miR-375 Regulates Intestinal Crypt Cell Landscape, Proliferation, and Regenerative Capacity

The role of miRNAs in small intestinal epithelial homeostasis is under-explored. In this study, we discovered that miR-375 is among the most significantly enriched miRNAs in crypts, and in both slowly- and actively-cycling intestinal stem cells (ISCs). We then showed by multiple manipulations, including CRISPR/Cas9 editing, of mouse enteroids that miR-375 is strongly suppressed by Wnt signaling. Single cell RNA-seq analysis of jejunal crypt cells from miR-375 knockout (375-KO) mice revealed elevated numbers of tuft cells and increased expression of Wnt-pathway genes in ISCs. In accordance with these findings, 375-KO mice displayed significant improvement in the clearance of helminth infection and in the regenerative response to whole-body irradiation. The effects of miR-375 on gut epithelial survival and proliferation were further confirmed by ex vivo perturbations in murine enteroids and in vivo over-expression experiments in Drosophila stem/progenitor cells. Functional studies in enteroids revealed that suppression of miR-375 partially compensates for the effects of Yap1 inhibition on cell survival. Consistent with these results, we also find that miR-375 is significantly reduced in mouse and human intestinal tumors. Taken together, this study demonstrates that miR-375 is a master regulator of intestinal epithelial function, proliferation, and regenerative capacity.