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Patini R, Cordaro M, Marchesini D, Scilla F, Gioco G, Rupe C, D'Agostino MA, Lajolo C. Is Systemic Immunosuppression a Risk Factor for Oral Cancer? A Systematic Review and Meta-Analysis. Cancers (Basel) 2023; 15:3077. [PMID: 37370688 DOI: 10.3390/cancers15123077] [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: 04/30/2023] [Revised: 05/30/2023] [Accepted: 06/01/2023] [Indexed: 06/29/2023] Open
Abstract
Even if the relationship between immunosuppression and increased incidence of systemic cancers is well known, there is less awareness about the risk of developing oral cancer in immunosuppressed patients. The aim of this review was to evaluate the association between immunosuppression and the development of oral cancer. Two authors independently and, in duplicate, conducted a systematic literature review of international journals and electronic databases (MEDLINE via OVID, Scopus, and Web of Science) from their inception to 28 April 2023. The assessment of risk of bias and overall quality of evidence was performed using the Newcastle-Ottawa Scale and GRADE system. A total of 2843 articles was identified, of which 44 met the inclusion criteria and were included in either the qualitative or quantitative analysis. The methodological quality of the included studies was generally high or moderate. The quantitative analysis of the studies revealed that immunosuppression should be considered a risk factor for the development of oral cancer, with a percentage of increased risk ranging from 0.2% to 1% (95% CI: 0.2% to 1.4%). In conclusion, the results suggest that a constant and accurate follow-up should be reserved for all immunosuppressed patients as a crucial strategy to intercept lesions that have an increased potential to evolve into oral cancer.
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Affiliation(s)
- Romeo Patini
- Department of Head, Neck and Sense Organs, School of Dentistry, Catholic University of Sacred Heart, Fondazione Policlinico Universitario "A. Gemelli"-IRCCS Rome, 00135 Rome, Italy
| | - Massimo Cordaro
- Department of Head, Neck and Sense Organs, School of Dentistry, Catholic University of Sacred Heart, Fondazione Policlinico Universitario "A. Gemelli"-IRCCS Rome, 00135 Rome, Italy
| | - Denise Marchesini
- Department of Head, Neck and Sense Organs, School of Dentistry, Catholic University of Sacred Heart, Fondazione Policlinico Universitario "A. Gemelli"-IRCCS Rome, 00135 Rome, Italy
| | - Francesco Scilla
- Department of Head, Neck and Sense Organs, School of Dentistry, Catholic University of Sacred Heart, Fondazione Policlinico Universitario "A. Gemelli"-IRCCS Rome, 00135 Rome, Italy
| | - Gioele Gioco
- Department of Head, Neck and Sense Organs, School of Dentistry, Catholic University of Sacred Heart, Fondazione Policlinico Universitario "A. Gemelli"-IRCCS Rome, 00135 Rome, Italy
| | - Cosimo Rupe
- Department of Head, Neck and Sense Organs, School of Dentistry, Catholic University of Sacred Heart, Fondazione Policlinico Universitario "A. Gemelli"-IRCCS Rome, 00135 Rome, Italy
| | - Maria Antonietta D'Agostino
- Department of Geriatric and Orthopedic Sciences, Catholic University of Sacred Heart, Fondazione Policlinico Universitario "A. Gemelli"-IRCCS Rome, 00135 Rome, Italy
| | - Carlo Lajolo
- Department of Head, Neck and Sense Organs, School of Dentistry, Catholic University of Sacred Heart, Fondazione Policlinico Universitario "A. Gemelli"-IRCCS Rome, 00135 Rome, Italy
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Mohtasham N, Najafi-Ghobadi K, Abbaszadeh H. The XRCC1 Arg194Trp polymorphism was associated with the risk of head and neck squamous cell carcinoma development: Results from a systematic review and meta-analysis. Cancer Rep (Hoboken) 2023; 6:e1776. [PMID: 36573562 PMCID: PMC10026292 DOI: 10.1002/cnr2.1776] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2022] [Revised: 12/05/2022] [Accepted: 12/13/2022] [Indexed: 12/28/2022] Open
Abstract
BACKGROUND The X-ray repair cross complementing group 1 (XRCC1) is a DNA repair gene. Various studies have examined the association between XRCC1 Arg194Trp polymorphism and head and neck squamous cell carcinoma (HNSCC) susceptibility with contradictory results. So, this systematic review and meta-analysis aimed to assess whether variants of this polymorphism increase the HNSCC risk or not. RECENT FINDINGS Thirty three studies consisting of 14282 subjects (6012 cases and 8270 controls) were included in this meta-analysis. Variants of XRCC1 Arg194Trp polymorphism were associated with increased HNSCC risk and the associations were significant based on heterozygous and dominant models (heterozygous model: OR = 1.182, 95%CI = 1.015-1.377, P = 0.032; homozygous model: OR = 1.274, 95%CI = 0.940-1.727, P = 0.119; dominant model: OR = 1.194, 95%CI = 1.027-1.388, P = 0.021; recessive model: OR = 1.181, 95%CI = 0.885-1.576, P = 0.119). There were significant associations between variants of this polymorphism and HNSCC risk based on Asian ethnicity under dominant model, hospital control source under different genetic models, PCR-RFLP genotyping method under dominant model and oral cavity tumor site under heterozygous and dominant models. OBJECTIVE The X-ray repair cross complementing group 1 (XRCC1) is a DNA repair gene. Various studies have examined the association between XRCC1 Arg194Trp polymorphism and head and neck squamous cell carcinoma (HNSCC) susceptibility with contradictory results. So, this systematic review and meta-analysis aimed to assess whether variants of this polymorphism increase the HNSCC risk or not. METHODS A systematic search of the literatures published till April 2022 was conducted using Google Scholar, Scopus, PubMed, Web of Science, Cochrane Library and Embase databases. The heterogeneity was assessed with the I-Square statistic. A random effects model or fixed effects model was used to analyze the data. Data were reported by odds ratio (OR) and 95% confidence interval (CI). The p value was considered significant if p < .05. RESULTS Thirty three studies consisting of 14 282 subjects (6012 cases and 8270 controls) were included in this meta-analysis. Variants of XRCC1 Arg194Trp polymorphism were associated with increased HNSCC risk and the associations were significant based on heterozygous and dominant models (heterozygous model: OR = 1.182, 95%CI = 1.015-1.377, p = .032; homozygous model: OR = 1.274, 95%CI = 0.940-1.727, p = .119; dominant model: OR = 1.194, 95%CI = 1.027-1.388, p = .021; recessive model: OR = 1.181, 95%CI = 0.885-1.576, p = .119). There were significant associations between variants of this polymorphism and HNSCC risk based on Asian ethnicity under dominant model, hospital control source under different genetic models, PCR-RFLP genotyping method under dominant model and oral cavity tumor site under heterozygous and dominant models. CONCLUSION Variants of XRCC1 Arg194Trp polymorphism were significantly associated with increased risk of HNSCC development based on heterozygous and dominant genetic models.
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Affiliation(s)
- Nooshin Mohtasham
- Oral and Maxillofacial Diseases Research Center, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Khadijeh Najafi-Ghobadi
- Department of Biostatistics, School of Public Health, Hamadan University of Medical Sciences, Hamadan, Iran
| | - Hamid Abbaszadeh
- Department of Oral and Maxillofacial Pathology, School of Dentistry, Birjand University of Medical Sciences, Birjand, Iran
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Association of XRCC3, XRCC4, BAX, and BCL-2 Polymorphisms with the Risk of Breast Cancer. Int J Breast Cancer 2022; 2022:5817841. [PMID: 35320970 PMCID: PMC8938079 DOI: 10.1155/2022/5817841] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2021] [Revised: 12/06/2021] [Accepted: 12/20/2021] [Indexed: 11/23/2022] Open
Abstract
Background Breast cancer is the most common malignancy in women. Genetic risk factors associated with breast cancer incidence have been identified. Aims This study is aimed at determining the association of XRCC3 Thr241Met (rs861539), XRCC4 G(-1394) T (rs6869366) DNA repair and BAX G(-248) A (rs4645878), and BCL2 C(-938) A (rs2279115) apoptotic gene polymorphisms with breast cancer. Materials and Methods Genetic analysis was performed using peripheral blood samples. Gene polymorphisms were detected by using polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) technique. 175 patients and 158 healthy controls were enrolled in the study. Results Breast cancer risk was 5.43 times more in individuals with AA genotype of Bax G(-248) A (rs4645878) (P = 0.002). The risk of metastasis was 11 times with this genotype. It was associated with 6 times more risk of having a tumor larger than 2 cm. The risk of breast cancer was 2.77 times more in individuals carrying the Met/Met genotype of XRCC3 Thr241Met (rs861539) (P = 0.009). The risk of having advanced clinical stage (stage III+IV) with the Met/Met genotype was 4 times more increased. No relationship with breast cancer was found with XRCC4 G(-1394) T (rs6869366) and BCL2 C(-938) A (rs2279115) gene polymorphisms. Conclusion Multicenter trials using subjects with genetic variations are needed to establish the relationship between breast cancer and single gene polymorphism.
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Association between RAD51, XRCC2 and XRCC3 gene polymorphisms and risk of ovarian cancer: a case control and an in silico study. Mol Biol Rep 2021; 48:4209-4220. [PMID: 34097201 DOI: 10.1007/s11033-021-06434-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2021] [Accepted: 05/21/2021] [Indexed: 12/28/2022]
Abstract
Homologous recombination (HR) is one of the important mechanisms in repairing double-strand breaks to maintain genomic integrity and DNA stability from the cytotoxic effects and mutations. Various studies have reported that single nucleotide polymorphisms (SNPs) in the HR-associated genes may have a significant association with ovarian cancer (OCa) risk but the results were inconclusive. In the present study, five polymorphisms of HR-associated genes (RAD51, XRCC2 and XRCC3) were genotyped by allelic discrimination assay in 200 OCa cases and 200 healthy individuals. The association with OCa risk was evaluated by unconditional logistic regression analyses. The results revealed that the mutant allele in both rs1801320 (CC) and rs1801321 (TT) of RAD51 gene was associated with increased risk of OCa (odds ratio [OR] 3.79, 95% confidence interval [CI] 1.21-11.78, p = 0.014 and OR 1.61, 95% CI 1.06-2.45, p = 0.025, respectively). Moreover, a significant association of TT allele (OR 4.68, 95% CI 1.27-17.15, p = 0.011) of rs3218536 of XRCC2 gene with OCa was observed. Stratified analysis results showed that patients with early menarche and stages 3 and 4 were found to be associated with rs1801321 of RAD51 gene and rs1799794 of XRCC3 gene. In silico analysis predicted that the two missense SNPs (rs3218536 and rs1799794) were found to have an impact on the protein structure, stability and function. The present study suggested that RAD51 and XRCC2 gene polymorphisms might have an impact on the OCa risk in the South Indian population. However, studies with a larger sample and on different populations are needed to support the conclusions.
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Balabanski L, Serbezov D, Nikolova D, Antonova O, Nesheva D, Hammoudeh Z, Vazharova R, Karachanak-Yankova S, Staneva R, Mihaylova M, Damyanova V, Hadjidekova S, Toncheva D. Centenarian Exomes as a Tool for Evaluating the Clinical Relevance of Germline Tumor Suppressor Mutations. Technol Cancer Res Treat 2020; 19:1533033820911082. [PMID: 32233832 PMCID: PMC7132786 DOI: 10.1177/1533033820911082] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022] Open
Abstract
Objectives: The aim of the present study was to evaluate the clinical relevance of mutations in
tumor suppressor genes using whole-exome sequencing data from centenarians and young
healthy individuals. Methods: Two pools, one of centenarians and one of young individuals, were constructed and
whole-exome sequencing was performed. We examined the whole-exome sequencing data of
Bulgarian individuals for carriership of tumor suppressor gene variants. Results: Of all variants annotated in both pools, 5080 (0.06%) are variants in tumor suppressor
genes but only 46 show significant difference in allele frequencies between the two
studied groups. Four variants (0.004%) are pathogenic/risk factors according to single
nucleotide polymorphism database: rs1566734 in PTPRJ, rs861539 in
XRCC3, rs203462 in AKAP10, and rs486907 in
RNASEL. Discussion: Based on their high minor allele frequencies and presence in the centenarian group, we
could reclassify them from pathogenic/risk factors to benign. Our study shows that
centenarian exomes can be used for re-evaluating the clinically uncertain variants.
