scholarly journals A New Survival Model Based on ADAMTSs for Prognostic Prediction in Clear Cell Renal Cell Carcinoma

2021 ◽  
Vol 2021 ◽  
pp. 1-10
Author(s):  
Guangzhen Wu ◽  
Jianyi Li ◽  
Yingkun Xu ◽  
Xiangyu Che ◽  
Feng Chen ◽  
...  
Keyword(s):  
Gene Expression ◽  
Renal Cell Carcinoma ◽  
Regression Analysis ◽  
Cell Carcinoma ◽  
Renal Cell ◽  
Prognostic Model ◽  
Clear Cell ◽  
Survival Model ◽  
Cell Renal Cell Carcinoma ◽  
Cancer Types

The main purpose of this study was to explore the genetic variation, gene expression, and clinical significance of ADAMTSs (a disintegrin and metalloprotease domains with thrombospondin motifs) across cancer types. Analysis of data from the TCGA (The Cancer Genome Atlas) database showed that the ADAMTSs have extensive CNV (copy number variation) and SNV (single nucleotide variation) across cancer types. Compared with normal tissues, the methylation of ADAMTSs in cancer tissues is also significantly different, which affects the expression of ADAMTS gene and the prognosis of cancer patients. Through gene expression analysis, we found that ADAMTS family has significant changes in gene expression across cancer types and is closely related to the prognosis of carcinoma, especially in ccRCC (clear cell renal cell carcinoma). LASSO regression analysis was used to establish a prognostic model based on the ADAMTSs to judge the prognosis of patients with ccRCC. Multiple Cox regression analysis suggested that age, grade, stage, and risk score of the prognostic model of ccRCC were independent prognostic factors in patients with renal clear cell carcinoma. These findings indicate that the ADAMTSs-based survival model can accurately predict the prognosis of patients with ccRCC and suggest that ADAMTSs are a potential prognostic biomarker and therapeutic target in ccRCC.

scholarly journals An optimal prognostic model based on gene expression for clear cell renal cell carcinoma

2020 ◽  
Vol 20 (3) ◽  
pp. 2420-2434 ◽  
Author(s):  
Dan Xu ◽  
Wantai Dang ◽  
Shaoqing Wang ◽  
Bo Hu ◽  
Lianghong Yin ◽  
...  
Keyword(s):  
Gene Expression ◽  
Renal Cell Carcinoma ◽  
Cell Carcinoma ◽  
Renal Cell ◽  
Prognostic Model ◽  
Clear Cell ◽  
Cell Renal Cell Carcinoma ◽  
Model Based

scholarly journals Patterns of gene expression characterize T1 and T3 clear cell renal cell carcinoma subtypes

PLoS ONE ◽  
2019 ◽  
Vol 14 (5) ◽  
pp. e0216793 ◽  
Author(s):  
Agnieszka M. Borys ◽  
Michał Seweryn ◽  
Tomasz Gołąbek ◽  
Łukasz Bełch ◽  
Agnieszka Klimkowska ◽  
...  
Keyword(s):  
Gene Expression ◽  
Renal Cell Carcinoma ◽  
Cell Carcinoma ◽  
Renal Cell ◽  
Clear Cell ◽  
Cell Renal Cell Carcinoma

scholarly journals Personalised drug repositioning for Clear Cell Renal Cell Carcinoma using gene expression

2018 ◽  
Vol 8 (1) ◽  
Author(s):  
Karel K. M. Koudijs ◽  
Anton G. T. Terwisscha van Scheltinga ◽  
Stefan Böhringer ◽  
Kirsten J. M. Schimmel ◽  
Henk-Jan Guchelaar
Keyword(s):  
Gene Expression ◽  
Renal Cell Carcinoma ◽  
Cell Carcinoma ◽  
Renal Cell ◽  
Clear Cell ◽  
Drug Repositioning ◽  
Cell Renal Cell Carcinoma

scholarly journals Prognostic Value of DNA Methylation-Driven Genes in Clear Cell Renal Cell Carcinoma: A Study Based on Methylation and Transcriptome Analyses

2020 ◽  
Vol 2020 ◽  
pp. 1-14
Author(s):  
Maolin Hu ◽  
Jiangling Xie ◽  
Huiming Hou ◽  
Ming Liu ◽  
Jianye Wang
Keyword(s):  
Gene Expression ◽  
Dna Methylation ◽  
Renal Cell Carcinoma ◽  
Cell Carcinoma ◽  
Risk Score ◽  
Renal Cell ◽  
Methylation Level ◽  
Cox Regression ◽  
Clear Cell ◽  
Cell Renal Cell Carcinoma

