A decade of DNA methylation profiling in cancer: What have we learned?

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Aditya Sharma Steven J Kuerbitz


Investigators have studied DNA methylation in tumor cells for nearly 50 years. Differences in gene-specific methylation between cancer cells and their normal counterparts were described more than 30 years ago. From early techniques that measured overall DNA methylation levels to enzyme-associated techniques that interrogated methylation at a single CpG dinucleotide to present day assays that catalogue the methylation of every cytosine in the genome, technical advancement progressively has brought increasing clarity to our understanding of the complex epigenomes of normal and neoplastic cells. Over the past 10 years we have been witness to an explosion of investigation into the epigenetic basis of cancer, and application of the powerful genome-wide DNA methylation profiling techniques to be reviewed have yielded critical insights into the organization of the cancer methylome with its broad regions of hypomethylation and foci of hypermethylation resulting in critical differences in gene expression and chromosomal stability compared to normal cells. These insights, in turn, have prompted novel, testable hypotheses, to be discussed, pertaining to fundamental aspects of cancer biology including the potential stem cell/progenitor cell origins of cancer and the plasticity of gene expression that may underlie tumor heterogeneity and tumor progression. Finally to be discussed is the growing portfolio of epigenetic tools being provided by modern methylome profiling analyses. These biomarker tools are complementing and extending the current genomic tests that are improving cancer diagnosis and that increasingly will facilitate highly individualized cancer treatment in the upcoming decade.

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SHARMA, Aditya; KUERBITZ, Steven J. A decade of DNA methylation profiling in cancer: What have we learned?. Medical Research Archives, [S.l.], n. 3, june 2015. ISSN 2375-1924. Available at: <https://esmed.org/MRA/mra/article/view/254>. Date accessed: 30 nov. 2023.
epigenetics, genome-wide methylation, CpG hypermethylation, hypomethylation, microRNA
Review Articles


Akao, Y., Y. Nakagawa, and T. Naoe. 2006. "let-7 microRNA functions as a potential growth suppressor in human colon cancer cells." Biol Pharm Bull 29 (5):903-6.

Andresen, K., K. M. Boberg, H. M. Vedeld, H. Honne, M. Hektoen, C. A. Wadsworth, O. P. Clausen, T. H. Karlsen, A. Foss, O. Mathisen, E. Schrumpf, R. A. Lothe, and G. E. Lind. 2012. "Novel target genes and a valid biomarker panel identified for cholangiocarcinoma." Epigenetics 7 (11):1249-57. doi: 10.4161/epi.22191.

Arai, E., S. Chiku, T. Mori, M. Gotoh, T. Nakagawa, H. Fujimoto, and Y. Kanai. 2012. "Single-CpG-resolution methylome analysis identifies clinicopathologically aggressive CpG island methylator phenotype clear cell renal cell carcinomas." Carcinogenesis 33 (8):1487-93. doi: 10.1093/carcin/bgs177.

Baylin, S. B., J. G. Herman, J. R. Graff, P. M. Vertino, and J. P. Issa. 1998. "Alterations in DNA methylation: a fundamental aspect of neoplasia." Adv Cancer Res 72:141-96.

Baylin, S. B., J. W. Hoppener, A. de Bustros, P. H. Steenbergh, C. J. Lips, and B. D. Nelkin. 1986. "DNA methylation patterns of the calcitonin gene in human lung cancers and lymphomas." Cancer Res 46 (6):2917-22.

Berman, B. P., D. J. Weisenberger, J. F. Aman, T. Hinoue, Z. Ramjan, Y. Liu, H. Noushmehr, C. P. Lange, C. M. van Dijk, R. A. Tollenaar, D. Van Den Berg, and P. W. Laird. 2012. "Regions of focal DNA hypermethylation and long-range hypomethylation in colorectal cancer coincide with nuclear lamina-associated domains." Nat Genet 44 (1):40-6. doi: 10.1038/ng.969.

Bianco, T., D. Hussey, and A. Dobrovic. 1999. "Methylation-sensitive, single-strand conformation analysis (MS-SSCA): A rapid method to screen for and analyze methylation." Hum Mutat 14 (4):289-93. doi: 10.1002/(SICI)1098-1004(199910)14:4<289::AID-HUMU3>3.0.CO;2-A.

Bibikova, M., J. Le, B. Barnes, S. Saedinia-Melnyk, L. Zhou, R. Shen, and K. L. Gunderson. 2009. "Genome-wide DNA methylation profiling using Infinium(R) assay." Epigenomics 1 (1):177-200. doi: 10.2217/epi.09.14.
Bibikova, M., Z. Lin, L. Zhou, E. Chudin, E. W. Garcia, B. Wu, D. Doucet, N. J. Thomas, Y. Wang, E. Vollmer, T. Goldmann, C. Seifart, W. Jiang, D. L. Barker, M. S. Chee, J. Floros, and J. B. Fan. 2006. "High-throughput DNA methylation profiling using universal bead arrays." Genome Res 16 (3):383-93. doi: 10.1101/gr.4410706.

Boland, C. R., and A. Goel. 2010. "Microsatellite instability in colorectal cancer." Gastroenterology 138 (6):2073-2087 e3. doi: 10.1053/j.gastro.2009.12.064.

Borssen, M., L. Palmqvist, K. Karrman, J. Abrahamsson, M. Behrendtz, J. Heldrup, E. Forestier, G. Roos, and S. Degerman. 2013. "Promoter DNA methylation pattern identifies prognostic subgroups in childhood T-cell acute lymphoblastic leukemia." PLoS One 8 (6):e65373. doi: 10.1371/journal.pone.0065373.

Charlton, J., R. D. Williams, N. J. Sebire, S. Popov, G. Vujanic, T. Chagtai, M. Alcaide-German, T. Morris, L. M. Butcher, P. Guilhamon, S. Beck, and K. Pritchard-Jones. 2015. "Comparative methylome analysis identifies new tumour subtypes and biomarkers for transformation of nephrogenic rests into Wilms tumour." Genome Med 7 (1):11. doi: 10.1186/s13073-015-0136-4.

Chatterton, Z., L. Morenos, F. Mechinaud, D. M. Ashley, J. M. Craig, A. Sexton-Oates, M. S. Halemba, M. Parkinson-Bates, J. Ng, D. Morrison, W. L. Carroll, R. Saffery, and N. C. Wong. 2014. "Epigenetic deregulation in pediatric acute lymphoblastic leukemia." Epigenetics 9 (3):459-67. doi: 10.4161/epi.27585.