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Affiliation(s)
- Lubomir Balabanski
- Department of Medical Genetics, Medical University-Sofia, Sofia, Bulgaria.,Hospital"Malinov," Sofia, Bulgaria
| | - Dimitar Serbezov
- Department of Medical Genetics, Medical University-Sofia, Sofia, Bulgaria
| | - Dragomira Nikolova
- Department of Medical Genetics, Medical University-Sofia, Sofia, Bulgaria
| | - Olga Antonova
- Department of Medical Genetics, Medical University-Sofia, Sofia, Bulgaria
| | - Desislava Nesheva
- Department of Medical Genetics, Medical University-Sofia, Sofia, Bulgaria
| | - Zora Hammoudeh
- Department of Medical Genetics, Medical University-Sofia, Sofia, Bulgaria
| | - Radoslava Vazharova
- Hospital"Malinov," Sofia, Bulgaria.,Medical Faculty, Sofia University "St Kliment Ohridski," Sofia, Bulgaria
| | | | - Rada Staneva
- Department of Medical Genetics, Medical University-Sofia, Sofia, Bulgaria
| | - Marta Mihaylova
- Department of Medical Genetics, Medical University-Sofia, Sofia, Bulgaria.,Bulgarian Academy of Science-BAS, Sofia, Bulgaria
| | - Vera Damyanova
- Department of Medical Genetics, Medical University-Sofia, Sofia, Bulgaria
| | - Savina Hadjidekova
- Department of Medical Genetics, Medical University-Sofia, Sofia, Bulgaria
| | - Draga Toncheva
- Department of Medical Genetics, Medical University-Sofia, Sofia, Bulgaria.,Bulgarian Academy of Science-BAS, Sofia, Bulgaria
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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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Senghore T, Chien HT, Wang WC, Chen YX, Young CK, Huang SF, Yeh CC. Predictive value of genetic variants XRCC1 rs1799782, APEX1 rs1760944, and MUTYH rs3219489 for adjuvant concurrent chemoradiotherapy outcomes in oral squamous cell carcinoma patients. THE PHARMACOGENOMICS JOURNAL 2020; 20:813-822. [PMID: 32461665 DOI: 10.1038/s41397-020-0170-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/30/2019] [Revised: 05/10/2020] [Accepted: 05/18/2020] [Indexed: 12/24/2022]
Abstract
Genetic variations in DNA base excision repair (BER) genes may affect tumor sensitivity to chemotherapy and radiotherapy. Thus, we investigated the effects of single-nucleotide polymorphisms (SNPs) in key BER pathway genes on clinical outcomes in male patients who received concurrent chemoradiotherapy (CCRT). Seven SNPs from XRCC1, OGG1, APEX1, and MUTYH were genotyped using the Sequenom iPLEX MassARRAY system in samples from 319 men with advanced oral squamous cell carcinoma. The disease-free survival (DFS) rates of the MUTYH rs3219489 genotypes and those of the other genotypes differed significantly (log-rank test p = 0.027). Multivariate Cox proportional hazard analysis showed that the MUTYH rs3219489 GG genotype was associated with poor DFS (recessive model: hazard ratio [HR] = 2.01, 95% confidence interval [CI] = 1.31-3.10; p = 0.002). The CT + TT genotypes of XRCC1 rs1799782 (dominant model: HR = 0.65, 95% CI = 0.43-0.99; p = 0.044) and GG genotype of APEX1 rs1760944 (recessive model: HR = 1.64, 95% CI = 1.00-2.70; p = 0.050) were associated with overall survival (OS). Carrying the two risk genotypes, CC and GG of XRCC1 rs1799782 and APEX1 rs1760944, respectively, (HR = 2.95, 95% CI = 1.47-5.88; p = 0.002) increased mortality risk. Our findings showed that carrying the two risk genotypes of XRCC1 rs1799782 and APEX1 rs1760944 was associated with poor OS, while the GG genotype of MUTYH rs3219489 was associated with poor DFS. Patients carrying the risk genotypes may not benefit from CCRT; therefore, they will need alternative treatments.
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Affiliation(s)
- Thomas Senghore
- School of Public Health, College of Public Health, Taipei Medical University, Taipei, 11031, Taiwan.,Department of Nursing, School of Medicine and Allied Health Sciences, University of The Gambia, Independence Drive, Banjul, P. O. Box 1646, Banjul, The Gambia
| | - Huei-Tzu Chien
- Department of Public Health, Chang Gung University, Taoyuan, 33302, Taiwan.,Department of Nutrition and Health Sciences, Chang Gung University of Science and Technology, Taoyuan, 33303, Taiwan
| | - Wen-Chang Wang
- Ph.D. Program for Translational Medicine, College of Medical Science and Technology, Taipei Medical University, Taipei, 11031, Taiwan
| | - You-Xin Chen
- School of Public Health, College of Public Health, Taipei Medical University, Taipei, 11031, Taiwan
| | - Chi-Kuang Young
- Department of Otolaryngology, Chang Gung Memorial Hospital, Keelung, 20401, Taiwan
| | - Shiang-Fu Huang
- Department of Public Health, Chang Gung University, Taoyuan, 33302, Taiwan. .,Graduate Institute of Clinical Medical Sciences, Chang Gung University, Taoyuan, 33302, Taiwan. .,Department of Otolaryngology, Head and Neck Surgery, Chang Gung Memorial Hospital, Linkou, Taoyuan, 33305, Taiwan.
| | - Chih-Ching Yeh
- School of Public Health, College of Public Health, Taipei Medical University, Taipei, 11031, Taiwan. .,Department of Public Health, College of Public Health, China Medical University, Taichung, 40402, Taiwan. .,Cancer Center, Wan Fang Hospital, Taipei Medical University, Taipei, 11696, Taiwan.
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Kaur J, Sambyal V, Guleria K, Singh NR, Uppal MS, Manjari M, Sudan M. Association of XRCC1, XRCC2 and XRCC3 Gene Polymorphism with Esophageal Cancer Risk. Clin Exp Gastroenterol 2020; 13:73-86. [PMID: 32214837 PMCID: PMC7083648 DOI: 10.2147/ceg.s232961] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/08/2019] [Accepted: 02/04/2020] [Indexed: 12/30/2022] Open
Abstract
Aim The X-ray repair cross-complementing (XRCC) gene polymorphisms influence esophageal carcinogenesis by altering the DNA repair capacity. The present study was designed to screen five single nucleotide polymorphisms (SNPs) of XRCC genes for their susceptibility to esophageal cancer (EC) risk. There is no previous report on these polymorphisms for EC from India, where EC frequency is high. Methods The present study included 497 subjects (213 EC patients and 284 healthy controls). The polymorphisms were screened using the PCR-RFLP method and allele and genotype distribution were compared using chi-square test. Association analysis was done by haplotype analysis and linkage disequilibrium (LD) analysis. Gene–gene interactions were identified using multifactor dimensionality reduction (MDR). The risk was calculated using binary logistic regression. Results For XRCC1 p.Arg399Gln, a decreased risk for EC was associated with the AA genotype [OR (95% CI): 0.53 (0.3–0.95), p=0.03] even after adjusting for various covariates [OR (95% CI): 0.49 (0.26–0.9), p=0.024] and with the recessive model [OR (95% CI): 0.49 (0.27–0.8), p=0.016]. The GA genotype of p.Arg280His was associated with an increased risk for EC [OR (95% CI): 1.7 (1.0–2.82), p= 0.045] after adjustments. The two XRCC1 polymorphisms, p.Arg399Gln and p.Arg194Trp were in slight LD among EC patients (D̍́=0.845, r2=0.042). XRCC2 and XRCC3 polymorphisms were not associated with EC risk. Conclusion XRCC1 p.Arg399Gln plays a protective role in the development of the EC. The study is the first report from India, providing baseline data about genetic polymorphisms in DNA repair genes XRCC1, XRCC2 and XRCC3 modulating overall EC risk.
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Affiliation(s)
- Jagjeet Kaur
- Human Cytogenetics Laboratory, Department of Human Genetics, Guru Nanak Dev University, Amritsar, India
| | - Vasudha Sambyal
- Human Cytogenetics Laboratory, Department of Human Genetics, Guru Nanak Dev University, Amritsar, India
| | - Kamlesh Guleria
- Human Cytogenetics Laboratory, Department of Human Genetics, Guru Nanak Dev University, Amritsar, India
| | | | | | | | - Meena Sudan
- Department of Radiotherapy, Sri Guru Ram Das Institute of Medical Sciences and Research, Amritsar, Punjab, India
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Alterations in XRCC1 gene profile in pathogenesis of oral cavity cancer: A population-based study from Kamrup Urban District of Assam, India. Curr Probl Cancer 2020; 44:100473. [DOI: 10.1016/j.currproblcancer.2019.03.003] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2019] [Accepted: 03/19/2019] [Indexed: 11/21/2022]
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10
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Raturi V, Hojo H, Bhatt MLB, Suhel M, Wu C, Bei Y, Nakamura M, Okumura M, Zhang H, Parmar D, Badajena A, Singh R, Kumar S, Katiyar T, Gaur J. Prospective evaluation of XRCC‐1 Arg194Trp polymorphism as bio‐predictor for clinical outcome in locally advanced laryngeal cancer undergoing cisplatin‐based chemoradiation. Head Neck 2020; 42:1045-1056. [DOI: 10.1002/hed.26083] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2019] [Revised: 12/08/2019] [Accepted: 01/10/2020] [Indexed: 12/30/2022] Open
Affiliation(s)
- Vijay Raturi
- Department of Radiation Oncology King George's Medical University Lucknow India
- Division of Radiation Oncology and Particle therapy National Cancer Center Hospital East Chiba Japan
| | - Hidehiro Hojo
- Division of Radiation Oncology and Particle therapy National Cancer Center Hospital East Chiba Japan
| | - M. L. B. Bhatt
- Department of Radiation Oncology King George's Medical University Lucknow India
| | - Mohammad Suhel
- Department of Radiation Oncology King George's Medical University Lucknow India
| | - Chen‐Ta Wu
- Department of Radiation Oncology, Graduate school of medicine Keio University Japan
| | - Yanping Bei
- Division of Radiation Oncology and Particle therapy National Cancer Center Hospital East Chiba Japan
| | - Masaki Nakamura
- Division of Radiation Oncology and Particle therapy National Cancer Center Hospital East Chiba Japan
| | - Masayuki Okumura
- Division of Radiation Oncology and Particle therapy National Cancer Center Hospital East Chiba Japan
| | - Haiqin Zhang
- Division of Radiation Oncology and Particle therapy National Cancer Center Hospital East Chiba Japan
| | | | - Avinash Badajena
- Department of Radiation Oncology King George's Medical University Lucknow India
| | - Rahul Singh
- Department of Radiation Oncology King George's Medical University Lucknow India
| | - Saurabh Kumar
- Department of Radiology King George's Medical University Lucknow India
| | - Tridev Katiyar
- Indian Institute of Toxicology and Research Lucknow India
| | - Jalaj Gaur
- Department of Radiation Oncology King George's Medical University Lucknow India
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Application of simulation-based CYP26 SNP-environment barcodes for evaluating the occurrence of oral malignant disorders by odds ratio-based binary particle swarm optimization: A case-control study in the Taiwanese population. PLoS One 2019; 14:e0220719. [PMID: 31465460 PMCID: PMC6715230 DOI: 10.1371/journal.pone.0220719] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2019] [Accepted: 07/22/2019] [Indexed: 12/15/2022] Open
Abstract
Introduction Genetic polymorphisms and social factors (alcohol consumption, betel quid (BQ) usage, and cigarette consumption), both separately or jointly, play a crucial role in the occurrence of oral malignant disorders such as oral and pharyngeal cancers and oral potentially malignant disorders (OPMD). Material and methods Simultaneous analyses of multiple single nucleotide polymorphisms (SNPs) and environmental effects on oral malignant disorders are essential to examine, albeit challenging. Thus, we conducted a case-control study (N = 576) to analyze the risk of occurrence of oral malignant disorders by using binary particle swarm optimization (BPSO) with an odds ratio (OR)-based method. Results We demonstrated that a combination of SNPs (CYP26B1 rs887844 and CYP26C1 rs12256889) and socio-demographic factors (age, ethnicity, and BQ chewing), referred to as the combined effects of SNP-environment, correlated with maximal risk diversity of occurrence observed between the oral malignant disorder group and the control group. The risks were more prominent in the oral and pharyngeal cancers group (OR = 10.30; 95% confidence interval (CI) = 4.58–23.15) than in the OPMD group (OR = 5.42; 95% CI = 1.94–15.12). Conclusions Simulation-based “SNP-environment barcodes” may be used to predict the risk of occurrence of oral malignant disorders. Applying simulation-based “SNP-environment barcodes” may provide insight into the importance of screening tests in preventing oral and pharyngeal cancers and OPMD.
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12
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Garcia JA, Kalacas NA, Sy Ortin T, Ramos MC, Albano PM. XRCC4 c.1394G>T Single Nucleotide Polymorphisms and
Breast Cancer Risk among Filipinos. Asian Pac J Cancer Prev 2019; 20:1097-1101. [PMID: 31030479 PMCID: PMC6948885 DOI: 10.31557/apjcp.2019.20.4.1097] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023] Open
Abstract
Background: The identification of cancer-associated single nucleotide polymorphisms (SNP) and mutation genes is a promising approach in recognizing individuals who are at risk of developing cancer. Hence, this study was conducted to determine the association between XRCC4 c.1394G>T SNP and breast cancer development among Filipinos. Methods: Genotyping for XRCC4 c.1394G>T SNP was performed on breast cancer patients (n=103) and their age- and sex- matched clinically healthy controls (n=103) by polymerase chain reaction – restriction fragment length polymorphism. Results: Significant difference in genotype (p=0.007) and allele (p=0.003) frequencies in XRCC4 c.1394G>T was observed between the breast cancer cases and controls. Carriers of the XRCC4 c.1394 G>T genotype were observed to have significantly higher risk of developing breast cancer compared to individuals with T/T genotype (OR=2.67, 95% CI: 1.36 – 5.25). XRCC4 c.1394G>T combined with passive smoking may also significantly increase risk of breast cancer (OR=14.73; 95% CI= 9.88-18.86). Conclusion: XRCC4 c. 1394G>T may be associated with breast cancer development among Filipinos.
