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Wang Y, Wan F, Chang K, Lu X, Dai B, Ye D. NUDT expression is predictive of prognosis in patients with clear cell renal cell carcinoma. Oncol Lett 2017; 14:6121-6128. [PMID: 29113256 DOI: 10.3892/ol.2017.6997] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2016] [Accepted: 07/27/2017] [Indexed: 01/20/2023] Open
Abstract
The nudix hydroxylase (NUDT) family of genes may have notable roles in cancer growth and metastasis. The present study aimed to determine the prognostic ability of NUDT genes in clear cell renal cell carcinoma (ccRCC). Data from 509 patients with ccRCC was obtained from The Cancer Genome Atlas (TCGA) database and 192 patient samples from Fudan University Shanghai Cancer Center (FUSCC) were analyzed in the present study. The expression profile of NUDT gene family members in the TCGA cohort was obtained from the TCGA RNA sequencing database. Pathological characteristics, including age, sex, tumor size, tumor grade, stage, laterality and overall survival were collected. Cox proportional hazards regression model and Kaplan-Meier survival analysis were performed to assess the associations between pathological characteristics and expression levels of NUDT family genes. NUDT family genes that exhibited associations with overall survival (OS) were further validated in the FUSCC cohort. In the TCGA cohort, Cox proportional hazards analysis found that NUDT5 [hazards ratio (HR)=1.676; 95% confidence interval (CI), 1.097-2.559] and NUDT17 (HR=1.375; 95% CI, 1.092-1.732) were predictive of ccRCC prognosis. Further analysis revealed that low NUDT5 (P<0.0001) and NUDT17 (P<0.0001) expression were associated with poorer OS rates in the TCGA cohort. In the FUSCC cohort, low NUDT5 expression was also associated with poor OS rates (P=0.0116), and tumor grade was a factor that influenced the expression level of NUDT5 (P=0.016).
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Affiliation(s)
- Yue Wang
- Department of Urology, Fudan University Shanghai Cancer Center, Shanghai 20032, P.R. China.,Department of Oncology, Shanghai Medical College, Fudan University, Shanghai 20032, P.R. China
| | - Fangning Wan
- Department of Urology, Fudan University Shanghai Cancer Center, Shanghai 20032, P.R. China.,Department of Oncology, Shanghai Medical College, Fudan University, Shanghai 20032, P.R. China
| | - Kun Chang
- Department of Urology, Fudan University Shanghai Cancer Center, Shanghai 20032, P.R. China.,Department of Oncology, Shanghai Medical College, Fudan University, Shanghai 20032, P.R. China
| | - Xiaolin Lu
- Department of Urology, Fudan University Shanghai Cancer Center, Shanghai 20032, P.R. China.,Department of Oncology, Shanghai Medical College, Fudan University, Shanghai 20032, P.R. China
| | - Bo Dai
- Department of Urology, Fudan University Shanghai Cancer Center, Shanghai 20032, P.R. China.,Department of Oncology, Shanghai Medical College, Fudan University, Shanghai 20032, P.R. China
| | - Dingwei Ye
- Department of Urology, Fudan University Shanghai Cancer Center, Shanghai 20032, P.R. China.,Department of Oncology, Shanghai Medical College, Fudan University, Shanghai 20032, P.R. China
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Choi JS, Dasari A, Hu P, Benkovic SJ, Berdis AJ. The use of modified and non-natural nucleotides provide unique insights into pro-mutagenic replication catalyzed by polymerase eta. Nucleic Acids Res 2015; 44:1022-35. [PMID: 26717984 PMCID: PMC4756837 DOI: 10.1093/nar/gkv1509] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2014] [Accepted: 12/10/2015] [Indexed: 12/25/2022] Open
Abstract
This report evaluates the pro-mutagenic behavior of 8-oxo-guanine (8-oxo-G) by quantifying the ability of high-fidelity and specialized DNA polymerases to incorporate natural and modified nucleotides opposite this lesion. Although high-fidelity DNA polymerases such as pol δ and the bacteriophage T4 DNA polymerase replicating 8-oxo-G in an error-prone manner, they display remarkably low efficiencies for TLS compared to normal DNA synthesis. In contrast, pol η shows a combination of high efficiency and low fidelity when replicating 8-oxo-G. These combined properties are consistent with a pro-mutagenic role for pol η when replicating this DNA lesion. Studies using modified nucleotide analogs show that pol η relies heavily on hydrogen-bonding interactions during translesion DNA synthesis. However, nucleobase modifications such as alkylation to the N2 position of guanine significantly increase error-prone synthesis catalyzed by pol η when replicating 8-oxo-G. Molecular modeling studies demonstrate the existence of a hydrophobic pocket in pol η that participates in the increased utilization of certain hydrophobic nucleotides. A model is proposed for enhanced pro-mutagenic replication catalyzed by pol η that couples efficient incorporation of damaged nucleotides opposite oxidized DNA lesions created by reactive oxygen species. The biological implications of this model toward increasing mutagenic events in lung cancer are discussed.
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Affiliation(s)
- Jung-Suk Choi
- Department of Chemistry, Cleveland State University, 2351 Euclid Avenue, Cleveland, OH 44115, USA
| | - Anvesh Dasari
- Department of Chemistry, Cleveland State University, 2351 Euclid Avenue, Cleveland, OH 44115, USA
| | - Peter Hu
- Department of Chemistry, The Pennsylvania State University, 413 Wartik Building, University Park, PA 16802, USA
| | - Stephen J Benkovic
- Department of Chemistry, The Pennsylvania State University, 413 Wartik Building, University Park, PA 16802, USA
| | - Anthony J Berdis
- Department of Chemistry, Cleveland State University, 2351 Euclid Avenue, Cleveland, OH 44115, USA Center for Gene Regulation in Health and Disease, Cleveland State University, 2351 Euclid Avenue, Cleveland, OH 44115, USA Case Comprehensive Cancer Center, 10900 Euclid Avenue, Cleveland OH 44106, USA
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Ghosh S, Dixit MK, Chakrabarti R. Thermodynamics of site-specific small molecular ion interactions with DNA duplex: a molecular dynamics study. MOLECULAR SIMULATION 2015. [DOI: 10.1080/08927022.2015.1085123] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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