A spatially organized immune-stromal program drives the fissure-to-fistula continuum in Crohn's disease.

BACKGROUND & AIMS: Fistulizing Crohn's disease represents a severe and disabling complication characterized by transmural inflammation and aberrant tissue remodeling. Although fissures are considered precursors of fistulas, the cellular and molecular mechanisms driving this transition remain poorly defined. We aimed to characterize the spatial immune-stromal interactions underlying fissure formation and progression toward fistula.

METHODS

Spatial transcriptomics was performed on intestinal surgical specimens from Crohn's disease patients with inflamed tissue, fissures of increasing depth, and entero-enteric fistulas. Spatial data were integrated with single-cell reference and ligand-receptor analysis to define cellular programs and signaling networks across tissue niches.

RESULTS

Fissure-associated regions were enriched in inflammatory fibroblasts and inflammatory monocytes, identifying fissures as active immune-stromal niches rather than passive structural defects. Integration with independent single-cell datasets confirmed the association of these signatures with Crohn's disease fistulae, while comparison with non-Crohn's fistulas and ulcerative colitis supported disease specificity. Single-cell-informed pseudotime analysis identified coordinated stromal and myeloid remodeling programs associated with inflammatory fibroblast enrichment and macrophage/LAMP3 + dendritic cell states. Ligand-receptor analysis demonstrated a progressive shift from CXCL12-CXCR4-mediated immune recruitment toward Complement activation and adhesion-mediated retention circuits involving ADGRE5-CD55 and THY1-integrin pathways, defining a spatially organized fistula-associated immune-stromal niche.

CONCLUSIONS

Fissures represent active immune-stromal niches in which coordinated remodeling programs support the development of the fistula microenvironment. These findings identify early fissure-associated remodeling as a potential therapeutic window and highlight CXCR4, complement, and immune-stromal adhesion pathways as candidate targets to intercept fistula progression in Crohn's disease.