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Wang S, Liu T, Ren C, Zhao Y, Qiao S, Zhang Y, Pang S. Heterogeneous graph inference with range constrainted L 2,1-collaborative matrix factorization for small molecule-miRNA association prediction. Comput Biol Chem 2024; 110:108078. [PMID: 38677013 DOI: 10.1016/j.compbiolchem.2024.108078] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2024] [Revised: 04/03/2024] [Accepted: 04/16/2024] [Indexed: 04/29/2024]
Abstract
MicroRNAs (miRNAs) play a vital role in regulating gene expression and various biological processes. As a result, they have been identified as effective targets for small molecule (SM) drugs in disease treatment. Heterogeneous graph inference stands as a classical approach for predicting SM-miRNA associations, showcasing commendable convergence accuracy and speed. However, most existing methods do not adequately address the inherent sparsity in SM-miRNA association networks, and imprecise SM/miRNA similarity metrics reduce the accuracy of predicting SM-miRNA associations. In this research, we proposed a heterogeneous graph inference with range constrained L2,1-collaborative matrix factorization (HGIRCLMF) method to predict potential SM-miRNA associations. First, we computed the multi-source similarities of SM/miRNA and integrated these similarity information into a comprehensive SM/miRNA similarity. This step improved the accuracy of SM and miRNA similarity, ensuring reliability for the subsequent inference of the heterogeneity map. Second, we used a range constrained L2,1-collaborative matrix factorization (RCLMF) model to pre-populate the SM-miRNA association matrix with missing values. In this step, we developed a novel matrix decomposition method that enhances the robustness and formative nature of SM-miRNA edges between SM networks and miRNA networks. Next, we built a well-established SM-miRNA heterogeneous network utilizing the processed biological information. Finally, HGIRCLMF used this network data to infer unknown association pair scores. We implemented four cross-validation experiments on two distinct datasets, and HGIRCLMF acquired the highest areas under the curve, surpassing six state-of-the-art computational approaches. Furthermore, we performed three case studies to validate the predictive power of our method in practical application.
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Affiliation(s)
- Shudong Wang
- College of Computer Science and Technology, Qingdao Institute of Software, China University of Petroleum, Qingdao 266580, China
| | - Tiyao Liu
- College of Computer Science and Technology, Qingdao Institute of Software, China University of Petroleum, Qingdao 266580, China
| | - Chuanru Ren
- College of Computer Science and Technology, Qingdao Institute of Software, China University of Petroleum, Qingdao 266580, China
| | - Yawu Zhao
- College of Computer Science and Technology, Qingdao Institute of Software, China University of Petroleum, Qingdao 266580, China
| | - Sibo Qiao
- College of Computer Science and Technology, Qingdao Institute of Software, China University of Petroleum, Qingdao 266580, China
| | - Yuanyuan Zhang
- School of Information and Control Engineering, Qingdao University of Technology, Qingdao 266525, China.
| | - Shanchen Pang
- College of Computer Science and Technology, Qingdao Institute of Software, China University of Petroleum, Qingdao 266580, China
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Lai J, Liang J, Zhang Y, Zhang B, Wei J, Fan J, Chen L, Chen Z, Li Q, Guo D, Lin J, Chen Q. A drug-delivery depot for epigenetic modulation and enhanced cancer immunotherapy. Biomed Pharmacother 2023; 168:115687. [PMID: 37837882 DOI: 10.1016/j.biopha.2023.115687] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2023] [Revised: 10/02/2023] [Accepted: 10/09/2023] [Indexed: 10/16/2023] Open
Abstract
DNA methyltransferase inhibitors (DNMTis) have found widespread application in the management of cancer. Zebularine (Zeb), functioning as a demethylating agent, has exhibited notable advantages and enhanced therapeutic efficacy in the realm of tumour immunotherapy. Nevertheless, due to its lack of targeted functionality, standalone Zeb therapy necessitates the administration of a substantially higher dosage. In this investigation, we have devised an innovative nanodrug formulation, comprising the DNA methyltransferase inhibitor Zeb and pH-responsive chitosan (CS), hereinafter referred to as CS-Zeb nanoparticles (NPs). Our findings have unveiled that CS-Zeb NPs manifest heightened drug release within an acidic milieu (pH 5.5) in comparison to a neutral environment (pH 7.4). Furthermore, in vivo studies have conclusively affirmed that, in contrast to equivalent quantities of Zeb in isolation, the nanocomplex significantly curtailed tumour burden and protracted the survival duration of the B16F10 tumour-bearing murine model. Additionally, CS-Zeb NPs elicited an augmentation of CD8+ T cells within the peripheral circulation of mice and tumour-infiltrating lymphocytes (TILs). Notably, the dosage of CS-Zeb NPs was reduced by a remarkable 70-fold when juxtaposed with Zeb administered in isolation. To summarise, our study underscores the potential of CS-Zeb NPs as an alternative chemotherapeutic agent for cancer treatment.
