Single cell and genetic analyses reveal conserved cell populations and signaling mechanisms of stomach and intestinal stromal stem cell niches

Stomach and intestinal epithelial cells are maintained by the activity of stem cells located in the isthmus and crypt, respectively1,2. Recent studies have demonstrated a surprisingly conserved role for Wnt signaling in stomach and intestinal development and stem cells3,4. Although accumulating evidence suggests that intestinal stromal cells secrete Wnt ligands to promote stem cell renewal5-10, the source of stomach Wnt ligands is still unclear. Moreover, how these gastrointestinal stem cell niche signals are produced is currently unknown. By performing single cell analysis of gastrointestinal stromal cells, we identified cell populations with transcriptome signatures that are conserved between the stomach and intestine. In close proximity to gastrointestinal epithelial cells, these cells highly expressed pericyte markers and Wnt ligands. They also were enriched for Hh signaling, which plays a key role in gut development11,12. A recent study has shown that intestinal pericryptal cells co-express Hh target and Wnt ligand genes8. To define their relationship, we analyzed mice with Hh gain of function in the pericyte-like stromal cells conserved between the stomach and intestine, and found increased levels of Wnt ligands, supporting Hh regulation of stromal Wnt ligand expression. Moreover, utilizing Sufu and Spop double knockout mice, which stabilized GLI2, a key Hh mediator in the gut, we were able to map GLI2 binding sites genome-wide and analyze super enhancers. This work demonstrates GLI2 activation of stromal Wnt ligands through enhancers that are conserved between the stomach and intestine. To determine the significance of Wnt secreting gastrointestinal stromal cells, we genetically inhibited Wnt secretion from the perictye-like or broad stromal cells, demonstrating their roles in gastrointestinal regeneration and development, respectively. Our work not only identifies the conserved gastrointestinal stromal niche cell populations but also reveals their underlying signaling and epigenetic mechanisms.