Chen, W. D., Z. J. Han, J. Skoletsky, J. Olson, J. Sah, L. Myeroff, P. Platzer, S. Lu, D. Dawson, J. Willis, T. P. Pretlow, J. Lutterbaugh, L. Kasturi, J. K. Willson, J. S. Rao, A. Shuber, and S. D. Markowitz. 2005. "Detection in fecal DNA of colon cancer-specific methylation of the nonexpressed vimentin gene." J Natl Cancer Inst 97 (15):1124-32. doi: 10.1093/jnci/dji204.

Chiu, W. T., H. T. Lee, F. J. Huang, K. D. Aldape, J. Yao, P. S. Steeg, C. Y. Chou, Z. Lu, K. Xie, and S. Huang. 2011. "Caveolin-1 upregulation mediates suppression of primary breast tumor growth and brain metastases by stat3 inhibition." Cancer Res 71 (14):4932-43. doi: 10.1158/0008-5472.CAN-10-4249.

Choudhry, H., and J. W. Catto. 2011. "Epigenetic regulation of microRNA expression in cancer." Methods Mol Biol 676:165-84. doi: 10.1007/978-1-60761-863-8_12.

Christman, J. K., P. Price, L. Pedrinan, and G. Acs. 1977. "Correlation between hypomethylation of DNA and expression of globin genes in Friend erythroleukemia cells." Eur J Biochem 81 (1):53-61.

Collado, M., M. A. Blasco, and M. Serrano. 2007. "Cellular senescence in cancer and aging." Cell 130 (2):223-33. doi: 10.1016/j.cell.2007.07.003.

Costa, F. F., V. A. Paixao, F. P. Cavalher, K. B. Ribeiro, I. W. Cunha, J. A. Rinck, Jr., M. O'Hare, A. Mackay, F. A. Soares, R. R. Brentani, and A. A. Camargo. 2006. "SATR-1 hypomethylation is a common and early event in breast cancer." Cancer Genet Cytogenet 165 (2):135-43. doi: 10.1016/j.cancergencyto.2005.07.023.

Costello, J. F., M. C. Fruhwald, D. J. Smiraglia, L. J. Rush, G. P. Robertson, X. Gao, F. A. Wright, J. D. Feramisco, P. Peltomaki, J. C. Lang, D. E. Schuller, L. Yu, C. D. Bloomfield, M. A. Caligiuri, A. Yates, R. Nishikawa, H. Su Huang, N. J. Petrelli, X. Zhang, M. S. O'Dorisio, W. A. Held, W. K. Cavenee, and C. Plass. 2000. "Aberrant CpG-island methylation has non-random and tumour-type-specific patterns." Nat Genet 24 (2):132-8. doi: 10.1038/72785.

Cunningham, J. M., E. R. Christensen, D. J. Tester, C. Y. Kim, P. C. Roche, L. J. Burgart, and S. N. Thibodeau. 1998. "Hypermethylation of the hMLH1 promoter in colon cancer with microsatellite instability." Cancer Res 58 (15):3455-60.

Dante, R. 1988. "Quantitative determination of methylated CpG in satellite DNA I and in L1Rn DNA sequences extracted from rat kidney tissue and from rat kidney cell lines." Eur J Biochem 175 (1):135-9.

Daskalos, A., G. Nikolaidis, G. Xinarianos, P. Savvari, A. Cassidy, R. Zakopoulou, A. Kotsinas, V. Gorgoulis, J. K. Field, and T. Liloglou. 2009. "Hypomethylation of retrotransposable elements correlates with genomic instability in non-small cell lung cancer." Int J Cancer 124 (1):81-7. doi: 10.1002/ijc.23849.

Davidsson, J., H. Lilljebjorn, A. Andersson, S. Veerla, J. Heldrup, M. Behrendtz, T. Fioretos, and B. Johansson. 2009. "The DNA methylome of pediatric acute lymphoblastic leukemia." Hum Mol Genet 18 (21):4054-65. doi: 10.1093/hmg/ddp354.

de Bustros, A., B. D. Nelkin, A. Silverman, G. Ehrlich, B. Poiesz, and S. B. Baylin. 1988. "The short arm of chromosome 11 is a "hot spot" for hypermethylation in human neoplasia." Proc Natl Acad Sci U S A 85 (15):5693-7.

Decock, A., M. Ongenaert, J. Hoebeeck, K. De Preter, G. Van Peer, W. Van Criekinge, R. Ladenstein, J. H. Schulte, R. Noguera, R. L. Stallings, A. Van Damme, G. Laureys, J. Vermeulen, T. Van Maerken, F. Speleman, and J. Vandesompele. 2012. "Genome-wide promoter methylation analysis in neuroblastoma identifies prognostic methylation biomarkers." Genome Biol 13 (10):R95. doi: 10.1186/gb-2012-13-10-r95.

deVos, T., R. Tetzner, F. Model, G. Weiss, M. Schuster, J. Distler, K. V. Steiger, R. Grutzmann, C. Pilarsky, J. K. Habermann, P. R. Fleshner, B. M. Oubre, R. Day, A. Z. Sledziewski, and C. Lofton-Day. 2009. "Circulating methylated SEPT9 DNA in plasma is a biomarker for colorectal cancer." Clin Chem 55 (7):1337-46. doi: 10.1373/clinchem.2008.115808.

Djos, A., T. Martinsson, P. Kogner, and H. Caren. 2012. "The RASSF gene family members RASSF5, RASSF6 and RASSF7 show frequent DNA methylation in neuroblastoma." Mol Cancer 11:40. doi: 10.1186/1476-4598-11-40.

Dobrovic, A., and D. Simpfendorfer. 1997. "Methylation of the BRCA1 gene in sporadic breast cancer." Cancer Res 57 (16):3347-50.

Eads, C. A., K. D. Danenberg, K. Kawakami, L. B. Saltz, C. Blake, D. Shibata, P. V. Danenberg, and P. W. Laird. 2000. "MethyLight: a high-throughput assay to measure DNA methylation." Nucleic Acids Res 28 (8):E32.

