Integrated analysis of genetic and epigenetic alterations reveals CpG island methylator phenotype associated with distinct clinical characters of lung adenocarcinoma

Carcinogenesis

Volumn 33, Issue 7, 2012, Pages 1277-1285

  Shinjo, Keiko ^a,b   Okamoto, Yasuyuki ^a   An, Byonggu ^a   Yokoyama, Toshihiko ^b   Takeuchi, Ichiro ^c   Fujii, Makiko ^a   Osada, Hirotaka ^a,b   Usami, Noriyasu ^b   Hasegawa, Yoshinori ^b   Ito, Hidemi ^a   Hida, Toyoaki ^a   Fujimoto, Nobukazu ^d   Kishimoto, Takumi ^d   Sekido, Yoshitaka ^a,b   Kondo, Yutaka ^a,e  

^a AICHI CANCER CENTER HOSPITAL   (Japan)

^b NAGOYA UNIVERSITY GRADUATE SCHOOL OF MEDICINE   (Japan)

^c NAGOYA INSTITUTE OF TECHNOLOGY   (Japan)

^d OKAYAMA ROSAI HOSPITAL   (Japan)

^e JAPAN SCIENCE AND TECHNOLOGY AGENCY   (Japan)

Author keywords

[No Author keywords available]

Indexed keywords

B RAF KINASE; BISULFITE; EPIDERMAL GROWTH FACTOR RECEPTOR; PROTEIN P53;

ADULT; AGED; ARTICLE; CANCER PATIENT; CANCER PROGNOSIS; CLINICAL FEATURE; CONTROLLED STUDY; CPG ISLAND; CPG ISLAND METHYLATOR PHENOTYPE; DNA METHYLATION; FEMALE; GENE MUTATION; GENETIC ASSOCIATION; HUMAN; LUNG ADENOCARCINOMA; MAJOR CLINICAL STUDY; MALE; MICROARRAY ANALYSIS; PRIORITY JOURNAL; PYROSEQUENCING; SMOKING; WILD TYPE;

ADENOCARCINOMA; AGED; CPG ISLANDS; DNA METHYLATION; EPIGENESIS, GENETIC; FEMALE; HUMANS; LUNG NEOPLASMS; MALE; MIDDLE AGED; PHENOTYPE;

EID: 84865160485     PISSN: 01433334     EISSN: 14602180     Source Type: Journal    
DOI: 10.1093/carcin/bgs154     Document Type: Article

References (45)

