic pluripotent state, peripheral cells differentiate to a primitive streak like state. These two populations then cause gastruloids to break radial symmetry, allowing axial elongation and commitment to the three embryonic germ layers. Finally by performing a phenotypic compound screen, we perturb thousands of gastruloids at relevant developmental time points deriving a phenotypic landscape and inferring molecular regulator networks underlying gastruloid development. Employing this resource, we improve the formation of anterior structures in the existing gastruloid model, using a dual Wnt modulation approach to differentiate an anterior ectopic pluripotent core to anterior ecto- and endodermal structures. This work gives is a resource to understand how gastruloids develop and, more generally, how homogenous cell populations can generate complex patterns in vitro. RNAseq from different timing of Wnt Pulse