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Curtis AA, Yu Y, Carey M, Parfrey P, Yilmaz YE, Savas S. Multifactor dimensionality reduction method identifies novel SNP interactions in the WNT protein interaction networks that are associated with recurrence risk in colorectal cancer. Front Oncol 2023; 13:1122229. [PMID: 36998434 PMCID: PMC10043327 DOI: 10.3389/fonc.2023.1122229] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2022] [Accepted: 02/27/2023] [Indexed: 03/18/2023] Open
Abstract
BackgroundInteractions among genetic variants are rarely studied but may explain a part of the variability in patient outcomes.ObjectivesIn this study, we aimed to identify 1 to 3 way interactions among SNPs from five Wnt protein interaction networks that predict the 5-year recurrence risk in a cohort of stage I-III colorectal cancer patients.Methods423 patients recruited to the Newfoundland Familial Colorectal Cancer Registry were included. Five Wnt family member proteins (Wnt1, Wnt2, Wnt5a, Wnt5b, and Wnt11) were selected. The BioGRID database was used to identify the proteins interacting with each of these proteins. Genotypes of the SNPs located in the interaction network genes were retrieved from a genome-wide SNP genotype data previously obtained in the patient cohort. The GMDR 0.9 program was utilized to examine 1-, 2-, and 3-SNP interactions using a 5-fold cross validation step. Top GMDR 0.9 models were assessed by permutation testing and, if significant, prognostic associations were verified by multivariable logistic regression models.ResultsGMDR 0.9 has identified novel 1, 2, and 3-way SNP interactions associated with 5-year recurrence risk in colorectal cancer. Nine of these interactions were multi loci interactions (2-way or 3-way). Identified interaction models were able to distinguish patients based on their 5-year recurrence-free status in multivariable regression models. The significance of interactions was the highest in the 3-SNP models. Several of the identified SNPs were eQTLs, indicating potential biological roles of the genes they were associated with in colorectal cancer recurrence.ConclusionsWe identified novel interacting genetic variants that associate with 5-year recurrence risk in colorectal cancer. A significant portion of the genes identified were previously linked to colorectal cancer pathogenesis or progression. These variants and genes are of interest for future functional and prognostic studies. Our results provide further evidence for the utility of GMDR models in identifying novel prognostic biomarkers and the biological importance of the Wnt pathways in colorectal cancer.
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Affiliation(s)
- Aaron A. Curtis
- Division of Biomedical Sciences, Faculty of Medicine, Memorial University, St. John’s, NL, Canada
| | - Yajun Yu
- Institute of Cardiovascular Research, Southwest Medical University, Luzhou, Sichuan, China
| | - Megan Carey
- Division of Biomedical Sciences, Faculty of Medicine, Memorial University, St. John’s, NL, Canada
| | - Patrick Parfrey
- Discipline of Medicine, Faculty of Medicine, Memorial University, St. John’s, NL, Canada
| | - Yildiz E. Yilmaz
- Department of Mathematics and Statistics, Faculty of Science, Memorial University, St. John’s, NL, Canada
| | - Sevtap Savas
- Division of Biomedical Sciences, Faculty of Medicine, Memorial University, St. John’s, NL, Canada
- Discipline of Oncology, Faculty of Medicine, Memorial University, St. John’s, NL, Canada
- *Correspondence: Sevtap Savas,
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Wang Y, Du M, Vallis J, Shariati M, Parfrey PS, Mclaughlin JR, Wang PP, Zhu Y. The Roles of MTRR and MTHFR Gene Polymorphisms in Colorectal Cancer Survival. Nutrients 2022; 14:nu14214594. [PMID: 36364857 PMCID: PMC9658674 DOI: 10.3390/nu14214594] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2022] [Revised: 10/25/2022] [Accepted: 10/28/2022] [Indexed: 11/06/2022] Open
Abstract
Background: Paradoxically epidemiological data illustrate a negative relationship between dietary folate intake and colorectal cancer (CRC) risk. The occurrence and progression of CRC may be influenced by variants in some key enzyme coding genes in the folate metabolic pathway. We investigated the correlation between genetic variants in methionine synthase reductase (MTRR) and methylenetetrahydrofolate reductase (MTHFR) and CRC survival. Methods: This study used data collected from the Newfoundland Familial Colorectal Cancer Study. A total of 532 patients diagnosed with CRC for the first time from 1999 to 2003 were enrolled, and their mortality were tracked until April 2010. DNA samples were genotyped by Illumina’s integrated quantum 1 million chip. Cox models were established to assess 33 tag single-nucleotide polymorphisms in MTRR and MTHFR in relation to overall survival (OS), disease-free survival (DFS) and CRC-specific survival. Results: The MTRR and MTHFR genes were associated with DFS and CRC-specific survival in CRC patients at the gene level. After multiple comparison adjustment, MTRR rs1801394 A (vs. G) allele was associated with increased DFS (p = 0.024), while MTHRT rs3737966 (G vs. A), rs4846049 (T vs. G), rs1476413 (A vs. G), rs1801131 (C vs. A), rs12121543 (A vs. C), rs1801133 (C vs. T), rs4846052 (T vs. C), rs2066471 (A vs. G) and rs7533315 (T vs. C) were related to worse CRC-specific survival. Additionally, significant interactions were seen among pre-diagnostic alcohol consumption with MTRR rs1801394, rs3776467, rs326124, rs162040, and rs3776455, with superior OS associated with those protective variant alleles limited to patients with alcohol consumption under the median. The MTHFR rs3737966 (G vs. A) allele seemed to be detrimental to CRC survival only among subjects with fruit intake below the median. Conclusions: Polymorphic variants in MTRR and MTHFR genes that code for key enzymes for folate metabolism may be associated with survival in patients with CRC. The gene-CRC outcome association seems modulated by alcohol drinking and fruit intake.
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Affiliation(s)
- Yu Wang
- Department of Epidemiology and Biostatistics, School of Public Health, Tianjin Medical University, Tianjin 300070, China
| | - Meizhi Du
- Department of Epidemiology and Biostatistics, School of Public Health, Tianjin Medical University, Tianjin 300070, China
| | - Jillian Vallis
- Division of Community Health and Humanities, Faculty of Medicine, Memorial University of Newfoundland, St. John’s, NL A1B 3V6, Canada
| | - Matin Shariati
- Division of Community Health and Humanities, Faculty of Medicine, Memorial University of Newfoundland, St. John’s, NL A1B 3V6, Canada
| | - Patrick S. Parfrey
- Clinical Epidemiology Unit, Faculty of Medicine, Memorial University of Newfoundland, St. John’s, NL A1B 3V6, Canada
| | - John R. Mclaughlin
- Dalla Lana School of Public Health, University of Toronto, Toronto, ON M5T 3M7, Canada
| | - Peizhong Peter Wang
- Division of Community Health and Humanities, Faculty of Medicine, Memorial University of Newfoundland, St. John’s, NL A1B 3V6, Canada
- Dalla Lana School of Public Health, University of Toronto, Toronto, ON M5T 3M7, Canada
- Correspondence: (P.P.W.); (Y.Z.); Tel.: +1-(709)-777-8571 (P.P.W.); +86-(022)-8333-6118 (Y.Z.)
| | - Yun Zhu
- Department of Epidemiology and Biostatistics, School of Public Health, Tianjin Medical University, Tianjin 300070, China
- Correspondence: (P.P.W.); (Y.Z.); Tel.: +1-(709)-777-8571 (P.P.W.); +86-(022)-8333-6118 (Y.Z.)
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Curtis A, Yu Y, Carey M, Parfrey P, Yilmaz YE, Savas S. Examining SNP-SNP interactions and risk of clinical outcomes in colorectal cancer using multifactor dimensionality reduction based methods. Front Genet 2022; 13:902217. [PMID: 35991579 PMCID: PMC9385108 DOI: 10.3389/fgene.2022.902217] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2022] [Accepted: 06/30/2022] [Indexed: 12/24/2022] Open
Abstract
Background: SNP interactions may explain the variable outcome risk among colorectal cancer patients. Examining SNP interactions is challenging, especially with large datasets. Multifactor Dimensionality Reduction (MDR)-based programs may address this problem.Objectives: 1) To compare two MDR-based programs for their utility; and 2) to apply these programs to sets of MMP and VEGF-family gene SNPs in order to examine their interactions in relation to colorectal cancer survival outcomes.Methods: This study applied two data reduction methods, Cox-MDR and GMDR 0.9, to study one to three way SNP interactions. Both programs were run using a 5-fold cross validation step and the top models were verified by permutation testing. Prognostic associations of the SNP interactions were verified using multivariable regression methods. Eight datasets, including SNPs from MMP family genes (n = 201) and seven sets of VEGF-family interaction networks (n = 1,517 SNPs) were examined.Results: ∼90 million potential interactions were examined. Analyses in the MMP and VEGF gene family datasets found several novel 1- to 3-way SNP interactions. These interactions were able to distinguish between the patients with different outcome risks (regression p-values 0.03–2.2E-09). The strongest association was detected for a 3-way interaction including CHRM3.rs665159_EPN1.rs6509955_PTGER3.rs1327460 variants.Conclusion: Our work demonstrates the utility of data reduction methods while identifying potential prognostic markers in colorectal cancer.
