Remodeling of the SAMP1/YitFc mouse ileum during chronic ileitis

Inflammatory bowel disease (IBD) is marked by progressive epithelial, immune, and stromal dysfunction. While human datasets have yielded important insights, they are inherently descriptive and limited in their ability to support in vivo mechanistic interrogation. The SAMP1/YitFc (SAMP) mouse model develops spontaneous ileitis, providing an experimental system that reflects human disease progression while allowing controlled manipulation of pathophysiologic pathways. To understand cell-specific gene expression changes in the diseased ileum, we defined the single nucleus transcriptomes of chronically inflamed SAMP ileum using single nucleus RNA sequencing (snRNA-seq). Whole-ileum snRNA-seq was performed from SAMP (n=4) and AKR (n=3) mice using the gut-optimized CitraPrep protocol, generating 58,349 high-quality nuclei across epithelial, immune, and stromal lineages. We corroborated SAMP-associated changes using immunofluorescence, western blotting, spatial transcriptomics, and integration with human single cell IBD data. We observed a shift to Th2 response and an expansion of ILC2 and mast cells in SAMP mice compared to AKR. Stromal remodeling in SAMP mice included increased expression of Igf1 in fibroblasts. In addition to observing previously validated Paneth cell expansion, a new expansion of tuft cells and emergence of SAMP-only Pcsk6⁺ crypt enterocytes were observed and confirmed in human Crohn’s patients. Finally, interactome analyses revealed cross-compartment changes in cell-cell signaling, including enterocyte-to-ILC3 communication and enhanced tissue-wide Igf1 signaling. These features mirror known and novel aspects of Crohn’s disease and extend our understanding of disease-associated multicellular networks. This atlas of spontaneous ileitis in SAMP mice provides a high-resolution resource for dissecting conserved and novel mechanisms of chronic inflammation and tissue remodeling. It demonstrates that the SAMP ileum recapitulates key transcriptomic features of human Crohn’s disease, validating it as a translational platform for mechanistic and therapeutic studies.