Cancer and Metastasis Reviews

, Volume 29, Issue 1, pp 95–107 | Cite as

Lung cancer: From single-gene methylation to methylome profiling

  • Gerwin Heller
  • Christoph C. Zielinski
  • Sabine Zöchbauer-Müller
Article

Abstract

DNA methylation as part of the epigenetic gene-silencing complex is a universal occurring change in lung cancer. Numerous studies investigated methylation of specific genes in primary tumors, in serum or plasma samples, and in specimens from the aerodigestive tract epithelium of lung cancer patients. In most studies, single genes or small numbers of genes were analyzed. Moreover, it has been observed that methylation of certain genes can already be detected in samples from the upper aerodigestive tract epithelium of cancer-free heavy smokers. These findings indicated that methylation of certain genes may be a useful biomarker for prognosis, disease recurrence, early detection, and lung cancer risk assessment. So far, several genes were identified which seem to be of worse prognostic relevance when they were found to be methylated. In addition, it has been shown that a panel of markers may be relevant to predict disease recurrence after surgery. In comparison to analysis of single or small numbers of genes, methods for genome-wide detection of methylation were developed recently. These approaches are focused on either pharmacological re-activation of methylated genes followed by expression microarray analysis or on microarray analysis of sodium bisulfite-treated or affinity-enriched methylated DNA sequences. With currently available methods for the simultaneous detection of methylation, up to 28,000 CpG islands can be analyzed. Overall, we are just at the beginning of translating these findings into the clinic and there is hope that future patients will benefit from these results.

Keywords

Lung cancer Epigenetics DNA methylation High throughput analysis 

Notes

Acknowledgment

This work was supported by the Vienna Science and Technology Fund (project number LS07-019).

