Epigenetics is a rapidly expanding field that focuses on stable changes in gene expression that are not accompanied by changes in DNA sequence and that are mediated primarily by DNA methylation and histone modifications. Disruption of the epigenome is a fundamental mechanism in cancer, and several epigenetic drugs that have proved to prolong survival and to be less toxic than conventional chemotherapy were recently approved by the FDA for cancer treatment. These include azacitidine (Vidaza), decitabine (Dacogen), vorinostat (Zolinza), and romidepsin (Istodax). Promising results of combination clinical trials with DNA methylation inhibitors and histone deacetylase inhibitors have recently been reported, and data are emerging that describe molecular determinants of clinical responses. Despite significant advances, challenges remain, including a lack of predictive markers, unclear mechanisms of response and resistance, and rare responses in solid tumors. Preclinical studies are ongoing with novel classes of agents that target various components of the epigenetic machinery. In this review, we focus on recent clinical and translational data in the epigenetics field that have potential in cancer therapy.
Epigenetics is defined as the study of stable changes in gene expression that are not accompanied by changes in DNA sequence. Epigenetic changes are important biological processes with relevance to all multicellular organisms. Studies in various models have shown that epigenetic regulation is critical for proper embryogenesis and development. Several mechanisms of epigenetic change have been described, and all seem to be interdependent to some degree. DNA methylation, posttranslational modifications of histones, and chromatin remodeling enzymes mediate epigenetic changes in many organisms. It has become clear that disruption of the epigenetic machinery plays a fundamental role in cancer development. Tumors often exhibit global hypomethylation, hypermethylation of CpG islands, and genome-wide alterations in the levels of histone modifications. These abnormalities are associated with widespread changes in gene expression, which are thought to contribute to tumor formation by affecting oncogenes and tumor suppressor genes.
What Is Epigenetic Therapy?
The understanding that epigenetic changes are prevalent in cancer and play a causative role in its biology has led to the development of new therapeutic approaches that target the epigenetic machinery. The first successful drugs developed as epigenetic agents were DNA methyltransferase inhibitors; these were followed by histone deacetylase inhibitors (HDIs). Both classes of drugs aim at reversing gene silencing and demonstrate antitumor activity in vitro and in vivo. Several other classes of drugs have been developed that target various other components of the epigenetic machinery; one such class is the histone methyltransferases, with new drugs in this class currently in early preclinical development (Table 1).
What Has Been Done?
The inhibitors of DNA methylation used clinically are nucleoside analogues that get converted into deoxy-nucleotide-triphosphates (dNTPs) and become incorporated into DNA in place of cytosine during DNA replication. They trap all DNA methyltransferases and target them for degradation. At low doses these drugs do not inhibit proliferation; they reactivate gene expression and have shown clinical activity as anticancer agents. Azacitidine (AZA; Vidaza) was the first hypomethylating agent approved by the FDA; its approval, in 2004, for the treatment of myelodysplastic disorders and leukemia, was followed by the approval, in 2006, of decitabine (DAC; 5-aza-2′-deoxyctidine; Dacogen).[2,3] Both drugs produce remissions or clinical improvements in more than 30% of patients treated. Features of responses have included the requirement for multiple cycles of therapy, slow response, and relatively few side effects. On the molecular level, demethylation, gene reactivation, and clonal elimination were observed in treated patients. The data in myelodysplastic syndrome (MDS) represent a proof-of-principle for epigenetic therapy for cancer, in particular in myeloid disorders.
HDIs work by preventing histone deacetylation, thereby facilitating an open chromatin structure and leading to the activation of genes, including the p21 cyclin-dependent kinase inhibitor. Several HDIs have shown antitumor activity in vitro with little toxicity in preclinical studies, suggesting selectivity for neoplastic cells. This has prompted the development of additional compounds, many of which have entered phase 1 trials in various malignancies. Two HDIs have shown particular efficacy against cutaneous T cell lymphoma (CTCL)—response rates of over 30%—which led to the FDA approval of vorinostat (suberoylanilide hydroxamic acid; Zolinza) in 2007 and of romidepsin (depsipeptide; Istodax) in 2009.[5,6]
1. Jones PA, Baylin SB. The epigenomics of cancer. Cell. 2007;128:683-92.
2. Issa JP, Kantarjian HM, Kirkpatrick P: Azacitidine. Nat Rev Drug Discov. 2005;4:275-6.
3. Kantarjian H, Issa JP, Rosenfeld CS, et al. Decitabine improves patient outcomes in myelodysplastic syndromes: results of a phase III randomized study. Cancer. 2006;106:1794-1803.