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Affiliation(s)
- Julius Adrie Garcia
- The Graduate School, University of Santo Tomas, Manila, Philippines. ,Research Center for the Natural and Applied Sciences, University of Santo Tomas, Manila, Philippines
| | - Noel Angelo Kalacas
- The Graduate School, University of Santo Tomas, Manila, Philippines. ,Research Center for the Natural and Applied Sciences, University of Santo Tomas, Manila, Philippines
| | - Teresa Sy Ortin
- The Graduate School, University of Santo Tomas, Manila, Philippines. ,University of Santo Tomas Hospital, Benavides Cancer Institute, Manila, Philippines
| | - Maria Cristina Ramos
- The Graduate School, University of Santo Tomas, Manila, Philippines. ,Research Center for the Natural and Applied Sciences, University of Santo Tomas, Manila, Philippines.,College of Science, University of Santo Tomas, Manila, Philippines
| | - Pia Marie Albano
- The Graduate School, University of Santo Tomas, Manila, Philippines. ,Research Center for the Natural and Applied Sciences, University of Santo Tomas, Manila, Philippines.,College of Science, University of Santo Tomas, Manila, Philippines
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13
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Liu Y, Zhao XX, Hu XJ, Yang F, Lin P, Cui SC, Zhao W, Cao XY, Wang YS. Effect of sex hormone-binding globulin polymorphisms on the outcome of in vitro fertilization-embryo transfer for polycystic ovary syndrome patients: A case-control study. J Cell Biochem 2018; 120:4675-4686. [PMID: 30520140 DOI: 10.1002/jcb.27756] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2018] [Accepted: 09/06/2018] [Indexed: 01/11/2023]
Abstract
Polycystic ovary syndrome (PCOS), known as a common endocrine disorder among females, plagues many PCOS patients. The current study aimed to explore the correlations of sex hormone-binding globulin (SHBG) polymorphisms with the outcome of in vitro fertilization-embryo transfer (IVF-ET) in PCOS patients. PCOS patients who underwent IVF-ET and patients with non-PCOS-related infertility were selected in the study. Correlations of SHBG rs6259 and rs727428 with the risk factors in PCOS were analyzed, followed by the evaluation of the effect of SHBG polymorphisms on the outcome of IVF-ET in PCOS patients. At last, unconditional logistic regression analysis was performed to study the risk factors for IVF-ET treatment outcome. Compared with SHBG rs6259 GG carriers, the incidence of PCOS was found to be elevated in SHBG rs6259 GA+AA carriers which indicated that the A allele was a risk factor for PCOS. Compared with SHBG rs6259 TT carriers, the number of retrieved oocytes and embryo as well as the fertility rate in SHBG rs6259 GA+AA carriers was found to be decreased, while the abortion rate, incidence of ovarian hyperstimulation syndrome, transplant rejection rate, estradiol, and testosterone in serum, as well as testosterone in follicular fluid were elevated. The luteal hormone, serum testosterone, and progesterone and GA+AA genotype of rs6259 were the risk factors for IVF-ET treatment outcome. Taken together, the study showed that SHBG rs6259 polymorphisms might be correlated with the risk of PCOS and the outcome of IVF-ET treatment.
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Affiliation(s)
- Yang Liu
- Department of Obstetrics, Linyi Central Hospital, Linyi, China
| | - Xi-Xi Zhao
- Intensive Care Unit, Linyi Central Hospital, Linyi, China
| | - Xiang-Juan Hu
- Department of Obstetrics and Gynecology, Economic and Technological Development Zone People's Hospital of Linyi, Linyi, China
| | - Feng Yang
- Operating Room, Economic and Technological Development Zone People's Hospital of Linyi, Linyi, China
| | - Ping Lin
- Department of Obstetrics, Linyi Central Hospital, Linyi, China
| | - Shi-Chang Cui
- Department of General Surgery, Linyi Central Hospital, Linyi, China
| | - Wei Zhao
- Department of Obstetrics, Linyi Central Hospital, Linyi, China
| | - Xiao-Yun Cao
- Medical Insurance Management Office, Economic and Technological Development Zone People's Hospital of Linyi, Linyi, China
| | - Yong-Sheng Wang
- Department of Gynecology, Linyi People's Hospital, Linyi, China
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14
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Santos EDM, Santos HBDP, de Matos FR, Machado RA, Coletta RD, Galvão HC, Freitas RDA. Clinicopathological significance of SNPs in
RAD51
and
XRCC3
in oral and oropharyngeal carcinomas. Oral Dis 2018; 25:54-63. [DOI: 10.1111/odi.12943] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2018] [Revised: 07/05/2018] [Accepted: 07/14/2018] [Indexed: 02/06/2023]
Affiliation(s)
- Edilmar de Moura Santos
- Department of Dentistry Federal University of Rio Grande do Norte Natal Rio Grande do Norte Brazil
| | | | | | - Renato Assis Machado
- Department of Oral Diagnosis, Dental School University of Campinas Piracicaba São Paulo Brazil
| | - Ricardo D. Coletta
- Department of Oral Diagnosis, Dental School University of Campinas Piracicaba São Paulo Brazil
| | - Hébel Cavalcanti Galvão
- Department of Dentistry Federal University of Rio Grande do Norte Natal Rio Grande do Norte Brazil
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15
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Nanda SS, Gandhi AK, Rastogi M, Khurana R, Hadi R, Sahni K, Mishra SP, Srivastava AK, Bhatt MLB, Parmar D. Evaluation of XRCC1 Gene Polymorphism as a Biomarker in Head and Neck Cancer Patients Undergoing Chemoradiation Therapy. Int J Radiat Oncol Biol Phys 2018; 101:593-601. [DOI: 10.1016/j.ijrobp.2018.03.039] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2017] [Revised: 03/26/2018] [Accepted: 03/26/2018] [Indexed: 12/29/2022]
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16
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Xiao S, Sun S, Long W, Kuang S, Liu Y, Huang H, Zhou J, Zhou Y, Lu X. A meta-analytic review of the association between two common SNPs in miRNAs and lung cancer susceptibility. Onco Targets Ther 2018; 11:2419-2427. [PMID: 29750042 PMCID: PMC5935188 DOI: 10.2147/ott.s156505] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Background MicroRNAs (miRNAs) are involved in many biological processes, including tumor suppression. Multiple studies have shown an association between the miRNA-196a2 rs11614913 and miRNA-146a rs2910164 polymorphisms and cancer risk. However, the implications of the reported data are debatable and inconclusive. Materials and methods Relevant articles were retrieved from the PubMed, EMBASE, China National Knowledge Infrastructure, and WanFang databases from January 1, 2007, to April 30, 2017. Studies were assessed based on designated inclusion and exclusion criteria, and data were manually extracted from relevant studies by two investigators. Pooled odds ratios (ORs) and 95% confidence intervals (CIs) were calculated to explore the association between two single-nucleotide polymorphisms (SNPs) in miRNAs and lung cancer susceptibility. Results Nine eligible articles were included, consisting of 3,101 cancer cases and 3,234 controls for miRNA-196a2 rs11614913, and 3,483 cases and 3,578 controls for miRNA-146a rs2910164. For studies evaluating miRNA-196a2 rs11614913, significant associations with lung cancer risk were discovered. Overall, the pooled analysis showed that miRNA-196a2 rs11614913 was associated with a decreased cancer risk (CC vs TT: OR = 1.25, 95% CI: 1.09–1.44; CT vs TT: OR = 1.26, 95% CI: 1.03–1.53). For miRNA-146a rs2910164, only the CC genotype was found to be associated with high lung cancer risk (OR = 1.30, 95% CI: 1.13–1.49). Subgroup analyses based on ethnicity, source of control group, and country indicated that there were strong associations between miRNA-146a rs2910164 and cancer risk. Conclusion The results indicated that lung cancer risk was significantly associated with miRNA-196a2 rs11614913 and miRNA-146a rs2910164. These two common SNPs in miRNAs may be potential biomarkers of lung cancer.
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Affiliation(s)
- Sha Xiao
- Department of Environmental and Occupational Health, School of Public Health, Hainan Medical University, Haikou, People's Republic of China
| | - Songzan Sun
- Department of Environmental and Occupational Health, School of Public Health, Hainan Medical University, Haikou, People's Republic of China
| | - Wenfang Long
- Department of Environmental and Occupational Health, School of Public Health, Hainan Medical University, Haikou, People's Republic of China
| | - Shicheng Kuang
- Department of Pharmacy, Hainan General Hospital, Haikou, People's Republic of China
| | - Yunru Liu
- Department of Environmental and Occupational Health, School of Public Health, Hainan Medical University, Haikou, People's Republic of China
| | - Hairong Huang
- Department of Environmental and Occupational Health, School of Public Health, Hainan Medical University, Haikou, People's Republic of China
| | - Jing Zhou
- Department of Environmental and Occupational Health, School of Public Health, Hainan Medical University, Haikou, People's Republic of China
| | - Yongjiang Zhou
- Department of Environmental and Occupational Health, School of Public Health, Hainan Medical University, Haikou, People's Republic of China
| | - Xiaobo Lu
- Department of Toxicology, School of Public Health, China Medical University, Shenyang, People's Republic of China
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17
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Cheng HL, Liu YF, Su CW, Su SC, Chen MK, Yang SF, Lin CW. Functional genetic variant in the Kozak sequence of WW domain-containing oxidoreductase (WWOX) gene is associated with oral cancer risk. Oncotarget 2018; 7:69384-69396. [PMID: 27655721 PMCID: PMC5342485 DOI: 10.18632/oncotarget.12082] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2016] [Accepted: 09/10/2016] [Indexed: 12/11/2022] Open
Abstract
In Taiwan, oral cancer is the fourth leading cancer in males and is associated with exposure to environmental carcinogens. WW domain-containing oxidoreductase (WWOX), a tumor suppressor gene, is associated with the development of various cancers. We hypothesized that genetic variants of WWOX influence the susceptibility to oral cancer. Five polymorphisms of WWOX gene from 761 male patients with oral cancer and 1199 male cancer-free individuals were genotyped. We observed that individuals carrying the polymorphic allele of WWOX rs11545028 are more susceptible to oral cancer. Furthermore, patients with advanced-stage oral cancer were associated with a higher frequency of WWOX rs11545028 polymorphisms with the variant genotype TT than did patients with the wild-type gene. An additional integrated in silico analysis confirmed that rs11545028 affects WWOX expression, which significantly correlates with tumor expression and subsequently with tumor development and aggressiveness. In conclusion, genetic variants of WWOX contribute to the occurrence of oral cancer, and the findings regarding these biomarkers provided a prediction model for risk assessment.
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Affiliation(s)
- Hsin-Lin Cheng
- Institute of Medicine, Chung Shan Medical University, Taichung, Taiwan
| | - Yu-Fan Liu
- Department of Biomedical Sciences, Chung Shan Medical University, Taichung, Taiwan
| | - Chun-Wen Su
- Institute of Medicine, Chung Shan Medical University, Taichung, Taiwan
| | - Shih-Chi Su
- Whole-Genome Research Core Laboratory of Human Diseases, Chang Gung Memorial Hospital, Keelung, Taiwan
| | - Mu-Kuan Chen
- Institute of Medicine, Chung Shan Medical University, Taichung, Taiwan.,Department of Otorhinolaryngology-Head and Neck Surgery, Changhua Christian Hospital, Changhua, Taiwan
| | - Shun-Fa Yang
- Institute of Medicine, Chung Shan Medical University, Taichung, Taiwan.,Department of Medical Research, Chung Shan Medical University Hospital, Taichung, Taiwan
| | - Chiao-Wen Lin
- Institute of Oral Sciences, Chung Shan Medical University, Taichung, Taiwan.,Department of Dentistry, Chung Shan Medical University Hospital, Taichung, Taiwan
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18
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Lu Z, Sturgis EM, Zhu L, Zhang H, Tao Y, Wei P, Wei Q, Li G. Mouse double minute 4 variants modify susceptibility to risk of recurrence in patients with squamous cell carcinoma of the oropharynx. Mol Carcinog 2017; 57:361-369. [PMID: 29073727 DOI: 10.1002/mc.22760] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2017] [Revised: 09/14/2017] [Accepted: 10/23/2017] [Indexed: 12/11/2022]
Abstract
Given the crucial role of Mouse double minute 4 (MDM4) oncoprotein in p53 pathway, single nucleotide polymorphisms (SNPs) could serve as such biomarkers for prediction of SCCOP recurrence. Thus, we investigated associations between three tagging putatively functional variants of MDM4, two in the 3' untranslated region of 3' UTR [rs11801299 (NC_000001.10:g.204529084G>A) and rs10900598(NC_000001.10:g.204525568G>T)] and one in intron 1 [rs1380576(NC_000001.10:g.204488278G>C)], and recurrence risk of SCCOP in 1,008 incident patients. A log-rank test and multivariable Cox models were used to assess associations. Patients with MDM4-rs10900598 GT/TT had a worse disease-free survival (DFS) compared with corresponding GG genotype, while those with rs11801299 AG/AA genotypes had a lower recurrence risk than the cases with rs11801299 GG genotype (both log-rank, P < 0.001). Multivariable analysis showed that significantly different recurrence risk were found among patients with MDM4-rs10900598 GT/TT and rs11801299 AG/AA variant genotypes (HR, 2.0, 95% CI, 1.4-2.9 and HR, 0.4, 95% CI, 0.3-0.6, respectively) compared with their corresponding common homozygous genotypes. Furthermore, after combining the risk genotypes of the three SNPs, patients among low-risk group had a significantly lower risk of SCCOP recurrence than those in high-risk group (HR, 0.2, 95% CI, 0.1-0.3). The risk for both individual SNPs or combined risk genotypes was restricted to HPV-positive SCCOP patients. Our findings suggest that the MDM4 polymorphisms may, individually or in combination, confer an independent risk of SCCOP recurrence, particularly in HPV-positive SCCOP patients. However, larger studies are needed to validate our findings.
