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Wojciechowski M, Czapinska H, Krwawicz J, Rafalski D, Bochtler M. Cytosine analogues as DNA methyltransferase substrates. Nucleic Acids Res 2024:gkae568. [PMID: 38966999 DOI: 10.1093/nar/gkae568] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2023] [Revised: 05/23/2024] [Accepted: 06/20/2024] [Indexed: 07/06/2024] Open
Abstract
DNA methyltransferases are drug targets for myelodysplastic syndrome (MDS), chronic myelomonocytic leukemia (CMML), acute myelogenous leukemia (AML) and possibly β-hemoglobinopathies. We characterize the interaction of nucleoside analogues in DNA with a prokaryotic CpG-specific DNA methyltransferase (M.MpeI) as a model for mammalian DNMT1 methyltransferases. We tested DNA containing 5-hydroxymethylcytosine (5hmC), 5-hydroxycytosine (5OHC), 5-methyl-2-pyrimidinone (in the ribosylated form known as 5-methylzebularine, 5mZ), 5,6-dihydro-5-azacytosine (dhaC), 5-fluorocytosine (5FC), 5-chlorocytosine (5ClC), 5-bromocytosine (5BrC) and 5-iodocytosine (5IC). Covalent complex formation was by far most efficient for 5FC. Non-covalent complexes were most abundant for dhaC and 5mZ. Surprisingly, we observed methylation of 5IC and 5BrC, and to a lesser extent 5ClC and 5FC, in the presence, but not the absence of small molecule thiol nucleophiles. For 5IC and 5BrC, we demonstrated by mass spectrometry that the reactions were due to methyltransferase driven dehalogenation, followed by methylation. Crystal structures of M.MpeI-DNA complexes capture the 'in' conformation of the active site loop for analogues with small or rotatable (5mZ) 5-substituents and its 'out' form for bulky 5-substituents. Since very similar 'in' and 'out' loop conformations were also observed for DNMT1, it is likely that our conclusions generalize to other DNA methyltransferases.
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Affiliation(s)
- Marek Wojciechowski
- International Institute of Molecular and Cell Biology, Trojdena 4, 02-109 Warsaw, Poland
- Plant Breeding and Acclimatization Institute - National Research Institute, 05-870 Radzikow, Poland
| | - Honorata Czapinska
- International Institute of Molecular and Cell Biology, Trojdena 4, 02-109 Warsaw, Poland
- Institute of Biochemistry and Biophysics PAS, Pawinskiego 5a, 02-106 Warsaw, Poland
| | - Joanna Krwawicz
- International Institute of Molecular and Cell Biology, Trojdena 4, 02-109 Warsaw, Poland
- Institute of Biochemistry and Biophysics PAS, Pawinskiego 5a, 02-106 Warsaw, Poland
- Department of Biochemistry, University of Oxford, Oxford, UK
| | - Dominik Rafalski
- International Institute of Molecular and Cell Biology, Trojdena 4, 02-109 Warsaw, Poland
- Institute of Biochemistry and Biophysics PAS, Pawinskiego 5a, 02-106 Warsaw, Poland
| | - Matthias Bochtler
- International Institute of Molecular and Cell Biology, Trojdena 4, 02-109 Warsaw, Poland
- Institute of Biochemistry and Biophysics PAS, Pawinskiego 5a, 02-106 Warsaw, Poland
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Fàbrega C, Clua A, Eritja R, Aviñó A. Oligonucleotides Carrying Nucleoside Antimetabolites as Potential Prodrugs. Curr Med Chem 2023; 30:1304-1319. [PMID: 34844535 DOI: 10.2174/0929867328666211129124039] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2021] [Revised: 09/07/2021] [Accepted: 09/27/2021] [Indexed: 11/22/2022]
Abstract
BACKGROUND Nucleoside and nucleobase antimetabolites are an important class of chemotherapeutic agents for the treatment of cancer as well as other diseases. INTRODUCTION In order to avoid undesirable side effects, several prodrug strategies have been developed. In the present review, we describe a relatively unknown strategy that consists of using oligonucleotides modified with nucleoside antimetabolites as prodrugs. METHODS The active nucleotides are generated by enzymatic degradation once incorporated into cells. This strategy has attracted large interest and is widely utilized at present due to the continuous developments made in therapeutic oligonucleotides and the recent advances in nanomaterials and nanomedicine. RESULTS A large research effort was made mainly in the improvement of the antiproliferative properties of nucleoside homopolymers, but recently, chemically modified aptamers, antisense oligonucleotides and/or siRNA carrying antiproliferative nucleotides have demonstrated a great potential due to the synergetic effect of both therapeutic entities. In addition, DNA nanostructures with interesting properties have been built to combine antimetabolites and enhancers of cellular uptake in the same scaffold. Finally, protein nanoparticles functionalized with receptor-binders and antiproliferative oligomers represent a new avenue for a more effective treatment in cancer therapy. CONCLUSION It is expected that oligonucleotides carrying nucleoside antimetabolites will be considered as potential drugs in the near future for biomedical applications.
