MICROBIAL DRIVERS OF REGION-SPECIFIC SUSCEPTIBILITY TO CHRONIC, TNF-INDUCED INTESTINAL INFLAMMATION

Abstract

Abstract BACKGROUND The majority of Crohn’s disease patients present with ileitis or ileocolitis, however, the factors that drive the development of inflammation in these different sites remain elusive. The TnfΔARE mouse model recapitulates many features of Crohn’s disease and is driven by systemic overexpression of TNF. AIMS To-date, the TnfΔARE model is published as a spontaneous intestinal inflammation model that is specific to the ileum, however, we observe severe colonic inflammation that is dependent on the murine housing facility. We aimed to use experimental approaches to investigate the epithelial and microbial factors that drive ileal and colonic inflammation in the TnfΔARE model of Crohn’s disease. METHODS Tnf ΔARE mice were housed in two murine housing facilities, termed “restrictive” and “permissive”. Pathological scoring was used to assess intestinal inflammation in TnfΔARE mice. Murine co-housing methods were used to expose non-colitic mice to those with colitis. Shotgun metagenomics was performed to determine differences in the intestinal microbiota between the two murine housing facilities. Doxycycline treatment was used to treat Chlamydia muridarum (CM) infection in mice. Various in vivo and in vitro perturbations were performed to test the role of intestinal epithelial cell expression of indoleamine 2,3-dioxygenase (IDO1) in ileal and colonic inflammation. Human single-cell RNA-sequencing (scRNA-seq) data, along with tissue samples, were analyzed to determine whether epithelial cell signaling pathways and microbiota were conserved in Crohn’s disease patients. RESULTS Tnf ΔARE mice from the restrictive murine housing facility developed the expected phenotype of ileitis, while TnfΔARE mice from the permissive murine housing facility developed ileocolitis. Upon co-housing, restrictive facility TnfΔARE mice develop ileocolitis. Permissive facility mice, but not restrictive facility mice, harbored the obligate intracellular bacterium CM in proximal colonic epithelia. Doxycycline treatment effectively cleared CM colonization and was associated with a reduction in colonic inflammation. IDO1 expression was upregulated in intestinal epithelial secretory cells in CM-infected mice and perturbation of this pathway resulted in a reduction of intestinal inflammation. Analysis of patient scRNA-seq and tissue samples revealed IDO1-expressing epithelial cells in the ascending colon and the presence of epithelia-associated microbiota. CONCLUSION Here, we associate CM infection with the development of ileocolitis the TnfΔARE mouse model of Crohn’s disease. We reveal the role of IDO1-expressing intestinal secretory cells in TnfΔARE mice with and without colonic involvement. Finally, we demonstrate conservation of these pathways and microbiota in human Crohn’s disease samples.