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Affiliation(s)
- Aaron Curtis
- Discipline of Genetics, Faculty of Medicine, Memorial University, St. John’s, NL, Canada
- Division of Biomedical Sciences, Faculty of Medicine, Memorial University, St. John’s, NL, Canada
| | - Yajun Yu
- Discipline of Genetics, Faculty of Medicine, Memorial University, St. John’s, NL, Canada
- Division of Biomedical Sciences, Faculty of Medicine, Memorial University, St. John’s, NL, Canada
| | - Megan Carey
- Discipline of Genetics, Faculty of Medicine, Memorial University, St. John’s, NL, Canada
| | - Patrick Parfrey
- Discipline of Medicine, Faculty of Medicine, Memorial University, St. John’s, NL, Canada
| | - Yildiz E. Yilmaz
- Discipline of Genetics, Faculty of Medicine, Memorial University, St. John’s, NL, Canada
- Discipline of Medicine, Faculty of Medicine, Memorial University, St. John’s, NL, Canada
- Department of Mathematics and Statistics, Faculty of Science, Memorial University, St. John’s, NL, Canada
| | - Sevtap Savas
- Discipline of Genetics, Faculty of Medicine, Memorial University, St. John’s, NL, Canada
- Division of Biomedical Sciences, Faculty of Medicine, Memorial University, St. John’s, NL, Canada
- Discipline of Oncology, Faculty of Medicine, Memorial University, St. John’s, NL, Canada
- *Correspondence: Sevtap Savas,
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Yu Y, Werdyani S, Carey M, Parfrey P, Yilmaz YE, Savas S. A comprehensive analysis of SNPs and CNVs identifies novel markers associated with disease outcomes in colorectal cancer. Mol Oncol 2021; 15:3329-3347. [PMID: 34309201 PMCID: PMC8637572 DOI: 10.1002/1878-0261.13067] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2021] [Revised: 05/29/2021] [Accepted: 07/24/2021] [Indexed: 12/15/2022] Open
Abstract
We aimed to examine the associations of a genome-wide set of single nucleotide polymorphisms (SNPs) and 254 copy number variations (CNVs) and/or insertion/deletions (INDELs) with clinical outcomes in colorectal cancer patients (n = 505). We also aimed to investigate whether their associations changed (e.g., appeared, diminished) over time. Multivariable Cox proportional hazards and piece-wise Cox regression models were used to examine the associations. The Cancer Genome Atlas (TCGA) datasets were used for replication purposes and to examine the gene expression differences between tumor and nontumor tissue samples. A common SNP (WBP11-rs7314075) was associated with disease-specific survival with P-value of 3.2 × 10-8 . Association of this region with disease-specific survival was also detected in the TCGA patient cohort. Two expression quantitative trait loci (eQTLs) were identified in this locus that were implicated in the regulation of ERP27 expression. Interestingly, expression levels of ERP27 and WBP11 were significantly different between colorectal tumors and nontumor tissues. Three SNPs predicted the risk of recurrent disease only after 5 years postdiagnosis. Overall, our study identified novel variants, one of which also showed an association in the TCGA dataset, but no CNVs/INDELs, that associated with outcomes in colorectal cancer. Three SNPs were candidate predictors of long-term recurrence/metastasis risk.
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Affiliation(s)
- Yajun Yu
- Discipline of Genetics, Faculty of Medicine, Memorial University, St. John's, NL, Canada
| | - Salem Werdyani
- Discipline of Genetics, Faculty of Medicine, Memorial University, St. John's, NL, Canada
| | - Megan Carey
- Discipline of Genetics, Faculty of Medicine, Memorial University, St. John's, NL, Canada
| | - Patrick Parfrey
- Discipline of Medicine, Faculty of Medicine, Memorial University, St. John's, NL, Canada
| | - Yildiz E Yilmaz
- Discipline of Genetics, Faculty of Medicine, Memorial University, St. John's, NL, Canada.,Discipline of Medicine, Faculty of Medicine, Memorial University, St. John's, NL, Canada.,Department of Mathematics and Statistics, Faculty of Science, Memorial University, St. John's, NL, Canada
| | - Sevtap Savas
- Discipline of Genetics, Faculty of Medicine, Memorial University, St. John's, NL, Canada.,Discipline of Oncology, Faculty of Medicine, Memorial University, St. John's, NL, Canada
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Association of XRCC2 rs2040639 with the survival of patients with oral squamous cell carcinoma undergoing concurrent chemoradiotherapy. Gene 2020; 768:145283. [PMID: 33144272 DOI: 10.1016/j.gene.2020.145283] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2020] [Revised: 10/15/2020] [Accepted: 10/26/2020] [Indexed: 11/22/2022]
Abstract
OBJECTIVE To investigate the association between the variants of DNA double-strand break repair genes and the clinical outcomes of patients with oral squamous cell carcinoma (OSCC) undergoing concurrent chemoradiotherapy. METHODS Five variants of DNA double-strand break repair genes in samples from 319 patients with OSCC were genotyped using the Sequenom iPLEX MassARRAY system. Kaplan-Meier curves and Cox proportional hazards analysis were used to identify the factors associated with patient survival. RESULTS The XRCC2 rs2040639 (G3063A) polymorphism in the codominant model was associated with decreased recurrence risk (hazard ratio [HR] = 0.55, 95% confidence interval [CI] = 0.31-0.98; p = 0.042). A marginally significant interaction was observed between XRCC2 rs2040639 and PRKDC rs7003908 in patients carrying the AA and AA genotypes; these patients showed reduced recurrence risk (HR = 0.36, 95% CI = 0.17-0.79; p = 0.010). CONCLUSION The A-allele of XRCC2 rs2040639 is a favorable prognostic factor for disease-free survival. Patients with these genotypes may benefit from concurrent chemoradiotherapy. Additional confirmation from studies with larger samples or other ethnic populations is warranted.
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Chen XL, Wang YM, Zhao F, Chen Z, Yang X, Sun C, Gao Y, Yang TG, Tian G, Chen YM, Zhu SL, Lin XB, Liu FB. Methylenetetrahydrofolate reductase polymorphisms and colorectal cancer prognosis: A meta-analysis. J Gene Med 2019; 21:e3114. [PMID: 31330573 PMCID: PMC6851539 DOI: 10.1002/jgm.3114] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2018] [Revised: 05/30/2019] [Accepted: 07/15/2019] [Indexed: 12/31/2022] Open
Abstract
Background The present study focused on understanding the prognostic value of the methylenetetrahydrofolate reductase (MTHFR) single nucleotide polymorphisms rs1801133 (C667T) and rs1801131 (A1298C) in patients with colorectal cancer (CRC). Methods A systematic literature search was conducted in March 2016. Databases, including Medline, EMBASE, Cochrane and Chinese databases (including CNKI, Wanfang and VIP), were searched to identify the relevant articles describing MTHFR polymorphisms in patients with CRC. Data regarding overall survival (OS), progression‐free survival (PFS) and disease‐free survival (DFS) were collected and analysed. Results Twenty‐four studies with 5423 patients with CRC were included. Significant differences in OS, PFS and DFS were not observed among the different comparisons of patients carrying different alleles of the MTHFR rs1801133 polymorphism (including TT versus CC, TT versus CT + CC, CT + TT versus CC and CT versus CC). Compared with patients with the rs1801131 CA + AA genotypes, patients with the CC genotype had a shorter OS (hazard ratio = 1.85; 95% confidence interval = 1.30–2.65) and DFS (hazard ratio = 2.16; 95% confidence interval= 1.19–3.93). Significant differences in OS, PFS and DFS were not observed among the other patient groups (including CC versus AA, CC + CA versus AA and CA versus AA). Subgroup analysis of rs1801133 and rs1801131 showed that patients with CRC from Asian regions and Western regions demonstrated similar results. Conclusions The MTHFR rs1801133 polymorphism was not associated with the prognosis of patients with CRC; however, rs1801131 may be associated with the prognosis of patients with CRC. Well‐designed prospective studies are necessary to obtain a better understanding of the prognostic value of rs1801133 and rs1801131.
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Affiliation(s)
- Xin-Lin Chen
- School of Basic Medical Science, Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Yu-Mei Wang
- Department of Pharmacology, School of Chinese Material Medicine, Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Fei Zhao
- School of Basic Medical Science, Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Zheng Chen
- The Third Affiliated Hospital, Sun Yat-Sen University, Guangzhou, China
| | - Xiaofei Yang
- The Second Clinical College, Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Cong Sun
- Zhongshan School of Medicine, Sun Yat-Sen University, Guangzhou, China
| | - Yunpeng Gao
- Eugene McDermott Center for Human Growth & Development, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Tian-Ge Yang
- School of Acupuncture and Rehabilitation, Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Guo Tian
- School of Acupuncture and Rehabilitation, Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Yi-Ming Chen
- School of Basic Medical Science, Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Shui-Lian Zhu
- The First Clinical College, The First Affiliated Hospital, Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Xiao-Bing Lin
- Personnel Department, Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Feng-Bin Liu
- The First Clinical College, The First Affiliated Hospital, Guangzhou University of Chinese Medicine, Guangzhou, China
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Yu Y, Carey M, Pollett W, Green J, Dicks E, Parfrey P, Yilmaz YE, Savas S. The long-term survival characteristics of a cohort of colorectal cancer patients and baseline variables associated with survival outcomes with or without time-varying effects. BMC Med 2019; 17:150. [PMID: 31352904 PMCID: PMC6661748 DOI: 10.1186/s12916-019-1379-5] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/02/2019] [Accepted: 06/27/2019] [Indexed: 12/27/2022] Open
Abstract
BACKGROUND Colorectal cancer is the third most common cancer in the world. In this study, we assessed the long-term survival characteristics and prognostic associations and potential time-varying effects of clinico-demographic variables and two molecular markers (microsatellite instability (MSI) and BRAF Val600Glu mutation) in a population-based patient cohort followed up to ~ 19 years. METHODS The patient cohort included 738 incident cases diagnosed between 1999 and 2003. Cox models were used to analyze the association between the variables and a set of survival outcome measures (overall survival (OS), disease-specific survival (DSS), recurrence-free survival (RFS), metastasis-free survival (MFS), recurrence/metastasis-free survival (RMFS), and event-free survival (EFS)). Cox proportional hazard (PH) assumption was tested for all variables, and Cox models with time-varying effects were used if any departure from the PH assumption was detected. RESULTS During the follow-up, ~ 61% patients died from any cause, ~ 26% died from colorectal cancer, and ~ 10% and ~ 20% experienced recurrences and distant metastases, respectively. Stage IV disease and post-diagnostic recurrence or metastasis were strongly linked to risk of death from colorectal cancer. If a patient had survived the first 6 years without any disease-related event (i.e., recurrence, metastasis, or death from colorectal cancer), their risks became very minimal after this time period. Distinct sets of markers were associated with different outcome measures. In some cases, the effects by variables were constant throughout the follow-up. For example, MSI-high tumor phenotype and older age at diagnosis predicted longer MFS times consistently over the follow-up. However, in some other cases, the effects of the variables varied with time. For example, adjuvant radiotherapy treatment was associated with increased risk of metastasis in patients who received this treatment after 5.5 years post-diagnosis, but not before that. CONCLUSIONS This study describes the long-term survival characteristics of a prospective cohort of colorectal cancer patients, relationships between baseline variables and a detailed set of patient outcomes over a long time, and time-varying effects of a group of variables. The results presented advance our understanding of the long-term prognostic characteristics in colorectal cancer and are expected to inspire future studies and clinical care strategies.
