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

IF 1.7 4区 医学 Q4 ONCOLOGY
Translational cancer research Pub Date : 2025-07-30 Epub Date: 2025-07-23 DOI:10.21037/tcr-2024-2607
Yiwen Huang, Guangpeng Chen, Hong Fan, Shangzi Wang, Huangbo Yuan, Zhengqiu Liu, Tiejun Zhang
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引用次数: 0

摘要

背景:乙型肝炎病毒相关的肝细胞癌(HBV-HCC)和丙型肝炎病毒相关的肝细胞癌(HCV-HCC)之间的遗传和表观遗传差异尚不清楚。本研究旨在利用一种创新的方法,从比较的角度阐明HBV-HCC和HCV-HCC的DNA甲基化模式和特征。方法:基于The Cancer Genome Atlas (TCGA)数据库,进行基因表达和甲基化分析,鉴定差异表达基因(DEGs)和差异甲基化探针(DMPs)。采用Cox生存分析来确定与预后相关的DEGs (Pro-DEGs)。一种新的序列最小绝对收缩和选择算子(Seq-Lasso)技术用于整合基因表达和DNA甲基化数据,随后生成基因水平的DNA甲基化摘要。这些总结分别用于从HBV-HCC和HCV-HCC的pro - deg中选择甲基化表达的数量性状位点(甲基- eqtl)。结果:无论在哪个基因组区域,低甲基化在HBV-HCC中比在HCV-HCC中更为普遍。值得注意的是,HBV-HCC患者组的公海区域包含功能最显著的甲基化位点,而在HCV-HCC患者组中,功能最重要的胞嘧啶-磷酸-鸟嘌呤(CpG)位点通常位于架子区域,与基因内的基因表达呈正相关。我们进一步构建并验证了基于6个与HCC预后相关的甲基- eqtl的预后指数(PI)。结论:我们的研究发现CpG岛位点在HBV-HCC和HCV-HCC中功能重要性最低。此外,我们还构建并验证了基于6个甲基- eqtl的PI,这些甲基- eqtl可能通过RFC3与HCC预后相关。
本文章由计算机程序翻译,如有差异,请以英文原文为准。

A comparison of hepatitis B virus- and hepatitis C virus-related hepatocellular carcinoma: a bioinformatics analysis.

A comparison of hepatitis B virus- and hepatitis C virus-related hepatocellular carcinoma: a bioinformatics analysis.

A comparison of hepatitis B virus- and hepatitis C virus-related hepatocellular carcinoma: a bioinformatics analysis.

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.

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来源期刊
CiteScore
2.10
自引率
0.00%
发文量
252
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.
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