Cancer Epigenetics: An introduction

Methods in Molecular Biology

Volumn 1238, Issue , 2015, Pages 3-25

  Kanwal, Rajnee ^a   Gupta, Karishma ^a   Gupta, Sanjay ^a  

^a NONE

Author keywords

Cancer; DNA methylation; Epigenetics; Histone modification; microRNA

Indexed keywords

BIOLOGICAL MARKER; DNA; HISTONE; TUMOR MARKER;

ARTICLE; CANCER GENETICS; CANCER PREVENTION; CANCER THERAPY; CARCINOGENESIS; CHROMOSOME; DNA METHYLATION; EPIGENETICS; GENETIC MARKER; HISTONE MODIFICATION; HUMAN; MALIGNANT NEOPLASTIC DISEASE; NUCLEOSOME; PHASE 1 CLINICAL TRIAL (TOPIC); PRIORITY JOURNAL;

EID: 84921746859     PISSN: 10643745     EISSN: None     Source Type: Book Series    
DOI: 10.1007/978-1-4939-1804-1_1     Document Type: Article

References (121)

1. Tsai HC, Baylin SB (2011) Cancer epigenetics: linking basic biology to clinical medicine. Cell Res 21:502–517
2. Kanwal R, Gupta S (2010) Epigenetics and cancer. J Appl Physiol 109:598–605
3. Sharma S, Kelly TK, Jones PA (2010) Epigenetics in cancer. Carcinogenesis 31:27–36
4. Lo PK, Sukumar S (2008) Epigenomics and breast cancer. Pharmacogenomics 9: 1879–1902
5. Kinney SR, Pradhan S (2011) Regulation of expression and activity of DNA (cytosine-5) methyltransferases in mammalian cells. Prog Mol Biol Transl Sci 101:311–333
6. Smith ZD, Meissner A (2013) DNA methylation: roles in mammalian development. Nat Rev Genet 14:204–220
7. Hatziapostolou M, Iliopoulos D (2011) Epigenetic aberrations during oncogenesis. Cell Mol Life Sci 68:1681–1702
8. Baylin SB, Jones PA (2011) A decade of exploring the cancer epigenome - biological and translational implications. Nat Rev Cancer 11:726–734
9. Robertson KD (2001) DNA methylation, methyltransferases, and cancer. Oncogene 20: 3139–3155
10. Deaton AM, Bird A (2011) CpG islands and the regulation of transcription. Genes Dev 25:1010–1022
11. Le Guezennec X, Vermeulen M, Brinkman AB, Hoeijmakers WA, Cohen A, Lasonder E, Stunnenberg HG (2006) MBD2/NuRD and MBD3/NuRD, two distinct complexes with different biochemical and functional properties. Mol Cell Biol 26:843–851
12. Parry L, Clarke AR (2011) The roles of the methyl-CpG binding proteins in cancer. Genes Cancer 2:618–630
13. Dillon N (2006) Gene regulation and largescale chromatin organization in the nucleus. Chromosome Res 14:117–126
14. Fischle W, Wang Y, Allis CD (2003) Histone and chromatin cross-talk. Curr Opin Cell Biol 15:172–183
15. Rodriguez-Paredes M, Esteller M (2011) Cancer epigenetics reaches mainstream oncology. Nat Med 17:330–339
16. Sana J, Faltejskova P, Svoboda M, Slaby O (2012) Novel classes of non-coding RNAs and cancer. J Transl Med 10:103
17. Lee Y, Kim M, Han J, Yeom KH, Lee S, Baek SH, Kim VN (2004) MicroRNA genes are transcribed by RNA polymerase II. EMBO J 23:4051–4060
18. Hauptman N, Glavac D (2013) Long noncoding RNA in cancer. Int J Mol Sci 14: 4655–4669
19. Mitra SA, Mitra AP, Triche TJ (2012) A central role for long non-coding RNA in cancer. Front Genet 3:17
20. Calin GA, Croce CM (2006) MicroRNA signatures in human cancers. Nat Rev Cancer 6:857–866
21. Chuang JC, Jones PA (2007) Epigenetics and microRNAs. Pediatr Res 61:24R–29R
