Lin Chen, Man Wang, Meng Pan, Qiang Wang, Hong Zheng, Huimin Li, Xiangqian Guo
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Protein expression levels of PUS1 and PUS7 were examined using The Human Protein Atlas (HPA) database, and the overexpression of PUS7 was further validated by immunohistochemistry staining. Univariate and multivariate COX regression analyses were performed to analyze the prognostic value of PUS7. Nomograms were built based on COX regression analytic results to predict patient survival. The tumor immune microenvironment was characterized using TIMER2.0, EPIC, and xCell algorithms to estimate the immune cell infiltration.</p><p><strong>Results: </strong>The results showed that PUS7 mRNA and protein levels are significantly over-expressed in hepatocellular carcinoma tissues compared to normal tissues. PUS7 overexpression is associated with poor prognosis and may serve as an independent prognostic factor for overall survival in hepatocellular carcinoma. Functional enrichment analysis indicated that PUS7 is involved in key oncogenic pathways, including cell cycle, DNA replication, homologous recombination, oocyte meiosis, mismatch repair, and spliceosome signaling pathways. Immune microenvironment analysis revealed a significant correlation between PUS7 expression and immune cell infiltration in hepatocellular carcinoma, suggesting a potential role in modulating tumor immunity.</p><p><strong>Conclusion: </strong>Our findings suggest that PUS7 is a novel and promising biomarker for diagnosis and prognosis of hepatocellular carcinoma. This study provides preliminary insights into the functional roles and underlying mechanisms of PUS7 in HCC progression, offering theoretical support for improving patient outcomes and identifying potential therapeutic targets.</p>","PeriodicalId":10624,"journal":{"name":"Computer methods and programs in biomedicine","volume":"273 ","pages":"109114"},"PeriodicalIF":4.8000,"publicationDate":"2025-10-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":"0","resultStr":"{\"title\":\"Integrative analysis of RNA modification-related gene PUS7 in diagnosis, prognosis, and tumor microenvironment of hepatocellular carcinoma.\",\"authors\":\"Lin Chen, Man Wang, Meng Pan, Qiang Wang, Hong Zheng, Huimin Li, Xiangqian Guo\",\"doi\":\"10.1016/j.cmpb.2025.109114\",\"DOIUrl\":null,\"url\":null,\"abstract\":\"<p><strong>Background: </strong>Hepatocellular carcinoma is a highly aggressive cancer with a poor prognosis. 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引用次数: 0
摘要
背景：肝细胞癌是一种侵袭性强、预后差的肿瘤。RNA修饰在调节癌症的各种生物学功能中起着关键作用。然而，RNA修饰相关假尿嘧啶合成酶（PUS）基因在肝细胞癌中的作用尚不清楚。方法：分析肿瘤基因组图谱（TCGA）转录组学和临床数据，探讨肝细胞癌中PUS基因的诊断和预后意义。采用差异分析和ROC分析评价PUS基因的诊断潜力。利用The Human Protein Atlas （HPA）数据库检测PUS1和PUS7的蛋白表达水平，并通过免疫组织化学染色进一步验证PUS7的过表达。采用单因素和多因素COX回归分析PUS7的预后价值。根据COX回归分析结果建立nomogram预测患者生存期。采用TIMER2.0、EPIC和xCell算法对肿瘤免疫微环境进行表征，估计免疫细胞浸润情况。结果：与正常组织相比，肝细胞癌组织中PUS7 mRNA和蛋白水平明显过表达。PUS7过表达与预后不良相关，可能是影响肝细胞癌总生存率的独立预后因素。功能富集分析表明，PUS7参与细胞周期、DNA复制、同源重组、卵母细胞减数分裂、错配修复和剪接体信号通路等关键的致癌途径。免疫微环境分析显示，在肝细胞癌中，PUS7的表达与免疫细胞浸润之间存在显著相关性，提示其可能在调节肿瘤免疫中发挥作用。结论：PUS7是一种新的、有前景的肝细胞癌诊断和预后生物标志物。本研究初步揭示了PUS7在HCC进展中的功能作用和潜在机制，为改善患者预后和确定潜在治疗靶点提供了理论支持。
Integrative analysis of RNA modification-related gene PUS7 in diagnosis, prognosis, and tumor microenvironment of hepatocellular carcinoma.
Background: Hepatocellular carcinoma is a highly aggressive cancer with a poor prognosis. RNA modifications play critical roles in regulating various biological functions in cancers. However, the involvement of RNA modification-related pseudouridine synthase (PUS) genes in hepatocellular carcinoma remains unclear.
Methods: To explore the diagnostic and prognostic significance of PUS genes in hepatocellular carcinoma, we analysed the transcriptomic and clinical data from The Cancer Genome Atlas (TCGA). Differential analysis and ROC analysis were conducted to evaluate the diagnostic potential of PUS genes. Protein expression levels of PUS1 and PUS7 were examined using The Human Protein Atlas (HPA) database, and the overexpression of PUS7 was further validated by immunohistochemistry staining. Univariate and multivariate COX regression analyses were performed to analyze the prognostic value of PUS7. Nomograms were built based on COX regression analytic results to predict patient survival. The tumor immune microenvironment was characterized using TIMER2.0, EPIC, and xCell algorithms to estimate the immune cell infiltration.
Results: The results showed that PUS7 mRNA and protein levels are significantly over-expressed in hepatocellular carcinoma tissues compared to normal tissues. PUS7 overexpression is associated with poor prognosis and may serve as an independent prognostic factor for overall survival in hepatocellular carcinoma. Functional enrichment analysis indicated that PUS7 is involved in key oncogenic pathways, including cell cycle, DNA replication, homologous recombination, oocyte meiosis, mismatch repair, and spliceosome signaling pathways. Immune microenvironment analysis revealed a significant correlation between PUS7 expression and immune cell infiltration in hepatocellular carcinoma, suggesting a potential role in modulating tumor immunity.
Conclusion: Our findings suggest that PUS7 is a novel and promising biomarker for diagnosis and prognosis of hepatocellular carcinoma. This study provides preliminary insights into the functional roles and underlying mechanisms of PUS7 in HCC progression, offering theoretical support for improving patient outcomes and identifying potential therapeutic targets.
期刊介绍：
To encourage the development of formal computing methods, and their application in biomedical research and medical practice, by illustration of fundamental principles in biomedical informatics research; to stimulate basic research into application software design; to report the state of research of biomedical information processing projects; to report new computer methodologies applied in biomedical areas; the eventual distribution of demonstrable software to avoid duplication of effort; to provide a forum for discussion and improvement of existing software; to optimize contact between national organizations and regional user groups by promoting an international exchange of information on formal methods, standards and software in biomedicine.
Computer Methods and Programs in Biomedicine covers computing methodology and software systems derived from computing science for implementation in all aspects of biomedical research and medical practice. It is designed to serve: biochemists; biologists; geneticists; immunologists; neuroscientists; pharmacologists; toxicologists; clinicians; epidemiologists; psychiatrists; psychologists; cardiologists; chemists; (radio)physicists; computer scientists; programmers and systems analysts; biomedical, clinical, electrical and other engineers; teachers of medical informatics and users of educational software.
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