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Affiliation(s)
- Junzhong Lai
- The Cancer Center, Fujian Medical University Union Hospital, Fuzhou, Fujian 350001, PR China
| | - Jiadi Liang
- Fujian Key Laboratory of Innate Immune Biology, Biomedical Research Center of South China, Fujian Normal University, Fuzhou, Fujian 350117, PR China
| | - Yong Zhang
- Fujian Key Laboratory of Innate Immune Biology, Biomedical Research Center of South China, Fujian Normal University, Fuzhou, Fujian 350117, PR China
| | - Bingchen Zhang
- Department of Oncology, Affiliated Dongguan Hospital, Southern Medical University, Dongguan, Guangdong 523058, PR China
| | - Jianhui Wei
- Fujian Key Laboratory of Innate Immune Biology, Biomedical Research Center of South China, Fujian Normal University, Fuzhou, Fujian 350117, PR China
| | - Jiqiang Fan
- Fujian Key Laboratory of Innate Immune Biology, Biomedical Research Center of South China, Fujian Normal University, Fuzhou, Fujian 350117, PR China
| | - Linqin Chen
- Fujian Key Laboratory of Innate Immune Biology, Biomedical Research Center of South China, Fujian Normal University, Fuzhou, Fujian 350117, PR China
| | - Zhirong Chen
- Fujian Key Laboratory of Innate Immune Biology, Biomedical Research Center of South China, Fujian Normal University, Fuzhou, Fujian 350117, PR China
| | - Qiumei Li
- Fujian Key Laboratory of Innate Immune Biology, Biomedical Research Center of South China, Fujian Normal University, Fuzhou, Fujian 350117, PR China
| | - Dong Guo
- Fujian Key Laboratory of Innate Immune Biology, Biomedical Research Center of South China, Fujian Normal University, Fuzhou, Fujian 350117, PR China
| | - Jizhen Lin
- The Cancer Center, Fujian Medical University Union Hospital, Fuzhou, Fujian 350001, PR China.
| | - Qi Chen
- Fujian Key Laboratory of Innate Immune Biology, Biomedical Research Center of South China, Fujian Normal University, Fuzhou, Fujian 350117, PR China.
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3
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Lyu SY, Xiao W, Cui GZ, Yu C, Liu H, Lyu M, Kuang QY, Xiao EH, Luo YH. Role and mechanism of DNA methylation and its inhibitors in hepatic fibrosis. Front Genet 2023; 14:1124330. [PMID: 37056286 PMCID: PMC10086238 DOI: 10.3389/fgene.2023.1124330] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2022] [Accepted: 03/15/2023] [Indexed: 03/30/2023] Open
Abstract
Liver fibrosis is a repair response to injury caused by various chronic stimuli that continually act on the liver. Among them, the activation of hepatic stellate cells (HSCs) and their transformation into a myofibroblast phenotype is a key event leading to liver fibrosis, however the mechanism has not yet been elucidated. The molecular basis of HSC activation involves changes in the regulation of gene expression without changes in the genome sequence, namely, via epigenetic regulation. DNA methylation is a key focus of epigenetic research, as it affects the expression of fibrosis-related, metabolism-related, and tumor suppressor genes. Increasing studies have shown that DNA methylation is closely related to several physiological and pathological processes including HSC activation and liver fibrosis. This review aimed to discuss the mechanism of DNA methylation in the pathogenesis of liver fibrosis, explore DNA methylation inhibitors as potential therapies for liver fibrosis, and provide new insights on the prevention and clinical treatment of liver fibrosis.
