Molecular Oncology
Volume 1, Issue 1 , Pages 26-41 , June 2007

Genetic and epigenetic alterations as biomarkers for cancer detection, diagnosis and prognosis

Received 16 January 2007 ,Revised 31 January 2007 ,Accepted 31 January 2007.

References 

  1. Abdel-Rahman WM, Mecklin JP, Peltomaki P. The genetics of HNPCC: application to diagnosis and screening. Critical Reviews in Oncology–Hematology. 2006;58:208–220
  2. Abe M, Ohira M, Kaneda A, Yagi Y, Yamamoto S, Kitano Y, et al. CpG island methylator phenotype is a strong determinant of poor prognosis in neuroblastomas. Cancer Research. 2005;65:828–834
  3. Ahuja N, Mohan AL, Li Q, Stolker JM, Herman JG, Hamilton SR, et al. Association between CpG island methylation and microsatellite instability in colorectal cancer. Cancer Research. 1997;57:3370–3374
  4. An Q, Liu Y, Gao Y, Huang J, Fong X, Li L, et al. Detection of p16 hypermethylation in circulating plasma DNA of non-small cell lung cancer patients. Cancer Letters. 2002;188:109–114
  5. An C, Choi IS, Yao JC, Worah S, Xie K, Mansfield PF, et al. Prognostic significance of CpG island methylator phenotype and microsatellite instability in gastric carcinoma. Clinical Cancer Research. 2005;11:656–663
  6. Balko JM, Potti A, Saunders C, Stromberg A, Haura EB, Black EP. Gene expression patterns that predict sensitivity to epidermal growth factor receptor tyrosine kinase inhibitors in lung cancer cell lines and human lung tumors. BMC Genomics. 2006;7:289
  7. Bartel DP. MicroRNAs: genomics, biogenesis, mechanism, and function. Cell. 2004;116:281–297
  8. Bazan V, Bruno L, Augello C, Agnese V, Calo V, Corsale S, et al. Molecular detection of TP53, Ki-Ras and p16INK4A promoter methylation in plasma of patients with colorectal cancer and its association with prognosis. Results of a 3-year GOIM (Gruppo Oncologico dell'Italia Meridionale) prospective study. Annals of Oncology. 2006;17(Suppl. 7):vii84–vii90
  9. Bearzatto A, Conte D, Frattini M, Zaffaroni N, Andriani F, Balestra D, et al. p16(INK4A) Hypermethylation detected by fluorescent methylation-specific PCR in plasmas from non-small cell lung cancer. Clinical Cancer Research. 2002;8:3782–3787
  10. Belinsky SA. Gene-promoter hypermethylation as a biomarker in lung cancer. Nature Reviews Cancer. 2004;4:707–717
  11. Belinsky SA, Nikula KJ, Palmisano WA, Michels R, Saccomanno G, Gabrielson E, et al. Aberrant methylation of p16(INK4a) is an early event in lung cancer and a potential biomarker for early diagnosis. Proceedings of the National Academy of Sciences of the United States of America. 1998;95:11891–11896
  12. Belinsky SA, Palmisano WA, Gilliland FD, Crooks LA, Divine KK, Winters SA, et al. Aberrant promoter methylation in bronchial epithelium and sputum from current and former smokers. Cancer Research. 2002;62:2370–2377
  13. Belinsky SA, Klinge DM, Dekker JD, Smith MW, Bocklage TJ, Gilliland FD, et al. Gene promoter methylation in plasma and sputum increases with lung cancer risk. Clinical Cancer Research. 2005;11:6505–6511
  14. Bielas JH, Loeb KR, Rubin BP, True LD, Loeb LA. Human cancers express a mutator phenotype. Proceedings of the National Academy of Sciences of the United States of America. 2006;103:18238–18242
  15. Bird A. DNA methylation patterns and epigenetic memory. Genes and Development. 2002;16:6–21
  16. Cairns BR. Emerging roles for chromatin remodeling in cancer biology. Trends in Cell Biology. 2001;11:S15–S21
  17. Calin GA, Croce CM. MicroRNA signatures in human cancers. Nature Reviews Cancer. 2006;6:857–866
  18. Cao R, Wang L, Wang H, Xia L, Erdjument-Bromage H, Tempst P, et al. Role of histone H3 lysine 27 methylation in polycomb-group silencing. Science. 2002;298:1039–1043
