Integrated analysis of RNA binding proteins in human colorectal cancer

Abstract

Background: Though RNA-binding proteins play an essential role in a variety of different tumors, there is still limited effort made on the systematic analysis of RNA binding proteins (RBPs) in the survival of colorectal cancer(CRC).Methods: An analysis was conducted of the CRC transcriptome data collected from the TCGA database and RBPs were extracted from CRC. R software was applied to analyze the differentially expressed genes (DEGs) of RBPs. To identify the pathways and functional annotation of RBPs DEGs, Gene Ontology (GO) function, Kyoto Encyclopedia of Genes and Genomes(KEGG) pathway enrichment analysis were carried out using the database for annotation, visualization and integrated discovery. The interactive gene database search tool was employed to conduct protein-protein interaction analysis, while Cytoscape software was applied for visual processing. Based on the COX regression analysis of the prognostic value of interacting RBPs and survival time, the RBPs related to survival were screened out, and a prognostic model was constructed. The data stored in TCGA database was taken as the Train group, while the chip data obtained from the GEO database was treated as the Test group to verify the model. Then, both survival analysis and ROC curve verification were conducted. Finally, the risk curves and nomograms of the two groups were drawn to predict the survival period.Results: There were 314 genes up-regulated by RBPs DEGs and 155 genes down-regulated, from which twelve RBPs (NOP14, MRPS23, MAK16, TDRD6, POP1, TDRD5, TDRD7, PPARGC1A, LIN28B, CELF4, LRRFIP2, MSI2) with prognostic markers were obtained.Conclusions: These twelve genes may be applicable as the predictor of CRC and play an essential role in the pathogenesis of CRC. In spite of this, it remains necessary to further explore the underlying mechanism.

Identification of Key Iron Metabolism-Related Long Non-Coding RNAs in Hepatocellular Carcinoma Based on Bioinformatics Analysis

“…For example, Liu et al suggested that fetal-lethal noncoding developmental regulatory RNA (FENDRR) as an anti brotic long noncoding RNA can reduced pulmonary brosis by inhibiting broblast activation by reducing iron concentration, which may act as a potential therapeutic target for pulmonary brosis [16] . Aberrant expression of lncRNAs related with iron metabolism has been participated in regulating critical physiological functions which were linked to different types of cancer in present studies [17][18][19]. Moreover, a review revealed that hepatic iron accumulation can lead to brotic responses, and the signi cance and potential of iron-related proteins in the progression and development of liver brosis [20] .…”

Identification of a Three-RNA Binding Proteins (RBPs) Signature Predicting Prognosis for Breast Cancer

“…Given that RBPs are critical regulators and effectors of cancer, they also should be regarded as hallmarks and potential targets for early diagnosis, prognosis and clinical intervention of cancer. NOP14/MRPS23/POP1 exhibit prognostic value in colorectal cancer, while APOBEC3C/DCAF13/EIF4E3/EZR possess significance in predicting prognosis of breast cancer ( 17 , 18 ). Moreover, the Ribavirin, an antiviral guanosine analog, is able to slacken tumorigenesis by competitively interacting with the 5’-Cap of eIF4E mRNA, subsequently impeding the translation and transposition of eIF4E-regualted Cyclin D1 ( 19 ).…”

Identification of RNA Binding Protein Signature to Predict Overall Survival for Bladder Cancer

“…Moreover, several studies showed that the abnormality of RBPs was related to lung cancer [11], glioma [12], colorectal cancer [13]and hepatocarcinoma [14]. It was reported that human ribosomal protein S3 (RPS3) served as a variety of novel pro-tumorigenic RBP in hepatocarcinoma, and RPS3 could bind to the 3' UTR of SIRT1 mRNA in hepatocarcinoma, resulting in the stable expression of the oncogene SIRT1 [14].…”