The cumulative effects of polymorphisms in the DNA mismatch repair genes and tobacco smoking in oesophageal cancer risk

PLoS ONE

Volumn 7, Issue 5, 2012, Pages

  Vogelsang, Matjaz ^a,b   Wang, Yabing ^a   Veber, Nika ^a   Mwapagha, Lamech M ^a   Parker, M Iqbal ^a  

^a UNIVERSITY OF CAPE TOWN   (South Africa)

^b NATIONAL INSTITUTE OF CHEMISTRY   (Slovenia)

Author keywords

[No Author keywords available]

Indexed keywords

ADULT; ARTICLE; BLACK AFRICAN; CANCER RISK; CASE CONTROL STUDY; CAUCASIAN; CONTROLLED STUDY; ESOPHAGEAL SQUAMOUS CELL CARCINOMA; ETHNIC GROUP; EXPOSURE; FEMALE; GENE; GENE FREQUENCY; GENE INTERACTION; GENETIC ANALYSIS; GENETIC ASSOCIATION; GENETIC SELECTION; GENETIC SUSCEPTIBILITY; GENETIC VARIABILITY; GENOTYPE; GENOTYPE ENVIRONMENT INTERACTION; GENOTYPING TECHNIQUE; HUMAN; MAJOR CLINICAL STUDY; MALE; MISMATCH REPAIR; MISMATCH REPAIR GENE; MLH1 GENE; MLH3 GENE; MSH2 GENE; MSH3 GENE; PATHOGENESIS; PMS1 GENE; POPULATION GENETIC STRUCTURE; SINGLE NUCLEOTIDE POLYMORPHISM; SMOKING; SOUTH AFRICA; ESOPHAGUS TUMOR; GENETICS; HAPLOTYPE; NEGRO; RISK FACTOR;

NICOTIANA TABACUM;

POLYDEOXYRIBONUCLEOTIDE SYNTHASE;

AFRICAN CONTINENTAL ANCESTRY GROUP; CASE-CONTROL STUDIES; DNA REPAIR ENZYMES; ESOPHAGEAL NEOPLASMS; EUROPEAN CONTINENTAL ANCESTRY GROUP; GENETIC ASSOCIATION STUDIES; GENOTYPE; HAPLOTYPES; HUMANS; POLYMORPHISM, SINGLE NUCLEOTIDE; RISK FACTORS; SMOKING; SOUTH AFRICA;

EID: 84862109148     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0036962     Document Type: Article

References (63)

