Hu Xueting, Zhou Jian, Zhang Yan, Zeng Yindi, Jie Guitao, Wang Sheng, Yang Aixiang, Zhang Menghui
Department of Intensive Care Unit, The Affiliated Suzhou Hospital of Nanjing Medical University, Suzhou Municipal Hospital, Gusu School, Nanjing Medical University, Suzhou, Jiangsu, China.
Department of Hematology, The Affiliated Hospital of Xuzhou Medical University, Xuzhou, Jiangsu, China.
Front Genet. 2022 Jul 19;13:942454. doi: 10.3389/fgene.2022.942454. eCollection 2022.
Hepatocellular carcinoma is one kind of clinical common malignant tumor with a poor prognosis, and its pathogenesis remains to be clarified urgently. This study was performed to elucidate key genes involving HCC by bioinformatics analysis and experimental evaluation. We identified common differentially expressed genes (DEGs) based on gene expression profile data of GSE60502 and GSE84402 from the Gene Expression Omnibus (GEO) database. Gene Ontology enrichment analysis (GO), Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis, REACTOME pathway enrichment analysis, and Gene Set Enrichment Analysis (GSEA) were used to analyze functions of these genes. The protein-protein interaction (PPI) network was constructed using Cytoscape software based on the STRING database, and Molecular Complex Detection (MCODE) was used to pick out two significant modules. Hub genes, screened by the CytoHubba plug-in, were validated by Gene Expression Profiling Interactive Analysis (GEPIA) and the Human Protein Atlas (HPA) database. Then, the correlation between hub genes expression and immune cell infiltration was evaluated by Tumor IMmune Estimation Resource (TIMER) database, and the prognostic values were analyzed by Kaplan-Meier plotter. Finally, biological experiments were performed to illustrate the functions of RRM2. Through integrated bioinformatics analysis, we found that the upregulated DEGs were related to cell cycle and cell division, while the downregulated DEGs were associated with various metabolic processes and complement cascade. RRM2, MAD2L1, MELK, NCAPG, and ASPM, selected as hub genes, were all correlated with poor overall prognosis in HCC. The novel RRM2 inhibitor osalmid had anti-tumor activity, including inhibiting proliferation and migration, promoting cell apoptosis, blocking cell cycle, and inducing DNA damage of HCC cells. The critical pathways and hub genes in HCC progression were screened out, and targeting RRM2 contributed to developing new therapeutic strategies for HCC.
肝细胞癌是一种临床常见的恶性肿瘤，预后较差，其发病机制亟待阐明。本研究通过生物信息学分析和实验评估来阐明与肝癌相关的关键基因。我们基于基因表达综合数据库（GEO）中GSE60502和GSE84402的基因表达谱数据鉴定了常见的差异表达基因（DEG）。使用基因本体富集分析（GO）、京都基因与基因组百科全书（KEGG）通路分析、REACTOME通路富集分析和基因集富集分析（GSEA）来分析这些基因的功能。基于STRING数据库，使用Cytoscape软件构建蛋白质-蛋白质相互作用（PPI）网络，并使用分子复合物检测（MCODE）挑选出两个重要模块。通过CytoHubba插件筛选出的枢纽基因，经基因表达谱交互式分析（GEPIA）和人类蛋白质图谱（HPA）数据库验证。然后，通过肿瘤免疫估计资源（TIMER）数据库评估枢纽基因表达与免疫细胞浸润之间的相关性，并通过Kaplan-Meier绘图仪分析预后价值。最后，进行生物学实验以阐明核糖核苷酸还原酶M2亚基（RRM2）的功能。通过综合生物信息学分析，我们发现上调的DEG与细胞周期和细胞分裂相关，而下调的DEG与各种代谢过程和补体级联反应相关。被选为枢纽基因的RRM2、有丝分裂后期促进复合物2（MAD2L1）、母体胚胎亮氨酸拉链激酶（MELK）、核仁磷酸蛋白（NCAPG）和异常纺锤体微管蛋白（ASPM）均与肝癌患者总体预后不良相关。新型RRM2抑制剂奥沙拉嗪具有抗肿瘤活性，包括抑制肝癌细胞增殖和迁移、促进细胞凋亡、阻断细胞周期以及诱导DNA损伤。筛选出了肝癌进展中的关键通路和枢纽基因，靶向RRM2有助于开发肝癌的新治疗策略。