22. Fabian MR, Sonenberg N, Filipowicz W (2010) Regulation of mRNA translation and stability by microRNAs. Annu Rev Biochem 79:351–379
23. Lee DH, O'Connor TR, Pfeifer GP (2002) Oxidative DNA damage induced by copper and hydrogen peroxide promotes CG TT tandem mutations at methylated CpG dinucleotides in nucleotide excision repairdefi cient cells. Nucleic Acids Res 30: 3566–3573
24. Macfarlane LA, Murphy PR (2010) MicroRNA: biogenesis, function and role in cancer. Curr Genomics 11:537–561
25. Lopez-Serra P, Esteller M (2012) DNA methylation- associated silencing of tumorsuppressor microRNAs in cancer. Oncogene 31:1609–1622
26. Henikoff S (2008) Nucleosome destabilization in the epigenetic regulation of gene expression. Nat Rev Genet 9:15–26
27. Verschure PJ (2004) Positioning the genome within the nucleus. Biol Cell 96:569–577
28. Hesson LB, Patil V, Sloane MA, Nunez AC, Liu J, Pimanda JE, Ward RL (2013) Reassembly of nucleosomes at the MLH1 promoter initiates resilencing following decitabine exposure. PLoS Genet 9:e1003636
29. Schneider R, Grosschedl R (2007) Dynamics and interplay of nuclear architecture, genome organization, and gene expression. Genes Dev 21:3027–3043
30. Ellis L, Atadja PW, Johnstone RW (2009) Epigenetics in cancer: targeting chromatin modifi cations. Mol Cancer Ther 8:1409–1420
31. Lonergan PE, Tindall DJ (2011) Androgen receptor signaling in prostate cancer development and progression. J Carcinog 10:20
32. Gupta GP, Massague J (2006) Cancer metastasis: building a framework. Cell 127:679–695
33. Ribarska T, Bastian KM, Koch A, Schulz WA (2012) Specific changes in the expression of imprinted genes in prostate cancer–implications for cancer progression and epigenetic regulation. Asian J Androl 14:436–450
34. Ducasse M, Brown MA (2006) Epigenetic aberrations and cancer. Mol Cancer 5:60
35. Miremadi A, Oestergaard MZ, Pharoah PD, Caldas C (2007) Cancer genetics of epigenetic genes. Hum Mol Genet 16 Spec No 1:R28–R49
36. Pareek CS, Smoczynski R, Tretyn A (2011) Sequencing technologies and genome sequencing. J Appl Genet 52:413–435
37. Soon WW, Hariharan M, Snyder MP (2013) High-throughput sequencing for biology and medicine. Mol Syst Biol 9:640
38. Hassler MR, Egger G (2012) Epigenomics of cancer - emerging new concepts. Biochimie 94:2219–2230
39. Madu CO, Lu Y (2010) Novel diagnostic biomarkers for prostate cancer. J Cancer 1: 150–177
40. Borinstein SC, Conerly M, Dzieciatkowski S, Biswas S, Washington MK, Trobridge P, Henikoff S, Grady WM (2010) Aberrant DNA methylation occurs in colon neoplasms arising in the azoxymethane colon cancer model. Mol Carcinog 49:94–103
41. Ehrlich M (2002) DNA methylation in cancer: too much, but also too little. Oncogene 21:5400–5413
42. De Smet C, Loriot A, Boon T (2004) Promoter-dependent mechanism leading to selective hypomethylation within the 5' region of gene MAGE-A1 in tumor cells. Mol Cell Biol 24:4781–4790
43. Robertson KD, Jones PA (2000) DNA methylation: past, present and future directions. Carcinogenesis 21:461–467
44. Jin B, Robertson KD (2013) DNA methyltransferases, DNA damage repair, and cancer. Adv Exp Med Biol 754:3–29
45. Kanwal R, Gupta S (2012) Epigenetic modifi - cations in cancer. Clin Genet 81:303–311
