Abstract Background Refractory perianal fistula in Crohn’s disease (CD) still present an unmet clinical need with a high disease burden. Despite increasing interest, pathophysiology leading to the refractory phenotype remains unclear, with only epithelial-to-mesenchymal-transitioning (EMT) commonly mentioned as a contributing factor. Using a systematic approach comparing therapy refractory CD fistula, therapy responsive non-IBD fistula and normal rectum, we aimed to differentiate between general healing responses and dysregulation thereof in refractory CD fistula. Methods Total RNASeq (n=51), single cell RNASeq (n=31) and spatial transcriptomic (n=8) analysis were performed on the internal opening and tract of CD fistula and idiopathic fistula. Results were validated using immunohistochemistry. Functional studies were performed in human adult organoid cultures and intestinal cell lines. Results In the fistula tracts we identified development of a squamous epithelium characterized by expression of WFDC2, keratin 5 and keratin 13. Although some EMT markers were expressed in the squamous epithelium or its intermediates, no activation of a complete EMT program could be detected in any of the tissue types, regardless of the underlying diagnosis. Upstream analysis indicated TNFα, IL6 and TGFβ as inducers of WFDC2+ epithelium, and human adult colon organoids stimulated with these cytokines (but not TGFβ alone) indeed showed a transciptional profile similar to the fistula epithelium, confirming redifferentiation potential. While WFDC2+ epithelium did occur in CD fistula, abundance was strongly decreased compared to non-IBD fistula. In addition, those WFDC2+ cells present had a more pro-inflammatory profile and were morphologically disorganized. Surprisingly, pseudotime analysis indicated epithelial calprotectin (S100A8/9) as a key factor in the aberrant development of WFDC2+ tissue in CD. Normal intestinal epithelium does not express calprotectin, but a mix of cytokines present in fistula induced clear intracellular expression of S100A8/9 in both epithelial cell lines and primary colon organoids. In CD fistula, calprotectin expression was particularly intranuclear, suggesting a transcriptional role. CHIP analysis indeed showed binding of calprotectin to various inflammatory genes and knockdown of calprotectin abrogated expression of these genes supporting a crucial regulatory role. Conclusion These data identify redifferentiation of rectal mucosa to a squamous phenotype as a normal damage response during fistula formation. However, in CD patients, transcriptional effects of calprotectin derail this process, resulting in disorganized inflammatory tissue not amenable for surgical closure and contributing to refractory disease.
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