Identifying the novel key genes in renal cell carcinoma by bioinformatics analysis and cell experiments
Identifying the novel key genes in renal cell carcinoma by bioinformatics analysis and cell experiments
复制标题
通过生物信息学分析和细胞实验鉴定肾细胞癌的新关键基因
DOI：
10.1186/s12935-020-01405-6
复制
发表时间：
2020-07-21
影响因子：
5.8
通讯作者：
Zeng, Guohua
中科院分区：
文献类型：
--
作者：
Chen, Yeda;Gu, Di;Zeng, Guohua
研究背景肾细胞癌（renal cell cancer，RCC）的主要驱动基因已被发现，但其复杂的分子异质性尚不清楚。方法基因芯片数据集GSE 781、GSE 6344、GSE 53000和GSE 68417均来自Gene Expression Omnibus（GEO）数据库。采用GEO 2 R工具筛选差异表达基因，并利用大卫软件进行功能富集分析。构建了蛋白质相互作用网络（PPI），并利用STRING和Cytoscape进行了模块分析。使用GEPIA进行生存分析。在Oncomine中验证了差异表达。利用细胞实验（细胞活力测定、transwell迁移和侵袭测定、伤口愈合测定、流式细胞术）验证hub基因对肾癌细胞（A498和OSRC-2细胞系）增殖的作用。6个hub基因（SUCLG 1、PCK 2、GLDC、SLC 12 A1、ATP 1A 1、PDHA 1）的表达与肾癌患者的总生存期显著相关。与293 t细胞株相比，这六个基因在六个RCC细胞株（A498、OSRC-2、786- O、Caki-1、ACHN、769-P）中的表达水平显著降低。与癌旁正常肾组织相比，肾癌组织中这些基因的mRNA和蛋白表达水平均下调。细胞活力测定显示SUCLG 1、PCK 2、GLDC过表达可明显抑制RCC的增殖。Transwell迁移、侵袭、伤口愈合实验显示SUCLG 1、PCK 2、GLDC三个基因的过表达明显抑制RCC的迁移、侵袭。结论SUCLG 1、PCK 2、GLDC基因的高表达可诱导肾癌细胞发生G1/S/G2期阻滞，提示SUCLG 1、PCK 2、GLDC基因的高表达可作为肾癌的预后指标。
BackgroundAlthough major driver gene have been identified, the complex molecular heterogeneity of renal cell cancer (RCC) remains unclear. Therefore, more relevant genes need to be identified to explain the pathogenesis of renal cancer.MethodsMicroarray datasets GSE781, GSE6344, GSE53000 and GSE68417 were downloaded from Gene Expression Omnibus (GEO) database. The differentially expressed genes (DEGs) were identified by employing GEO2R tool, and function enrichment analyses were performed by using DAVID. The protein-protein interaction network (PPI) was constructed and the module analysis was performed using STRING and Cytoscape. Survival analysis was performed using GEPIA. Differential expression was verified in Oncomine. Cell experiments (cell viability assays, transwell migration and invasion assays, wound healing assay, flow cytometry) were utilized to verify the roles of the hub genes on the proliferation of kidney cancer cells (A498 and OSRC-2 cell lines).ResultsA total of 215 DEGs were identified from four datasets. Six hub gene (SUCLG1, PCK2, GLDC, SLC12A1, ATP1A1, PDHA1) were identified and the overall survival time of patients with RCC were significantly shorter. The expression levels of these six genes were significantly decreased in six RCC cell lines(A498, OSRC-2, 786- O, Caki-1, ACHN, 769-P) compared to 293t cell line. The expression level of both mRNA and protein of these genes were downregulated in RCC samples compared to those in paracancerous normal tissues. Cell viability assays showed that overexpressions of SUCLG1, PCK2, GLDC significantly decreased proliferation of RCC. Transwell migration, invasion, wound healing assay showed overexpression of three genes(SUCLG1, PCK2, GLDC) significantly inhibited the migration, invasion of RCC. Flow cytometry analysis showed that overexpression of three genes(SUCLG1, PCK2, GLDC) induced G1/S/G2 phase arrest of RCC cells.ConclusionBased on our current findings, it is concluded that SUCLG1, PCK2, GLDC may serve as a potential prognostic marker of RCC.