4. Issa JP. DNA methylation as a therapeutic target in cancer. Clin Cancer Res. 2007;13:1634-7.
5. Duvic M, Vu J. Vorinostat: a new oral histone deacetylase inhibitor approved for cutaneous T-cell lymphoma. Expert Opin Investig Drugs. 2007;16:1111-20.
6. Grant C, Rahman F, Piekarz R, et al. A new therapy for cutaneous T-cell lymphoma and a potential therapy for solid tumors. Expert Rev Anticancer Ther. 2010;10:997-1008.
7. Fenaux P, Mufti GJ, Hellstrom-Lindberg E, et al. Efficacy of azacitidine compared with that of conventional care regimens in the treatment of higher-risk myelodysplastic syndromes: a randomised, open-label, phase III study. Lancet Oncol. 2009;10:223-32.
8. Fenaux P, Gattermann N, Seymour JF, et al. Prolonged survival with improved tolerability in higher-risk myelodysplastic syndromes: azacitidine compared with low dose ara-C. Br J Haematol. 2010;149:244-9.
9. Fenaux P, Mufti GJ, Hellstrom-Lindberg E, et al. Azacitidine prolongs overall survival compared with conventional care regimens in elderly patients with low bone marrow blast count acute myeloid leukemia. J Clin Oncol. 2010;28:562-9.
10. Sekeres MA, List AF, Cuthbertson D, et al. Phase I combination trial of lenalidomide and azacitidine in patients with higher-risk myelodysplastic syndromes. J Clin Oncol. 2010;28:2253-8.
11. Kantarjian HM, Giles FJ, Greenberg PL, et al. Phase II study of romiplostim in patients with low- or intermediate-risk myelodysplastic syndrome receiving azacitidine therapy. Blood. 2010;116:3163-70.
12. Blum W, Garzon R, Klisovic RB, et al. Clinical response and miR-29b predictive significance in older AML patients treated with a 10-day schedule of decitabine. Proc Natl Acad Sci U S A. 2010;107:7473-8.
13. Cashen AF, Schiller GJ, O'Donnell MR, et al. Multicenter, phase II study of decitabine for the first-line treatment of older patients with acute myeloid leukemia. J Clin Oncol. 2010;28:556-61.
14. Fang F, Balch C, Schilder J, et al. A phase 1 and pharmacodynamic study of decitabine in combination with carboplatin in patients with recurrent, platinum-resistant, epithelial ovarian cancer. Cancer. 2010;116:4043-53.
15. Garcia-Manero G, Yang H, Bueso-Ramos C, et al. Phase 1 study of the histone deacetylase inhibitor vorinostat (suberoylanilide hydroxamic acid [SAHA]) in patients with advanced leukemias and myelodysplastic syndromes. Blood. 2008;111:1060-6.
16. Ramalingam SS, Maitland ML, Frankel P, et al. Carboplatin and paclitaxel in combination with either vorinostat or placebo for first-line therapy of advanced non-small-cell lung cancer. J Clin Oncol. 2010;28:56-62.
17. Watanabe T, Kato H, Kobayashi Y, et al. Potential efficacy of the oral histone deacetylase inhibitor vorinostat in a phase I trial in follicular and mantle cell lymphoma. Cancer Sci. 2010;101:196-200.
18. Galanis E, Jaeckle KA, Maurer MJ, et al. Phase II trial of vorinostat in recurrent glioblastoma multiforme: a North Central Cancer Treatment Group study. J Clin Oncol. 2009;27:2052-8.
19. Ree AH, Dueland S, Folkvord S, et al. Vorinostat, a histone deacetylase inhibitor, combined with pelvic palliative radiotherapy for gastrointestinal carcinoma: the Pelvic Radiation and Vorinostat (PRAVO) phase 1 study. Lancet Oncol. 2010;11:459-64.
20. Whittaker SJ, Demierre MF, Kim EJ, et al. Final results from a multicenter, international, pivotal study of romidepsin in refractory cutaneous T-cell lymphoma. J Clin Oncol. 2010;28:4485-91.
21. Klimek VM, Fircanis S, Maslak P, et al. Tolerability, pharmacodynamics, and pharmacokinetics studies of depsipeptide (romidepsin) in patients with acute myelogenous leukemia or advanced myelodysplastic syndromes. Clin Cancer Res. 2008;14:826-32.
