References
- Vogelstein B, Papadopoulos N, Velculescu VE, et al. Cancer genome landscapes. Science. 2013;339(6127):1546–1558.
- Jones P. The cancer epigenome. Genome. 2013;56(10):540–541.
- Liu L, Jin G, Zhou X. Modeling the relationship of epigenetic modifications to transcription factor binding. Nucleic Acids Res. 2015;43(8):3873–3885.
- Yoo CB, Jones PA. Epigenetic therapy of cancer: past, present and future. Nat Rev Drug Discovery. 2006;5(1):37–50.
- Berger SL, Kouzarides T, Shiekhattar R, et al. An operational definition of epigenetics. Genes Dev. 2009;23(7):781–783.
- Dawson MA, Kouzarides T. Cancer epigenetics: from mechanism to therapy. Cell. 2012;150(1):12–27.
- Berdasco M, Esteller M. Aberrant epigenetic landscape in cancer: how cellular identity goes awry. Dev Cell. 2010;19(5):698–711.
- Bedi U, Mishra VK, Wasilewski D, et al. Epigenetic plasticity: a central regulator of epithelial-to-mesenchymal transition in cancer. Oncotarget. 2014;5(8):2016–2029.
- Tam WL, Weinberg RA. The epigenetics of epithelial-mesenchymal plasticity in cancer. Nature med. 2013;19(11):1438–1449.
- Mani SA, Guo W, Liao MJ, et al. The epithelial-mesenchymal transition generates cells with properties of stem cells. Cell. 2008;133(4):704–715.
- Chaffer CL, Brennan JP, Slavin JL, et al. Mesenchymal-to-epithelial transition facilitates bladder cancer metastasis: role of fibroblast growth factor receptor-2. Cancer Res. 2006;66(23):11271–11278.
- Mir N, Jayachandran A, Dhungel B, et al. Epithelial-to-mesenchymal transition: a mediator of sorafenib resistance in advanced hepatocellular carcinoma. Curr Cancer Drug Targets. 2017;17(8):698–706.
- Kanwal R, Gupta K, Gupta S. Cancer epigenetics: an introduction. Methods Mol Biol. 2015;1238:3–25.
- Wang Z, Tang B, He Y, et al. DNA methylation dynamics in neurogenesis. Epigenomics. 2016;8(3):401–414.
- Kazanets A, Shorstova T, Hilmi K, et al. Epigenetic silencing of tumor suppressor genes: paradigms, puzzles, and potential. Biochim Biophys Acta. 2016;1865(2):275–288.
- Shi YX, Wang Y, Li X, et al. Genome-wide DNA methylation profiling reveals novel epigenetic signatures in squamous cell lung cancer. BMC Genomics. 2017;18(1):901.
- Suzuki H, Yamamoto E, Maruyama R, et al. Biological significance of the CpG island methylator phenotype. Biochem Biophys Res Commun. 2014;455(1–2):35–42.
- Hanahan D, Weinberg RA. Hallmarks of cancer: the next generation. Cell. 2011;144(5):646–674.
- Castillo J, Lopez-Rodas G, Franco L. Histone post-translational modifications and nucleosome organisation in transcriptional regulation: some open questions. Adv Exp Med Biol. 2017;966:65–92.
- Lawrence M, Daujat S, Schneider R. Lateral thinking: how histone modifications regulate gene expression. Trends Genet. 2016;32(1):42–56.
- Barski A, Cuddapah S, Cui K, et al. High-resolution profiling of histone methylations in the human genome. Cell. 2007;129(4):823–837.
- Ntranos A, Casaccia P. Bromodomains: translating the words of lysine acetylation into myelin injury and repair. Neurosci lett. 2016;625:4–10.
- Workman JL, Kingston RE. Alteration of nucleosome structure as a mechanism of transcriptional regulation. Annu revi biochem. 1998;67:545–579.
- Khan SA, Reddy D, Gupta S. Global histone post-translational modifications and cancer: biomarkers for diagnosis, prognosis and treatment? World J Biol Chem. 2015;6(4):333–345.
