Integrated analysis of RNA-binding proteins in human colorectal cancer
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(2020) 18:222
RESEARCH
Open Access
Integrated analysis of RNA-binding proteins in human colorectal cancer Xuehui Fan, Lili Liu, Yue Shi, Fanghan Guo, Haining Wang, Xiuli Zhao, Di Zhong and Guozhong Li*
Abstract Background: Although RNA-binding proteins play an essential role in a variety of different tumours, there are still limited efforts made to systematically analyse the role of RNA-binding proteins (RBPs) in the survival of colorectal cancer (CRC) patients. Methods: Analysis of CRC transcriptome data collected from the TCGA database was conducted, and RBPs were extracted from CRC. R software was applied to analyse the differentially expressed genes (DEGs) of RBPs. To identify related pathways and perform functional annotation of RBP DEGs, Gene Ontology (GO) function and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analyses were carried out using the database for annotation, visualization and integrated discovery. Protein-protein interactions (PPIs) of these DEGs were analysed based on the Search Tool for the Retrieval of Interacting Genes (STRING) database and visualized by Cytoscape software. Based on the Cox regression analysis of the prognostic value of RBPs (from the PPI network) with survival time, the RBPs related to survival were identified, and a prognostic model was constructed. To verify the model, the data stored in the TCGA database were designated as the training set, while the chip data obtained from the GEO database were treated as the test set. Then, both survival analysis and ROC curve verification were conducted. Finally, the risk curves and nomograms of the two groups were generated to predict the survival period. Results: Among RBP DEGs, 314 genes were upregulated while 155 were downregulated, of which twelve RBPs (NOP14, MRPS23, MAK16, TDRD6, POP1, TDRD5, TDRD7, PPARGC1A, LIN28B, CELF4, LRRFIP2, MSI2) with prognostic value were obtained. Conclusions: The twelve identified genes may be promising predictors of CRC and play an essential role in the pathogenesis of CRC. However, further investigation of the underlying mechanism is needed. Keywords: Colorectal cancer (CRC), RNA-binding protein (RBP), Prognostic model construction, Survival analysis
Introduction As a significant class of cellular proteins, RNA-binding proteins (RBPs) can interact with RNA by recognizing special RNA-binding domains and are widely involved in multiple posttranscriptional regulatory processes, such as RNA shearing, transport, sequence editing, intracellular localization and translation control [1]. It is estimated that there are up to 1500 different proteins that have the * Correspondence: [email protected] Department of Neurology, The First Affiliated Hospital of Harbin Medical University, 23 You Zheng Street, Harbin 150001, Heilongjiang Province, People’s Republic of China
potential to bind RNA in the human genome [2]. RBPs are characterized by the presence of an RNA-binding domain (RBD) that contains 60–100 residues and usually adopts an αβ topology. Found in single or multiple copies
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