References

  1. 1.
    Travis, W. D., Travis, L. B., & Devesa, S. S. (1995). Lung cancer. Cancer, 75, 191–202.PubMedGoogle Scholar
  2. 2.
    Shogren-Knaak, M., Ishii, H., Sun, J. M., Pazin, M. J., Davie, J. R., & Peterson, C. L. (2006). Histone H4-K16 acetylation controls chromatin structure and protein interactions. Science, 311, 844–847.PubMedGoogle Scholar
  3. 3.
    Vettese-Dadey, M., Grant, P. A., Hebbes, T. R., Crane- Robinson, C., Allis, C. D., & Workman, J. L. (1996). Acetylation of histone H4 plays a primary role in enhancing transcription factor binding to nucleosomal DNA in vitro. Embo Journal, 15, 2508–2518.PubMedGoogle Scholar
  4. 4.
    Esteller, M. (2008). Epigenetics in cancer. New England Journal of Medicine, 358, 1148–1159.PubMedGoogle Scholar
  5. 5.
    Espada, J., Ballestar, E., Fraga, M. F., Villar-Garea, A., Juarranz, A., Stockert, J. C., et al. (2004). Human DNA methyltransferase 1 is required for maintenance of the histone H3 modification pattern. Journal of Biological Chemistry, 279, 37175–37184.PubMedGoogle Scholar
  6. 6.
    Ikegami, K., Ohgane, J., Tanaka, S., Yagi, S., & Shiota, K. (2009). Interplay between DNA methylation, histone modification and chromatin remodeling in stem cells and during development. International Journal of Developmental Biology, 53, 203–214.PubMedGoogle Scholar
  7. 7.
    Eden, S., Hashimshony, T., Keshet, I., Cedar, H., & Thorne, A. W. (1998). DNA methylation models histone acetylation. Nature, 394, 842.PubMedGoogle Scholar
  8. 8.
    Rhee, I., Jair, K. W., Yen, R. W., Lengauer, C., Herman, J. G., Kinzler, K. W., et al. (2000). CpG methylation is maintained in human cancer cells lacking DNMT1. Nature, 404, 1003–1007.PubMedGoogle Scholar
  9. 9.
    Gowher, H., & Jeltsch, A. (2001). Enzymatic properties of recombinant Dnmt3a DNA methyltransferase from mouse: the enzyme modifies DNA in a non-processive manner and also methylates non-CpG [correction of non-CpA] sites. Journal of Molecular Biology, 309, 1201–1208.PubMedGoogle Scholar
  10. 10.
    Okano, M., Xie, S., & Li, E. (1998). Cloning and characterization of a family of novel mammalian DNA (cytosine-5) methyltransferases. Nature Genetics, 19, 219–220.PubMedGoogle Scholar
  11. 11.
    Matsuo, K., Clay, O., Takahashi, T., Silke, J., & Schaffner, W. (1993). Evidence for erosion of mouse CpG islands during mammalian evolution. Somatic Cell and Molecular Genetics, 19, 543–555.PubMedGoogle Scholar
  12. 12.
    Wang, Y., & Leung, F. C. (2004). An evaluation of new criteria for CpG islands in the human genome as gene markers. Bioinformatics, 20, 1170–1177.PubMedGoogle Scholar
  13. 13.
    Lander, E. S., Linton, L. M., Birren, B., Nusbaum, C., Zody, M. C., Baldwin, J., et al. (2001). Initial sequencing and analysis of the human genome. Nature, 409, 860–921.PubMedGoogle Scholar
  14. 14.
    Venter, J. C., Adams, M. D., Myers, E. W., Li, P. W., Mural, R. J., Sutton, G. G., et al. (2001). The sequence of the human genome. Science, 291, 1304–1351.PubMedGoogle Scholar
  15. 15.
    Bird, A. P. (1986). CpG-rich islands and the function of DNA methylation. Nature, 321, 209–213.PubMedGoogle Scholar
  16. 16.
    Gardiner-Garden, M., & Frommer, M. (1987). CpG islands in vertebrate genomes. Journal of Molecular Biology, 196, 261–282.PubMedGoogle Scholar
  17. 17.
    Razin, A., & Cedar, H. (1994). DNA methylation and genomic imprinting. Cell, 77, 473–476.PubMedGoogle Scholar
  18. 18.
    Jones, P. A., & Baylin, S. B. (2002). The fundamental role of epigenetic events in cancer. Nature Reviews. Genetics, 3, 415–428.PubMedGoogle Scholar
  19. 19.
    Fraga, M. F., Ballestar, E., Villar-Garea, A., Boix-Chornet, M., Espada, J., Schotta, G., et al. (2005). Loss of acetylation at Lys16 and trimethylation at Lys20 of histone H4 is a common hallmark of human cancer. Nature Genetics, 37, 391–400.PubMedGoogle Scholar
  20. 20.
    Cameron, E. E., Bachman, K. E., Myohanen, S., Herman, J. G., & Baylin, S. B. (1999). Synergy of demethylation and histone deacetylase inhibition in the re-expression of genes silenced in cancer. Nature Genetics, 21, 103–107.PubMedGoogle Scholar
  21. 21.
    Calin, G. A., & Croce, C. M. (2006). MicroRNA signatures in human cancers. Nature Reviews. Cancer, 6, 857–866.PubMedGoogle Scholar
  22. 22.
    He, L., & Hannon, G. J. (2004). MicroRNAs: small RNAs with a big role in gene regulation. Nature Reviews. Genetics, 5, 522–531.PubMedGoogle Scholar
  23. 23.
