ORIGINAL RESEARCH article
Front. Genet.
Sec. Epigenomics and Epigenetics
Volume 16 - 2025 | doi: 10.3389/fgene.2025.1584986
This article is part of the Research TopicEffects of Lactic Acid and Lactylation on Epigenetic Modifications and Gene Expression in TumorView all 3 articles
Prediction of NR3C1 as a Methylation Marker for Prevention and Treatment of Gastric Cancer in Rhizoma Atractylodis Macrocephalae based on Machine Learning Algorithm and Bioinformatics Analysis
Provisionally accepted
- 1School of Pharmacy, Ningxia Medical University, Yinchuan, China
- 2Health Administration and Social Services College, Yinchuan, China
- 3Ningxia Chinese Medicine Research Center, Yinchuan, China
- 4Ningxia Medical University General Hospital, Yinchuan, China
- 5Key Laboratory of Ningxia Ethnomedicine Modernization, Ministry of Education, Yinchuan, China
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OBJECTIVE: To identify the markers of Rhizoma Atractylodis Macrocephalae(RAM) for the prevention and treatment of gastric cancer using bioinformatics analysis. METHODS: The main active components of RAM were screened using TCMSP and SwissADME, the target genes of RAM were screened using WGCNA and three machine learning algorithms, and the target genes were analyzed clinically as well as by methylation. RESULTS: Three core genes CA2, HSP90AA1 and NR3C1 were screened by WGCNA and three machine learning algorithms. Clinical correlation analysis and epigenetic analyses showed that these genes play the most important role in gastric cancer. In gastric cancer, there was a strong correlation between methylated expression of NR3C1 and mRNA expression, suggesting that methylation of NR3C1 may be involved in the regulation of its expression. Therefore, methylation correlation analysis of NR3C1 was performed, and it was found that the methylation type of NR3C1 was mainly m6A methylation, and the frequency of methylation hypermutation in the CDS region was also high, and the homologous region and promoter of the NR3C1 gene showed hypomethylation and hypermethylation differences in the analyses of gastric tissues, races and gastric cancer subtypes, respectively. Among the methylated peninsular mutations, the TSS200; 5'UTR, 5'UTR and TSS1500; 5'UTR regions were statistically significant. CONCLUSION: NR3C1 can be used as a potential methylation marker of RAM for the prevention and treatment of gastric cancer.
Keywords: RhizomaAtractylodis Macrocephalae, gastric cancer, Methylation, NR3C1, WGCNA, machine learning
Received: 28 Feb 2025; Accepted: 13 Aug 2025.
Copyright: © 2025 Huang, Gu, Chen, Huang, Du, Zhou, Nan and Yuan. 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:
Yi Nan, Key Laboratory of Ningxia Ethnomedicine Modernization, Ministry of Education, Yinchuan, China
Ling Yuan, School of Pharmacy, Ningxia Medical University, Yinchuan, China
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