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Affiliation(s)
- Zhongming Lu
- Department of Otolaryngology-Head and Neck Surgery, Guangdong General Hospital and Guangdong Academy of Medical Sciences, Guangzhou, Guangdong, China.,Department of Head and Neck Surgery, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Erich M Sturgis
- Department of Head and Neck Surgery, The University of Texas MD Anderson Cancer Center, Houston, Texas.,Department of Epidemiology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Lijun Zhu
- Department of Head and Neck Surgery, The University of Texas MD Anderson Cancer Center, Houston, Texas.,Department of Oral and Maxillofacial Surgery, Guangdong General Hospital and Guangdong Academy of Medical Sciences, Guangzhou, Guangdong, China
| | - Hua Zhang
- Department of Head and Neck Surgery, The University of Texas MD Anderson Cancer Center, Houston, Texas.,Department of Otolaryngology-Head and Neck Surgery, the Affiliated Yantai Yuhuangding Hospital of Qingdao University, Yantai, Shandong, China
| | - Ye Tao
- Department of Head and Neck Surgery, The University of Texas MD Anderson Cancer Center, Houston, Texas.,Department of Otolaryngology and Head and Neck Surgery, the 2nd Affiliated Hospital of Anhui Medical University, Hefei, Anhui, China
| | - Peng Wei
- Department of Biostatistics, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Qingyi Wei
- Duke Cancer Institute, Duke University Medical Center, Durham, North Carolina
| | - Guojun Li
- Department of Head and Neck Surgery, The University of Texas MD Anderson Cancer Center, Houston, Texas.,Department of Epidemiology, The University of Texas MD Anderson Cancer Center, Houston, Texas
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19
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Haplotype analysis of XRCC2 gene polymorphisms and association with increased risk of head and neck cancer. Sci Rep 2017; 7:13210. [PMID: 29038438 PMCID: PMC5643489 DOI: 10.1038/s41598-017-13461-6] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2016] [Accepted: 09/15/2017] [Indexed: 12/14/2022] Open
Abstract
We aimed to investigate the effect of hotspot variations of XRCC2 gene on the risk of head and neck cancer (HNC) in 400 patients and 400 controls. Five polymorphisms of XRCC2 gene G4234C (rs3218384), G4088T (rs3218373), G3063A (rs2040639), R188H (rs3218536) and rs7802034 were analyzed using Allele- specific polymerase chain reaction (ARMS-PCR) followed by sequence analysis. For rs3218373, the GG genotype indicated a statistically significant 3-fold increased risk of HNC (P < 0.001) after multivariate adjustment. For rs7802034, the GG genotype suggested statistically significant 2-fold increased risk of HNC (P < 0.001). For SNP of rs3218536, the AA genotype indicated a significant 3-fold increased risk of HNC (P < 0.001). Additionally, haplotype analysis revealed that TACAG, TGGAG, TACGG and TAGGA haplotypes of XRCC2 polymorphisms are associated with HNC risk. Two SNPs in XRCC2 (rs2040639 and rs3218384) were found increased in strong linkage disequilibrium. Furthermore, joint effect model showed 20 fold (OR = 19.89; 95% CI = 2.65–149.36, P = 0.003) increased HNC risk in patients carrying four homozygous risk alleles of selected polymorphisms. These results show that allele distributions and genotypes of XRCC2 SNPs are significantly associated with increased HNC risk and could be a genetic adjuster for the said disease.
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20
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Yang CH, Lin YD, Chuang LY, Chen JB, Chang HW. Joint Analysis of SNP-SNP-Environment Interactions for Chronic Dialysis by an Improved Branch and Bound Algorithm. J Comput Biol 2017; 24:1212-1225. [PMID: 28876085 DOI: 10.1089/cmb.2017.0090] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
In previous studies, both single-nucleotide polymorphism (SNP)-SNP or gene-gene (G × G) interactions and SNP-environmental factor (G × E) interactions were reported to partially account for "missing" heritability. However, (G × G) × E interactions were less commonly addressed. The purpose of this study was to develop a novel strategy to evaluate possible (G × G) × E interactions in D-loop-based chronic dialysis association. Using values from our previously published data set (704 controls and 193 cases) of 77 D-loop SNPs and 7 environmental factors (coronary heart disease, hypertension, diabetes mellitus, triglyceride, cholesterol, blood thiol, and TBARS levels), we compared the performances of G, G × G, G × E, and (G × G) × E. We found that the interactions of four individual SNPs previously associated with a significantly high risk of chronic dialysis [odds ratio (OR) = 1.56-4.93] with environmental factors (G × E) increased the risk of chronic dialysis (maximum OR = 35.43). We then used an improved branch and bound algorithm to identify combinations of two to four SNPs that were most highly associated with chronic dialysis (OR = 9.27-34.39). When the interactions of the two- and three-SNP combinations with environmental factors were evaluated, we found that the (G × G) × E effects increased the risk of chronic dialysis (maximum OR = 8.32-57.54 and OR = 12.52-57.81, respectively; adjusted OR = 8.67-81.81 and OR = 12.29-81.95, respectively). Taken together, the (G × G) × E interactions identified chronic dialysis-associated SNPs that would not have been found using G × G or G × E interactions, suggesting that (G × G) × E interactions may be helpful to solve the problems of missing heritability in association studies.
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Affiliation(s)
- Cheng-Hong Yang
- 1 Department of Electronic Engineering, National Kaohsiung University of Applied Sciences , Kaohsiung, Taiwan .,2 Graduate Institute of Clinical Medicine, Kaohsiung Medical University , Kaohsiung, Taiwan
| | - Yu-Da Lin
- 1 Department of Electronic Engineering, National Kaohsiung University of Applied Sciences , Kaohsiung, Taiwan
| | - Li-Yeh Chuang
- 3 Department of Chemical Engineering & Institute of Biotechnology and Chemical Engineering, I-Shou University , Kaohsiung, Taiwan
| | - Jin-Bor Chen
- 4 Division of Nephrology, Department of Internal Medicine, Mitochondrial Research Unit, Kaohsiung Chang Gung Memorial Hospital, Chang Gung University College of Medicine , Kaohsiung, Taiwan
| | - Hsueh-Wei Chang
- 5 Institute of Medical Science and Technology, National Sun Yat-Sen University , Kaohsiung, Taiwan .,6 Department of Medical Research, Kaohsiung Medical University Hospital , Kaohsiung, Taiwan .,7 Department of Biomedical Science and Environmental Biology, Kaohsiung Medical University , Kaohsiung, Taiwan
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21
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Chen WC, Wang WC, Okada Y, Chang WP, Chou YH, Chang HH, Huang JD, Chen DY, Chang WC. rs2841277 ( PLD4) is associated with susceptibility and rs4672495 is associated with disease activity in rheumatoid arthritis. Oncotarget 2017; 8:64180-64190. [PMID: 28969061 PMCID: PMC5609993 DOI: 10.18632/oncotarget.19419] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2017] [Accepted: 06/05/2017] [Indexed: 12/16/2022] Open
Abstract
Rheumatoid arthritis (RA) is one of the most common autoimmune diseases, can lead to long-term joint damage, chronic pain, and loss of motor function in the hands, and may share some common genetic factors with other autoimmune disorders, such as ankylosing spondylitis (AS). Many single-nucleotide polymorphisms (SNPs) were reported by genome-wide association studies (GWASs) of RA, but some of them have not been examined in the Taiwanese population. In this study, for 15 SNPs reported in previous RA and AS GWASs, we investigated their association with RA in a Taiwanese population. Based on 334 RA patients recruited from the Taichung Veterans General Hospital and 16,036 healthy subjects from the Taiwan Biobank (TWB) project, we observed that subjects having minor allele C at rs2841277 (phospholipase D family, member 4 (PLD4)) have lower susceptibility of RA, compare to those having genotype TT (Odds ratio (OR) = 0.6, p = 3.0 × 10−6). Among the RA patients, we observed that subjects having GG at rs4672495 have a lower proportion of severe RA, compare to other subjects (OR = 0.09, p = 5.6 × 10−3). Results of a bioinformatics approach showed that rs2841277 is able to influence expression of LINC00638 and AHNAK2 and rs4672495 is able to influence the expression of B3GNT2. In summary, this study replicated an association of rs2841277 with RA susceptibility and showed an AS-associated SNP, rs4672495, is associated with RA activity in the Taiwanese population.
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Affiliation(s)
- Wei-Chiao Chen
- Institute of Clinical Pharmacy and Pharmaceutical Sciences, College of Medicine, National Cheng Kung University, Tainan, Taiwan
| | - Wen-Chang Wang
- The Ph.D. Program for Translational Medicine, College of Medical Science and Technology, Taipei Medical University, Taipei, Taiwan
| | - Yukinori Okada
- Department of Statistical Genetics, Graduate School of Medicine, Osaka University, Osaka, Japan
| | - Wei-Pin Chang
- School of Health Care Administration, College of Management, Taipei Medical University, Taipei, Taiwan
| | - Yii-Her Chou
- Department of Urology, Kaohsiung Medical University Hospital, Kaohsiung, Taiwan.,Department of Urology, School of Medicine, College of Medicine, Kaohsiung Medical University, Kaohsiung, Taiwan
| | - Hui-Hua Chang
- Institute of Clinical Pharmacy and Pharmaceutical Sciences, College of Medicine, National Cheng Kung University, Tainan, Taiwan.,School of Pharmacy, College of Medicine, National Cheng Kung University, Tainan, Taiwan
| | - Jin-Ding Huang
- Institute of Clinical Pharmacy and Pharmaceutical Sciences, College of Medicine, National Cheng Kung University, Tainan, Taiwan
| | - Der-Yuan Chen
- Department of Internal Medicine and Medical Education, Taichung Veterans General Hospital, Taichung, Taiwan.,Faculty of Medicine, National Yang Ming University, Taipei, Taiwan.,Ph.D. Program in Translational Medicine, National Chung Hsing University, Taichung, Taiwan.,Institute of Biomedical Science and Rong Hsing Research Center for Translational Medicine, National Chung Hsing University, Taichung, Taiwan
| | - Wei-Chiao Chang
- The Ph.D. Program for Translational Medicine, College of Medical Science and Technology, Taipei Medical University, Taipei, Taiwan.,Master Program for Clinical Pharmacogenomics and Pharmacoproteomics, School of Pharmacy, Taipei Medical University, Taipei, Taiwan.,Department of Clinical Pharmacy, School of Pharmacy, Taipei Medical University, Taipei, Taiwan.,Center for Biomarkers and Biotech Drugs, Kaohsiung Medical University, Kaohsiung, Taiwan.,Department of Pharmacy, Taipei Medical University-Wanfang Hospital, Taipei, Taiwan
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22
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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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23
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Genetic variants of the DNA repair genes from Exome Aggregation Consortium (EXAC) database: significance in cancer. DNA Repair (Amst) 2017; 52:92-102. [DOI: 10.1016/j.dnarep.2017.02.013] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2016] [Revised: 01/11/2017] [Accepted: 02/20/2017] [Indexed: 12/29/2022]
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24
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Laytragoon Lewin N, Lewin F, Andersson BÅ, Löfgren S, Rutqvist LE. The use of rapid and cost-effective blood-based biomarkers in combination with tumour TNM stage for individual head and neck cancer patient treatment selection. Med Oncol 2017; 34:63. [PMID: 28316053 PMCID: PMC5357467 DOI: 10.1007/s12032-017-0912-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2017] [Accepted: 02/28/2017] [Indexed: 01/09/2023]
Abstract
Head and neck (H&N) cancer is an aggressive disease and the incidence has increased in younger population worldwide. Tumour TNM staging is the main basis for treatment decision despite significant variation in clinical outcome. Survival time of these patients has marginally improved during the last 30 years. Various biomarkers with cumbersome analysis, high cost, time consumption and requirement of special laboratory facilities have been investigated. However, none of these biomarkers have been shown to be suitable to use for individual H&N cancer patient treatment selection in the clinic. For practical use in clinical settings, the given biomarkers must be simple to analyse, rapid, cost effective and available in routine laboratories. With this intension, we suggested the combination of standard TNM staging and biomarkers associated with inflammation such as neutrophils, neutrophil to lymphocyte ratio, plasma C-reactive protein or plasma tumour necrosis factor alpha (TNFa) and single-nucleotide polymorphism in TNFa rs1800629 using blood-based analysis. The optimal treatment outcome of H&N cancer by using combination of TNM stage and these blood-based biomarkers for individual patient selection need further investigation.
