Reconstructing regulative progenitor behaviors in synthetic embryos

Advanced stem cell-based in vitro models of embryogenesis offer great promise to decipher developmental programs with high-throughput and resolution. However, the rapid changes in morphology and cell state that underly these models mask multiple higher order parameters, including the regulative balance between differentiation and self-renewal that govern transient progenitor cell populations. Here, we apply a continuous single-cell Cas9-based molecular recorder to mouse embryonic stem cells, which enables the recovery of can reproducibly recovere and high-content information regarding the historical relationship between individual cells. We apply our system to Trunk-Like Structures (TLS), a complex in vitro model of embryogenesis that captures differentiation and morphological dynamics from pluripotency exit to the specification of the somitic and neural lineages. By recording cell lineages alongside the transcriptional identities of extant cells, we are able to build high-resolution phylogenetic trees, identify clonal subpopulations, and reveal recover the step-wisestepwise series of events that govern germ layer specification. Moreover, we examine are able to functionally characterize the specification and maintenance of multipotent neuro-mesodermal progenitor (NMP) populations as they coordinate self-renewal and commitment into more specialized cell types, including how thehow highly disparateplastic individual nature of individual branches trajectories ultimately aggregateultimately aggregate to ensure to generate the generation of highly consistent embryonic structures. Finally, we demonstrate the potential of this technology for high-throughput perturbation screening by combining small molecule treatment with individual structure labeling, allowing us to we demonstrate that these parameters can be independently tuned to modulate TLS morphology, including in reversible ways that extend the duration through which NMPs can contribute to both lineages of the embryonic trunkconnect perturbation of early differentiation pathways to progenitor cell behavior and structure morphology. Our work represents the first continuous molecular recording approach applied to dynamic in vitro models, a toolkit that can be combined with inhibitor libraries or other screening modalities to uncover the genetic and epigenetic mechanisms that enable highly orchestrated and robust changes in cell state composition during critical windows of morphogenesis.