Single-cell transcriptomes of the regenerating intestine reveal a revival stem cell

Abstract

The turnover of the intestinal epithelium is driven by multipotent LGR5⁺ crypt-base columnar cells (CBCs) located at the bottom of crypt zones¹. However, CBCs are lost following injury, such as irradiation², but the intestinal epithelium is nevertheless able to recover³. Thus, a second population of quiescent '+4' cells, or reserve stem cells (RSCs), has previously been proposed to regenerate the damaged intestine^4-7. Although CBCs and RSCs were thought to be mutually exclusive^4,8, subsequent studies have found that LGR5⁺ CBCs express RSC markers⁹ and that RSCs were dispensable-whereas LGR5⁺ cells were essential-for repair of the damaged intestine³. In addition, progenitors of absorptive enterocytes¹⁰, secretory cells^11-15 and slow cycling LGR5⁺ cells¹⁶ 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⁺ cells¹⁷. 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.