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Affiliation(s)
- Nongnit Laytragoon Lewin
- Division of Medical Diagnostic, Ryhov Hospital, 55322, Jönköping, Sweden. .,Department of Clinical and Experimental Medicine, Linköping University, 58185, Linköping, Sweden.
| | - Freddi Lewin
- Department of Oncology, Ryhov Hospital, 55322, Jönköping, Sweden
| | - Bengt-Åke Andersson
- Division of Medical Diagnostic, Ryhov Hospital, 55322, Jönköping, Sweden.,Department of Clinical and Experimental Medicine, Linköping University, 58185, Linköping, Sweden
| | - Sture Löfgren
- Division of Medical Diagnostic, Ryhov Hospital, 55322, Jönköping, Sweden
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Multani S, Saranath D. Genotypic distribution of single nucleotide polymorphisms in oral cancer: global scene. Tumour Biol 2016; 37:14501-14512. [PMID: 27651159 DOI: 10.1007/s13277-016-5322-5] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2016] [Accepted: 09/05/2016] [Indexed: 12/22/2022] Open
Abstract
Globocan 2012 reports the global oral cancer incidence of 300,373 new oral cancer cases annually, contributing to 2.1 % of the world cancer burden. The major well-established risk factors for oral cancer include tobacco, betel/areca nut, alcohol and high-risk oncogenic human papilloma virus (HPV) 16/18. However, only 5-10 % of individuals with high-risk lifestyle develop oral cancer. Thus, genomic variants in individuals represented as single nucleotide polymorphisms (SNPs) influence susceptibility to oral cancer. With a view to understanding the role of genomic variants in oral cancer, we reviewed SNPs in case-control studies with a minimum of 100 cases and 100 controls. PubMed and HuGE navigator search engines were used to obtain data published from 1990 to 2015, which identified 67 articles investigating the role of SNPs in oral cancer. Single publications reported 93 SNPs in 55 genes, with 34 SNPs associated with a risk of oral cancer. Meta-analysis of data in multiple studies defined nine SNPs associated with a risk of oral cancer. The genes were associated with critical functions deregulated in cancers, including cell proliferation, immune function, inflammation, transcription, DNA repair and xenobiotic metabolism.
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Affiliation(s)
- Shaleen Multani
- Department of Biological Sciences, Sunandan Divatia School of Science, NMIMS (Deemed-to-be) University, Mumbai, Maharashtra, 400056, India
| | - Dhananjaya Saranath
- Department of Biological Sciences, Sunandan Divatia School of Science, NMIMS (Deemed-to-be) University, Mumbai, Maharashtra, 400056, India.
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Xu Y, Yan C, Hao Z, Zhou J, Fan S, Tai S, Yang C, Zhang L, Liang C. Association between BHMT gene rs3733890 polymorphism and cancer risk: evidence from a meta-analysis. Onco Targets Ther 2016; 9:5225-33. [PMID: 27578989 PMCID: PMC5001659 DOI: 10.2147/ott.s103901] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
BACKGROUND AND OBJECTIVE The gene betaine-homocysteine methyltransferase (BHMT) has drawn much attention during the past decades. An increasing number of clinical and genetic investigations have supposed that BHMT rs3733890 polymorphism might be associated with risk of breast cancer and ovarian cancer. As no consistent conclusion has been achieved, we conducted an up-to-date summary of BHMT rs3733890 polymorphism and cancer risk through a meta-analysis. MATERIALS AND METHODS The articles were collected from PubMed, Google Scholar, and CNKI (Chinese) databases up to December 2015. Then, the correlations were determined by reading the titles and abstracts and by further reading the full text to filter the unqualified articles. Odds ratio (OR) and the corresponding 95% confidence intervals (CI) were used to assess the results. RESULTS Among 187 articles collected in the analysis, seven studies with a total of 2,832 cases and 3,958 controls were included for evaluation of the association between BHMT rs3733890 polymorphism and susceptibility of cancer risk. The heterogeneity test showed no significant differences. Furthermore, we found that BHMT -742G>A polymorphism in case and control groups showed no statistically significant association with susceptibility in various cancer types except for uterine cervical cancer (A vs G: OR =0.641, 95% CI =0.445-0.923, P=0.017; AA+AG vs GG: OR =0.579, 95% CI =0.362-0.924, P=0.022). In addition, no statistically significant association was uncovered when stratification analyses were conducted by ethnicity and genotyping methods. CONCLUSION Our results have shown no obvious evidence that rs3733890 polymorphism in BHMT gene affected the susceptibility of head and neck squamous cell carcinoma, breast cancer, ovarian cancer, colorectal adenoma, and liver cancer. In contrast, we found the protective role of BHMT -742G>A polymorphism in uterine cervical cancer incidence. Future well-designed studies comprising larger sample size are warranted to verify our findings.
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Affiliation(s)
- Yue Xu
- Department of Urology, The First Affiliated Hospital of Anhui Medical University and Institute of Urology
| | - Cunye Yan
- First School of Clinical Medicine, Anhui Medical University, Hefei, Anhui, People's Republic of China
| | - Zongyao Hao
- Department of Urology, The First Affiliated Hospital of Anhui Medical University and Institute of Urology
| | - Jun Zhou
- Department of Urology, The First Affiliated Hospital of Anhui Medical University and Institute of Urology
| | - Song Fan
- Department of Urology, The First Affiliated Hospital of Anhui Medical University and Institute of Urology
| | - Sheng Tai
- Department of Urology, The First Affiliated Hospital of Anhui Medical University and Institute of Urology
| | - Cheng Yang
- Department of Urology, The First Affiliated Hospital of Anhui Medical University and Institute of Urology
| | - Li Zhang
- Department of Urology, The First Affiliated Hospital of Anhui Medical University and Institute of Urology
| | - Chaozhao Liang
- Department of Urology, The First Affiliated Hospital of Anhui Medical University and Institute of Urology
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Yang CH, Lin YD, Yen CY, Chuang LY, Chang HW. A systematic gene-gene and gene-environment interaction analysis of DNA repair genes XRCC1, XRCC2, XRCC3, XRCC4, and oral cancer risk. OMICS-A JOURNAL OF INTEGRATIVE BIOLOGY 2016; 19:238-47. [PMID: 25831063 DOI: 10.1089/omi.2014.0121] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Oral cancer is the sixth most common cancer worldwide with a high mortality rate. Biomarkers that anticipate susceptibility, prognosis, or response to treatments are much needed. Oral cancer is a polygenic disease involving complex interactions among genetic and environmental factors, which require multifaceted analyses. Here, we examined in a dataset of 103 oral cancer cases and 98 controls from Taiwan the association between oral cancer risk and the DNA repair genes X-ray repair cross-complementing group (XRCCs) 1-4, and the environmental factors of smoking, alcohol drinking, and betel quid (BQ) chewing. We employed logistic regression, multifactor dimensionality reduction (MDR), and hierarchical interaction graphs for analyzing gene-gene (G×G) and gene-environment (G×E) interactions. We identified a significantly elevated risk of the XRCC2 rs2040639 heterozygous variant among smokers [adjusted odds ratio (OR) 3.7, 95% confidence interval (CI)=1.1-12.1] and alcohol drinkers [adjusted OR=5.7, 95% CI=1.4-23.2]. The best two-factor based G×G interaction of oral cancer included the XRCC1 rs1799782 and XRCC2 rs2040639 [OR=3.13, 95% CI=1.66-6.13]. For the G×E interaction, the estimated OR of oral cancer for two (drinking-BQ chewing), three (XRCC1-XRCC2-BQ chewing), four (XRCC1-XRCC2-age-BQ chewing), and five factors (XRCC1-XRCC2-age-drinking-BQ chewing) were 32.9 [95% CI=14.1-76.9], 31.0 [95% CI=14.0-64.7], 49.8 [95% CI=21.0-117.7] and 82.9 [95% CI=31.0-221.5], respectively. Taken together, the genotypes of XRCC1 rs1799782 and XRCC2 rs2040639 DNA repair genes appear to be significantly associated with oral cancer. These were enhanced by exposure to certain environmental factors. The observations presented here warrant further research in larger study samples to examine their relevance for routine clinical care in oncology.
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Affiliation(s)
- Cheng-Hong Yang
- 1 Department of Electronic Engineering, National Kaohsiung University of Applied Sciences , Kaohsiung, Taiwan
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dos Santos Pereira J, Fontes FL, de Medeiros SRB, de Almeida Freitas R, de Souza LB, da Costa Miguel MC. Association of the XPD and XRCC3 gene polymorphisms with oral squamous cell carcinoma in a Northeastern Brazilian population: A pilot study. Arch Oral Biol 2015; 64:19-23. [PMID: 26742000 DOI: 10.1016/j.archoralbio.2015.12.004] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2015] [Revised: 10/06/2015] [Accepted: 12/19/2015] [Indexed: 10/22/2022]
Abstract
OBJECTIVE to evaluate the association between XPD and XRCC3 polymorphisms and oral squamous cell carcinoma (OSCC). DESIGN the sample consisted of 54 cases of OSCC and 40 cases of inflammatory fibrous hyperplasia (IFH). Genotypes were determined by the polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) method. RESULTS XPD-Lys/Gln was more common in IFH (n=28; 70%) than in OSCC (n=24; 44.4%) (OR: 0.3; p<0.05). XPD-Gln was more frequent in high-grade lesions (0.48) than in low-grade lesions (0.21) (OR: 3.4; p<0.05). The Gln/Gln genotype was associated with III and IV clinical stages (OR: 0.07; p<0.05). XRCC3-Met was more frequent in OSCC (0.49) than in IFH (0.35) (OR: 2.6; p<0.05). The Met/Met genotype was associated with the presence of metastases (OR: 8.1; p<0.05) and with III and IV clinical stages (OR: 0.07; p<0.05). CONCLUSIONS in this sample, the frequency of XPD-Gln in IFH suggests that this variant may protect against OSCC. The presence of the XRCC3-Met allele seems to contribute to the development of OSCC, metastases and more advanced stages in these lesions.
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Affiliation(s)
- Joabe dos Santos Pereira
- Departament of Pathology, Federal University of Rio Grande do Norte, Natal, Rio Grande do Norte, Brazil
| | - Fabrícia Lima Fontes
- Department of Cellular Biology and Genetics, Federal University of Rio Grande do Norte, Natal, Rio Grande do Norte, Brazil
| | | | - Roseana de Almeida Freitas
- Post-Graduation Program of Oral Pathology, Departament of Dentistry, Federal University of Rio Grande do Norte, Natal, Rio Grande do Norte, Brazil
| | - Lélia Batista de Souza
- Post-Graduation Program of Oral Pathology, Departament of Dentistry, Federal University of Rio Grande do Norte, Natal, Rio Grande do Norte, Brazil
| | - Márcia Cristina da Costa Miguel
- Post-Graduation Program of Oral Pathology, Departament of Dentistry, Federal University of Rio Grande do Norte, Natal, Rio Grande do Norte, Brazil.
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Chuang LY, Cheng YH, Yang CH. PCR-CTPP design for enzyme-free SNP genotyping using memetic algorithm. IEEE Trans Nanobioscience 2015; 14:13-23. [PMID: 25730498 DOI: 10.1109/tnb.2015.2392782] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
In recent years, many single nucleotide polymorphisms (SNPs) have been successfully genotyped by polymerase chain reaction with confronting two-pair primers (PCR-CTPP). However, computation experiments of feasible CTPP primers are still challenging. The melting temperatures between four primers must be within a very narrow range, and many primer constraints need to be conformed to. PCR-CTPP is a simple, time- and cost-effective SNP genotyping method applied in molecular biology and biomedical fields. In this study, an MA (memetic algorithm)-based method is proposed to enable the design of feasible CTPP primer sets. Overall, 288 SNPs which exclude the deletion/insertion polymorphisms (DIPs) and multi-nucleotide polymorphisms (MNPs) in the SLC6A4 gene were tested in silico. The results were compared with a GA (genetic algorithm)-based method and indicate that the proposed method provides more feasible CTPP primers than the GA-based method. The MA-based CTPP primer design method provides critical melting temperatures and all kinds of evaluation of the common primer constraints. It could conceivably assist biologists and other researchers in obtaining feasible CTTP primer sets. The MA-CTPP algorithm is implemented in JAVA and a user-friendly input interface is freely available at http://bio.kuas.edu.tw/ma-ctpp/.
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The Combinational Polymorphisms of ORAI1 Gene Are Associated with Preventive Models of Breast Cancer in the Taiwanese. BIOMED RESEARCH INTERNATIONAL 2015; 2015:281263. [PMID: 26380267 PMCID: PMC4561876 DOI: 10.1155/2015/281263] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/04/2014] [Accepted: 01/21/2015] [Indexed: 11/26/2022]
Abstract
The ORAI calcium release-activated calcium modulator 1 (ORAI1) has been proven to be an important gene for breast cancer progression and metastasis. However, the protective association model between the single nucleotide polymorphisms (SNPs) of ORAI1 gene was not investigated. Based on a published data set of 345 female breast cancer patients and 290 female controls, we used a particle swarm optimization (PSO) algorithm to identify the possible protective models of breast cancer association in terms of the SNPs of ORAI1 gene. Results showed that the PSO-generated models of 2-SNP (rs12320939-TT/rs12313273-CC), 3-SNP (rs12320939-TT/rs12313273-CC/rs712853-(TT/TC)), 4-SNP (rs12320939-TT/rs12313273-CC/rs7135617-(GG/GT)/rs712853-(TT/TC)), and 5-SNP (rs12320939-TT/rs12313273-CC/rs7135617-(GG/GT)/rs6486795-CC/rs712853-(TT/TC)) displayed low values of odds ratios (0.409–0.425) for breast cancer association. Taken together, these results suggested that our proposed PSO strategy is powerful to identify the combinational SNPs of rs12320939, rs12313273, rs7135617, rs6486795, and rs712853 of ORAI1 gene with a strongly protective association in breast cancer.