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Affiliation(s)
- Carme Fàbrega
- Institute for Advanced Chemistry of Catalonia (IQAC), Spanish National Research Council (CSIC), Barcelona, Spain.,Networking Center on Bioengineering, Biomaterials and Nanomedicine (CIBER-BBN), E-08034 Barcelona, Spain
| | - Anna Clua
- Institute for Advanced Chemistry of Catalonia (IQAC), Spanish National Research Council (CSIC), Barcelona, Spain.,Networking Center on Bioengineering, Biomaterials and Nanomedicine (CIBER-BBN), E-08034 Barcelona, Spain
| | - Ramon Eritja
- Institute for Advanced Chemistry of Catalonia (IQAC), Spanish National Research Council (CSIC), Barcelona, Spain.,Networking Center on Bioengineering, Biomaterials and Nanomedicine (CIBER-BBN), E-08034 Barcelona, Spain
| | - Anna Aviñó
- Institute for Advanced Chemistry of Catalonia (IQAC), Spanish National Research Council (CSIC), Barcelona, Spain.,Networking Center on Bioengineering, Biomaterials and Nanomedicine (CIBER-BBN), E-08034 Barcelona, Spain
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3
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Inhibitors of DNA Methylation. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2022; 1389:471-513. [DOI: 10.1007/978-3-031-11454-0_17] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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The antihypertensive drug hydralazine activates the intrinsic pathway of apoptosis and causes DNA damage in leukemic T cells. Oncotarget 2017; 7:21875-86. [PMID: 26942461 PMCID: PMC5008330 DOI: 10.18632/oncotarget.7871] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2015] [Accepted: 02/20/2016] [Indexed: 12/20/2022] Open
Abstract
Epigenetic therapies have emerged as promising anticancer approaches, since epigenetic modifications play a major role in tumor initiation and progression. Hydralazine, an approved vasodilator and antihypertensive drug, has been recently shown to act as a DNA methylation inhibitor. Even though hydralazine is already tested in clinical cancer trials, its mechanism of antitumor action remains undefined. Here, we show that hydralazine induced caspase-dependent apoptotic cell death in human p53-mutant leukemic T cells. Moreover, we demonstrate that hydralazine triggered the mitochondrial pathway of apoptosis by inducing Bak activation and loss of the mitochondrial membrane potential. Hydralazine treatment further resulted in the accumulation of reactive oxygen species, whereas a superoxide dismutase mimetic inhibited hydralazine-induced cell death. Interestingly, caspase-9-deficient Jurkat cells or Bcl-2- and Bcl-xL-overexpressing cells were strongly resistant to hydralazine treatment, thereby demonstrating the dependence of hydralazine-induced apoptosis on the mitochondrial death pathway. Furthermore, we demonstrate that hydralazine treatment triggered DNA damage which might contribute to its antitumor effect.