  19. Chan MW, Chan LW, Tang NL, Tong JH, Lo KW, Lee TL, et al. Hypermethylation of multiple genes in tumor tissues and voided urine in urinary bladder cancer patients. Clinical Cancer Research. 2002;8:464–470
  20. Costello JF, Fruhwald MC, Smiraglia DJ, Rush LJ, Robertson GP, Gao X, et al. Aberrant CpG-island methylation has non-random and tumour-type-specific patterns. Nature Genetics. 2000;24:132–138
  21. Cui H, Horon IL, Ohlsson R, Hamilton SR, Feinberg AP. Loss of imprinting in normal tissue of colorectal cancer patients with microsatellite instability. Nature Medicine. 1998;4:1276–1280
  22. Cui H, Cruz-Correa M, Giardiello FM, Hutcheon DF, Kafonek DR, Brandenburg S, et al. Loss of IGF2 imprinting: a potential marker of colorectal cancer risk. Science. 2003;299:1753–1755
  23. Dominguez G, Carballido J, Silva J, Silva JM, Garcia JM, Menendez J, et al. p14ARF promoter hypermethylation in plasma DNA as an indicator of disease recurrence in bladder cancer patients. Clinical Cancer Research. 2002;8:980–985
  24. Dulaimi E, Uzzo RG, Greenberg RE, Al-Saleem T, Cairns P. Detection of bladder cancer in urine by a tumor suppressor gene hypermethylation panel. Clinical Cancer Research. 2004;10:1887–1893
  25. Eads CA, Danenberg KD, Kawakami K, Saltz LB, Danenberg PV, Laird PW. CpG island hypermethylation in human colorectal tumors is not associated with DNA methyltransferase overexpression. Cancer Research. 1999;59:2302–2306
  26. Eads CA, Lord RV, Wickramasinghe K, Long TI, Kurumboor SK, Bernstein L, et al. Epigenetic patterns in the progression of esophageal adenocarcinoma. Cancer Research. 2001;61:3410–3418
  27. Egger G, Liang G, Aparicio A, Jones PA. Epigenetics in human disease and prospects for epigenetic therapy. Nature. 2004;429:457–463
  28. Elenbaas B, Spirio L, Koerner F, Fleming MD, Zimonjic DB, Donaher JL, et al. Human breast cancer cells generated by oncogenic transformation of primary mammary epithelial cells. Genes and Development. 2001;15:50–65
  29. Esteller M, Herman JG. Generating mutations but providing chemosensitivity: the role of O6-methylguanine DNA methyltransferase in human cancer. Oncogene. 2004;23:1–8
  30. Esteller M, Levine R, Baylin SB, Ellenson LH, Herman JG. MLH1 promoter hypermethylation is associated with the microsatellite instability phenotype in sporadic endometrial carcinomas. Oncogene. 1998;17:2413–2417
  31. Esteller M, Sanchez-Cespedes M, Rosell R, Sidransky D, Baylin SB, Herman JG. Detection of aberrant promoter hypermethylation of tumor suppressor genes in serum DNA from non-small cell lung cancer patients. Cancer Research. 1999;59:67–70
  32. 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. Journal of the National Cancer Institute. 2002;94:26–32
  33. Fackler MJ, Malone K, Zhang Z, Schilling E, Garrett-Mayer E, Swift-Scanlan T, et al. Quantitative multiplex methylation-specific PCR analysis doubles detection of tumor cells in breast ductal fluid. Clinical Cancer Research. 2006;12:3306–3310
  34. Fearon ER, Vogelstein B. A genetic model for colorectal tumorigenesis. Cell. 1990;61:759–767
  35. Feinberg AP, Tycko B. The history of cancer epigenetics. Nature Reviews in Cancer. 2004;4:143–153
  36. Feinberg AP, Ohlsson R, Henikoff S. The epigenetic progenitor origin of human cancer. Nature Reviews. 2006;7:21–33
  37. Fishel R, Wilson T. MutS homologs in mammalian cells. Current Opinion in Genetics and Development. 1997;7:105–113
  38. Forbes S, Clements J, Dawson E, Bamford S, Webb T, Dogan A, et al. Cosmic 2005. British Journal of Cancer. 2006;94:318–322