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Farnebo L, Stjernström A, Fredrikson M, Ansell A, Garvin S, Thunell LK. DNA repair genes XPC, XPD, XRCC1, and XRCC3 are associated with risk and survival of squamous cell carcinoma of the head and neck. DNA Repair (Amst) 2015; 31:64-72. [DOI: 10.1016/j.dnarep.2015.05.003] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2014] [Revised: 05/03/2015] [Accepted: 05/05/2015] [Indexed: 12/25/2022]
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Association study between novel CYP26 polymorphisms and the risk of betel quid-related malignant oral disorders. ScientificWorldJournal 2015; 2015:160185. [PMID: 25839051 PMCID: PMC4369936 DOI: 10.1155/2015/160185] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2014] [Accepted: 06/26/2014] [Indexed: 01/14/2023] Open
Abstract
BQ chewing may produce significant amounts of reactive oxygen species (ROS), resulting in oral mucosa damage, and ROS may be metabolized by CYP26 families. Because the CYP26 polymorphisms associated with malignant oral disorders are not well known, we conducted an association study on the associations between the single nucleotide polymorphisms (SNP) of CYP26 families and the risks of malignant oral disorders. BQ chewers with the CYP26A1 rs4411227 C/C+C/G genotype and C allele showed an increased risk of oral and pharyngeal cancer (adjusted odds ratio (aOR) = 2.30 and 1.93, respectively). The CYP26B1 rs3768647 G allele may be associated with oral and pharyngeal cancer (aOR = 3.12) and OPMDs (aOR = 2.23). Subjects with the rs9309462 CT genotype and C allele had an increased risk of oral and pharyngeal cancer (aOR = 9.24 and 8.86, respectively) and OPMDs (aOR = 8.17 and 7.87, respectively). The analysis of joint effects between the CYP26A1 rs4411227 and CYP26B1 rs3768647/rs9309462 polymorphisms revealed statistical significance (aOR = 29.91 and 10.03, respectively). Additionally, we observed a significant mRNA expression of CY26A1 and CYP26B1 in cancerous tissues compared with adjacent noncancerous tissues. Our findings suggest that novel CYP26 polymorphisms are associated with an increased risk of malignant oral disorders, particularly among BQ chewers.
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Xu K, Song X, Chen Z, Qin C, He Y, Zhan W. XRCC2 promotes colorectal cancer cell growth, regulates cell cycle progression, and apoptosis. Medicine (Baltimore) 2014; 93:e294. [PMID: 25526472 PMCID: PMC4603138 DOI: 10.1097/md.0000000000000294] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
X-ray repair complementing defective repair in Chinese hamster cells 2 (XRCC2) and poly(ADP-ribose) polymerase 1 (PARP1) both play important roles in homologous recombination DNA repair. According to the theory of synthetic lethality, XRCC2-deficient cells are more sensitive to PARP1 inhibitors compared to XRCC2-expressing cells. We investigated XRCC2 expression and function in colorectal cancer (CRC), and the characteristics of sensitivity to PARP1 inhibitor in CRC cells with different XRCC2 levels. We enrolled 153 patients with CRC who had undergone surgery in this study. XRCC2 expression was assessed using immunohistochemistry. Stable CRC SW480 cell lines with low or high XRCC2 expression were constructed. Following treatment with the PARP1 inhibitor olaparib, the viability of cells with different XRCC2 levels was determined; cell cycle distribution and apoptosis were analyzed using flow cytometry. B-cell lymphoma-2 (Bcl-2) protein expression was measured by Western blotting. The positive rates of XRCC2 in primary CRC tissue were significantly higher than that in the matched adjacent noncancerous tissue, and XRCC2 expression status in primary CRC was related to tumor site, Dukes' stage, and tumor-nodes-metastasis (TNM) stage. XRCC2 overexpression inhibited CRC cell apoptosis and promoted proliferation by enriching cells in the G0/G1 phase. Moreover, olaparib suppressed proliferation, and olaparib sensitivity in CRC cells with high XRCC2 expression was greater. High XRCC2 expression promotes CRC cell proliferation and enriches cells in the G0/G1 phase but inhibits apoptosis. High XRCC2 expression cells are more sensitive to olaparib, which inhibits their viability.
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Affiliation(s)
- Kaiwu Xu
- From the Gastrointestinal and Pancreatic Surgery Department, The First Affiliated Hospital of Sun Yat-Sen University, Guangzhou, Guangdong Province, People's Republic of China
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SNP 1772 C > T of HIF-1α gene associates with breast cancer risk in a Taiwanese population. Cancer Cell Int 2014; 14:87. [PMID: 25302049 PMCID: PMC4190286 DOI: 10.1186/s12935-014-0087-7] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2014] [Accepted: 08/25/2014] [Indexed: 02/07/2023] Open
Abstract
Background Hypoxia inducible factor 1α (HIF-1α) is a stress-responsive transcription factor to hypoxia and its expression is correlated to tumor progression and angiogenesis. Several single nucleotide polymorphisms (SNPs) of HIF-1α gene in the oxygen-dependent degradation (ODD) domain was reportedly associated with increased HIF-1α activity. Results In this study, we focused on the relationship between SNP 1772 C > T (rs11549465) of HIF-1α gene and its breast cancer risk, as well as its correlation with HIF-1α expression and tumor angiogenesis. Ninety six breast cancer patients and 120 age-matched controls were enrolled. We found that 1772 T allele of HIF-1α gene was associated with increased breast cancer risk (adjusted OR = 14.51; 95% CI: 6.74-31.24). This SNP was not associated with clinicopathologic features of angiogenesis such as VEGF activity and the micro-vessel density and survival of breast cancer patients. Conclusion Taken together, the 1772 C > T of HIF-1α gene is a potential biomarker for breast cancer susceptibility.
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Gok I, Baday M, Cetinkunar S, Kilic K, Bilgin BC. Polymorphisms in DNA repair genes XRCC2 and XRCC3 risk of gastric cancer in Turkey. Bosn J Basic Med Sci 2014; 14:214-8. [PMID: 25428673 DOI: 10.17305/bjbms.2014.4.7] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2014] [Revised: 09/06/2014] [Accepted: 09/06/2014] [Indexed: 01/27/2023] Open
Abstract
We studied the prevalence of polymorphisms in genes XRCC2 and XRCC3 in stomach cancer patients who lived in North Eastern Turkey. A total of 61 cancer patients and 78 controls were included in this study. Single nucleotide changes were studied in XRCC2 and XRCC3 genes at locus Arg188His and Thr241Met. Blood samples were taken from the patients and controls, and DNA was isolated. The regions of interest were amplified using a polymerase chain reaction method. After amplification, we used restriction enzymes (HphI and NcoI) to digest the amplified product. Digested product was then run through gel electrophoresis. We identified changes in the nucleotides in these specific regions. It was found that the Arg188His polymorphism of the XRCC2 gene was about 39% (24 out of the 61) among cancer patients. However, only 15% (12 out of 78) of the control group indicated this polymorphism. We also observed that 18 of the 61 cancer patients (29%) carried the Thr241Met polymorphism of the XRCC3 gene whereas 11 of the 78 (14%) individuals in the control group had the polymorphism. Our results showed a significant difference in polymorphism ratios between the cancer patients and health control group for the regions of interest. This result clearly showed that these polymorphisms increase the risk of stomach cancer and might be a strong marker for early diagnosis of gastric cancer.
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Affiliation(s)
- Ilhami Gok
- Department of Bioengineering, Faculty of Engineering & Architecture Kafkas University, 36100 Kars/ Turkey Phone: Fax : +90 474 225 12 82.
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Feng YZ, Liu YL, He XF, Wei W, Shen XL, Xie DL. Association between the XRCC1 Arg194Trp polymorphism and risk of cancer: evidence from 201 case-control studies. Tumour Biol 2014; 35:10677-97. [PMID: 25064613 DOI: 10.1007/s13277-014-2326-x] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2014] [Accepted: 07/07/2014] [Indexed: 12/11/2022] Open
Abstract
The Arg194Trp polymorphism in the X-ray cross-complementing group 1 (XRCC1) had been implicated in cancer susceptibility. The previous published data on the association between XRCC1 Arg194Trp polymorphism and cancer risk remained controversial. Hence, we performed a meta-analysis to investigate the association between cancer susceptibility and XRCC1 Arg194Trp (59,227 cases and 81,587 controls from 201 studies) polymorphism in different inheritance models. We used odds ratios with 95 % confidence intervals to assess the strength of the association. Overall, significantly increased cancer risk was found (recessive model: (odds ration [OR] = 1.18, 95% confidence interval [CI] = 1.09-1.27; homozygous model: OR = 1.21, 95% CI = 1.10-1.33; additive model: OR = 1.05, 95% CI = 1.01-1.09) when all eligible studies were pooled into the meta-analysis. In further stratified and sensitivity analyses, significantly increased glioma risk was found among Asians, significantly decreased lung cancer risk was found among Caucasians, and significant increased breast cancer risk was found among hospital-based studies. In summary, this meta-analysis suggests that Arg194Trp polymorphism may be associated with increased breast cancer risk, Arg194Trp polymorphism is associated with increased glioma risk among Asians, and Arg194Trp polymorphism is associated with decreased lung cancer risk among Caucasians. In addition, our work also points out the importance of new studies for Arg194Trp association in some cancer types, such as gastric, pancreatic, prostate, and nasopharyngeal cancers, where at least some of the covariates responsible for heterogeneity could be controlled, to obtain a more conclusive understanding about the function of the XRCC1 Arg194Trp polymorphism in cancer development (I (2) > 75%).
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Affiliation(s)
- Yan-Zhong Feng
- Department of maternity, Peace Hospital of Changzhi Medical College, Changzhi, 046000, China
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Zhou X, Gu L, Zeng Y, Wei L, Ying M, Wang N, Su C, Wang Y, Liu C. The XRCC1 Arg194Trp and Arg280His polymorphisms in head and neck cancer susceptibility: a meta-analysis. Tumour Biol 2014; 35:10665-76. [PMID: 25062722 DOI: 10.1007/s13277-014-2247-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2014] [Accepted: 06/18/2014] [Indexed: 01/11/2023] Open
Abstract
The XRCC1 Arg194Trp and Arg280His polymorphisms are likely to be implicated with the development of head and neck cancer. However, studies of association have been inconsistent. This meta-analysis of the available literature was performed to make a more precise estimation of the risk associated with these polymorphisms. A comprehensive literature search was conducted to identify all case-control studies of the XRCC1 Arg194Trp and Arg280His polymorphisms in head and neck cancer. Summary odds ratios (ORs) with 95% confidence intervals (CIs) were used to assess the strength of association. A total of 20 eligible studies were selected for this meta-analysis, including 3,362 cases and 5,796 controls for the XRCC1 Arg194Trp polymorphism and 1,932 cases and 2,757 controls for the XRCC1 Arg280His polymorphism. Overall, no significant associations were found in all genetic models when the studies were pooled into the meta-analysis for the Arg194Trp and Arg280His polymorphisms. When stratified by ethnicity, significant associations were found for Arg194Trp polymorphism in CT vs CC (OR = 1.26, 95% CI = 1.05-1.52) and the recessive model (OR = 1.28, 95% CI = 1.07-1.53) in Asian population, and no significant associations were found in non-Asian population in all genetic models. This meta-analysis suggests that the XRCC1 Arg194Trp polymorphism is a risk factor for head and neck cancer in Asian populations.
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Affiliation(s)
- Xue Zhou
- Department of Obstetrics and Gynecology, Shanghai Jiao Tong University Affiliated First People's Hospital, Shanghai, People's Republic of China,
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Farooqi AA, Yaylim I, Ozkan NE, Zaman F, Halim TA, Chang HW. Restoring TRAIL mediated signaling in ovarian cancer cells. Arch Immunol Ther Exp (Warsz) 2014; 62:459-74. [PMID: 25030086 DOI: 10.1007/s00005-014-0307-9] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2013] [Accepted: 06/26/2014] [Indexed: 02/08/2023]
Abstract
Ovarian cancer has emerged as a multifaceted and genomically complex disease. Genetic/epigenetic mutations, suppression of tumor suppressors, overexpression of oncogenes, rewiring of intracellular signaling cascades and loss of apoptosis are some of the deeply studied mechanisms. In vitro and in vivo studies have highlighted different molecular mechanisms that regulate tumor necrosis factor-related apoptosis-inducing ligand (TRAIL) mediated apoptosis in ovarian cancer. In this review, we bring to limelight, expansion in understanding systematical characterization of ovarian cancer cells has led to the rapid development of new drugs and treatments to target negative regulators of TRAIL mediated signaling pathway. Wide ranging synthetic and natural agents have been shown to stimulate mRNA and protein expression of death receptors. This review is compartmentalized into programmed cell death protein 4, platelet-derived growth factor signaling and miRNA control of TRAIL mediated signaling to ovarian cancer. Mapatumumab and PRO95780 have been tested for efficacy against ovarian cancer. Use of high-throughput screening assays will aid in dissecting the heterogeneity of this disease and increasing a long-term survival which might be achieved by translating rapidly accumulating information obtained from molecular and cellular studies to clinic researches.
