Clinical and Translational Research
Copyright ©The Author(s) 2024. Published by Baishideng Publishing Group Inc. All rights reserved.
World J Clin Cases. Apr 6, 2024; 12(10): 1750-1765
Published online Apr 6, 2024. doi: 10.12998/wjcc.v12.i10.1750
Identification of marker genes associated with N6-methyladenosine and autophagy in ulcerative colitis
Xiao-Yan Liu, Dan Qiao, Ya-Li Zhang, Zi-Xuan Liu, You-Lan Chen, Ren-Ye Que, Hong-Yan Cao, Yan-Cheng Dai
Xiao-Yan Liu, Dan Qiao, Zi-Xuan Liu, Ren-Ye Que, Hong-Yan Cao, Yan-Cheng Dai, Department of Gastroenterology, Shanghai Traditional Chinese Medicine-Integrated Hospital, Shanghai University of Traditional Chinese Medicine, Shanghai 200082, China
Ya-Li Zhang, Institute of Digestive Diseases, Long Hua Hospital Shanghai University of Traditional Chinese Medicine, Shanghai 200032, China
You-Lan Chen, Department of Gastroenterology, Shu Guang Hospital, Shanghai University of Traditional Chinese Medicine, Shanghai 201203, China
Author contributions: Liu XY and Qian D authored the paper and contributed equally to this work; Dai YC conceived and designed the experiments; Zhang YL, Liu ZX, and Chen YL performed the experiments; Que RY analyzed the data; Cao HY provided reagents/materials/analysis tools; all authors have read and approved the final manuscript.
Supported by the National Natural Science Foundation of China, No. 81873253; the Shanghai Natural Science Foundation, No. 22ZR1458800; the scientific research Project Plan of Shanghai Municipal Health Commission, No. 202240385; and the Xinglin Scholar Program of Shanghai University of Traditional Chinese Medicine, No. [2020]23; the Hongkou District Health Committee, No. HKZK2020A01.
Institutional review board statement: This article is a bioinformatic analysis of the Gene Expression Omnibus (GEO) database and involve animal experiments.
Institutional animal care and use committee statement: All animal experiments conformed to the internationally accepted principles for the care and use of laboratory animals (No. PZSHUTCM210611001, the Animal Ethics Committee of the Shanghai University of Traditional Chinese Medicine).
Clinical trial registration statement: This study is registered at Chinese Clinical Trial Registry. The registration identification number is ChiCTR2300068348.
Informed consent statement: All study participants or their legal guardian provided informed written consent about personal and medical data collection prior to study enrolment.
Conflict-of-interest statement: All authors report no conflicts of interest in this work.
Data sharing statement: The following publicly available datasets were analyzed in this study: https://www.ncbi.nlm.nih.gov/, http://www.autophagy.lu/index.html.
ARRIVE guidelines statement: The authors have read the ARRIVE guidelines, and the manuscript was prepared and revised according to the ARRIVE guidelines.
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: Yan-Cheng Dai, PhD, Chief Doctor, Department of Gastroenterology, Shanghai Traditional Chinese Medicine-Integrated Hospital Shanghai University of Traditional Chinese Medicine, No. 230 Baoding Road, Hongkou District, Shanghai 200082, China. daiyancheng2005@126.com
Received: January 1, 2024
Peer-review started: January 1, 2024
First decision: January 16, 2024
Revised: January 21, 2024
Accepted: February 29, 2024
Article in press: February 29, 2024
Published online: April 6, 2024
ARTICLE HIGHLIGHTS
Research background

Both N6-methyladenosine (m6A) methylation and autophagy are considered relevant to the pathogenesis of ulcerative colitis (UC). However, a systematic exploration of the role of the combination of m6A methylation and autophagy in UC remains to be performed.

Research motivation

In this study, we used publicly available data related to UC and comprehensive bioinformatics methods to elucidate the autophagy-related genes of m6A with a diagnostic value for UC, thereby contributing to the development of treatment options for patients with UC.

Research objectives

To elucidate the autophagy-related genes of m6A with a diagnostic value for UC.

Research methods

The correlation between m6A-related genes and autophagy-related genes (ARGs) was analysed. Finally, gene set enrichment analysis (GSEA) was performed on the characteristic genes. Additionally, the expression levels of four characteristic genes were verified in DSS-induced colitis in mice.

Research results

GSEA indicated that BAG3, P4HB and TP53INP2 were involved in the inflammatory response and TNF-α signalling via NF- κB. Furthermore, polymerase chain reaction results showed significantly higher mRNA levels of BAG3 and P4HB and lower mRNA levels of FMR1 and TP53INP2 in the DSS group compared to the control group.

Research conclusions

This study identified four m6A-ARGs that predict the occurrence of UC, thus providing a scientific reference for further studies on the pathogenesis of UC.

Research perspectives

The specific regulatory mechanisms of these genes need further experimental research and clinical application research.