DNA methylation profiles in precancerous tissue and cancers: Carcinogenetic risk estimation and prognostication based on DNA methylation status

Epigenomics

Volumn 2, Issue 3, 2010, Pages 467-481

  Arai, Eri ^a   Kanai, Yae ^a  

^a NATIONAL CANCER CENTER RESEARCH INSTITUTE   (Japan)

Author keywords

bacterial artificial chromosome array based methylated CpG island amplification; DNA methylation; DNA methyltransferase; precancerous condition; prognostication; risk estimation

Indexed keywords

DNA; DNA METHYLTRANSFERASE;

BACTERIAL ARTIFICIAL CHROMOSOME; CANCER CELL; CANCER RISK; CHROMOSOMAL INSTABILITY; CHRONIC HEPATITIS; CPG ISLAND; DNA METHYLATION; EPIGENETICS; GENOME; HUMAN; KIDNEY CARCINOMA; LIVER CELL CARCINOMA; NEOPLASM; NONHUMAN; PRECANCER; PRIORITY JOURNAL; PROGNOSIS; REVIEW; TUMOR GENE; VIRUS HEPATITIS;

CHROMOSOMES, ARTIFICIAL, BACTERIAL; CPG ISLANDS; DNA METHYLATION; EPIGENOMICS; GENE EXPRESSION REGULATION, NEOPLASTIC; GENOMICS; HUMANS; NEOPLASMS; NUCLEIC ACID AMPLIFICATION TECHNIQUES; PRECANCEROUS CONDITIONS; PROGNOSIS; RISK ASSESSMENT;

BACTERIA (MICROORGANISMS);

EID: 77954133525     PISSN: 17501911     EISSN: 1750192X     Source Type: Journal    
DOI: 10.2217/epi.10.16     Document Type: Review

References (70)

