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

2021 ◽  
Vol 2021 ◽  
pp. 1-18
Author(s):  
Bowen Wang ◽  
Haoran Zhao ◽  
Shaobin Ni ◽  
Beichen Ding
Keyword(s):  
Renal Cell Carcinoma ◽  
Cell Carcinoma ◽  
Roc Curve ◽  
Renal Cell ◽  
Prognostic Value ◽  
Prognostic Model ◽  
Rna Binding ◽  
Clear Cell ◽  
Rna Binding Proteins ◽  
Cell Renal Cell Carcinoma

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.

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

2020 ◽  
Vol 11 (22) ◽  
pp. 6591-6600 ◽  
Author(s):  
Zhenpeng Zhu ◽  
Anbang He ◽  
Lanruo Lin ◽  
Chunru Xu ◽  
Tianyu Cai ◽  
...  
Keyword(s):  
Renal Cell Carcinoma ◽  
Cell Carcinoma ◽  
Renal Cell ◽  
Prognostic Value ◽  
Binding Proteins ◽  
Rna Binding ◽  
Clear Cell ◽  
Rna Binding Proteins ◽  
Biological Functions ◽  
Cell Renal Cell Carcinoma

scholarly journals The expression and prognostic value of RNA binding proteins in clear cell renal cell carcinoma

2020 ◽  
Vol 9 (12) ◽  
pp. 7415-7431
Author(s):  
Can-Xuan Li ◽  
Jie Chen ◽  
Zheng-Guang Xu ◽  
Wing-Keung Yiu ◽  
Yen-Ting Lin
Keyword(s):  
Renal Cell Carcinoma ◽  
Cell Carcinoma ◽  
Renal Cell ◽  
Prognostic Value ◽  
Binding Proteins ◽  
Rna Binding ◽  
Clear Cell ◽  
Rna Binding Proteins ◽  
Cell Renal Cell Carcinoma

scholarly journals A Valuable Plasma Membrane Protein Prognostic Model in Clear Cell Renal Cell Carcinoma

2020 ◽  
Author(s):  
Haosheng Liu ◽  
Jianxiong Fang ◽  
Tianqi Liu ◽  
Zhenhui Zhang ◽  
Chao Zhao ◽  
...  
Keyword(s):  
Renal Cell Carcinoma ◽  
Plasma Membrane ◽  
Membrane Proteins ◽  
Cell Carcinoma ◽  
Renal Cell ◽  
Prognostic Value ◽  
Prognostic Model ◽  
Clear Cell ◽  
Plasma Membrane Proteins ◽  
Cell Renal Cell Carcinoma

Abstract Background: Renal cell cacinoma (RCC) accounts for 3% of human cancers, and clear cell renal cell carcinoma (ccRCC) is the most common pathological type of RCC. Cell surface proteins have been shown to play an important role in the occurrence and progression of various cancers. In this study, we focused on plasma membrane proteins (PMPs), to explore their potential value in ccRCC. Methods: The PMPs expression profiles and ccRCC patients’ clinical information were downloaded from TCGA database. Through a series of bioinformatic methods, we established a plasma membrane proteins prognostic model and verify its value in multiple ways. Results: Multivariate cox regression analysis and area under receiver operating characteristic curve indicated that this model was an effective independent predictor of ccRCC clinical outcomes. It has good prognostic value in different groups of clinical features. Combined with other two clinical characteristics, a nomogram was constructed to predict patient survival at 1, 3, and 5 years. Conclusions: Our study is the first to explore the prognostic value of plasma membrane proteins in clear cell renal cell carcinoma. We hope our work could provide a new viewpoint for ccRCC prognosis and drawn people’s attention to plasma membrane proteins in clear cell renal cell carcinoma.

scholarly journals Identification of a glycolysis-related lncRNA prognostic signature for clear cell renal cell carcinoma

2021 ◽  
Vol 41 (8) ◽  
Author(s):  
Wei Ma ◽  
Manli Zhong ◽  
Xiaowu Liu
Keyword(s):  
Renal Cell Carcinoma ◽  
Cell Carcinoma ◽  
Roc Curve ◽  
Renal Cell ◽  
Prognostic Value ◽  
Risk Model ◽  
Cox Regression ◽  
Clear Cell ◽  
Cell Renal Cell Carcinoma ◽  
Kaplan Meier

Abstract Background: The present study investigated the independent prognostic value of glycolysis-related long noncoding (lnc)RNAs in clear cell renal cell carcinoma (ccRCC). Methods: A coexpression analysis of glycolysis-related mRNAs–long noncoding RNAs (lncRNAs) in ccRCC from The Cancer Genome Atlas (TCGA) was carried out. Clinical samples were randomly divided into training and validation sets. Univariate Cox regression and least absolute shrinkage and selection operator (LASSO) regression analyses were performed to establish a glycolysis risk model with prognostic value for ccRCC, which was validated in the training and validation sets and in the whole cohort by Kaplan–Meier, univariate and multivariate Cox regression, and receiver operating characteristic (ROC) curve analyses. Principal component analysis (PCA) and functional annotation by gene set enrichment analysis (GSEA) were performed to evaluate the risk model. Results: We identified 297 glycolysis-associated lncRNAs in ccRCC; of these, 7 were found to have prognostic value in ccRCC patients by Kaplan–Meier, univariate and multivariate Cox regression, and ROC curve analyses. The results of the GSEA suggested a close association between the 7-lncRNA signature and glycolysis-related biological processes and pathways. Conclusion: The seven identified glycolysis-related lncRNAs constitute an lncRNA signature with prognostic value for ccRCC and provide potential therapeutic targets for the treatment of ccRCC patients.

scholarly journals Prognostic value of immune-related genes in clear cell renal cell carcinoma

Aging ◽  
2019 ◽  
Vol 11 (23) ◽  
pp. 11474-11489 ◽  
Author(s):  
Bangbei Wan ◽  
Bo Liu ◽  
Yuan Huang ◽  
Gang Yu ◽  
Cai Lv
Keyword(s):  
Renal Cell Carcinoma ◽  
Cell Carcinoma ◽  
Renal Cell ◽  
Prognostic Value ◽  
Clear Cell ◽  
Cell Renal Cell Carcinoma ◽  
Immune Related Genes

scholarly journals Prognostic Value of an m5C RNA Methylation Regulator-Related Signature for Clear Cell Renal Cell Carcinoma

2021 ◽  
Vol Volume 13 ◽  
pp. 6673-6687
Author(s):  
Hanrong Li ◽  
Huiming Jiang ◽  
Zhicheng Huang ◽  
Zhilin Chen ◽  
Nanhui Chen
Keyword(s):  
Renal Cell Carcinoma ◽  
Cell Carcinoma ◽  
Renal Cell ◽  
Prognostic Value ◽  
Clear Cell ◽  
Cell Renal Cell Carcinoma ◽  
Rna Methylation
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