Easwaran, H., S. E. Johnstone, L. Van Neste, J. Ohm, T. Mosbruger, Q. Wang, M. J. Aryee, P. Joyce, N. Ahuja, D. Weisenberger, E. Collisson, J. Zhu, S. Yegnasubramanian, W. Matsui, and S. B. Baylin. 2012. "A DNA hypermethylation module for the stem/progenitor cell signature of cancer." Genome Res 22 (5):837-49. doi: 10.1101/gr.131169.111.

Ehrlich, M., C. B. Woods, M. C. Yu, L. Dubeau, F. Yang, M. Campan, D. J. Weisenberger, T. Long, B. Youn, E. S. Fiala, and P. W. Laird. 2006. "Quantitative analysis of associations between DNA hypermethylation, hypomethylation, and DNMT RNA levels in ovarian tumors." Oncogene 25 (18):2636-45. doi: 10.1038/sj.onc.1209145.

Eis, P. S., W. Tam, L. Sun, A. Chadburn, Z. Li, M. F. Gomez, E. Lund, and J. E. Dahlberg. 2005. "Accumulation of miR-155 and BIC RNA in human B cell lymphomas." Proc Natl Acad Sci U S A 102 (10):3627-32. doi: 10.1073/pnas.0500613102.

Esteller, M., J. Garcia-Foncillas, E. Andion, S. N. Goodman, O. F. Hidalgo, V. Vanaclocha, S. B. Baylin, and J. G. Herman. 2000. "Inactivation of the DNA-repair gene MGMT and the clinical response of gliomas to alkylating agents." N Engl J Med 343 (19):1350-4. doi: 10.1056/NEJM200011093431901.

Esteller, M., S. R. Hamilton, P. C. Burger, S. B. Baylin, and J. G. Herman. 1999. "Inactivation of the DNA repair gene O6-methylguanine-DNA methyltransferase by promoter hypermethylation is a common event in primary human neoplasia." Cancer Res 59 (4):793-7.

Esteller, M., J. M. Silva, G. Dominguez, F. Bonilla, X. Matias-Guiu, E. Lerma, E. Bussaglia, J. Prat, I. C. Harkes, E. A. Repasky, E. Gabrielson, M. Schutte, S. B. Baylin, and J. G. Herman. 2000. "Promoter hypermethylation and BRCA1 inactivation in sporadic breast and ovarian tumors." J Natl Cancer Inst 92 (7):564-9.

Falette, N. S., S. A. Fuqua, G. C. Chamness, M. S. Cheah, G. L. Greene, and W. L. McGuire. 1990. "Estrogen receptor gene methylation in human breast tumors." Cancer Res 50 (13):3974-8.

Fang, F., S. Turcan, A. Rimner, A. Kaufman, D. Giri, L. G. Morris, R. Shen, V. Seshan, Q. Mo, A. Heguy, S. B. Baylin, N. Ahuja, A. Viale, J. Massague, L. Norton, L. T. Vahdat, M. E. Moynahan, and T. A. Chan. 2011. "Breast cancer methylomes establish an epigenomic foundation for metastasis." Sci Transl Med 3 (75):75ra25. doi: 10.1126/scitranslmed.3001875.

Feinberg, A. P. 2004. "The epigenetics of cancer etiology." Semin Cancer Biol 14 (6):427-32. doi: 10.1016/j.semcancer.2004.06.005.

Feinberg, A. P., and B. Vogelstein. 1983. "Hypomethylation distinguishes genes of some human cancers from their normal counterparts." Nature 301 (5895):89-92.

Frigola, J., M. Ribas, R. A. Risques, and M. A. Peinado. 2002. "Methylome profiling of cancer cells by amplification of inter-methylated sites (AIMS)." Nucleic Acids Res 30 (7):e28.

Frommer, M., L. E. McDonald, D. S. Millar, C. M. Collis, F. Watt, G. W. Grigg, P. L. Molloy, and C. L. Paul. 1992. "A genomic sequencing protocol that yields a positive display of 5-methylcytosine residues in individual DNA strands." Proc Natl Acad Sci U S A 89 (5):1827-31.

Gama-Sosa, M. A., V. A. Slagel, R. W. Trewyn, R. Oxenhandler, K. C. Kuo, C. W. Gehrke, and M. Ehrlich. 1983. "The 5-methylcytosine content of DNA from human tumors." Nucleic Acids Res 11 (19):6883-94.

Gibson, S. L., A. Boquoi, T. Chen, N. E. Sharpless, C. Brensinger, and G. H. Enders. 2005. "p16(Ink4a) inhibits histologic progression and angiogenic signaling in min colon tumors." Cancer Biol Ther 4 (12):1389-94.

Gitan, R. S., H. Shi, C. M. Chen, P. S. Yan, and T. H. Huang. 2002. "Methylation-specific oligonucleotide microarray: a new potential for high-throughput methylation analysis." Genome Res 12 (1):158-64. doi: 10.1101/gr.202801.

Goelz, S. E., B. Vogelstein, S. R. Hamilton, and A. P. Feinberg. 1985. "Hypomethylation of DNA from benign and malignant human colon neoplasms." Science 228 (4696):187-90.

Gonzalgo, M. L., G. Liang, C. H. Spruck, 3rd, J. M. Zingg, W. M. Rideout, 3rd, and P. A. Jones. 1997. "Identification and characterization of differentially methylated regions of genomic DNA by methylation-sensitive arbitrarily primed PCR." Cancer Res 57 (4):594-9.

Graziano, F., F. Arduini, A. Ruzzo, A. Mandolesi, I. Bearzi, R. Silva, P. Muretto, E. Testa, D. Mari, M. Magnani, M. Scartozzi, and S. Cascinu. 2004. "Combined analysis of E-cadherin gene (CDH1) promoter hypermethylation and E-cadherin protein expression in patients with gastric cancer: implications for treatment with demethylating drugs." Ann Oncol 15 (3):489-92.

Graff, J.R., J.G. Herman, R.G. Lapidus, H. Chopra, R. Xu, D.F. Jarrard, W.B. Isaacs, P.M. Pitha, N.E. Davidson, and S.B. Baylin. 1995l. "E-cadherin expression is silenced by DNA hypermethylation in human breast and prostate carcinomas." Cancer Res 55 (22):5195-5199.

Greger, V., E. Passarge, W. Hopping, E. Messmer, and B. Horsthemke. 1989. "Epigenetic changes may contribute to the formation and spontaneous regression of retinoblastoma." Hum Genet 83 (2):155-8.

