{"title":"乙型肝炎病毒和丙型肝炎病毒相关肝细胞癌的比较:生物信息学分析","authors":"Yiwen Huang, Guangpeng Chen, Hong Fan, Shangzi Wang, Huangbo Yuan, Zhengqiu Liu, Tiejun Zhang","doi":"10.21037/tcr-2024-2607","DOIUrl":null,"url":null,"abstract":"<p><strong>Background: </strong>The genetic and epigenetic differences between hepatitis B virus-related hepatocellular carcinoma (HBV-HCC) and hepatitis C virus-related hepatocellular carcinoma (HCV-HCC) remain underexplored. This study aimed to elucidate DNA methylation patterns and features of HBV-HCC and HCV-HCC through use of an innovative method from a comparative perspective.</p><p><strong>Methods: </strong>We conducted gene expression and methylation analyses to identify differentially expressed genes (DEGs) and differentially methylated probes (DMPs) based on The Cancer Genome Atlas (TCGA) database. Cox survival analysis was employed to identify prognosis-related DEGs (Pro-DEGs). A novel sequential least absolute shrinkage and selection operator (Seq-Lasso) technique was used to integrate gene expression and DNA methylation data, subsequently generating gene-level DNA methylation summaries. These summaries were used to select methylation-expression quantitative trait loci (methyl-eQTLs) from Pro-DEGs for HBV-HCC and HCV-HCC, respectively.</p><p><strong>Results: </strong>Hypomethylation was more prevalent in HBV-HCC than in HCV-HCC in regardless of the genome region. Notably, open sea regions of the HBV-HCC patient group contained the most functionally significant methylation sites, whereas in the HCV-HCC patient group, the most functionally important cytosine-phosphate-guanine (CpG) sites were typically located in shelf regions when positively associated with gene expression within genes. We further constructed and validated a prognostic index (PI) based on six methyl-eQTLs associated with HCC prognosis.</p><p><strong>Conclusions: </strong>Our study found that CpG island sites had the least functional importance in both HBV-HCC and HCV-HCC. And, we also constructed and validated a PI based on six methyl-eQTLs that may be related to HCC prognosis via RFC3.</p>","PeriodicalId":23216,"journal":{"name":"Translational cancer research","volume":"14 7","pages":"4243-4259"},"PeriodicalIF":1.7000,"publicationDate":"2025-07-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12335692/pdf/","citationCount":"0","resultStr":"{\"title\":\"A comparison of hepatitis B virus- and hepatitis C virus-related hepatocellular carcinoma: a bioinformatics analysis.\",\"authors\":\"Yiwen Huang, Guangpeng Chen, Hong Fan, Shangzi Wang, Huangbo Yuan, Zhengqiu Liu, Tiejun Zhang\",\"doi\":\"10.21037/tcr-2024-2607\",\"DOIUrl\":null,\"url\":null,\"abstract\":\"<p><strong>Background: </strong>The genetic and epigenetic differences between hepatitis B virus-related hepatocellular carcinoma (HBV-HCC) and hepatitis C virus-related hepatocellular carcinoma (HCV-HCC) remain underexplored. This study aimed to elucidate DNA methylation patterns and features of HBV-HCC and HCV-HCC through use of an innovative method from a comparative perspective.</p><p><strong>Methods: </strong>We conducted gene expression and methylation analyses to identify differentially expressed genes (DEGs) and differentially methylated probes (DMPs) based on The Cancer Genome Atlas (TCGA) database. Cox survival analysis was employed to identify prognosis-related DEGs (Pro-DEGs). A novel sequential least absolute shrinkage and selection operator (Seq-Lasso) technique was used to integrate gene expression and DNA methylation data, subsequently generating gene-level DNA methylation summaries. These summaries were used to select methylation-expression quantitative trait loci (methyl-eQTLs) from Pro-DEGs for HBV-HCC and HCV-HCC, respectively.</p><p><strong>Results: </strong>Hypomethylation was more prevalent in HBV-HCC than in HCV-HCC in regardless of the genome region. Notably, open sea regions of the HBV-HCC patient group contained the most functionally significant methylation sites, whereas in the HCV-HCC patient group, the most functionally important cytosine-phosphate-guanine (CpG) sites were typically located in shelf regions when positively associated with gene expression within genes. We further constructed and validated a prognostic index (PI) based on six methyl-eQTLs associated with HCC prognosis.