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  • Expert Reviews in Molecular Medicine, Volume 12
  • 2010, e23

DNA methylation profiling in cancer

  • Yutaka Kondo (a1) and Jean-Pierre J. Issa (a2)
  • DOI: http://dx.doi.org/10.1017/S1462399410001559
  • Published online: 28 July 2010
Abstract

Aberrant DNA methylation in the genome is found in almost all types of cancer and contributes to malignant transformation by silencing multiple tumour-suppressor genes, sometimes simultaneously. Therefore, deciphering the signature of DNA methylation in each tumour is required to better understand tumour behaviour and might be of benefit for clinical diagnostics and therapy. Recent technologies for high-throughput genome-wide DNA methylation analyses are promising and potent tools for epigenetic profiling. Since epigenetic therapy is now in clinical use or trials for several types of cancers, efficient epigenetic profiling is required. In this review, the current key technologies available to assess genome-wide DNA methylation are introduced and the implications of DNA methylation profiling in human cancers are discussed.

Copyright
Corresponding author
*Corresponding author: Yutaka Kondo, Division of Molecular Oncology, Aichi Cancer Center Research Institute, 1-1 Kanokoden, Chikusa-ku, Nagoya 464-8681, Japan. E-mail: ykondo@aichi-cc.jp
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This list contains references from the content that can be linked to their source. For a full set of references and notes please see the PDF or HTML where available.

1B.H. Ramsahoye (2000) Non-CpG methylation is prevalent in embryonic stem cells and may be mediated by DNA methyltransferase 3a. Proceedings of the National Academy of Sciences of the United States of America 97, 5237-5242

2R. Lister (2009) Human DNA methylomes at base resolution show widespread epigenomic differences. Nature 462, 315-322

3T.H. Bestor (1992) CpG islands in mammalian gene promoters are inherently resistant to de novo methylation. Genetic Analysis, Techniques and Applications 9, 48-53

4S.H. Cross and A.P. Bird (1995) CpG islands and genes. Current Opinion in Genetics and Development 5, 309-314

5R. Illingworth (2008) A novel CpG island set identifies tissue-specific methylation at developmental gene loci. PLoS Biology 6, e22

6A. Bird (2002) DNA methylation patterns and epigenetic memory. Genes and Development 16, 6-21

7P.A. Jones and P.W. Laird (1999) Cancer epigenetics comes of age. Nature Genetics 21, 163-167

8P.A. Jones and S.B. Baylin (2007) The epigenomics of cancer. Cell 128, 683-692

10L. Shen (2010) DNA methylation predicts survival and response to therapy in patients with myelodysplastic syndromes. Journal of Clinical Oncology 28, 605-613

11C.B. Yoo and P.A. Jones (2006) Epigenetic therapy of cancer: past, present and future. Nature Reviews Drug Discovery 5, 37-50

12P.A. Marks and W.S. Xu (2009) Histone deacetylase inhibitors: Potential in cancer therapy. Journal of Cellular Biochemistry 107, 600-608

13S. Beck and V.K. Rakyan (2008) The methylome: approaches for global DNA methylation profiling. Trends in Genetics 24, 231-237

15Y. Hayashizaki (1993) Restriction landmark genomic scanning method and its various applications. Electrophoresis 14, 251-258

16J. Kawai (1993) Methylation profiles of genomic DNA of mouse developmental brain detected by restriction landmark genomic scanning (RLGS) method. Nucleic Acids Research 21, 5604-5608

17M. Okano (1999) DNA methyltransferases Dnmt3a and Dnmt3b are essential for de novo methylation and mammalian development. Cell 99, 247-257

18A. Eden (2003) Chromosomal instability and tumors promoted by DNA hypomethylation. Science 300, 455

19B. Cadieux (2006) Genome-wide hypomethylation in human glioblastomas associated with specific copy number alteration, methylenetetrahydrofolate reductase allele status, and increased proliferation. Cancer Research 66, 8469-8476

20C. De Smet (1999) DNA methylation is the primary silencing mechanism for a set of germ line- and tumor-specific genes with a CpG-rich promoter. Molecular and Cellular Biology 19, 7327-7335