1. Jones PA, Baylin SB: The fundamental role of epigenetic events in cancer. Nat. Rev. Genet. 3, 415-428 (2002).
2. Jones PA, Baylin SB: The epigenomics of cancer. Cell 128, 683-692 (2007).
3. Sharma S, Kelly TK, Jones PA: Epigenetics in cancer. Carcinogenesis 31, 27-36 (2009).
4. Cedar H, Bergman Y: Linking DNA methylation and histone modifcation: patterns and paradigms. Nat. Rev. Genet. 10, 295-304 (2009).
5. Delcuve GP, Rastegar M, Davie JR: Epigenetic control. J. Cell Physiol. 219, 243-250 (2009).
6. Illingworth RS, Bird AP: CpG islands-'a rough guide'. FEBS Lett. 583, 1713-1720 (2009).
7. Mohn F, Schubeler D: Genetics and epigenetics: stability and plasticity during cellular differentiation. Trends. Genet. 25, 129-136 (2009).
8. Yoshiura K, Kanai Y, Ochiai A, Shimoyama Y, Sugimura T, Hirohashi S: Silencing of the E-cadherin invasion-suppressor gene by CpG methylation in human carcinomas. Proc. Natl Acad. Sci. USA 92, 7416-7419 (1995).
9. Baylin SB, Ohm JE: Epigenetic gene silencing in cancer-a mechanism for early oncogenic pathway addiction? Nat. Rev. Cancer 6, 107-116 (2006).
10. Shibata D: Inferring human stem cell behaviour from epigenetic drift. J. Pathol. 217, 199-205 (2009).
11. Ohm JE, McGarvey KM, Yu X et al.: A stem cell-like chromatin pattern may predispose tumor suppressor genes to DNA hypermethylation and heritable silencing. Nat. Genet. 39, 237-242 (2007).
12. Pogribny IP, Beland FA: DNA hypomethylation in the origin and pathogenesis of human diseases. Cell Mol. Life Sci. 66, 2249-2261 (2009).
13. Wong N, Lam WC, Lai PB, Pang E, Lau WY, Johnson PJ: Hypomethylation of chromosome 1 heterochromatin DNA correlates with q-arm copy gain in human hepatocellular carcinoma. Am. J. Pathol. 159, 465-471 (2001).
14. Nakagawa T, Kanai Y, Ushijima S, Kitamura T, Kakizoe T, Hirohashi S: DNA hypomethylation on pericentromeric satellite regions signifcantly correlates with loss of heterozygosity on chromosome 9 in urothelial carcinomas. J. Urol. 173, 243-246 (2005).
15. Okano M, Bell DW, Haber DA, Li E: DNA methyltransferases DNMT3a and Dnmt3b are essential for de novo methylation and mammalian development. Cell 99, 247-257 (1999).
16. Saito Y, Kanai Y, Sakamoto M, Saito H, Ishii H, Hirohashi S: Overexpression of a splice variant of DNA methyltransferase 3b, DNMT3b4, associated with DNA hypomethylation on pericentromeric satellite regions during human hepatocarcinogenesis. Proc. Natl Acad. Sci. USA 99, 10060-10065 (2002).
17. Laird PW: The power and the promise of DNA methylation markers. Nat. Rev. Cancer 3, 253-266 (2003).
18. Issa JP, Kantarjian HM: Targeting DNA methylation. Clin. Cancer Res. 15, 3938-3946 (2009).
19. Swanton C, Caldas C: Molecular classifcation of solid tumours: towards pathway-driven therapeutics. Br. J. Cancer 100, 1517-1522 (2009).
20. Kanai Y, Hirohashi S: Alterations of DNA methylation associated with abnormalities of DNA methyltransferases in human cancers during transition from a precancerous to a malignant state. Carcinogenesis 28, 2434-2442 (2007).
21. Kanai Y: Alterations of DNA methylation and clinicopathological diversity of human cancers. Pathol. Int. 58, 544-558 (2008).
22. Kanai Y: Genome-wide DNA methylation profles in precancerous conditions and cancers. Cancer Sci. 101, 36-45 (2010).
23. Kanai Y, Ushijima S, Tsuda H, Sakamoto M, Sugimura T, Hirohashi S: Aberrant DNA methylation on chromosome 16 is an early event in hepatocarcinogenesis. Jpn. J. Cancer Res. 87, 1210-1217 (1996).
24. Kanai Y, Hui AM, Sun L et al.: DNA hypermethylation at the D17S5 locus and reduced HIC-1 mRNA expression are associated with hepatocarcinogenesis. Hepatology 29, 703-709 (1999).
25. Kondo Y, Kanai Y, Sakamoto M, Mizokami M, Ueda R, Hirohashi S: Genetic instability and aberrant DNA methylation in chronic hepatitis and cirrhosis-a comprehensive study of loss of heterozygosity and microsatellite instability at 39 loci and DNA hypermethylation on 8 CpG islands in microdissected specimens from patients with hepatocellular carcinoma. Hepatology 32, 970-979 (2000).
26. Etoh T, Kanai Y, Ushijima S et al.: Increased DNA methyltransferase 1 (DNMT1) protein expression correlates signifcantly with poorer tumor differentiation and frequent DNA hypermethylation of multiple CpG islands in gastric cancers. Am. J. Pathol. 164, 689-699 (2004).
