Single-cell Transcriptomes of the Regenerating Intestine Reveal a Revival Stem Cell

The turnover of the intestinal epithelium is driven by multipotent LGR5 crypt-base columnar cells (CBCs) located at the bottom of crypt zones. However, CBCs are lost following injury, such as irradiation, but the intestinal epithelium is nevertheless able to recover. Thus, a second population of quiescent '+4' cells, or reserve stem cells (RSCs), has previously been proposed to regenerate the damaged intestine. Although CBCs and RSCs were thought to be mutually exclusive, subsequent studies have found that LGR5 CBCs express RSC markers and that RSCs were dispensable-whereas LGR5 cells were essential-for repair of the damaged intestine. In addition, progenitors of absorptive enterocytes, secretory cells and slow cycling LGR5 cells have been shown to contribute to regeneration whereas the transcriptional regulator YAP1, which is important for intestinal regeneration, was suggested to induce a pro-survival phenotype in LGR5 cells. Thus, whether cellular plasticity or distinct cell populations are critical for intestinal regeneration remains unknown. Here we applied single-cell RNA sequencing to profile the regenerating mouse intestine and identified a distinct, damage-induced quiescent cell type that we term the revival stem cell (revSC). revSCs are marked by high clusterin expression and are extremely rare under homoeostatic conditions, yet give rise-in a temporal hierarchy-to all the major cell types of the intestine, including LGR5 CBCs. After intestinal damage by irradiation, targeted ablation of LGR5 CBCs, or treatment with dextran sodium sulfate, revSCs undergo a YAP1-dependent transient expansion, reconstitute the LGR5 CBC compartment and are required to regenerate a functional intestine. These studies thus define a unique stem cell that is mobilized by damage to revive the homoeostatic stem cell compartment and regenerate the intestinal epithelium.