DNA methylation and cancer diagnosis: New methods and applications

Expert Review of Molecular Diagnostics

Volumn 9, Issue 7, 2009, Pages 651-657

  Dehan, Pierre ^a   Kustermans, Gaelle ^a   Guenin, Samuel ^a   Horion, Julie ^a   Boniver, Jacques ^a   Delvenne, Philippe ^a  

^a UNIVERSITY OF LIÈGE   (Belgium)

Author keywords

Biomarker; Cancer; CpG island; Diagnosis; DNA methylation; Microarray

Indexed keywords

BISULFITE; CPG OLIGODEOXYNUCLEOTIDE; CYTOSINE; METHYLCYTOSINE; TUMOR MARKER; UNCLASSIFIED DRUG;

CANCER DIAGNOSIS; CARCINOGENESIS; DEVICE; DNA METHYLATION; EPIGENETICS; GENE IDENTIFICATION; GENE SILENCING; GENOME; HUMAN; NEOPLASM; POLYMERASE CHAIN REACTION; PROMOTER REGION; REVIEW; TUMOR SUPPRESSOR GENE;

DNA METHYLATION; EPIGENESIS, GENETIC; HUMANS; NEOPLASMS; TUMOR MARKERS, BIOLOGICAL;

EID: 70350068690     PISSN: 14737159     EISSN: 17448352     Source Type: Journal    
DOI: 10.1586/erm.09.53     Document Type: Review

References (70)

