ORIGINAL RESEARCH article
Front. Mol. Biosci.
Sec. Molecular Diagnostics and Therapeutics
Volume 12 - 2025 | doi: 10.3389/fmolb.2025.1621643
This article is part of the Research TopicAdvancements in Immune Heterogeneity in Inflammatory Diseases and Cancer: New Targets, Mechanisms, and StrategiesView all 18 articles
Expression of Immune Related Genes and Possible Regulatory Mechanisms in Ulcerative Colitis
Provisionally accepted
- 1First Teaching Hospital of Tianjin University of Traditional Chinese Medicine, National Clinical Research Center for Chinese Medicine Acupuncture and Moxibustion, Tianjin, China
- 2Tianjin University of Traditional Chinese Medicine, Tianjin, China
- 3Medical College, Yanbian University, Yanji, China
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Background: The abnormal immune response may lead to lesions of the intestinal mucosal layer in ulcerative colitis (UC). Immunity-related genes (IRGs) are crucial for the immunological reaction in UC. However, the IRGs and potential regulatory mechanisms in UC are still unknown. Identification of immune-related genes of UC is essential to understand its pathogenesis and to develop new targeted therapeutic modalities. Methods: In this study, we combined the R package "Single R" with manual inspection methods to annotate single-cell RNA-seq data. We then performed differentially expressed genes (DEGs) analysis and pseudo-time analysis. Additionally, we performed weighted co-expression network (WGCNA) and immunity-related gene analyses in bulk sequencing of UC intestinal tissues. Afterward, GO and KEGG analyses were performed on scRNA and bulk sequencing data. From the Human TFDB database, pertinent regulatory transcription factors (TFs) were found. Using the STRING database, the protein-protein interaction network of important TFs was created. Finally, the IRGs were verified by experiments. Results: We verified that the relevant IRGs were highly expressed in T and B cells of UC patients by the single-cell technique. Moreover, analysis of IRGs' regulatory TFs revealed that 11 TFs were associated with the expression of IRGs, and the PPI network indicated that Hnf4a was the hub tf. In addition, we confirmed the high expression of CD28 in ulcerative colitis tissues by qRT-PCR and immunohistochemistry. Single-cell analysis of possible regulatory mechanisms of immune-related genes in Ulcerative Colitis Conclusions: We preliminarily discovered that Hnf4a contributes to T cell activation, infiltration, and transcriptional regulation of CD28. Importantly, we improved our understanding of the immune landscape in UC inflammatory tissue using scRNA and bulk sequencing data.
Keywords: ulcerative colitis, single-cell sequencing, Weighted Co-expression NetworkAnalysis, Biomarker genes, immunity related genes
Received: 01 May 2025; Accepted: 12 Sep 2025.
Copyright: © 2025 Qu, Xu, Zhou, He, Wang, Li, Li and Shen. This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) or licensor are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.
* Correspondence: Aihua Shen, shenaihua1128@163.com
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