This study comprehensively解析es the cellular composition, gene expression characteristics, and spatial organization of intestinal fibrosis in Crohn's disease using single-cell and spatial transcriptomic technologies. It reveals the interaction network between inflammatory-associated fibroblasts (IAF), immune cells, and endothelial cells, offering new insights into the mechanisms and therapeutic strategies for fibrotic diseases.
Literature Overview
This article, 'Single-cell and spatial transcriptomics of stricturing Crohn’s disease highlights a fibrosis-associated network', published in the journal Nature Genetics, reviews and summarizes the cellular and gene expression atlas of Crohn’s disease (CD)-related intestinal fibrosis. Based on 61 samples covering 21 CD patients and 10 non-IBD controls, the study utilized single-cell RNA sequencing (scRNA-seq) and spatial transcriptomic technology (Visium) to reveal dynamic changes in fibroblasts, immune cells, and the enteric nervous system in fibrotic regions. It also identifies tissue microenvironments highly correlated with Crohn's disease risk gene modules.Background Knowledge
Crohn's disease is a chronic inflammatory bowel disease often accompanied by fibrotic complications following prolonged inflammation, leading to intestinal lumen stenosis and functional impairment. Currently, there are limited effective anti-fibrotic treatment options, and traditional mouse models fail to accurately replicate the complex pathology of human CD. In recent years, single-cell sequencing and spatial transcriptomic techniques have emerged as critical tools for analyzing disease microenvironments, enabling the identification of cell subtypes, their gene expression programs, and intercellular communication networks. This study combines both omics approaches to reveal the spatial organization of fibrotic Crohn's disease tissue at single-cell resolution and identifies multicellular networks associated with disease progression, offering novel insights into understanding intestinal fibrosis mechanisms.
Research Methods and Experiments
The study included 61 intestinal tissue samples from 21 CD patients and 10 non-IBD controls, including biopsies and surgically resected tissues. The samples were classified into four categories—non-IBD, non-stricturing, inflamed non-stricturing, and stricturing—based on macroscopic pathology and endoscopic scoring. scRNA-seq was performed to isolate and sequence epithelial and non-epithelial cells, while spatial transcriptomics (Visium) was used to map gene expression within tissue sections. Cellular composition changes and gene expression patterns were evaluated using Bray-Curtis dissimilarity analysis, Dirichlet regression, and Lasso regression modeling. Additionally, an inflammatory-associated fibroblast (IAF) scoring system was developed to identify core cellular programs associated with fibrosis.Key Conclusions and Perspectives
Research Significance and Prospects
This study, for the first time at single-cell and spatial resolution, reveals the cellular composition and gene networks of intestinal fibrosis in Crohn’s disease, highlighting the central role of fibroblast-immune cell interactions in fibrosis. Future research may further investigate the dynamic regulatory mechanisms of IAF programs and validate subcellular RNA localization using high-resolution spatial techniques to identify potential therapeutic targets for anti-fibrotic treatment. Additionally, integrating multi-omics and longitudinal studies could track fibrosis progression and evaluate molecular signatures of therapeutic responses.
Conclusion
This study systematically characterizes cellular heterogeneity and gene expression programs in stricturing Crohn's disease tissues through integrated single-cell and spatial transcriptomic approaches. It identifies fibroblast subtypes and their spatial localization patterns that are highly associated with intestinal fibrosis. The study also reveals gene module enrichment in tertiary lymphoid structures and spatially specific expression of CD risk genes, providing key clues for fibrosis mechanism research and therapeutic interventions. These findings not only deepen our understanding of CD-associated fibrosis but also provide an analytical framework applicable to other fibrotic diseases such as pulmonary fibrosis and cirrhosis.