27. Wentzensen N, Sherman ME, Schiffman M, Wang SS: Utility of methylation markers in cervical cancer early detection: appraisal of the state-of-the-science. Gynecol. Oncol. 112, 293-299 (2009).
28. Ushijima T: Epigenetic feld for cancerization. J. Biochem. Mol. Biol. 40, 142-150 (2007).
29. Eguchi K, Kanai Y, Kobayashi K, Hirohashi S: DNA hypermethylation at the D17S5 locus in non-small cell lung cancers: its association with smoking history. Cancer Res. 57, 4913-4915 (1997).
30. Toyota M, Ahuja N, Ohe-Toyota M, Herman JG, Baylin SB, Issa JP: CpG island methylator phenotype in colorectal cancer. Proc. Natl Acad. Sci. USA 96, 8681-8686 (1999). (Pubitemid 29354851)
31. Kanai Y, Ushijima S, Hui AM et al.: The E-cadherin gene is silenced by CpG methylation in human hepatocellular carcinomas. Int. J. Cancer 71, 355-359 (1997).
32. Saito Y, Kanai Y, Sakamoto M, Saito H, Ishii H, Hirohashi S: Expression of mRNA for DNA methyltransferases and methyl-CpG-binding proteins and DNA methylation status on CpG islands and pericentromeric satellite regions during human hepatocarcinogenesis. Hepatology 33, 561-568 (2001).
33. Saito Y, Kanai Y, Nakagawa T et al.: Increased protein expression of DNA methyltransferase (DNMT) 1 is signifcantly correlated with the malignant potential and poor prognosis of human hepatocellular carcinomas. Int. J. Cancer 105, 527-532 (2003).
34. Peng DF, Kanai Y, Sawada M et al.: Increased DNA methyltransferase 1 (DNMT1) protein expression in precancerous conditions and ductal carcinomas of the pancreas. Cancer Sci. 96, 403-408 (2005).
35. Peng DF, Kanai Y, Sawada M et al.: DNA methylation of multiple tumor-related genes in association with overexpression of DNA methyltransferase 1 (DNMT1) during multistage carcinogenesis of the pancreas. Carcinogenesis 27, 1160-1168 (2006).
36. Ooi SK, O'Donnell AH, Bestor TH: Mammalian cytosine methylation at a glance. J. Cell Sci. 122, 2787-2791 (2009).
37. Chuang LS, Ian HI, Koh TW, Ng HH, Xu G, Li BF: Human DNA-(cytosine-5) methyltransferase-PCNA complex as a target for p21WAF1. Science 277, 1996-2000 (1997).
38. Kanai Y, Ushijima S, Kondo Y, Nakanishi Y, Hirohashi S: DNA methyltransferase expression and DNA methylation of CpG islands and peri-centromeric satellite regions in human colorectal and stomach cancers. Int. J. Cancer 91, 205-212 (2001).
39. Damiani LA, Yingling CM, Leng S, Romo PE, Nakamura J, Belinsky SA: Carcinogen-induced gene promoter hypermethylation is mediated by DNMT1 and causal for transformation of immortalized bronchial epithelial cells. Cancer Res. 68, 9005-9014 (2008).
40. Liao X, Siu MK, Chan KY et al.: Hypermethylation of RAS effector related genes and DNA methyltransferase 1 expression in endometrial carcinogenesis. Int. J. Cancer 123, 296-302 (2008).
41. Hino R, Uozaki H, Murakami N et al.: Activation of DNA methyltransferase 1 by EBV latent membrane protein 2A leads to promoter hypermethylation of PTEN gene in gastric carcinoma. Cancer Res. 69, 2766-2774 (2009).
42. Gao P, Yang X, Xue YW et al.: Promoter methylation of glutathione S-transferase pi1 and multidrug resistance gene 1 in bronchioloalveolar carcinoma and its correlation with DNA methyltransferase 1 expression. Cancer 115, 3222-3232 (2009).
43. Lin RK, Hsieh YS, Lin P et al.: The tobacco-specifc carcinogen NNK induces DNA methyltransferase 1 accumulation and tumor suppressor gene hypermethylation in mice and lung cancer patients. J. Clin. Invest. 120, 521-532 (2010).
44. 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 Res. 59, 2302-2306 (1999).
45. Park HJ, Yu E, Shim YH: DNA methyltransferase expression and DNA hypermethylation in human hepatocellular carcinoma. Cancer Lett. 233, 271-278 (2006).
46. Kondo Y, Shen L, Suzuki S et al.: Alterations of DNA methylation and histone modifcations contribute to gene silencing in hepatocellular carcinomas. Hepatol. Res. 37, 974-983 (2007).
47. Estecio MR, Yan PS, Ibrahim AE et al.: High-throughput methylation profling by MCA coupled to CpG island microarray. Genome Res. 17, 1529-1536 (2007).
