Single-cell analysis of colonic organoids deficient for tumor necrosis factor receptor 2

Colonic epithelial repair is a key determinant of health. After injury, repair initiates through phenotypic reprogramming of wounded epithelium to a regenerative state permissive for the activation of alternative stem cell populations and healing. Although cytokine signals such as interferon help induce regenerative reprogramming, the signals that modify this state as the wound resolves remain largely unknown. Here we show that, during healing, the late upregulation of a cytokine receptor, tumor necrosis factor (TNF) receptor 2 (R2, TNFR2, Tnfrsf1b), clears the phenotype of regenerative signaling and restores homeostatic patterns of epithelial differentiation. Mice lacking epithelial-specific expression of TNFR2 also failed to complete colon ulcer healing, suggesting that full repair requires coordination of both regenerative and homeostatic epithelial phenotypes. In single-cell RNA-seq experiments, we find that colonic epithelial organoids grown from Tnfr2-/- mice retain a highly enriched census of progenitor cells and reduced representation of differentiated cells, consistent with TNFR2's role in promoting differentiation. These results demonstrate how epithelial cells adapt to inflammatory cues to choreograph repair. Colonic organoids from wildtype or Tnfr2-/- mice were grown in the presence or absence of tumor necrosis factor (TNF), n=1 culture per condition.