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Affiliation(s)
- Yajun Yu
- Discipline of Genetics, Faculty of Medicine, Memorial University, 300 Prince Philip Drive, New Medical Education Building, St. John's, NL, A1B 3V6, Canada
| | - Megan Carey
- Discipline of Genetics, Faculty of Medicine, Memorial University, 300 Prince Philip Drive, New Medical Education Building, St. John's, NL, A1B 3V6, Canada
| | - William Pollett
- Discipline of Surgery, Faculty of Medicine, Memorial University, St. John's, NL, Canada
| | - Jane Green
- Discipline of Genetics, Faculty of Medicine, Memorial University, 300 Prince Philip Drive, New Medical Education Building, St. John's, NL, A1B 3V6, Canada
| | - Elizabeth Dicks
- Discipline of Medicine, Faculty of Medicine, Memorial University, St. John's, NL, Canada
| | - Patrick Parfrey
- Discipline of Medicine, Faculty of Medicine, Memorial University, St. John's, NL, Canada
| | - Yildiz E Yilmaz
- Discipline of Genetics, Faculty of Medicine, Memorial University, 300 Prince Philip Drive, New Medical Education Building, St. John's, NL, A1B 3V6, Canada.,Discipline of Medicine, Faculty of Medicine, Memorial University, St. John's, NL, Canada.,Department of Mathematics and Statistics, Faculty of Science, Memorial University, St. John's, NL, Canada
| | - Sevtap Savas
- Discipline of Genetics, Faculty of Medicine, Memorial University, 300 Prince Philip Drive, New Medical Education Building, St. John's, NL, A1B 3V6, Canada. .,Discipline of Oncology, Faculty of Medicine, Memorial University, St. John's, NL, Canada.
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Penney ME, Parfrey PS, Savas S, Yilmaz YE. A genome-wide association study identifies single nucleotide polymorphisms associated with time-to-metastasis in colorectal cancer. BMC Cancer 2019; 19:133. [PMID: 30738427 PMCID: PMC6368959 DOI: 10.1186/s12885-019-5346-5] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2018] [Accepted: 02/04/2019] [Indexed: 12/16/2022] Open
Abstract
Background Differentiating between cancer patients who will experience metastasis within a short time and who will be long-term survivors without metastasis is a critical aim in healthcare. The microsatellite instability (MSI)-high tumor phenotype is such a differentiator in colorectal cancer, as patients with these tumors are unlikely to experience metastasis. Our aim in this study was to determine if germline genetic variations could further differentiate colorectal cancer patients based on the long-term risk and timing of metastasis. Methods The patient cohort consisted of 379 stage I-III Caucasian colorectal cancer patients with microsatellite stable or MSI-low tumors. We performed univariable analysis on 810,622 common single nucleotide polymorphisms (SNPs) under different genetic models. Depending on the long-term metastasis-free survival probability estimates, we applied a mixture cure model, Cox proportional hazards regression model, or log-rank test. For SNPs reaching Bonferroni-corrected significance (p < 6.2 × 10− 8) having valid genetic models, multivariable analysis adjusting for significant baseline characteristics was conducted. Results After adjusting for significant baseline characteristics, specific genotypes of ten polymorphisms were significantly associated with time-to-metastasis. These polymorphisms are three intergenic SNPs, rs5749032 (p = 1.28 × 10− 10), rs2327990 (p = 9.59 × 10− 10), rs1145724 (p = 3 × 10− 8), and seven SNPs within the non-coding sequences of three genes: FHIT (p = 2.59 × 10− 9), EPHB1 (p = 8.23 × 10− 9), and MIR7515 (p = 4.87 × 10− 8). Conclusions Our results suggest novel associations of specific genotypes of SNPs with early metastasis in Caucasian colorectal cancer patients. These associations, once replicated in other patient cohorts, could assist in the development of personalized treatment strategies for colorectal cancer patients. Electronic supplementary material The online version of this article (10.1186/s12885-019-5346-5) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Michelle E Penney
- Discipline of Genetics, Faculty of Medicine, Memorial University of Newfoundland, St. John's, Canada
| | - Patrick S Parfrey
- Discipline of Medicine, Faculty of Medicine, Memorial University of Newfoundland, St. John's, Canada
| | - Sevtap Savas
- Discipline of Genetics, Faculty of Medicine, Memorial University of Newfoundland, St. John's, Canada.,Discipline of Oncology, Faculty of Medicine, Memorial University of Newfoundland, St. John's, Canada
| | - Yildiz E Yilmaz
- Discipline of Genetics, Faculty of Medicine, Memorial University of Newfoundland, St. John's, Canada. .,Discipline of Medicine, Faculty of Medicine, Memorial University of Newfoundland, St. John's, Canada. .,Department of Mathematics and Statistics, Faculty of Science, Memorial University of Newfoundland, St. John's, Canada.
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9
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Yang L, Xu M, Cui CB, Wei PH, Wu SZ, Cen ZJ, Meng XX, Huang QG, Xie ZC. Diagnostic and prognostic values of the mRNA expression of excision repair cross-complementation enzymes in hepatitis B virus-related hepatocellular carcinoma. Cancer Manag Res 2018; 10:5313-5328. [PMID: 30464628 PMCID: PMC6225908 DOI: 10.2147/cmar.s179043] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
Background The current study aims at using the whole genome expression profile chips for systematically investigating the diagnostic and prognostic values of excision repair cross-complementation (ERCC) genes in hepatitis B virus (HBV)-related hepatocellular carcinoma (HCC). Materials and methods Whole genome expression profile chips were obtained from the GSE14520. The receiver-operating characteristic (ROC) curve, survival analysis, and nomogram were used to investigate the diagnostic and prognostic values of ERCC genes. Investigation of the potential function of ERCC8 was carried out by gene set enrichment analysis (GSEA) and genome-wide coexpression analysis. Results ROC analysis suggests that six ERCC genes (ERCC1, ERCC2, ERCC3, ERCC4, ERCC5, and ERCC8) were dysregulated and may have potential to distinguish between HBV-related HCC tumor and paracancerous tissues (area under the curve of ROC ranged from 0.623 to 0.744). Survival analysis demonstrated that high ERCC8 expression was associated with a significantly decreased risk of recurrence (adjusted P=0.021; HR=0.643; 95% CI=0.442–0.937) and death (adjusted P=0.049; HR=0.631; 95% CI=0.399–0.998) in HBV-related HCC. Then, we also developed two nomograms for the HBV-related HCC individualized prognosis predictions. GSEA suggests that the high expression of ERCC8 may have involvement in the energy metabolism biological processes. As the genome-wide coexpression analysis and functional assessment of ERCC8 suggest, those coexpressed genes were significantly enriched in multiple biological processes of DNA damage and repair. Conclusion The present study indicates that six ERCC genes (ERCC1, ERCC2, ERCC3, ERCC4, ERCC5, and ERCC8) were dysregulated between HBV-related HCC tumor and paracancerous tissues and that the mRNA expression of ERCC8 may serve as a potential biomarker for the HBV-related HCC prognosis.