</p><p><strong>Conclusions: </strong>Our study found that CpG island sites had the least functional importance in both HBV-HCC and HCV-HCC. And, we also constructed and validated a PI based on six methyl-eQTLs that may be related to HCC prognosis via RFC3.</p>\",\"PeriodicalId\":23216,\"journal\":{\"name\":\"Translational cancer research\",\"volume\":\"14 7\",\"pages\":\"4243-4259\"},\"PeriodicalIF\":1.7000,\"publicationDate\":\"2025-07-30\",\"publicationTypes\":\"Journal Article\",\"fieldsOfStudy\":null,\"isOpenAccess\":false,\"openAccessPdf\":\"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12335692/pdf/\",\"citationCount\":\"0\",\"resultStr\":null,\"platform\":\"Semanticscholar\",\"paperid\":null,\"PeriodicalName\":\"Translational cancer research\",\"FirstCategoryId\":\"3\",\"ListUrlMain\":\"https://doi.org/10.21037/tcr-2024-2607\",\"RegionNum\":4,\"RegionCategory\":\"医学\",\"ArticlePicture\":[],\"TitleCN\":null,\"AbstractTextCN\":null,\"PMCID\":null,\"EPubDate\":\"2025/7/23 0:00:00\",\"PubModel\":\"Epub\",\"JCR\":\"Q4\",\"JCRName\":\"ONCOLOGY\",\"Score\":null,\"Total\":0}","platform":"Semanticscholar","paperid":null,"PeriodicalName":"Translational cancer research","FirstCategoryId":"3","ListUrlMain":"https://doi.org/10.21037/tcr-2024-2607","RegionNum":4,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":null,"EPubDate":"2025/7/23 0:00:00","PubModel":"Epub","JCR":"Q4","JCRName":"ONCOLOGY","Score":null,"Total":0}
A comparison of hepatitis B virus- and hepatitis C virus-related hepatocellular carcinoma: a bioinformatics analysis.
Background: The genetic and epigenetic differences between hepatitis B virus-related hepatocellular carcinoma (HBV-HCC) and hepatitis C virus-related hepatocellular carcinoma (HCV-HCC) remain underexplored. This study aimed to elucidate DNA methylation patterns and features of HBV-HCC and HCV-HCC through use of an innovative method from a comparative perspective.
Methods: We conducted gene expression and methylation analyses to identify differentially expressed genes (DEGs) and differentially methylated probes (DMPs) based on The Cancer Genome Atlas (TCGA) database. Cox survival analysis was employed to identify prognosis-related DEGs (Pro-DEGs). A novel sequential least absolute shrinkage and selection operator (Seq-Lasso) technique was used to integrate gene expression and DNA methylation data, subsequently generating gene-level DNA methylation summaries. These summaries were used to select methylation-expression quantitative trait loci (methyl-eQTLs) from Pro-DEGs for HBV-HCC and HCV-HCC, respectively.
Results: Hypomethylation was more prevalent in HBV-HCC than in HCV-HCC in regardless of the genome region. Notably, open sea regions of the HBV-HCC patient group contained the most functionally significant methylation sites, whereas in the HCV-HCC patient group, the most functionally important cytosine-phosphate-guanine (CpG) sites were typically located in shelf regions when positively associated with gene expression within genes. We further constructed and validated a prognostic index (PI) based on six methyl-eQTLs associated with HCC prognosis.
Conclusions: Our study found that CpG island sites had the least functional importance in both HBV-HCC and HCV-HCC. And, we also constructed and validated a PI based on six methyl-eQTLs that may be related to HCC prognosis via RFC3.
期刊介绍:
Translational Cancer Research (Transl Cancer Res TCR; Print ISSN: 2218-676X; Online ISSN 2219-6803; http://tcr.amegroups.com/) is an Open Access, peer-reviewed journal, indexed in Science Citation Index Expanded (SCIE). TCR publishes laboratory studies of novel therapeutic interventions as well as clinical trials which evaluate new treatment paradigms for cancer; results of novel research investigations which bridge the laboratory and clinical settings including risk assessment, cellular and molecular characterization, prevention, detection, diagnosis and treatment of human cancers with the overall goal of improving the clinical care of cancer patients. The focus of TCR is original, peer-reviewed, science-based research that successfully advances clinical medicine toward the goal of improving patients'' quality of life. The editors and an international advisory group of scientists and clinician-scientists as well as other experts will hold TCR articles to the high-quality standards. We accept Original Articles as well as Review Articles, Editorials and Brief Articles.