SNP rs16906252C>T is an expression and methylation quantitative trait locus associated with an increased risk of developing MGMT-methylated colorectal cancer

Clinical Cancer Research

Volumn 22, Issue 24, 2016, Pages 6266-6277

  Kuroiwa Trzmielina, Joice ^a   Wang, Fan ^b,c   Rapkins, Robert W ^a   Ward, Robyn L ^a   Buchanan, Daniel D ^d,e   Win, Aung Ko ^e   Clendenning, Mark ^d   Rosty, Christophe ^d,f,g   Southey, Melissa C ^d   Winship, Ingrid M ^d,h   Hopper, John L ^e,i   Jenkins, Mark A ^e   Olivier, Jake ^j   Hawkins, Nicholas J ^j   Hitchins, Megan P ^b  

^a UNIVERSITY OF NEW SOUTH WALES   (Australia)

^b STANFORD UNIVERSITY   (United States)

^c HARBIN MEDICAL UNIVERSITY   (China)

^d UNIVERSITY OF MELBOURNE   (Australia)

^e UNIVERSITY OF MELBOURNE   (Australia)

^f Envoi Specialist Pathologists   (Australia)

^g UNIVERSITY OF QUEENSLAND   (Australia)

^h ROYAL MELBOURNE HOSPITAL   (Australia)

ⁱ Seoul National University   (South Korea)

^j UNIVERSITY OF NEW SOUTH WALES   (Australia)

more..

Author keywords

[No Author keywords available]

Indexed keywords

METHYLATED DNA PROTEIN CYSTEINE METHYLTRANSFERASE; DNA LIGASE; DNA METHYLTRANSFERASE; MGMT PROTEIN, HUMAN; TUMOR SUPPRESSOR PROTEIN;

ARTICLE; AUSTRALIA; CANCER RISK; CANCER SUSCEPTIBILITY; COLORECTAL CANCER; DNA METHYLATION; EPIGENETICS; EXON; GENE EXPRESSION; GENE FREQUENCY; GENETIC VARIABILITY; GENOTYPE; HETEROZYGOTE; HOMOZYGOSITY; HUMAN; MAJOR CLINICAL STUDY; METHYLATION; PRIORITY JOURNAL; PYROSEQUENCING; QUANTITATIVE TRAIT LOCUS; RISK ASSESSMENT; RISK FACTOR; SINGLE NUCLEOTIDE POLYMORPHISM; AGED; ALLELE; CASE CONTROL STUDY; COLORECTAL TUMOR; FEMALE; GENETIC EPIGENESIS; GENETICS; MALE; PROMOTER REGION; RETROSPECTIVE STUDY; RISK;

AGED; ALLELES; CASE-CONTROL STUDIES; COLORECTAL NEOPLASMS; DNA METHYLATION; DNA MODIFICATION METHYLASES; DNA REPAIR ENZYMES; EPIGENESIS, GENETIC; FEMALE; GENOTYPE; HUMANS; MALE; O(6)-METHYLGUANINE-DNA METHYLTRANSFERASE; POLYMORPHISM, SINGLE NUCLEOTIDE; PROMOTER REGIONS, GENETIC; QUANTITATIVE TRAIT LOCI; RETROSPECTIVE STUDIES; RISK; TUMOR SUPPRESSOR PROTEINS;

EID: 85006980125     PISSN: 10780432     EISSN: 15573265     Source Type: Journal    
DOI: 10.1158/1078-0432.CCR-15-2765     Document Type: Article

References (38)