Guenther, M. G., S. S. Levine, L. A. Boyer, R. Jaenisch, and R. A. Young. 2007. "A chromatin landmark and transcription initiation at most promoters in human cells." Cell 130 (1):77-88. doi: 10.1016/j.cell.2007.05.042.

Hammond, S. M. 2006. "MicroRNAs as oncogenes." Curr Opin Genet Dev 16 (1):4-9. doi: 10.1016/j.gde.2005.12.005.

Hansen, K. D., W. Timp, H. C. Bravo, S. Sabunciyan, B. Langmead, O. G. McDonald, B. Wen, H. Wu, Y. Liu, D. Diep, E. Briem, K. Zhang, R. A. Irizarry, and A. P. Feinberg. 2011. "Increased methylation variation in epigenetic domains across cancer types." Nat Genet 43 (8):768-75. doi: 10.1038/ng.865.

He, L., J. M. Thomson, M. T. Hemann, E. Hernando-Monge, D. Mu, S. Goodson, S. Powers, C. Cordon-Cardo, S. W. Lowe, G. J. Hannon, and S. M. Hammond. 2005. "A microRNA polycistron as a potential human oncogene." Nature 435 (7043):828-33. doi: 10.1038/nature03552.

Heller, G., M. Weinzierl, C. Noll, V. Babinsky, B. Ziegler, C. Altenberger, C. Minichsdorfer, G. Lang, B. Dome, A. End-Pfutzenreuter, B. M. Arns, Y. Grin, W. Klepetko, C. C. Zielinski, and S. Zochbauer-Muller. 2012. "Genome-wide miRNA expression profiling identifies miR-9-3 and miR-193a as targets for DNA methylation in non-small cell lung cancers." Clin Cancer Res 18 (6):1619-29. doi: 10.1158/1078-0432.CCR-11-2450.

Herman, J. G., J. R. Graff, S. Myohanen, B. D. Nelkin, and S. B. Baylin. 1996. "Methylation-specific PCR: a novel PCR assay for methylation status of CpG islands." Proc Natl Acad Sci U S A 93 (18):9821-6.

Herman, J. G., A. Merlo, L. Mao, R. G. Lapidus, J. P. Issa, N. E. Davidson, D. Sidransky, and S. B. Baylin. 1995. "Inactivation of the CDKN2/p16/MTS1 gene is frequently associated with aberrant DNA methylation in all common human cancers." Cancer Res 55 (20):4525-30.

Herman, J. G., A. Umar, K. Polyak, J. R. Graff, N. Ahuja, J. P. Issa, S. Markowitz, J. K. Willson, S. R. Hamilton, K. W. Kinzler, M. F. Kane, R. D. Kolodner, B. Vogelstein, T. A. Kunkel, and S. B. Baylin. 1998. "Incidence and functional consequences of hMLH1 promoter hypermethylation in colorectal carcinoma." Proc Natl Acad Sci U S A 95 (12):6870-5.

Hernandez-Vargas, H., M. Ouzounova, F. Le Calvez-Kelm, M. P. Lambert, S. McKay-Chopin, S. V. Tavtigian, A. Puisieux, C. Matar, and Z. Herceg. 2011. "Methylome analysis reveals Jak-STAT pathway deregulation in putative breast cancer stem cells." Epigenetics 6 (4):428-39.

Hill, V. K., C. Ricketts, I. Bieche, S. Vacher, D. Gentle, C. Lewis, E. R. Maher, and F. Latif. 2011. "Genome-wide DNA methylation profiling of CpG islands in breast cancer identifies novel genes associated with tumorigenicity." Cancer Res 71 (8):2988-99. doi: 10.1158/0008-5472.CAN-10-4026.

Hinoue, T., D. J. Weisenberger, C. P. Lange, H. Shen, H. M. Byun, D. Van Den Berg, S. Malik, F. Pan, H. Noushmehr, C. M. van Dijk, R. A. Tollenaar, and P. W. Laird. 2012. "Genome-scale analysis of aberrant DNA methylation in colorectal cancer." Genome Res 22 (2):271-82. doi: 10.1101/gr.117523.110.

Hon, G. C., R. D. Hawkins, O. L. Caballero, C. Lo, R. Lister, M. Pelizzola, A. Valsesia, Z. Ye, S. Kuan, L. E. Edsall, A. A. Camargo, B. J. Stevenson, J. R. Ecker, V. Bafna, R. L. Strausberg, A. J. Simpson, and B. Ren. 2012. "Global DNA hypomethylation coupled to repressive chromatin domain formation and gene silencing in breast cancer." Genome Res 22 (2):246-58. doi: 10.1101/gr.125872.111.

Hotchkiss, R. D. 1948. "The quantitative separation of purines, pyrimidines, and nucleosides by paper chromatography." J Biol Chem 175 (1):315-32.

Hughes, L. A., V. Melotte, J. de Schrijver, M. de Maat, V. T. Smit, J. V. Bovee, P. J. French, P. A. van den Brandt, L. J. Schouten, T. de Meyer, W. van Criekinge, N. Ahuja, J. G. Herman, M. P. Weijenberg, and M. van Engeland. 2013. "The CpG island methylator phenotype: what's in a name?" Cancer Res 73 (19):5858-68. doi: 10.1158/0008-5472.CAN-12-4306.

Itzkowitz, S., R. Brand, L. Jandorf, K. Durkee, J. Millholland, L. Rabeneck, P. C. Schroy, 3rd, S. Sontag, D. Johnson, S. Markowitz, L. Paszat, and B. M. Berger. 2008. "A simplified, noninvasive stool DNA test for colorectal cancer detection." Am J Gastroenterol 103 (11):2862-70. doi: 10.1111/j.1572-0241.2008.02088.x.

Jadhav, R. R., Z. Ye, R. L. Huang, J. Liu, P. Y. Hsu, Y. W. Huang, L. B. Rangel, H. C. Lai, J. C. Roa, N. B. Kirma, T. H. Huang, and V. X. Jin. 2015. "Genome-wide DNA methylation analysis reveals estrogen-mediated epigenetic repression of metallothionein-1 gene cluster in breast cancer." Clin Epigenetics 7 (1):13. doi: 10.1186/s13148-015-0045-9.