  39. Fraga MF, Ballestar E, Villar-Garea A, Boix-Chornet M, Espada J, Schotta G, et al. Loss of acetylation at Lys16 and trimethylation at Lys20 of histone H4 is a common hallmark of human cancer. Nature Genetics. 2005;37:391–400
  40. Frolov MV, Dyson NJ. Molecular mechanisms of E2F-dependent activation and pRB-mediated repression. Journal of Cell Science. 2004;117:2173–2181
  41. Futreal PA, Coin L, Marshall M, Down T, Hubbard T, Wooster R, et al. A census of human cancer genes. Nature Reviews in Cancer. 2004;4:177–183
  42. Garnis C, Buys TP, Lam WL. Genetic alteration and gene expression modulation during cancer progression. Molecular Cancer. 2004;3:9
  43. Gayther SA, Batley SJ, Linger L, Bannister A, Thorpe K, Chin SF, et al. Mutations truncating the EP300 acetylase in human cancers. Nature Genetics. 2000;24:300–303
  44. Gil J, Peters G. Regulation of the INK4b-ARF-INK4a tumour suppressor locus: all for one or one for all. Nature Reviews in Molecular and Cellular Biology. 2006;7:667–677
  45. Goel A, Nagasaka T, Arnold CN, Inoue T, Hamilton C, Niedzwiecki D, et al. The CpG Island Methylator Phenotype and Chromosomal Instability Are Inversely Correlated in Sporadic Colorectal Cancer. Gastroenterology. 2006;
  46. Goessl C, Sauter T, Michael T, Berge B, Staehler M, Miller K. Efficacy and tolerability of tolterodine in children with detrusor hyperreflexia. Urology. 2000;55:414–418
  47. Goessl C, Muller M, Straub B, Miller K. DNA alterations in body fluids as molecular tumor markers for urological malignancies. European Urology. 2002;41:668–676
  48. Gormally, E., Caboux, E., Vineis, P., Hainaut, P. Circulating free DNA in plasma or serum as biomarker of carcinogenesis: practical aspects and biological significance. Mutation Research, in press. (Epub ahead of print). doi:10.1016/j.mrrev.2006.11.002.
  49. Gormally E, Vineis P, Matullo G, Veglia F, Caboux E, Le Roux E, et al. TP53 and KRAS2 mutations in plasma DNA of healthy subjects and subsequent cancer occurrence: a prospective study. Cancer Research. 2006;66:6871–6876
  50. Grady WM, Rajput A, Lutterbaugh JD, Markowitz SD. Detection of aberrantly methylated hMLH1 promoter DNA in the serum of patients with microsatellite unstable colon cancer. Cancer Research. 2001;61:900–902
  51. Guo M, Akiyama Y, House MG, Hooker CM, Heath E, Gabrielson E, et al. Hypermethylation of the GATA genes in lung cancer. Clinical Cancer Research. 2004;10:7917–7924
  52. Hainaut P, Hollstein M. p53 and human cancer: the first ten thousand mutations. Advances in Cancer Research. 2000;77:81–137
  53. Hanahan D, Weinberg RA. The hallmarks of cancer. Cell. 2000;100:57–70
  54. Harari D, Yarden Y. Molecular mechanisms underlying ErbB2/HER2 action in breast cancer. Oncogene. 2000;19:6102–6114
  55. Herman JG, Umar A, Polyak K, Graff JR, Ahuja N, Issa JP, et al. Incidence and functional consequences of hMLH1 promoter hypermethylation in colorectal carcinoma. Proceedings of the National Academy of Sciences of the United States of America. 1998;95:6870–6875
  56. Issa JP. Methylation and prognosis: of molecular clocks and hypermethylator phenotypes. Clinical Cancer Research. 2003;9:2879–2881
  57. Issa JP. CpG island methylator phenotype in cancer. Nature Reviews in Cancer. 2004;4:988–993
  58. Jackson PE, Kuang SY, Wang JB, Strickland PT, Munoz A, Kensler TW, et al. Prospective detection of codon 249 mutations in plasma of hepatocellular carcinoma patients. Carcinogenesis. 2003;24:1657–1663
  59. Jaenisch R. DNA methylation and imprinting: why bother?. Trends in Genetics. 1997;13:323–329