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Aranda J, Attana F, Tuñón I. Molecular Mechanism of Inhibition of DNA Methylation by Zebularine. ACS Catal 2017. [DOI: 10.1021/acscatal.6b03381] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Affiliation(s)
- Juan Aranda
- Departamento Química
Física, Universitat de València, 46100 Burjassot, Spain
| | - Fedaa Attana
- Departamento Química
Física, Universitat de València, 46100 Burjassot, Spain
| | - Iñaki Tuñón
- Departamento Química
Física, Universitat de València, 46100 Burjassot, Spain
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Lukashevich OV, Cherepanova NA, Jurkovska RZ, Jeltsch A, Gromova ES. Conserved motif VIII of murine DNA methyltransferase Dnmt3a is essential for methylation activity. BMC BIOCHEMISTRY 2016; 17:7. [PMID: 27001594 PMCID: PMC4802922 DOI: 10.1186/s12858-016-0064-y] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/24/2015] [Accepted: 03/02/2016] [Indexed: 11/10/2022]
Abstract
BACKGROUND Dnmt3a is a DNA methyltransferase that establishes de novo DNA methylation in mammals. The structure of the Dnmt3a C-terminal domain is similar to the bacterial M. HhaI enzyme, a well-studied prokaryotic DNA methyltransferase. No X-ray structure is available for the complex of Dnmt3a with DNA and the mechanistic details of DNA recognition and catalysis by mammalian Dnmts are not completely understood. RESULTS Mutant variants of the catalytic domain of the murine Dnmt3a carrying substitutions of highly conserved N167, R200, and R202 have been generated by site directed mutagenesis and purified. Their methylation activity, DNA binding affinity, ability to flip the target cytosine out of the DNA double helix and covalent complex formation with DNA have been examined. Substitutions of N167 lead to reduced catalytic activity and reduced base flipping. Catalytic activity, base flipping, and covalent conjugate formation were almost completely abolished for the mutant enzymes with substitutions of R200 or R202. CONCLUSIONS We conclude that R202 plays a similar role in catalysis in Dnmt3a-CD as R232 in M.SssI and R165 in M.HhaI, which could be positioning of the cytosine for nucleophilic attack by a conserved Cys. R200 of Dnmt3a-CD is important in both catalysis and cytosine flipping. Both conserved R200 and R202 are involved in creating and stabilizing of the transient covalent intermediate of the methylation reaction. N167 might contribute to the positioning of the residues from the motif VI, but does not play a direct role in catalysis.
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Affiliation(s)
- Olga V Lukashevich
- Department of Chemistry, Moscow State University, 119991, Moscow, Russia
| | | | - Renata Z Jurkovska
- BioMedX Innovation Center, Im Neuenheimer Feld 583, 69120, Heidelberg, Germany
| | - Albert Jeltsch
- Institute of Biochemistry, Faculty of Chemistry, University Stuttgart, Pfaffenwaldring 55, 70569, Stuttgart, Germany
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Lopez M, Halby L, Arimondo PB. DNA Methyltransferase Inhibitors: Development and Applications. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2016; 945:431-473. [DOI: 10.1007/978-3-319-43624-1_16] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
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8
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Erdmann A, Halby L, Fahy J, Arimondo PB. Targeting DNA Methylation with Small Molecules: What’s Next? J Med Chem 2014; 58:2569-83. [DOI: 10.1021/jm500843d] [Citation(s) in RCA: 93] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Affiliation(s)
- Alexandre Erdmann
- Epigenetic Targeting of Cancer,
USR3388 ETaC, CNRS-Pierre Fabre, 3 Avenue H. Curien, 31035 Toulouse Cedex 01, France
| | - Ludovic Halby
- Epigenetic Targeting of Cancer,
USR3388 ETaC, CNRS-Pierre Fabre, 3 Avenue H. Curien, 31035 Toulouse Cedex 01, France
| | - Jacques Fahy
- Epigenetic Targeting of Cancer,
USR3388 ETaC, CNRS-Pierre Fabre, 3 Avenue H. Curien, 31035 Toulouse Cedex 01, France
| | - Paola B Arimondo
- Epigenetic Targeting of Cancer,
USR3388 ETaC, CNRS-Pierre Fabre, 3 Avenue H. Curien, 31035 Toulouse Cedex 01, France
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Moon HJ, Redman KL. Trm4 and Nsun2 RNA:m5C Methyltransferases Form Metabolite-Dependent, Covalent Adducts with Previously Methylated RNA. Biochemistry 2014; 53:7132-44. [DOI: 10.1021/bi500882b] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Affiliation(s)
- Haley J. Moon
- Indiana University School of Medicine-Fort Wayne, 2101 Coliseum Boulevard East, Fort Wayne, Indiana 46805, United States
| | - Kent L. Redman
- Indiana University School of Medicine-Fort Wayne, 2101 Coliseum Boulevard East, Fort Wayne, Indiana 46805, United States
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Ebenryter-Olbinska K, Karolak-Wojciechowska J, Sochacka E. Efficient synthesis of 2'-deoxyzebularine and its α-anomer by the silyl method of N-glycosylation. Crystal structures and conformational study in solution. Carbohydr Res 2014; 392:7-15. [PMID: 24814656 DOI: 10.1016/j.carres.2014.03.018] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2014] [Revised: 03/17/2014] [Accepted: 03/18/2014] [Indexed: 10/25/2022]
Abstract
2'-Deoxyzebularine and its α-anomer have been efficiently synthesized with relatively high stereoselectivity by a modified procedure of the silyl method of the N-glycosidic bond formation. An SnCl4-catalyzed condensation of silylated pyrimidin-2-one with 1-α-chloro-3,5-di-O-p-toluoyl-2-deoxy-d-ribofuranose under kinetic control condition (-33°C, 1,2-dichloroethane) led to the mixture of β- and α-anomeric nucleosides in 3:1 ratio. Analogous condensation at +35°C (thermodynamic control conditions) provided mainly p-toluoyl protected α-2'-deoxyzebularine (α:β=4:1), easily separated by crystallization from the anomeric mixture. The structures of both 2'-deoxyzebularine anomers were confirmed by X-ray analysis of the crystals and conformational studies in solution performed using an NMR method.