21T. Sakatani (2005) Loss of imprinting of Igf2 alters intestinal maturation and tumorigenesis in mice. Science 307, 1976-1978

22S.B. Baylin (1998) Alterations in DNA methylation: a fundamental aspect of neoplasia. Advances in Cancer Research 72, 141-196

24A.H. Ting , K.M. McGarvey and S.B. Baylin (2006) The cancer epigenome–components and functional correlates. Genes and Development 20, 3215-3231

25Y. Kondo and J.P. Issa (2004) Epigenetic changes in colorectal cancer. Cancer and Metastasis Reviews 23, 29-39

26I. Keshet (2006) Evidence for an instructive mechanism of de novo methylation in cancer cells. Natue Genetics 38, 149-153

27F.A. Feltus (2003) Predicting aberrant CpG island methylation. Proceedings of the National Academy of Sciences of the United States of America 100, 12253-12258

28J.E. Ohm (2007) A stem cell-like chromatin pattern may predispose tumor suppressor genes to DNA hypermethylation and heritable silencing. Nature Genetics 39, 237-242

29M. Widschwendter (2007) Epigenetic stem cell signature in cancer. Nature Genetics 39, 157-158

30Y. Schlesinger (2007) Polycomb-mediated methylation on Lys27 of histone H3 pre-marks genes for de novo methylation in cancer. Nature Genetics 39, 232-236

31Y. Kondo (2008) Gene silencing in cancer by histone H3 lysine 27 trimethylation independent of promoter DNA methylation. Nature Genetics 40, 741-750

32E.N. Gal-Yam (2008) Frequent switching of Polycomb repressive marks and DNA hypermethylation in the PC3 prostate cancer cell line. Proceedings of the National Academy of Sciences of the United States of America 105, 12979-12984

33H. Takeshima (2009) The presence of RNA polymerase II, active or stalled, predicts epigenetic fate of promoter CpG islands. Genome Research 19, 1974-1982

34M. Toyota (1999) CpG island methylator phenotype in colorectal cancer. Proceedings of the National Academy of Sciences of the United States of America 96, 8681-8686

35L. Shen (2007) Integrated genetic and epigenetic analysis identifies three different subclasses of colon cancer. Proceedings of the National Academy of Sciences of the United States of America 104, 18654-18659

36S. Ogino (2006) CpG island methylator phenotype-low (CIMP-low) in colorectal cancer: possible associations with male sex and KRAS mutations. Journal of Molecular Diagnostics 8, 582-588

37K. Yagi Three DNA methylation epigenotypes in human colorectal cancer. Clinical Cancer Research 16, 21-33

38S.B. Baylin and J.E. Ohm (2006) Epigenetic gene silencing in cancer – a mechanism for early oncogenic pathway addiction? Nature Reviews Cancer 6, 107-116

39J.P. Issa (2004) CpG island methylator phenotype in cancer. Nature Reviews Cancer 4, 988-993

40J.P. Issa (2008) Colon cancer: it's CIN or CIMP. Clinical Cancer Research 14, 5939-5940

41Y. Kanai (2001) DNA methyltransferase expression and DNA methylation of CPG islands and peri-centromeric satellite regions in human colorectal and stomach cancers. International Journal of Cancer 91, 205-212

44H. Kim (2003) Concerted promoter hypermethylation of hMLH1, p16INK4A, and E-cadherin in gastric carcinomas with microsatellite instability. Journal of Pathology 200, 23-31

45M. Kusano (2006) Genetic, epigenetic, and clinicopathologic features of gastric carcinomas with the CpG island methylator phenotype and an association with Epstein-Barr virus. Cancer 106, 1467-1479

46M. Weber (2005) Chromosome-wide and promoter-specific analyses identify sites of differential DNA methylation in normal and transformed human cells. Nature Genetics 37, 853-862

47X. Zhang (2006) Genome-wide high-resolution mapping and functional analysis of DNA methylation in arabidopsis. Cell 126, 1189-1201