  60. Jaenisch R, Bird A. Epigenetic regulation of gene expression: how the genome integrates intrinsic and environmental signals. Nature Genetics. 2003;33(Suppl.):245–254
  61. Jenuwein T, Allis CD. Translating the histone code. Science. 2001;293:1074–1080
  62. Jeronimo C, Usadel H, Henrique R, Silva C, Oliveira J, Lopes C, et al. Quantitative GSTP1 hypermethylation in bodily fluids of patients with prostate cancer. Urology. 2002;60:1131–1135
  63. John RM, Surani MA. Genomic imprinting, mammalian evolution, and the mystery of egg-laying mammals. Cell. 2000;101:585–588
  64. Jones PA, Baylin SB. The fundamental role of epigenetic events in cancer. Nature Reviews. 2002;3:415–428
  65. Kambara T, Simms LA, Whitehall VL, Spring KJ, Wynter CV, Walsh MD, et al. BRAF mutation is associated with DNA methylation in serrated polyps and cancers of the colorectum. Gut. 2004;53:1137–1144
  66. Kane MF, Loda M, Gaida GM, Lipman J, Mishra R, Goldman H, et al. Methylation of the hMLH1 promoter correlates with lack of expression of hMLH1 in sporadic colon tumors and mismatch repair-defective human tumor cell lines. Cancer Research. 1997;57:808–811
  67. Kaneda A, Kaminishi M, Yanagihara K, Sugimura T, Ushijima T. Identification of silencing of nine genes in human gastric cancers. Cancer Research. 2002;62:6645–6650
  68. Kawakami K, Brabender J, Lord RV, Groshen S, Greenwald BD, Krasna MJ, et al. Hypermethylated APC DNA in plasma and prognosis of patients with esophageal adenocarcinoma. Journal of the National Cancer Institute. 2000;92:1805–1811
  69. Kim CF, Jackson EL, Woolfenden AE, Lawrence S, Babar I, Vogel S, et al. Identification of bronchioalveolar stem cells in normal lung and lung cancer. Cell. 2005;121:823–835
  70. King CM, Gillespie ES, McKenna PG, Barnett YA. An investigation of mutation as a function of age in humans. Mutation Research. 1994;316:79–90
  71. Kurakawa E, Shimamoto T, Utsumi K, Hirano T, Kato H, Ohyashiki K. Hypermethylation of p16(INK4a) and p15(INK4b) genes in non-small cell lung cancer. International Journal of Oncology. 2001;19:277–281
  72. Laird PW. The power and the promise of DNA methylation markers. Nature Reviews in Cancer. 2003;3:253–266
  73. Lecomte T, Berger A, Zinzindohoue F, Micard S, Landi B, Blons H, et al. Detection of free-circulating tumor-associated DNA in plasma of colorectal cancer patients and its association with prognosis. International Journal of Cancer. 2002;100:542–548
  74. Lee TL, Leung WK, Chan MW, Ng EK, Tong JH, Lo KW, et al. Detection of gene promoter hypermethylation in the tumor and serum of patients with gastric carcinoma. Clinical Cancer Research. 2002;8:1761–1766
  75. Liang G, Salem CE, Yu MC, Nguyen HD, Gonzales FA, Nguyen TT, et al. DNA methylation differences associated with tumor tissues identified by genome scanning analysis. Genomics. 1998;53:260–268
  76. Loizou JI, Murr R, Finkbeiner MG, Sawan C, Wang ZQ, Herceg Z. Epigenetic information in chromatin: the code of entry for DNA repair. Cell Cycle. 2006;5:696–701
  77. Lu J, Getz G, Miska EA, Alvarez-Saavedra E, Lamb J, Peck D, et al. MicroRNA expression profiles classify human cancers. Nature. 2005;435:834–838
  78. Luedi PP, Hartemink AJ, Jirtle RL. Genome-wide prediction of imprinted murine genes. Genome Research. 2005;15:875–884
  79. Marsit CJ, McClean MD, Furniss CS, Kelsey KT. Epigenetic inactivation of the SFRP genes is associated with drinking, smoking and HPV in head and neck squamous cell carcinoma. International Journal of Cancer. 2006;119:1761–1766
  80. Moulton T, Crenshaw T, Hao Y, Moosikasuwan J, Lin N, Dembitzer F, et al Epigenetic lesions at the H19 locus in Wilms' tumour patients. Nature Genetics. 1994;7:440–447
