J Cancer 2020; 11(22):6591-6600. doi:10.7150/jca.49175 This issue

Research Paper

Biological functions and prognostic value of RNA Binding Proteins in clear cell Renal Cell Carcinoma

Zhenpeng Zhu1,2*, Anbang He1,2, Lanruo Lin3, Chunru Xu1,2, Tianyu Cai1,2, Jian Lin1,2✉

1. Department of Urology, Peking University First Hospital, Beijing 100034, China
2. Institute of Urology, Peking University, Beijing 100034, China
3. Capital Medical University, Beijing 100069, China
*Contributed equally

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Citation:
Zhu Z, He A, Lin L, Xu C, Cai T, Lin J. Biological functions and prognostic value of RNA Binding Proteins in clear cell Renal Cell Carcinoma. J Cancer 2020; 11(22):6591-6600. doi:10.7150/jca.49175. Available from https://www.jcancer.org/v11p6591.htm

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Abstract

Early detection and accurate evaluation were both critical to improving the prognosis of clear cell Renal Cell Carcinoma (ccRCC) patients. More importantly, RNA Binding Proteins (RBPs) play a vital role in the tumorigenesis and progression of numerous cancers. However, the relationship between RBPs and ccRCC is still unclear. Exploring the potential biological functions of RBPs in ccRCC and establishing a prognostic signature to predict the survival probability remains meaningful. In this study, transcriptome profiling and the corresponding clinical information were obtained from the TCGA database, GEO database, and ICGC database. By using the "edgeR" R package, 200 DERBPs were found, including 128 up-regulated and 72 down-regulated RBPs. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analyses showed that DERBPs were mainly involved in regulating transcriptional processes and metabolism. Furthermore, there were 4 hub genes (RPS2, RPS14, RPS20, and RPLP0) were found in the PPI network, which may play vital biological roles among those DERBPs. Then we used LASSO regression to construct a prognostic signature and validated the signature in the GEO and ICGC cohort. The time-dependent receiver operating characteristic (ROC) curve showed that the signature could accurately predict the prognosis of ccRCC patients. Then we established a nomogram, and the calibration curve and ROC curve showed that the nomogram could accurately predict 1-year, 3-year, and 5-year overall survival (OS) of ccRCC patients (The AUC value: 0.871, 0.829, and 0.816). In conclusion, we constructed a 10-RBPs-based prognostic signature integrating clinical parameters to predict the prognosis of ccRCC patients. The prognostic signature based on the differentially expressed RBPs (DERBPs) might serve as promising diagnostic and prognostic biomarkers in ccRCC.

Keywords: clear cell renal cell carcinoma, RNA Binding Proteins, Bioinformatics analysis, Prognostic signature, Overall survival.