46. Khin SS, Kitazawa R, Kondo T, Idei Y, Fujimoto M, Haraguchi R, Mori K, Kitazawa S (2011) Epigenetic alteration by DNA promoter hypermethylation of genes related to transforming growth factor-beta (TGF-beta) signaling in cancer. Cancers (Basel) 3:982–993
47. Kotake Y, Nakagawa T, Kitagawa K, Suzuki S, Liu N, Kitagawa M, Xiong Y (2011) Long non-coding RNA ANRIL is required for the PRC2 recruitment to and silencing of p15(INK4B) tumor suppressor gene. Oncogene 30:1956–1962
48. Koturbash I, Beland FA, Pogribny IP (2011) Role of epigenetic events in chemical carcinogenesis– a justifi cation for incorporating epigenetic evaluations in cancer risk assessment. Toxicol Mech Methods 21:289–297
49. Ross SA, Milner JA (2007) Epigenetic modulation and cancer: effect of metabolic syndrome? Am J Clin Nutr 86:s872–s877
50. Ehrlich M (2009) DNA hypomethylation in cancer cells. Epigenomics 1:239–259
51. Sadikovic B, Al-Romaih K, Squire JA, Zielenska M (2008) Cause and consequences of genetic and epigenetic alterations in human cancer. Curr Genomics 9:394–408
52. Cheung HH, Lee TL, Rennert OM, Chan WY (2009) DNA methylation of cancer genome. Birth Defects Res C Embryo Today 87:335–350
53. Fearon ER (2011) Molecular genetics of colorectal cancer. Annu Rev Pathol 6:479–507
54. Plass C, Soloway PD (2002) DNA methylation, imprinting and cancer. Eur J Hum Genet 10:6–16
55. Choi SW, Friso S (2010) Epigenetics: a new bridge between nutrition and health. Adv Nutr 1:8–16
56. Esteller M (2007) Cancer epigenomics: DNA methylomes and histone-modifi cation maps. Nat Rev Genet 8:286–298
57. Kelly TK, De Carvalho DD, Jones PA (2010) Epigenetic modifi cations as therapeutic targets. Nat Biotechnol 28:1069–1078
58. Dalgliesh GL, Furge K, Greenman C, Chen L, Bignell G, Butler A, Davies H, Edkins S, Hardy C, Latimer C, Teague J, Andrews J, Barthorpe S, Beare D, Buck G, Campbell PJ, Forbes S, Jia M, Jones D, Knott H, Kok CY, Lau KW, Leroy C, Lin ML, McBride DJ, Maddison M, Maguire S, McLay K, Menzies A, Mironenko T, Mulderrig L, Mudie L, O’Meara S, Pleasance E, Rajasingham A, Shepherd R, Smith R, Stebbings L, Stephens P, Tang G, Tarpey PS, Turrell K, Dykema KJ, Khoo SK, Petillo D, Wondergem B, Anema J, Kahnoski RJ, Teh BT, Stratton MR, Futreal PA (2010) Systematic sequencing of renal carcinoma reveals inactivation of histone modifying genes. Nature 463:360–363
59. Seidel C, Florean C, Schnekenburger M, Dicato M, Diederich M (2012) Chromatinmodifying agents in anti-cancer therapy. Biochimie 94:2264–2279
60. Jonasch E, Futreal PA, Davis IJ, Bailey ST, Kim WY, Brugarolas J, Giaccia AJ, Kurban G, Pause A, Frydman J, Zurita AJ, Rini BI, Sharma P, Atkins MB, Walker CL, Rathmell WK (2012) State of the science: an update on renal cell carcinoma. Mol Cancer Res 10:859–880
61. Liu L, Xu Z, Zhong L, Wang H, Jiang S, Long Q, Xu J, Guo J (2013) Prognostic value of EZH2 expression and activity in renal cell carcinoma: a prospective study. PLoS One 8:e81484
62. Albany C, Alva AS, Aparicio AM, Singal R, Yellapragada S, Sonpavde G, Hahn NM (2011) Epigenetics in prostate cancer. Prostate Cancer 2011:580318
