Quantitative DNA methylation and recurrence of breast cancer: A study of 30 candidate genes

Cancer Biomarkers

Volumn 11, Issue 2-3, 2012, Pages 75-88

  Cheol Kim, Dae ^a,b   Thorat, Mangesh A ^b   Lee, Mi Ri ^a   Cho, Se Heon ^a   Vasiljević, Nataša ^b   Scibior Bentkowska, Dorota ^b   Wu, Keqiang ^b   Ahmad, Amar S ^b   Duffy, Stephen ^b   Cuzick, Jack M ^b   Lorincz, Attila T ^b  

^a Dong A University   (South Korea)

^b QUEEN MARY UNIVERSITY OF LONDON   (United Kingdom)

Author keywords

biomarker; Breast cancer; DNA Methylation; prognosis; pyrosequencing

Indexed keywords

BISULFITE; HLA A ANTIGEN; SLIT2 PROTEIN; TRANSCRIPTION FACTOR NKX2.5;

ADULT; ARTICLE; BREAST CANCER; CANCER PROGNOSIS; CANCER REGRESSION; CANCER RISK; CANCER SURVIVAL; CONTROLLED STUDY; DNA METHYLATION; FOLLOW UP; HUMAN; HUMAN TISSUE; KOREA; MAJOR CLINICAL STUDY; MULTIVARIATE ANALYSIS; PRIORITY JOURNAL; PYROSEQUENCING; QUANTITATIVE ANALYSIS; SERPINB5 GENE; SFN GENE; TUMOR GENE; TUMOR SUPPRESSOR GENE; TWIST1 GENE;

BREAST NEOPLASMS; DISEASE PROGRESSION; DNA METHYLATION; FEMALE; HUMANS; KAPLAN-MEIER ESTIMATE; MIDDLE AGED; NEOPLASM RECURRENCE, LOCAL; PROGNOSIS; SURVIVAL ANALYSIS; TUMOR MARKERS, BIOLOGICAL;

EID: 84867519436     PISSN: 15740153     EISSN: 18758592     Source Type: Journal    
DOI: 10.3233/CBM-2012-0266     Document Type: Article

References (44)