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Affiliation(s)
- Ammad Ahmad Farooqi
- Laboratory for Translational Oncology and Personalized Medicine, RLMC, 35 km Ferozepur Road, Lahore, Pakistan,
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Choudhury JH, Choudhury B, Kundu S, Ghosh SK. Combined effect of tobacco and DNA repair genes polymorphisms of XRCC1 and XRCC2 influence high risk of head and neck squamous cell carcinoma in northeast Indian population. Med Oncol 2014; 31:67. [PMID: 24958516 DOI: 10.1007/s12032-014-0067-8] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2014] [Accepted: 06/03/2014] [Indexed: 01/12/2023]
Abstract
Tobacco consumption in various forms is one of the major risk factor for the development of head and neck squamous cell carcinoma. Polymorphisms in XRCC1 and XRCC2 genes may alter an individual's susceptibility to tobacco-related cancers. Here, we have investigated the interaction of XRCC1 (Arg399Gln) and XRCC2 (Arg188His) polymorphism and tobacco exposure in the progression of HNSCC in northeast Indian population. The population-based case-control study includes 110 HNSCC patients and 140 controls. The polymorphisms of XRCC1 and XRCC2 were studied by means of PCR-RFLP, and the results were confirmed by DNA sequencing. Smokers and tobacco-betel quid chewers were significantly higher in cases (P = 0.045 and 0.033). The variant homozygote AA genotype of XRCC1 Arg399Gln and heterozygote GA genotype of XRCC2 Arg188His has an increased risk toward HNSCC (OR 2.43; P = 0.031 and OR 3.29; P < 0.01, respectively). The interaction between tobacco-betel quid chewing and variant genotypes of XRCC1 and XRCC2 resulted in several fold increase the risk of HNSCC, when compared to non-chewers. Heavy smokers carrying XRCC1 AA and XRCC2 GA genotypes had a significantly higher risk of HNSCC compared to never smokers (P = 0.017 and 0.003, respectively). Upon gene-gene interaction analysis, individuals carrying both XRCC1 GA (Arg/Gln) and XRCC2 GA (Arg/His) genotypes had the highest risk of HNSCC (P = 0.001).Our finding suggests that interaction of tobacco and polymorphisms of XRCC1 and XRCC2 increases the risk of HNSCC. Furthermore, cross talk between these two DNA repair genes might modulate susceptibility toward HNSCC.
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Affiliation(s)
- Javed Hussain Choudhury
- Department of Biotechnology, Assam University (A Central University), Silchar, 788011, Assam, India
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Xu K, Song X, Chen Z, Qin C, He Y. XRCC2 rs3218536 polymorphism decreases the sensitivity of colorectal cancer cells to poly(ADP-ribose) polymerase 1 inhibitor. Oncol Lett 2014; 8:1222-1228. [PMID: 25120693 PMCID: PMC4114618 DOI: 10.3892/ol.2014.2236] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2013] [Accepted: 05/29/2014] [Indexed: 12/18/2022] Open
Abstract
Single nucleotide polymorphisms (SNPs) are associated with the development of certain types of cancer. The present study aimed to investigate the association between X-ray repair complementing defective repair in Chinese hamster cells 2 (XRCC2) SNPs and colorectal cancer (CRC) cell sensitivity to the poly(ADP-ribose) polymerase (PARP) 1 inhibitor olaparib (AZD2281). SNaPshot® analysis of XRCC2 SNPs was performed in five CRC cell lines. The AZD2281-sensitivities of the CRC cells were also analyzed using MTT assays. The effect of AZD2281 on XRCC2 and PARP1 expression was investigated in the five cell lines using quantitative polymerase chain reaction and western blot analyses. Parallel investigations were performed using a cisplatin (DDP) model of DNA damage. The XRCC2 rs3218536 SNP was found to be associated with the LoVo microsatellite instability CRC cell line. The relative rate of growth inhibition was found to be lower in the LoVo cells following treatment with AZD2281 compared with the other four cell lines (P=0.002). Furthermore, the XRCC2 mRNA level in the LoVo cells was observed to be significantly higher than that in the other four cell lines (P<0.05). Similar results were found using the DDP model of DNA damage (P<0.05). The present study indicated that the XRCC2 rs3218536 polymorphism decreases the sensitivity of CRC cells to AZD2281.
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Affiliation(s)
- Kaiwu Xu
- Department of Gastrointestinal and Pancreatic Surgery, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou, Guangdong 510080, P.R. China
| | - Xinming Song
- Department of Gastrointestinal and Pancreatic Surgery, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou, Guangdong 510080, P.R. China
| | - Zhihui Chen
- Department of Gastrointestinal and Pancreatic Surgery, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou, Guangdong 510080, P.R. China
| | - Changjiang Qin
- Department of Gastrointestinal and Pancreatic Surgery, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou, Guangdong 510080, P.R. China
| | - Yulong He
- Department of Gastrointestinal and Pancreatic Surgery, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou, Guangdong 510080, P.R. China
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Double-bottom chaotic map particle swarm optimization based on chi-square test to determine gene-gene interactions. BIOMED RESEARCH INTERNATIONAL 2014; 2014:172049. [PMID: 24895547 PMCID: PMC4033510 DOI: 10.1155/2014/172049] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/20/2013] [Accepted: 04/16/2014] [Indexed: 11/19/2022]
Abstract
Gene-gene interaction studies focus on the investigation of the association between the single nucleotide polymorphisms (SNPs) of genes for disease susceptibility. Statistical methods are widely used to search for a good model of gene-gene interaction for disease analysis, and the previously determined models have successfully explained the effects between SNPs and diseases. However, the huge numbers of potential combinations of SNP genotypes limit the use of statistical methods for analysing high-order interaction, and finding an available high-order model of gene-gene interaction remains a challenge. In this study, an improved particle swarm optimization with double-bottom chaotic maps (DBM-PSO) was applied to assist statistical methods in the analysis of associated variations to disease susceptibility. A big data set was simulated using the published genotype frequencies of 26 SNPs amongst eight genes for breast cancer. Results showed that the proposed DBM-PSO successfully determined two- to six-order models of gene-gene interaction for the risk association with breast cancer (odds ratio > 1.0; P value <0.05). Analysis results supported that the proposed DBM-PSO can identify good models and provide higher chi-square values than conventional PSO. This study indicates that DBM-PSO is a robust and precise algorithm for determination of gene-gene interaction models for breast cancer.
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Guha N, Warnakulasuriya S, Vlaanderen J, Straif K. Betel quid chewing and the risk of oral and oropharyngeal cancers: A meta-analysis with implications for cancer control. Int J Cancer 2014; 135:1433-43. [DOI: 10.1002/ijc.28643] [Citation(s) in RCA: 136] [Impact Index Per Article: 13.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2013] [Revised: 10/28/2013] [Accepted: 11/18/2013] [Indexed: 11/09/2022]
Affiliation(s)
- Neela Guha
- International Agency for Research on Cancer; Lyon France
| | - Saman Warnakulasuriya
- Division of Oral Medicine; Department of Clinical and Diagnostic Sciences; King's College London Dental Institute at Guy's, King's & St. Thomas' Hospitals; London United Kingdom
- WHO Collaborating Centre for Oral Cancer/Precancer; London United Kingdom
| | | | - Kurt Straif
- International Agency for Research on Cancer; Lyon France
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Chang WC, Fang YY, Chang HW, Chuang LY, Lin YD, Hou MF, Yang CH. Identifying association model for single-nucleotide polymorphisms of ORAI1 gene for breast cancer. Cancer Cell Int 2014; 14:29. [PMID: 24685237 PMCID: PMC3994227 DOI: 10.1186/1475-2867-14-29] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2013] [Accepted: 03/07/2014] [Indexed: 12/20/2022] Open
Abstract
Background ORAI1 channels play an important role for breast cancer progression and metastasis. Previous studies indicated the strong correlation between breast cancer and individual single nucleotide polymorphisms (SNPs) of ORAI1 gene. However, the possible SNP-SNP interaction of ORAI1 gene was not investigated. Results To develop the complex analyses of SNP-SNP interaction, we propose a genetic algorithm (GA) to detect the model of breast cancer association between five SNPs (rs12320939, rs12313273, rs7135617, rs6486795 and rs712853) of ORAI1 gene. For individual SNPs, the differences between case and control groups in five SNPs of ORAI1 gene were not significant. In contrast, GA-generated SNP models show that 2-SNP (rs12320939-GT/rs6486795-CT), 3-SNP (rs12320939-GT/rs12313273-TT/rs6486795-TC), 5-SNP (rs12320939-GG/rs12313273-TC/rs7135617-TT/rs6486795-TT/rs712853-TT) have higher risks for breast cancer in terms of odds ratio analysis (1.357, 1.689, and 13.148, respectively). Conclusion Taken together, the cumulative effects of SNPs of ORAI1 gene in breast cancer association study were well demonstrated in terms of GA-generated SNP models.
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Affiliation(s)
- Wei-Chiao Chang
- Master Program for Clinical Pharmacogenomics and Pharmacoproteomics, School of Pharmacy, Taipei Medical University, Taipei, Taiwan.,Department of Clinical Pharmacy, School of Pharmacy, Taipei Medical University, Taipei, Taiwan.,Cancer Center, Kaohsiung Medical University Hospital, Kaohsiung, Taiwan.,Institute of Clinical Medicine, Kaohsiung Medical University, Kaohsiung, Taiwan
| | - Yong-Yuan Fang
- Labor Safety and Health Office, Kaohsiung Municipal Ta-Tung Hospital, Kaohsiung, Taiwan
| | - Hsueh-Wei Chang
- Cancer Center, Kaohsiung Medical University Hospital, Kaohsiung, Taiwan.,Department of Biomedical Science and Environmental Biology, Kaohsiung Medical University, Kaohsiung, Taiwan.,Institute of Medical Science and Technology, National Sun Yat-sen University, Kaohsiung, Taiwan
| | - Li-Yeh Chuang
- Department of Chemical Engineering & Institute of Biotechnology and Chemical Engineering, I-Shou University, Kaohsiung, Taiwan
| | - Yu-Da Lin
- Department of Electronic Engineering, National Kaohsiung University of Applied Sciences, Kaohsiung, Taiwan
| | - Ming-Feng Hou
- Cancer Center, Kaohsiung Medical University Hospital, Kaohsiung, Taiwan.,Institute of Clinical Medicine, Kaohsiung Medical University, Kaohsiung, Taiwan.,Kaohsiung Municipal Ta-Tung Hospital, Kaohsiung, Taiwan
| | - Cheng-Hong Yang
- Department of Electronic Engineering, National Kaohsiung University of Applied Sciences, Kaohsiung, Taiwan
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Wu W, Liu L, Yin Z, Guan P, Li X, Zhou B. Association of X-ray repair cross-complementing group 1 Arg194Trp, Arg399Gln and Arg280His polymorphisms with head and neck cancer susceptibility: a meta-analysis. PLoS One 2014; 9:e86798. [PMID: 24497981 PMCID: PMC3907446 DOI: 10.1371/journal.pone.0086798] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2013] [Accepted: 12/13/2013] [Indexed: 12/16/2022] Open
Abstract
Background Previous studies on the association of X-ray repair cross-complementing group 1 (XRCC1) Arg194Trp, Arg399Gln, and Arg280His polymorphisms with head and neck cancer (HNC) have produced inconsistent results. The aim of the present study was to evaluate the effects of these three polymorphic variants on HNC risk. Methods The PubMed and EMBASE databases were searched for genetic association studies on the XRCC1 Arg194Trp, Arg399Gln, and Arg280His polymorphisms and HNC risk. (The most recent search was conducted on 20 August, 2013.) Twenty-six studies were identified and meta-analysis was performed to evaluate the association between the polymorphism and HNC by calculating combined odds ratios and 95% confidence intervals. Results No significant association was found under the allelic, homozygous, heterozygote, and dominant genetic models in the overall comparison. Further, no significant association between the XRCC1 Arg399Gln and Arg280His polymorphisms and HNC risk was detected under the four genetic models in subgroup analyses based on ethnicity, cancer site, and whether or not the studies had been adjusted for cigarette smoking and alcohol. However, in stratified analyses based on cancer site, a significant association was found between the XRCC1 Arg194Trp polymorphism and oral cancer under the allelic, heterozygote, and dominant models. The XRCC1 Arg194Trp polymorphism was significantly associated with HNC risk in studies that were adjusted for smoking and alcohol under the homozygous and heterozygote models. Conclusion The meta-analysis results suggest that the XRCC1 Arg399Gln and Arg280His polymorphisms are probably not associated with the risk of HNC, but the XRCC1 Arg194Trp polymorphism was associated with increased risk of HNC in the subgroup analysis of studies adjusted for smoking and alcohol and with increased risk of oral cancer in the stratified analyses based on cancer site. Further studies with larger samples are needed to confirm these findings.