1. National Health Laboratory Service, National Cancer Registry of South Africa (2004) Incidence of histologically diagnosed Cancer in South Africa. 19 Available: http://www.nioh.ac.za/assets/files/cancer%20%202004pdf. Accessed 2012 March.
2. Hendricks D, Parker MI, (2002) Oesophageal cancer in Africa. IUBMB Life 53: 263-268.
3. Layke JC, Lopez PP, (2006) Esophageal cancer: a review and update. Am Fam Physician 73: 2187-2194.
4. Cheung WY, Liu G, (2009) Genetic variations in esophageal cancer risk and prognosis. Gastroenterol Clin North Am 38: 75-91, viii.
5. Hiyama T, Yoshihara M, Tanaka S, Chayama K, (2007) Genetic polymorphisms and esophageal cancer risk. Int J Cancer 121: 1643-1658.
6. Liu CY, Wu MC, Chen F, Ter-Minassian M, Asomaning K, et al. (2010) A Large-scale genetic association study of esophageal adenocarcinoma risk. Carcinogenesis 31: 1259-1263.
7. Abnet CC, Freedman ND, Hu N, Wang Z, Yu K, et al. (2010) A shared susceptibility locus in PLCE1 at 10q23 for gastric adenocarcinoma and esophageal squamous cell carcinoma. Nat Genet 42: 764-767.
8. McKay JD, Truong T, Gaborieau V, Chabrier A, Chuang SC, et al. (2011) A genome-wide association study of upper aerodigestive tract cancers conducted within the INHANCE consortium. PLoS Genet 7: e1001333.
9. Wang LD, Zhou FY, Li XM, Sun LD, Song X, et al. (2010) Genome-wide association study of esophageal squamous cell carcinoma in Chinese subjects identifies susceptibility loci at PLCE1 and C20orf54. Nat Genet 42: 759-763.
10. An Y, Jin G, Wang H, Wang Y, Liu H, et al. (2008) Polymorphisms in hMLH1 and risk of early-onset lung cancer in a southeast Chinese population. Lung Cancer 59: 164-170.
11. Hirao T, Nelson HH, Ashok TD, Wain JC, Mark EJ, et al. (2001) Tobacco smoke-induced DNA damage and an early age of smoking initiation induce chromosome loss at 3p21 in lung cancer. Cancer Res 61: 612-615.
12. Lo YL, Hsiao CF, Jou YS, Chang GC, Tsai YH, et al. (2011) Polymorphisms of MLH1 and MSH2 genes and the risk of lung cancer among never smokers. Lung Cancer 72: 280-286.
13. Park SH, Lee GY, Jeon HS, Lee SJ, Kim KM, et al. (2004)-93G->A polymorphism of hMLH1 and risk of primary lung cancer. Int J Cancer 112: 678-682.
14. Wei Q, Eicher SA, Guan Y, Cheng L, Xu J, et al. (1998) Reduced expression of hMLH1 and hGTBP/hMSH6: a risk factor for head and neck cancer. Cancer Epidemiol Biomarkers Prev 7: 309-314.
15. Li GM, (2008) Mechanisms and functions of DNA mismatch repair. Cell Res 18: 85-98.
16. Evans SC, Gillis A, Geldenhuys L, Vaninetti NM, Malatjalian DA, et al. (2004) Microsatellite instability in esophageal adenocarcinoma. Cancer Lett 212: 241-251.
17. Gleeson CM, Sloan JM, McGuigan JA, Ritchie AJ, Weber JL, et al. (1996) Ubiquitous somatic alterations at microsatellite alleles occur infrequently in Barrett's-associated esophageal adenocarcinoma. Cancer Res 56: 259-263.
18. Ikeguchi M, Unate H, Maeta M, Kaibara N, (1999) Detection of loss of heterozygosityat microsatellite loci in esophageal squamous-cell carcinoma. Oncology 56: 164-168.
19. Kagawa Y, Yoshida K, Hirai T, Toge T, Yokozaki H, et al. (2000) Microsatellite instability in squamous cell carcinomas and dysplasias of the esophagus. Anticancer Res 20: 213-217.
20. Kulke MH, Thakore KS, Thomas G, Wang H, Loda M, et al. (2001) Microsatellite instability and hMLH1/hMSH2 expression in Barrett esophagus-associated adenocarcinoma. Cancer 91: 1451-1457.
21. Meltzer SJ, Yin J, Manin B, Rhyu MG, Cottrell J, et al. (1994) Microsatellite instability occurs frequently and in both diploid and aneuploid cell populations of Barrett's-associated esophageal adenocarcinomas. Cancer Res 54: 3379-3382.
22. Muzeau F, Flejou JF, Belghiti J, Thomas G, Hamelin R, (1997) Infrequent microsatellite instability in oesophageal cancers. Br J Cancer 75: 1336-1339.