1. Jemal A, Siegel R, Ward E et al. Cancer statistics, 2008. CA Cancer J. Clin. 58(2), 71-96 (2008).
2. Gal-Yam EN, Saito Y, Egger G, Jones PA. Cancer epigenetics: modifications, screening, and therapy. Annu. Rev. Med. 59, 267-280 (2008). •• Comprehensive review and an excellent introduction to cancer epigenetics. (Pubitemid 351287937)
3. Esteller M. Cancer epigenomics: DNA methylomes and histone-modification maps. Nat. Rev. Genet. 8(4), 286-298 (2007). (Pubitemid 46439286)
4. Illingworth R, Kerr A, Desousa D et al. A novel CpG island set identifies tissue-specific methylation at developmental gene loci. PLoS Biol. 6(1), E22 (2008). (Pubitemid 351226045)
5. Saxonov S, Berg P, Brutlag DL. A genome-wide analysis of CpG dinucleotides in the human genome distinguishes two distinct classes of promoters. Proc. Natl Acad. Sci. USA 103(5), 1412-1417 (2006). (Pubitemid 43191179)
6. Bird A. DNA methylation patterns and epigenetic memory. Genes Dev. 16(1), 6-21 (2002). (Pubitemid 34049633)
7. Kwabi-Addo B, Chung W, Shen L et al. Age-related DNA methylation changes in normal human prostate tissues. Clin. Cancer Res. 13(13), 3796-3802 (2007). • Interesting study demonstrating age-related DNA methylation in normal tissue. (Pubitemid 47037584)
8. Cedar H, Bergman Y. Linking DNA methylation and histone modification: patterns and paradigms. Nat. Rev. Genet. 10(5), 295-304 (2009). •• Comprehensive review introducing to epigenetic complexity.
9. McCabe MT, Lee EK, Vertino PM. A multifactorial signature of DNA sequence and polycomb binding predicts aberrant CpG island methylation. Cancer Res. 69(1), 282-291 (2009).
10. Takeshima H, Yamashita S, Shimazu T, Niwa T, Ushijima T. The presence of RNA polymerase II, active or stalled, predicts epigenetic fate of promoter CpG islands. Genome Res. DOI: 10.1101/gr.093310.109 (2009) (Epub ahead of print).
11. Esteller M, Corn PG, Baylin SB, Herman JG. A gene hypermethylation profile of human cancer. Cancer Res. 61(8), 3225-3229 (2001). (Pubitemid 32695003)
12. Laird PW. The power and the promise of DNA methylation markers. Nat. Rev. Cancer 3(4), 253-266 (2003). •• Review with prospective insight on methylation biomarkers.
13. Keshet I, Schlesinger Y, Farkash S et al. Evidence for an instructive mechanism of de novo methylation in cancer cells. Nat. Genet. 38(2), 149-153 (2006). (Pubitemid 43177227)
14. Wilson AS, Power BE, Molloy PL. DNA hypomethylation and human diseases. Biochim. Biophys. Acta 1775(1), 138-162 (2007). • Comprehensive review on the less studied hypomethylation process.
15. Wu H, Chen Y, Liang J et al. Hypomethylation-linked activation of PAX2 mediates tamoxifen-stimulated endometrial carcinogenesis. Nature 438(7070), 981-987 (2005). (Pubitemid 43093965)
16. Yegnasubramanian S, Haffner MC, Zhang Y et al. DNA hypomethylation arises later in prostate cancer progression than CpG island hypermethylation and contributes to metastatic tumor heterogeneity. Cancer Res. 68(21), 8954-8967 (2008).
17. Bariol C, Suter C, Cheong K et al. The relationship between hypomethylation and CpG island methylation in colorectal neoplasia. Am. J. Pathol. 162(4), 1361-1371 (2003). (Pubitemid 36350680)
18. Chuang JC, Jones PA. Epigenetics and microRNAs. Pediatr. Res. 61(5), R24-R29 (2007).
19. Datta J, Kutay H, Nasser MW et al. Methylation mediated silencing of MicroRNA-1 gene and its role in hepatocellular carcinogenesis. Cancer Res. 68(13), 5049-5058 (2008).
20. Toyota M, Suzuki H, Sasaki Y et al. Epigenetic silencing of microRNA-34b/c and B-cell translocation gene 4 is associated with CpG island methylation in colorectal cancer. Cancer Res. 68(11), 4123-4132 (2008).
21. Zilberman D, Henikoff S. Genome-wide analysis of DNA methylation patterns. Development 134(22), 3959-3965 (2007). (Pubitemid 350269413)
22. Mund C, Brueckner B, Lyko F. Reactivation of epigenetically silenced genes by DNA methyltransferase inhibitors: basic concepts and clinical applications. Epigenetics 1(1), 7-13 (2006).
