DNA hypermethylation in lung cancer is targeted at differentiation- associated genes

Oncogene

Volumn 31, Issue 9, 2012, Pages 1181-1188

  Helman, E ^a   Naxerova, K ^b   Kohane, I S ^a  

^a HARVARD MIT DIVISION OF HEALTH SCIENCES AND TECHNOLOGY   (United States)

^b MASSACHUSETTS GENERAL HOSPITAL   (United States)

Author keywords

development; gene expression; Hypermethylation; non small cell lung cancer

Indexed keywords

ARTICLE; CANCER CELL CULTURE; CARCINOGENESIS; CELL DEDIFFERENTIATION; CPG ISLAND; DEVELOPMENTAL STAGE; DNA METHYLATION; EPIGENETICS; GENE EXPRESSION; GENE SILENCING; GENETIC TRANSCRIPTION; HUMAN; HUMAN CELL; LUNG CANCER; LUNG DEVELOPMENT; MORPHOGENESIS; PRIORITY JOURNAL; TUMOR SUPPRESSOR GENE;

ANIMALS; CARCINOMA, NON-SMALL-CELL LUNG; CELL TRANSFORMATION, NEOPLASTIC; CPG ISLANDS; DNA METHYLATION; EPIGENOMICS; GENE EXPRESSION REGULATION, NEOPLASTIC; GENES, TUMOR SUPPRESSOR; HUMANS; LUNG NEOPLASMS; MICE; MICE, INBRED C57BL;

MURINAE;

EID: 84857785696     PISSN: 09509232     EISSN: 14765594     Source Type: Journal    
DOI: 10.1038/onc.2011.307     Document Type: Article

References (49)