- Keppler BR, Archer TK. Chromatin-modifying enzymes as therapeutic targets–part 1. Expert Opin Ther Targets. 2008;12(10):1301–1312.
- Sidhu H, Capalash N. UHRF1: the key regulator of epigenetics and molecular target for cancer therapeutics. Tumour Biol. 2017;39(2):1010428317692205.
- Alhosin M, Omran Z, Zamzami MA, et al. Signalling pathways in UHRF1-dependent regulation of tumor suppressor genes in cancer. J Exp Clin Cancer Res. 2016;35(1):174.
- Wu R, Su Y, Wu H, et al. Characters, functions and clinical perspectives of long non-coding RNAs. Mol genet genomics. 2016;291(3):1013–1033.
- Roberts TC, Morris KV, Weinberg MS. Perspectives on the mechanism of transcriptional regulation by long non-coding RNAs. Epigenetics. 2014;9(1):13–20.
- Li H, Ma SQ, Huang J, et al. Roles of long noncoding RNAs in colorectal cancer metastasis. Oncotarget. 2017;8(24):39859–39876.
- Nie L, Wu HJ, Hsu JM, et al. Long non-coding RNAs: versatile master regulators of gene expression and crucial players in cancer. Am J Transl Res. 2012;4(2):127–150.
- Liu H, Lei C, He Q, et al. Nuclear functions of mammalian microRNAs in gene regulation, immunity and cancer. Mol Cancer. 2018;17(1):64.
- Cech TR, Steitz JA. The noncoding RNA revolution-trashing old rules to forge new ones. Cell. 2014;157(1):77–94.
- Pagano F, De Marinis E, Grignani F, et al. Epigenetic role of miRNAs in normal and leukemic hematopoiesis. Epigenomics. 2013;5(5):539–552.
- Wee S, Dhanak D, Li H, et al. Targeting epigenetic regulators for cancer therapy. Ann N Y Acad Sci. 2014;1309:30–36.
- Kadoch C, Crabtree GR. Mammalian SWI/SNF chromatin remodeling complexes and cancer: mechanistic insights gained from human genomics. Sci Adv. 2015;1(5):e1500447.
- Sturm D, Bender S, Jones DT, et al. Paediatric and adult glioblastoma: multiform (epi)genomic culprits emerge. Nat Rev Cancer. 2014;14(2):92–107.
- Morel D, Almouzni G, Soria JC, et al. Targeting chromatin defects in selected solid tumors based on oncogene addiction, synthetic lethality and epigenetic antagonism. Ann oncol. 2017;28(2):254–269.
- West AC, Johnstone RW. New and emerging HDAC inhibitors for cancer treatment. J Clin Invest. 2014;124(1):30–39.
- Roy DM, Walsh LA, Chan TA. Driver mutations of cancer epigenomes. Protein Cell. 2014;5(4):265–296.
- Lauschke VM, Barragan I, Ingelman-Sundberg M. Pharmacoepigenetics and toxicoepigenetics: novel mechanistic insights and therapeutic opportunities. Annu rev pharmacol toxicol. 2018;58:161–185.
- Nervi C, De Marinis E, Codacci-Pisanelli G. Epigenetic treatment of solid tumours: a review of clinical trials. Clin Epigenetics. 2015;7:127.
- Goffin J, Eisenhauer E. DNA methyltransferase inhibitors-state of the art. Ann oncol. 2002;13(11):1699–1716.
- Santini V, Kantarjian HM, Issa JP. Changes in DNA methylation in neoplasia: pathophysiology and therapeutic implications. Ann Internal Med. 2001;134(7):573–586.
- Dhanak D, Jackson P. Development and classes of epigenetic drugs for cancer. Biochem Biophys Res Commun. 2014;455(1–2):58–69.
- Dunn J, Rao S. Epigenetics and immunotherapy: the current state of play. Mol Immunol. 2017;87:227–239.
- Heyn H, Esteller M. DNA methylation profiling in the clinic: applications and challenges. Nat Rev Genet. 2012;13(10):679–692.