Johnson, S. M., H. Grosshans, J. Shingara, M. Byrom, R. Jarvis, A. Cheng, E. Labourier, K. L. Reinert, D. Brown, and F. J. Slack. 2005. "RAS is regulated by the let-7 microRNA family." Cell 120 (5):635-47. doi: 10.1016/j.cell.2005.01.014.

Jones, P. A., and S. B. Baylin. "The Fundamental Role of Epigenetic Events in Cancer." Nature Reviews Genetics 3, no. 6 (2002): 415-28.

Kang, J. Y., S. H. Song, J. Yun, M. S. Jeon, Y. Cha, S. H. Lee, H. P. Kim, E. G. Jeong, S. W. Han, N. Y. Cho, M. C. Kook, G. H. Kang, and T. Y. Kim. 2015. "Identification of long-range epigenetic silencing on chromosome 15q25 and its clinical implication in gastric cancer." Am J Pathol 185 (3):666-78. doi: 10.1016/j.ajpath.2014.11.022.

Katzenellenbogen, R. A., S. B. Baylin, and J. G. Herman. 1999. "Hypermethylation of the DAP-kinase CpG island is a common alteration in B-cell malignancies." Blood 93 (12):4347-53.

Kelley, D. E., B. A. Pollok, M. L. Atchison, and R. P. Perry. 1988. "The coupling between enhancer activity and hypomethylation of kappa immunoglobulin genes is developmentally regulated." Mol Cell Biol 8 (2):930-7.

Keshet, I., Y. Schlesinger, S. Farkash, E. Rand, M. Hecht, E. Segal, E. Pikarski, R. A. Young, A. Niveleau, H. Cedar, and I. Simon. 2006. "Evidence for an instructive mechanism of de novo methylation in cancer cells." Nat Genet 38 (2):149-53. doi: 10.1038/ng1719.

Khulan, B., R. F. Thompson, K. Ye, M. J. Fazzari, M. Suzuki, E. Stasiek, M. E. Figueroa, J. L. Glass, Q. Chen, C. Montagna, E. Hatchwell, R. R. Selzer, T. A. Richmond, R. D. Green, A. Melnick, and J. M. Greally. 2006. "Comparative isoschizomer profiling of cytosine methylation: the HELP assay." Genome Res 16 (8):1046-55. doi: 10.1101/gr.5273806.

Kissil, J. L., E. Feinstein, O. Cohen, P. A. Jones, Y. C. Tsai, M. A. Knowles, M. E. Eydmann, and A. Kimchi. 1997. "DAP-kinase loss of expression in various carcinoma and B-cell lymphoma cell lines: possible implications for role as tumor suppressor gene." Oncogene 15 (4):403-7. doi: 10.1038/sj.onc.1201172.

Kneip, C., B. Schmidt, A. Seegebarth, S. Weickmann, M. Fleischhacker, V. Liebenberg, J. K. Field, and D. Dietrich. 2011. "SHOX2 DNA methylation is a biomarker for the diagnosis of lung cancer in plasma." J Thorac Oncol 6 (10):1632-8. doi: 10.1097/JTO.0b013e318220ef9a.

Kunej, T., I. Godnic, J. Ferdin, S. Horvat, P. Dovc, and G. A. Calin. 2011. "Epigenetic regulation of microRNAs in cancer: an integrated review of literature." Mutat Res 717 (1-2):77-84. doi: 10.1016/j.mrfmmm.2011.03.008.

Lehmann, U., B. Hasemeier, M. Christgen, M. Muller, D. Romermann, F. Langer, and H. Kreipe. 2008. "Epigenetic inactivation of microRNA gene hsa-mir-9-1 in human breast cancer." J Pathol 214 (1):17-24. doi: 10.1002/path.2251.

Lesch, B. J., and D. C. Page. 2014. "Poised chromatin in the mammalian germ line." Development 141 (19):3619-26. doi: 10.1242/dev.113027.

Lewis, B. P., C. B. Burge, and D. P. Bartel. 2005. "Conserved seed pairing, often flanked by adenosines, indicates that thousands of human genes are microRNA targets." Cell 120 (1):15-20. doi: 10.1016/j.cell.2004.12.035.

Lister, R., R. C. O'Malley, J. Tonti-Filippini, B. D. Gregory, C. C. Berry, A. H. Millar, and J. R. Ecker. 2008. "Highly integrated single-base resolution maps of the epigenome in Arabidopsis." Cell 133 (3):523-36. doi: 10.1016/j.cell.2008.03.029.

Lister, R., M. Pelizzola, Y. S. Kida, R. D. Hawkins, J. R. Nery, G. Hon, J. Antosiewicz-Bourget, R. O'Malley, R. Castanon, S. Klugman, M. Downes, R. Yu, R. Stewart, B. Ren, J. A. Thomson, R. M. Evans, and J. R. Ecker. 2011. "Hotspots of aberrant epigenomic reprogramming in human induced pluripotent stem cells." Nature 471 (7336):68-73. doi: 10.1038/nature09798.

Liteplo, R. G., P. Frost, and R. S. Kerbel. 1984. "5-azacytidine induction of thymidine kinase in a spontaneously enzyme-deficient murine tumor line." Exp Cell Res 150 (2):499-504.

Liu, P., M. Rudick, and R. G. Anderson. 2002. "Multiple functions of caveolin-1." J Biol Chem 277 (44):41295-8. doi: 10.1074/jbc.R200020200.

Loriot, A., A. Van Tongelen, J. Blanco, S. Klaessens, J. Cannuyer, N. van Baren, A. Decottignies, and C. De Smet. 2014. "A novel cancer-germline transcript carrying pro-metastatic miR-105 and TET-targeting miR-767 induced by DNA hypomethylation in tumors." Epigenetics 9 (8):1163-71. doi: 10.4161/epi.29628.

Lu, C., P. S. Ward, G. S. Kapoor, D. Rohle, S. Turcan, O. Abdel-Wahab, C. R. Edwards, R. Khanin, M. E. Figueroa, A. Melnick, K. E. Wellen, D. M. O'Rourke, S. L. Berger, T. A. Chan, R. L. Levine, I. K. Mellinghoff, and C. B. Thompson. 2012. "IDH mutation impairs histone demethylation and results in a block to cell differentiation." Nature 483 (7390):474-8. doi: 10.1038/nature10860.

