J Cancer 2019; 10(25):6384-6394. doi:10.7150/jca.30656

Research Paper

The screening of pivotal gene expression signatures and biomarkers in renal carcinoma

Hailong Ruan1,2*, Sen Li1,2*, Junwei Tong1,2*, Qi Cao1,2*, Zhengshuai Song1,2, Keshan Wang1,2, Yu huang1,2, Lin Bao1,2, Xuanyu Chen1,2, Hongmei Yang3, Ke Chen1,2✉, Xiaoping Zhang1,2✉

1. Department of Urology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430022, China
2. Institute of Urology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430022, China
3. Department of Pathogenic Biology, School of Basic Medicine, Huazhong University of Science and Technology, Wuhan 430030, China
*Contributed equally

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Citation:
Ruan H, Li S, Tong J, Cao Q, Song Z, Wang K, huang Y, Bao L, Chen X, Yang H, Chen K, Zhang X. The screening of pivotal gene expression signatures and biomarkers in renal carcinoma. J Cancer 2019; 10(25):6384-6394. doi:10.7150/jca.30656. Available from http://www.jcancer.org/v10p6384.htm

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Abstract

Renal cell carcinoma (RCC) is one of the most common malignancies in the urinary system, among which the proportion of clear cell RCC (ccRCC) is over 80%. This study aims to explore potential signaling pathways and key biomarkers that drive RCC progression. The RCC GEO Datasets GSE15641 was featured to screen differentially expressed genes (DEGs). The pathway enrichment and functional annotation of differentially expressed genes were analyzed using the Kyoto Encyclopedia of Genes and Genomes (KEGG) and the Gene Ontology (GO). We screened Hub genes from DEGs using protein-protein interaction (PPI) networks and Cytoscape software. The survival and diagnostic analysis of these hub genes was performed to evaluate their potential prognostic and diagnostic value for ccRCC. In GSE15641 dataset, 598 DEGs were captured according to screening criteria (406 up-regulated genes and 192 down-regulated genes). Meanwhile, 15 hub genes were screened out from DEGs using PPI and Cytoscape. Kaplan Meier and ROC curve analysis identified three potential prognostic and diagnostic biomarkers (TGFB1, TIMP1 and VIM) for ccRCC from 15 hub genes. Gene set enrichment analysis (GSEA) revealed that these three dysregulated genes are mainly enriched in primary immunodeficiency, ECM receptor interaction, cytokine receptor interaction and natural killer cell-mediated cytotoxicity pathway. In summary, our findings discovered pivotal gene expression signatures and signaling pathways in the progression of ccRCC. TGFB1, TIMP1 and VIM might contribute to the progression of ccRCC, which could have potential as biomarkers or therapeutic targets for ccRCC.

Keywords: hub genes, clear cell renal cell carcinoma, biomarkers, bioinformatics, differentially expressed gene