22. Odenike OM, Alkan S, Sher D, et al. Histone deacetylase inhibitor romidepsin has differential activity in core binding factor acute myeloid leukemia. Clin Cancer Res. 2008;14:7095-101.
23. Ellis L, Pan Y, Smyth GK, et al. Histone deacetylase inhibitor panobinostat induces clinical responses with associated alterations in gene expression profiles in cutaneous T-cell lymphoma. Clin Cancer Res. 2008;14:4500-510.
24. Dickinson M, Ritchie D, DeAngelo DJ, et al. Preliminary evidence of disease response to the pan deacetylase inhibitor panobinostat (LBH589) in refractory Hodgkin lymphoma. Br J Haematol. 2009;147:
25. Rathkopf D, Wong BY, Ross RW, et al. A phase I study of oral panobinostat alone and in combination with docetaxel in patients with castration-resistant prostate cancer. Cancer Chemother Pharmacol. 2010;66:181-9.
26. Lassen U, Molife LR, Sorensen M, et al. A phase I study of the safety and pharmacokinetics of the histone deacetylase inhibitor belinostat administered in combination with carboplatin and/or paclitaxel in patients with solid tumours. Br J Cancer. 2010;103:12-17.
27. Mackay HJ, Hirte H, Colgan T, et al. Phase II trial of the histone deacetylase inhibitor belinostat in women with platinum resistant epithelial ovarian cancer and micropapillary (LMP) ovarian tumours. Eur J Cancer. 2010;46:1573-9.
28. Kuendgen A, Strupp C, Aivado M, et al. Treatment of myelodysplastic syndromes with valproic acid alone or in combination with all-trans retinoic acid. Blood. 2004;104:1266-9.
29. Munster P, Marchion D, Bicaku E, et al. Clinical and biological effects of valproic acid as a histone deacetylase inhibitor on tumor and surrogate tissues: phase I/II trial of valproic acid and epirubicin/FEC. Clin Cancer Res. 2009;15:2488-96.
30. Daud AI, Dawson J, Deconti RC, et al. Potentiation of a topoisomerase I inhibitor, karenitecin, by the histone deacetylase inhibitor valproic acid in melanoma: translational and phase I/II clinical trial. Clin Cancer Res. 2009;15:2479-87.
31. Kantarjian H, Oki Y, Garcia-Manero G, et al. Results of a randomized study of 3 schedules of low-dose decitabine in higher-risk myelodysplastic syndrome and chronic myelomonocytic leukemia. Blood. 2007;109:52-7.
32. Yang AS, Doshi KD, Choi SW, et al. DNA methylation changes after 5-aza-2'-deoxycytidine therapy in patients with leukemia. Cancer Res. 2006;66:5495-503.
33. Mund C, Hackanson B, Stresemann C, et al. Characterization of DNA demethylation effects induced by 5-aza-2'-deoxycytidine in patients with myelodysplastic syndrome. Cancer Res. 2005;65:7086-90.
34. Jiemjit A, Fandy TE, Carraway H, et al. p21(WAF1/CIP1) induction by 5-azacytosine nucleosides requires DNA damage. Oncogene. 2008;27:3615-23.
35. Fandy TE, Herman JG, Kerns P, et al. Early epigenetic changes and DNA damage do not predict clinical response in an overlapping schedule of 5-azacytidine and entinostat in patients with myeloid malignancies. Blood. 2009;114:2764-73.
36. Halaban R, Krauthammer M, Pelizzola M, et al. Integrative analysis of epigenetic modulation in melanoma cell response to decitabine: clinical implications. PLoS One. 2009;4:e4563.
37. Goodyear O, Agathanggelou A, Novitzky-Basso I, et al. Induction of a CD8+ T-cell response to the MAGE cancer testis antigen by combined treatment with azacitidine and sodium valproate in patients with acute myeloid leukemia and myelodysplasia. Blood. 2010;116:1908-18.
38. Musch T, Oz Y, Lyko F, Breiling A. Nucleoside drugs induce cellular differentiation by caspase-dependent degradation of stem cell factors. PLoS One. 2010;5:e10726.
39. Fotheringham S, Epping MT, Stimson L, et al. Genome-wide loss-of-function screen reveals an important role for the proteasome in HDAC inhibitor-induced apoptosis. Cancer Cell. 2009;15:57-66.
40. Khan O, Fotheringham S, Wood V, et al. HR23B is a biomarker for tumor sensitivity to HDAC inhibitor-based therapy. Proc Natl Acad Sci U S A. 2010;107:6532-7.