23. Naidoo R, Ramburan A, Reddi A, Chetty R, (2005) Aberrations in the mismatch repair genes and the clinical impact on oesophageal squamous carcinomas from a high incidence area in South Africa. J Clin Pathol 58: 281-284.
24. Nakashima H, Mori M, Mimori K, Inoue H, Shibuta K, et al. (1995) Microsatellite instability in Japanese esophageal carcinoma. Int J Cancer 64: 286-289.
25. Ogasawara S, Maesawa C, Tamura G, Satodate R, (1995) Frequent microsatellite alterations on chromosome 3p in esophageal squamous cell carcinoma. Cancer Res 55: 891-894.
26. Uehara H, Miyamoto M, Kato K, Cho Y, Kurokawa T, et al. (2005) Deficiency of hMLH1 and hMSH2 expression is a poor prognostic factor in esophageal squamous cell carcinoma. J Surg Oncol 92: 109-115.
27. Uchida N, Kumimoto H, Nishizawa K, Tokumasu S, Harada H, et al. (2001) Mismatch repair and microsatellite instability in esophageal cancer cells. Int J Cancer 91: 687-691.
28. Wang L, Li W, Wang X, Zhang C, Zhang T, et al. (1996) Genetic alterations on chromosomes 3 and 9 of esophageal cancer tissues from China. Oncogene 12: 699-703.
29. Yanagi M, Keller G, Mueller J, Walch A, Werner M, et al. (2000) Comparison of loss of heterozygosity and microsatellite instability in adenocarcinomas of the distal esophagus and proximal stomach. Virchows Arch 437: 605-610.
30. Conde J, Silva SN, Azevedo AP, Teixeira V, Pina JE, et al. (2009) Association of common variants in mismatch repair genes and breast cancer susceptibility: a multigene study. BMC Cancer 9: 344.
31. Hirata H, Hinoda Y, Kawamoto K, Kikuno N, Suehiro Y, et al. (2008) Mismatch repair gene MSH3 polymorphism is associated with the risk of sporadic prostate cancer. J Urol 179: 2020-2024.
32. Boland CR, Goel A, (2010) Microsatellite instability in colorectal cancer. Gastroenterology 138: 2073-2087 e2073.
33. Doss CG, Sethumadhavan R, (2009) Investigation on the role of nsSNPs in HNPCC genes-a bioinformatics approach. J Biomed Sci 16: 42.
34. Michiels S, Danoy P, Dessen P, Bera A, Boulet T, et al. (2007) Polymorphism discovery in 62 DNA repair genes and haplotype associations with risks for lung and head and neck cancers. Carcinogenesis 28: 1731-1739.
35. Gabriel SB, Schaffner SF, Nguyen H, Moore JM, Roy J, et al. (2002) The structure of haplotype blocks in the human genome. Science 296: 2225-2229.
36. Reich DE, Cargill M, Bolk S, Ireland J, Sabeti PC, et al. (2001) Linkage disequilibrium in the human genome. Nature 411: 199-204.
37. Tishkoff SA, Williams SM, (2002) Genetic analysis of African populations: human evolution and complex disease. Nat Rev Genet 3: 611-621.
38. Calle ML, Urrea V, Vellalta G, Malats N, Steen KV, (2008) Improving strategies for detecting genetic patterns of disease susceptibility in association studies. Stat Med 27: 6532-6546.
39. Dodd LE, Sengupta S, Chen IH, den Boon JA, Cheng YJ, et al. (2006) Genes involved in DNA repair and nitrosamine metabolism and those located on chromosome 14q32 are dysregulated in nasopharyngeal carcinoma. Cancer Epidemiol Biomarkers Prev 15: 2216-2225.
40. Jin Z, May WS, Gao F, Flagg T, Deng X, (2006) Bcl2 suppresses DNA repair by enhancing c-Myc transcriptional activity. J Biol Chem 281: 14446-14456.
41. Jorquera R, Castonguay A, Schuller HM, (1994) DNA single-strand breaks and toxicity induced by 4-(methyl-nitrosamino)-1-(3- pyridyl)-1-butanone or N-nitrosodimethylamine in hamster and rat liver. Carcinogenesis 15: 389-394.
42. Mijal RS, Thomson NM, Fleischer NL, Pauly GT, Moschel RC, et al. (2004) The repair of the tobacco specific nitrosamine derived adduct O6-[4-Oxo-4-(3-pyridyl)butyl]guanine by O6-alkylguanine-DNA alkyltransferase variants. Chem Res Toxicol 17: 424-434.
