Yuan YY, Wu H, Chen QY, Fan H, Shuai B. Construction of the underlying circRNA-miRNA-mRNA regulatory network and a new diagnostic model in ulcerative colitis by bioinformatics analysis. World J Clin Cases 2024; 12(9): 1606-1621 [PMID: 38576737 DOI: 10.12998/wjcc.v12.i9.1606]
Corresponding Author of This Article
Heng Fan, PhD, MD, Chief Physician, Department of Integrated Traditional Chinese and Western Medicine, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, No. 1277 Jie Fang Avenue, Wuhan 430022, Hubei Province, China. fanheng009@aliyun.com
Research Domain of This Article
Immunology
Article-Type of This Article
Clinical and Translational Research
Open-Access Policy of This Article
This article is an open-access article which was selected by an in-house editor and fully peer-reviewed by external reviewers. It is distributed in accordance with the Creative Commons Attribution Non Commercial (CC BY-NC 4.0) license, which permits others to distribute, remix, adapt, build upon this work non-commercially, and license their derivative works on different terms, provided the original work is properly cited and the use is non-commercial. See: http://creativecommons.org/licenses/by-nc/4.0/
World J Clin Cases. Mar 26, 2024; 12(9): 1606-1621 Published online Mar 26, 2024. doi: 10.12998/wjcc.v12.i9.1606
Construction of the underlying circRNA-miRNA-mRNA regulatory network and a new diagnostic model in ulcerative colitis by bioinformatics analysis
Yu-Yi Yuan, Hui Wu, Qian-Yun Chen, Heng Fan, Bo Shuai
Yu-Yi Yuan, Hui Wu, Qian-Yun Chen, Heng Fan, Bo Shuai, Department of Integrated Traditional Chinese and Western Medicine, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430022, Hubei Province, China
Co-first authors: Yu-Yi Yuan, Hui Wu and Qian-Yun Chen.
Co-corresponding authors: Heng Fan and Bo Shuai.
Author contributions: Yuan YY, Fan H and Shuai B designed the research study; Yuan YY, Wu H and Chen QY performed the research; Fan H and Shuai B contributed new reagents and analytic tools; Yuan YY, Wu H and Chen QY analyzed the data and wrote the manuscript; all authors have read and approve the final manuscript.
Supported bythe National Natural Science Foundation of China, No. 81774093, No. 81904009, No. 81974546 and No. 82174182; and Key R&D Project of Hubei Province, No. 2020BCB001.
Institutional review board statement: This study dealt with published data only, no ethical approval.
Conflict-of-interest statement: All the authors report no relevant conflicts of interest for this article.
Data sharing statement: Further inquiries can be directed to the corresponding author.
Open-Access: This article is an open-access article that was selected by an in-house editor and fully peer-reviewed by external reviewers. It is distributed in accordance with the Creative Commons Attribution NonCommercial (CC BY-NC 4.0) license, which permits others to distribute, remix, adapt, build upon this work non-commercially, and license their derivative works on different terms, provided the original work is properly cited and the use is non-commercial. See: https://creativecommons.org/Licenses/by-nc/4.0/
Corresponding author: Heng Fan, PhD, MD, Chief Physician, Department of Integrated Traditional Chinese and Western Medicine, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, No. 1277 Jie Fang Avenue, Wuhan 430022, Hubei Province, China. fanheng009@aliyun.com
Received: October 19, 2023 Peer-review started: October 19, 2023 First decision: January 25, 2024 Revised: February 2, 2024 Accepted: March 4, 2024 Article in press: March 4, 2024 Published online: March 26, 2024 Processing time: 157 Days and 17.6 Hours
Abstract
BACKGROUND
Circular RNAs (circRNAs) are involved in the pathogenesis of many diseases through competing endogenous RNA (ceRNA) regulatory mechanisms.
AIM
To investigate a circRNA-related ceRNA regulatory network and a new predictive model by circRNA to understand the diagnostic mechanism of circRNAs in ulcerative colitis (UC).
METHODS
We obtained gene expression profiles of circRNAs, miRNAs, and mRNAs in UC from the Gene Expression Omnibus dataset. The circRNA-miRNA-mRNA network was constructed based on circRNA-miRNA and miRNA-mRNA interactions. Functional enrichment analysis was performed to identify the biological mechanisms involved in circRNAs. We identified the most relevant differential circRNAs for diagnosing UC and constructed a new predictive nomogram, whose efficacy was tested with the C-index, receiver operating characteristic curve (ROC), and decision curve analysis (DCA).
RESULTS
A circRNA-miRNA-mRNA regulatory network was obtained, containing 12 circRNAs, three miRNAs, and 38 mRNAs. Two optimal prognostic-related differentially expressed circRNAs, hsa_circ_0085323 and hsa_circ_0036906, were included to construct a predictive nomogram. The model showed good discrimination, with a C-index of 1(> 0.9, high accuracy). ROC and DCA suggested that the nomogram had a beneficial diagnostic ability.
CONCLUSION
This novel predictive nomogram incorporating hsa_circ_0085323 and hsa_circ_0036906 can be conveniently used to predict the risk of UC. The circRNa-miRNA-mRNA network in UC could be more clinically significant.
Core Tip: In this study, we constructed a circRNA-miRNA-mRNA regulatory network to investigate the probable mechanism of circRNAs in ulcerative colitis. Initially, differentially expressed circRNAs (DEcircRNAs), differentially expressed miRNAs (DEmiRNAs), and differentially expressed mRNAs (DEmRNAs) were retrieved using the RNA expression spectrum of circRNA, miRNA, and mRNA in the Gene Expression Omnibus dataset. The competing endogenous RNA (ceRNA) network was then established after determining the DEcircRNA-DEmiRNA and DEmiRNA-DEmRNA interactions using bioinformatics analysis methods. Functional enrichment analysis was performed to evaluate the biological functions of DEmRNAs in the ceRNA network. Ultimately, DEcircRNAs in the circRNA-miRNA-mRNA network were used to construct a new diagnostic model.