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Affiliation(s)
| | - Janina Karolak-Wojciechowska
- Institute of General and Ecological Chemistry, Lodz University of Technology, Zeromskiego 116, 90-924 Lodz, Poland
| | - Elzbieta Sochacka
- Institute of Organic Chemistry, Lodz University of Technology, Zeromskiego 116, 90-924 Lodz, Poland.
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11
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Zebularine induces chemosensitization to methotrexate and efficiently decreases AhR gene methylation in childhood acute lymphoblastic leukemia cells. Anticancer Drugs 2014; 25:72-81. [DOI: 10.1097/cad.0000000000000028] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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12
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Gertych A, Oh JH, Wawrowsky KA, Weisenberger DJ, Tajbakhsh J. 3-D DNA methylation phenotypes correlate with cytotoxicity levels in prostate and liver cancer cell models. BMC Pharmacol Toxicol 2013; 14:11. [PMID: 23394161 PMCID: PMC3598242 DOI: 10.1186/2050-6511-14-11] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2012] [Accepted: 01/14/2013] [Indexed: 11/10/2022] Open
Abstract
Background The spatial organization of the genome is being evaluated as a novel indicator of toxicity in conjunction with drug-induced global DNA hypomethylation and concurrent chromatin reorganization. 3D quantitative DNA methylation imaging (3D-qDMI) was applied as a cell-by-cell high-throughput approach to investigate this matter by assessing genome topology through represented immunofluorescent nuclear distribution patterns of 5-methylcytosine (MeC) and global DNA (4,6-diamidino-2-phenylindole = DAPI) in labeled nuclei. Methods Differential progression of global DNA hypomethylation was studied by comparatively dosing zebularine (ZEB) and 5-azacytidine (AZA). Treated and untreated (control) human prostate and liver cancer cells were subjected to confocal scanning microscopy and dedicated 3D image analysis for the following features: differential nuclear MeC/DAPI load and codistribution patterns, cell similarity based on these patterns, and corresponding differences in the topology of low-intensity MeC (LIM) and low in intensity DAPI (LID) sites. Results Both agents generated a high fraction of similar MeC phenotypes across applied concentrations. ZEB exerted similar effects at 10–100-fold higher drug concentrations than its AZA analogue: concentration-dependent progression of global cytosine demethylation, validated by measuring differential MeC levels in repeat sequences using MethyLight, and the concurrent increase in nuclear LIM densities correlated with cellular growth reduction and cytotoxicity. Conclusions 3D-qDMI demonstrated the capability of quantitating dose-dependent drug-induced spatial progression of DNA demethylation in cell nuclei, independent from interphase cell-cycle stages and in conjunction with cytotoxicity. The results support the notion of DNA methylation topology being considered as a potential indicator of causal impacts on chromatin distribution with a conceivable application in epigenetic drug toxicology.