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Affiliation(s)
- Shi-Yi Lyu
- Department of Radiology, The Second Xiangya Hospital, Central-South University, Changsha, Hunan, China
| | - Wang Xiao
- Department of Gastrointestinal Surgery, The Second Xiangya Hospital, Central-South University, Changsha, Hunan, China
| | - Guang-Zu Cui
- XiangYa School of Medicine, Central South University, Changsha, Hunan, China
| | - Cheng Yu
- Department of Radiology, The Second Xiangya Hospital, Central-South University, Changsha, Hunan, China
| | - Huan Liu
- Department of Radiology, The Second Xiangya Hospital, Central-South University, Changsha, Hunan, China
| | - Min Lyu
- Department of Radiology, The Second Xiangya Hospital, Central-South University, Changsha, Hunan, China
| | - Qian-Ya Kuang
- Department of Radiology, The Second Xiangya Hospital, Central-South University, Changsha, Hunan, China
| | - En-Hua Xiao
- Department of Radiology, The Second Xiangya Hospital, Central-South University, Changsha, Hunan, China
| | - Yong-Heng Luo
- Department of Radiology, The Second Xiangya Hospital, Central-South University, Changsha, Hunan, China
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Sass P, Sosnowski P, Kamińska J, Deptuła M, Skoniecka A, Zieliński J, Rodziewicz-Motowidło S, Pikuła M, Sachadyn P. Examination of epigenetic inhibitor zebularine in treatment of skin wounds in healthy and diabetic mice. J Tissue Eng Regen Med 2022; 16:1238-1248. [PMID: 36350668 PMCID: PMC10099879 DOI: 10.1002/term.3365] [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: 04/12/2022] [Revised: 10/11/2022] [Accepted: 10/28/2022] [Indexed: 11/11/2022]
Abstract
DNA methyltransferase inhibitor zebularine was proven to induce regeneration in the ear pinna in mice. We utilized a dorsal skin wound model to further evaluate this epigenetic inhibitor in wound healing. Full-thickness excisional wounds were made on the dorsum of 2 and 10-month-old healthy BALB/c and 3 and 8-month-old diabetic (db/db) mice, followed by topical or intraperitoneal zebularine delivery. Depending on the strain, age, dose, and delivery, the zebularine treatments either had no effect or accelerated or delayed wound closure. In principle, zebularine applied topically moderately promoted wound closure in the healthy but markedly delayed in the diabetic mice, which was in line with decreased viability of cultured keratinocytes from diabetic patients exposed to zebularine. The histological analysis revealed an improvement in the architecture of restored skin in zebularine-treated mice, manifested as a distinct layered pattern resembling panniculus carnosus. The finding corresponds with the zebularine-mediated activation of the Wnt5a gene, an essential regulator of Wnt signaling, the pathway involved in hair follicle development, the process which in turn is connected with regenerative skin healing. Although zebularine did not remarkably accelerate wound healing, zebularine and other epigenetic inhibitors deserve further testing as potential drugs to improve the quality of restored skin.
