Upregulated VEGFA and DLL4 act as potential prognostic genes for clear cell renal cell carcinoma
Authors Wang X, Zhang J, Wang Y, Tu M, Wang Y, Shi G
Received 1 September 2017
Accepted for publication 8 December 2017
Published 26 March 2018 Volume 2018:11 Pages 1697—1706
Checked for plagiarism Yes
Review by Single-blind
Peer reviewers approved by Dr Akshita Wason
Peer reviewer comments 2
Editor who approved publication: Professor Jianmin Xu
Xilong Wang, Jun Zhang, Yangyun Wang, Minqi Tu, Ying Wang, Guowei Shi
Department of Urology, The Fifth People’s Hospital of Shanghai, Fudan University, Shanghai, China
Purpose: As a typical hypervascular tumor, clear cell renal cell carcinoma (ccRCC) is the most common type of RCC. This study was aimed to explore the prognostic genes for ccRCC, focusing on the roles of vascular endothelial growth factor A (VEGFA) and Delta-like ligand 4 (DLL4) in the disease.
Materials and methods: The mRNA-sequencing data of kidney renal clear cell carcinoma (KIRC) were obtained from The Cancer Genome Atlas (TCGA) database, including 469 tumor samples and 68 adjacent normal samples. Using limma package, differentially expressed genes (DEGs) were analyzed by differential expression and subgroup analyses and confirmed using validation dataset GSE53757. Followed by enrichment analysis, protein–protein interaction (PPI) network analysis and protein subcellular localization were performed using multifaceted analysis tool for human transcriptome tool, and Cytoscape software and InnateDB database, respectively. Moreover, survival analysis was conducted to identify key prognosis-associated genes. In addition, VEGFA and DLL4 levels were detected using real-time quantitative PCR (qRT-PCR).
Results: A total of 1,984 DEGs were screened in the KIRC tumor samples. VEGFA was located in extracellular space and could interact with placental growth factor (PGF) and angiopoietin 2 (ANGPT2) in the PPI network. Subgroup analysis suggested that VEGFA was significantly upregulated in stages I, II, and III ccRCC tumor samples. Survival analysis showed that TIMP1 was among the top four prognosis-associated genes. qRT-PCR analysis confirmed that the expression levels of DLL4 and VEGFA were significantly upregulated in tumor samples.
Conclusion: VEGFA and DLL4 might be prognostic genes for ccRCC. Besides, PGF, ANGPT2, and TIMP1 might also be related to the prognosis of ccRCC patients.
Keywords: clear cell renal cell carcinoma, differentially expressed genes, protein–protein interaction network, subgroup analysis, survival analysis
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