1. Antequera F, Boyes J, Bird A. (1990). High levels of de novo methylation and altered chromatin structure at CpG islands in cell lines. Cell 62: 503-514.
2. Armstrong L, Lako M, Dean W, Stojkovic M. (2006). Epigenetic modification is central to genome reprogramming in somatic cell nuclear transfer. Stem Cells 24: 805-814.
3. Banerjee S, Bacanamwo M. (2010). DNA methyltransferase inhibition induces mouse embryonic stem cell differentiation into endothelial cells. Exp Cell Res 316: 172-180.
4. Baylin SB, Herman JG. (2000). DNA hypermethylation in tumorigenesis: epigenetics joins genetics. Trends Genet 16: 168-174.
5. Baylin SB, Herman JG, Graff JR, Vertino PM, Issa JP. (1998). Alterations in DNA methylation: a fundamental aspect of neoplasia. Adv Cancer Res 72: 141-196.
6. Belinsky SA. (2004). Gene-promoter hypermethylation as a biomarker in lung cancer. Nat Rev Cancer 4: 707-717.
7. Belinsky SA, Nikula KJ, Palmisano WA, Michels R, Saccomanno G, Gabrielson E et al. (1998). Aberrant methylation of p16INK4a is an early event in lung cancer and a potential biomarker for early diagnosis. Proc Natl Acad Sci USA 95: 11891-11896.
8. Borczuk AC, Gorenstein L, Walter KL, Assaad AA, Wang L, Powell CA. (2003). Non-small-cell lung cancer molecular signatures recapitulate lung developmental pathways. Am J Pathol 163: 1949-1960.
9. Costello JF, Frü hwald MC, Smiraglia DJ, Rush LJ, Robertson GP, Gao X et al. (2000). Aberrant CpG-island methylation has non-random and tumor-type-specific patterns. Nat Genet 24: 132-138.
10. Delgado S, Gómez M, Bird A, Antequera F. (1998). Initiation of DNA replication at CpG islands in mammalian chromosomes. EMBO J 17: 2426-2435.
11. Esteller M. (2002). CpG island hypermethylation and tumor suppressor genes: a booming present, a brighter future. Oncogene 21: 5427-5440.
12. Esteller M. (2005). Aberrant DNA methylation as a cancer-inducing mechanism. Annu Rev Pharmacol Toxicol 45: 629-656.
13. Esteller M, Corn PG, Baylin SB, Herman JG. (2001). A gene hypermethylation profile of human cancer. Cancer Res 61: 3225-3229.
14. Falcon S, Gentleman R. (2007). Using GOstats to test gene lists for GO term association. Bioinformatics 23: 257-258.
15. Feinberg AP, Vogelstein B. (1983). Hypomethylation distinguishes genes of some human cancers from their normal counterparts. Nature 301: 89-92.
16. Fraga MF, Ballestar E, Paz MF, Ropero S, Setien F, Ballestar ML et al. (2005). Epigenetic differences arise during the lifetime of monozygotic twins. Proc Natl Acad Sci USA 102: 10604-10609.
17. Gentleman RC, Carey VJ, Bates DM, Bolstad B, Dettling M, Dudoit S et al. (2004). Bioconductor: open software development for computational biology and bioinformatics. Genome Biol 5: R80.
18. Gonzalez-Zulueta M, Bender CM, Yang AS, Nguyen T, Beart RW, Van Tornout JM et al. (1995). Methylation of the 50 CpG island of the p16/CDKN2 tumor suppressor gene in normal and transformed human tissues correlates with gene silencing. Cancer Res 55: 4531-4535.
19. Greger V, Passarge E, Höpping W, Messmer E, Horsthemke B. (1989). Epigenetic changes may contribute to the formation and spontaneous regression of retinoblastoma. Hum Genet 83: 155-158.
20. Hajkova P, Erhardt S, Lane N, Haaf T, El-Maarri O, Reik W et al. (2002). Epigenetic reprogramming in mouse primordial germ cells. Mech Dev 117: 15-23.
21. Hayslip J, Montero A. (2006). Tumor suppressor gene methylation in follicular lymphoma: a comprehensive review. Mol Cancer 5: 44.
22. Heller G, Zielinski CC, Zö chbauer-Müller S. (2010). Lung cancer: from single-gene methylation to methylome profiling. Cancer Metastasis Rev 29: 95-107.
23. Herman JG, Merlo A, Mao L, Lapidus RG, Issa JP, Davidson NE et al. (1995). Inactivation of the CDKN2/p16/MTS1 gene is frequently associated with aberrant DNA methylation in all common human cancers. Cancer Res 55: 4525-4530.
24. Irizarry RA, Hobbs B, Collin F, Beazer-Barclay YD, Antonellis KJ, Scherf U et al. (2003). Exploration, normalization, and summaries of high density oligonucleotide array probe level data. Biostatistics 4: 249-264.
25. Keshet I, Lieman-Hurwitz J, Cedar H. (1986). DNA methylation affects the formation of active chromatin. Cell 44: 535-543.