23. Kongkham PN, Northcott PA, Ra YS et al. An epigenetic genome-wide screen identifies SPINT2 as a novel tumor suppressor gene in pediatric medulloblastoma. Cancer Res. 68(23), 9945-9953 (2008).
24. Lippman Z, Gendrel AV, Colot V, Martienssen R. Profiling DNA methylation patterns using genomic tiling microarrays. Nat. Methods 2(3), 219-224 (2005). (Pubitemid 41122130)
25. Hatada I, Fukasawa M, Kimura M et al. Genome-wide profiling of promoter methylation in human. Oncogene 25(21), 3059-3064 (2006). (Pubitemid 43780470)
26. Rush LJ, Plass C. Restriction landmark genomic scanning for DNA methylation in cancer: past, present, and future applications. Anal. Biochem. 307(2), 191-201 (2002). (Pubitemid 35026191)
27. Yamagata Y, Maekawa R, Asada H et al. Aberrant DNA methylation status in human uterine leiomyoma. Mol. Hum. Reprod. 15(4), 259-267 (2009).
28. Hu M, Yao J, Polyak K. Methylation-specific digital karyotyping. Nat. Protoc. 1(3), 1621-1636 (2006).
29. Shen L, Kondo Y, Guo Y et al. Genome-wide profiling of DNA methylation reveals a class of normally methylated CpG island promoters. PLoS Genet. 3(10), 2023-2036 (2007). (Pubitemid 350072065)
30. Khulan B, Thompson RF, Ye K et al. Comparative isoschizomer profiling of cytosine methylation: the HELP assay. Genome Res. 16(8), 1046-1055 (2006). (Pubitemid 44162264)
31. Jacinto FV, Ballestar E, Esteller M. Methyl-DNA immunoprecipitation (MeDIP): hunting down the DNA methylome. Biotechniques 44(1), 35-39 (2008). (Pubitemid 351251659)
32. Gebhard C, Schwarzfischer L, Pham TH et al. Genome-wide profiling of CpG methylation identifies novel targets of aberrant hypermethylation in myeloid leukemia. Cancer Res. 66(12), 6118-6128 (2006).
33. Rauch TA, Pfeifer GP. The MIRA method for DNA methylation analysis. Methods Mol. Biol. 507, 65-75 (2009).
34. Weber M, Davies JJ, Wittig D et al. Chromosome-wide and promoter-specific analyses identify sites of differential DNA methylation in normal and transformed human cells. Nat. Genet. 37(8), 853-862 (2005). (Pubitemid 41077111)
35. Wang S-C, Petronis A. DNA Methylation Microarrays : Experimental Design and Statistical Analysis. CRC Press, FL, USA (2008).
36. Beck S, Rakyan VK. The methylome: approaches for global DNA methylation profiling. Trends Genet. 24(5), 231-237 (2008).
37. Fraga MF, Esteller M. DNA methylation: a profile of methods and applications. Biotechniques 33(3), 632, 634, 636-649 (2002). (Pubitemid 35277569)
38. Shames DS, Minna JD, Gazdar AF. Methods for detecting DNA methylation in tumors: from bench to bedside. Cancer Lett. 251(2), 187-198 (2007). • Describes many methods for detecting DNA methylation in tumors.
39. Clark SJ, Harrison J, Paul CL, Frommer M. High sensitivity mapping of methylated cytosines. Nucleic Acids Res. 22(15), 2990-2997 (1994). (Pubitemid 24260626)
40. Herman JG, Graff JR, Myohanen S, Nelkin BD, Baylin SB. Methylation-specific PCR: a novel PCR assay for methylation status of CpG islands. Proc. Natl Acad. Sci. USA 93(18), 9821-9826 (1996).
41. Licchesi JD, Herman JG. Methylation-specific PCR. Methods Mol. Biol. 507, 305-323 (2009).
42. Eads CA, Danenberg KD, Kawakami K et al. MethyLight: a high-throughput assay to measure DNA methylation. Nucleic Acids Res. 28(8), E32 (2000).
43. Gustafson KS. Locked nucleic acids can enhance the analytical performance of quantitative methylation-specific polymerase chain reaction. J. Mol. Diagn. 10(1), 33-42 (2008).
44. Zhang Y, Rohde C, Tierling S et al. DNA methylation analysis by bisulfite conversion, cloning, and sequencing of individual clones. Methods Mol. Biol. 507, 177-187 (2009).
45. Weisenberger DJ, Trinh BN, Campan M et al. DNA methylation analysis by digital bisulfite genomic sequencing and digital MethyLight. Nucleic Acids Res. 36(14), 4689-4698 (2008).
46. Wojdacz TK, Dobrovic A. Melting curve assays for DNA methylation analysis. Methods Mol. Biol. 507, 229-240 (2009).
47. Brena RM, Plass C. Bio-COBRA: absolute quantification of DNA methylation in electrofluidics chips. Methods Mol. Biol. 507, 257-269 (2009).