1. Esteller M, Hamilton SR, Burger PC, Baylin SB, Herman JG. Inactivation of the DNA repair gene O6-methylguanine-DNA methyltransferase by promoter hypermethylation is a common event in primary human neoplasia. Cancer Res 1999;59:793-7.
2. Hawkins NJ, Lee JH, Wong JJ, Kwok CT, Ward RL, Hitchins MP. MGMT methylation is associated primarily with the germline C>T SNP (rs16906252) in colorectal cancer and normal colonic mucosa. Mod Pathol 2009;22:1588-99.
3. Esteller M, Garcia-Foncillas J, Andion E, Goodman SN, Hidalgo OF, Vanaclocha V, et al. Inactivation of the DNA-repair gene MGMT and the clinical response of gliomas to alkylating agents. N Engl J Med 2000;343:1350-4.
4. Esteller M, Gaidano G, Goodman SN, Zagonel V, Capello D, Botto B, et al. Hypermethylation of the DNA repair gene O(6)-methylguanine DNA methyltransferase and survival of patients with diffuse large B-cell lymphoma. J Natl Cancer Inst 2002;94:26-32.
5. Hegi ME, Diserens AC, Gorlia T, Hamou MF, de Tribolet N, Weller M, et al. MGMT gene silencing and benefit from temozolomide in glioblastoma. N Engl J Med 2005;352:997-1003.
6. Kreth S, Thon N, Eigenbrod S, Lutz J, Ledderose C, Egensperger R, et al. O-methylguanine-DNA methyltransferase (MGMT) mRNA expression predicts outcome in malignant glioma independent of MGMT promoter methylation. PLoS One 2011;6:e17156.
7. Brown CC, Havener TM, Medina MW, Auman JT, Mangravite LM, Krauss RM, et al. A genome-wide association analysis of temozolomide response using lymphoblastoid cell lines shows a clinically relevant association with MGMT. Pharmacogenet Genomics 2012;22:796-802.
8. Rapkins RW, Wang F, Nguyen HN, Cloughesy TF, Lai A, Ha W, et al. The MGMT promoter SNP rs16906252 is a risk factor for MGMT methylation in glioblastoma and is predictive of response to temozolomide. Neuro Oncol 2015;17:1589-98.
9. Hinoue T, Weisenberger DJ, Lange CP, Shen H, Byun HM, Van Den Berg D, et al. Genome-scale analysis of aberrant DNA methylation in colorectal cancer. Genome Res 2012;22:271-82.
10. Guinney J, Dienstmann R, Wang X, de Reynies A, Schlicker A, Soneson C, et al. The consensus molecular subtypes of colorectal cancer. Nat Med 2015;21:1350-6.
11. Weisenberger DJ, Siegmund KD, Campan M, Young J, Long TI, Faasse MA, et al. CpG island methylator phenotype underlies sporadic microsatellite instability and is tightly associated with BRAF mutation in colorectal cancer. Nat Genet 2006;38:787-93.
12. Shen L, Toyota M, Kondo Y, Lin E, Zhang L, Guo Y, et al. Integrated genetic and epigenetic analysis identifies three different subclasses of colon cancer. Proc Natl Acad Sci U S A 2007;104:18654-9.
13. Ogino S, Kawasaki T, Kirkner GJ, Loda M, Fuchs CS. CpG island methylator phenotype-low (CIMP-low) in colorectal cancer: possible associations with male sex and KRAS mutations. J Mol Diagn 2006;8:582-8.
14. Esteller M, Toyota M, Sanchez-Cespedes M, Capella G, Peinado MA, Watkins DN, et al. Inactivation of the DNA repair gene O6-methylguanine-DNA methyltransferase by promoter hypermethylation is associated with G to A mutations in K-ras in colorectal tumorigenesis. Cancer Res 2000;60:2368-71.
15. Nagasaka T, Goel A, Notohara K, Takahata T, Sasamoto H, Uchida T, et al. Methylation pattern of the O6-methylguanine-DNA methyltransferase gene in colon during progressive colorectal tumorigenesis. Int J Cancer 2008;122:2429-36.
16. Shen L, Kondo Y, Rosner GL, Xiao L, Hernandez NS, Vilaythong J, et al. MGMT promoter methylation and field defect in sporadic colorectal cancer. J Natl Cancer Inst 2005;97:1330-8.
17. Whitehall VL, Walsh MD, Young J, Leggett BA, Jass JR. Methylation of O-6-methylguanine DNA methyltransferase characterizes a subset of colorectal cancer with low-level DNA microsatellite instability. Cancer Res 2001;61:827-30.
18. Deng G, Kakar S, Tanaka H, Matsuzaki K, Miura S, Sleisenger MH, et al. Proximal and distal colorectal cancers show distinct gene-specific methylation profiles and clinical and molecular characteristics. Eur J Cancer 2008;44:1290-301.