    Eulalio, A., Huntzinger, E., & Izaurralde, E. (2008). Getting to the root of miRNA-mediated gene silencing. Cell, 132, 9–14.PubMedGoogle Scholar
  24. 24.
    Bueno, M. J., Perez de Castro, I., Gomez de Cedron, M., Santos, J., Calin, G. A., Cigudosa, J. C., et al. (2008). Genetic and epigenetic silencing of microRNA-203 enhances ABL1 and BCR-ABL1 oncogene expression. Cancer Cell, 13, 496–506.PubMedGoogle Scholar
  25. 25.
    Brueckner, B., Stresemann, C., Kuner, R., Mund, C., Musch, T., Meister, M., et al. (2007). The human let-7a-3 locus contains an epigenetically regulated microRNA gene with oncogenic function. Cancer Research, 67, 1419–1423.PubMedGoogle Scholar
  26. 26.
    Fazi, F., Racanicchi, S., Zardo, G., Starnes, L. M., Mancini, M., Travaglini, L., et al. (2007). Epigenetic silencing of the myelopoiesis regulator microRNA-223 by the AML1/ETO oncoprotein. Cancer Cell, 12, 457–466.PubMedGoogle Scholar
  27. 27.
    Lujambio, A., Ropero, S., Ballestar, E., Fraga, M. F., Cerrato, C., Setien, F., et al. (2007). Genetic unmasking of an epigenetically silenced microRNA in human cancer cells. Cancer Research, 67, 1424–1429.PubMedGoogle Scholar
  28. 28.
    Lodygin, D., Tarasov, V., Epanchintsev, A., Berking, C., Knyazeva, T., Korner, H., et al. (2008). Inactivation of miR-34a by aberrant CpG methylation in multiple types of cancer. Cell Cycle, 7, 2591–2600.PubMedGoogle Scholar
  29. 29.
    Corney, D. C., Flesken-Nikitin, A., Godwin, A. K., Wang, W., & Nikitin, A. Y. (2007). MicroRNA-34b and MicroRNA-34c are targets of p53 and cooperate in control of cell proliferation and adhesion-independent growth. Cancer Research, 67, 8433–8438.PubMedGoogle Scholar
  30. 30.
    Fabbri, M., Garzon, R., Cimmino, A., Liu, Z., Zanesi, N., Callegari, E., et al. (2007). MicroRNA-29 family reverts aberrant methylation in lung cancer by targeting DNA methyltransferases 3A and 3B. Proceedings of the National Academy of Sciences of the United States of America, 104, 15805–15810.PubMedGoogle Scholar
  31. 31.
    Shames, D. S., Minna, J. D., & Gazdar, A. F. (2007). Methods for detecting DNA methylation in tumors: from bench to bedside. Cancer Letters, 251, 187–198.PubMedGoogle Scholar
  32. 32.
    Herman, J. G., & Baylin, S. B. (2001). Methylation-specific PCR. Current Protocols in Human Genetics, Chapter 10, Unit 10 16.Google Scholar
  33. 33.
    Herman, J. G., Graff, J. R., Myohanen, S., Nelkin, B. D., & Baylin, S. B. (1996). Methylation-specific PCR: a novel PCR assay for methylation status of CpG islands. Proceedings of the National Academy of Sciences of the United States of America, 93, 9821–9826.PubMedGoogle Scholar
  34. 34.
    Fraga, M. F., & Esteller, M (2002). DNA methylation: a profile of methods and applications. Biotechniques, 33, 632, 634, 636-649.Google Scholar
  35. 35.
    Campan, M., Weisenberger, D. J., Trinh, B., & Laird, P. W. (2009). MethyLight. Methods in Molecular Biology, 507, 325–337.PubMedGoogle Scholar
  36. 36.
    Dammann, R., Li, C., Yoon, J. H., Chin, P. L., Bates, S., & Pfeifer, G. P. (2000). Epigenetic inactivation of a RAS association domain family protein from the lung tumour suppressor locus 3p21.3. Nature Genetics, 25, 315–319.PubMedGoogle Scholar
  37. 37.
    Esteller, M., Corn, P. G., Baylin, S. B., & Herman, J. G. (2001). A gene hypermethylation profile of human cancer. Cancer Research, 61, 3225–3229.PubMedGoogle Scholar
  38. 38.
    Zöchbauer-Müller, S., Fong, K. M., Virmani, A. K., Geradts, J., Gazdar, A. F., & Minna, J. D. (2001). Aberrant promoter methylation of multiple genes in non-small cell lung cancers. Cancer Research, 61, 249–255.PubMedGoogle Scholar
  39. 39.
    Virmani, A. K., Rathi, A., Sathyanarayana, U. G., Padar, A., Huang, C. X., Cunnigham, H. T., et al. (2001). Aberrant methylation of the adenomatous polyposis coli (APC) gene promoter 1A in breast and lung carcinomas. Clinical Cancer Research, 7, 1998–2004.PubMedGoogle Scholar
  40. 40.
    Virmani, A. K., Rathi, A., Zöchbauer-Müller, S., Sacchi, N., Fukuyama, Y., Bryant, D., et al. (2000). Promoter methylation and silencing of the retinoic acid receptor-beta gene in lung carcinomas. Journal of the National Cancer Institute, 92, 1303–1307.PubMedGoogle Scholar
  41. 41.
    Toyooka, K. O., Toyooka, S., Virmani, A. K., Sathyanarayana, U. G., Euhus, D. M., Gilcrease, M., et al. (2001). Loss of expression and aberrant methylation of the CDH13 (H-cadherin) gene in breast and lung carcinomas. Cancer Research, 61, 4556–4560.PubMedGoogle Scholar
