Sui Yingli, Lu Kun, Fu Lin
Institute of Chronic Disease, School of Basic Medicine, Qingdao University, Qingdao, Shandong, China.
PeerJ. 2021 Apr 20;9:e11272. doi: 10.7717/peerj.11272. eCollection 2021.
Clear Cell Renal Cell Carcinoma (CCRCC) is the most aggressive subtype of Renal Cell Carcinoma (RCC) with high metastasis and recurrence rates. This study aims to find new potential key genes of CCRCC.
Four gene expression profiles (GSE12606, GSE53000, GSE68417, and GSE66272) were downloaded from the Gene Expression Omnibus (GEO) database. The TCGA KIRC data was downloaded from The Cancer Genome Atlas (TCGA). Using GEO2R, the differentially expressed genes (DEG) in CCRCC tissues and normal samples were analyzed. Gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analyses were performed in DAVID database. A protein-protein interaction (PPI) network was constructed and the hub gene was predicted by STRING and Cytoscape. GEPIA and Kaplan-Meier plotter databases were used for further screening of Key genes. Expression verification and survival analysis of key genes were performed using TCGA database, GEPIA database, and Kaplan-Meier plotter. Receiver operating characteristic (ROC) curve was used to analyze the diagnostic value of key genes in CCRCC, which is plotted by R software based on TCGA database. UALCAN database was used to analyze the relationship between key genes and clinical pathology in CCRCC and the methylation level of the promoter of key genes in CCRCC.
A total of 289 up-regulated and 449 down-regulated genes were identified based on GSE12606, GSE53000, GSE68417, and GSE66272 profiles in CCRCC. The upregulated DEGs were mainly enriched with protein binding and PI3K-Akt signaling pathway, whereas down-regulated genes were enriched with the integral component of the membrane and metabolic pathways. Next, the top 35 genes were screened out from the PPI network according to Degree, and three new key genes ITGAX, LAPTM5 and SERPINE1 were further screened out through survival and prognosis analysis. Further results showed that the ITGAX, LAPTM5, and SERPINE1 levels in CCRCC tumor tissues were significantly higher than those in normal tissues and were associated with poor prognosis. ROC curve shows that ITGAX, LAPTM5, and SERPINE1 have good diagnostic value with good specificity and sensitivity. The promoter methylation levels of ITGAX, LAPTM5 and SERPINE1 in CCRCC tumor tissues were significantly lower than those in normal tissues. We also found that key genes were associated with clinical pathology in CCRCC.
ITGAX, LAPTM5, and SERPINE1 were identified as novel key candidate genes that could be used as prognostic biomarkers and potential therapeutic targets for CCRCC.
透明细胞肾细胞癌（CCRCC）是肾细胞癌（RCC）中侵袭性最强的亚型，具有高转移率和复发率。本研究旨在寻找CCRCC新的潜在关键基因。
从基因表达综合数据库（GEO）下载了四个基因表达谱（GSE12606、GSE53000、GSE68417和GSE66272）。从癌症基因组图谱（TCGA）下载了TCGA KIRC数据。使用GEO2R分析CCRCC组织和正常样本中的差异表达基因（DEG）。在DAVID数据库中进行基因本体论（GO）和京都基因与基因组百科全书（KEGG）富集分析。构建蛋白质-蛋白质相互作用（PPI）网络，并通过STRING和Cytoscape预测枢纽基因。利用GEPIA和Kaplan-Meier plotter数据库进一步筛选关键基因。使用TCGA数据库、GEPIA数据库和Kaplan-Meier plotter对关键基因进行表达验证和生存分析。采用受试者工作特征（ROC）曲线分析关键基因在CCRCC中的诊断价值，该曲线由基于TCGA数据库的R软件绘制。使用UALCAN数据库分析CCRCC中关键基因与临床病理的关系以及CCRCC中关键基因启动子的甲基化水平。
基于CCRCC中的GSE12606、GSE53000、GSE68417和GSE66272谱，共鉴定出289个上调基因和449个下调基因。上调的DEG主要富集于蛋白质结合和PI3K-Akt信号通路，而下调基因则富集于膜的整合成分和代谢途径。接下来，根据Degree从PPI网络中筛选出前35个基因，并通过生存和预后分析进一步筛选出三个新的关键基因ITGAX、LAPTM5和SERPINE1。进一步结果显示，CCRCC肿瘤组织中ITGAX、LAPTM5和SERPINE1的水平显著高于正常组织，且与预后不良相关。ROC曲线显示，ITGAX、LAPTM5和SERPINE1具有良好的诊断价值，特异性和敏感性良好。CCRCC肿瘤组织中ITGAX、LAPTM5和SERPINE1的启动子甲基化水平显著低于正常组织。我们还发现关键基因与CCRCC的临床病理相关。
ITGAX、LAPTM5和SERPINE1被鉴定为新的关键候选基因，可作为CCRCC的预后生物标志物和潜在治疗靶点。
