Objective: To explore the marker genes correlated with the prognosis, progression and clinical diagnosis of hepatocellular carcinoma (HCC) based on bioinformatics methods.
Methods: The TCGA-LIHC, GSE84432, GSE143233 and GSE63898 datasets from The Cancer Genome Atlas (TCGA) and Gene Expression Omnibus (GEO) were analyzed. The differentially expressed genes (DEGs) shared by different disease types were obtained using GEO2R and edge R packages, and Gene Ontology (GO) and Kyoto Gene and Genome Encyclopedia (KEGG) enrichment analyses of the DEGs were performed. The expression levels of these DEGs in normal and cancerous tissues were verified in TCGA-LIHC to identify the upregulated genes in HCC. Survival analysis, receiver-operating characteristic (ROC) curve analysis, and correlation analysis between the key genes and the clinical features of the patients were carried out using the R language. The differential expressions of 15 key genes were verified in clinical samples of HCC and adjacent tissues using RT-qPCR.
Results: A total of 118 common DEGs were obtained in the database, and among them two genes, namely ATPase Na +/K + transport subunit beta 3 (ATP1B3) and actin regulator (ENAH), showed increased expressions with disease progression. Survival analysis combined with the TCGA-LIHC dataset suggested that high expressions of ATP1B3 and ENAH were both significantly correlated with a poor prognosis of HCC patients (P < 0.05), and their AUC values were 0.821 and 0.933, respectively. A high expression of ATP1B3 was correlated with T stage, pathological stage and pathological grade of the tumors (P < 0.05), while that of ENAH was associated only with an advanced tumor grade (P < 0.05). The results of RT-qPCR showed that ATP1B3 and ENAH were both significantly upregulated in clinical HCC tissues (P < 0.05).
Conclusion: ATPIB3 and ENAH are both upregulated in HCC, and their high expressions may serve as biomarkers of progression of liver diseases and a poor prognosis of HCC.
目的: 筛选与肝细胞癌（HCC）预后、进展和临床诊断相关标记物。
方法: 分析来自癌症基因组图谱数据库（TCGA）和基因表达综合（GEO）的TCGA-LIHC、GSE84432、GSE14323和GSE63898数据集。利用GEO2R和edge R包获得各疾病类型之间共同差异基因（DEG），并对DEG进行基因本体论（GO）和京都基因与基因组百科全书（KEGG）富集分析。将DEG在TCGA-LIHC中正常和癌组织进行差异表达验证分析，挑选在HCC中上调基因。利用R语言进行生存分析、受试者工作特征（ROC）曲线分析、基因与患者临床特征关系分析。再通过RT-qPCR验证15对临床HCC和癌旁组织中基因的差异表达。
结果: 数据库挖掘共获得118个共同DEG，挑选出2个基因：ATP酶Na+/K+转运亚基Beta 3（ATP1B3）和肌动蛋白调节器（ENAH），其表达随疾病进展升高。结合TCGA-LIHC数据集生存分析发现两者高表达与HCC患者不良预后显著相关（P＜0.05）。ROC曲线分析ATP1B3和ENAH的AUC值分别是0.821和0.933。ATP1B3高表达与晚期病理T分期、Stage和Grade相关（P＜0.05），而ENAH高表达仅与晚期病理Grade有关（P＜0.05）。RT-qPCR结果发现，ATP1B3和ENAH在临床HCC组织中表达上调（P＜0.05）。
结论: ATPIB3和ENAH有望成为肝脏疾病恶化和肝细胞癌的不良预后标志物。
Keywords: ATP1B3; ENAH; hepatocellular carcinoma; liver cirrhosis; liver fibrosis.