Abstract Background Fibroblasts play a key role in stricture formation in Crohn’s disease (CD), but their mechanistic role in ulcerative colitis (UC) is unclear. Understanding fibrogenesis in UC requires a systems-level investigation to uncover new treatment targets. We studied full-thickness UC tissues to characterize fibroblast heterogeneity and function by generating the first single-cell RNA sequencing (scRNAseq) atlas of transmural UC bowel and providing proof of principle for therapeutic target validation. Methods We performed scRNAseq of nine fresh full-thickness UC resections containing non-involved and inflamed segments as well as seven normal non-CD (non-CD or non-IBD) colon segments. Each segment was separated into mucosa/submucosa or muscularis propria and analyzed separately for a total of 64 tissue samples and 287,279 cells. We tested integrin a5b1 and avb1 heterodimers as potential anti-fibrotic therapeutic targets in UC with blocking antibody and small molecule respectively by using whole tissues, isolated intestinal cells, next-generation sequencing (NGS), and two mouse models. Results Our integrated dataset revealed fibroblast heterogeneity in inflamed UC with the majority of changes detected in the mucosa/submucosa, but also alterations in the muscle layer. Cell-cell interaction modeling revealed multiple fibroblast populations displaying a central signaling role in inflamed UC, including adventitial, MMP-expressing, and inflammatory fibroblasts. Fibroblasts emerged as major signal senders and interacted with each other through secretion of fibronectin (FN) and integrin signaling network. a5b1 and avb1 were fibroblast predominant integrins in UC, and inhibiting these heterodimers showed fibrosis resolution in our in vitro and in vivo experimental systems. Their function was validated by target expression, ECM deposition, migration, NGS and two animal models with a5b1 and avb1 blocking antibodies and small molecules. Conclusion The first UC full-thickness bowel scRNAseq atlas revealed previously unrecognized fibroblast heterogeneity and interactions. Integrins a5b1 and avb1 were validated as a potential therapeutic target. These results provide a new resource for a better understanding of UC fibrosis and open a potential therapeutic vulnerability of integrin heterodimers. Conflict of interest: Dr. Mukherjee, Pranab: No conflict of interest Chauhan, Gaurav: No conflict of interest Christensen, Stephen: No conflict of interest Khan, Afshin: None West, Gail: No conflict of interest Banerjee, Suhanti: No conflict of interest Chandra, Jyotsna: No conflict of interest Prasad, Ankita: No conflict of interest Czarnecki, Douglas: No conflict of interest Liu, Weiwei: No conflict of interest Larsen, Catherine: No conflict of interest Kirstein, Matthew: No conflict of interest Wong, Jamie: No conflict of interest Lu, Min: No conflict of interest Jain, Dhawal: Dhawal Jain is an employee and shareholder of Eli Lilly and Company Veisman, Ido: No conflict of interest Massey, William: No conflict of interest Wang, Yan: No conflict of interest Lal, Samir: No conflict of interest Fienman, Joshua: No conflict of interest Kravarik, Kellie: No conflict of interest Rieder, Florian: Personal Fees: Adiso, Adnovate, Agomab, Allergan, AbbVie, Arena, Astra Zeneca, Boehringer-Ingelheim, Celgene/BMS, Celltrion, CDISC, Celsius, Cowen, Ferring, Galapagos, Galmed, Genentech, Gilead, Gossamer, Granite, Guidepoint, Helmsley, Horizon Therapeutics, Image Analysis Limited, Index Pharma, Landos, Jannsen, Koutif, Mestag, Metacrine, Mopac, Morphic, Organovo, Origo, Palisade, Pfizer, Pliant, Prometheus Biosciences, Receptos, RedX, Roche, Samsung, Sanofi, Surmodics, Surrozen, Takeda, Techlab, Teva, Theravance, Thetis, UCB, Ysios, 89Bio
Mukherjee et al. (2026) studied this question.