  81. Muller HM, Widschwendter A, Fiegl H, Ivarsson L, Goebel G, Perkmann E, et al. DNA methylation in serum of breast cancer patients: an independent prognostic marker. Cancer Research. 2003;63:7641–7645
  82. Nakayama H, Hibi K, Taguchi M, Takase T, Yamazaki T, Kasai Y, et al. Molecular detection of p16 promoter methylation in the serum of colorectal cancer patients. Cancer Letters. 2002;188:115–119
  83. Nuovo GJ, Plaia TW, Belinsky SA, Baylin SB, Herman JG. In situ detection of the hypermethylation-induced inactivation of the p16 gene as an early event in oncogenesis. Proceedings of the National Academy of Sciences of the United States of America. 1999;96:12754–12759
  84. Oakey RJ, Beechey CV. Imprinted genes: identification by chromosome rearrangements and post-genomic strategies. Trends in Genetics. 2002;18:359–366
  85. Olivier M, Eeles R, Hollstein M, Khan MA, Harris CC, Hainaut P. The IARC TP53 database: new online mutation analysis and recommendations to users. Human Mutation. 2002;19:607–614
  86. Olivier M, Langerod A, Carrieri P, Bergh J, Klaar S, Eyfjord J, et al. The clinical value of somatic TP53 gene mutations in 1,794 patients with breast cancer. Clinical Cancer Research. 2006;12:1157–1167
  87. Paez JG, Janne PA, Lee JC, Tracy S, Greulich H, Gabriel S, et al. EGFR mutations in lung cancer: correlation with clinical response to gefitinib therapy. Science. 2004;304:1497–1500
  88. Pao W, Miller V, Zakowski M, Doherty J, Politi K, Sarkaria I, et al. EGF receptor gene mutations are common in lung cancers from “never smokers” and are associated with sensitivity of tumors to gefitinib and erlotinib. Proceedings of the National Academy of Sciences of the United States of America. 2004;101:13306–13311
  89. Pao W, Miller VA, Politi KA, Riely GJ, Somwar R, Zakowski MF, et al. Acquired resistance of lung adenocarcinomas to gefitinib or erlotinib is associated with a second mutation in the EGFR kinase domain. PLoS Medicine. 2005;2:e73
  90. Papadopoulou E, Davilas E, Sotiriou V, Koliopanos A, Aggelakis F, Dardoufas K, et al. Cell-free DNA and RNA in plasma as a new molecular marker for prostate cancer. Oncology Research. 2004;14:439–445
  91. Papadopoulou E, Davilas E, Sotiriou V, Georgakopoulos E, Georgakopoulou S, Koliopanos A, et al. Cell-free DNA and RNA in plasma as a new molecular marker for prostate and breast cancer. Annals of the New York Academy of Sciences. 2006;1075:235–243
  92. Pardal R, Clarke MF, Morrison SJ. Applying the principles of stem-cell biology to cancer. Nature Reviews in Cancer. 2003;3:895–902
  93. Pasquinelli AE, Hunter S, Bracht J. MicroRNAs: a developing story. Current Opinion in Genetics and Development. 2005;15:200–205
  94. Peterson CL, Cote J. Cellular machineries for chromosomal DNA repair. Genes and Development. 2004;18:602–616
  95. Pray-Grant MG, Daniel JA, Schieltz D, Yates JR, Grant PA. Chd1 chromodomain links histone H3 methylation with SAGA- and SLIK-dependent acetylation. Nature. 2005;433:434–438
  96. Pulling LC, Vuillemenot BR, Hutt JA, Devereux TR, Belinsky SA. Aberrant promoter hypermethylation of the death-associated protein kinase gene is early and frequent in murine lung tumors induced by cigarette smoke and tobacco carcinogens. Cancer Research. 2004;64:3844–3848
  97. Ravenel JD, Broman KW, Perlman EJ, Niemitz EL, Jayawardena TM, Bell DW, et al. Loss of imprinting of insulin-like growth factor-II (IGF2) gene in distinguishing specific biologic subtypes of Wilms tumor. Journal of the National Cancer Institute. 2001;93:1698–1703