43. Hou Y, Gao F, Wang Q, Zhao J, Flagg T, et al. (2007) Bcl2 impedes DNA mismatch repair by directly regulating the hMSH2-hMSH6 heterodimeric complex. J Biol Chem 282: 9279-9287.
44. Dandara C, Li DP, Walther G, Parker MI, (2006) Gene-environment interaction: the role of SULT1A1 and CYP3A5 polymorphisms as risk modifiers for squamous cell carcinoma of the oesophagus. Carcinogenesis 27: 791-797.
45. Lukanich JM, (2003) Section I: epidemiological review. Semin Thorac Cardiovasc Surg 15: 158-166.
46. Yang CX, Wang HY, Wang ZM, Du HZ, Tao DM, et al. (2005) Risk factors for esophageal cancer: a case-control study in South-western China. Asian Pac J Cancer Prev 6: 48-53.
47. Bye H, Prescott NJ, Matejcic M, Rose E, Lewis CM, et al. (2011) Population-specific genetic associations with oesophageal squamous cell carcinoma in South Africa. Carcinogenesis 32: 1855-1861.
48. Li D, Dandara C, Parker MI, (2010) The 341C/T polymorphism in the GSTP1 gene is associated with increased risk of oesophageal cancer. BMC Genet 11: 47.
49. Matejcic M, Li D, Prescott NJ, Lewis CM, Mathew CG, et al. (2011) Association of a deletion of GSTT2B with an altered risk of oesophageal squamous cell carcinoma in a South African population: a case-control study. PLoS One 6: e29366.
50. Dutra LA, Costa PG, Velasco LF, Amato AA, Barra GB, (2008) Allele-specific PCR assay to genotype SNP rs7903146 in TCF7L2 gene for rapid screening of diabetes susceptibility. Arq Bras Endocrinol Metabol 52: 1362-1366.
51. Germer S, Higuchi R, (2003) Homogeneous allele-specific PCR in SNP genotyping. Methods Mol Biol 212: 197-214.
52. Wangkumhang P, Chaichoompu K, Ngamphiw C, Ruangrit U, Chanprasert J, et al. (2007) WASP: a Web-based Allele-Specific PCR assay designing tool for detecting SNPs and mutations. BMC Genomics 8: 275.
53. Benjamini Y, Hochberg Y, (1995) Controlling the False Discovery Rate: a Practical and Powerful Approach to Multiple Testing. Journal of the Royal Statistical Society B 57: 289-300.
54. Gauderman WJ, Morrison JM, (2006) QUANTO 1.1: A computer program for power and sample size calculations for genetic-epidemiology studies. Available:http://hydrauscedu/gxe.
55. Stephens M, Donnelly P, (2003) A comparison of bayesian methods for haplotype reconstruction from population genotype data. Am J Hum Genet 73: 1162-1169.
56. Stephens M, Smith NJ, Donnelly P, (2001) A new statistical method for haplotype reconstruction from population data. Am J Hum Genet 68: 978-989.
57. Calle ML, Urrea V, Malats N, Van Steen K, (2010) mbmdr: an R package for exploring gene-gene interactions associated with binary or quantitative traits. Bioinformatics 26: 2198-2199.
58. Ramakers C, Ruijter JM, Deprez RH, Moorman AF, (2003) Assumption-free analysis of quantitative real-time polymerase chain reaction (PCR) data. Neurosci Lett 339: 62-66.
59. Kumar P, Henikoff S, Ng PC, (2009) Predicting the effects of coding non-synonymous variants on protein function using the SIFT algorithm. Nat Protoc 4: 1073-1081.
60. Ng PC, Henikoff S, (2003) SIFT: Predicting amino acid changes that affect protein function. Nucleic Acids Res 31: 3812-3814.
61. Ramensky V, Bork P, Sunyaev S, (2002) Human non-synonymous SNPs: server and survey. Nucleic Acids Res 30: 3894-3900.
62. Mathe E, Olivier M, Kato S, Ishioka C, Hainaut P, et al. (2006) Computational approaches for predicting the biological effect of p53 missense mutations: a comparison of three sequence analysis based methods. Nucleic Acids Res 34: 1317-1325.
63. Tavtigian SV, Deffenbaugh AM, Yin L, Judkins T, Scholl T, et al. (2006) Comprehensive statistical study of 452 BRCA1 missense substitutions with classification of eight recurrent substitutions as neutral. J Med Genet 43: 295-305.