48. Kaminsky Z, Petronis A. Methylation SNaPshot: a method for the quantification of site-specific DNA methylation levels. Methods Mol. Biol. 507, 241-255 (2009).
49. van den Boom D, Ehrich M. Mass spectrometric analysis of cytosine methylation by base-specific cleavage and primer extension methods. Methods Mol. Biol. 507, 207-227 (2009).
50. Dejeux E, El abdalaoui H, Gut IG, Tost J. Identification and quantification of differentially methylated loci by the pyrosequencing technology. Methods Mol. Biol. 507, 189-205 (2009).
51. Bibikova M, Lin Z, Zhou L et al. High-throughput DNA methylation profiling using universal bead arrays. Genome Res. 16(3), 383-393 (2006). (Pubitemid 43327509)
52. Meissner A, Gnirke A, Bell GW et al. Reduced representation bisulfite sequencing for comparative high-resolution DNA methylation analysis. Nucleic Acids Res. 33(18), 5868-5877 (2005). (Pubitemid 41742606)
53. Oakes CC, La Salle S, Trasler JM, Robaire B. Restriction digestion and real-time PCR (qAMP). Methods Mol. Biol. 507, 271-280 (2009).
54. Yegnasubramanian S, Lin X, Haffner MC, DeMarzo AM, Nelson WG. Combination of methylated-DNA precipitation and methylation-sensitive restriction enzymes (COMPARE-MS) for the rapid, sensitive and quantitative detection of DNA methylation. Nucleic Acids Res. 34(3), E19 (2006). (Pubitemid 43380693)
55. Kholod N, Boniver J, Delvenne P. A new dimethyl sulfoxide-based method for gene promoter methylation detection. J. Mol. Diagn. 9(5), 574-581 (2007). (Pubitemid 350158415)
56. Wong N, Morley R, Saffery R, Craig J. Archived Guthrie blood spots as a novel source for quantitative DNA methylation analysis. Biotechniques 45(4), 423-428 (2008).
57. Cairns P. Gene methylation and early detection of genitourinary cancer: the road ahead. Nat. Rev. Cancer 7(7), 531-543 (2007). • Comprehensive review introducing prospective views. (Pubitemid 46985397)
58. Lee WH, Morton RA, Epstein JI et al. Cytidine methylation of regulatory sequences near the pi-class glutathione S-transferase gene accompanies human prostatic carcinogenesis. Proc. Natl Acad. Sci. USA 91(24), 11733-11737 (1994).
59. Meiers I, Shanks JH, Bostwick DG. Glutathione S-transferase pi (GSTP1) hypermethylation in prostate cancer: review 2007. Pathology 39(3), 299-304 (2007). (Pubitemid 46897603)
60. Ongenaert M, Van Neste L, De Meyer T et al. PubMeth: a cancer methylation database combining text-mining and expert annotation. Nucleic Acids Res. 36, D842-D846 (2008). (Pubitemid 351149833)
61. 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(2), 293-299 (2009).
62. Docherty SJ, Davis OS, Haworth CM, Plomin R, Mill J. Bisulfite-based epityping on pooled genomic DNA provides an accurate estimate of average group DNA methylation. Epigenetics Chromatin 2(1), 3 (2009).
63. Berman BP, Weisenberger DJ, Laird PW. Locking in on the human methylome. Nat. Biotechnol. 27(4), 341-342 (2009).
64. Clarke J, Wu HC, Jayasinghe L et al. Continuous base identification for singlemolecule nanopore DNA sequencing. Nat. Nanotechnol. 4(4), 265-270 (2009). •• Study that holds promise as new tool for DNA methylation detection.
65. Moving AHEAD with an international human epigenome project. Nature 454(7205), 711-715 (2008).
66. Akhtar A, Cavalli G. The epigenome network of excellence. PLoS Biol. 3(5), E177 (2005).
67. Clement G, Benhattar J. A methylation sensitive dot blot assay (MS-DBA) for the quantitative analysis of DNA methylation in clinical samples. J. Clin. Pathol. 58(2), 155-158 (2005). (Pubitemid 40193800)
68. Kristensen LS, Mikeska T, Krypuy M, Dobrovic A. Sensitive melting analysis after real time-methylation specific PCR (SMART-MSP): high-throughput and probe-free quantitative DNA methylation detection. Nucleic Acids Res. 36(7), E42 (2008). (Pubitemid 351567020)
69. Dugast-Darzacq C, Grange T. MethylQuant: a real-time PCR-based method to quantify DNA methylation at single specific cytosines. Methods Mol. Biol. 507, 281-303 (2009).
70. Campan M, Weisenberger DJ, Trinh B, Laird PW. MethyLight. Methods Mol. Biol. 507, 325-337 (2009).