41. Mandawat A, Fiskus W, Buckley KM, et al. Pan-histone deacetylase (HDAC) inhibitor panobinostat depletes CXCR4 levels and signaling and exerts synergistic anti-myeloid activity in combination with CXCR4 antagonists. Blood. 2010;Epub ahead of print.
42. Fiskus W, Wang Y, Sreekumar A, et al. Combined epigenetic therapy with the histone methyltransferase EZH2 inhibitor 3-deazaneplanocin A and the histone deacetylase inhibitor panobinostat against human AML cells. Blood. 2009;114:2733-43.
43. Hacker S, Dittrich A, Mohr A, et al. Histone deacetylase inhibitors cooperate with IFN-gamma to restore caspase-8 expression and overcome TRAIL resistance in cancers with silencing of caspase-8. Oncogene. 2009;28:3097-110.
44. Sharma SV, Lee DY, Li B, et al. A chromatin-mediated reversible drug-tolerant state in cancer cell subpopulations. Cell. 2010;141:69-80.
45. Yoo CB, Jeong S, Egger G, et al. Delivery of 5-aza-2'-deoxycytidine to cells using oligodeoxynucleotides. Cancer Res. 2007;67:6400-408.
46. Brueckner B, Rius M, Markelova MR, et al. Delivery of 5-azacytidine to human cancer cells by elaidic acid esterification increases therapeutic drug efficacy. Mol Cancer Ther. 2010;9:1256-64.
47. Kuck D, Caulfield T, Lyko F, Medina-Franco JL. Nanaomycin A selectively inhibits DNMT3B and reactivates silenced tumor suppressor genes in human cancer cells. Mol Cancer Ther. 2010;9:3015-23.
48. Mandl-Weber S, Meinel FG, Jankowsky R, et al. The novel inhibitor of histone deacetylase resminostat (RAS2410) inhibits proliferation and induces apoptosis in multiple myeloma (MM) cells. Br J Haematol. 2010;149:518-28.
49. Lucas DM, Alinari L, West DA, et al. The novel deacetylase inhibitor AR-42 demonstrates pre-clinical activity in B-cell malignancies in vitro and in vivo. PLoS One. 2010;5:e10941.
50. Tang YA, Wen WL, Chang JW, et al. A novel histone deacetylase inhibitor exhibits antitumor activity via apoptosis induction, F-actin disruption and gene acetylation in lung cancer. PLoS One. 2010;5:e12417.
51. Varambally S, Dhanasekaran SM, Zhou M, et al. The polycomb group protein EZH2 is involved in progression of prostate cancer. Nature. 2002;419:624-9.
52. Morin RD, Johnson NA, Severson TM, et al. Somatic mutations altering EZH2 (Tyr641) in follicular and diffuse large B-cell lymphomas of germinal-center origin. Nat Genet. 2010;42:181-5.
53. Tan J, Yang X, Zhuang L, et al. Pharmacologic disruption of Polycomb-repressive complex 2-mediated gene repression selectively induces apoptosis in cancer cells. Genes Dev. 2007;21:1050-63.
54. Suva ML, Riggi N, Janiszewska M, et al. EZH2 is essential for glioblastoma cancer stem cell maintenance. Cancer Res. 2009;69:9211-8.
55. Puppe J, Drost R, Liu X, et al. BRCA1-deficient mammary tumor cells are dependent on EZH2 expression and sensitive to Polycomb repressive complex 2-inhibitor 3-deazaneplanocin A. Breast Cancer Res. 2009;11:R63.
56. Kondo Y, Shen L, Ahmed S, et al. Downregulation of histone H3 lysine 9 methyltransferase G9a induces centrosome disruption and chromosome instability in cancer cells. PLoS One. 2008;3:e2037.
57. Liu F, Chen X, Allali-Hassani A, et al. Discovery of a 2,4-diamino-7-aminoalkoxyquinazoline as a potent and selective inhibitor of histone lysine methyltransferase G9a. J Med Chem. 2009;52:7950-3.
58. Liu F, Chen X, Allali-Hassani A, et al. Protein lysine methyltransferase G9a inhibitors: design, synthesis, and structure activity relationships of 2,4-diamino-7-aminoalkoxy-quinazolines. J Med Chem. 2010;53:
59. Kubicek S, O'Sullivan RJ, August EM, et al. Reversal of H3K9me2 by a small-molecule inhibitor for the G9a histone methyltransferase. Mol Cell. 2007;25:473-81. 60. Majumder S, Liu Y, Ford OH, III, et al. Involvement of arginine methyltransferase CARM1 in androgen receptor function and prostate cancer cell viability. Prostate. 2006;66:1292-1301.