  42. 42.
    Toyooka, S., Toyooka, K. O., Miyajima, K., Reddy, J. L., Toyota, M., Sathyanarayana, U. G., et al. (2003). Epigenetic down-regulation of death-associated protein kinase in lung cancers. Clinical Cancer Research, 9, 3034–3041.PubMedGoogle Scholar
  43. 43.
    Burbee, D. G., Forgacs, E., Zöchbauer-Müller, S., Shivakumar, L., Fong, K. M., Gao, B., et al. (2001). Epigenetic inactivation of RASSF1A in lung and breast cancers and malignant phenotype suppression. Journal of the National Cancer Institute, 93, 691–699.PubMedGoogle Scholar
  44. 44.
    Virmani, A., Rathi, A., Sugio, K., Sathyanarayana, U. G., Toyooka, S., Kischel, F. C., et al. (2003). Aberrant methylation of TMS1 in small cell, non small cell lung cancer and breast cancer. International Journal of Cancer, 106, 198–204.Google Scholar
  45. 45.
    Zöchbauer-Müller, S., Fong, K. M., Maitra, A., Lam, S., Geradts, J., Ashfaq, R., et al. (2001). 5′ CpG island methylation of the FHIT gene is correlated with loss of gene expression in lung and breast cancer. Cancer Research, 61, 3581–3585.PubMedGoogle Scholar
  46. 46.
    Zöchbauer-Müller, S., Fong, K. M., Geradts, J., Xu, X., Seidl, S., End-Pfutzenreuter, A., et al. (2005). Expression of the candidate tumor suppressor gene hSRBC is frequently lost in primary lung cancers with and without DNA methylation. Oncogene, 24, 6249–6255.PubMedGoogle Scholar
  47. 47.
    Heller, G., Fong, K. M., Girard, L., Seidl, S., End-Pfützenreuter, A., Lang, G., et al. (2006). Expression and methylation pattern of TSLC1 cascade genes in lung carcinomas. Oncogene, 25, 959–968.PubMedGoogle Scholar
  48. 48.
    Kikuchi, S., Yamada, D., Fukami, T., Masuda, M., Sakurai-Yageta, M., Williams, Y. N., et al. (2005). Promoter methylation of DAL-1/4.1B predicts poor prognosis in non-small cell lung cancer. Clinical Cancer Research, 11, 2954–2961.PubMedGoogle Scholar
  49. 49.
    Kikuchi, S., Yamada, D., Fukami, T., Maruyama, T., Ito, A., Asamura, H., et al. (2006). Hypermethylation of the TSLC1/IGSF4 promoter is associated with tobacco smoking and a poor prognosis in primary nonsmall cell lung carcinoma. Cancer, 106, 1751–1758.PubMedGoogle Scholar
  50. 50.
    Esteller, M., Sanchez-Cespedes, M., Rosell, R., Sidransky, D., Baylin, S. B., & Herman, J. G. (1999). Detection of aberrant promoter hypermethylation of tumor suppressor genes in serum DNA from non-small cell lung cancer patients. Cancer Research, 59, 67–70.PubMedGoogle Scholar
  51. 51.
    Usadel, H., Brabender, J., Danenberg, K. D., Jeronimo, C., Harden, S., Engles, J., et al. (2002). Quantitative adenomatous polyposis coli promoter methylation analysis in tumor tissue, serum, and plasma DNA of patients with lung cancer. Cancer Research, 62, 371–375.PubMedGoogle Scholar
  52. 52.
    Hsu, H. S., Chen, T. P., Hung, C. H., Wen, C. K., Lin, R. K., Lee, H. C., et al. (2007). Characterization of a multiple epigenetic marker panel for lung cancer detection and risk assessment in plasma. Cancer, 110, 2019–2026.PubMedGoogle Scholar
  53. 53.
    Fujiwara, K., Fujimoto, N., Tabata, M., Nishii, K., Matsuo, K., Hotta, K., et al. (2005). Identification of epigenetic aberrant promoter methylation in serum DNA is useful for early detection of lung cancer. Clinical Cancer Research, 11, 1219–1225.PubMedGoogle Scholar
  54. 54.
    Wang, Y., Yu, Z., Wang, T., Zhang, J., Hong, L., & Chen, L. (2007). Identification of epigenetic aberrant promoter methylation of RASSF1A in serum DNA and its clinicopathological significance in lung cancer. Lung Cancer, 56, 289–294.PubMedGoogle Scholar
  55. 55.
    Belinsky, S. A., Klinge, D. M., Dekker, J. D., Smith, M. W., Bocklage, T. J., Gilliland, F. D., et al. (2005). Gene promoter methylation in plasma and sputum increases with lung cancer risk. Clinical Cancer Research, 11, 6505–6511.PubMedGoogle Scholar
  56. 56.
    Anglim, P. P., Alonzo, T. A., & Laird-Offringa, I. A. (2008). DNA methylation-based biomarkers for early detection of non-small cell lung cancer: an update. Mol Cancer, 7, 81.PubMedGoogle Scholar
  57. 57.
    Wang, Y. C., Lu, Y. P., Tseng, R. C., Lin, R. K., Chang, J. W., Chen, J. T., et al. (2003). Inactivation of hMLH1 and hMSH2 by promoter methylation in primary non-small cell lung tumors and matched sputum samples. Journal of Clinical Investigation, 111, 887–895.PubMedGoogle Scholar
  58. 58.