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Affiliation(s)
- Lu Yang
- Department of Epidemiology, Guangxi Medical University, Nanning 530021, Guangxi Zhuang Autonomous Region, People's Republic of China,
| | - Ming Xu
- Department of Human Anatomy and Histology and Embryology, Qilu Medical University, Zibo 255213, Shandong Province, People's Republic of China
| | - Chuan-Bao Cui
- Department of Epidemiology, Guangxi Medical University, Nanning 530021, Guangxi Zhuang Autonomous Region, People's Republic of China,
| | - Peng-Hai Wei
- Department of Epidemiology, Guangxi Medical University, Nanning 530021, Guangxi Zhuang Autonomous Region, People's Republic of China,
| | - Shu-Zhi Wu
- Department of Epidemiology, Guangxi Medical University, Nanning 530021, Guangxi Zhuang Autonomous Region, People's Republic of China,
| | - Zuo-Jie Cen
- Department of Epidemiology, Guangxi Medical University, Nanning 530021, Guangxi Zhuang Autonomous Region, People's Republic of China,
| | - Xing-Xing Meng
- Department of Epidemiology, Guangxi Medical University, Nanning 530021, Guangxi Zhuang Autonomous Region, People's Republic of China,
| | - Qiong-Guang Huang
- Department of Epidemiology, Guangxi Medical University, Nanning 530021, Guangxi Zhuang Autonomous Region, People's Republic of China,
| | - Zhi-Chun Xie
- Department of Epidemiology, Guangxi Medical University, Nanning 530021, Guangxi Zhuang Autonomous Region, People's Republic of China,
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10
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Yu Y, Cheng D, Parfrey P, Liu G, Savas S. Two functional indel polymorphisms in the promoter region of the Brahma gene (BRM) and disease risk and progression-free survival in colorectal cancer. PLoS One 2018; 13:e0198873. [PMID: 29894502 PMCID: PMC5997361 DOI: 10.1371/journal.pone.0198873] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2018] [Accepted: 05/25/2018] [Indexed: 01/28/2023] Open
Abstract
Background and objective The Brahma gene (BRM) encodes a catalytic ATPase subunit of the Switch/Sucrose non-fermentable (SWI/SNF) complex, which modulates gene expression and many important cellular processes. Two indel polymorphisms in the promoter region of BRM (BRM-741 and BRM-1321) are associated with its reduced expression and the risk of susceptibility or survival outcomes in multiple solid cancers. In this study, we have examined these variants in relation to susceptibility and survival outcomes in colorectal cancer. Methods Genotypes were obtained using TaqMan assays in 427 cases and 408 controls. Multivariate logistic and Cox regression models were fitted to examine the associations of the BRM-741 and BRM-1321 genotypes adjusting for relevant covariates. Sub-group analyses based on tumor location and patient sex were also performed. In all analyses, indels were examined individually as well as in combination. Results Our results showed that there was no association between the BRM polymorphisms and the risk of colorectal cancer. However, genotype combinations of the BRM-741 and BRM-1321 variants were associated with the risk of colon cancer. Particularly, patients having at least one variant allele had increased risk of colon cancer when compared to patients with the double wild-type genotype. In the survival analyses, BRM-741 heterozygosity was associated with longer progression-free survival time in the colorectal cancer patients. A stronger association was detected in the male patients under the recessive genetic model where the homozygosity for the variant allele of BRM-741 was associated with shorter progression-free survival time. Conclusions Our analyses suggest that BRM-741 and BRM-1321 indels are associated with the risk of developing colon cancer and the BRM-741 indel is associated with the disease progression in colorectal cancer patients, especially in the male patients. Although our results show a different relationship between these indels and colorectal cancer compared to other cancer sites, they also suggest that BRM and its promoter variants may have biological roles in susceptibility and survival outcomes in colorectal cancers. Performing further analyses in additional and larger cohorts are needed to confirm our conclusions.
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Affiliation(s)
- Yajun Yu
- Discipline of Genetics, Faculty of Medicine, Memorial University, St. John’s, Newfoundland and Labrador, Canada
| | - Dangxiao Cheng
- Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada
| | - Patrick Parfrey
- Clinical Epidemiology Unit, Faculty of Medicine, Memorial University, St. John’s, Newfoundland and Labrador, Canada
| | - Geoffrey Liu
- Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada
- Division of Medical Oncology and Hematology, Department of Medicine, Princess Margaret Cancer Centre and University of Toronto, Toronto, Ontario, Canada
- Epidemiology, Dalla Lana School of Public Health, University of Toronto, Toronto, Ontario, Canada
| | - Sevtap Savas
- Discipline of Genetics, Faculty of Medicine, Memorial University, St. John’s, Newfoundland and Labrador, Canada
- Discipline of Oncology, Faculty of Medicine, Memorial University, St. John’s, Newfoundland and Labrador, Canada
- * E-mail:
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11
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He Y, Penney ME, Negandhi AA, Parfrey PS, Savas S, Yilmaz YE. XRCC3 Thr241Met and TYMS variable number tandem repeat polymorphisms are associated with time-to-metastasis in colorectal cancer. PLoS One 2018; 13:e0192316. [PMID: 29394274 PMCID: PMC5796722 DOI: 10.1371/journal.pone.0192316] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2017] [Accepted: 01/20/2018] [Indexed: 01/13/2023] Open
Abstract
Background Metastasis is a major cause of mortality in cancer. Identifying prognostic factors that distinguish patients who will experience metastasis in the short-term and those that will be free of metastasis in the long-term is of particular interest in current medical research. The objective of this study was to examine if select genetic polymorphisms can differentiate colorectal cancer patients based on timing and long-term risk of metastasis. Methods The patient cohort consisted of 402 stage I-III colorectal cancer patients with microsatellite instability (MSI)-low (MSI-L) or microsatellite stable (MSS) tumors. We applied multivariable mixture cure model, which is the proper model when there is a substantial group of patients who remain free of metastasis in the long-term, to 26 polymorphisms. Time-dependent receiver operator characteristic (ROC) curve analysis was performed to determine the change in discriminatory accuracy of the models when the significant SNPs were included. Results After adjusting for significant baseline characteristics, two polymorphisms were significantly associated with time-to-metastasis: TT and TC genotypes of the XRCC3 Thr241Met (p = 0.042) and the 3R/3R genotype of TYMS 5’-UTR variable number tandem repeat (VNTR) (p = 0.009) were associated with decreased time-to-metastasis. ROC curves showed that the discriminatory accuracy of the model is increased slightly when these polymorphisms were added to the significant baseline characteristics. Conclusions Our results indicate XRCC3 Thr241Met and TYMS 5’-UTR VNTR polymorphisms are associated with time-to-metastasis, and may have potential biological roles in expediting the metastatic process. Once replicated, these associations could contribute to the development of precision medicine for colorectal cancer patients.
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Affiliation(s)
- Yanjing He
- Department of Mathematics and Statistics, Faculty of Science, Memorial University of Newfoundland, St. John's, Canada
- Discipline of Genetics, Faculty of Medicine, Memorial University of Newfoundland, St. John’s, Canada
| | - Michelle E. Penney
- Discipline of Genetics, Faculty of Medicine, Memorial University of Newfoundland, St. John’s, Canada
| | - Amit A. Negandhi
- Discipline of Genetics, Faculty of Medicine, Memorial University of Newfoundland, St. John’s, Canada
| | - Patrick S. Parfrey
- Discipline of Medicine, Faculty of Medicine, Memorial University of Newfoundland, St. John’s, Canada
| | - Sevtap Savas
- Discipline of Genetics, Faculty of Medicine, Memorial University of Newfoundland, St. John’s, Canada
- Discipline of Oncology, Faculty of Medicine, Memorial University of Newfoundland, St. John’s, Canada
| | - Yildiz E. Yilmaz
- Department of Mathematics and Statistics, Faculty of Science, Memorial University of Newfoundland, St. John's, Canada
- Discipline of Genetics, Faculty of Medicine, Memorial University of Newfoundland, St. John’s, Canada
- Discipline of Medicine, Faculty of Medicine, Memorial University of Newfoundland, St. John’s, Canada
- * E-mail:
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12
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Xu M, Liu Y, Li D, Wang X, Liang S, Zhang G, Yang X. Chinese C allele carriers of the ERCC5 rs1047768 polymorphism are more sensitive to platinum-based chemotherapy: a meta-analysis. Oncotarget 2018; 9:1248-1256. [PMID: 29416691 PMCID: PMC5787435 DOI: 10.18632/oncotarget.18981] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2016] [Accepted: 06/17/2017] [Indexed: 12/11/2022] Open
Abstract
It is suspected that ERCC5 rs1047768 and rs17655 polymorphisms influence the response to platinum-based chemotherapy. This meta-analysis was performed to summarize the scattered evidence regarding the association between these two polymorphisms and sensitivity to platinum-based treatment. Thirteen studies were included after a comprehensive literature search. The pooled odds ratios and 95% confidence intervals suggested that the C allele of the ERCC5 rs1047768 polymorphism is associated with elevated sensitivity to platinating agents, especially for Chinese patients. However, no difference among rs17655 genotypes could be detected.
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Affiliation(s)
- Meizhen Xu
- School of Biology and Basic Medical Sciences, Soochow University, Suzhou, China
| | - Yina Liu
- School of Biology and Basic Medical Sciences, Soochow University, Suzhou, China
| | - Dan Li
- Clinical Translational Research Center, Shanghai Pulmonary Hospital, Tongji University, Shanghai, China.,School of Life Science and Technology, Tongji University, Shanghai, China.,Present address: Jiayin BioTechnology Co., Ltd., Shanghai, China
| | | | | | - Gaochuan Zhang
- School of Biology and Basic Medical Sciences, Soochow University, Suzhou, China
| | - Xiaoqin Yang
- School of Biology and Basic Medical Sciences, Soochow University, Suzhou, China
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13
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Werdyani S, Yu Y, Skardasi G, Xu J, Shestopaloff K, Xu W, Dicks E, Green J, Parfrey P, Yilmaz YE, Savas S. Germline INDELs and CNVs in a cohort of colorectal cancer patients: their characteristics, associations with relapse-free survival time, and potential time-varying effects on the risk of relapse. Cancer Med 2017; 6:1220-1232. [PMID: 28544645 PMCID: PMC5463068 DOI: 10.1002/cam4.1074] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2017] [Revised: 03/13/2017] [Accepted: 03/16/2017] [Indexed: 12/24/2022] Open
Abstract
INDELs and CNVs are structural variations that may play roles in cancer susceptibility and patient outcomes. Our objectives were a) to computationally detect and examine the genome‐wide INDEL/CNV profiles in a cohort of colorectal cancer patients, and b) to examine the associations of frequent INDELs/CNVs with relapse‐free survival time. We also identified unique variants in 13 Familial Colorectal Cancer Type X (FCCX) cases. The study cohort consisted of 495 colorectal cancer patients. QuantiSNP and PennCNV algorithms were utilized to predict the INDELs/CNVs using genome‐wide signal intensity data. Duplex PCR was used to validate predictions for 10 variants. Multivariable Cox regression models were used to test the associations of 106 common variants with relapse‐free survival time. Score test and the multivariable Cox proportional hazards models with time‐varying coefficients were applied to identify the variants with time‐varying effects on the relapse‐free survival time. A total of 3486 distinct INDELs/CNVs were identified in the patient cohort. The majority of these variants were rare (83%) and deletion variants (81%). The results of the computational predictions and duplex PCR results were highly concordant (93–100%). We identified four promising variants significantly associated with relapse‐free survival time (P < 0.05) in the multivariable Cox proportional hazards regression models after adjustment for clinical factors. More importantly, two additional variants were identified to have time‐varying effects on the risk of relapse. Finally, 58 rare variants were identified unique to the FCCX cases; none of them were detected in more than one patient. This is one of the first genome‐wide analyses that identified the germline INDEL/CNV profiles in colorectal cancer patients. Our analyses identified novel variants and genes that can biologically affect the risk of relapse in colorectal cancer patients. Additionally, for the first time, we identified germline variants that can potentially be early‐relapse markers in colorectal cancer.