26. Kho AT, Zhao Q, Cai Z, Butte AJ, Kim JY, Pomeroy SL et al. (2004). Conserved mechanisms across development and tumorigenesis revealed by a mouse development perspective of human cancers. Genes Dev 18: 629-640.
27. Laird PW. (2003). The power and the promise of DNA methylation markers. Nat Rev Cancer 3: 253-266.
28. Liu H, Kho AT, Kohane IS, Sun Y. (2006). Predicting survival within the lung cancer histopathological hierarchy using a multi-scale genomic model of development. PLoS Med 3: e232.
29. Marchevsky AM, Tsou JA, Laird-Offringa IA. (2004). Classification of individual lung cancer cell lines based on DNA methylation markers: use of linear discriminant analysis and artificial neural networks. J Mol Diagn 6: 28-36.
30. McLaren A. (2000). Germ and somatic cell lineages in the developing gonad. Mol Cell Endocrinol 163: 3-9.
31. Meissner A, Mikkelsen TS, Gu H, Wernig M, Hanna J, Sivachenko A et al. (2008). Genome-scale DNA methylation maps of pluripotent and differentiated cells. Nature 454: 766-770.
32. Merlo A, Herman JG, Mao L, Lee DJ, Gabrielson E, Burger PC et al. (1995). 5' CpG island methylation is associated with transcriptional silencing of the tumor suppressor p16/CDKN2/MTS1 in human cancers. Nat Med 1: 686-692.
33. Momparler RL, Bouchard J, Samson J. (1985). Induction of differentiation and inhibition of DNA methylation in HL-60 myeloid leukemic cells by 5-AZA-20-deoxycytidine. Leuk Res 9: 1361-1366.
34. Naxerova K, Bult CJ, Peaston A, Fancher K, Knowles BB, Kasif S et al. (2008). Analysis of gene expression in a developmental context emphasizes distinct biological leitmotifs in human cancers. Genome Biol 9: R108.
35. Nephew K. (2003). Epigenetic gene silencing in cancer initiation and progression. Cancer Lett 190: 125-133.
36. Nuovo GJ, Plaia TW, Belinsky SA, Baylin SB, Herman JG. (1999). In situ detection of the hypermethylation-induced inactivation of the p16 gene as an early event in oncogenesis. Proc Natl Acad Sci USA 96: 12754-12759.
37. Pfeifer GP, Rauch TA. (2009). DNA methylation patterns in lung carcinomas. Semin Cancer Biol 19: 181-187.
38. Rauch T, Wang Z, Zhang X, Zhong X, Wu X, Lau SK et al. (2007). Homeobox gene methylation in lung cancer studied by genome-wide analysis with a microarray-based methylated CpG island recovery assay. Proc Natl Acad Sci USA 104: 5527-5532.
39. Rauch TA, Zhong X, Wu X, Wang M, Kernstine KH, Wang Z et al. (2008). High-resolution mapping of DNA hypermethylation and hypomethylation in lung cancer. Proc Natl Acad Sci USA 105: 252-257.
40. Safar AM, Spencer III H, Su X, Coffey M, Cooney CA, Ratnasinghe LD et al. (2005). Methylation profiling of archived non-small cell lung cancer: a promising prognostic system. Clin Cancer Res 11: 4400-4405.
41. Sakai T, Toguchida J, Ohtani N, Yandell DW, Rapaport JM, Dryja TP et al. (1991). Allele-specific hypermethylation of the retinoblastoma tumor-suppressor gene. Am J Hum Genet 48: 880-888.
42. Sasaki H, Matsui Y. (2008). Epigenetic events in mammalian germ-cell development: reprogramming and beyond. Nat Rev Genet 9: 129-140.
43. Shames DS, Girard L, Gao B, Sato M, Lewis CM, Shivapurkar N et al. (2006). A genome-wide screen for promoter methylation inlung cancer identifies novel methylation markers for multiple malignancies. PLoS Med 3: e486.
44. Taylor SM, Jones PA. (1979). Multiple new phenotypes induced in 10T1/2 and 3T3 cells treated with 5-azacytidine. Cell 17: 771-779.
45. Tsou JA, Hagen JA, Carpenter CL, Laird-Offringa IA. (2002). DNA methylation analysis: a powerful new tool for lung cancer diagnosis. Oncogene 21: 5450-5461.
46. Ushijima T. (2005). Detection and interpretation of altered methylation patterns in cancer cells. Nat Rev Cancer 5: 223-231.
47. Wang Y, Leung FCC. (2004). An evaluation of new criteria for CpG islands in the human genome as gene markers. Bioinformatics 20: 1170-1177.
48. Xu C, Police S, Rao N, Carpenter MK. (2002). Characterization and enrichment of cardiomyocytes derived from human embryonic stem cells. Circ Res 91: 501-508.
49. Yoon BS, Yoo SJ, Lee JE, You S, Lee HT, Yoon HS. (2006). Enhanced differentiation of human embryonic stem cells into cardiomyocytes by combining hanging drop culture and 5-azacytidine treatment. Differentiation 74: 149-159.