48. Estecio MR, Issa JP: Tackling the methylome: recent methodological advances in genome-wide methylation profling. Genome Med. 1, 106 (2009).
49. Bibikova M, Fan JB: GoldenGate assay for DNA methylation profling. Methods Mol. Biol. 507, 149-163 (2009).
50. Gunderson KL: Whole-genome genotyping on bead arrays. Methods Mol. Biol. 529, 197-213 (2009).
51. Eid J, Fehr A, Gray J et al.: Real-time DNA sequencing from single polymerase molecules. Science 323, 133-138 (2009).
52. Maekita T, Nakazawa K, Mihara M et al.: High levels of aberrant DNA methylation in Helicobacter pylori-infected gastric mucosae and its possible association with gastric cancer risk. Clin. Cancer Res. 12, 989-995 (2006).
53. Clark SJ: Action at a distance: epigenetic silencing of large chromosomal regions in carcinogenesis. Hum. Mol. Genet. 16(Spec. No. 1), R88-R95 (2007).
54. Inazawa J, Inoue J, Imoto I: Comparative genomic hybridization (CGH)-arrays pave the way for identifcation of novel cancer-related genes. Cancer Sci. 95, 559-563 (2004).
55. Nishiyama N, Arai E, Chihara Y et al.: Genome-wide DNA methylation profles in urothelial carcinomas and urothelia at the precancerous stage. Cancer Sci. 101, 231-240 (2010).
56. Misawa A, Inoue J, Sugino Y et al.: Methylation-associated silencing of the nuclear receptor 1I2 gene in advanced-type neuroblastomas, identifed by bacterial artifcial chromosome array-based methylated CpG island amplifcation. Cancer Res. 65, 10233-10242 (2005).
57. Tanaka K, Imoto I, Inoue J et al.: Frequent methylation-associated silencing of a candidate tumor-suppressor, CRABP1, in esophageal squamous-cell carcinoma. Oncogene 26, 6456-6468 (2007).
58. Sugino Y, Misawa A, Inoue J et al.: Epigenetic silencing of prostaglandin E receptor 2 (PTGER2) is associated with progression of neuroblastomas. Oncogene 26, 7401-7413 (2007).
59. McRonald FE, Morris MR, Gentle D et al.: CpG methylation profling in VHL related and VHL unrelated renal cell carcinoma. Mol. Cancer 8, 31-41 (2009).
60. Arai E, Ushijima S, Fujimoto H et al.: Genome-wide DNA methylation profles in both precancerous conditions and clear cell renal cell carcinomas are correlated with malignant potential and patient outcome. Carcinogenesis 30, 214-221 (2009).
61. Arai E, Kanai Y, Ushijima S, Fujimoto H, Mukai K, Hirohashi S: Regional DNA hypermethylation and DNA methyltransferase (DNMT) 1 protein overexpression in both renal tumors and corresponding nontumorous renal tissues. Int. J. Cancer 119, 288-296 (2006).
62. Arai E, Ushijima S, Tsuda H et al.: Genetic clustering of clear cell renal cell carcinoma based on array-comparative genomic hybridization: its association with DNA methylation alteration and patient outcome. Clin. Cancer Res. 14, 5531-5539 (2008).
63. Lee HS, Kim BH, Cho NY et al.: Prognostic implications of and relationship between CpG island hypermethylation and repetitive DNA hypomethylation in hepatocellular carcinoma. Clin. Cancer Res. 15, 812-820 (2009).
64. Moribe T, Iizuka N, Miura T et al.: Methylation of multiple genes as molecular markers for diagnosis of a small, well-differentiated hepatocellular carcinoma. Int. J. Cancer 125, 388-397 (2009).
65. Arai E, Ushijima S, Gotoh M et al.: Genome-wide DNA methylation profles in liver tissue at the precancerous stage and in hepatocellular carcinoma. Int. J. Cancer 125, 2854-2862 (2009).
66. Kakizoe T: Development and progression of urothelial carcinoma. Cancer Sci. 97, 821-828 (2006).
67. Nakagawa T, Kanai Y, Ushijima S, Kitamura T, Kakizoe T, Hirohashi S: DNA hypermethylation on multiple CpG islands associated with increased DNA methyltransferase DNMT1 protein expression during multistage urothelial carcinogenesis. J. Urol. 173, 1767-1771 (2005).
68. Nakagawa T, Kanai Y, Saito Y, Kitamura T, Kakizoe T, Hirohashi S: Increased DNA methyltransferase 1 protein expression in human transitional cell carcinoma of the bladder. J. Urol. 170, 2463-2466 (2003).
69. Manabe D, Saika T, Ebara S et al.: Comparative study of oncologic outcome of laparoscopic nephroureterectomy and standard nephroureterectomy for upper urinary tract transitional cell carcinoma. Urology 69, 457-461 (2007).
70. Kim WJ, Kim YJ: Epigenetic markers as promising prognosticators for bladder cancer. Int. J. Urol. 16, 17-22 (2009).