scholarly journals LAT, HOXD3 and NFE2L3 identified as novel DNA methylation-driven genes and prognostic markers in human clear cell renal cell carcinoma by integrative bioinformatics approaches

2019 ◽  
Vol 10 (26) ◽  
pp. 6726-6737 ◽  
Author(s):  
Jie Wang ◽  
Hu Zhao ◽  
Huiyue Dong ◽  
Ling Zhu ◽  
Shuiliang Wang ◽  
...  
Keyword(s):  
Dna Methylation ◽  
Renal Cell Carcinoma ◽  
Cell Carcinoma ◽  
Renal Cell ◽  
Prognostic Markers ◽  
Clear Cell ◽  
Cell Renal Cell Carcinoma

scholarly journals Downregulation of lncRNA ZNF582-AS1 due to DNA hypermethylation promotes clear cell renal cell carcinoma growth and metastasis by regulating the N(6)-methyladenosine modification of MT-RNR1

2021 ◽  
Vol 40 (1) ◽  
Author(s):  
Wuping Yang ◽  
Kenan Zhang ◽  
Lei Li ◽  
Yawei Xu ◽  
Kaifang Ma ◽  
...  
Keyword(s):  
Dna Methylation ◽  
Renal Cell Carcinoma ◽  
Protein Expression ◽  
Cell Carcinoma ◽  
Clinical Significance ◽  
Renal Cell ◽  
Clear Cell ◽  
Expression Level ◽  
Cell Renal Cell Carcinoma ◽  
Qrt Pcr

Abstract Background Emerging evidence confirms that lncRNAs (long non-coding RNAs) are potential biomarkers that play vital roles in tumors. ZNF582-AS1 is a novel lncRNA that serves as a potential prognostic marker of cancers. However, the specific clinical significance and molecular mechanism of ZNF582-AS1 in ccRCC (clear cell renal cell carcinoma) are unclear. Methods Expression level and clinical significance of ZNF582-AS1 were determined by TCGA-KIRC data and qRT-PCR results of 62 ccRCCs. DNA methylation status of ZNF582-AS1 promoter was examined by MSP, MassARRAY methylation and demethylation analysis. Gain-of-function experiments were conducted to investigate the biological roles of ZNF582-AS1 in the phenotype of ccRCC. The subcellular localization of ZNF582-AS1 was detected by RNA FISH. iTRAQ, RNA pull-down and RIP-qRT-PCR were used to identify the downstream targets of ZNF582-AS1. rRNA MeRIP-seq and MeRIP-qRT-PCR were utilized to examine the N(6)-methyladenosine modification status. Western blot and immunohistochemistry assays were used to determine the protein expression level. Results ZNF582-AS1 was downregulated in ccRCC, and decreased ZNF582-AS1 expression was significantly correlated with advanced tumor stage, higher pathological stage, distant metastasis and poor prognosis. Decreased ZNF582-AS1 expression was caused by DNA methylation at the CpG islands within its promoter. ZNF582-AS1 overexpression inhibited cell proliferative, migratory and invasive ability, and increased cell apoptotic rate in vitro and in vivo. Mechanistically, we found that ZNF582-AS1 overexpression suppressed the N(6)-methyladenosine modification of MT-RNR1 by reducing rRNA adenine N(6)-methyltransferase A8K0B9 protein level, resulting in the decrease of MT-RNR1 expression, followed by the inhibition of MT-CO2 protein expression. Furthermore, MT-RNR1 overexpression reversed the decreased MT-CO2 expression and phenotype inhibition of ccRCC induced by increased ZNF582-AS1 expression. Conclusions This study demonstrates for the first time that ZNF582-AS1 functions as a tumor suppressor gene in ccRCC and ZNF582-AS1 may serve as a potential biomarker and therapeutic target of ccRCC.

Molecular characterization of clear cell renal cell carcinoma identifies CSNK2A1, SPP1 and DEFB1 as promising novel prognostic markers

Apmis ◽  
2016 ◽  
Vol 124 (5) ◽  
pp. 372-383 ◽  
Author(s):  
Maj Rabjerg ◽  
Henriette Bjerregaard ◽  
Ulrich Halekoh ◽  
Boye L. Jensen ◽  
Steen Walter ◽  
...  
Keyword(s):  
Renal Cell Carcinoma ◽  
Cell Carcinoma ◽  
Molecular Characterization ◽  
Renal Cell ◽  
Prognostic Markers ◽  
Clear Cell ◽  
Cell Renal Cell Carcinoma

scholarly journals Analysis of various potential prognostic markers and survival data in clear cell renal cell carcinoma

2017 ◽  
Vol 43 (3) ◽  
pp. 440-454 ◽  
Author(s):  
Tastekin Ebru ◽  
Oz Puyan Fulya ◽  
Akdere Hakan ◽  
Yurut-Caloglu Vuslat ◽  
Sut Necdet ◽  
...  
Keyword(s):  
Renal Cell Carcinoma ◽  
Cell Carcinoma ◽  
Survival Data ◽  
Renal Cell ◽  
Prognostic Markers ◽  
Clear Cell ◽  
Cell Renal Cell Carcinoma

scholarly journals A Two-DNA Methylation Signature to Improve Prognosis Prediction of Clear Cell Renal Cell Carcinoma

2019 ◽  
Vol 60 (11) ◽  
pp. 1013 ◽  
Author(s):  
Shanping Shi ◽  
Shazhou Ye ◽  
Xiaoyue Wu ◽  
Mingjun Xu ◽  
Renjie Zhuo ◽  
...  
Keyword(s):  
Dna Methylation ◽  
Renal Cell Carcinoma ◽  
Cell Carcinoma ◽  
Renal Cell ◽  
Clear Cell ◽  
Cell Renal Cell Carcinoma ◽  
Prognosis Prediction

Abstract LB-130: Simultaneous evaluation of chromatin accessibility and DNA methylation in clear cell renal cell carcinoma by a newly developed assay, AcceSssIble

2014 ◽  
Author(s):  
Elinne Becket ◽  
Christopher Duymich ◽  
Yin-Wei Chang ◽  
Kurinji Pandiyan ◽  
Peter A. Jones ◽  
...  
Keyword(s):  
Dna Methylation ◽  
Renal Cell Carcinoma ◽  
Cell Carcinoma ◽  
Renal Cell ◽  
Clear Cell ◽  
Chromatin Accessibility ◽  
Cell Renal Cell Carcinoma ◽  
Simultaneous Evaluation

scholarly journals DNA methylation of CRB3 is a prognostic biomarker in clear cell renal cell carcinoma

2019 ◽  
Vol 46 (4) ◽  
pp. 4377-4383 ◽  
Author(s):  
Pingping Li ◽  
Jie Liu ◽  
Juan Li ◽  
Peijun Liu
Keyword(s):  
Dna Methylation ◽  
Renal Cell Carcinoma ◽  
Cell Carcinoma ◽  
Renal Cell ◽  
Clear Cell ◽  
Prognostic Biomarker ◽  
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 Identification of DNA Methylation–Independent Epigenetic Events Underlying Clear Cell Renal Cell Carcinoma

2016 ◽  
Vol 76 (7) ◽  
pp. 1954-1964 ◽  
Author(s):  
Elinne Becket ◽  
Sameer Chopra ◽  
Christopher E. Duymich ◽  
Justin J. Lin ◽  
Jueng Soo You ◽  
...  
Keyword(s):  
Dna Methylation ◽  
Renal Cell Carcinoma ◽  
Cell Carcinoma ◽  
Renal Cell ◽  
Clear Cell ◽  
Cell Renal Cell Carcinoma ◽  
Epigenetic Events
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