19. Rosty C, Young JP, Walsh MD, Clendenning M, Walters RJ, Pearson S, et al. Colorectal carcinomas with KRAS mutation are associated with distinctive morphological and molecular features. Mod Pathol 2013;26:825-34.
20. Ogino S, Kawasaki T, Kirkner GJ, Suemoto Y, Meyerhardt JA, Fuchs CS. Molecular correlates with MGMT promoter methylation and silencing support CpG island methylator phenotype-low (CIMP-low) in colorectal cancer. Gut 2007;56:1564-71.
21. Ogino S, Hazra A, Tranah GJ, Kirkner GJ, Kawasaki T, Nosho K, et al. MGMT germline polymorphism is associated with somatic MGMT promoter methylation and gene silencing in colorectal cancer. Carcinogenesis 2007;28:1985-90.
22. Leng S, Bernauer AM, Hong C, Do KC, Yingling CM, Flores KG, et al. The A/G allele of rs16906252 predicts for MGMT methylation and is selectively silenced in premalignant lesions from smokers and in lung adenocarcinomas. Clin Cancer Res 2011;17:2014-23.
23. Kristensen LS, Nielsen HM, Hager H, Hansen LL. Methylation of MGMT in malignant pleural mesothelioma occurs in a subset of patients and is associated with the T allele of the rs16906252 MGMT promoter SNP. Lung Cancer 2011;71:130-6.
24. McDonald KL, Rapkins RW, Olivier J, Zhao L, Nozue K, Lu D, et al. The T genotype of the MGMT C>T (rs16906252) enhancer single-nucleotide polymorphism (SNP) is associated with promoter methylation and longer survival in glioblastoma patients. Eur J Cancer 2013;49:360-8.
25. Kristensen LS, Treppendahl MB, Asmar F, Girkov MS, Nielsen HM, Kjeldsen TE, et al. Investigation of MGMT and DAPK1 methylation patterns in diffuse large B-cell lymphoma using allelic MSP-pyrosequencing. Sci Rep 2013;3:2789.
26. Candiloro IL, Dobrovic A. Detection of MGMT promoter methylation in normal individuals is strongly associated with the T allele of the rs16906252 MGMT promoter single nucleotide polymorphism. Cancer Prev Res 2009;2:862-7.
27. Slaughter DP, Southwick HW, Smejkal W. Field cancerization in oral stratified squamous epithelium; clinical implications of multicentric origin. Cancer 1953;6:963-8.
28. Harris LC, Remack JS, Brent TP. Identification of a 59 bp enhancer located at the first exon/intron boundary of the human O6-methylguanine DNA methyltransferase gene. Nucleic Acids Res 1994;22:4614-9.
29. Chen FY, Harris LC, Remack JS, Brent TP. Cytoplasmic sequestration of an O6-methylguanine-DNA methyltransferase enhancer binding protein in DNA repair-deficient human cells. Proc Natl Acad Sci U S A 1997;94:4348-53.
30. Stirzaker C, Song JZ, Davidson B, Clark SJ. Transcriptional gene silencing promotes DNA hypermethylation through a sequential change in chromatin modifications in cancer cells. Cancer Res 2004;64:3871-7.
31. Winship I, Win AK. The Australasian Colorectal Cancer Family Registry. Med J Aust 2012;197:480-1.
32. Ogino S, Kawasaki T, Brahmandam M, Cantor M, Kirkner GJ, Spiegelman D, et al. Precision and performance characteristics of bisulfite conversion and real-time PCR (MethyLight) for quantitative DNA methylation analysis. J Mol Diagn 2006;8:209-17.
33. Kwok CT, Hitchins MP. Allele Quantification Pyrosequencing(R) at designated SNP sites to detect allelic expression imbalance and loss-of-heterozygosity. Methods Mol Biol 2015;1315:153-71.
34. Ogino S, Stampfer M. Lifestyle factors and microsatellite instability in colorectal cancer: the evolving field of molecular pathological epidemiology. J Natl Cancer Inst 2010;102:365-7.
35. Ogino S, Chan AT, Fuchs CS, Giovannucci E. Molecular pathological epidemiology of colorectal neoplasia: an emerging transdisciplinary and interdisciplinary field. Gut 2011;60:397-411.
36. Ogino S, Campbell PT, Nishihara R, Phipps AI, Beck AH, Sherman ME, et al. Proceedings of the second international molecular pathological epidemiology (MPE) meeting. Cancer Causes Control 2015;26:959-72.
37. Ogino S, King EE, Beck AH, Sherman ME, Milner DA, Giovannucci E. Interdisciplinary education to integrate pathology and epidemiology: towards molecular and population-level health science. Am J Epidemiol 2012;176:659-67.
38. Heyn H, Sayols S, Moutinho C, Vidal E, Sanchez-Mut JV, Stefansson OA, et al. Linkage of DNA methylation quantitative trait loci to human cancer risk. Cell Rep 2014;7:331-8.