63. Bachmann IM, Halvorsen OJ, Collett K, Stefansson IM, Straume O, Haukaas SA, Salvesen HB, Otte AP, Akslen LA (2006) EZH2 expression is associated with high proliferation rate and aggressive tumor subgroups in cutaneous melanoma and cancers of the endometrium, prostate, and breast. J Clin Oncol 24:268–273
64. Li H, Cai Q, Godwin AK, Zhang R (2010) Enhancer of zeste homolog 2 promotes the proliferation and invasion of epithelial ovarian cancer cells. Mol Cancer Res 8:1610–1618
65. Gupta RA, Shah N, Wang KC, Kim J, Horlings HM, Wong DJ, Tsai MC, Hung T, Argani P, Rinn JL, Wang Y, Brzoska P, Kong B, Li R, West RB, van de Vijver MJ, Sukumar S, Chang HY (2010) Long non-coding RNA HOTAIR reprograms chromatin state to promote cancer metastasis. Nature 464:1071–1076
66. Congrains A, Kamide K, Ohishi M, Rakugi H (2013) ANRIL: molecular mechanisms and implications in human health. Int J Mol Sci 14:1278–1292
67. Deng G, Sui G (2013) Noncoding RNA in oncogenesis: a new era of identifying key players. Int J Mol Sci 14:18319–18349
68. Almeida MI, Reis RM, Calin GA (2012) Decoy activity through microRNAs: the therapeutic implications. Expert Opin Biol Ther 12:1153–1159
69. Marques AC, Tan J, Ponting CP (2011) Wrangling for microRNAs provokes much crosstalk. Genome Biol 12:132
70. Calore F, Lovat F, Garofalo M (2013) Noncoding RNAs and cancer. Int J Mol Sci 14:17085–17110
71. Fabbri M, Croce CM (2011) Role of microRNAs in lymphoid biology and disease. Curr Opin Hematol 18:266–272
72. Ouillette P, Collins R, Shakhan S, Li J, Li C, Shedden K, Malek SN (2011) The prognostic signifi cance of various 13q14 deletions in chronic lymphocytic leukemia. Clin Cancer Res 17:6778–6790
73. Shao Y, Qu Y, Dang S, Li J, Li C, Shedden K, Malek SN (2013) MiR-145 inhibits oral squamous cell carcinoma (OSCC) cell growth by targeting c-Myc and Cdk 6. Cancer Cell Int 13:51
74. Suh SO, Chen Y, Zaman M, Hirata H, Yamamura S, Shahryari V, Liu J, Tabatabai ZL, Kakar S, Deng G, Tanaka Y, Dahiya R (2011) MicroRNA-145 is regulated by DNA methylation and p53 gene mutation in prostate cancer. Carcinogenesis 32:772–778
75. Xu N, Papagiannakopoulos T, Pan G, Thomson JA, Kosik KS (2009) MicroRNA-145 regulates OCT4, SOX2, and KLF4 and represses pluripotency in human embryonic stem cells. Cell 137:647–658
76. Blair LP, Yan Q (2012) Epigenetic mechanisms in commonly occurring cancers. DNA Cell Biol 31(Suppl 1):S49–S61
77. Lund AH, van Lohuizen M (2004) Epigenetics and cancer. Genes Dev 18:2315–2335
78. Morita S, Horii T, Kimura M, Ochiya T, Tajima S, Hatada I (2013) miR-29 represses the activities of DNA methyltransferases and DNA demethylases. Int J Mol Sci 14:14647–14658
79. Choi JD, Lee JS (2013) Interplay between epigenetics and genetics in cancer. Genomics Inform 11:164–173
80. Parry TE (2006) Mutagenic mechanisms in leukemia and cancer: a new concept Cytosine lack could be as mutagenic as cytosine deamination. Leuk Res 30:1079–1083
81. Soussi T, Beroud C (2003) Signifi cance of TP53 mutations in human cancer: a critical analysis of mutations at CpG dinucleotides. Hum Mutat 21:192–200
82. Valinluck V, Tsai HH, Rogstad DK (2004) Oxidative damage to methyl-CpG sequences inhibits the binding of the methyl-CpG binding domain (MBD) of methyl-CpG binding protein 2 (MeCP2). Nucleic Acids Res 32:4100–4108
