Recording symmetry breaking during gastruloid morphogenesis with recombinase circuits

In vitro models of embryonic development and organogenesis have revealed the remarkable potential of stem cells to self-organize morphogenesis. While great progress has been made towards measuring the complexity of organoid morphologies and cell types, we have a less complete understanding of how signaling dynamics orchestrate this emergent biological complexity.

We study symmetry breaking in the gastruloid model of axial morphogenesis using genetic circuits recorders of signaling histories. Recombinase circuits encode permanent labels of cells' signaling states within a ‘listening window’ defined through addition of the small molecule doxycycline. Clonal mouse embryonic cell lines expressing morphogen recorders can achieve high fidelity labeling with temporal resolution between 1 and 3 hours. By sampling a Wnt morphogen recorder at different timepoints during gastruloid morphogenesis, we map how dynamics of Wnt signaling encode anterior-posterior positional information. These measurements localize the timepoint of Wnt symmetry breaking to within a 6 hour time window. Notably, this window occurs before any apparent polarization in either gastruloid morphology or Wnt signaling domains, suggesting a key role for cellular rearrangements in axial morphogenesis. In ongoing work, we are usings morphogen recorders to trace signaling lineages across cell types using single-cell transcriptomics.