Merlo, A., J. G. Herman, L. Mao, D. J. Lee, E. Gabrielson, P. C. Burger, S. B. Baylin, and D. Sidransky. 1995. "5' CpG island methylation is associated with transcriptional silencing of the tumour suppressor p16/CDKN2/MTS1 in human cancers." Nat Med 1 (7):686-92.

Nishida, N., M. Kudo, T. Nishimura, T. Arizumi, M. Takita, S. Kitai, N. Yada, S. Hagiwara, T. Inoue, Y. Minami, K. Ueshima, T. Sakurai, N. Yokomichi, T. Nagasaka, and A. Goel. 2013. "Unique association between global DNA hypomethylation and chromosomal alterations in human hepatocellular carcinoma." PLoS One 8 (9):e72312. doi: 10.1371/journal.pone.0072312.

Noushmehr, H., D. J. Weisenberger, K. Diefes, H. S. Phillips, K. Pujara, B. P. Berman, F. Pan, C. E. Pelloski, E. P. Sulman, K. P. Bhat, R. G. Verhaak, K. A. Hoadley, D. N. Hayes, C. M. Perou, H. K. Schmidt, L. Ding, R. K. Wilson, D. Van Den Berg, H. Shen, H. Bengtsson, P. Neuvial, L. M. Cope, J. Buckley, J. G. Herman, S. B. Baylin, P. W. Laird, K. Aldape, and Network Cancer Genome Atlas Research. 2010. "Identification of a CpG island methylator phenotype that defines a distinct subgroup of glioma." Cancer Cell 17 (5):510-22. doi: 10.1016/j.ccr.2010.03.017.

Novak, P., T. Jensen, M. M. Oshiro, G. S. Watts, C. J. Kim, and B. W. Futscher. 2008. "Agglomerative epigenetic aberrations are a common event in human breast cancer." Cancer Res 68 (20):8616-25. doi: 10.1158/0008-5472.CAN-08-1419.

Nyren, P. 1987. "Enzymatic method for continuous monitoring of DNA polymerase activity." Anal Biochem 167 (2):235-8.

Ogawa, H., X. Wu, K. Kawamoto, N. Nishida, M. Konno, J. Koseki, H. Matsui, K. Noguchi, N. Gotoh, T. Yamamoto, K. Miyata, N. Nishiyama, H. Nagano, H. Yamamoto, S. Obika, K. Kataoka, Y. Doki, M. Mori, and H. Ishii. 2015. "MicroRNAs Induce Epigenetic Reprogramming and Suppress Malignant Phenotypes of Human Colon Cancer Cells." PLoS One 10 (5):e0127119. doi: 10.1371/journal.pone.0127119.

Ohm, J. E., K. M. McGarvey, X. Yu, L. Cheng, K. E. Schuebel, L. Cope, H. P. Mohammad, W. Chen, V. C. Daniel, W. Yu, D. M. Berman, T. Jenuwein, K. Pruitt, S. J. Sharkis, D. N. Watkins, J. G. Herman, and S. B. Baylin. 2007. "A stem cell-like chromatin pattern may predispose tumor suppressor genes to DNA hypermethylation and heritable silencing." Nat Genet 39 (2):237-42. doi: 10.1038/ng1972.

Okochi-Takada, E., N. Hattori, T. Tsukamoto, K. Miyamoto, T. Ando, S. Ito,Y. Yamamura, M. Wakabayachi, Y. Nobeyama, and T. Ushijima. 2014. "ANGPTL4 is a secreted tumor suppressor that inhibits angiogenesis." Oncogene 33 (17):2273-2278.

Orita, M., H. Iwahana, H. Kanazawa, K. Hayashi, and T. Sekiya. 1989. "Detection of polymorphisms of human DNA by gel electrophoresis as single-strand conformation polymorphisms." Proc Natl Acad Sci U S A 86 (8):2766-70.

Palmisano, W. A., K. K. Divine, G. Saccomanno, F. D. Gilliland, S. B. Baylin, J. G. Herman, and S. A. Belinsky. 2000. "Predicting lung cancer by detecting aberrant promoter methylation in sputum." Cancer Res 60 (21):5954-8.

Payne, S. R. 2010. "From discovery to the clinic: the novel DNA methylation biomarker (m)SEPT9 for the detection of colorectal cancer in blood." Epigenomics 2 (4):575-85. doi: 10.2217/epi.10.35.

Piva, R., A. P. Rimondi, S. Hanau, I. Maestri, A. Alvisi, V. L. Kumar, and L. del Senno. 1990. "Different methylation of oestrogen receptor DNA in human breast carcinomas with and without oestrogen receptor." Br J Cancer 61 (2):270-5.

Rao, X., J. Evans, H. Chae, J. Pilrose, S. Kim, P. Yan, R. L. Huang, H. C. Lai, H. Lin, Y. Liu, D. Miller, J. K. Rhee, Y. W. Huang, F. Gu, J. W. Gray, T. M. Huang, and K. P. Nephew. 2013. "CpG island shore methylation regulates caveolin-1 expression in breast cancer." Oncogene 32 (38):4519-28. doi: 10.1038/onc.2012.474.

Reinders, J., C. Delucinge Vivier, G. Theiler, D. Chollet, P. Descombes, and J. Paszkowski. 2008. "Genome-wide, high-resolution DNA methylation profiling using bisulfite-mediated cytosine conversion." Genome Res 18 (3):469-76. doi: 10.1101/gr.7073008.

Reyngold, M., S. Turcan, D. Giri, K. Kannan, L. A. Walsh, A. Viale, M. Drobnjak, L. T. Vahdat, W. Lee, and T. A. Chan. 2014. "Remodeling of the methylation landscape in breast cancer metastasis." PLoS One 9 (8):e103896. doi: 10.1371/journal.pone.0103896.

Richards, K. L., B. Zhang, K. A. Baggerly, S. Colella, J. C. Lang, D. E. Schuller, and R. Krahe. 2009. "Genome-wide hypomethylation in head and neck cancer is more pronounced in HPV-negative tumors and is associated with genomic instability." PLoS One 4 (3):e4941. doi: 10.1371/journal.pone.0004941.

Robertson, G., M. Hirst, M. Bainbridge, M. Bilenky, Y. Zhao, T. Zeng, G. Euskirchen, B. Bernier, R. Varhol, A. Delaney, N. Thiessen, O. L. Griffith, A. He, M. Marra, M. Snyder, and S. Jones. 2007. "Genome-wide profiles of STAT1 DNA association using chromatin immunoprecipitation and massively parallel sequencing." Nat Methods 4 (8):651-7. doi: 10.1038/nmeth1068.