  98. Roman-Gomez J, Jimenez-Velasco A, Agirre X, Prosper F, Heiniger A, Torres A. Lack of CpG island methylator phenotype defines a clinical subtype of T-cell acute lymphoblastic leukemia associated with good prognosis. Journal of Clinical Oncology. 2005;23:7043–7049
  99. Rowley JD. The critical role of chromosome translocations in human leukemias. Annual Review of Genetics. 1998;32:495–519
  100. Safar AM, Spencer H, Su X, Coffey M, Cooney CA, Ratnasinghe LD, et al. Methylation profiling of archived non-small cell lung cancer: a promising prognostic system. Clinical Cancer Research. 2005;11:4400–4405
  101. Sakatani T, Kaneda A, Iacobuzio-Donahue CA, Carter MG, de Boom Witzel S, Okano H, et al. Loss of imprinting of Igf2 alters intestinal maturation and tumorigenesis in mice. Science. 2005;307:1976–1978
  102. Samowitz WS, Albertsen H, Herrick J, Levin TR, Sweeney C, Murtaugh MA, et al. Evaluation of a large, population-based sample supports a CpG island methylator phenotype in colon cancer. Gastroenterology. 2005;129:837–845
  103. Sanchez-Cespedes M, Esteller M, Wu L, Nawroz-Danish H, Yoo GH, Koch WM, et al. Gene promoter hypermethylation in tumors and serum of head and neck cancer patients. Cancer research. 2000;60:892–895
  104. Santos-Rosa H, Caldas C. Chromatin modifier enzymes, the histone code and cancer. European Journal of Cancer. 2005;41:2381–2402
  105. Schedin P, Elias A. Multistep tumorigenesis and the microenvironment. Breast Cancer Research. 2004;6:93–101
  106. Schlesinger Y, Straussman R, Keshet I, Farkash S, Hecht M, Zimmerman J, et al. Polycomb-mediated methylation on Lys27 of histone H3 pre-marks genes for de novo methylation in cancer. Nature Genetics. 2006;
  107. Schneider R, Bannister AJ, Kouzarides T. Unsafe SETs: histone lysine methyltransferases and cancer. Trends in Biochemical Sciences. 2002;27:396–402
  108. Seligson DB, Horvath S, Shi T, Yu H, Tze S, Grunstein M, et al. Global histone modification patterns predict risk of prostate cancer recurrence. Nature. 2005;435:1262–1266
  109. Sengupta S, Shimamoto A, Koshiji M, Pedeux R, Rusin M, Spillare EA, et al. Tumor suppressor p53 represses transcription of RECQ4 helicase. Oncogene. 2005;24:1738–1748
  110. Shaw RJ, Akufo-Tetteh EK, Risk JM, Field JK, Liloglou T. Methylation enrichment pyrosequencing: combining the specificity of MSP with validation by pyrosequencing. Nucleic Acids Research. 2006;34:e78
  111. Shen L, Kondo Y, Hamilton SR, Rashid A, Issa JP. P14 methylation in human colon cancer is associated with microsatellite instability and wild-type p53. Gastroenterology. 2003;124:626–633
  112. Sherr CJ, Roberts JM. CDK inhibitors: positive and negative regulators of G1-phase progression. Genes and Development. 1999;13:1501–1512
  113. Shibata DM, Sato F, Mori Y, Perry K, Yin J, Wang S, et al. Hypermethylation of HPP1 is associated with hMLH1 hypermethylation in gastric adenocarcinomas. Cancer Research. 2002;62:5637–5640
  114. Shigematsu H, Gazdar AF. Somatic mutations of epidermal growth factor receptor signaling pathway in lung cancers. International Journal of Cancer. 2006;118:257–262
  115. Shigeno K, Yoshida H, Pan L, Luo JM, Fujisawa S, Naito K, et al. Disease-related potential of mutations in transcriptional cofactors CREB-binding protein and p300 in leukemias. Cancer Letters. 2004;213:11–20
  116. Singh SK, Hawkins C, Clarke ID, Squire JA, Bayani J, Hide T, et al. Identification of human brain tumour initiating cells. Nature. 2004;432:396–401
  117. Sjoblom T, Jones S, Wood LD, Parsons DW, Lin J, Barber TD, et al. The consensus coding sequences of human breast and colorectal cancers. Science. 2006;314:268–274