61. Selvi BR, Batta K, Kishore AH, et al. Identification of a novel inhibitor of coactivator-associated arginine methyltransferase 1 (CARM1)-mediated methylation of histone H3 Arg-17. J Biol Chem. 2010;285:7143-52.
62. Metzger E, Wissmann M, Yin N, et al. LSD1 demethylates repressive histone marks to promote androgen-receptor-dependent transcription. Nature. 2005;437:436-9.
63. Wissmann M, Yin N, Muller JM, et al. Cooperative demethylation by JMJD2C and LSD1 promotes androgen receptor-dependent gene expression. Nat Cell Biol. 2007;9:347-53.
64. Kahl P, Gullotti L, Heukamp LC, et al. Androgen receptor coactivators lysine-specific histone demethylase 1 and four and a half LIM domain protein 2 predict risk of prostate cancer recurrence. Cancer Res. 2006;66:11341-7.
65. Lim S, Janzer A, Becker A, et al. Lysine-specific demethylase 1 (LSD1) is highly expressed in ER-negative breast cancers and a biomarker predicting aggressive biology. Carcinogenesis. 2010;31:512-20.
66. Schulte JH, Lim S, Schramm A, et al. Lysine-specific demethylase 1 is strongly expressed in poorly differentiated neuroblastoma: implications for therapy. Cancer Res. 2009;69:2065-71.
67. Huang Y, Stewart TM, Wu Y, et al. Novel oligoamine analogues inhibit lysine-specific demethylase 1 and induce reexpression of epigenetically silenced genes. Clin Cancer Res. 2009;15:7217-28.
68. Huang Y, Greene E, Murray ST, et al. Inhibition of lysine-specific demethylase 1 by polyamine analogues results in reexpression of aberrantly silenced genes. Proc Natl Acad Sci U S A. 2007;104:8023-8.
69. Huang Y, Marton LJ, Woster PM, Casero RA. Polyamine analogues targeting epigenetic gene regulation. Essays Biochem. 2009;46:95-110.
70. Liu G, Bollig-Fischer A, Kreike B, et al. Genomic amplification and oncogenic properties of the GASC1 histone demethylase gene in breast cancer. Oncogene. 2009;28:4491-500.
71. Cloos PA, Christensen J, Agger K, et al. The putative oncogene GASC1 demethylates tri- and dimethylated lysine 9 on histone H3. Nature. 2006;442:307-11.
72. Hamada S, Suzuki T, Mino K, et al. Design, synthesis, enzyme-inhibitory activity, and effect on human cancer cells of a novel series of jumonji domain-containing protein 2 histone demethylase inhibitors. J Med Chem. 2010;53:5629-38.
73. Kitabayashi I, Aikawa Y, Nguyen LA, et al. Activation of AML1-mediated transcription by MOZ and inhibition by the MOZ-CBP fusion protein. EMBO J. 2001;20:7184-96.
74. Perez-Campo FM, Borrow J, Kouskoff V, Lacaud G. The histone acetyl transferase activity of monocytic leukemia zinc finger is critical for the proliferation of hematopoietic precursors. Blood. 2009;113:4866-74.
75. Sobulo OM, Borrow J, Tomek R, et al. MLL is fused to CBP, a histone acetyltransferase, in therapy-related acute myeloid leukemia with a t(11;16)(q23;p13.3). Proc Natl Acad Sci U S A. 1997;94:8732-7.
76. Chen J, Odenike O, Rowley JD. Leukaemogenesis: more than mutant genes. Nat Rev Cancer. 2010;10:23-36.
77. Vernarecci S, Tosi F, Filetici P. Tuning acetylated chromatin with HAT inhibitors: a novel tool for therapy. Epigenetics. 2010;5:105-11.
78. Bandyopadhyay K, Baneres JL, Martin A, et al. Spermidinyl-CoA-based HAT inhibitors block DNA repair and provide cancer-specific chemo- and radiosensitization. Cell Cycle. 2009;8:2779-88.
79. Arif M, Vedamurthy BM, Choudhari R, et al. Nitric oxide-mediated histone hyperacetylation in oral cancer: target for a water-soluble HAT inhibitor, CTK7A. Chem Biol. 2010;17:903-13.
80. Bowers EM, Yan G, Mukherjee C, et al. Virtual ligand screening of the p300/CBP histone acetyltransferase: identification of a selective small molecule inhibitor. Chem Biol. 2010;17:471-82.