    Belinsky, S. A., Liechty, K. C., Gentry, F. D., Wolf, H. J., Rogers, J., Vu, K., et al. (2006). Promoter hypermethylation of multiple genes in sputum precedes lung cancer incidence in a high-risk cohort. Cancer Research, 66, 3338–3344.PubMedGoogle Scholar
  59. 59.
    Belinsky, S. A., Grimes, M. J., Casas, E., Stidley, C. A., Franklin, W. A., Bocklage, T. J., et al. (2007). Predicting gene promoter methylation in non-small-cell lung cancer by evaluating sputum and serum. British Journal of Cancer, 96, 1278–1283.PubMedGoogle Scholar
  60. 60.
    Machida, E. O., Brock, M. V., Hooker, C. M., Nakayama, J., Ishida, A., Amano, J., et al. (2006). Hypermethylation of ASC/TMS1 is a sputum marker for late-stage lung cancer. Cancer Research, 66, 6210–6218.PubMedGoogle Scholar
  61. 61.
    Shivapurkar, N., Stastny, V., Suzuki, M., Wistuba, I. I., Li, L., Zheng, Y., et al. (2007). Application of a methylation gene panel by quantitative PCR for lung cancers. Cancer Letter, 247, 56–71.Google Scholar
  62. 62.
    Schmiemann, V., Bocking, A., Kazimirek, M., Onofre, A. S., Gabbert, H. E., Kappes, R., et al. (2005). Methylation assay for the diagnosis of lung cancer on bronchial aspirates: a cohort study. Clinical Cancer Research, 11, 7728–7734.PubMedGoogle Scholar
  63. 63.
    Grote, H. J., Schmiemann, V., Geddert, H., Rohr, U. P., Kappes, R., Gabbert, H. E., et al. (2005). Aberrant promoter methylation of p16(INK4a), RARB2 and SEMA3B in bronchial aspirates from patients with suspected lung cancer. International Journal of Cancer, 116, 720–725.Google Scholar
  64. 64.
    Grote, H. J., Schmiemann, V., Kiel, S., Bocking, A., Kappes, R., Gabbert, H. E., et al. (2004). Aberrant methylation of the adenomatous polyposis coli promoter 1A in bronchial aspirates from patients with suspected lung cancer. International Journal of Cancer, 110, 751–755.Google Scholar
  65. 65.
    Kim, H., Kwon, Y. M., Kim, J. S., Lee, H., Park, J. H., Shim, Y. M., et al. (2004). Tumor-specific methylation in bronchial lavage for the early detection of non-small-cell lung cancer. Journal of Clinical Oncology, 22, 2363–2370.PubMedGoogle Scholar
  66. 66.
    Chan, E. C., Lam, S. Y., Tsang, K. W., Lam, B., Ho, J. C., Fu, K. H., et al. (2002). Aberrant promoter methylation in Chinese patients with non-small cell lung cancer: patterns in primary tumors and potential diagnostic application in bronchoalevolar lavage. Clinical Cancer Research, 8, 3741–3746.PubMedGoogle Scholar
  67. 67.
    Han, W., Wang, T., Reilly, A. A., Keller, S. M., & Spivack, S. D. (2009). Gene promoter methylation assayed in exhaled breath, with differences in smokers and lung cancer patients. Respiratory Research, 10, 86.PubMedGoogle Scholar
  68. 68.
    Toyooka, S., Toyooka, K. O., Maruyama, R., Virmani, A. K., Girard, L., Miyajima, K., et al. (2001). DNA methylation profiles of lung tumors. Mol Cancer Therapeutics, 1, 61–67.Google Scholar
  69. 69.
    Gu, J., Berman, D., Lu, C., Wistuba, I. I., Roth, J. A., Frazier, M., et al. (2006). Aberrant promoter methylation profile and association with survival in patients with non-small cell lung cancer. Clinical Cancer Research, 12, 7329–7338.PubMedGoogle Scholar
  70. 70.
    Ehrich, M., Field, J. K., Liloglou, T., Xinarianos, G., Oeth, P., Nelson, M. R., et al. (2006). Cytosine methylation profiles as a molecular marker in non-small cell lung cancer. Cancer Research, 66, 10911–10918.PubMedGoogle Scholar
  71. 71.
    Toyooka, S., Tokumo, M., Shigematsu, H., Matsuo, K., Asano, H., Tomii, K., et al. (2006). Mutational and epigenetic evidence for independent pathways for lung adenocarcinomas arising in smokers and never smokers. Cancer Research, 66, 1371–1375.PubMedGoogle Scholar
  72. 72.
    Tang, X., Khuri, F. R., Lee, J. J., Kemp, B. L., Liu, D., Hong, W. K., et al. (2000). Hypermethylation of the death-associated protein (DAP) kinase promoter and aggressiveness in stage I non-small-cell lung cancer. Journal of the National Cancer Institute, 92, 1511–1516.PubMedGoogle Scholar
  73. 73.
    Lu, C., Soria, J. C., Tang, X., Xu, X. C., Wang, L., Mao, L., et al. (2004). Prognostic factors in resected stage I non-small-cell lung cancer: a multivariate analysis of six molecular markers. Journal of Clinical Oncology, 22, 4575–4583.PubMedGoogle Scholar
  74. 74.
    Kim, D. H., Kim, J. S., Ji, Y. I., Shim, Y. M., Kim, H., Han, J., et al. (2003). Hypermethylation of RASSF1A promoter is associated with the age at starting smoking and a poor prognosis in primary non-small cell lung cancer. Cancer Research, 63, 3743–3746.PubMedGoogle Scholar