  118. Slattery ML, Curtin K, Sweeney C, Levin TR, Potter J, Wolff RK, et al. Diet and lifestyle factor associations with CpG island methylator phenotype and BRAF mutations in colon cancer. International Journal of Cancer. 2007;120:656–663
  119. Sparmann A, van Lohuizen M. Polycomb silencers control cell fate, development and cancer. Nature Reviews in Cancer. 2006;6:846–856
  120. Steenman MJ, Rainier S, Dobry CJ, Grundy P, Horon IL, Feinberg AP. Loss of imprinting of IGF2 is linked to reduced expression and abnormal methylation of H19 in Wilms' tumour. Nature Genetics. 1994;7:433–439
  121. Strahl BD, Allis CD. The language of covalent histone modifications. Nature. 2000;403:41–45
  122. Sugimura T, Terada M, Yokota J, Hirohashi S, Wakabayashi K. Multiple genetic alterations in human carcinogenesis. Environmental Health Perspectives. 1992;98:5–12
  123. Surani MA, Barton SC, Norris ML. Development of reconstituted mouse eggs suggests imprinting of the genome during gametogenesis. Nature. 1984;308:548–550
  124. Taback B, Saha S, Hoon DS. Comparative analysis of mesenteric and peripheral blood circulating tumor DNA in colorectal cancer patients. Annals of the New York Academy of Sciences. 2006;1075:197–203
  125. Tada Y, Wada M, Taguchi K, Mochida Y, Kinugawa N, Tsuneyoshi M, et al. The association of death-associated protein kinase hypermethylation with early recurrence in superficial bladder cancers. Cancer Research. 2002;62:4048–4053
  126. Takano T, Ohe Y, Sakamoto H, Tsuta K, Matsuno Y, Tateishi U, et al. Epidermal growth factor receptor gene mutations and increased copy numbers predict gefitinib sensitivity in patients with recurrent non-small-cell lung cancer. Journal of Clinical Oncology. 2005;23:6829–6837
  127. Thibodeau SN, French AJ, Roche PC, Cunningham JM, Tester DJ, Lindor NM, et al. Altered expression of hMSH2 and hMLH1 in tumors with microsatellite instability and genetic alterations in mismatch repair genes. Cancer Research. 1996;56:4836–4840
  128. Toyooka S, Kiura K, Mitsudomi T. EGFR mutation and response of lung cancer to gefitinib. The New England Journal of Medicine. 2005;352:2136;(author reply 2136)
  129. Toyota M, Ahuja N, Ohe-Toyota M, Herman JG, Baylin SB, Issa JP. CpG island methylator phenotype in colorectal cancer. Proceedings of the National Academy of Sciences of the United States of America. 1999;96:8681–8686
  130. Toyota M, Ohe-Toyota M, Ahuja N, Issa JP. Distinct genetic profiles in colorectal tumors with or without the CpG island methylator phenotype. Proceedings of the National Academy of Sciences of the United States of America. 2000;97:710–715
  131. Usadel H, Brabender J, Danenberg KD, Jeronimo C, Harden S, Engles J, et al. Quantitative adenomatous polyposis coli promoter methylation analysis in tumor tissue, serum, and plasma DNA of patients with lung cancer. Cancer Research. 2002;62:371–375
  132. Valenzuela MT, Galisteo R, Zuluaga A, Villalobos M, Nunez MI, Oliver FJ, et al. Assessing the use of p16(INK4a) promoter gene methylation in serum for detection of bladder cancer. European Urology. 2002;42:622–628discussion 628–630
  133. Varambally S, Dhanasekaran SM, Zhou M, Barrette TR, Kumar-Sinha C, Sanda MG, et al. The polycomb group protein EZH2 is involved in progression of prostate cancer. Nature. 2002;419:624–629
  134. Volinia S, Calin GA, Liu CG, Ambs S, Cimmino A, Petrocca F, et al. A microRNA expression signature of human solid tumors defines cancer gene targets. Proceedings of the National Academy of Sciences of the United States of America. 2006;103:2257–2261
  135. Wang YC, Hsu HS, Chen TP, Chen JT. Molecular diagnostic markers for lung cancer in sputum and plasma. Annals of the New York Academy of Sciences. 2006;1075:179–184
