Abstract Background Intestinal fibrostenosis in Crohn’s disease (CD) represents a significant clinical challenge, driven by the absence of reliable early biomarkers, limited therapeutic options, and high postoperative recurrence rates, all of which contribute to poor patient outcomes. This study aims to elucidate the role of Gli1+ mesenchymal cells in the pathogenesis of intestinal fibrostenosis and to explore their potential as a novel therapeutic target. Methods CD patients who underwent surgery for intestinal obstruction due to fibrosis were included in this study, and intestinal tissues were collected from both fibrotic and normal sites. Dextrose sodium sulfate (DSS)-induced and 2,4,6-Trinitrobenzenesulfonic acid (TNBS)-induced chronic colitis mouse models and their normal controls were also included. Single-cell RNA sequencing was performed on both human and murine tissues. Gli1-CreERT2; R26-tdTomato mice were generated for lineage tracing. Cell sorting combined with Smart-seq was used to isolate Gli1+ mesenchymal cells, revealing their pathogenic determinants. Results Single-cell RNA sequencing data and immunofluorescence staining from surgical patients revealed an enrichment of Gli1+ mesenchymal cells at fibrotic sites. Lineage tracing of Gli1+ mesenchymal cells demonstrated their proliferation and acquisition of a myofibroblast phenotype following chronic colitis. In vivo ablation of Gli1+ mesenchymal cells attenuated the severity of intestinal fibrosis. Compared to Gli1- cells, Gli1+ mesenchymal cells expressed a distinct gene expression profile, including markers of extracellular matrix (ECM)-related genes and Smoc2 (SPARC Related Modular Calcium Binding 2, encodes an extracellular matrix protein). Elevated Smoc2 expression was confirmed in both human and murine tissues, and Smoc2 knockdown further supported its role in promoting intestinal fibrosis. Mechanistically, Gli1+ mesenchymal cells establish a pro-fibrotic niche through the endocrine and exocrine functions of SMOC2, promoting ECM deposition and the activation of other fibroblasts. Additionally, a predictive and diagnostic model was established by assessing SMOC2 levels in tissue and plasma samples from CD patients with intestinal fibrosis, highlighting its potential as a biomarker for postoperative recurrence and as a therapeutic target. Conclusion Our results demonstrate that Gli1+ mesenchymal cells are key drivers of intestinal fibrostenosis, forming a pro-fibrotic niche through their unique secretion of the SMOC2 protein at fibrotic sites. SMOC2 could therefore be used as a predictive biomarker for postoperative recurrence and as a potential therapeutic target.
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