Identification of rare post-mitotic cell states induced by injury and required for whole-body regeneration in Schmidtea mediterranea

Regeneration requires coordination of stem cells, their progeny, and distant differentiated tissues. Here, we present a comprehensive atlas of whole-body regeneration in Schmidtea mediterranea and identify wound-induced cell states. Analysis of 299,998 single-cell transcriptomes captured from regeneration-competent and regeneration-incompetent fragments identified transient regeneration-activated cell states (TRACS) in the muscle, epidermis, and intestine. TRACS were stem-cell-division-independent with distinct spatiotemporal distributions and RNAi depletion of TRACS-enriched genes produced regeneration defects. Muscle expression of notum, follistatin, evi/wls, glypican-1, and junctophilin-1 was required for tissue polarity. Epidermal expression of agat-1/2/3, cyp3142a1, zfhx3, and atp1a1 was important for stem cell proliferation. Finally, expression of spectrinβ and atp12a in intestinal basal cells and lrrk2, cathepsinB, myosin1e, polybromo-1, and talin-1 in intestinal enterocytes regulated stem cell proliferation and tissue remodeling. respectively. Our results identify cell types and molecules important for regeneration, indicating that regenerative capacity can emerge from coordinated transcriptional plasticity across all three germ layers.