Abstract

Organoids are a major tool to study tissue renewal. However, characterizing the underlying differentiation dynamics in space and time remains challenging. We developed TypeTracker, which identifies cell fates by AI-enabled cell tracking and propagating measured endpoint fates back along the branched lineage trees. TypeTracker provides cell fates during growth and division for all cells, which allows us to pinpoint the moments and locations where cells commit to a new fate for all major cell types. Our application of this approach to intestinal organoids indicates a new ‘commit-then-sort’ model of organ renewal at the cellular level, which contrast with the conventional conveyor belt picture where cells differentiate when moving up the crypt-villus axis. Specifically, cells that ultimately migrate to the villus in intestinal organoids commit to their new type early, when still deep inside the crypt, which has several important consequences: 1) Secretory cells commit before terminal division, with secretory fates emerging symmetrically in sister cells. 2) Different secretory types descend from distinct stem cell lineages rather than an omni-potent secretory progenitor. 3) The ratio between secretory and absorptive cells is strongly affected by proliferation of absorptive cells after commitment. 4) Spatial patterning occurs after commitment through type-dependent cell rearrangements. Our approach and resulting model upend our understanding of intestinal cell fate dynamics, raises new questions about the underlying commitment and sorting mechanisms, and may be used more broadly to study spatio-temporal differentiation programs in diverse organoid systems. If time allows I will also discuss recent results on the dynamics of WNT signaling and cell extrusion from the epithelial layer.

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