1. J. Ferlay, H. R. Shin, F. Bray, D. Forman, C. Mathers and D. M. Parkin, Estimates of worldwide burden of cancer in 2008: GLOBOCAN 2008. Int J Cancer, 127(12), (2010), 2893-917.
2. M. A. Thorat, What caused the decline in US breast cancer incidence? Nat Clin Pract Oncol, 5(6), (2008), 314-5. (Pubitemid 351780948)
3. I. Jatoi and A. B. Miller, Why is breast-cancer mortality declining? Lancet Oncol, 4(4), (2003), 251-4. (Pubitemid 36503323)
4. D. A. Berry, K. A. Cronin, S. K. Plevritis, D. G. Fryback, L. Clarke, M. Zelen, et al., Effect of screening and adjuvant therapy on mortality from breast cancer. N Engl J Med, 353(17), (2005), 1784-92. (Pubitemid 41549890)
5. L. Harris, H. Fritsche, R. Mennel, L. Norton, P. Ravdin, S. Taube, et al., American Society of Clinical Oncology 2007 update of recommendations for the use of tumor markers in breast cancer. J Clin Oncol, 25(33), (2007), 5287-312. (Pubitemid 350232263)
6. J. A. Sparano, TAILORx: trial assigning individualized options for treatment (Rx). Clin Breast Cancer, 7(4), (2006), 347-50. (Pubitemid 44717771)
7. J. Bogaerts, F. Cardoso, M. Buyse, S. Braga, S. Loi, J. A. Harrison, et al., Gene signature evaluation as a prognostic tool: challenges in the design of theMINDACT trial. Nat Clin Pract Oncol, 3(10), (2006), 540-51. (Pubitemid 44781724)
8. F. O. Ademuyiwa, A. Miller, T. O'Connor, S. B. Edge, M. A. Thorat, G. W. Sledge, et al., The effects of oncotype DX recurrence scores on chemotherapy utilization in a multiinstitutional breast cancer cohort. Breast Cancer Res Treat, 126(3), (2011), 797-802.
9. M. A. Thorat, Gene-signature-based prognostic tools in breast cancer: not yet. Lancet, 369(9571), (2007), 1428. (Pubitemid 46646953)
10. M. A. Thorat, Herceptin in early breast cancer: a call for judicious use. Natl Med J India, 18(6), (2005), 315-7.
11. S. B. Baylin, S. A. Belinsky and J. G. Herman, Aberrant methylation of gene promoters in cancer-concepts, misconcepts, and promise. J Natl Cancer Inst, 92(18), (2000), 1460-1.
12. P. A. Jones, DNA methylation errors and cancer. Cancer Res, 56(11), (1996), 2463-7. (Pubitemid 26170673)
13. P. A. Jones and P.W. Laird, Cancer epigenetics comes of age. Nat Genet, 21(2), (1999), 163-7. (Pubitemid 29070360)
14. J. A. Ronneberg, T. Fleischer, H. K. Solvang, S. H. Nordgard, H. Edvardsen, I. Potapenko, et al., Methylation profiling with a panel of cancer related genes: association with estrogen receptor, TP53 mutation status and expression subtypes in sporadic breast cancer. Mol Oncol, 5(1), 61-76.
15. S. Kamalakaran, V. Varadan, H. E. Giercksky Russnes, D. Levy, J.Kendall, A. Janevski, et al., DNAmethylation patterns in luminal breast cancers differ from non-luminal subtypes and can identify relapse risk independent of other clinical variables. Mol Oncol, 5(1), 77-92.
16. D. F. Ransohoff, Rules of evidence for cancer molecularmarker discovery and validation. Nat Rev Cancer, 4(4), (2004), 309-14. (Pubitemid 38525286)
17. M. A. Cobleigh, P. Bitterman, J. Baker, M. Cronin, M. L. Liu, R. Borchik, et al., Tumor Gene Expression Predicts Distant Disease-Free Survival (DDFS) in Breast Cancer Patients with 10 or More Positive Nodes: High Throughput RT-PCR Assay of Paraffin-Embedded Tumor Tissues. Proc Am Soc Clin Oncol, 22, (2003), 850.
18. S. Marsh, Pyrosequencing applications. Methods Mol Biol, 373, (2007), 15-24.
19. N. Vasiljevic, K. Wu, A. R. Brentnall, D. C. Kim, M. A. Thorat, S. C. Kudahetti, et al., Absolute quantitation of DNA methylation of 28 candidate genes in prostate cancer using pyrosequencing. Dis Markers, 30(4), 151-61.
20. R. L. Camp, M. Dolled-Filhart and D. L. Rimm, X-tile: a new bio-informatics tool for biomarker assessment and outcomebased cut-point optimization. Clin Cancer Res, 10(21), (2004), 7252-9. (Pubitemid 39487712)
21. R. D. C. Team. R: A Language and Environment for Statistical Computing. In R Foundation for Statistical Computing: Vienna, Austria, 2009.
22. M. Esteller, P. G. Corn, S. B. Baylin and J. G. Herman, A gene hypermethylation profile of human cancer. Cancer Res, 61(8), (2001), 3225-9. (Pubitemid 32695003)
23. J. Singer-Sam, M. Grant, J. M. LeBon, K. Okuyama, V. Chapman, M. Monk, et al., Use of a HpaII-polymerase chain reaction assay to study DNA methylation in the Pgk-1 CpG island of mouse embryos at the time of X-chromosome inactivation. Mol Cell Biol, 10(9), (1990), 4987-9.