- Lakshmaiah KC, Jacob LA, Aparna S, et al. Epigenetic therapy of cancer with histone deacetylase inhibitors. J Cancer Res Ther. 2014;10(3):469–478.
- Hojfeldt JW, Agger K, Helin K. Histone lysine demethylases as targets for anticancer therapy. Nat Rev Drug Discovery. 2013;12(12):917–930.
- Lu X, Ning Z, Li Z, et al. Development of chidamide for peripheral T-cell lymphoma, the first orphan drug approved in China. Intractable Rare Dis Res. 2016;5(3):185–191.
- Meighan-Mantha R. Epigenetic drugs in oncology: current clinical landscape and emerging trends. Informa’s Pharma intelligence. 2017; 1(1):1–16.
- Prachayasittikul V, Prathipati P, Pratiwi R, et al. Exploring the epigenetic drug discovery landscape. Expert Opin Drug Discov. 2017;12(4):345–362.
- Kim KH, Roberts CW. Targeting EZH2 in cancer. Nature med. 2016;22(2):128–134.
- Slany RK. The molecular mechanics of mixed lineage leukemia. Oncogene. 2016;35(40):5215–5223.
- Pedersen MT, Helin K. Histone demethylases in development and disease. Trends Cell Biol. 2010;20(11):662–671.
- Takeuchi T, Watanabe Y, Takano-Shimizu T, et al. Roles of jumonji and jumonji family genes in chromatin regulation and development. Dev Dyn. 2006;235(9):2449–2459.
- Ling H, Fabbri M, Calin GA. MicroRNAs and other non-coding RNAs as targets for anticancer drug development. Nat Rev Drug Discovery. 2013;12(11):847–865.
- Shi L, Peng F, Tao Y, et al. Roles of long noncoding RNAs in hepatocellular carcinoma. Virus res. 2016;223:131–139.
- Uhlmann S, Mannsperger H, Zhang JD, et al. Global microRNA level regulation of EGFR-driven cell-cycle protein network in breast cancer. Mol syst biol. 2012;8:570.
- Wheeler DL, Dunn EF, Harari PM. Understanding resistance to EGFR inhibitors-impact on future treatment strategies. Nat Rev Clin Oncol. 2010;7(9):493–507.
- Melo S, Villanueva A, Moutinho C, et al. Small molecule enoxacin is a cancer-specific growth inhibitor that acts by enhancing TAR RNA-binding protein 2-mediated microRNA processing. Proc Natl Acad Sci USA. 2011;108(11):4394–4399.
- Beg MS, Brenner AJ, Sachdev J, et al. Phase I study of MRX34, a liposomal miR-34a mimic, administered twice weekly in patients with advanced solid tumors. Invest New Drugs. 2017;35(2):180–188.
- Campbell RM, Tummino PJ. Cancer epigenetics drug discovery and development: the challenge of hitting the mark. J Clin Invest. 2014;124(1):64–69.
- Nie J, Liu L, Li X, et al. Decitabine, a new star in epigenetic therapy: the clinical application and biological mechanism in solid tumors. Cancer Lett. 2014;354(1):12–20.
- Connolly RM, Rudek MA, Piekarz R. Entinostat: a promising treatment option for patients with advanced breast cancer. Future Oncol. 2017;13(13):1137–1148.
- Yardley DA, Ismail-Khan RR, Melichar B, et al. Randomized phase II, double-blind, placebo-controlled study of exemestane with or without entinostat in postmenopausal women with locally recurrent or metastatic estrogen receptor-positive breast cancer progressing on treatment with a nonsteroidal aromatase inhibitor. J Clin Oncol. 2013;31(17):2128–2135.
- Minucci S, Pelicci PG. Histone deacetylase inhibitors and the promise of epigenetic (and more) treatments for cancer. Nat Rev Cancer. 2006;6(1):38–51.
- Robertson KD, Uzvolgyi E, Liang G, et al. The human DNA methyltransferases (DNMTs) 1, 3a and 3b: coordinate mRNA expression in normal tissues and overexpression in tumors. Nucleic Acids Res. 1999;27(11):2291–2298.
