Single-cell and spatial multi-omics reveal interferon signaling in the pathogenesis of perianal fistulizing Crohn’s disease 4670

Abstract Description Perianal fistulizing Crohn’s disease (PCD) is a common and debilitating complication with elusive pathophysiology. We recruited patients with PCD (n = 24), CD without perianal disease (NPCD, n = 10), and idiopathic perianal fistulas (IPF, n = 29). Biopsies were taken from fistula tracts, fistula opening, and rectal mucosa. Single-cell RNA-sequencing (scRNAseq), mass cytometry (CyTOF), spatial transcriptomics (ST), immunohistochemistry, and integrated analysis were performed. ScRNAseq, CyTOF, and ST unraveled immune and non-immune cell compartments in PCD and IPF fistula tracts. PCD fistula cells showed hyperactivated pathogenic pathways including IFNg response and TNF signaling. Intestinal cells from PCD patients also expressed greater levels of IFNg-responsive and EMT genes compared to NPCD patients. Furthermore, both fistula tracts and ileal mucosa from PCD patients harbored expanded IFNg+ pathogenic Th17 cells. CyTOF data corroborated transcriptomic findings and revealed additional characteristics indicative of IFNg signaling in PCD fistula tracts, external fistula opening, and rectum. Further analysis also revealed cellular modules associated with anti-TNF therapy in PCD patients. In conclusion, multi-omics analysis revealed immune, stromal, and epithelial cell landscapes of PCD, which highlight the pathogenic role of hyperactivated IFNG signaling in both fistula tracts and luminal mucosa and identified IFNG as a novel therapeutic target for PCD. Funding Sources Supported by AGA2023-32-03, P30 DK052574,1K08DK140612, CCF1062472, WashU CTRFP1714, WashU PHIA101, R01 DK126969, R01 DK132327. Topic Categories Immune Mechanisms of Human Disease (HUM)