通过生物信息学分析和细胞实验鉴定肾细胞癌中的新型关键基因。
Identifying the novel key genes in renal cell carcinoma by bioinformatics analysis and cell experiments.
作者信息
Chen Yeda, Gu Di, Wen Yaoan, Yang Shuxin, Duan Xiaolu, Lai Yongchang, Yang Jianan, Yuan Daozhang, Khan Aisha, Wu Wenqi, Zeng Guohua
机构信息
Department of Urology, Minimally Invasive Surgery Center, The First Affiliated Hospital of Guangzhou Medical University, Guangdong Key Laboratory of Urology, Kangda Road 1#, Haizhu District, Guangzhou, 510230 Guangdong China.
Department of Urology, Affiliated Cancer Hospital and Institute of Guangzhou Medical University, Guangzhou, China.
出版信息
Cancer Cell Int. 2020 Jul 21;20:331. doi: 10.1186/s12935-020-01405-6. eCollection 2020.
BACKGROUND
Although 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.
METHODS
Microarray 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).
RESULTS
A 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.
CONCLUSION
Based on our current findings, it is concluded that SUCLG1, PCK2, GLDC may serve as a potential prognostic marker of RCC.
背景
尽管已鉴定出主要驱动基因，但肾细胞癌（RCC）复杂的分子异质性仍不清楚。因此，需要鉴定更多相关基因来解释肾癌的发病机制。
方法
从基因表达综合数据库（GEO）下载微阵列数据集GSE781、GSE6344、GSE53000和GSE68417。使用GEO2R工具鉴定差异表达基因（DEG），并使用DAVID进行功能富集分析。构建蛋白质-蛋白质相互作用网络（PPI），并使用STRING和Cytoscape进行模块分析。使用GEPIA进行生存分析。在Oncomine中验证差异表达。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）验证枢纽基因对肾癌细胞（A498和OSRC-2细胞系）增殖的作用。
结果
从四个数据集中共鉴定出215个DEG。鉴定出六个枢纽基因（SUCLG1、PCK2、GLDC、SLC12A1、ATP1A1、PDHA1），RCC患者的总生存时间显著缩短。与293t细胞系相比，这六个基因在六种RCC细胞系（A498、OSRC-2、786-O、Caki-1、ACHN、769-P）中的表达水平显著降低。与癌旁正常组织相比，这些基因在RCC样本中的mRNA和蛋白质表达水平均下调。细胞活力测定表明，SUCLG1、PCK2、GLDC的过表达显著降低RCC的增殖。Transwell迁移、侵袭、伤口愈合测定表明，三个基因（SUCLG1、PCK2、GLDC）的过表达显著抑制RCC的迁移和侵袭。流式细胞术分析表明，三个基因（SUCLG1、PCK2、GLDC）的过表达诱导RCC细胞的G1/S/G2期阻滞。
结论
基于我们目前的研究结果，得出结论：SUCLG1、PCK2、GLDC可能作为RCC的潜在预后标志物。
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