J Cancer 2018; 9(21):3912-3922. doi:10.7150/jca.25900

Research Paper

Identifying a Novel Biomarker TOP2A of Clear Cell Renal Cell Carcinoma (ccRCC) Associated with Smoking by Co-Expression Network Analysis

Yaoyi Xiong1, Lushun Yuan1, Liang Chen1, Yuan Zhu2,3,4, Shanshan Zhang2,3,4, Xuefeng Liu5, Yu Xiao1,2,3,4✉, Xinghuan Wang1✉

1. Department of Urology, Zhongnan Hospital of Wuhan University, Wuhan, China
2. Department of Biological Repositories, Zhongnan Hospital of Wuhan University, Wuhan, China
3. Laboratory of Precision Medicine, Zhongnan Hospital of Wuhan University, Wuhan, China
4. Human Genetics Resource Preservation Center of Hubei Province, Wuhan, China
5. Department of Pathology, Lombardi Comprehensive Cancer Center, Georgetown University Medical School, Washington DC, USA

Abstract

Although it is well known that smoking is one of pathogenesis of clear cell renal cell carcinoma (ccRCC), the underlying molecular mechanism is still unclear. In our study, the microarray dataset GSE46699 is analyzed by weighted gene co-expression network analysis (WGCNA). Then we identify 15 co-expressed gene modules in which the lightcyan module (R2 = 0.30) is the most significant. Combined with the protein-protein interaction (PPI) network and WGCNA, two hub genes are identified. Meanwhile, linear regression analyses indicate that TOP2A has a higher connection with smoking in ccRCC, survival analysis proved that overexpression of TOP2A in ccRCC could lead to shorter survival time. Furthermore, bioinformatical analyses based on GSE46699 and GSE2109 as well as qRT-PCR experiment show similar results that TOP2A is significantly up-regulated in smoking ccRCC compared to non-smoking ccRCC samples. In addition, Functional analysis, pathway enrichment analysis and gene set enrichment analysis (GSEA) indicate that high expression of TOP2A is related to cell cycle and p53 signaling pathway in ccRCC samples. Moreover, in vitro experiments revealed that TOP2A induced cell cycle arrest at G2 phase and proliferation inhibition via p53 phosphorylation. Taken together, by using WGCNA, we have identified a novel biomarker named TOP2A, which could affect the development of smoking-related ccRCC by regulating cell cycle and p53 signaling pathway.

Keywords: weighted gene co-expression network analysis (WGCNA), TOP2A, biomarker, smoking, clear cell renal cell carcinoma (ccRCC)

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How to cite this article:
Xiong Y, Yuan L, Chen L, Zhu Y, Zhang S, Liu X, Xiao Y, Wang X. Identifying a Novel Biomarker TOP2A of Clear Cell Renal Cell Carcinoma (ccRCC) Associated with Smoking by Co-Expression Network Analysis. J Cancer 2018; 9(21):3912-3922. doi:10.7150/jca.25900. Available from http://www.jcancer.org/v09p3912.htm