Comparative Single-Cell Profiling of Mucosa and Organoids Implicates Altered Epithelial-Mesenchymal Interactions Mediated by PTGER4 in Perianal Fistulizing Crohns Disease
Background and aims: Perianal fistulizing Crohns disease (CD) is severe and often more difficult to treat than luminal CD. Current therapeutics focusing solely on the immune system neither target epithelial and mesenchymal compartments nor consider genetic/epigenetic mechanisms, potentially missing causative aspects of the disease. Thus, the mucosal cells and organoids from a cohort of perianal fistulizing CD patients and controls with diverse genetic backgrounds were experimentally examined. Methods: Patient mucosal biopsies (n = 37 patients; 11 inflamed, 26 non-inflamed) and organoids were subjected to single cell RNA sequencing, biochemical, and microscopic analysis. Single-cell transcriptional activity was investigated via principal components, cell type proportions, enriched pathways, and receptor-ligand interactions. Results: Overall, 140,503 mucosa and 77,044 organoid cells were sequenced. Inflamed perianal CD showed changes across the mucosal compartments (epithelium, immune, stromal), the most dramatic taking place in the epithelium. Epithelial changes occurring in the rectum of perianal CD patients associated with inflammation, gender, and ancestry, and were accompanied by a reduction in differentiated lineages. Organoids from the patient cohort retained both the gender- and ancestral-specific gene expression but did not overwhelmingly reflect their disease status. Organoids lacked bona fide differentiated lineages, but secretory pathways were promoted through PGE2-PTGER4 signaling and HDAC function. Conclusion: Epigenetic modifications are disrupted in the epithelium during inflammation and perianal fistulizing CD that affect the differentiation capacity of those cells, limiting their production/function and thus diminishing the ability of the mucosal tissue to heal. These epigenetic modifications appear to be modulated by crosstalk between the epithelial and mesenchymal cells, and thus might be leveraged therapeutically.