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Affiliation(s)
- Arkadiusz Gertych
- Translational Cytomics Group, Department of Surgery, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
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Biergans SD, Jones JC, Treiber N, Galizia CG, Szyszka P. DNA methylation mediates the discriminatory power of associative long-term memory in honeybees. PLoS One 2012; 7:e39349. [PMID: 22724000 PMCID: PMC3377632 DOI: 10.1371/journal.pone.0039349] [Citation(s) in RCA: 59] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2012] [Accepted: 05/23/2012] [Indexed: 12/30/2022] Open
Abstract
Memory is created by several interlinked processes in the brain, some of which require long-term gene regulation. Epigenetic mechanisms are likely candidates for regulating memory-related genes. Among these, DNA methylation is known to be a long lasting genomic mark and may be involved in the establishment of long-term memory. Here we demonstrate that DNA methyltransferases, which induce and maintain DNA methylation, are involved in a particular aspect of associative long-term memory formation in honeybees, but are not required for short-term memory formation. While long-term memory strength itself was not affected by blocking DNA methyltransferases, odor specificity of the memory (memory discriminatory power) was. Conversely, perceptual discriminatory power was normal. These results suggest that different genetic pathways are involved in mediating the strength and discriminatory power of associative odor memories and provide, to our knowledge, the first indication that DNA methyltransferases are involved in stimulus-specific associative long-term memory formation.
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Martinet N, Michel BY, Bertrand P, Benhida R. Small molecules DNAmethyltransferasesinhibitors. MEDCHEMCOMM 2012. [DOI: 10.1039/c1md00194a] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/16/2022]
Abstract
This review describes current knowledge concerning DNA methyltransferases (DNMT) biology and the two main classes of DNMT inhibtors.
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Affiliation(s)
- Nadine Martinet
- Laboratoire de Chimie des Molécules Bioactives et des Arômes
- UMR 6001 CNRS
- Institut de Chimie de Nice
- Université de Nice-Sophia Antipolis
- 06108 Nice Cedex 2
| | - Benoît Y. Michel
- Laboratoire de Chimie des Molécules Bioactives et des Arômes
- UMR 6001 CNRS
- Institut de Chimie de Nice
- Université de Nice-Sophia Antipolis
- 06108 Nice Cedex 2
| | - Philippe Bertrand
- Laboratory of reactivity and synthesis of natural substances
- UMR 6514 Poitiers
- France
| | - Rachid Benhida
- Laboratoire de Chimie des Molécules Bioactives et des Arômes
- UMR 6001 CNRS
- Institut de Chimie de Nice
- Université de Nice-Sophia Antipolis
- 06108 Nice Cedex 2
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Ruiz-Magaña MJ, Rodríguez-Vargas JM, Morales JC, Saldivia MA, Schulze-Osthoff K, Ruiz-Ruiz C. The DNA methyltransferase inhibitors zebularine and decitabine induce mitochondria-mediated apoptosis and DNA damage in p53 mutant leukemic T cells. Int J Cancer 2011; 130:1195-207. [PMID: 21455989 DOI: 10.1002/ijc.26107] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2010] [Accepted: 03/15/2011] [Indexed: 12/23/2022]
Abstract
DNA methyltransferase (DNMT)-inhibiting nucleoside analogs reactivate the expression of tumor suppressor genes and apoptosis-related genes silenced by methylation, thus favoring the induction of apoptosis in tumor cells. Moreover, induction of DNA damage seems to contribute to their antitumor effect. However, the apoptotic signaling pathway induced by these demethylating drugs is not well understood. Here, we have investigated the induction of apoptosis by two nucleoside DNMT inhibitors, decitabine and zebularine, in leukemic T cells. Both inhibitors induced caspase-dependent apoptosis in Jurkat, CEM-6 and MOLT-4 leukemia T cell lines, all with mutant p53, whereas resting and activated normal T lymphocytes were highly resistant to these demethylating agents. Although decitabine and zebularine showed different ability to induce apoptosis and cell cycle arrest among the three cell lines, they similarly activated the intrinsic apoptotic pathway by inducing mitochondrial alterations such as Bak activation, loss of transmembrane potential and generation of reactive oxygen species (ROS). Accordingly, Bcl-2- and Bcl-x(L) -overexpressing Jurkat cells, as well as caspase-9-deficient Jurkat cells, were resistant to apoptosis induced by decitabine and zebularine. Interestingly, ROS production seemed to be necessary for the induction of apoptosis. Apoptotic events, such as Bak and caspase activation, started as soon as 20 hr after treatment with either decitabine or zebularine. In addition, progression of apoptosis triggered by both DNMT inhibitors was paralleled by the induction of DNA damage. Our results suggest that the mitochondrial apoptotic pathway activated by decitabine and zebularine in p53 mutant leukemic T cells depends mainly on the induction of DNA damage.
