Epithelial and stromal remodelling in murine Crohn’s disease-like ileitis

Background Inflammatory bowel disease is characterised by progressive epithelial, immune and stromal dysfunction. Human datasets yield important insights yet are inherently descriptive, requiring animal models for in vivo mechanistic interrogation. The SAMP1/YitFc (SAMP) mouse model develops spontaneous Crohn’s disease (CD)-like ileitis, allowing for the controlled manipulation of pathophysiological pathways. Objective To define cell-specific disease-associated transcriptional changes and their translational relevance, we profiled inflamed SAMP ilea by single-nucleus RNA-sequencing (snRNA-seq) and compared identified programmes with human IBD single-cell RNA-seq datasets. Design We performed whole-ileum snRNA-seq on SAMP (n=4) and control AKR/J (n=3) mice using the gut-optimised CitraPrep protocol, generating 58 349 high-quality nuclei across epithelial, immune and stromal lineages. We corroborated SAMP-associated changes with immunofluorescent staining, western blotting, spatial transcriptomic and human single-cell RNA-seq data. Results We observed a primary type 2 immune phenotype in SAMP compared with AKR mice, but most transcriptional changes occurred in stromal and epithelial, not immune, cells. Stromal remodelling included increased fibroblast-derived Igf1 . In SAMP epithelium, expansion of tuft cells and emergence of SAMP-specific Pcsk6+ crypt enterocytes were observed and confirmed in patients with CD. Finally, we identified cross-compartmental changes in cell–cell signalling, including enterocyte-to-type three innate lymphoid cell communication and enhanced global Igf1 signalling. These features recapitulate both known and novel characteristics of CD, thereby extending our understanding of disease-associated multicellular networks. Conclusion This atlas of ileitis-prone SAMP mice provides a high-resolution resource for dissecting conserved and novel mechanisms of inflammation and tissue remodelling. In this study, we uncover disease-associated transcriptional changes conserved in human CD, presenting a translational platform for future mechanistic and therapeutic studies.