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bioRxiv · 10.1101/2025.09.08.674957

TNF Receptor 1 regulates colonic mesenchymal cell diversity and the epithelial stem cell niche.

Gadeock, S.·Girish, N.·Liu, C. Y.·Huang, Y.·Grikscheit, T. C.·Polk, D. B.
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Abstract

BACKGROUND & AIMSAnti-tumor necrosis factor (anti-TNF) is a mainstay of inflammatory bowel disease (IBD) therapy but fails in many patients. Although TNF has pro-inflammatory effects, depletion of TNF receptor 1 (TNFR1) paradoxically exacerbates chronic colitis. Because colitis induces remodeling of mesenchymal cell populations, which provide a niche for epithelial stem cells involved in mucosal healing, we hypothesized that TNFR1 promotes colonic mesenchymal cell diversity and stem cell niche function. METHODSMesenchymal TNFR1 function was studied using TNFR1-/-, platelet derived growth factor receptor alpha (PDGFR)-Cre;TNFR1fl/fl mice, and mixed-genotype mesenchymal-epithelial co-cultures. Mesenchymal cell diversity and gene function were assessed using single-cell RNA-Seq of primary colonic myofibroblasts (CMFs) and via anti-integrin A6 (ITGA6) antibody treatment and exogenous R-spondin 3 (RSPO3) supplementation. RESULTSTNFR1-/- mesenchyme exhibits reduced cell diversity, with specific depletion of specialized TNF- and interferon-signaling pericryptal cell-type. Deletion of TNFR1 in the pericryptal mesenchyme diminished the (PDGFR)+ CMF population and reduced RSPO3 expression, but increased ITGA6 expression relative to controls (TNFR1+/-). Moreover, inhibition of ITGA6 reversed the proliferative and migratory phenotype of TNFR1-/- CMFs and restored expression of PDGFR and RSPO3. Co-cultures of colonoids with TNFR1-/- CMFs resulted in downregulation of stem cell marker expression; this was rescued by supplementation with RSPO3. Supporting the role for mesenchymal TNFR1 in regulating colonic epithelial stem cells, mice deficient for TNFR1 in PDGFR+ cells showed a 40% loss of Lgr5+ stem cells, consistent with the global TNFR1-deficient mouse. CONCLUSIONTNFR1-mediated signaling regulates specification and function of colonic mesenchyme, performing an integral role in the maintenance of the crypt stem cell population.

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Gadeock, S., Girish, N., Liu, C. Y., Huang, Y., Grikscheit, T. C., Polk, D. B.. 2025-09-09. TNF Receptor 1 regulates colonic mesenchymal cell diversity and the epithelial stem cell niche.. https://doi.org/10.1101/2025.09.08.674957

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