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Affiliation(s)
- Wei Wu
- Department of Epidemiology, School of Public Health, China Medical University, Shenyang, China
- Key Laboratory of Cancer Etiology and Intervention, University of Liaoning Province, Shenyang, China
| | - Lu Liu
- Department of Preventive Dentistry, School of Stomatology, China Medical University, Shenyang, China
| | - Zhihua Yin
- Department of Epidemiology, School of Public Health, China Medical University, Shenyang, China
- Key Laboratory of Cancer Etiology and Intervention, University of Liaoning Province, Shenyang, China
| | - Peng Guan
- Department of Epidemiology, School of Public Health, China Medical University, Shenyang, China
- Key Laboratory of Cancer Etiology and Intervention, University of Liaoning Province, Shenyang, China
| | - Xuelian Li
- Department of Epidemiology, School of Public Health, China Medical University, Shenyang, China
- Key Laboratory of Cancer Etiology and Intervention, University of Liaoning Province, Shenyang, China
| | - Baosen Zhou
- Department of Epidemiology, School of Public Health, China Medical University, Shenyang, China
- Key Laboratory of Cancer Etiology and Intervention, University of Liaoning Province, Shenyang, China
- * E-mail:
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Chuang LY, Lane HY, Lin YD, Lin MT, Yang CH, Chang HW. Identification of SNP barcode biomarkers for genes associated with facial emotion perception using particle swarm optimization algorithm. Ann Gen Psychiatry 2014; 13:15. [PMID: 24955105 PMCID: PMC4050220 DOI: 10.1186/1744-859x-13-15] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/01/2014] [Accepted: 04/23/2014] [Indexed: 01/04/2023] Open
Abstract
BACKGROUND Facial emotion perception (FEP) can affect social function. We previously reported that parts of five tested single-nucleotide polymorphisms (SNPs) in the MET and AKT1 genes may individually affect FEP performance. However, the effects of SNP-SNP interactions on FEP performance remain unclear. METHODS This study compared patients with high and low FEP performances (n = 89 and 93, respectively). A particle swarm optimization (PSO) algorithm was used to identify the best SNP barcodes (i.e., the SNP combinations and genotypes that revealed the largest differences between the high and low FEP groups). RESULTS The analyses of individual SNPs showed no significant differences between the high and low FEP groups. However, comparisons of multiple SNP-SNP interactions involving different combinations of two to five SNPs showed that the best PSO-generated SNP barcodes were significantly associated with high FEP score. The analyses of the joint effects of the best SNP barcodes for two to five interacting SNPs also showed that the best SNP barcodes had significantly higher odds ratios (2.119 to 3.138; P < 0.05) compared to other SNP barcodes. In conclusion, the proposed PSO algorithm effectively identifies the best SNP barcodes that have the strongest associations with FEP performance. CONCLUSIONS This study also proposes a computational methodology for analyzing complex SNP-SNP interactions in social cognition domains such as recognition of facial emotion.
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Affiliation(s)
- Li-Yeh Chuang
- Department of Chemical Engineering & Institute of Biotechnology and Chemical Engineering, I-Shou University, Kaohsiung 84001, Taiwan
| | - Hsien-Yuan Lane
- Institute of Clinical Medical Science, China Medical University, Taichung 40402, Taiwan ; Department of Psychiatry, China Medical University Hospital, Taichung 40402, Taiwan
| | - Yu-Da Lin
- Department of Electronic Engineering, National Kaohsiung University of Applied Sciences, Kaohsiung 80778, Taiwan
| | - Ming-Teng Lin
- Department of Chemical Engineering & Institute of Biotechnology and Chemical Engineering, I-Shou University, Kaohsiung 84001, Taiwan ; Department of Psychiatry, Taipei Veterans General Hospital, Hsinchu Branch, Hsinchu 31064, Taiwan
| | - Cheng-Hong Yang
- Department of Electronic Engineering, National Kaohsiung University of Applied Sciences, Kaohsiung 80778, Taiwan
| | - Hsueh-Wei Chang
- Cancer Center, Translational Research Center, Kaohsiung Medical University Hospital, Kaohsiung Medical University, Kaohsiung 80708, Taiwan ; Institute of Medical Science and Technology, National Sun Yat-sen University, Kaohsiung 80424, Taiwan ; Department of Biomedical Science and Environmental Biology, Kaohsiung Medical University, Kaohsiung 80708, Taiwan
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Genome stability pathways in head and neck cancers. Int J Genomics 2013; 2013:464720. [PMID: 24364026 PMCID: PMC3834617 DOI: 10.1155/2013/464720] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2013] [Revised: 09/19/2013] [Accepted: 09/20/2013] [Indexed: 12/12/2022] Open
Abstract
Genomic instability underlies the transformation of host cells toward malignancy, promotes development of invasion and metastasis and shapes the response of established cancer to treatment. In this review, we discuss recent advances in our understanding of genomic stability in squamous cell carcinoma of the head and neck (HNSCC), with an emphasis on DNA repair pathways. HNSCC is characterized by distinct profiles in genome stability between similarly staged cancers that are reflected in risk, treatment response and outcomes. Defective DNA repair generates chromosomal derangement that can cause subsequent alterations in gene expression, and is a hallmark of progression toward carcinoma. Variable functionality of an increasing spectrum of repair gene polymorphisms is associated with increased cancer risk, while aetiological factors such as human papillomavirus, tobacco and alcohol induce significantly different behaviour in induced malignancy, underpinned by differences in genomic stability. Targeted inhibition of signalling receptors has proven to be a clinically-validated therapy, and protein expression of other DNA repair and signalling molecules associated with cancer behaviour could potentially provide a more refined clinical model for prognosis and treatment prediction. Development and expansion of current genomic stability models is furthering our understanding of HNSCC pathophysiology and uncovering new, promising treatment strategies.
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Chen JB, Chuang LY, Lin YD, Liou CW, Lin TK, Lee WC, Cheng BC, Chang HW, Yang CH. Preventive SNP–SNP interactions in the mitochondrial displacement loop (D-loop) from chronic dialysis patients. Mitochondrion 2013; 13:698-704. [DOI: 10.1016/j.mito.2013.01.013] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2012] [Revised: 01/24/2013] [Accepted: 01/31/2013] [Indexed: 12/01/2022]
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DNA repair gene XRCC1 polymorphisms and head and neck cancer risk: an updated meta-analysis including 16344 subjects. PLoS One 2013; 8:e74059. [PMID: 24086310 PMCID: PMC3781168 DOI: 10.1371/journal.pone.0074059] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2013] [Accepted: 07/29/2013] [Indexed: 12/20/2022] Open
Abstract
BACKGROUND DNA repair gene X-ray repair cross complementing group 1 (XRCC1) plays an important role in the maintenance of the genomic integrity and protection of cells from DNA damage. Sequence variation in XRCC1 gene may alter head and neck cancer (HNC) susceptibility. However, these results are inconclusive. To derive a more precise estimation of the relationship between XRCC1 polymorphism and HNC risk, we undertook a meta-analysis involving 16,344 subjects. METHODS A search of the literature by PubMed, Embase, Web of Science and China National Knowledge Infrastructure was performed to identify studies based on the predetermined inclusion criteria. The odds ratio (OR) with 95% confidence interval (CI) was combined using a random-effects model or a fixed-effects model. RESULTS Twenty-nine studies consisting of 6,719 cases and 9,627 controls were identified and analyzed. Overall, no evidence of significant association was observed between XRCC1 Arg194Trp, XRCC1 Arg280His, XRCC1 Arg399Gln genotypes and the risk of HNC in any genetic models. Subgroup analyses according to ethnicity, tumor site, publication year, genotyping method also detected no significant association in any subgroup, except that oral cancer was associated with Arg194Trp variant in recessive model. Furthermore, no significant effect of these polymorphisms interacted with smoking on HNC risk was detected but Arg194Trp homozygous variant. CONCLUSION In conclusion, this meta-analysis suggests that the XRCC1 Arg194Trp, Arg280His and Arg399Gln polymorphism may not involve in HNC susceptibility. Further studies about gene-gene and gene-environment interactions in different populations are required.
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da Silva ALG, da Rosa HT, Karnopp TE, Charlier CF, Ellwanger JH, Moura DJ, Possuelo LG, Valim ARDM, Guecheva TN, Henriques JAP. Evaluation of DNA damage in COPD patients and its correlation with polymorphisms in repair genes. BMC MEDICAL GENETICS 2013; 14:93. [PMID: 24053728 PMCID: PMC3848611 DOI: 10.1186/1471-2350-14-93] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/17/2013] [Accepted: 09/11/2013] [Indexed: 02/07/2023]
Abstract
BACKGROUND We investigated a potential link between genetic polymorphisms in genes XRCC1 (Arg399Gln), OGG1 (Ser326Cys), XRCC3 (Thr241Met), and XRCC4 (Ile401Thr) with the level of DNA damage and repair, accessed by comet and micronucleus test, in 51 COPD patients and 51 controls. METHODS Peripheral blood was used to perform the alkaline and neutral comet assay; and genetic polymorphisms by PCR/RFLP. To assess the susceptibility to exogenous DNA damage, the cells were treated with methyl methanesulphonate for 1-h or 3-h. After 3-h treatment the % residual damage was calculated assuming the value of 1-h treatment as 100%. The cytogenetic damage was evaluated by buccal micronucleus cytome assay (BMCyt). RESULTS COPD patients with the risk allele XRCC1 (Arg399Gln) and XRCC3 (Thr241Met) showed higher DNA damage by comet assay. The residual damage was higher for COPD with risk allele in the four genes. In COPD patients was showed negative correlation between BMCyt (binucleated, nuclear bud, condensed chromatin and karyorrhexic cells) with pulmonary function and some variant genotypes. CONCLUSION Our results suggest a possible association between variant genotypes in XRCC1 (Arg399Gln), OGG1 (Ser326Cys), XRCC3 (Thr241Met), and XRCC4 (Ile401Thr), DNA damage and progression of COPD.
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Affiliation(s)
- Andréa Lúcia Gonçalves da Silva
- Santa Cruz Hospital and Department of Health and Physical Education, University of Santa Cruz do Sul - UNISC, Avenida Independência, 2293, Bloco 42, Bairro Universitário, Santa Cruz do Sul, RS, Brazil.
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Lin CW, Chuang CY, Tang CH, Chang JL, Lee LM, Lee WJ, Chow JM, Yang SF, Chien MH. Combined effects of icam-1 single-nucleotide polymorphisms and environmental carcinogens on oral cancer susceptibility and clinicopathologic development. PLoS One 2013; 8:e72940. [PMID: 24069166 PMCID: PMC3771971 DOI: 10.1371/journal.pone.0072940] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2013] [Accepted: 07/14/2013] [Indexed: 12/15/2022] Open
Abstract
BACKGROUND In Taiwan, oral cancer has causally been associated with environmental carcinogens. Intercellular adhesion molecule (ICAM)-1, a cell adhesion molecule with a key role in inflammation and immunosurveillance, was implicated in carcinogenesis by facilitating instability in the tumor environment. The current study explored the combined effect of ICAM-1 gene polymorphisms and exposure to environmental carcinogens on the susceptibility of developing oral squamous cell carcinoma (OSCC) and the clinicopathological characteristics of the tumors. METHODOLOGY AND PRINCIPAL FINDINGS Four single-nucleotide polymorphisms (SNPs) of the ICAM-1 gene from 595 patients with oral cancer and 561 non-cancer controls were analyzed by a real-time PCR. We found that the ICAM-1 rs5498 polymorphism and the TAGG or TACG haplotype of 4 ICAM-1 SNPs (rs3093030, rs5491, rs281432, and rs5498) combined were associated with oral-cancer susceptibility. Among 727 smokers, ICAM-1 polymorphisms carriers with the betel-nut chewing habit had a 27.49-36.23-fold greater risk of having oral cancer compared to ICAM-1 wild-type (WT) carriers without the betel-nut chewing habit. Among 549 betel-nut chewers, ICAM-1 polymorphisms carriers who smoked had a 9.93-14.27-fold greater risk of having oral cancer compared to those who carried the WT but did not smoke. Finally, patients with oral cancer who had at least 1 T allele of ICAM-1 rs5491 or 1 G allele of rs281432 were at lower risk of developing an advanced clinical stage (III/IV) (p<0.05), compared to those patients with AA or CC homozygotes. CONCLUSIONS Our results suggest that the ICAM-1 rs5498 SNP and either of 2 haplotypes of 4 SNPs combined have potential predictive significance in oral carcinogenesis. Gene-environment interactions of ICAM-1 polymorphisms, smoking, and betel-nut chewing might alter oral-cancer susceptibility. ICAM-1 rs5491 and rs281432 may be applied as factors to predict the clinical stage in OSCC patients.
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Affiliation(s)
- Chiao-Wen Lin
- Institute of Oral Sciences, Chung Shan Medical University, Taichung, Taiwan
- Department of Dentistry, Chung Shan Medical University Hospital, Taichung, Taiwan
| | - Chun-Yi Chuang
- School of Medicine, Chung Shan Medical University, Taichung, Taiwan
- Department of Otolaryngology, Chung Shan Medical University Hospital, Taichung, Taiwan
| | - Chih-Hsin Tang
- Graduate Institute of Basic Medical Science, China Medical University, Taichung, Taiwan
- Department of Biotechnology, College of Health Science, Asia University, Taichung, Taiwan
| | - Junn-Liang Chang
- Department of Medical Management, Taoyuan Armed Forces General Hospital, Taoyuan County, Taiwan
- School of Medicine, Pathology Department, National Defense Medical Center, Taipei, Taiwan
| | - Liang-Ming Lee
- Department of Urology, Wan Fan Hospital, Taipei Medical University, Taipei, Taiwan
| | - Wei-Jiunn Lee
- Department of Urology, Wan Fan Hospital, Taipei Medical University, Taipei, Taiwan
| | - Jyh-Ming Chow
- Section of Hematology-Oncology, Department of Internal Medicine, Wan Fang Hospital, Taipei Medical University, Taipei, Taiwan
| | - Shun-Fa Yang
- Institute of Medicine, Chung Shan Medical University, Taichung, Taiwan
- Department of Medical Research, Chung Shan Medical University Hospital, Taichung, Taiwan
- * E-mail: (MHC); (SFY)
| | - Ming-Hsien Chien
- Wan Fang Hospital, Taipei Medical University, Taipei, Taiwan
- Graduate Institute of Clinical Medicine, College of Medicine, Taipei Medical University, Taipei, Taiwan
- * E-mail: (MHC); (SFY)
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