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Joshi JS, Vora HH, Ghosh NR, Tankshali RN, Jetly DH, Trivedi TI. Nonhomologous end joining repair pathway molecules as predictive biomarkers for patients with oral squamous cell carcinoma. J Cancer Res Ther 2021; 17:1031-1038. [PMID: 34528560 DOI: 10.4103/jcrt.jcrt_582_19] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
Abstract
Purpose Nonhomologous end-joining (NHEJ) is critical for the repair of either pathologic double-strand breaks (DSBs) and/or for the repair of physiologic DSBs created during radiotherapy to kill the tumor cell. Therefore, patients with higher expression of NHEJ repair proteins might develop resistance to ionizing radiation, allowing the disease to recur. As cancer of the oral cavity is a serious health problem globally, the present study aimed to examine the expression of Ku70/80, X-ray repair cross-complementing protein 4 (XRCC4) and DNA ligase IV-core molecules of the NHEJ pathway in patients with oral cancer. Materials and Methods Protein expression of Ku70/80, XRCC4, and DNA ligase IV were studied by Immunohistochemistry and mRNA expression of Ku70 and Ku80 were studied using reverse transcription polymerase chain reaction. Data were analyzed statistically using SPSS. Results A univariate survival analysis revealed an association of Ku70 mRNA with shorter overall survival (OS). While protein expression of XRCC4 showed an association with reduced relapse-free survival and shorter OS. Multivariate survival analysis demonstrated that XRCC4 and DNA ligase IV are independent prognosticators for predicting adverse disease outcomes. Conclusion Strong expression of repair proteins - XRCC4 and DNA ligase IV is associated with unfavorable disease outcome in patients with oral squamous cell carcinoma.
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Affiliation(s)
- Jigna S Joshi
- Stem Cell Biology Lab, Department of Cancer Biology, The Gujarat Cancer & Research Institute, Ahmedabad, Gujarat, India
| | - Hemangini H Vora
- Immunohematology Lab, Department of Cancer Biology, The Gujarat Cancer & Research Institute, Ahmedabad, Gujarat, India
| | - Nandita R Ghosh
- Tumor Biology Lab, Department of Cancer Biology, The Gujarat Cancer & Research Institute, Ahmedabad, Gujarat, India
| | - Rajen N Tankshali
- Department of Surgical Oncology, Gujarat Cancer & Research Institute, Ahmedabad, Gujarat, India
| | - Dhaval H Jetly
- Department of Onco-Pathology, Gujarat Cancer & Research Institute, Ahmedabad, Gujarat, India
| | - Trupti I Trivedi
- Clinical Carcinogenesis Lab, Department of Cancer Biology, The Gujarat Cancer & Research Institute, Ahmedabad, Gujarat, India
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2
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Ye ZM, Li LJ, Luo MB, Qing HY, Zheng JH, Zhang C, Lu YX, Tang YM. A systematic review and network meta-analysis of single nucleotide polymorphisms associated with pancreatic cancer risk. Aging (Albany NY) 2020; 12:25256-25274. [PMID: 33226370 PMCID: PMC7803556 DOI: 10.18632/aging.104128] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2020] [Accepted: 09/19/2020] [Indexed: 12/12/2022]
Abstract
In this meta-analysis, we systematically investigated the correlation between single nucleotide polymorphisms (SNPs) and pancreatic cancer (PC) risk. We searched PubMed, Network Science, EMBASE, Cochrane Library, China National Knowledge Infrastructure (CNKI), China Science and Technology Periodical Database (VIP), and Wanfang databases up to January 2020 for studies on PC risk-associated SNPs. We identified 45 case-control studies (36,360 PC patients and 54,752 non-cancer individuals) relating to investigations of 27 genes and 54 SNPs for this meta-analysis. Direct meta-analysis followed by network meta-analysis and Thakkinstian algorithm analysis showed that homozygous genetic models for CTLA-4 rs231775 (OR =0.326; 95% CI: 0.218-0.488) and VDR rs2228570 (OR = 1.976; 95% CI: 1.496-2.611) and additive gene model for TP53 rs9895829 (OR = 1.231; 95% CI: 1.143-1.326) were significantly associated with PC risk. TP53 rs9895829 was the most optimal SNP for diagnosing PC susceptibility with a false positive report probability < 0.2 at a stringent prior probability value of 0.00001. This systematic review and meta-analysis suggest that TP53 rs9895829, VDR rs2228570, and CTLA-4 rs231775 are significantly associated with PC risk. We also demonstrate that TP53 rs9895829 is a potential diagnostic biomarker for estimating PC risk.
