Jing Feng , Li-Na He , Ruchen Yao , Yuqi Qiao , Tian Yang , Zhe Cui , Xiangjun Meng , Jinlu Tong , Keyu Jia , Zhixiang Zuo , Jun Shen
{"title":"Comprehensive analysis of heterogeneity and cell-cell interactions in Crohn’s disease reveals novel location-specific insights","authors":"Jing Feng , Li-Na He , Ruchen Yao , Yuqi Qiao , Tian Yang , Zhe Cui , Xiangjun Meng , Jinlu Tong , Keyu Jia , Zhixiang Zuo , Jun Shen","doi":"10.1016/j.jare.2024.12.042","DOIUrl":null,"url":null,"abstract":"<div><h3>Introduction</h3><div>In Crohn’s disease (CD), lesions are mainly distributed in a segmental manner, with the primary sites of involvement being the ileum and colon. Heterogeneity in colon and ileum results in location-specific clinical presentations and therapeutic responses. Mucosal healing tends to be more readily and quickly achieved in the colon than in the ileum, where lesions are more likely to develop into complex behaviors. The heterogeneity of colon and ileum in CD, which is essential for tailored therapeutic approaches, has not yet been systematically illustrated.</div></div><div><h3>Objectives</h3><div>CD presents with unique intestinal lesions, mainly impacting the terminal ileum and colon. It is essential to comprehend the diversity in pathogenesis and treatment response among various segments.</div></div><div><h3>Methods</h3><div>We conducted comparative single-cell RNA sequencing analysis in treatment-naïve CD patients, concentrating on the colon and ileum.</div></div><div><h3>Results</h3><div>A novel subset of epithelial cells expressing high levels of <em>DUOX2</em> and <em>DUOXA2</em> (DUOX2-epi) was discovered. This DUOX2-epi subcluster predominantly distributed in the tip epithelium of the inflamed colon, potentially in response to microbial infection, as evidenced by the significant enrichment of inflammatory and microbial response pathways. The colonic and ileal DUOX2-epi subsets trigger inflammatory responses through distinct mechanisms. The colonic DUOX2-epi primarily affects monocytes via the SAA1-FPR2 ligand-receptor interaction, whereas the ileal DUOX2-epi directly interacts with regulate T cells through the CXCL16-CXCR6 ligand-receptor pair. Moreover, the cell–cell communication networks involving DUOX2-epi in the colon and ileum can help predict the location-specific effects of biological therapies.</div></div><div><h3>Conclusion</h3><div>This study delves into the heterogeneity within the ileum and colon of Crohn’s disease at the single-cell level, identifying a new epithelial subset DUOX2-epi. Predictive gene modules tailored to different locations for biological therapies are developed as well, based on the cell–cell communication network modulated by DUOX2-epi.</div></div>","PeriodicalId":14952,"journal":{"name":"Journal of Advanced Research","volume":"76 ","pages":"Pages 679-694"},"PeriodicalIF":13.0000,"publicationDate":"2025-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":"0","resultStr":null,"platform":"Semanticscholar","paperid":null,"PeriodicalName":"Journal of Advanced Research","FirstCategoryId":"103","ListUrlMain":"https://www.sciencedirect.com/science/article/pii/S2090123224006209","RegionNum":1,"RegionCategory":"综合性期刊","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":null,"EPubDate":"","PubModel":"","JCR":"Q1","JCRName":"MULTIDISCIPLINARY SCIENCES","Score":null,"Total":0}
引用次数: 0
Abstract
Introduction
In Crohn’s disease (CD), lesions are mainly distributed in a segmental manner, with the primary sites of involvement being the ileum and colon. Heterogeneity in colon and ileum results in location-specific clinical presentations and therapeutic responses. Mucosal healing tends to be more readily and quickly achieved in the colon than in the ileum, where lesions are more likely to develop into complex behaviors. The heterogeneity of colon and ileum in CD, which is essential for tailored therapeutic approaches, has not yet been systematically illustrated.
Objectives
CD presents with unique intestinal lesions, mainly impacting the terminal ileum and colon. It is essential to comprehend the diversity in pathogenesis and treatment response among various segments.
Methods
We conducted comparative single-cell RNA sequencing analysis in treatment-naïve CD patients, concentrating on the colon and ileum.
Results
A novel subset of epithelial cells expressing high levels of DUOX2 and DUOXA2 (DUOX2-epi) was discovered. This DUOX2-epi subcluster predominantly distributed in the tip epithelium of the inflamed colon, potentially in response to microbial infection, as evidenced by the significant enrichment of inflammatory and microbial response pathways. The colonic and ileal DUOX2-epi subsets trigger inflammatory responses through distinct mechanisms. The colonic DUOX2-epi primarily affects monocytes via the SAA1-FPR2 ligand-receptor interaction, whereas the ileal DUOX2-epi directly interacts with regulate T cells through the CXCL16-CXCR6 ligand-receptor pair. Moreover, the cell–cell communication networks involving DUOX2-epi in the colon and ileum can help predict the location-specific effects of biological therapies.
Conclusion
This study delves into the heterogeneity within the ileum and colon of Crohn’s disease at the single-cell level, identifying a new epithelial subset DUOX2-epi. Predictive gene modules tailored to different locations for biological therapies are developed as well, based on the cell–cell communication network modulated by DUOX2-epi.
期刊介绍:
Journal of Advanced Research (J. Adv. Res.) is an applied/natural sciences, peer-reviewed journal that focuses on interdisciplinary research. The journal aims to contribute to applied research and knowledge worldwide through the publication of original and high-quality research articles in the fields of Medicine, Pharmaceutical Sciences, Dentistry, Physical Therapy, Veterinary Medicine, and Basic and Biological Sciences.
The following abstracting and indexing services cover the Journal of Advanced Research: PubMed/Medline, Essential Science Indicators, Web of Science, Scopus, PubMed Central, PubMed, Science Citation Index Expanded, Directory of Open Access Journals (DOAJ), and INSPEC.