  75. 75.
    Tomizawa, Y., Kohno, T., Kondo, H., Otsuka, A., Nishioka, M., Niki, T., et al. (2002). Clinicopathological significance of epigenetic inactivation of RASSF1A at 3p21.3 in stage I lung adenocarcinoma. Clinical Cancer Research, 8, 2362–2368.PubMedGoogle Scholar
  76. 76.
    Toyooka, S., Suzuki, M., Maruyama, R., Toyooka, K. O., Tsukuda, K., Fukuyama, Y., et al. (2004). The relationship between aberrant methylation and survival in non-small-cell lung cancers. British Journal of Cancer, 91, 771–774.PubMedGoogle Scholar
  77. 77.
    Yanagawa, N., Tamura, G., Oizumi, H., Kanauchi, N., Endoh, M., Sadahiro, M., et al. (2007). Promoter hypermethylation of RASSF1A and RUNX3 genes as an independent prognostic prediction marker in surgically resected non-small cell lung cancers. Lung Cancer, 58, 131–138.PubMedGoogle Scholar
  78. 78.
    Seng, T. J., Currey, N., Cooper, W. A., Lee, C. S., Chan, C., Horvath, L., et al. (2008). DLEC1 and MLH1 promoter methylation are associated with poor prognosis in non-small cell lung carcinoma. British Journal of Cancer, 99, 375–382.PubMedGoogle Scholar
  79. 79.
    Brock, M. V., Hooker, C. M., Ota-Machida, E., Han, Y., Guo, M., Ames, S., et al. (2008). DNA methylation markers and early recurrence in stage I lung cancer. New England Journal of Medicine, 358, 1118–1128.PubMedGoogle Scholar
  80. 80.
    Parkin, D. M., Pisani, P., Lopez, A. D., & Masuyer, E. (1994). At least one in seven cases of cancer is caused by smoking. Global estimates for 1985. International Journal of Cancer, 59, 494–504.Google Scholar
  81. 81.
    Sun, S., Schiller, J. H., & Gazdar, A. F. (2007). Lung cancer in never smokers—a different disease. Nature Reviews Cancer, 7, 778–790.PubMedGoogle Scholar
  82. 82.
    Toyooka, S., Maruyama, R., Toyooka, K. O., McLerran, D., Feng, Z., Fukuyama, Y., et al. (2003). Smoke exposure, histologic type and geography-related differences in the methylation profiles of non-small cell lung cancer. International Journal of Cancer, 103, 153–160.Google Scholar
  83. 83.
    Belinsky, S. A., Palmisano, W. A., Gilliland, F. D., Crooks, L. A., Divine, K. K., Winters, S. A., et al. (2002). Aberrant promoter methylation in bronchial epithelium and sputum from current and former smokers. Cancer Research, 62, 2370–2377.PubMedGoogle Scholar
  84. 84.
    Damiani, L. A., Yingling, C. M., Leng, S., Romo, P. E., Nakamura, J., & Belinsky, S. A. (2008). Carcinogen-induced gene promoter hypermethylation is mediated by DNMT1 and causal for transformation of immortalized bronchial epithelial cells. Cancer Research, 68, 9005–9014.PubMedGoogle Scholar
  85. 85.
    Shen, H., Spitz, M. R., Qiao, Y., Guo, Z., Wang, L. E., Bosken, C. H., et al. (2003). Smoking, DNA repair capacity and risk of nonsmall cell lung cancer. International Journal of Cancer, 107, 84–88.Google Scholar
  86. 86.
    Leng, S., Stidley, C. A., Willink, R., Bernauer, A., Do, K., Picchi, M. A., et al. (2008). Double-strand break damage and associated DNA repair genes predispose smokers to gene methylation. Cancer Research, 68, 3049–3056.PubMedGoogle Scholar
  87. 87.
    Kersting, M., Friedl, C., Kraus, A., Behn, M., Pankow, W., & Schuermann, M. (2000). Differential frequencies of p16(INK4a) promoter hypermethylation, p53 mutation, and K-ras mutation in exfoliative material mark the development of lung cancer in symptomatic chronic smokers. Journal of Clinical Oncology, 18, 3221–3229.PubMedGoogle Scholar
  88. 88.
    Honorio, S., Agathanggelou, A., Schuermann, M., Pankow, W., Viacava, P., Maher, E. R., et al. (2003). Detection of RASSF1A aberrant promoter hypermethylation in sputum from chronic smokers and ductal carcinoma in situ from breast cancer patients. Oncogene, 22, 147–150.PubMedGoogle Scholar
  89. 89.
    Lamy, A., Sesboue, R., Bourguignon, J., Dautreaux, B., Metayer, J., Frebourg, T., et al. (2002). Aberrant methylation of the CDKN2a/p16INK4a gene promoter region in preinvasive bronchial lesions: a prospective study in high-risk patients without invasive cancer. International Journal of Cancer, 100, 189–193.Google Scholar
  90. 90.
    Soria, J. C., Rodriguez, M., Liu, D. D., Lee, J. J., Hong, W. K., & Mao, L. (2002). Aberrant promoter methylation of multiple genes in bronchial brush samples from former cigarette smokers. Cancer Research, 62, 351–355.PubMedGoogle Scholar
  91. 91.