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Affiliation(s)
- Piotr Sass
- Laboratory for Regenerative Biotechnology, Gdańsk University of Technology, Gdańsk, Poland
| | - Paweł Sosnowski
- Laboratory for Regenerative Biotechnology, Gdańsk University of Technology, Gdańsk, Poland
| | - Jolanta Kamińska
- Laboratory for Regenerative Biotechnology, Gdańsk University of Technology, Gdańsk, Poland
| | - Milena Deptuła
- Laboratory of Tissue Engineering and Regenerative Medicine, Division of Embryology, Medical University of Gdańsk, Gdańsk, Poland
| | - Aneta Skoniecka
- Laboratory of Tissue Engineering and Regenerative Medicine, Division of Embryology, Medical University of Gdańsk, Gdańsk, Poland
| | - Jacek Zieliński
- Department of Oncologic Surgery, Medical University of Gdańsk, Gdańsk, Poland
| | | | - Michał Pikuła
- Laboratory of Tissue Engineering and Regenerative Medicine, Division of Embryology, Medical University of Gdańsk, Gdańsk, Poland
| | - Paweł Sachadyn
- Laboratory for Regenerative Biotechnology, Gdańsk University of Technology, Gdańsk, Poland
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Kong J, Garcia V, Zehraoui E, Stammitti L, Hilbert G, Renaud C, Maury S, Delaunay A, Cluzet S, Lecourieux F, Lecourieux D, Teyssier E, Gallusci P. Zebularine, a DNA Methylation Inhibitor, Activates Anthocyanin Accumulation in Grapevine Cells. Genes (Basel) 2022; 13:genes13071256. [PMID: 35886036 PMCID: PMC9316115 DOI: 10.3390/genes13071256] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2022] [Revised: 07/07/2022] [Accepted: 07/12/2022] [Indexed: 02/01/2023] Open
Abstract
Through its role in the regulation of gene expression, DNA methylation can participate in the control of specialized metabolite production. We have investigated the link between DNA methylation and anthocyanin accumulation in grapevine using the hypomethylating drug, zebularine and Gamay Teinturier cell suspensions. In this model, zebularine increased anthocyanin accumulation in the light, and induced its production in the dark. To unravel the underlying mechanisms, cell transcriptome, metabolic content, and DNA methylation were analyzed. The up-regulation of stress-related genes, as well as a decrease in cell viability, revealed that zebularine affected cell integrity. Concomitantly, the global DNA methylation level was only slightly decreased in the light and not modified in the dark. However, locus-specific analyses demonstrated a decrease in DNA methylation at a few selected loci, including a CACTA DNA transposon and a small region upstream from the UFGT gene, coding for the UDP glucose:flavonoid-3-O-glucosyltransferase, known to be critical for anthocyanin biosynthesis. Moreover, this decrease was correlated with an increase in UFGT expression and in anthocyanin content. In conclusion, our data suggest that UFGT expression could be regulated through DNA methylation in Gamay Teinturier, although the functional link between changes in DNA methylation and UFGT transcription still needs to be demonstrated.
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Affiliation(s)
- Junhua Kong
- UMR Ecophysiologie et Génomique Fonctionnelle de la Vigne, Université de Bordeaux, INRAE, Bordeaux Science Agro, 210 Chemin de Leysotte—33140 Villenave d’Ornon, France; (J.K.); (V.G.); (E.Z.); (L.S.); (G.H.); (C.R.); (F.L.); (D.L.); (P.G.)
| | - Virginie Garcia
- UMR Ecophysiologie et Génomique Fonctionnelle de la Vigne, Université de Bordeaux, INRAE, Bordeaux Science Agro, 210 Chemin de Leysotte—33140 Villenave d’Ornon, France; (J.K.); (V.G.); (E.Z.); (L.S.); (G.H.); (C.R.); (F.L.); (D.L.); (P.G.)
| | - Enric Zehraoui
- UMR Ecophysiologie et Génomique Fonctionnelle de la Vigne, Université de Bordeaux, INRAE, Bordeaux Science Agro, 210 Chemin de Leysotte—33140 Villenave d’Ornon, France; (J.K.); (V.G.); (E.Z.); (L.S.); (G.H.); (C.R.); (F.L.); (D.L.); (P.G.)
| | - Linda Stammitti
- UMR Ecophysiologie et Génomique Fonctionnelle de la Vigne, Université de Bordeaux, INRAE, Bordeaux Science Agro, 210 Chemin de Leysotte—33140 Villenave d’Ornon, France; (J.K.); (V.G.); (E.Z.); (L.S.); (G.H.); (C.R.); (F.L.); (D.L.); (P.G.)
| | - Ghislaine Hilbert
- UMR Ecophysiologie et Génomique Fonctionnelle de la Vigne, Université de Bordeaux, INRAE, Bordeaux Science Agro, 210 Chemin de Leysotte—33140 Villenave d’Ornon, France; (J.K.); (V.G.); (E.Z.); (L.S.); (G.H.); (C.R.); (F.L.); (D.L.); (P.G.)
| | - Christel Renaud
- UMR Ecophysiologie et Génomique Fonctionnelle de la Vigne, Université de Bordeaux, INRAE, Bordeaux Science Agro, 210 Chemin de Leysotte—33140 Villenave d’Ornon, France; (J.K.); (V.G.); (E.Z.); (L.S.); (G.H.); (C.R.); (F.L.); (D.L.); (P.G.)