- Waltregny D, North B, Van Mellaert F, et al. Screening of histone deacetylases (HDAC) expression in human prostate cancer reveals distinct class I HDAC profiles between epithelial and stromal cells. Eur j histochem. 2004;48(3):273–290.
- Unoki M. Current and potential anticancer drugs targeting members of the UHRF1 complex including epigenetic modifiers. Recent Pat Anticancer Drug Discov. 2011;6(1):116–130.
- Unoki M, Daigo Y, Koinuma J, et al. UHRF1 is a novel diagnostic marker of lung cancer. Br j cancer. 2010;103(2):217–222.
- Jenkins Y, Markovtsov V, Lang W, et al. Critical role of the ubiquitin ligase activity of UHRF1, a nuclear RING finger protein, in tumor cell growth. Mol Biol Cell. 2005;16(12):5621–5629.
- Azad N, Zahnow CA, Rudin CM, et al. The future of epigenetic therapy in solid tumours–lessons from the past. Nat Rev Clin Oncol. 2013;10(5):256–266.
- Falahi F, van Kruchten M, Martinet N, et al. Current and upcoming approaches to exploit the reversibility of epigenetic mutations in breast cancer. Breast Cancer Res. 2014;16(4):412.
- Kinnaird A, Zhao S, Wellen KE, et al. Metabolic control of epigenetics in cancer. Nat Rev Cancer. 2016;16(11):694–707.
- Brown JM, Giaccia AJ. The unique physiology of solid tumors: opportunities (and problems) for cancer therapy. Cancer Res. 1998;58(7):1408–1416.
- Wang Y, Zhang H, Chen Y, et al. LSD1 is a subunit of the NuRD complex and targets the metastasis programs in breast cancer. Cell. 2009;138(4):660–672.
- Raynal NJ, Da Costa EM, Lee JT, et al. Repositioning FDA-approved drugs in combination with epigenetic drugs to reprogram colon cancer epigenome. Mol Cancer Ther. 2017;16(2):397–407.
- Cameron EE, Bachman KE, Myohanen S, et al. Synergy of demethylation and histone deacetylase inhibition in the re-expression of genes silenced in cancer. Nature Genet. 1999;21(1):103–107.
- Zhu WG, Otterson GA. The interaction of histone deacetylase inhibitors and DNA methyltransferase inhibitors in the treatment of human cancer cells. Curr Med Chem Anticancer Agents. 2003;3(3):187–199.
- Griffiths EA, Gore SD. DNA methyltransferase and histone deacetylase inhibitors in the treatment of myelodysplastic syndromes. Semin hematol. 2008;45(1):23–30.
- Gilan O, Lam EY, Becher I, et al. Functional interdependence of BRD4 and DOT1L in MLL leukemia. Nat Struct Mol Biol. 2016;23(7):673–681.
- Li J, Hao D, Wang L, et al. Epigenetic targeting drugs potentiate chemotherapeutic effects in solid tumor therapy. Sci Rep. 2017;7(1):4035.
- Appleton K, Mackay HJ, Judson I, et al. Phase I and pharmacodynamic trial of the DNA methyltransferase inhibitor decitabine and carboplatin in solid tumors. J Clin Oncol. 2007;25(29):4603–4609.
- Tawbi HA, Beumer JH, Tarhini AA, et al. Safety and efficacy of decitabine in combination with temozolomide in metastatic melanoma: a phase I/II study and pharmacokinetic analysis. Ann oncol. 2013;24(4):1112–1119.
- 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(1):56–62.
- Groselj B, Sharma NL, Hamdy FC, et al. Histone deacetylase inhibitors as radiosensitisers: effects on DNA damage signalling and repair. Br j cancer. 2013;108(4):748–754.
- Witta SE, Jotte RM, Konduri K, et al. Randomized phase II trial of erlotinib with and without entinostat in patients with advanced non-small-cell lung cancer who progressed on prior chemotherapy. J Clin Oncol. 2012;30(18):2248–2255.