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Affiliation(s)
- Salem Werdyani
- Discipline of Genetics, Faculty of Medicine, Memorial University, St. John's, Newfoundland and Labrador, Canada
| | - Yajun Yu
- Discipline of Genetics, Faculty of Medicine, Memorial University, St. John's, Newfoundland and Labrador, Canada
| | - Georgia Skardasi
- Discipline of Genetics, Faculty of Medicine, Memorial University, St. John's, Newfoundland and Labrador, Canada
| | - Jingxiong Xu
- Department of Biostatistics, Princess Margaret Hospital, University of Toronto, Toronto, Ontario, Canada
| | | | - Wei Xu
- Department of Biostatistics, Princess Margaret Hospital, University of Toronto, Toronto, Ontario, Canada.,Dalla Lana School of Public Health, University of Toronto, Toronto, Ontario, Canada
| | - Elizabeth Dicks
- Clinical Epidemiology Unit, Faculty of Medicine, Memorial University, St. John's, Newfoundland and Labrador, Canada
| | - Jane Green
- Discipline of Genetics, Faculty of Medicine, Memorial University, St. John's, Newfoundland and Labrador, Canada.,Discipline of Oncology, Faculty of Medicine, Memorial University, St. John's, Newfoundland and Labrador, Canada
| | - Patrick Parfrey
- Clinical Epidemiology Unit, Faculty of Medicine, Memorial University, St. John's, Newfoundland and Labrador, Canada
| | - Yildiz E Yilmaz
- Discipline of Genetics, Faculty of Medicine, Memorial University, St. John's, Newfoundland and Labrador, Canada.,Clinical Epidemiology Unit, Faculty of Medicine, Memorial University, St. John's, Newfoundland and Labrador, Canada.,Department of Mathematics and Statistics, Faculty of Science, Memorial University, St. John's, Newfoundland and Labrador, Canada
| | - Sevtap Savas
- Discipline of Genetics, Faculty of Medicine, Memorial University, St. John's, Newfoundland and Labrador, Canada.,Discipline of Oncology, Faculty of Medicine, Memorial University, St. John's, Newfoundland and Labrador, Canada
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14
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Xiang T, Kang X, Gong Z, Bai W, Chen C, Zhang W. XPG genetic polymorphisms and clinical outcome of patients with advanced non-small cell lung cancer under platinum-based treatment: a meta-analysis of 12 studies. Cancer Chemother Pharmacol 2017; 79:791-800. [PMID: 28314991 DOI: 10.1007/s00280-017-3280-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2016] [Accepted: 03/07/2017] [Indexed: 01/10/2023]
Abstract
PURPOSE A number of studies on the relationship between xeroderma pigmentosum group G (XPG) polymorphisms and clinical outcomes in non-small cell cancer (NSCLC) have led to inconclusive results. This meta-analysis evaluates the predictive value of XPG polymorphisms on the treatment response rate and overall survival of patients with NSCLC. METHODS To measure the correlative strength of the relationship between XPG polymorphisms and outcomes of patients with NSCLC, we searched electronic databases, including PubMed and China National Knowledge Infrastructure, to retrieve studies up to August 2016. We also employed pooled odds ratios (ORs) and hazard ratios (HRs) corresponding to 95% confidence intervals (95% CIs). RESULTS Twelve studies involving 2877 patients with NSCLC were included: 8 studies involving 1473 patients examined the correlation between XPG polymorphisms and tumor response rate and 7 studies involving 2329 patients reported on the correlation of XPG polymorphisms with overall survival. None of the XPG His1104Asp(C>G)/His46His(C>T) polymorphisms exhibited a correlation with treatment response rate or overall survival. However, in a further stratified analysis by ethnicity, carriers of the 1104G allele were associated with good response among Asians in the homozygote model (GG vs. CC: OR = 1.57, 95% CI: 1.05-2.34, P = 0.027). Meanwhile, further stratified by ethnicity, His46His polymorphism was not associated with RR and OS in any genetic models. CONCLUSIONS No strong evidence was found to support the use of XPG polymorphisms as tumor response and prognostic factors of patients with NSCLC receiving a platinum-based treatment regimen, which is attributed to marginal association. Studies with large-scale and multiple ethnicities need to be conducted to verify the conclusion.
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Affiliation(s)
- Tianxin Xiang
- Department of Infectious Diseases, The First Affiliated Hospital of Nanchang University, Nanchang, China
| | - Xiuhua Kang
- Department of Respiratory Diseases, The First Affiliated Hospital of Nanchang University, Nanchang, China
| | - Zhenghua Gong
- Shenzhen Peking University and Hong Kong University of Science and Technology Medical Center, FuTian District, Shenzhen, China
| | - Wei Bai
- Department of Respiratory Diseases, The First Affiliated Hospital of Nanchang University, Nanchang, China
| | - Chuanhui Chen
- Department of Respiratory Diseases, The First Affiliated Hospital of Nanchang University, Nanchang, China
| | - Wei Zhang
- Department of Respiratory Diseases, The First Affiliated Hospital of Nanchang University, Nanchang, China.
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15
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Yeh CC, Lai CY, Chang SN, Hsieh LL, Tang R, Sung FC, Lin YK. Polymorphisms of MTHFR C677T and A1298C associated with survival in patients with colorectal cancer treated with 5-fluorouracil-based chemotherapy. Int J Clin Oncol 2017; 22:484-493. [DOI: 10.1007/s10147-016-1080-z] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2016] [Accepted: 12/19/2016] [Indexed: 02/07/2023]
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16
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Botticelli A, Borro M, Onesti CE, Strigari L, Gentile G, Cerbelli B, Romiti A, Occhipinti M, Sebastiani C, Lionetto L, Marchetti L, Simmaco M, Marchetti P, Mazzuca F. Degradation Rate of 5-Fluorouracil in Metastatic Colorectal Cancer: A New Predictive Outcome Biomarker? PLoS One 2016; 11:e0163105. [PMID: 27656891 PMCID: PMC5033390 DOI: 10.1371/journal.pone.0163105] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2016] [Accepted: 09/04/2016] [Indexed: 12/12/2022] Open
Abstract
Background 5-FU based chemotherapy is the most common first line regimen used for metastatic colorectal cancer (mCRC). Identification of predictive markers of response to chemotherapy is a challenging approach for drug selection. The present study analyzes the predictive role of 5-FU degradation rate (5-FUDR) and genetic polymorphisms (MTHFR, TSER, DPYD) on survival. Materials and Methods Genetic polymorphisms of MTHFR, TSER and DPYD, and the 5-FUDR of homogenous patients with mCRC were retrospectively studied. Genetic markers and the 5-FUDR were correlated with clinical outcome. Results 133 patients affected by mCRC, treated with fluoropyrimidine-based chemotherapy from 2009 to 2014, were evaluated. Patients were classified into three metabolic classes, according to normal distribution of 5-FUDR in more than 1000 patients, as previously published: poor-metabolizer (PM) with 5-FU-DR ≤ 0,85 ng/ml/106 cells/min (8 pts); normal metabolizer with 0,85 < 5-FU-DR < 2,2 ng/ml/106 cells/min (119 pts); ultra-rapid metabolizer (UM) with 5-FU-DR ≥ 2,2 ng/ml/106 cells/min (6 pts). PM and UM groups showed a longer PFS respect to normal metabolizer group (14.5 and 11 months respectively vs 8 months; p = 0.029). A higher G3-4 toxicity rate was observed in PM and UM, respect to normal metabolizer (50% in both PM and UM vs 18%; p = 0.019). No significant associations between genes polymorphisms and outcomes or toxicities were observed. Conclusion 5-FUDR seems to be significantly involved in predicting survival of patients who underwent 5-FU based CHT for mCRC. Although our findings require confirmation in large prospective studies, they reinforce the concept that individual genetic variation may allow personalized selection of chemotherapy to optimize clinical outcomes.