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Affiliation(s)
- Zhuo-Miao Ye
- Department of Oncology, Xiangya Hospital, Central South University, Changsha 410008, China; Ruikang School of Clinical Medicine, Guangxi University of Chinese Medicine, Nanning 530001, China.,Ruikang School of Clinical Medicine, Guangxi University of Chinese Medicine, Nanning 530001, China
| | - Li-Juan Li
- The First Clinical Faculty of Guangxi University of Chinese Medicine, Guangxi University of Chinese Medicine, Nanning 530222, China
| | - Ming-Bo Luo
- Ruikang School of Clinical Medicine, Guangxi University of Chinese Medicine, Nanning 530001, China
| | - Hong-Yuan Qing
- Ruikang School of Clinical Medicine, Guangxi University of Chinese Medicine, Nanning 530001, China
| | - Jing-Hui Zheng
- Department of Cardiology, Ruikang Hospital Affiliated to Guangxi University of Chinese Medicine, Nanning 530011, China
| | - Chi Zhang
- Graduate School, Guangxi University of Chinese Medicine, Nanning 530001, Guangxi, China
| | - Yun-Xin Lu
- Department of Oncology, Ruikang Hospital Affiliated to Guangxi University of Chinese Medicine, Nanning 530011, China
| | - You-Ming Tang
- Department of Gastroenterology, Ruikang Hospital Affiliated to Guangxi University of Chinese Medicine, Nanning, China
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Ye ZM, Li LJ, Zheng JH, Zhang C, Lu YX, Tang Y. A comprehensive assessment of single nucleotide polymorphisms associated with pancreatic cancer risk: A protocol for systematic review and network meta-analysis. Medicine (Baltimore) 2020; 99:e20345. [PMID: 32541456 PMCID: PMC7302655 DOI: 10.1097/md.0000000000020345] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/16/2020] [Revised: 04/22/2020] [Accepted: 04/22/2020] [Indexed: 12/29/2022] Open
Abstract
BACKGROUND Single nucleotide polymorphisms (SNPs) have been inconsistently associated with pancreatic cancer (PC) risk. This meta-analysis aimed to synthesize relevant data on SNPs associated with PC. METHODS Databases were searched to identify association studies of SNPs and PC published through January 2020 from the databases of PubMed, Web of Science, Embase, Cochrane Library, China National Knowledge Infrastructure, the Chinese Science and Technology Periodical Database (VIP) and Wanfang databases. Network meta-analysis and Thakkinstian algorithm were used to select the most appropriate genetic model, along with false positive report probability (FPRP) for noteworthy associations. The methodological quality of data was assessed based on the STREGA statement Stata 14.0 will be used for systematic review and meta-analysis. RESULTS This study will provide a high-quality evidence to find the SNP most associated with pancreatic cancer susceptibility and the best genetic model. CONCLUSIONS This study will explore which SNP is most associated with pancreatic cancer susceptibility.Registration: INPLASY202040023.
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Affiliation(s)
- Zhuo-Miao Ye
- Ruikang School of Clinical Medicine, Guangxi University of Chinese Medicine
| | - Li-Juan Li
- The First Clinical Faculty of Guangxi University of Chinese Medicine
| | - Jing-Hui Zheng
- Department of Cardiology, Ruikang Hospital Affiliated to Guangxi University of Chinese Medicine, Nanning
| | - Chi Zhang
- Graduate School, Guangxi University of Chinese Medicine
| | | | - Youming Tang
- Department of Gastroenterology, Ruikang Hospital Affiliated to Guangxi University of Chinese Medicine, Nanning, China
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Zhang XY, Wei XH, Wang BJ, Yao J. The XRCC4rs1805377 polymorphism is not associated with the risk of cancer: An updated meta-analysis. J Int Med Res 2020; 48:300060520926364. [PMID: 32493081 PMCID: PMC7273771 DOI: 10.1177/0300060520926364] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
ObjectivesA growing number of studies have reported that genes involved in the repair of DNA double-strand breaks might be cancer-susceptibility genes. The x-ray cross-complementing group 4 gene ( XRCC4) encodes a protein that functions in the repair of DNA double-strand breaks, and this meta-analysis aimed to investigate the relationship between the XRCC4 rs1805377 polymorphism and cancer occurrence.MethodsWe retrieved case–control studies that met the inclusion criteria from PubMed, Web of Science, Embase, and China National Knowledge Infrastructure databases. Associations between rs1805377 and cancer risk were evaluated by odds ratios (ORs) using a random effects model and 95% confidence intervals (CIs) as well as sensitivity and subgroup analyses.ResultsAfter inclusion criteria were met, the meta-analysis involved 24 studies that included 9,633 cancer patients and 10,544 healthy controls. No significant association was found between rs1805377 and the risk of cancer (pooled OR = 1.107; 95% CI = 0.955–1.284) in the dominant genetic model. Similarly, no significant association was observed in the subgroup analysis.ConclusionsThrough this meta-analysis, we found no association between the rs1805377 polymorphism and cancer occurrence. This may provide useful information for relevant future studies into the etiology of cancer.