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Andersen JB, Factor VM, Marquardt JU, Raggi C, Lee YH, Seo D, Conner EA, Thorgeirsson SS. An integrated genomic and epigenomic approach predicts therapeutic response to zebularine in human liver cancer. Sci Transl Med 2011; 2:54ra77. [PMID: 20962331 DOI: 10.1126/scitranslmed.3001338] [Citation(s) in RCA: 80] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Epigenomic changes such as aberrant hypermethylation and subsequent atypical gene silencing are characteristic features of human cancer. Here, we report a comprehensive characterization of epigenomic modulation caused by zebularine, an effective DNA methylation inhibitor, in human liver cancer. Using transcriptomic and epigenomic profiling, we identified a zebularine response signature that classified liver cancer cell lines into two major subtypes with different drug responses. In drug-sensitive cell lines, zebularine caused inhibition of proliferation coupled with increased apoptosis, whereas drug-resistant cell lines showed up-regulation of oncogenic networks (for example, E2F1, MYC, and TNF) that drive liver cancer growth in vitro and in preclinical mouse models. Assessment of zebularine-based therapy in xenograft mouse models demonstrated potent therapeutic effects against tumors established from zebularine-sensitive but not zebularine-resistant liver cancer cells, leading to increased survival and decreased pulmonary metastasis. Integration of the zebularine gene expression and demethylation response signatures allowed differentiation of patients with hepatocellular carcinoma according to their survival and disease recurrence. This integrated signature identified a subclass of patients within the poor-survivor group that is likely to benefit from therapeutic agents that target the cancer epigenome.
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Affiliation(s)
- Jesper B Andersen
- Laboratory of Experimental Carcinogenesis, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892-4262, USA
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Cherepanova NA, Zhuze AL, Gromova ES. Inhibition of murine DNA methyltransferase Dnmt3a by DNA duplexes containing pyrimidine-2(1H)-one. BIOCHEMISTRY (MOSCOW) 2010; 75:1115-25. [DOI: 10.1134/s000629791009004x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
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Champion C, Guianvarc'h D, Sénamaud-Beaufort C, Jurkowska RZ, Jeltsch A, Ponger L, Arimondo PB, Guieysse-Peugeot AL. Mechanistic insights on the inhibition of c5 DNA methyltransferases by zebularine. PLoS One 2010; 5:e12388. [PMID: 20808780 PMCID: PMC2927531 DOI: 10.1371/journal.pone.0012388] [Citation(s) in RCA: 83] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2010] [Accepted: 07/03/2010] [Indexed: 12/22/2022] Open
Abstract
In mammals DNA methylation occurs at position 5 of cytosine in a CpG context and regulates gene expression. It plays an important role in diseases and inhibitors of DNA methyltransferases (DNMTs)—the enzymes responsible for DNA methylation—are used in clinics for cancer therapy. The most potent inhibitors are 5-azacytidine and 5-azadeoxycytidine. Zebularine (1-(β-D-ribofuranosyl)-2(1H)- pyrimidinone) is another cytidine analog described as a potent inhibitor that acts by forming a covalent complex with DNMT when incorporated into DNA. Here we bring additional experiments to explain its mechanism of action. First, we observe an increase in the DNA binding when zebularine is incorporated into the DNA, compared to deoxycytidine and 5-fluorodeoxycytidine, together with a strong decrease in the dissociation rate. Second, we show by denaturing gel analysis that the intermediate covalent complex between the enzyme and the DNA is reversible, differing thus from 5-fluorodeoxycytidine. Third, no methylation reaction occurs when zebularine is present in the DNA. We confirm that zebularine exerts its demethylation activity by stabilizing the binding of DNMTs to DNA, hindering the methylation and decreasing the dissociation, thereby trapping the enzyme and preventing turnover even at other sites.
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Affiliation(s)
| | - Dominique Guianvarc'h
- Laboratoire des Biomolécules, UPMC Université Paris 06, CNRS, ENS, FR, Paris, France
| | | | - Renata Z. Jurkowska
- Jacobs University Bremen, School of Engineering and Science, Bremen, Germany
| | - Albert Jeltsch
- Jacobs University Bremen, School of Engineering and Science, Bremen, Germany
| | - Loïc Ponger
- MNHN CNRS UMR7196, Paris, France
- INSERM U565, Paris, France
| | - Paola B. Arimondo
- MNHN CNRS UMR7196, Paris, France
- INSERM U565, Paris, France
- * E-mail: (PBA); (ALGP)
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