Ronaghi, M. 2001. "Pyrosequencing sheds light on DNA sequencing." Genome Res 11 (1):3-11.

Ronaghi, M., S. Karamohamed, B. Pettersson, M. Uhlen, and P. Nyren. 1996. "Real-time DNA sequencing using detection of pyrophosphate release." Anal Biochem 242 (1):84-9. doi: 10.1006/abio.1996.0432.

Sakai, T., J. Toguchida, N. Ohtani, D. W. Yandell, J. M. Rapaport, and T. P. Dryja. 1991. "Allele-specific hypermethylation of the retinoblastoma tumor-suppressor gene." Am J Hum Genet 48 (5):880-8.

Samowitz, W. S., H. Albertsen, J. Herrick, T. R. Levin, C. Sweeney, M. A. Murtaugh, R. K. Wolff, and M. L. Slattery. 2005. "Evaluation of a large, population-based sample supports a CpG island methylator phenotype in colon cancer." Gastroenterology 129 (3):837-45. doi: 10.1053/j.gastro.2005.06.020.

Sandoval, J., H. Heyn, J. Mendez-Gonzalez, A. Gomez, S. Moran, M. Baiget, M. Melo, I. Badell, J. F. Nomdedeu, and M. Esteller. 2013. "Genome-wide DNA methylation profiling predicts relapse in childhood B-cell acute lymphoblastic leukaemia." Br J Haematol 160 (3):406-9. doi: 10.1111/bjh.12113.

Savage, K., M. B. Lambros, D. Robertson, R. L. Jones, C. Jones, A. Mackay, M. James, J. L. Hornick, E. M. Pereira, F. Milanezi, C. D. Fletcher, F. C. Schmitt, A. Ashworth, and J. S. Reis-Filho. 2007. "Caveolin 1 is overexpressed and amplified in a subset of basal-like and metaplastic breast carcinomas: a morphologic, ultrastructural, immunohistochemical, and in situ hybridization analysis." Clin Cancer Res 13 (1):90-101. doi: 10.1158/1078-0432.CCR-06-1371.

Schmidt, B., V. Liebenberg, D. Dietrich, T. Schlegel, C. Kneip, A. Seegebarth, N. Flemming, S. Seemann, J. Distler, J. Lewin, R. Tetzner, S. Weickmann, U. Wille, T. Liloglou, O. Raji, M. Walshaw, M. Fleischhacker, C. Witt, and J. K. Field. 2010. "SHOX2 DNA methylation is a biomarker for the diagnosis of lung cancer based on bronchial aspirates." BMC Cancer 10:600. doi: 10.1186/1471-2407-10-600.

Sheffield, V. C., J. S. Beck, A. E. Kwitek, D. W. Sandstrom, and E. M. Stone. 1993. "The sensitivity of single-strand conformation polymorphism analysis for the detection of single base substitutions." Genomics 16 (2):325-32. doi: 10.1006/geno.1993.1193.

Shen, L., H. Kantarjian, Y. Guo, E. Lin, J. Shan, X. Huang, D. Berry, S. Ahmed, W. Zhu, S. Pierce, Y. Kondo, Y. Oki, J. Jelinek, H. Saba, E. Estey, and J. P. Issa. 2010. "DNA methylation predicts survival and response to therapy in patients with myelodysplastic syndromes." J Clin Oncol 28 (4):605-13. doi: 10.1200/JCO.2009.23.4781.

Shen, L., M. Toyota, Y. Kondo, E. Lin, L. Zhang, Y. Guo, N. S. Hernandez, X. Chen, S. Ahmed, K. Konishi, S. R. Hamilton, and J. P. Issa. 2007. "Integrated genetic and epigenetic analysis identifies three different subclasses of colon cancer." Proc Natl Acad Sci U S A 104 (47):18654-9. doi: 10.1073/pnas.0704652104.

Simons, C. C., L. A. Hughes, K. M. Smits, C. A. Khalid-de Bakker, A. P. de Bruine, B. Carvalho, G. A. Meijer, L. J. Schouten, P. A. van den Brandt, M. P. Weijenberg, and M. van Engeland. 2013. "A novel classification of colorectal tumors based on microsatellite instability, the CpG island methylator phenotype and chromosomal instability: implications for prognosis." Ann Oncol 24 (8):2048-56. doi: 10.1093/annonc/mdt076.

Spandidos, D. A. 1986. "A unified theory for the development of cancer." Biosci Rep 6 (8):691-708.

Strahl, B. D., and C. D. Allis. 2000. "The language of covalent histone modifications." Nature 403 (6765):41-5. doi: 10.1038/47412.

Tanemura, A., A. M. Terando, M. S. Sim, A. Q. van Hoesel, M. F. de Maat, D. L. Morton, and D. S. Hoon. 2009. "CpG island methylator phenotype predicts progression of malignant melanoma." Clin Cancer Res 15 (5):1801-7. doi: 10.1158/1078-0432.CCR-08-1361.

Tanzer, M., B. Balluff, J. Distler, K. Hale, A. Leodolter, C. Rocken, B. Molnar, R. Schmid, C. Lofton-Day, T. Schuster, and M. P. Ebert. 2010. "Performance of epigenetic markers SEPT9 and ALX4 in plasma for detection of colorectal precancerous lesions." PLoS One 5 (2):e9061. doi: 10.1371/journal.pone.0009061.

Taube, J. H., G. G. Malouf, E. Lu, N. Sphyris, V. Vijay, P. P. Ramachandran, K. R. Ueno, S. Gaur, M. S. Nicoloso, S. Rossi, J. I. Herschkowitz, J. M. Rosen, J. P. Issa, G. A. Calin, J. T. Chang, and S. A. Mani. 2013. "Epigenetic silencing of microRNA-203 is required for EMT and cancer stem cell properties." Sci Rep 3:2687. doi: 10.1038/srep02687.

Thirlwell, C., A. Feber, M. Lechner, A. E. Teschendorff, and S. Beck. 2012. "Comments on: Interpretation of genome-wide infinium methylation data from ligated DNA in formalin-fixed paraffin-embedded paired tumor and normal tissue." BMC Res Notes 5:631. doi: 10.1186/1756-0500-5-631.