    Zöchbauer-Müller, S., Lam, S., Toyooka, S., Virmani, A. K., Toyooka, K. O., Seidl, S., et al. (2003). Aberrant methylation of multiple genes in the upper aerodigestive tract epithelium of heavy smokers. International Journal of Cancer, 107, 612–616.Google Scholar
  92. 92.
    Bhutani, M., Pathak, A. K., Fan, Y. H., Liu, D. D., Lee, J. J., Tang, H., et al. (2008). Oral epithelium as a surrogate tissue for assessing smoking-induced molecular alterations in the lungs. Cancer Prevention Researcg (Philadelphia, PA), 1, 39–44.Google Scholar
  93. 93.
    Licchesi, J. D., Westra, W. H., Hooker, C. M., & Herman, J. G. (2008). Promoter hypermethylation of hallmark cancer genes in atypical adenomatous hyperplasia of the lung. Clinical Cancer Research, 14, 2570–2578.PubMedGoogle Scholar
  94. 94.
    Palmisano, W. A., Divine, K. K., Saccomanno, G., Gilliland, F. D., Baylin, S. B., Herman, J. G., et al. (2000). Predicting lung cancer by detecting aberrant promoter methylation in sputum. Cancer Research, 60, 5954–5958.PubMedGoogle Scholar
  95. 95.
    http://www.fda.gov/ Dacogen (decitabine), NDA# N21790.
  96. 96.
    Kaminskas, E., Farrell, A., Abraham, S., Baird, A., Hsieh, L. S., Lee, S. L., et al. (2005). Approval summary: azacitidine for treatment of myelodysplastic syndrome subtypes. Clinical Cancer Research, 11, 3604–3608.PubMedGoogle Scholar
  97. 97.
    Mann, B. S., Johnson, J. R., He, K., Sridhara, R., Abraham, S., Booth, B. P., et al. (2007). Vorinostat for treatment of cutaneous manifestations of advanced primary cutaneous T-cell lymphoma. Clinical Cancer Research, 13, 2318–2322.PubMedGoogle Scholar
  98. 98.
    Piekarz R, Wright J, Frye R, Allen SL, Craig M, Geskin L, et al. (2008). Results of a phase 2 NCI multicenter study of romidepsin in patients with relapsed peripheral T-cell lymphoma (PTCL). ASH Annual Meeting Abstracts, 112.Google Scholar
  99. 99.
    Juergens, R., Vendetti, F., Coleman, B., Sebree, R., Belinsky, S., Rudek, M., et al. (2009). A phase II-trial of 5-azacitidine (5AC) and entinostat (SNDX-275) in relapsed advanced lung cancer (NSCLC): an interim analysis. Abstract# A6.6, 13th World Conference on Lung Cancer (WCLC).Google Scholar
  100. 100.
    Costello, J. F., Fruhwald, M. C., Smiraglia, D. J., Rush, L. J., Robertson, G. P., Gao, X., et al. (2000). Aberrant CpG-island methylation has non-random and tumour-type-specific patterns. Nature Genetics, 24, 132–138.PubMedGoogle Scholar
  101. 101.
    Dai, Z., Lakshmanan, R. R., Zhu, W. G., Smiraglia, D. J., Rush, L. J., Fruhwald, M. C., et al. (2001). Global methylation profiling of lung cancer identifies novel methylated genes. Neoplasia, 3, 314–323.PubMedGoogle Scholar
  102. 102.
    Brena, R. M., Morrison, C., Liyanarachchi, S., Jarjoura, D., Davuluri, R. V., Otterson, G. A., et al. (2007). Aberrant DNA methylation of OLIG1, a novel prognostic factor in non-small cell lung cancer. PLoS Med, 4, e108.PubMedGoogle Scholar
  103. 103.
    Weber, M., Davies, J. J., Wittig, D., Oakeley, E. J., Haase, M., Lam, W. L., et al. (2005). Chromosome-wide and promoter-specific analyses identify sites of differential DNA methylation in normal and transformed human cells. Nature Genetics, 37, 853–862.PubMedGoogle Scholar
  104. 104.
    Dammann, R., Yang, G., & Pfeifer, G. P. (2001). Hypermethylation of the cpG island of Ras association domain family 1A (RASSF1A), a putative tumor suppressor gene from the 3p21.3 locus, occurs in a large percentage of human breast cancers. Cancer Research, 61, 3105–3109.PubMedGoogle Scholar
  105. 105.
    Suzuki, H., Gabrielson, E., Chen, W., Anbazhagan, R., van Engeland, M., Weijenberg, M. P., et al. (2002). A genomic screen for genes upregulated by demethylation and histone deacetylase inhibition in human colorectal cancer. Nature Genetics, 31, 141–149.PubMedGoogle Scholar
  106. 106.
    Shames, D. S., Girard, L., Gao, B., Sato, M., Lewis, C. M., Shivapurkar, N., et al. (2006). A genome-wide screen for promoter methylation in lung cancer identifies novel methylation markers for multiple malignancies. PLoS Medicine, 3, e486.PubMedGoogle Scholar
  107. 107.
    Zhong, S., Fields, C. R., Su, N., Pan, Y. X., & Robertson, K. D. (2007). Pharmacologic inhibition of epigenetic modifications, coupled with gene expression profiling, reveals novel targets of aberrant DNA methylation and histone deacetylation in lung cancer. Oncogene, 26, 2621–2634.PubMedGoogle Scholar
  108. 108.