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Affiliation(s)
- Andrea Botticelli
- Department of Clinical and Molecular Medicine, “Sapienza” University of Rome, Rome, Italy
| | - Marina Borro
- Department of Neurosciences, Mental Health and Sensory Organs (NESMOS), “Sapienza” University of Rome, Rome, Italy
| | | | - Lidia Strigari
- Laboratory of Medical Physics and Expert Systems, Regina Elena National Cancer Institute, Rome, Italy
| | | | - Bruna Cerbelli
- Department of Radiological Oncological and Pathological Sciences, “Sapienza” University of Rome, Rome, Italy
| | - Adriana Romiti
- Department of Clinical and Molecular Medicine, “Sapienza” University of Rome, Rome, Italy
| | | | | | | | - Luca Marchetti
- Department of Medical Oncology, Policlinico Umberto I, Rome, Italy
| | - Maurizio Simmaco
- Department of Neurosciences, Mental Health and Sensory Organs (NESMOS), “Sapienza” University of Rome, Rome, Italy
| | - Paolo Marchetti
- Department of Clinical and Molecular Medicine, “Sapienza” University of Rome, Rome, Italy
- Medical Oncology Unit, Sant’Andrea Hospital, Rome, Italy
- Istituto Dermopatico dell’Immacolata-IRCCS, Rome, Italy
| | - Federica Mazzuca
- Department of Clinical and Molecular Medicine, “Sapienza” University of Rome, Rome, Italy
- Medical Oncology Unit, Sant’Andrea Hospital, Rome, Italy
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17
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Hua RX, Zhuo ZJ, Zhu J, Zhang SD, Xue WQ, Zhang JB, Xu HM, Li XZ, Zhang PF, He J, Jia WH. XPG Gene Polymorphisms Contribute to Colorectal Cancer Susceptibility: A Two-Stage Case-Control Study. J Cancer 2016; 7:1731-1739. [PMID: 27698911 PMCID: PMC5039395 DOI: 10.7150/jca.15602] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2016] [Accepted: 07/09/2016] [Indexed: 02/07/2023] Open
Abstract
Previous studies have reported that xeroderma pigmentosum group G (XPG) gene polymorphisms may modulate colorectal cancer (CRC) susceptibility. In this study, we performed a two-stage case-control study to comprehensively investigate the associations of five polymorphisms in the XPG gene with CRC risk in 1,901 cases and 1,976 controls from Southern China, including rs2094258 C>T, rs751402 C>T, rs2296147 T>C, rs1047768 T>C and rs873601 G>A. After combining data from two stages, we found that three of the studied polymorphisms (rs2094258 C>T, rs751402 C>T, and rs873601 G>A) were significantly associated with CRC susceptibility. After adjustment for age and gender, multivariate logistic regression analysis indicated that carriers of the rs2094258 T alleles had an increased CRC risk [CT vs. CC: adjusted odds ratio (OR)=1.17, 95% confidence interval (CI)=1.01-1.36; TT vs. CC: adjusted OR=1.49, 95% CI=1.18-1.89; TT vs. CT/CC: adjusted OR=1.38, 95% CI=1.10-1.72]. Likely, rs873601 A allele also conferred increased CRC susceptibility. In contrast, a protective association was identified between rs751402 C>T polymorphism and the risk of CRC. In summary, our results indicated that these three polymorphisms were found to associate with CRC susceptibility in a Southern Chinese population.
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Affiliation(s)
- Rui-Xi Hua
- Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Department of Experimental Research, Collaborative Innovation Center for Cancer Medicine, Guangzhou 510060, Guangdong, China
- Department of Oncology, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou 510080, Guangdong, China
| | - Zhen-Jian Zhuo
- Guangdong Province Key Laboratory of Pharmacodynamic Constituents of TCM and New Drugs Research, College of Pharmacy, Jinan University, Guangzhou 510632, Guangdong, China
| | - Jinhong Zhu
- Molecular Epidemiology Laboratory and Department of Laboratory Medicine, Harbin Medical University Cancer Hospital, Harbin 150040, Heilongjiang, China
| | - Shao-Dan Zhang
- Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Department of Experimental Research, Collaborative Innovation Center for Cancer Medicine, Guangzhou 510060, Guangdong, China
| | - Wen-Qiong Xue
- Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Department of Experimental Research, Collaborative Innovation Center for Cancer Medicine, Guangzhou 510060, Guangdong, China
| | - Jiang-Bo Zhang
- Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Department of Experimental Research, Collaborative Innovation Center for Cancer Medicine, Guangzhou 510060, Guangdong, China
| | - Hong-Mei Xu
- Reproductive Medical Center, Department of Obstetrics and Gynecology, Sun Yat-sen Memorial Hospital, Guangzhou 510120, Guangdong, China
| | - Xi-Zhao Li
- Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Department of Experimental Research, Collaborative Innovation Center for Cancer Medicine, Guangzhou 510060, Guangdong, China
| | - Pei-Fen Zhang
- Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Department of Experimental Research, Collaborative Innovation Center for Cancer Medicine, Guangzhou 510060, Guangdong, China
| | - Jing He
- Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Department of Experimental Research, Collaborative Innovation Center for Cancer Medicine, Guangzhou 510060, Guangdong, China
- Department of Pediatric Surgery, Guangzhou Institute of Pediatrics, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou 510623, Guangdong, China
| | - Wei-Hua Jia
- Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Department of Experimental Research, Collaborative Innovation Center for Cancer Medicine, Guangzhou 510060, Guangdong, China
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18
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Dan LA, Werdyani S, Xu J, Shestopaloff K, Hyde A, Dicks E, Younghusband B, Green J, Parfrey P, Xu W, Savas S. No associations of a set of SNPs in the Vascular Endothelial Growth Factor (VEGF) and Matrix Metalloproteinase (MMP) genes with survival of colorectal cancer patients. Cancer Med 2016; 5:2221-31. [PMID: 27334288 PMCID: PMC5055182 DOI: 10.1002/cam4.796] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2016] [Revised: 05/18/2016] [Accepted: 05/19/2016] [Indexed: 02/06/2023] Open
Abstract
In this study, we aimed to investigate the associations of genetic variations within select genes functioning in angiogenesis, lymph‐angiogenesis, and metastasis pathways and the risk of outcome in colorectal cancer patients. We followed a two‐stage analysis: First, 381 polymorphisms from 30 genes (eight Vascular Endothelial Growth Factor (VEGF) and 22 Matrix Metalloproteinase [MMP] genes) were investigated in the discovery cohort (n = 505). Then, 16 polymorphisms with the lowest P‐value in this analysis were investigated in a separate replication cohort (n = 247). Genotypes were obtained using the Illumina® HumanOmni‐1‐Quad (discovery cohort) and Sequenom MassArray® (replication cohort) platforms. The primary outcome measure was overall survival (OS). Kaplan–Meier, univariate and multivariable Cox regression methods were used to test the associations between genotypes and OS. Four SNPs (rs12365082, rs11225389, rs11225388, and rs2846707) had the univariate analysis P < 0.05 in both the discovery and replication cohorts. These SNPs are in linkage disequilibrium with each other to varying extent and are located in the MMP8 and MMP27 genes. In the multivariable analysis adjusting for age, stage, and microsatellite instability status, three of these SNPs (rs12365082, rs11225389, rs11225388) were independent predictors of OS (P < 0.05) in the discovery cohort. However, the same analysis in the replication cohort did not yield statistically significant results. Overall, while the genetic variations in the VEGF and MMP genes are attractive candidates as prognostic markers, our study showed no evidence of associations of a large set of SNPs in these genes and overall survival of colorectal cancer patients in our study.
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Affiliation(s)
- Lydia A Dan
- Discipline of Genetics, Faculty of Medicine, Memorial University, St. John's, Newfoundland, Canada
| | - Salem Werdyani
- Discipline of Genetics, Faculty of Medicine, Memorial University, St. John's, Newfoundland, Canada
| | - Jingxiong Xu
- Department of Biostatistics, Princess Margaret Hospital, University of Toronto, Toronto, Ontario, Canada
| | | | - Angela Hyde
- Discipline of Genetics, Faculty of Medicine, Memorial University, St. John's, Newfoundland, Canada
| | - Elizabeth Dicks
- Clinical Epidemiology Unit, Faculty of Medicine, Memorial University, St. John's, Newfoundland, Canada
| | - Ban Younghusband
- Discipline of Genetics, Faculty of Medicine, Memorial University, St. John's, Newfoundland, Canada
| | - Jane Green
- Discipline of Genetics, Faculty of Medicine, Memorial University, St. John's, Newfoundland, Canada
| | - Patrick Parfrey
- Clinical Epidemiology Unit, Faculty of Medicine, Memorial University, St. John's, Newfoundland, Canada
| | - Wei Xu
- Department of Biostatistics, Princess Margaret Hospital, University of Toronto, Toronto, Ontario, Canada.,Dalla Lana School of Public Health, University of Toronto, Toronto, Ontario, Canada
| | - Sevtap Savas
- Discipline of Genetics, Faculty of Medicine, Memorial University, St. John's, Newfoundland, Canada. .,Discipline of Oncology, Faculty of Medicine, Memorial University, St. John's, Newfoundland, Canada.
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19
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Wang F, Zhang SD, Xu HM, Zhu JH, Hua RX, Xue WQ, Li XZ, Wang TM, He J, Jia WH. XPG rs2296147 T>C polymorphism predicted clinical outcome in colorectal cancer. Oncotarget 2016; 7:11724-32. [PMID: 26887052 PMCID: PMC4905506 DOI: 10.18632/oncotarget.7352] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2015] [Accepted: 01/23/2016] [Indexed: 02/07/2023] Open
Abstract
Xeroderma pigmentosum group G (XPG), one of key components of nucleotide excision repair pathway (NER), is involved in excision repair of UV-induced DNA damage. Single nucleotide polymorphisms (SNPs) in the XPG gene have been reported to associate with the clinical outcome of various cancer patients. We aimed to assess the impact of four potentially functional SNPs (rs2094258 C>T, rs2296147 T>C, rs751402 G>A, and rs873601 G>A) in the XPG gene on prognosis in colorectal cancer (CRC) patients. A total of 1901 patients diagnosed with pathologically confirmed CRC were genotyped for four XPG polymorphisms. Cox proportional hazards model analysis controlled for several confounding factors was conducted to compute hazard ratios (HRs) and 95% confidence intervals (CIs). Of the four included SNPs, only rs2296147 was shown to significantly affect progression-free survival (PFS) in CRC. Patients carrying rs2296147 CT/TT genotype had a significantly shorter median 10 years PFS than those carrying CC genotype (88.5 months vs. 118.1 months), and an increased progression risk were observed with rs2296147 (HR = 1.324, 95% CI = 1.046-1.667). Moreover, none of the four SNPs were associated with overall survival. In conclusion, our study showed that XPG rs2296147 CT/TT variants conferred significant survival disadvantage in CRC patients in term of PFS. XPG rs2296147 polymorphism could be predictive of unfavorable prognosis of CRC patients.
