Prediction of NR3C1 as a methylation marker for the prevention and treatment of gastric cancer in Rhizoma Atractylodis Macrocephalae based on machine learning algorithm and bioinformatics analysis.
Shicong Huang, Qian Gu, Yan Chen, Xiaofang Huang, Yuhua Du, Ziying Zhou, Yi Nan, Ling Yuan
{"title":"Prediction of NR3C1 as a methylation marker for the prevention and treatment of gastric cancer in Rhizoma Atractylodis Macrocephalae based on machine learning algorithm and bioinformatics analysis.","authors":"Shicong Huang, Qian Gu, Yan Chen, Xiaofang Huang, Yuhua Du, Ziying Zhou, Yi Nan, Ling Yuan","doi":"10.3389/fgene.2025.1584986","DOIUrl":null,"url":null,"abstract":"<p><strong>Objective: </strong>The aim of this study was to identify the markers of Rhizoma Atractylodis Macrocephalae (RAM) for the prevention and treatment of gastric cancer using bioinformatics analysis.</p><p><strong>Methods: </strong>The main active components of RAM were screened using the Traditional Chinese Medicine Systematic Pharmacology Profiling Platform (TCMSP) and SwissADME, the target genes of RAM were screened using WGCNA and three machine learning algorithms, and the target genes were analyzed clinically and by methylation.</p><p><strong>Results: </strong>Three core genes, namely, 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 NR3C1 methylation and its 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; the frequency of methylation hypermutation in the CDS region was also high, and the homologous region and the 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.</p><p><strong>Conclusion: </strong>NR3C1 can be used as a potential methylation marker of RAM for the prevention and treatment of gastric cancer.</p>","PeriodicalId":12750,"journal":{"name":"Frontiers in Genetics","volume":"16 ","pages":"1584986"},"PeriodicalIF":2.8000,"publicationDate":"2025-09-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12455331/pdf/","citationCount":"0","resultStr":null,"platform":"Semanticscholar","paperid":null,"PeriodicalName":"Frontiers in Genetics","FirstCategoryId":"99","ListUrlMain":"https://doi.org/10.3389/fgene.2025.1584986","RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":null,"EPubDate":"2025/1/1 0:00:00","PubModel":"eCollection","JCR":"Q2","JCRName":"GENETICS & HEREDITY","Score":null,"Total":0}
引用次数: 0
Abstract
Objective: The aim of this study was 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 the Traditional Chinese Medicine Systematic Pharmacology Profiling Platform (TCMSP) and SwissADME, the target genes of RAM were screened using WGCNA and three machine learning algorithms, and the target genes were analyzed clinically and by methylation.
Results: Three core genes, namely, 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 NR3C1 methylation and its 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; the frequency of methylation hypermutation in the CDS region was also high, and the homologous region and the 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.
Frontiers in GeneticsBiochemistry, Genetics and Molecular Biology-Molecular Medicine
CiteScore
5.50
自引率
8.10%
发文量
3491
审稿时长
14 weeks
期刊介绍：
Frontiers in Genetics publishes rigorously peer-reviewed research on genes and genomes relating to all the domains of life, from humans to plants to livestock and other model organisms. Led by an outstanding Editorial Board of the world’s leading experts, this multidisciplinary, open-access journal is at the forefront of communicating cutting-edge research to researchers, academics, clinicians, policy makers and the public.
The study of inheritance and the impact of the genome on various biological processes is well documented. However, the majority of discoveries are still to come. A new era is seeing major developments in the function and variability of the genome, the use of genetic and genomic tools and the analysis of the genetic basis of various biological phenomena.
求助内容：
应助结果提醒方式：
京公网安备 11010802042870号
