Stromal cell states are altered in active Crohn’s disease (CD), but their niche-specific localisation, origin and phenotypic stability is unknown. Using spatial transcriptomics, RNA-seq and ATAC-seq (~500,000 cells) we identify and map 20 distinct fibroblast states within their cellular and cytokine signalling environments in human full-thickness CD bowel. Inflammatory fibroblasts (IFs) reside in immune-rich mucosal ulcers of high cytokine signalling activity. We demonstrate that combinatorial cytokine exposure generates the IF state, whilst suppressing precursor universal fibroblast programs. Once generated, the IF state does not spontaneously revert, suggesting permanent reprogramming due to IF-specific gene regulatory networks including CEBPB and ETV4 transcription factors. This epigenetic reprogramming is distinct from contractile stroma (CS) populating immune-depleted submucosal fibrotic niches. Histone deacetylase inhibition destabilises IF, while demethylase inhibition promotes CS. Together, our findings establish that epigenetic reprogramming of stromal cell states underpins pathologic tissue niches that determine clinical outcomes in CD, offering novel therapeutic approaches. 

This data entry is part of multimodal series containing scRNA-seq (SCP3254) , scATAC-seq (SCP3258), and Xenium 5k (SCP3259).