Disrupted Vitamin D receptor in Paneth cells leads to ileitis and dysbiosis in the small intestine

Background: Vitamin D3 and its receptor vitamin D receptor (VDR) are implicated in the pathogenesis of inflammatory bowel disease and susceptibility to infection. Paneth cells (PCs) are specialized epithelial cells mainly found in the small intestine. PCs have a key role in shaping microbiome and inflammatory responses. However, there is limited study exploring PCs with VDR deficiency in ileitis and dysbiosis. Hypothesis: We hypothesize that VDR deficiency in Paneth cells alters the microbiome and makes the host susceptible to small intestinal inflammation (e.g., ileitis). Methods/Models: Small intestinal microbiome of VDRΔPC mice were detected by Fluorescence in situ hybridization. SAMP1/YitFc mice develop a spontaneous ileitis that is similar in many features to human Crohn’s Disease. We then examined the expression level of VDR in the SAMP1/YitFc mice with ileitis. To rule out confounding factors that may contribute to the intestinal epithelial VDR regulation, we have established a germ-free VDRΔIEC mouse model. We also cultured enteroids derived from the conditional PC KO (VDRΔPC) and VDRLoxp mice. Paneth cells isolated from VDRΔPC and VDRloxp mice were analyzed by single cell RNA sequencing. Results: We observed dislocation of small intestinal microbiome and penetration to epithelial cells in the VDRΔPC mice. The mucus thickness was significantly reduced in the small intestine of the VDRΔPC mice, compared to the VDRloxp mice. We found abnormal Paneth cells in the SAMP1/YitFc mice, compared with the control AKR mice. VDR and VDR target ATG16L1 were significantly reduced in the small intestine of the SAMP1/YitFc mice with ileitis via RT-PCR, WB, and IHC staining. Interestingly, the differences of PCs between specific pathogen free VDRΔIEC mice and VDRloxp controls were markedly reduced when both mice groups were germ-free. Paneth cells in the ileal organoids isolated from VDRloxp and VDRΔPC mice were labeled with lysozyme via immunofluorescence staining. The number of lysozyme-positive cell, i.e. Paneth cell, were counted in each bud of the organoids. There were significantly reduced number of Paneth cells in the VDRΔPC enteroids. At the molecular level, single cell RNA sequencing of Paneth cells isolated VDRΔPC mice and VDRloxp showed that changes of VDR target genes include AMPs and α-defensin. PC VDR involves processes in broad-spectrum humoral immune response, predominantly mediated by AMPs and a tissue repair mechanism for proliferation. Conclusion and Future Plan: PC VDR deletion makes the host susceptible to small intestinal inflammation. Insights gained from understanding how VDR is integrally involved in regulating PC function may serve as a novel paradigm for understanding host-microbial interactions and new therapeutic targets for ileitis. This abstract was presented at the American Physiology Summit 2026 and is only available in HTML format. There is no downloadable file or PDF version. The Physiology editorial board was not involved in the peer review process.