24. M. Frommer, L. E. McDonald, D. S. Millar, C. M. Collis, F. Watt, G.W. Grigg, et al., A genomic sequencing protocol that yields a positive display of 5-methylcytosine residues in individual DNA strands. Proc Natl Acad Sci USA, 89(5), (1992), 1827-31.
25. S. Huang, Gene expression profiling, genetic networks, and cellular states: an integrating concept for tumorigenesis and drug discovery. J MolMed, 77(6), (1999), 469-80. (Pubitemid 29372579)
26. J. G. Herman, J. R. Graff, S. Myohanen, B. D. Nelkin and S. B. Baylin, Methylation-specific PCR: a novel PCR assay for methylation status of CpG islands. Proc Natl Acad Sci USA, 93(18), (1996), 9821-6. (Pubitemid 26296693)
27. S. Derks, M. H. Lentjes, D. M. Hellebrekers, A. P. de Bruine, J. G. Herman andM. van Engeland, Methylation-specific PCR unraveled. Cell Oncol, 26(5-6), (2004), 291-9. (Pubitemid 40916730)
28. S. A. Belinsky, D.M. Klinge, J. D. Dekker, M.W. Smith, T. J. Bocklage, F. D. Gilliland, et al., Gene promoter methylation in plasma and sputum increases with lung cancer risk. Clin Cancer Res, 11(18), (2005), 6505-11. (Pubitemid 41338988)
29. K. Kawamoto, H. Enokida, T. Gotanda, H. Kubo, K. Nishiyama, M. Kawahara, et al., p16INK4a and p14ARF methylation as a potential biomarker for human bladder cancer. Biochem Biophys Res Commun, 339(3), (2006), 790-6. (Pubitemid 41772883)
30. T. Langaee and M. Ronaghi, Genetic variation analyses by Pyrosequencing. Mutat Res, 573(1-2), (2005), 96-102.
31. S. Ogino, T. Kawasaki, M. Brahmandam, L. Yan, M. Cantor, C. Namgyal, et al., Sensitive sequencing method for KRAS mutation detection by Pyrosequencing. J Mol Diagn, 7(3), (2005), 413-21. (Pubitemid 41149657)
32. S. C. Clarke, Pyrosequencing: nucleotide sequencing technology with bacterial genotyping applications. Expert Rev Mol Diagn, 5(6), (2005), 947-53. (Pubitemid 41666188)
33. J. Tost and I. G. Gut, DNA methylation analysis by pyrosequencing. Nat Protoc, 2(9), (2007), 2265-75. (Pubitemid 351575045)
34. Y. A. Cho, J. Kim, K. S. Park, S. Y. Lim, A. Shin, M. K. Sung, et al., Effect of dietary soy intake on breast cancer risk according to menopause and hormone receptor status. Eur J Clin Nutr, 64(9), 924-32.
35. A. Shin, J. Kim, S. Y. Lim, G. Kim, M. K. Sung, E. S. Lee, et al., Dietary mushroom intake and the risk of breast cancer based on hormone receptor status. Nutr Cancer, 62(4), 476-83.
36. B. A. Miller, L. N. Kolonel, L. Bernstein, J. J. L. Young, G. M. Swanson, D. West, et al. Racial/Ethnic Patterns of Cancer in the United States, 1988-1992. In National Cancer Institute. NIH Pub. No. 96-4104, Miller BA, ed.; Diane Publishing: Bethsda, MD, 1996.
37. L. A. Carey, C. M. Perou, C. A. Livasy, L. G. Dressler, D. Cowan, K. Conway, et al., Race, breast cancer subtypes, and survival in the Carolina Breast Cancer Study. JAMA, 295(21), (2006), 2492-502. (Pubitemid 43854964)
38. M. L. Telli, E. T. Chang, A. W. Kurian, T. H. Keegan, L. A. McClure, D. Lichtensztajn, et al., Asian ethnicity and breast cancer subtypes: a study from the California Cancer Registry. Breast Cancer Res Treat, 127(2), (2011), 471-478.
39. D. H. Choi, D. B. Shin, M. H. Lee, D.W. Lee, D. Dhandapani, D. Carter, et al., A comparison of five immunohistochemical biomarkers and HER-2/neu gene amplification by fluorescence in situ hybridization in white and Korean patients with early-onset breast carcinoma. Cancer, 98(8), (2003), 1587-95. (Pubitemid 37238613)
40. R. A. Whipple, M. A. Matrone, E. H. Cho, E. M. Balzer, M. I. Vitolo, J. R. Yoon, et al., Epithelial-to-mesenchymal transition promotes tubulin detyrosination and microtentacles that enhance endothelial engagement. Cancer Res, 70(20), 8127-37.
41. E. Foubert, B. De Craene and G. Berx, Key signalling nodes in mammary gland development and cancer. The Snail1-Twist1 conspiracy in malignant breast cancer progression. Breast Cancer Res, 12(3), 206.
42. F.Vesuna,A. Lisok, B. Kimble andV.Raman, Twistmodulates breast cancer stem cells by transcriptional regulation of CD24 expression. Neoplasia, 11(12), (2009), 1318-28.
43. E. W. Wilker, M. A. van Vugt, S. A. Artim, P. H. Huang, C. P. Petersen, H. C. Reinhardt, et al., 14-3-3sigma controls mitotic translation to facilitate cytokinesis. Nature, 446(7133), (2007), 329-32. (Pubitemid 46426148)
44. A. Dallol, N. F. Da Silva, P. Viacava, J. D.Minna, I. Bieche, E. R. Maher, et al., SLIT2, a human homologue of the Drosophila Slit2 gene, has tumor suppressor activity and is frequently inactivated in lung and breast cancers. Cancer Res, 62(20), (2002), 5874-80. (Pubitemid 35204748)