| | - Stéphane Maury
- INRAe, EA1207 USC1328 Laboratoire de Biologie des Ligneux et des Grandes Cultures, Université d’Orléans, 45067 Orléans, France; (S.M.); (A.D.)
| | - Alain Delaunay
- INRAe, EA1207 USC1328 Laboratoire de Biologie des Ligneux et des Grandes Cultures, Université d’Orléans, 45067 Orléans, France; (S.M.); (A.D.)
| | - Stéphanie Cluzet
- Unité de Recherche Oenologie, Faculté des Sciences Pharmaceutiques, University Bordeaux, EA4577, USC 1366 INRA, Equipe Molécules d’Intérêt Biologique (GESVAB), ISVV, CEDEX, 33882 Villenave d’Ornon, France;
| | - Fatma Lecourieux
- UMR Ecophysiologie et Génomique Fonctionnelle de la Vigne, Université de Bordeaux, INRAE, Bordeaux Science Agro, 210 Chemin de Leysotte—33140 Villenave d’Ornon, France; (J.K.); (V.G.); (E.Z.); (L.S.); (G.H.); (C.R.); (F.L.); (D.L.); (P.G.)
| | - David Lecourieux
- UMR Ecophysiologie et Génomique Fonctionnelle de la Vigne, Université de Bordeaux, INRAE, Bordeaux Science Agro, 210 Chemin de Leysotte—33140 Villenave d’Ornon, France; (J.K.); (V.G.); (E.Z.); (L.S.); (G.H.); (C.R.); (F.L.); (D.L.); (P.G.)
| | - Emeline Teyssier
- UMR Ecophysiologie et Génomique Fonctionnelle de la Vigne, Université de Bordeaux, INRAE, Bordeaux Science Agro, 210 Chemin de Leysotte—33140 Villenave d’Ornon, France; (J.K.); (V.G.); (E.Z.); (L.S.); (G.H.); (C.R.); (F.L.); (D.L.); (P.G.)
- Correspondence: ; Tel.: +33-5-5757-5928
| | - Philippe Gallusci
- UMR Ecophysiologie et Génomique Fonctionnelle de la Vigne, Université de Bordeaux, INRAE, Bordeaux Science Agro, 210 Chemin de Leysotte—33140 Villenave d’Ornon, France; (J.K.); (V.G.); (E.Z.); (L.S.); (G.H.); (C.R.); (F.L.); (D.L.); (P.G.)
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Sosnowski P, Sass P, Słonimska P, Płatek R, Kamińska J, Baczyński Keller J, Mucha P, Peszyńska-Sularz G, Czupryn A, Pikuła M, Piotrowski A, Janus Ł, Rodziewicz-Motowidło S, Skowron P, Sachadyn P. Regenerative Drug Discovery Using Ear Pinna Punch Wound Model in Mice. Pharmaceuticals (Basel) 2022; 15:ph15050610. [PMID: 35631437 PMCID: PMC9145447 DOI: 10.3390/ph15050610] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2022] [Revised: 05/04/2022] [Accepted: 05/06/2022] [Indexed: 01/25/2023] Open
Abstract
The ear pinna is a complex tissue consisting of the dermis, cartilage, muscles, vessels, and nerves. Ear pinna healing is a model of regeneration in mammals. In some mammals, including rabbits, punch wounds in the ear pinna close spontaneously; in common-use laboratory mice, they remain for life. Agents inducing ear pinna healing are potential regenerative drugs. We tested the effects of selected bioactive agents on 2 mm ear pinna wound closure in BALB/c mice. Our previous research demonstrated that a DNA methyltransferase inhibitor, zebularine, remarkably induced ear pinna regeneration. Although experiments with two other demethylating agents, RG108 and hydralazine, were unsuccessful, a histone deacetylase inhibitor, valproic acid, was another epigenetic agent found to increase ear hole closure. In addition, we identified a pro-regenerative activity of 4-ketoretinoic acid, a retinoic acid metabolite. Attempts to counteract the regenerative effects of the demethylating agent zebularine, with folates as methyl donors, failed. Surprisingly, a high dose of methionine, another methyl donor, promoted ear hole closure. Moreover, we showed that the regenerated areas of ear pinna were supplied with nerve fibre networks and blood vessels. The ear punch model proved helpful in testing the pro-regenerative activities of small-molecule compounds and observations of peripheral nerve regeneration.
