Single-cell RNA-sequencing combined with bulk RNA-sequencing analysis of peripheral blood reveals the characteristics and key immune cell genes of ulcerative colitis

Yan-Cheng Dai; Dan Qiao; Chen-Ye Fang; Qiu-Qin Chen; Ren-Ye Que; Tie-Gang Xiao; Lie Zheng; Li-Juan Wang; Ya-Li Zhang

doi:10.12998/wjcc.v10.i33.12116

Single-cell RNA-sequencing combined with bulk RNA-sequencing analysis of peripheral blood reveals the characteristics and key immune cell genes of ulcerative colitis

World J Clin Cases. 2022 Nov 26;10(33):12116-12135. doi: 10.12998/wjcc.v10.i33.12116.

Authors

Yan-Cheng Dai¹, Dan Qiao¹, Chen-Ye Fang², Qiu-Qin Chen³, Ren-Ye Que¹, Tie-Gang Xiao¹, Lie Zheng⁴, Li-Juan Wang⁵, Ya-Li Zhang⁶

Affiliations

¹ Department of Gastroenterology, Shanghai Traditional Chinese Medicine-Integrated Hospital, Shanghai University of Traditional Chinese Medicine, Shanghai 200082, China.
² Department of Gastroenterology, Traditional Chinese Medicine Hospital of Ningbo, Ningbo 315000, Zhejiang Province, China.
³ Department of Pathology, Shanghai Traditional Chinese Medicine-Integrated Hospital, Shanghai University of Traditional Chinese Medicine, Shanghai 200082, China.
⁴ Department of Gastroenterology, Traditional Chinese Medicine Hospital of Xi'an 730000, Shaanxi Province, China.
⁵ Experimental Education Center, Shanghai University of Traditional Chinese Medicine, Shanghai 201203, China.
⁶ Institute of Digestive Diseases, LongHua Hospital Shanghai University of Traditional Chinese Medicine, Shanghai 200032, China. zhanghappy181015@126.com.

Abstract

Background: Ulcerative colitis (UC) is a complicated disease caused by the interaction between genetic and environmental factors that affects mucosal homeostasis and triggers an inappropriate immune response. Single-cell RNA sequencing (scRNA-seq) can be used to rapidly obtain the precise gene expression patterns of thousands of cells in the intestine, analyze the characteristics of cells with the same phenotype, and provide new insights into the growth and development of intestinal organs, the clonal evolution of cells, and immune cell changes. These findings can provide new ideas for the diagnosis and treatment of intestinal diseases.

Aim: To identify clinical phenotypes and biomarkers that can predict the response of UC patients to specific therapeutic drugs and thus aid the diagnosis and treatment of UC.

Methods: Using the Gene Expression Omnibus (GEO) database, we analyzed peripheral blood cell subtypes of patients with UC by scRNA-seq combined with bulk RNA sequencing (RNA-seq) to reveal the core genes of UC. We then combined weighted gene correlation network analysis (WGCNA) and least absolute shrinkage and selection operator (LASSO) analysis to reveal diagnostic markers of UC.

Results: After processing the scRNA-seq data, we obtained data from approximately 24340 cells and identified 17 cell types. Through intercellular communication analysis, we selected monocyte marker genes as the candidate gene set for the prediction model. Construction of a WGCNA coexpression network identified RhoB, cathepsin D (CTSD) and zyxin (ZYX) as core genes. Immune infiltration analysis showed that these three core genes were strongly correlated with immune cells. Functional enrichment analysis showed that the differentially expressed genes were closely related to immune and inflammatory responses, which are associated with many challenges in the diagnosis and treatment of UC.

Conclusion: Through scRNA-seq analysis, LASSO diagnostic model building and WGCNA, we identified RhoB, CTSD and ZYX as core genes of UC that are closely related to monocyte infiltration that may serve as diagnostic markers and molecular targets for UC therapeutic intervention.

Keywords: Bulk RNA-seq; Key genes; Peripheral blood; Single-cell RNA-seq; Ulcerative colitis.