48T. Rauch (2006) MIRA-assisted microarray analysis, a new technology for the determination of DNA methylation patterns, identifies frequent methylation of homeodomain-containing genes in lung cancer cells. Cancer Research 66, 7939-7947

49B. Khulan (2006) Comparative isoschizomer profiling of cytosine methylation: the HELP assay. Genome Research 16, 1046-1055

50M.R. Estecio (2007) High-throughput methylation profiling by MCA coupled to CpG island microarray. Genome Research 17, 1529-1536

51L. Shen (2007) Genome-wide profiling of DNA methylation reveals a class of normally methylated CpG island promoters. PLoS Genetics 3, 2023-2036

52W. Gao (2008) Variable DNA methylation patterns associated with progression of disease in hepatocellular carcinomas. Carcinogenesis 29, 1901-1910

53N. Omura (2008) Genome-wide profiling of methylated promoters in pancreatic adenocarcinoma. Cancer Biology and Therapy 7, 1146-1156

56Z. Xiong and P.W. Laird (1997) COBRA: a sensitive and quantitative DNA methylation assay. Nucleic Acids Research 25, 2532-2534

57J.G. Herman (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

58M. Bibikova (2006) High-throughput DNA methylation profiling using universal bead arrays. Genome Research 16, 383-393

59T.J. Albert (2007) Direct selection of human genomic loci by microarray hybridization. Nature Methods 4, 903-905

61E. Hodges (2009) High definition profiling of mammalian DNA methylation by array capture and single molecule bisulfite sequencing. Genome Research 19, 1593-1605

62J.B. Li (2009) Multiplex padlock targeted sequencing reveals human hypermutable CpG variations. Genome Research 19, 1606-1615

64M. Esteller (2000) Inactivation of the DNA-repair gene MGMT and the clinical response of gliomas to alkylating agents. New England Journal of Medicine 343, 1350-1354

65M. Toyota (2003) Epigenetic inactivation of CHFR in human tumors. Proceedings of the National Academy of Sciences of the United States of America 100, 7818-7823

68M.E. Figueroa (2010) DNA methylation signatures identify biologically distinct subtypes in acute myeloid leukemia. Cancer Cell 17, 13-27

69Y. Goto (2009) Epigenetic profiles distinguish malignant pleural mesothelioma from lung adenocarcinoma. Cancer Research 69, 9073-9082

70E. Arai (2009) Genome-wide DNA methylation profiles in liver tissue at the precancerous stage and in hepatocellular carcinoma. International Journal of Cancer 125, 2854-2862

72M. Toyota (2000) 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 97, 710-715

73M. van Rijnsoever (2002) Characterisation of colorectal cancers showing hypermethylation at multiple CpG islands. Gut 51, 797-802

75R.L. Ward (2004) The CpG island methylator phenotype is not associated with a personal or family history of cancer. Cancer Research 64, 7618-7621

76W.S. Samowitz (2005) Evaluation of a large, population-based sample supports a CpG island methylator phenotype in colon cancer. Gastroenterology 129, 837-845

77Y. Suehiro (2008) Epigenetic-genetic interactions in the APC/WNT, RAS/RAF, and P53 pathways in colorectal carcinoma. Clinical Cancer Research 14, 2560-2569

78D.J. Weisenberger (2006) CpG island methylator phenotype underlies sporadic microsatellite instability and is tightly associated with BRAF mutation in colorectal cancer. Nature Genetics 38, 787-793

79S. Ogino (2006) CpG island methylator phenotype (CIMP) of colorectal cancer is best characterised by quantitative DNA methylation analysis and prospective cohort studies. Gut 55, 1000-1006

80Y.W. Cheng (2008) CpG island methylator phenotype associates with low-degree chromosomal abnormalities in colorectal cancer. Clinical Cancer Research 14, 6005-6013

81S. Ogino (2007) Molecular correlates with MGMT promoter methylation and silencing support CpG island methylator phenotype-low (CIMP-low) in colorectal cancer. Gut 56, 1564-1571