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Affiliation(s)
- Fang Wang
- 1 Sun Yat-Sen University Cancer Center, State Key Laboratory of Oncology in South China, Department of Experimental Research, Collaborative Innovation Center for Cancer Medicine, Guangzhou 510060, Guangdong, China
| | - Shao-Dan Zhang
- 1 Sun Yat-Sen University Cancer Center, State Key Laboratory of Oncology in South China, Department of Experimental Research, Collaborative Innovation Center for Cancer Medicine, Guangzhou 510060, Guangdong, China
| | - Hong-Mei Xu
- 3 Reproductive Medical Center, Department of Obstetrics and Gynecology, Sun Yat-Sen Memorial Hospital, Guangzhou 510120, Guangdong, China
| | - Jin-Hong Zhu
- 4 Molecular Epidemiology Laboratory and Department of Laboratory Medicine, Harbin Medical University Cancer Hospital, Harbin 150081, Heilongjiang, China
| | - Rui-Xi Hua
- 5 Department of Oncology, The First Affiliated Hospital of Sun Yat-Sen University, Guangzhou 510080, Guangdong, China
| | - Wen-Qiong Xue
- 1 Sun Yat-Sen University Cancer Center, State Key Laboratory of Oncology in South China, Department of Experimental Research, Collaborative Innovation Center for Cancer Medicine, Guangzhou 510060, Guangdong, China
| | - Xi-Zhao Li
- 1 Sun Yat-Sen University Cancer Center, State Key Laboratory of Oncology in South China, Department of Experimental Research, Collaborative Innovation Center for Cancer Medicine, Guangzhou 510060, Guangdong, China
| | - Tong-Min Wang
- 1 Sun Yat-Sen University Cancer Center, State Key Laboratory of Oncology in South China, Department of Experimental Research, Collaborative Innovation Center for Cancer Medicine, Guangzhou 510060, Guangdong, China
| | - Jing He
- 1 Sun Yat-Sen University Cancer Center, State Key Laboratory of Oncology in South China, Department of Experimental Research, Collaborative Innovation Center for Cancer Medicine, Guangzhou 510060, Guangdong, China
- 2 Department of Pediatric Surgery, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou 510623, Guangdong, China
| | - Wei-Hua Jia
- 1 Sun Yat-Sen University Cancer Center, State Key Laboratory of Oncology in South China, Department of Experimental Research, Collaborative Innovation Center for Cancer Medicine, Guangzhou 510060, Guangdong, China
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Glutathione S-transferase M1 null genotype related to poor prognosis of colorectal cancer. Tumour Biol 2016; 37:10229-34. [DOI: 10.1007/s13277-015-4676-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2015] [Accepted: 12/16/2015] [Indexed: 12/11/2022] Open
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Haerian BS, Haerian MS. Evaluation of association studies and meta-analyses of MTHFR gene polymorphisms in colorectal cancer. Pharmacogenomics 2016; 16:413-25. [PMID: 25823789 DOI: 10.2217/pgs.14.177] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
There is a discrepancy between the results of 89 original studies and 15 meta-analyses investigating the association of MTHFR rs1801133 and rs1801131 polymorphisms with colorectal cancer (CRC) risk. We examined this hypothesis through meta-analyses of both loci and their diplotypes as well as evaluation of previous meta-analyses. The present meta-analysis showed that rs1801133 and rs1801131 might be CRC susceptibility variants in Americans and Australians and rs1801133 in Brazilians and Japanese. A strong linkage disequilibrium was observed between both loci and their diplotypes were associated with CRC risk. Evaluation of 15 meta-analyses showed a high discrepancy among their findings, mainly caused by population stratification of original studies and data analysis strategies in meta-analysis. Population stratification was more dominant in the studies from Australia, America and Brazil leading to false positive or negative results. In conclusion, these loci alone might modify the development of CRC in some ethnicities.
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Affiliation(s)
- Batoul Sadat Haerian
- Department of Pharmacology, Faculty of Medicine, University of Malaya, Kuala Lumpur, Malaysia
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Mohideen AMSH, Dicks E, Parfrey P, Green R, Savas S. Mitochondrial DNA polymorphisms, its copy number change and outcome in colorectal cancer. BMC Res Notes 2015; 8:272. [PMID: 26116242 PMCID: PMC4482280 DOI: 10.1186/s13104-015-1250-5] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2015] [Accepted: 06/17/2015] [Indexed: 12/14/2022] Open
Abstract
Background Mitochondrion is a small organelle inside the eukaryotic cells. It has its own genome (mtDNA) and encodes for proteins that are critical for energy production and cellular metabolism. Mitochondrial dysfunctions have been implicated in cancer progression and may be related to poor prognosis in cancer patients. In this study we hypothesized that genetic variations in mtDNA are associated with clinical outcome in colorectal cancer patients. Methods We tested the associations of six mtDNA polymorphisms [MitoT479C, MitoT491C, MitoT10035C, MitoA13781G, 10398 (A/G), and 16189 (T/C)] and the mtDNA copy number change with overall survival (OS) and disease-free survival (DFS) times. Two mtDNA polymorphisms were genotyped using the TaqMan® SNP genotyping technique and the genotypes for the remaining four mtDNA polymorphisms were obtained by the Illumina® HumanOmni1-Quad genome wide SNP genotyping platform in 536 patients. The mtDNA copy number change (in tumor tissues with respect to non-tumor tissues) was estimated using the quantitative real time polymerase chain reaction for 274 patients. Associations of these mtDNA variations with OS and DFS were tested using the Cox regression method. Results In both univariate and multivariable analyses, none of the six mtDNA polymorphisms were associated with OS or DFS. 39.6 and 60.4% of the patients had increased and decreased mtDNA copy number in their tumor tissues when compared to their non-tumor rectum or colon tissues, respectively. However, in contrast to previous findings, the change in the mtDNA copy number was associated with neither OS nor DFS in our patient cohort. Conclusions Our results suggest that the mitochondrial genetic markers investigated in this study are not associated with outcome in colorectal cancer. Electronic supplementary material The online version of this article (doi:10.1186/s13104-015-1250-5) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Asan Meera Sahib Haja Mohideen
- Discipline of Genetics, Faculty of Medicine, Memorial University of Newfoundland, 300 Prince Philip Drive, HSC, Room H4333, St. John's, NL, A1B 3V6, Canada.
| | - Elizabeth Dicks
- Clinical Epidemiology Unit, Faculty of Medicine, Memorial University of Newfoundland, St. John's, NL, Canada.
| | - Patrick Parfrey
- Clinical Epidemiology Unit, Faculty of Medicine, Memorial University of Newfoundland, St. John's, NL, Canada.
| | - Roger Green
- Discipline of Genetics, Faculty of Medicine, Memorial University of Newfoundland, 300 Prince Philip Drive, HSC, Room H4333, St. John's, NL, A1B 3V6, Canada.
| | - Sevtap Savas
- Discipline of Genetics, Faculty of Medicine, Memorial University of Newfoundland, 300 Prince Philip Drive, HSC, Room H4333, St. John's, NL, A1B 3V6, Canada. .,Discipline of Oncology, Faculty of Medicine, Memorial University of Newfoundland, St. John's, NL, Canada.
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A Survival Association Study of 102 Polymorphisms Previously Associated with Survival Outcomes in Colorectal Cancer. BIOMED RESEARCH INTERNATIONAL 2015; 2015:968743. [PMID: 26064972 PMCID: PMC4443940 DOI: 10.1155/2015/968743] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/05/2015] [Accepted: 04/06/2015] [Indexed: 12/31/2022]
Abstract
Several published studies identified associations of a number of polymorphisms with a variety of survival outcomes in colorectal cancer. In this study, we aimed to explore 102 previously reported common genetic polymorphisms and their associations with overall survival (OS) and disease-free survival (DFS) in a colorectal cancer patient cohort from Newfoundland (n = 505). Genotypes were obtained using a genomewide SNP genotyping platform. For each polymorphism, the best possible genetic model was estimated for both overall survival and disease-free survival using a previously published approach. These SNPs were then analyzed under their genetic models by Cox regression method. Correction for multiple comparisons was performed by the False Discovery Rate (FDR) method. Univariate analysis results showed that RRM1-rs12806698, IFNGR1-rs1327474, DDX20-rs197412, and PTGS2-rs5275 polymorphisms were nominally associated with OS or DFS (p < 0.01). In stage-adjusted analysis, the nominal associations of DDX20-rs197412, PTGS2-rs5275, and HSPA5-rs391957 with DFS were detected. However, after FDR correction none of these polymorphisms remained significantly associated with the survival outcomes. We conclude that polymorphisms investigated in this study are not associated with OS or DFS in our colorectal cancer patient cohort.
