Integrated Analysis of the Roles of RNA Binding Proteins and Their Prognostic Value in Clear Cell Renal Cell Carcinoma

Abstract

Background and Purpose. The renal cell carcinoma is one of the main malignant tumors in the genitourinary system, which seriously affects human health. Unregulated expression of RNA binding proteins (RBPs) is thought to be involved in the progression of many cancers. However, the role of RBPs in the clear cell renal cell carcinoma (ccRCC) is not yet clear. Methods. We downloaded the RNA sequencing data of ccRCC from the Cancer Genome Atlas (TCGA) database and identified differently expressed RBPs in different tissues. In this study, we used bioinformatics to analyze the expression and prognostic value of RBPs; then, we performed functional analysis and constructed a protein interaction network for them. We also screened out some RBPs related to the prognosis of ccRCC. Finally, based on the identified RBPs, we constructed a prognostic model that can predict patients’ risk of illness and survival time. Also, the data in the HPA database were used for verification. Results. In our experiment, we obtained 539 ccRCC samples and 72 normal controls. In the subsequent analysis, 87 upregulated RBPs and 38 downregulated RBPs were obtained. In addition, 9 genes related to the prognosis of patients were selected, namely, RPL36A, THOC6, RNASE2, NOVA2, TLR3, PPARGC1A, DARS, LARS2, and U2AF1L4. We further constructed a prognostic model based on these genes and plotted the ROC curve. This ROC curve performed well in judgement and evaluation. A nomogram that can judge the patient’s life span is also made. Conclusion. In conclusion, we have identified differentially expressed RBPs in ccRCC and carried out a series of in-depth research studies, the results of which may provide ideas for the diagnosis of ccRCC and the research of new targeted drugs.

Identification of a Methylation-Regulating Genes Prognostic Signature to Predict the Prognosis and Aid Immunotherapy of Clear Cell Renal Cell Carcinoma

“…We observed good calibrations regarding the predicted vs observed 1-, 3-, and 5-years OS of the patients ( Figure 8B ). Moreover, the ROC curves exhibited better predictive capability in the current nomogram to predict the 1-, 3-, and 5-years OS than the MRGPS and risk scores published by Wang et al (2021) , Chen et al (2021) , and Zheng et al (2021) ( Figures 8C–E ). Additionally, DCA analysis revealed the superiority of the current nomogram over MRGPS and the published risk scores in predicting the 1-, 3-, and 5-years OS ( Figures 8F–H ).…”

MAGE enables population level RNAseq driven genotyping and (differential) allelic divergence detection in healthy kidney and carcinoma

“…Meanwhile, current and previous LOI results in breast cancer 16 , as well as functional studies 38,39 , support HM13 as a candidate oncogene. U2AF1L4 has been far less studied but is also of interest, being a homologue of a gene imprinted in mouse 40 and featuring prognostic value in renal clear cell carcinoma according to preliminary experimental research 41,42 .…”

Ribonuclease A Family Member 2 Promotes the Malignant Progression of Glioma Through the PI3K/Akt Signaling Pathway

“…RNASE2 mRNA is elevated in peripheral blood mononuclear cells from patients with systemic lupus erythematosus, and RNASE2 silencing suppresses the production of age-associated B cell subsets in vitro ( 8 ). Furthermore, it is differentially expressed and related to prognosis in gastric cancer and clear cell renal cell carcinoma ( 9 , 10 ). RNASE2 expression is also significantly higher in colorectal cancer stem cells (CD133 + ) than in CD133 − colorectal cancer cells ( 11 ).…”