Drug repurposing approach for the discovery of therapeutic agents for Crohn’s disease-associated intestinal fibrosis

Abstract Background and Aims Intestinal fibrosis in Crohn’s disease (CD) frequently leads to stricture formation, with current treatment options limited to endoscopic balloon dilation and surgery. This underscores the urgent need for anti-fibrotic therapies. Our objective was to identify therapeutic targets and compounds capable of reversing the fibrotic gene expression profile of mucosal fibroblasts in CD. Methods We derived a fibrotic gene signature via fibroblasts isolated from stricturing CD tissue and conducted a meta-regression analysis across three publicly available transcriptomic datasets, to identify key differentially expressed genes (DEGs) in fibrostenotic CD. Drug repurposing platforms (iLINCS, L1000, CLUE-io) were implemented to screen compounds with high druggability, for their potential to reverse this pro-fibrotic profile. Transcription factors, microRNAs, and drugs targeting the fibrostenotic signature were identified using the TRRUST, miRWalk, and DGIdb databases, ultimately forming a drug–gene interaction network. The STITCH platform was used to predict compound-protein binding affinities. Promising compounds were subsequently evaluated in vitro, using mucosal fibroblasts derived from fibrostenotic CD patients, and the effect on the expression of selected protein targets was measured via ELISA and immunofluorescence staining. Results The top upregulated DEGs included fibroblast activation protein (FAP), IL-7 receptor, and transcription factor AP-2 gamma. The drug–gene interaction network analysis identified IL-6 among the most druggable targets. Of 6783 pharmaceutical agents, PI3K inhibitors and histone deacetylase blockers were the most effective in reversing the fibrotic signature via a FAP- and IL-6-dependent mechanism. Conclusion This integrative approach identified potential anti-fibrotic compounds and molecular targets in CD-associated fibrostenosis, supporting future development of effective therapies.