  136. Ward RL, Cheong K, Ku SL, Meagher A, O'Connor T, Hawkins NJ. Adverse prognostic effect of methylation in colorectal cancer is reversed by microsatellite instability. Journal of Clinical Oncology. 2003;21:3729–3736
  137. 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. Nature Genetics. 2006;38:787–793
  138. Widschwendter M, Fiegl H, Egle D, Mueller-Holzner E, Spizzo G, Marth C, et al. Epigenetic stem cell signature in cancer. Nature Genetics. 2006;
  139. Wolffe AP. Chromatin remodeling: why it is important in cancer. Oncogene. 2001;20:2988–2990
  140. Wong IH, Lo YM, Zhang J, Liew CT, Ng MH, Wong N, et al. Detection of aberrant p16 methylation in the plasma and serum of liver cancer patients. Cancer Research. 1999;59:71–73
  141. Wong IH, Lo YM, Yeo W, Lau WY, Johnson PJ. Frequent p15 promoter methylation in tumor and peripheral blood from hepatocellular carcinoma patients. Clinical Cancer Research. 2000;6:3516–3521
  142. Wong TS, Chang HW, Tang KC, Wei WI, Kwong DL, Sham JS, et al. High frequency of promoter hypermethylation of the death-associated protein-kinase gene in nasopharyngeal carcinoma and its detection in the peripheral blood of patients. Clinical Cancer Research. 2002;8:433–437
  143. Wong TS, Man MW, Lam AK, Wei WI, Kwong YL, Yuen AP. The study of p16 and p15 gene methylation in head and neck squamous cell carcinoma and their quantitative evaluation in plasma by real-time PCR. European Journal of Cancer. 2003;39:1881–1887
  144. Wong TS, Kwong DL, Sham JS, Wei WI, Kwong YL, Yuen AP. Quantitative plasma hypermethylated DNA markers of undifferentiated nasopharyngeal carcinoma. Clinical Cancer Research. 2004;10:2401–2406
  145. Woodson K, Flood A, Green L, Tangrea JA, Hanson J, Cash B, et al. Loss of insulin-like growth factor-II imprinting and the presence of screen-detected colorectal adenomas in women. Journal of the National Cancer Institute. 2004;96:407–410
  146. Yamamoto H, Min Y, Itoh F, Imsumran A, Horiuchi S, Yoshida M, et al. Differential involvement of the hypermethylator phenotype in hereditary and sporadic colorectal cancers with high-frequency microsatellite instability. Genes, Chromosomes and Cancer. 2002;33:322–325
  147. Yan PS, Perry MR, Laux DE, Asare AL, Caldwell CW, Huang TH. CpG island arrays: an application toward deciphering epigenetic signatures of breast cancer. Clinical Cancer Research. 2000;6:1432–1438
  148. Yang XJ. The diverse superfamily of lysine acetyltransferases and their roles in leukemia and other diseases. Nucleic acids research. 2004;32:959–976
  149. Zhang L, Huang J, Yang N, Greshock J, Megraw MS, Giannakakis A, et al. microRNAs exhibit high frequency genomic alterations in human cancer. Proceedings of the National Academy of Sciences of the United States of America. 2006;103:9136–9141
  150. Zhang YJ, Rossner P, Chen Y, Agrawal M, Wang Q, Wang L, et al. Aflatoxin B1 and polycyclic aromatic hydrocarbon adducts, p53 mutations and p16 methylation in liver tissue and plasma of hepatocellular carcinoma patients. International Journal of Cancer. 2006;119:985–991
  151. Zhu P, Martin E, Mengwasser J, Schlag P, Janssen KP, Gottlicher M. Induction of HDAC2 expression upon loss of APC in colorectal tumorigenesis. Cancer Cell. 2004;5:455–463
  152. Zou HZ, Yu BM, Wang ZW, Sun JY, Cang H, Gao F, et al. Detection of aberrant p16 methylation in the serum of colorectal cancer patients. Clinical Cancer Research. 2002;8:188–191

PII: S1574-7891(07)00010-5

doi: 10.1016/j.molonc.2007.01.004

Molecular Oncology
Volume 1, Issue 1 , Pages 26-41 , June 2007

Article Tools

* Image Usage & Resolution