    Bestor, T. H. (2003). Unanswered questions about the role of promoter methylation in carcinogenesis. Annals of the New York Academy of Sciences, 983, 22–27.PubMedGoogle Scholar
  109. 109.
    Sato, N., Fukushima, N., Maitra, A., Matsubayashi, H., Yeo, C. J., Cameron, J. L., et al. (2003). Discovery of novel targets for aberrant methylation in pancreatic carcinoma using high-throughput microarrays. Cancer Research, 63, 3735–3742.PubMedGoogle Scholar
  110. 110.
    Bibikova, M., Lin, Z., Zhou, L., Chudin, E., Garcia, E. W., Wu, B., et al. (2006). High-throughput DNA methylation profiling using universal bead arrays. Genome Research, 16, 383–393.PubMedGoogle Scholar
  111. 111.
    Christensen, B. C., Marsit, C. J., Houseman, E. A., Godleski, J. J., Longacker, J. L., Zheng, S., et al. (2009). Differentiation of lung adenocarcinoma, pleural mesothelioma, and nonmalignant pulmonary tissues using DNA methylation profiles. Cancer Research, 69, 6315–6321.PubMedGoogle Scholar
  112. 112.
    Mockler, T. C., Chan, S., Sundaresan, A., Chen, H., Jacobsen, S. E., & Ecker, J. R. (2005). Applications of DNA tiling arrays for whole-genome analysis. Genomics, 85, 1–15.PubMedGoogle Scholar
  113. 113.
    Rauch, T. A., Zhong, X., Wu, X., Wang, M., Kernstine, K. H., Wang, Z., et al. (2008). High-resolution mapping of DNA hypermethylation and hypomethylation in lung cancer. Proceedings of the National Academy of Sciences of the United States of America, 105, 252–257.PubMedGoogle Scholar
  114. 114.
    Tessema, M., Willink, R., Do, K., Yu, Y. Y., Yu, W., Machida, E. O., et al. (2008). Promoter methylation of genes in and around the candidate lung cancer susceptibility locus 6q23-25. Cancer Research, 68, 1707–1714.PubMedGoogle Scholar
  115. 115.
    Zhang, Z., Tan, S., & Zhang, L. (2006). Prognostic value of apoptosis-associated speck-like protein containing a CARD gene promoter methylation in resectable non-small-cell lung cancer. Clinical Lung Cancer, 8, 62–65.PubMedGoogle Scholar
  116. 116.
    Nakata, S., Sugio, K., Uramoto, H., Oyama, T., Hanagiri, T., Morita, M., et al. (2006). The methylation status and protein expression of CDH1, p16(INK4A), and fragile histidine triad in nonsmall cell lung carcinoma: epigenetic silencing, clinical features, and prognostic significance. Cancer, 106, 2190–2199.PubMedGoogle Scholar
  117. 117.
    Maruyama, R., Sugio, K., Yoshino, I., Maehara, Y., & Gazdar, A. F. (2004). Hypermethylation of FHIT as a prognostic marker in nonsmall cell lung carcinoma. Cancer, 100, 1472–1477.PubMedGoogle Scholar
  118. 118.
    Brabender, J., Usadel, H., Danenberg, K. D., Metzger, R., Schneider, P. M., Lord, R. V., et al. (2001). Adenomatous polyposis coli gene promoter hypermethylation in non-small cell lung cancer is associated with survival. Oncogene, 20, 3528–3532.PubMedGoogle Scholar
  119. 119.
    Agathanggelou, A., Honorio, S., Macartney, D. P., Martinez, A., Dallol, A., Rader, J., et al. (2001). Methylation associated inactivation of RASSF1A from region 3p21.3 in lung, breast and ovarian tumours. Oncogene, 20, 1509–1518.PubMedGoogle Scholar
  120. 120.
    Dammann, R., Takahashi, T., & Pfeifer, G. P. (2001). The CpG island of the novel tumor suppressor gene RASSF1A is intensely methylated in primary small cell lung carcinomas. Oncogene, 20, 3563–3567.PubMedGoogle Scholar
  121. 121.
    Kashiwabara, K., Oyama, T., Sano, T., Fukuda, T., & Nakajima, T. (1998). Correlation between methylation status of the p16/CDKN2 gene and the expression of p16 and Rb proteins in primary non-small cell lung cancers. International Journal of Cancer, 79, 215–220.Google Scholar
  122. 122.
    Kuramochi, M., Fukuhara, H., Nobukuni, T., Kanbe, T., Maruyama, T., Ghosh, H. P., et al. (2001). TSLC1 is a tumor-suppressor gene in human non-small-cell lung cancer. Nature Genetics, 27, 427–430.PubMedGoogle Scholar
  123. 123.
    Brabender, J., Usadel, H., Metzger, R., Schneider, P. M., Park, J., Salonga, D., et al. (2003). Quantitative O(6)-methylguanine DNA methyltransferase methylation analysis in curatively resected non-small cell lung cancer: associations with clinical outcome. Clinical Cancer Research, 9, 223–227.PubMedGoogle Scholar

Copyright information

© Springer Science+Business Media, LLC 2010

Authors and Affiliations

  • Gerwin Heller
    • 1
  • Christoph C. Zielinski
    • 1
  • Sabine Zöchbauer-Müller
    • 1
  1. 1.Department of Medicine I, Clinical Division of OncologyMedical University of ViennaViennaAustria

Personalised recommendations