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Affiliation(s)
- Xin-yuan Zhang
- School of Forensic Medicine, China Medical University, Shenyang, Liaoning Province, P. R. China
| | - Xiao-han Wei
- School of Forensic Medicine, China Medical University, Shenyang, Liaoning Province, P. R. China
| | - Bao-jie Wang
- School of Forensic Medicine, China Medical University, Shenyang, Liaoning Province, P. R. China
| | - Jun Yao
- School of Forensic Medicine, China Medical University, Shenyang, Liaoning Province, P. R. China
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Mucaki EJ, Shirley BC, Rogan PK. Expression Changes Confirm Genomic Variants Predicted to Result in Allele-Specific, Alternative mRNA Splicing. Front Genet 2020; 11:109. [PMID: 32211018 PMCID: PMC7066660 DOI: 10.3389/fgene.2020.00109] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2019] [Accepted: 01/30/2020] [Indexed: 12/11/2022] Open
Abstract
Splice isoform structure and abundance can be affected by either noncoding or masquerading coding variants that alter the structure or abundance of transcripts. When these variants are common in the population, these nonconstitutive transcripts are sufficiently frequent so as to resemble naturally occurring, alternative mRNA splicing. Prediction of the effects of such variants has been shown to be accurate using information theory-based methods. Single nucleotide polymorphisms (SNPs) predicted to significantly alter natural and/or cryptic splice site strength were shown to affect gene expression. Splicing changes for known SNP genotypes were confirmed in HapMap lymphoblastoid cell lines with gene expression microarrays and custom designed q-RT-PCR or TaqMan assays. The majority of these SNPs (15 of 22) as well as an independent set of 24 variants were then subjected to RNAseq analysis using the ValidSpliceMut web beacon (http://validsplicemut.cytognomix.com), which is based on data from the Cancer Genome Atlas and International Cancer Genome Consortium. SNPs from different genes analyzed with gene expression microarray and q-RT-PCR exhibited significant changes in affected splice site use. Thirteen SNPs directly affected exon inclusion and 10 altered cryptic site use. Homozygous SNP genotypes resulting in stronger splice sites exhibited higher levels of processed mRNA than alleles associated with weaker sites. Four SNPs exhibited variable expression among individuals with the same genotypes, masking statistically significant expression differences between alleles. Genome-wide information theory and expression analyses (RNAseq) in tumor exomes and genomes confirmed splicing effects for 7 of the HapMap SNP and 14 SNPs identified from tumor genomes. q-RT-PCR resolved rare splice isoforms with read abundance too low for statistical significance in ValidSpliceMut. Nevertheless, the web-beacon provides evidence of unanticipated splicing outcomes, for example, intron retention due to compromised recognition of constitutive splice sites. Thus, ValidSpliceMut and q-RT-PCR represent complementary resources for identification of allele-specific, alternative splicing.
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Affiliation(s)
- Eliseos J Mucaki
- Department of Biochemistry, University of Western Ontario, London, ON, Canada
| | | | - Peter K Rogan
- Department of Biochemistry, University of Western Ontario, London, ON, Canada.,CytoGnomix, London, ON, Canada.,Department of Oncology University of Western Ontario, London, ON, Canada.,Department of Computer Science, University of Western Ontario, London, ON, Canada
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The Role of the Core Non-Homologous End Joining Factors in Carcinogenesis and Cancer. Cancers (Basel) 2017; 9:cancers9070081. [PMID: 28684677 PMCID: PMC5532617 DOI: 10.3390/cancers9070081] [Citation(s) in RCA: 103] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2017] [Revised: 06/30/2017] [Accepted: 07/03/2017] [Indexed: 12/20/2022] Open
Abstract
DNA double-strand breaks (DSBs) are deleterious DNA lesions that if left unrepaired or are misrepaired, potentially result in chromosomal aberrations, known drivers of carcinogenesis. Pathways that direct the repair of DSBs are traditionally believed to be guardians of the genome as they protect cells from genomic instability. The prominent DSB repair pathway in human cells is the non-homologous end joining (NHEJ) pathway, which mediates template-independent re-ligation of the broken DNA molecule and is active in all phases of the cell cycle. Its role as a guardian of the genome is supported by the fact that defects in NHEJ lead to increased sensitivity to agents that induce DSBs and an increased frequency of chromosomal aberrations. Conversely, evidence from tumors and tumor cell lines has emerged that NHEJ also promotes chromosomal aberrations and genomic instability, particularly in cells that have a defect in one of the other DSB repair pathways. Collectively, the data present a conundrum: how can a single pathway both suppress and promote carcinogenesis? In this review, we will examine NHEJ's role as both a guardian and a disruptor of the genome and explain how underlying genetic context not only dictates whether NHEJ promotes or suppresses carcinogenesis, but also how it alters the response of tumors to conventional therapeutics.
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