枢纽基因作为宫颈癌潜在诊断生物标志物的鉴定：一种生物信息学方法

IF 3.1 4区生物学 Q2 BIOLOGY

Computational Biology and Chemistry Pub Date : 2025-08-05 DOI:10.1016/j.compbiolchem.2025.108605

Tara Chand , Pankaj Vaishanavaa , Ashwini Kumar Dubey , Gauri Misra

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引用次数: 0

摘要

宫颈癌是一种发病率不断上升的普遍恶性肿瘤，主要是由于性传播、持续的HPV感染和延迟筛查。确定新的生物标志物对改善宫颈癌的诊断、预后和治疗至关重要。本研究利用综合生物信息学方法，通过分析GEO数据库中的基因表达数据，确定潜在的生物标志物。方法采用GEO2R分析4个GEO芯片数据集（GSE7410、GSE7803、GSE52903、GSE67522）的基因变异，校正p值为0.05。使用维恩图将常见的deg可视化。利用STRING构建蛋白-蛋白互作网络，鉴定中心基因。通过基因本体论（GO）和KEGG通路分析来研究生物功能和通路。人类蛋白图谱（Human Protein Atlas， HPA）通过免疫组织化学进行了蛋白表达的计算机验证。通过Kaplan-Meier生存分析来确定枢纽基因的预后价值。结果分析显示，数据集中共有684个共同的deg（446个上调，238个下调）。利用GSE67522中前20个上调的deg进行热图构建和PPI分析，最终鉴定出9个关键枢纽基因。GO和KEGG分析显示，其中6个显著参与细胞周期调节和致瘤途径。通过HPA数据验证了这些枢纽基因的蛋白表达。结论6个中心基因（CCNB2、AURKA、CDC20、CDT1、CENPF和KIF2C）被确定为宫颈癌治疗的潜在生物标志物。这些发现提供了有价值的见解，在宫颈癌的翻译结果诊断中发挥重要作用的基因的分子谱。

本文章由计算机程序翻译，如有差异，请以英文原文为准。

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Identification of hub genes as potential diagnostic biomarkers for cervical cancer: A bioinformatic approach

Background

Cervical cancer remains a prevalent malignancy with rising incidence, primarily due to sexual transmission, persistent HPV infection, and delayed screening. Identifying new biomarkers is critical for improved diagnosis, prognosis, and treatment of cervical cancer. This study utilized integrated bioinformatics to identify potential biomarkers by analysing gene expression data from the GEO database.

Methods

Four GEO microarray datasets (GSE7410, GSE7803, GSE52903, GSE67522) were analysed using GEO2R to identify DEGs with an adjusted p-value <0.05. Common DEGs were visualized using Venn diagrams. Protein-protein interaction network was constructed using STRING to identify hub genes. Gene Ontology (GO) and KEGG pathway analyses were performed to investigate biological functions and pathways. The Human Protein Atlas (HPA) was used for in silico validation of protein expression via immunohistochemistry. Kaplan-Meier survival analysis was performed to determine the prognostic value of hub genes.

Results

Analysis revealed 684 common DEGs across the datasets (446 upregulated, 238 downregulated). The top 20 upregulated DEGs from GSE67522 were used for heatmap construction and PPI analysis, leading to the identification of nine key hub genes. GO and KEGG analyses showed that six of these were significantly involved in cell cycle regulation and tumorigenic pathways. These hub genes were validated for their protein expression through HPA data.

Conclusion

Six hub genes (CCNB2, AURKA, CDC20, CDT1, CENPF, and KIF2C) were identified as potential biomarkers for cervical cancer management.

Impact

These findings provide valuable insight into the molecular profiles of genes that play significant roles in cervical cancer for translational outcomes in diagnosis.

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来源期刊

Computational Biology and Chemistry 生物-计算机：跨学科应用

CiteScore

6.10

自引率

3.20%

发文量

142

审稿时长

24 days

期刊介绍： Computational Biology and Chemistry publishes original research papers and review articles in all areas of computational life sciences. High quality research contributions with a major computational component in the areas of nucleic acid and protein sequence research, molecular evolution, molecular genetics (functional genomics and proteomics), theory and practice of either biology-specific or chemical-biology-specific modeling, and structural biology of nucleic acids and proteins are particularly welcome. Exceptionally high quality research work in bioinformatics, systems biology, ecology, computational pharmacology, metabolism, biomedical engineering, epidemiology, and statistical genetics will also be considered. Given their inherent uncertainty, protein modeling and molecular docking studies should be thoroughly validated. In the absence of experimental results for validation, the use of molecular dynamics simulations along with detailed free energy calculations, for example, should be used as complementary techniques to support the major conclusions. Submissions of premature modeling exercises without additional biological insights will not be considered. Review articles will generally be commissioned by the editors and should not be submitted to the journal without explicit invitation. However prospective authors are welcome to send a brief (one to three pages) synopsis, which will be evaluated by the editors.