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Xu W, Xu J, Shestopaloff K, Dicks E, Green J, Parfrey P, Green R, Savas S. A genome wide association study on Newfoundland colorectal cancer patients' survival outcomes. Biomark Res 2015; 3:6. [PMID: 25866641 PMCID: PMC4393623 DOI: 10.1186/s40364-015-0031-6] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2014] [Accepted: 02/23/2015] [Indexed: 01/14/2023] Open
Abstract
Background In this study we performed genome-wide association studies to identify candidate SNPs that may predict the risk of disease outcome in colorectal cancer. Methods Patient cohort consisted of 505 unrelated patients with Caucasian ancestry. Germline DNA samples were genotyped using the Illumina® human Omni-1quad SNP chip. Associations of SNPs with overall and disease free survivals were examined primarily for 431 patients with microsatellite instability-low (MSI-L) or stable (MSS) colorectal tumors using Cox proportional hazards method adjusting for clinical covariates. Bootstrap method was applied for internal validation of results. As exploratory analyses, association analyses for the colon (n = 334) and rectal (n = 171) cancer patients were also performed. Results As a result, there was no SNP that reached the genomewide significance levels (p < 5x10−8) in any of the analyses. A small number of genetic markers (n = 10) showed nominal associations (p <10−6) for MSS/MSI-L, colon, or rectal cancer patient groups. These markers were located in two non-coding RNA genes or intergenic regions and none were amino acid substituting polymorphisms. Bootstrap analysis for the MSS/MSI-L cohort data suggested the robustness of the observed nominal associations. Conclusions Likely due to small number of patients, our study did not identify an acceptable level of association of SNPs with outcome in MSS/MSI-L, colon, or rectal cancer patients. A number of SNPs with sub-optimal p-values were, however, identified; these loci may be promising and examined in other larger-sized patient cohorts. Electronic supplementary material The online version of this article (doi:10.1186/s40364-015-0031-6) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Wei Xu
- Department of Biostatistics, Princess Margaret Cancer Centre, Toronto, ON Canada M5G 2 M9 ; Dalla Lana School of Public Health, University of Toronto, Toronto, ON Canada M5T 3M7
| | - Jingxiong Xu
- Department of Biostatistics, Princess Margaret Cancer Centre, Toronto, ON Canada M5G 2 M9 ; Dalla Lana School of Public Health, University of Toronto, Toronto, ON Canada M5T 3M7
| | | | - Elizabeth Dicks
- Clinical Epidemiology Unit, Faculty of Medicine, Memorial University, St. John's, NL Canada A1B 3V6
| | - Jane Green
- Discipline of Genetics, Faculty of Medicine, Memorial University, St. John's, NL Canada A1B 3 V6
| | - Patrick Parfrey
- Clinical Epidemiology Unit, Faculty of Medicine, Memorial University, St. John's, NL Canada A1B 3V6
| | - Roger Green
- Discipline of Genetics, Faculty of Medicine, Memorial University, St. John's, NL Canada A1B 3 V6
| | - Sevtap Savas
- Discipline of Genetics, Faculty of Medicine, Memorial University, St. John's, NL Canada A1B 3 V6 ; Discipline of Oncology, Faculty of Medicine, Memorial University, St. John's, NL Canada A1B 3 V6
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Rao KS, Paul A, Kumar ASA, Umamaheswaran G, Dubashi B, Gunaseelan K, Dkhar SA. Allele and genotype distributions of DNA repair gene polymorphisms in South Indian healthy population. BIOMARKERS IN CANCER 2014; 6:29-35. [PMID: 25520562 PMCID: PMC4259864 DOI: 10.4137/bic.s19681] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/31/2014] [Revised: 11/11/2014] [Accepted: 11/13/2014] [Indexed: 12/11/2022]
Abstract
Various DNA repair pathways protect the structural and chemical integrity of the human genome from environmental and endogenous threats. Polymorphisms of genes encoding the proteins involved in DNA repair have been found to be associated with cancer risk and chemotherapeutic response. In this study, we aim to establish the normative frequencies of DNA repair genes in South Indian healthy population and compare with HapMap populations. Genotyping was done on 128 healthy volunteers from South India, and the allele and genotype distributions were established. The minor allele frequency of Xeroderma pigmentosum group A (XPA) G23A, Excision repair cross-complementing 2 (ERCC2)/Xeroderma pigmentosum group D (XPD) Lys751Gln, Xeroderma pigmentosum group G (XPG) His46His, XPG Asp1104His, and X-ray repair cross-complementing group 1 (XRCC1) Arg399Gln polymorphisms were 49.2%, 36.3%, 48.0%, 23.0%, and 34.0% respectively. Ethnic variations were observed in the frequency distribution of these polymorphisms between the South Indians and other HapMap populations. The present work forms the groundwork for cancer association studies and biomarker identification for treatment response and prognosis.
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Affiliation(s)
- Katiboina Srinivasa Rao
- Department of Pharmacology, Jawaharlal Institute of Postgraduate Medical Education and Research (JIPMER), Pondicherry, India
| | - Abialbon Paul
- Department of Pharmacology, Jawaharlal Institute of Postgraduate Medical Education and Research (JIPMER), Pondicherry, India
| | - Annan Sudarsan Arun Kumar
- Department of Pharmacology, Jawaharlal Institute of Postgraduate Medical Education and Research (JIPMER), Pondicherry, India
| | - Gurusamy Umamaheswaran
- Department of Pharmacology, Jawaharlal Institute of Postgraduate Medical Education and Research (JIPMER), Pondicherry, India
| | - Biswajit Dubashi
- Department of Medical Oncology, Jawaharlal Institute of Postgraduate Medical Education and Research (JIPMER), Pondicherry, India
| | - Karunanithi Gunaseelan
- Department of Radiotherapy, Jawaharlal Institute of Postgraduate Medical Education and Research (JIPMER), Pondicherry, India
| | - Steven Aibor Dkhar
- Department of Pharmacology, Jawaharlal Institute of Postgraduate Medical Education and Research (JIPMER), Pondicherry, India
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Haja Mohideen AMS, Hyde A, Squires J, Wang J, Dicks E, Younghusband B, Parfrey P, Green R, Savas S. Examining the polymorphisms in the hypoxia pathway genes in relation to outcome in colorectal cancer. PLoS One 2014; 9:e113513. [PMID: 25405996 PMCID: PMC4236175 DOI: 10.1371/journal.pone.0113513] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2014] [Accepted: 10/29/2014] [Indexed: 12/21/2022] Open
Abstract
Introduction Colorectal cancer is a common malignancy. Identification of genetic prognostic markers may help prognostic estimations in colorectal cancer. Genes that regulate response to hypoxia and other genes that are regulated under the hypoxic conditions have been shown to play roles in cancer progression. In this study, we hypothesized that genetic variations in the hypoxia pathway genes were associated with the risk of outcome in colorectal cancer patients. Methods This study was performed in two phases. In the first phase, 49 SNPs from six hypoxia pathway genes (HIF1A, HIF1B, HIF2A, LOX, MIF and CXCL12) in 272 colorectal cancer patients were analyzed. In the second phase, 77 SNPs from seven hypoxia pathway genes (HIF1A, HIF1B, HIF2A, HIF2B, HIF3A, LOX and CXCL12) were analyzed in an additional cohort of 535 patients. Kaplan Meier, Cox univariate and multivariable regression analyses were performed to analyze the relationship between the SNPs and overall survival (OS), disease free survival (DFS) or disease specific survival (DSS). Since this was a hypothesis-generating study, no correction for multiple testing was applied. Results In phase I, one SNP (HIF2A rs11125070) was found to be associated with DFS in multivariable analysis; yet association of a proxy polymorphism (HIF2A rs4953342) was not detected in the phase II patient cohort. In phase II, associations of two SNPs (HIF2A rs4953352 and HIF2B rs12593988) were significant in both OS and DFS multivariable analyses. However, association of HIF2A rs4953352 was not replicated in the phase I cohort using a proxy SNP (HIF2A rs6706003). Conclusion Overall, our study did not find a convincing evidence of association of the investigated polymorphisms with the disease outcomes in colorectal cancer.
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Affiliation(s)
- Asan M. S. Haja Mohideen
- Discipline of Genetics, Faculty of Medicine, Memorial University of Newfoundland, St. John's, NL, Canada
| | - Angela Hyde
- Discipline of Genetics, Faculty of Medicine, Memorial University of Newfoundland, St. John's, NL, Canada
| | - Jessica Squires
- Discipline of Genetics, Faculty of Medicine, Memorial University of Newfoundland, St. John's, NL, Canada
| | - Jing Wang
- Division of Community Health and Humanities, Faculty of Medicine, Memorial University of Newfoundland, St. John's, NL, Canada
| | - Elizabeth Dicks
- Clinical Epidemiology Unit, Faculty of Medicine, Memorial University of Newfoundland, St. John's, NL, Canada
| | - Ban Younghusband
- Discipline of Genetics, Faculty of Medicine, Memorial University of Newfoundland, St. John's, NL, Canada
| | - Patrick Parfrey
- Clinical Epidemiology Unit, Faculty of Medicine, Memorial University of Newfoundland, St. John's, NL, Canada
| | - Roger Green
- Discipline of Genetics, Faculty of Medicine, Memorial University of Newfoundland, St. John's, NL, Canada
| | - Sevtap Savas
- Discipline of Genetics, Faculty of Medicine, Memorial University of Newfoundland, St. John's, NL, Canada
- Discipline of Oncology, Faculty of Medicine, Memorial University of Newfoundland, St. John's, NL, Canada
- * E-mail:
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MTHFR-1298 A>C (rs1801131) is a predictor of survival in two cohorts of stage II/III colorectal cancer patients treated with adjuvant fluoropyrimidine chemotherapy with or without oxaliplatin. THE PHARMACOGENOMICS JOURNAL 2014; 15:219-25. [DOI: 10.1038/tpj.2014.64] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/02/2014] [Revised: 08/05/2014] [Accepted: 09/05/2014] [Indexed: 11/08/2022]
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Custodio A, Moreno-Rubio J, Aparicio J, Gallego-Plazas J, Yaya R, Maurel J, Rodríguez-Salas N, Burgos E, Ramos D, Calatrava A, Andrada E, Díaz-López E, Sánchez A, Madero R, Cejas P, Feliu J. Pharmacogenetic Predictors of Outcome in Patients with Stage II and III Colon Cancer Treated with Oxaliplatin and Fluoropyrimidine-Based Adjuvant Chemotherapy. Mol Cancer Ther 2014; 13:2226-37. [DOI: 10.1158/1535-7163.mct-13-1109] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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