Timp, W., and A. P. Feinberg. 2013. "Cancer as a dysregulated epigenome allowing cellular growth advantage at the expense of the host." Nat Rev Cancer 13 (7):497-510. doi: 10.1038/nrc3486.

Tiwari, N., V. K. Tiwari, L. Waldmeier, P. J. Balwierz, P. Arnold, M. Pachkov, N. Meyer-Schaller, D. Schubeler, E. van Nimwegen, and G. Christofori. 2013. "Sox4 is a master regulator of epithelial-mesenchymal transition by controlling Ezh2 expression and epigenetic reprogramming." Cancer Cell 23 (6):768-83. doi: 10.1016/j.ccr.2013.04.020.

Toyota, M., N. Ahuja, M. Ohe-Toyota, J. G. Herman, S. B. Baylin, and J. P. Issa. 1999. "CpG island methylator phenotype in colorectal cancer." Proc Natl Acad Sci U S A 96 (15):8681-6.

Toyota, M., C. Ho, N. Ahuja, K. W. Jair, Q. Li, M. Ohe-Toyota, S. B. Baylin, and J. P. Issa. 1999. "Identification of differentially methylated sequences in colorectal cancer by methylated CpG island amplification." Cancer Res 59 (10):2307-12.

Turcan, S., D. Rohle, A. Goenka, L. A. Walsh, F. Fang, E. Yilmaz, C. Campos, A. W. Fabius, C. Lu, P. S. Ward, C. B. Thompson, A. Kaufman, O. Guryanova, R. Levine, A. Heguy, A. Viale, L. G. Morris, J. T. Huse, I. K. Mellinghoff, and T. A. Chan. 2012. "IDH1 mutation is sufficient to establish the glioma hypermethylator phenotype." Nature 483 (7390):479-83. doi: 10.1038/nature10866.

Vedeld, H. M., K. Andresen, I. A. Eilertsen, A. Nesbakken, R. Seruca, I. P. Gladhaug, E. Thiis-Evensen, T. O. Rognum, K. M. Boberg, and G. E. Lind. 2015. "The novel colorectal cancer biomarkers CDO1, ZSCAN18 and ZNF331 are frequently methylated across gastrointestinal cancers." Int J Cancer 136 (4):844-53. doi: 10.1002/ijc.29039.

Vire, E., C. Brenner, R. Deplus, L. Blanchon, M. Fraga, C. Didelot, L. Morey, A. Van Eynde, D. Bernard, J. M. Vanderwinden, M. Bollen, M. Esteller, L. Di Croce, Y. de Launoit, and F.Fuks. 2006. "The Polycomb group protein EZH2 directly controls DNA methylation." Nature 439 (7078):871-4. doi: 10.1038/nature04431.

Waddington, C. H. 2012. "The epigenotype. 1942." Int J Epidemiol 41 (1):10-3. doi: 10.1093/ije/dyr184.

Weisenberger, D. J., K. D. Siegmund, M. Campan, J. Young, T. I. Long, M. A. Faasse, G. H. Kang, M. Widschwendter, D. Weener, D. Buchanan, H. Koh, L. Simms, M. Barker, B. Leggett, J. Levine, M. Kim, A. J. French, S. N. Thibodeau, J. Jass, R. Haile, and P. W. Laird. 2006. "CpG island methylator phenotype underlies sporadic microsatellite instability and is tightly associated with BRAF mutation in colorectal cancer." Nat Genet 38 (7):787-93. doi: 10.1038/ng1834.

Wong, N. C., D. Ashley, Z. Chatterton, M. Parkinson-Bates, H. K. Ng, M. S. Halemba, A. Kowalczyk, J. Bedo, Q. Wang, K. Bell, E. Algar, J. M. Craig, and R. Saffery. 2012. "A distinct DNA methylation signature defines pediatric pre-B cell acute lymphoblastic leukemia." Epigenetics 7 (6):535-41. doi: 10.4161/epi.20193.

Xu, Y., B. Hu, A. J. Choi, B. Gopalan, B. H. Lee, M. F. Kalady, J. M. Church, and A. H. Ting. 2012. "Unique DNA methylome profiles in CpG island methylator phenotype colon cancers." Genome Res 22 (2):283-91. doi: 10.1101/gr.122788.111.

Yan, P., D. Frankhouser, M. Murphy, H. H. Tam, B. Rodriguez, J. Curfman, M. Trimarchi, S. Geyer, Y. Z. Wu, S. P. Whitman, K. Metzeler, A. Walker, R. Klisovic, S. Jacob, M. R. Grever, J. C. Byrd, C. D. Bloomfield, R. Garzon, W. Blum, M. A. Caligiuri, R. Bundschuh, and G. Marcucci. 2012. "Genome-wide methylation profiling in decitabine-treated patients with acute myeloid leukemia." Blood 120 (12):2466-74. doi: 10.1182/blood-2012-05-429175.

Zhang, B., W. Zhu, P. Yang, T. Liu, M. Jiang, Z. N. He, S. X. Zhang, W. Q. Chen, and W. Chen. 2011. "Cigarette smoking and p16INK4alpha gene promoter hypermethylation in non-small cell lung carcinoma patients: a meta-analysis." PLoS One 6 (12):e28882. doi: 10.1371/journal.pone.0028882.

Zhang, X., J. Yazaki, A. Sundaresan, S. Cokus, S. W. Chan, H. Chen, I. R. Henderson, P. Shinn, M. Pellegrini, S. E. Jacobsen, and J. R. Ecker. 2006. "Genome-wide high-resolution mapping and functional analysis of DNA methylation in arabidopsis." Cell 126 (6):1189-201. doi: 10.1016/j.cell.2006.08.003.

Zhao, X., F. Yang, S. Li, M. Liu, S. Ying, X. Jia, and X. Wang. 2014. "CpG island methylator phenotype of myelodysplastic syndrome identified through genome-wide profiling of DNA methylation and gene expression." Br J Haematol 165 (5):649-58. doi: 10.1111/bjh.12811.

Zilberman, D., M. Gehring, R. K. Tran, T. Ballinger, and S. Henikoff. 2007. "Genome-wide analysis of Arabidopsis thaliana DNA methylation uncovers an interdependence between methylation and transcription." Nat Genet 39 (1):61-9. doi: 10.1038/ng1929.