82C.A. Messick (2009) Genetic and molecular diversity of colon cancer hepatic metastases. Surgery 146, 227-231

83S. Hiraoka (2006) Laterally spreading type of colorectal adenoma exhibits a unique methylation phenotype and K-ras mutations. Gastroenterology 131, 379-389

84S.J. Park (2003) Frequent CpG island methylation in serrated adenomas of the colorectum. American Journal of Pathology 162, 815-822

85A. Rashid (2001) CpG island methylation in colorectal adenomas. American Journal of Pathology 159, 1129-1135

86M.J. O'Brien (2004) Hyperplastic (serrated) polyps of the colorectum: relationship of CpG island methylator phenotype and K-ras mutation to location and histologic subtype. American Journal of Surgical Pathology 28, 423-434

87T. Kambara (2004) BRAF mutation is associated with DNA methylation in serrated polyps and cancers of the colorectum. Gut 53, 1137-1144

88A.O. Chan (2002) Concordant CpG island methylation in hyperplastic polyposis. American Journal of Pathology 160, 529-536

89N. Oue (2003) DNA methylation of multiple genes in gastric carcinoma: association with histological type and CpG island methylator phenotype. Cancer Science 94, 901-905

90T. Etoh (2004) Increased DNA methyltransferase 1 (DNMT1) protein expression correlates significantly with poorer tumor differentiation and frequent DNA hypermethylation of multiple CpG islands in gastric cancers. American Journal of Pathology 164, 689-699

92Y. Kaneko (2003) Distinct methylated profiles in Helicobacter pylori dependent and independent gastric MALT lymphomas. Gut 52, 641-646

93D.H. Sinn (2009) Methylation and API2/MALT1 fusion in colorectal extranodal marginal zone lymphoma. Modern Pathology 22, 314-320

95S. Lee (2002) Aberrant CpG island methylation of multiple genes in intrahepatic cholangiocarcinoma. American Journal of Pathology 161, 1015-1022

96L. Shen (2002) DNA methylation and environmental exposures in human hepatocellular carcinoma. Journal of the National Cancer Institute 94, 755-761

97C. Zhang (2008) CpG island methylator phenotype association with upregulated telomerase activity in hepatocellular carcinoma. International Journal of Cancer 123, 998-1004

98S.G. Kim (2003) Epigenetic and genetic alterations in duodenal carcinomas are distinct from biliary and ampullary carcinomas. Gastroenterology 124, 1300-1310

99M. Suzuki (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

100Z. Liu (2008) CpG island methylator phenotype involving tumor suppressor genes located on chromosome 3p in non-small cell lung cancer. Lung Cancer 62, 15-22

101M. Suzuki Molecular characterization of chronic obstructive pulmonary disease-related non-small cell lung cancer through aberrant methylation and alterations of EGFR signaling. Annals of Surgical Oncology 17, 878-888

103J. Roman-Gomez (2005) Lack of CpG island methylator phenotype defines a clinical subtype of T-cell acute lymphoblastic leukemia associated with good prognosis. Journal of Clinical Oncology 23, 7043-7049

104C.N. Arnold (2008) Molecular characteristics and predictors of survival in patients with malignant neuroendocrine tumors. International Journal of Cancer 123, 1556-1564

105J. Geli (2008) Global and regional CpG methylation in pheochromocytomas and abdominal paragangliomas: association to malignant behavior. Clinical Cancer Research 14, 2551-2559

106Y. Cohen (2008) Hypermethylation of CpG island loci of multiple tumor suppressor genes in retinoblastoma. Experimental Eye Research 86, 201-206

107E. Merhavi (2007) Promoter methylation status of multiple genes in uveal melanoma. Investigative Ophthalmology and Visual Science 48, 4403-4406

J.P. Issa and H.M. Kantarjian (2009) Targeting DNA methylation. Clinical Cancer Research 15, 3938-3946

P.W. Laird (2010) Principles and challenges of genome-wide DNA methylation analysis. Nature Reviews Genetics 11, 191-203

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Expert Reviews in Molecular Medicine
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