1. Jemal,A. et al. (2010) Cancer statistics, 2010. CA Cancer J. Clin., 60, 277-
2. Mitsudomi,T. et al. (2010) Gefitinib versus cisplatin plus docetaxel in patients with non-small-cell lung cancer harbouring mutations of the epidermal growth factor receptor (WJTOG3405): an open label, randomised phase 3 trial. Lancet Oncol., 11, 121-128.
3. Choi,Y.L. et al. (2010) EML4-ALK mutations in lung cancer that confer resistance to ALK inhibitors. N. Engl. J. Med., 363, 1734-1739.
4. Belinsky,S.A. (2004) Gene-promoter hypermethylation as a biomarker in lung cancer. Nat. Rev. Cancer, 4, 707-717.
5. Jones,P.A. et al. (2002) The fundamental role of epigenetic events in cancer. Nat. Rev. Genet., 3, 415-428.
6. Jones,P.A. et al. (2007) The epigenomics of cancer. Cell, 128, 683-692.
7. Toyota,M. et al. (1999) CpG island methylator phenotype in colorectal cancer. Proc. Natl Acad. Sci. USA, 96, 8681-8686.
8. Grady,W.M. (2007) CIMP and colon cancer gets more complicated. Gut, 56, 1498-1500.
9. Suzuki,M. et al. (2006) Exclusive mutation in epidermal growth factor receptor gene, HER-2, and KRAS, and synchronous methylation of nonsmall cell lung cancer. Cancer, 106, 2200-2207.
10. Marsit,C.J. et al. (2006) Examination of a CpG island methylator phenotype and implications of methylation profiles in solid tumors. Cancer Res., 66, 10621-10629.
11. Liu,Z. et al. (2008) CpG island methylator phenotype involving tumor suppressor genes located on chromosome 3p in non-small cell lung cancer. Lung Cancer, 62, 15-22.
12. Suzuki,M. et al. (2010) Molecular characterization of chronic obstructive pulmonary disease-related non-small cell lung cancer through aberrant methylation and alterations of EGFR signaling. Ann. Surg. Oncol., 17, 878-888.
13. Zhang,Y. et al. (2011) Methylation of multiple genes as a candidate biomarker in non-small cell lung cancer. Cancer Lett., 303, 21-28.
14. Weisenberger,D.J. et al. (2006) CpG island methylator phenotype underlies sporadic microsatellite instability and is tightly associated with BRAF mutation in colorectal cancer. Nat. Genet., 38, 787-793.
15. Ogino,S. et al. (2006) CpG island methylator phenotype-low (CIMP-low) in colorectal cancer: possible associations with male sex and KRAS mutations. J. Mol. Diagn., 8, 582-588.
16. Shen,L. et al. (2007) Integrated genetic and epigenetic analysis identifies three different subclasses of colon cancer. Proc. Natl Acad. Sci. USA, 104, 18654-18659.
17. Gao,W. et al. (2008) Variable DNA methylation patterns associated with progression of disease in hepatocellular carcinomas. Carcinogenesis, 29, 1901-1910.
18. Goto,Y. et al. (2009) Epigenetic profiles distinguish malignant pleural mesothelioma from lung adenocarcinoma. Cancer Res., 69, 9073-9082.
19. An,B. et al. (2010) A characteristic methylation profile in CpG island methylator phenotype-negative distal colorectal cancers. Int. J. Cancer, 127, 2095-2105.
20. Okamoto,Y. et al. (2012) Aberrant DNA methylation associated with aggressiveness of gastrointestinal stromal tumour. Gut, 61, 392-401.
21. Yang,A.S. et al. (2004) A simple method for estimating global DNA methylation using bisulfite PCR of repetitive DNA elements. Nucleic Acids Res., 32, e38.
22. Kondo,Y. et al. (2007) Alterations of DNA methylation and histone modifications contribute to gene silencing in hepatocellular carcinomas. Hepatol Res., 37, 974-983.
23. Eisen,M.B. et al. (1998) Cluster analysis and display of genome-wide expression patterns. Proc. Natl Acad. Sci. USA, 95, 14863-14868.
24. Cover,T. et al. (1967) Nearest neighbor pattern classification. IEEE Trans. Inform. Theory, 13, 21-27.
25. Yokoyama,T. et al. (2006) EGFR point mutation in non-small cell lung cancer is occasionally accompanied by a second mutation or amplification. Cancer Sci., 97, 753-759.
26. Ogino,S. et al. (2005) Sensitive sequencing method for KRAS mutation detection by pyrosequencing. J. Mol. Diagn., 7, 413-421.
27. Spittle,C. et al. (2007) Application of a BRAF pyrosequencing assay for mutation detection and copy number analysis in malignant melanoma. J. Mol. Diagn., 9, 464-471.
28. Monti,S. et al. (2003) Consensus clustering: a resampling-based method for class discovery and visualization of gene expression microarray data. Mach. Learn., 52, 91-118.
29. Toyota,M. et al. (2000) Distinct genetic profiles in colorectal tumors with or without the CpG island methylator phenotype. Proc. Natl Acad. Sci. USA, 97, 710-715.
30. Noushmehr,H. et al. (2010) Identification of a CpG island methylator phenotype that defines a distinct subgroup of glioma. Cancer Cell, 17, 510-
31. Fang,F. et al. (2011) Breast cancer methylomes establish an epigenomic foundation for metastasis. Sci. Transl. Med., 3, 75ra25.
32. Issa,J.P. (2004) CpG island methylator phenotype in cancer. Nat. Rev. Cancer, 4, 988-993.
33. Lu,K.H. et al. (2004) Selection of potential markers for epithelial ovarian cancer with gene expression arrays and recursive descent partition analysis. Clin. Cancer Res., 10, 3291-3300.
34. Eberhard,D.A. et al. (2005) Mutations in the epidermal growth factor receptor and in KRAS are predictive and prognostic indicators in patients with non-small-cell lung cancer treated with chemotherapy alone and in combination with erlotinib. J. Clin. Oncol., 23, 5900-5909.
35. Toyooka,S. et al. (2006) Mutational and epigenetic evidence for independent pathways for lung adenocarcinomas arising in smokers and never smokers. Cancer Res., 66, 1371-1375.
36. Samowitz,W.S. et al. (2006) Association of smoking, CpG island methylator phenotype, and V600E BRAF mutations in colon cancer. J. Natl Cancer Inst., 98, 1731-1738.
37. Limsui,D. et al. (2010) Cigarette smoking and colorectal cancer risk by molecularly defined subtypes. J. Natl Cancer Inst., 102, 1012-1022.
38. Shen,L. et al. (2010) DNA methylation predicts survival and response to therapy in patients with myelodysplastic syndromes. J. Clin. Oncol., 28, 605-613.
39. Ogino,S. et al. (2008) Molecular classification and correlates in colorectal cancer. J. Mol. Diagn., 10, 13-27.
40. Yagi,K. et al. (2010) Three DNA methylation epigenotypes in human colorectal cancer. Clin. Cancer Res., 16, 21-33.
41. Silverman,L.R. et al. (2002) Randomized controlled trial of azacitidine in patients with the myelodysplastic syndrome: a study of the cancer and leukemia group B. J. Clin. Oncol., 20, 2429-2440.
42. Kantarjian,H. et al. (2006) Decitabine improves patient outcomes in myelodysplastic syndromes: results of a phase III randomized study. Cancer, 106, 1794-1803.
43. Schrump,D.S. et al. (2006) Phase I study of decitabine-mediated gene expression in patients with cancers involving the lungs, esophagus, or pleura. Clin. Cancer Res., 12, 5777-5785.
44. Momparler,R.L. et al. (2001) Potential of 5-aza-2'-deoxycytidine (Decitabine) a potent inhibitor of DNA methylation for therapy of advanced non-small cell lung cancer. Lung Cancer, 34 (suppl. 4), S111-S115.
45. Garcia-Manero,G. (2010) Prognosis of myelodysplastic syndromes. Hematology Am. Soc. Hematol. Educ. Program, 2010, 330-337.