Atlas of innate immune responses to experimental cholera and IL22 treatment demonstrates protection by mucus-secreting cells

Abstract The diarrheal disease cholera remains a global threat. However, knowledge of the innate immune defenses in the small intestine that protect against the causative agent, Vibrio cholerae, is limited. Here, single-cell RNA-sequencing of epithelial and immune cells mapped gene expression patterns in the infant mouse small intestine and revealed changes in response to V. cholerae infection and treatment with an IL22 Fc-fusion protein. Infection increased the abundance of an enterocyte subtype that highly expressed defense-associated functions and stimulated production of IL22, a cytokine linked to epithelial integrity, from group 3 innate lymphoid cells. Administration of IL22Fc increased production of vibriocidal Reg3β from enterocytes and the abundance of secretory lineage and Muc2-producing goblet cells, which secreted mucus into the intestinal crypts, impairing V. cholerae association with the epithelium. These IL22-mediated responses limited V. cholerae intestinal colonization and protected mice from diarrhea and death. These observations suggest enterocyte specialization in mucosal defense, identify mechanisms of IL22-mediated protection, and point to host-directed approaches for cholera therapeutics. Competing Interest Statement The authors have declared no competing interest. Footnotes 1)Fate-mapping experiments using Edu and genetically labelled stem cells to decipher the origins of cluster 5 enterocytes, resulting in new Fig. 1h-j and Extended Data Fig.3c-f. Additionally, new RNA velocity analyses of our scRNA-Seq data corroborating the origin of cluster 5 enterocytes. 2)Edu labeling of proliferating cells to uncover how IL22 treatment increases the secretory progenitor cell population, resulting in a new Extended Data Fig. 9. 3)Several experiments, including intestinal proteomics, expand on the mechanisms of protection resulting from IL22 treatment, resulting in new Extended Data Fig. 8c. 4)New evidence using Muc2 -/- mice (new Fig. 6n) linking bacterial motility and mucus-mediated colonization restriction.