- Pulliam N, Fang F, Ozes AR, et al. An effective epigenetic-PARP inhibitor combination therapy for breast and ovarian cancers independent of BRCA mutations. Clin Cancer Res. 2018;24(13):3163–3175.
- Belinsky SA, Grimes MJ, Picchi MA, et al. Combination therapy with vidaza and entinostat suppresses tumor growth and reprograms the epigenome in an orthotopic lung cancer model. Cancer Res. 2011;71(2):454–462.
- Berndsen RH, Abdul UK, Weiss A, et al. Epigenetic approach for angiostatic therapy: promising combinations for cancer treatment. Angiogenesis. 2017;20(2):245–267.
- Kim R, Emi M, Tanabe K. Cancer immunoediting from immune surveillance to immune escape. Immunology. 2007;121(1):1–14.
- Sigalotti L, Fratta E, Coral S, et al. Epigenetic drugs as immunomodulators for combination therapies in solid tumors. Pharmacol Ther. 2014;142(3):339–350.
- Marchini A, Scott EM, Rommelaere J. Overcoming barriers in oncolytic virotherapy with HDAC inhibitors and immune checkpoint blockade. Viruses. 2016;8(1).
- Nguyen TL, Wilson MG, Hiscott J. Oncolytic viruses and histone deacetylase inhibitors–a multi-pronged strategy to target tumor cells. Cytokine Growth Factor Rev. 2010;21(2–3):153–159.
- Bartlett DL, Liu Z, Sathaiah M, et al. Oncolytic viruses as therapeutic cancer vaccines. Mol Cancer. 2013;12(1):103.
- Zheng H, Zhao W, Yan C, et al. HDAC inhibitors enhance T-cell chemokine expression and augment response to PD-1 immunotherapy in lung adenocarcinoma. Clin Cancer Res. 2016;22(16):4119–4132.
- Topper MJ, Vaz M, Chiappinelli KB, et al. Epigenetic therapy ties MYC depletion to reversing immune evasion and treating lung cancer. Cell. 2017;171(6):1284–1300 e21.
- Marrocco DL, Tilley WD, Bianco-Miotto T, et al. Suberoylanilide hydroxamic acid (vorinostat) represses androgen receptor expression and acts synergistically with an androgen receptor antagonist to inhibit prostate cancer cell proliferation. Mol Cancer Ther. 2007;6(1):51–60.
- Marrocco-Tallarigo DL, Centenera MM, Scher HI, et al. Finding the place of histone deacetylase inhibitors in prostate cancer therapy. Expert Rev Clin Pharmacol. 2009;2(6):619–630.
- Pfeiffer MJ, Mulders PF, Schalken JA. An in vitro model for preclinical testing of endocrine therapy combinations for prostate cancer. Prostate. 2010;70(14):1524–1532.
- Kanai Y, Arai E. Multilayer-omics analyses of human cancers: exploration of biomarkers and drug targets based on the activities of the international human epigenome consortium. Front Genet. 2014;5:24.
- Gul S. Epigenetic assays for chemical biology and drug discovery. Clin Epigenetics. 2017;9:41.
- Ladd-Acosta C. Epigenetic signatures as biomarkers of exposure. Curr Environ Health Rep. 2015;2(2):117–125.
- Valdespino V, Valdespino PM. Potential of epigenetic therapies in the management of solid tumors. Cancer Manag Res. 2015;7:241–251.
- Chiappinelli KB, Zahnow CA, Ahuja N, et al. Combining epigenetic and immunotherapy to combat cancer. Cancer Res. 2016;76(7):1683–1689.
- Orillion A, Hashimoto A, Damayanti N, et al. Entinostat neutralizes myeloid-derived suppressor cells and enhances the antitumor effect of PD-1 inhibition in murine models of lung and renal cell carcinoma. Clin Cancer Res off J Am Assoc Cancer Res. 2017;23(17):5187–5201.
- Li H, Chiappinelli KB, Guzzetta AA, et al. Immune regulation by low doses of the DNA methyltransferase inhibitor 5-azacitidine in common human epithelial cancers. Oncotarget. 2014;5(3):587–598.