Background. Few previous studies have comprehensively explored the level of DNA methylation and gene expression in ccRCC. The purpose of this study was to identify the key clear cell renal cell carcinoma- (ccRCC-) related DNA methylation-driven genes (MDG) and to build a prognostic model based on the level of DNA methylation. Methods. RNA-seq transcriptome data and DNA methylation data were obtained from The Cancer Genome Atlas. Based on the MethylMix algorithm, we obtain ccRCC-related MDG. The univariate and multivariate Cox regression analyses were employed to investigate the correlation between patient overall survival and the methylation level of each MDG. Finally, a prognosis risk score was established based on a linear combination of the regression coefficient derived from the multivariate Cox regression model (β) multiplied with the methylation level of the gene. Results. 19 ccRCC-related MDG were identified. Three MDG (NCKAP1L, EVI2A, and BATF) were further screened and integrated into a prognostic risk score model, risk score=3.710∗methylation level of NCKAP1L+−3.892∗methylation level of EVI2A+−3.907∗methylation level of BATF. The risk model was independent from conventional clinical characteristics as a prognostic factor for ccRCC (HR=1.221, 95% confidence interval: 1.063–1.402, and P=0.005). The joint survival analysis showed that the gene expression and methylation levels of the prognostic genes EVI2A and BATF were significantly related with prognosis. Conclusion. This study provided an important bioinformatics foundation for in-depth studies of ccRCC DNA methylation.

scholarly journals LRRC19—A Bridge between Selenium Adjuvant Therapy and Renal Clear Cell Carcinoma: A Study Based on Datamining

Genes ◽  
2020 ◽  
Vol 11 (4) ◽  
pp. 440
Author(s):  
Yitong Zhang ◽  
Jiaxing Wang ◽  
Xiqing Liu
Keyword(s):  
Gene Expression ◽  
Renal Cell Carcinoma ◽  
Cell Carcinoma ◽  
Renal Cell ◽  
Independent Risk Factor ◽  
Clear Cell ◽  
Clear Cell Carcinoma ◽  
Renal Clear Cell Carcinoma ◽  
Cell Renal Cell Carcinoma ◽  
Low Expression

Kidney renal clear cell carcinoma (KIRC) is the most common and fatal subtype of renal cancer. Antagonistic associations between selenium and cancer have been reported in previous studies. Selenium compounds, as anti-cancer agents, have been reported and approved for clinical trials. The main active form of selenium in selenoproteins is selenocysteine (Sec). The process of Sec biosynthesis and incorporation into selenoproteins plays a significant role in biological processes, including anti-carcinogenesis. However, a comprehensive selenoprotein mRNA analysis in KIRC remains absent. In the present study, we examined all 25 selenoproteins and identified key selenoproteins, glutathione peroxidase 3 (GPX3) and type 1 iodothyronine deiodinase (DIO1), with the associated prognostic biomarker leucine-rich repeat containing 19 (LRRC19) in clear cell renal cell carcinoma cases from The Cancer Genome Atlas (TCGA) database. We performed validations for the key gene expression levels by two individual clear cell renal cell carcinoma cohorts, GSE781 and GSE6344, datasets from the Gene Expression Omnibus (GEO) database. Multivariate survival analysis demonstrated that low expression of LRRC19 was an independent risk factor for OS. Gene set enrichment analysis (GSEA) identified tyrosine metabolism, metabolic pathways, peroxisome, and fatty acid degradation as differentially enriched with the high LRRC19 expression in KIRC cases, which are involved in selenium therapy of clear cell renal cell carcinoma. In conclusion, low expression of LRRC19 was identified as an independent risk factor, which will advance our understanding concerning the selenium adjuvant therapy of clear cell renal cell carcinoma.

Validation of Gene Expression Signatures to Identify Low-risk Clear-cell Renal Cell Carcinoma Patients at Higher Risk for Disease-related Death

2016 ◽  
Vol 2 (6) ◽  
pp. 608-615 ◽  
Author(s):  
Mansi Parasramka ◽  
Daniel J. Serie ◽  
Yan W. Asmann ◽  
Jeanette E. Eckel-Passow ◽  
Erik P. Castle ◽  
...  
Keyword(s):  
Gene Expression ◽  
Renal Cell Carcinoma ◽  
Cell Carcinoma ◽  
Renal Cell ◽  
Clear Cell ◽  
Low Risk ◽  
Cell Renal Cell Carcinoma ◽  
Gene Expression Signatures
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