83. Chen ZQ, Zhang CH, Kim CK, Xue Y (2011) Quantum mechanics study and Monte Carlo simulation on the hydrolytic deamination of 5-methylcytosine glycol. Phys Chem Chem Phys 13:6471–6483
84. Ziegel R, Shallop A, Upadhyaya P, Jones R, Tretyakova N (2004) Endogenous 5- methylcytosine protects neighboring guanines from N7 and O6-methylation and O6-pyridyloxobutylation by the tobacco carcinogen 4-(methylnitrosamino)-1-(3- pyridyl)- 1-butanone. Biochemistry 43:540–549
85. Donkena KV, Young CY, Tindall DJ (2010) Oxidative stress and DNA methylation in prostate cancer. Obstet Gynecol Int 2010: 302051
86. Maltseva DV, Baykov AA, Jeltsch A, Gromova ES (2009) Impact of 7,8-dihydro-8- oxoguanine on methylation of the CpG site by Dnmt3a. Biochemistry 48:1361–1368
87. Tudek B, Winczura A, Janik J, Siomek A, Foksinski M, Oliński R (2010) Involvement of oxidatively damaged DNA and repair in cancer development and aging. Am J Transl Res 2:254–284
88. Gargiulo G, Minucci S (2009) Epigenomic profi ling of cancer cells. Int J Biochem Cell Biol 41:127–135
89. Lin HJ, Zuo T, Chao JR, Peng Z, Asamoto LK, Yamashita SS, Huang TH (2009) Seed in soil, with an epigenetic view. Biochim Biophys Acta 1790:920–924
90. Wei SH, Balch C, Paik HH, Kim YS, Baldwin RL, Liyanarachchi S, Li L, Wang Z, Wan JC, Davuluri RV, Karlan BY, Gifford G, Brown R, Kim S, Huang TH, Nephew KP (2006) Prognostic DNA methylation biomarkers in ovarian cancer. Clin Cancer Res 12:2788–2794
91. Delpu Y, Cordelier P, Cho WC, Torrisani J (2013) DNA methylation and cancer diagnosis. Int J Mol Sci 14:15029–15058
92. Laird PW (2005) Cancer epigenetics. Hum Mol Genet 14 Spec No 1:R65–R76
93. Rivenbark AG, Coleman WB (2007) Practical applications for epigenetic biomarkers in cancer diagnostics. Expert Opin Med Diagn 1:17–30
94. Shivapurkar N, Gazdar AF (2010) DNA methylation based biomarkers in non-invasive cancer screening. Curr Mol Med 10:123–132
95. Wilson AS, Power BE, Molloy PL (2007) DNA hypomethylation and human diseases. Biochim Biophys Acta 1775:138–162
96. Patra SK, Deb M, Patra A (2011) Molecular marks for epigenetic identifi cation of developmental and cancer stem cells. Clin Epigenetics 2:27–53
97. Peter ME (2009) Let-7 and miR-200 microRNAs: guardians against pluripotency and cancer progression. Cell Cycle 8:843–852
98. Ardekani AM, Naeini MM (2010) The role of MicroRNAs in human diseases. Avicenna J Med Biotechnol 2:161–179
99. Paranjape T, Slack FJ, Weidhaas JB (2009) MicroRNAs: tools for cancer diagnostics. Gut 58:1546–1554
100. Cheng Q, Yi B, Wang A, Jiang X (2013) Exploring and exploiting the fundamental role of microRNAs in tumor pathogenesis. Onco Targets Ther 6:1675–1684
101. Metias SM, Lianidou E, Yousef GM (2009) MicroRNAs in clinical oncology: at the crossroads between promises and problems. J Clin Pathol 62:771–776
102. Olson P, Lu J, Zhang H, Shai A, Chun MG, Wang Y, Libutti SK, Nakakura EK, Golub TR, Hanahan D (2009) MicroRNA dynamics in the stages of tumorigenesis correlate with hallmark capabilities of cancer. Genes Dev 23:2152–2165
103. Gal-Yam EN, Saito Y, Egger G, Jones PA (2008) Cancer epigenetics: modifi cations, screening, and therapy. Annu Rev Med 59: 267–280
104. McCabe MT, Brandes JC, Vertino PM (2009) Cancer DNA methylation: molecular mechanisms and clinical implications. Clin Cancer Res 15:3927–3937
105. Plass C, Pfi ster SM, Lindroth AM, Bogatyrova O, Claus R, Lichter P (2013) Mutations in regulators of the epigenome and their connections to global chromatin patterns in cancer. Nat Rev Genet 14:765–780
106. Amatori S, Bagaloni I, Donati B, Fanelli M (2010) DNA demethylating antineoplastic strategies: a comparative point of view. Genes Cancer 1:197–209
107. Gryder BE, Sodji QH, Oyelere AK (2012) Targeted cancer therapy: giving histone deacetylase inhibitors all they need to succeed. Future Med Chem 4:505–524
108. Hagelkruys A, Sawicka A, Rennmayr M, Seiser C (2011) The biology of HDAC in cancer: the nuclear and epigenetic components. Handb Exp Pharmacol 206:13–37
109. Bots M, Johnstone RW (2009) Rational combinations using HDAC inhibitors. Clin Cancer Res 15:3970–3977
110. Singh BN, Zhang G, Hwa YL, Li J, Dowdy SC, Jiang SW (2010) Nonhistone protein acetylation as cancer therapy targets. Expert Rev Anticancer Ther 10:935–954
111. Pitts TM, Morrow M, Kaufman SA, Tentler JJ, Eckhardt SG (2009) Vorinostat and bort-ezomib exert synergistic antiproliferative and proapoptotic effects in colon cancer cell models. Mol Cancer Ther 8:342–349
112. Gong AY, Eischeid AN, Xiao J, Zhao J, Chen D, Wang ZY, Young CY, Chen XM (2012) miR-17-5p targets the p300/CBP-associated factor and modulates androgen receptor transcriptional activity in cultured prostate cancer cells. BMC Cancer 12:492
113. Nicoloso MS, Spizzo R, Shimizu M, Rossi S, Calin GA (2009) MicroRNAs–the micro steering wheel of tumour metastases. Nat Rev Cancer 9:293–302
114. Pan W, Zhu S, Yuan M, Cui H, Wang L, Luo X, Li J, Zhou H, Tang Y, Shen N (2010) MicroRNA-21 and microRNA-148a contribute to DNA hypomethylation in lupus CD4+ T cells by directly and indirectly targeting DNA methyltransferase 1. J Immunol 184: 6773–6781
115. Mathers JC, Strathdee G, Relton CL (2010) Induction of epigenetic alterations by dietary and other environmental factors. Adv Genet 71:3–39
116. Herceg Z (2007) Epigenetics and cancer: towards an evaluation of the impact of environmental and dietary factors. Mutagenesis 22:91–103
117. McKay JA, Mathers JC (2011) Diet induced epigenetic changes and their implications for health. Acta Physiol (Oxf) 202:103–118
118. Reik W, Dean W, Walter J (2001) Epigenetic reprogramming in mammalian development. Science 293:1089–1093
119. Nian H, Delage B, Ho E, Dashwood RH (2009) Modulation of histone deacetylase activity by dietary isothiocyanates and allyl sulfi des: studies with sulforaphane and garlic organosulfur compounds. Environ Mol Mutagen 50:213–221
120. Jang M, Cai L, Udeani GO, Slowing KV, Thomas CF, Beecher CW, Fong HH, Farnsworth NR, Kinghorn AD, Mehta RG, Moon RC, Pezzuto JM (1997) Cancer chemopreventive activity of resveratrol, a natural product derived from grapes. Science 275: 218–220
121. Pandey M, Shukla S, Gupta S (2010) Promoter demethylation and chromatin remodeling by green tea polyphenols leads to re-expression of GSTP1 in human prostate cancer cells. Int J Cancer 126:2520–2533