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Affiliation(s)
- Paweł Sosnowski
- Laboratory for Regenerative Biotechnology, Gdańsk University of Technology, 80-233 Gdańsk, Poland; (P.S.); (P.S.); (P.S.); (R.P.); (J.K.); (J.B.K.)
| | - Piotr Sass
- Laboratory for Regenerative Biotechnology, Gdańsk University of Technology, 80-233 Gdańsk, Poland; (P.S.); (P.S.); (P.S.); (R.P.); (J.K.); (J.B.K.)
| | - Paulina Słonimska
- Laboratory for Regenerative Biotechnology, Gdańsk University of Technology, 80-233 Gdańsk, Poland; (P.S.); (P.S.); (P.S.); (R.P.); (J.K.); (J.B.K.)
| | - Rafał Płatek
- Laboratory for Regenerative Biotechnology, Gdańsk University of Technology, 80-233 Gdańsk, Poland; (P.S.); (P.S.); (P.S.); (R.P.); (J.K.); (J.B.K.)
| | - Jolanta Kamińska
- Laboratory for Regenerative Biotechnology, Gdańsk University of Technology, 80-233 Gdańsk, Poland; (P.S.); (P.S.); (P.S.); (R.P.); (J.K.); (J.B.K.)
| | - Jakub Baczyński Keller
- Laboratory for Regenerative Biotechnology, Gdańsk University of Technology, 80-233 Gdańsk, Poland; (P.S.); (P.S.); (P.S.); (R.P.); (J.K.); (J.B.K.)
| | - Piotr Mucha
- Department of Molecular Biochemistry, Faculty of Chemistry, University of Gdańsk, 80-308 Gdańsk, Poland;
| | - Grażyna Peszyńska-Sularz
- Tri-City University Animal House—Research Service Centre, Medical University of Gdańsk, 80-211 Gdańsk, Poland;
| | - Artur Czupryn
- Laboratory of Neurobiology, Nencki Institute of Experimental Biology PAS, 02-093 Warsaw, Poland;
| | - Michał Pikuła
- Laboratory of Tissue Engineering and Regenerative Medicine, Department of Embryology, Medical University of Gdańsk, 80-211 Gdańsk, Poland;
| | - Arkadiusz Piotrowski
- Department of Biology and Pharmaceutical Botany, Faculty of Pharmacy, Medical University of Gdańsk, 80-416 Gdańsk, Poland;
| | | | | | - Piotr Skowron
- Department of Molecular Biotechnology, Faculty of Chemistry, University of Gdańsk, 80-308 Gdańsk, Poland;
| | - Paweł Sachadyn
- Laboratory for Regenerative Biotechnology, Gdańsk University of Technology, 80-233 Gdańsk, Poland; (P.S.); (P.S.); (P.S.); (R.P.); (J.K.); (J.B.K.)
- Correspondence:
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Prochazkova K, Finke A, Tomaštíková ED, Filo J, Bente H, Dvořák P, Ovečka M, Šamaj J, Pecinka A. Zebularine induces enzymatic DNA-protein crosslinks in 45S rDNA heterochromatin of Arabidopsis nuclei. Nucleic Acids Res 2021; 50:244-258. [PMID: 34904670 PMCID: PMC8754632 DOI: 10.1093/nar/gkab1218] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2021] [Accepted: 12/01/2021] [Indexed: 11/14/2022] Open
Abstract
Loss of genome stability leads to reduced fitness, fertility and a high mutation rate. Therefore, the genome is guarded by the pathways monitoring its integrity and neutralizing DNA lesions. To analyze the mechanism of DNA damage induction by cytidine analog zebularine, we performed a forward-directed suppressor genetic screen in the background of Arabidopsis thaliana zebularine-hypersensitive structural maintenance of chromosomes 6b (smc6b) mutant. We show that smc6b hypersensitivity was suppressed by the mutations in EQUILIBRATIVE NUCLEOSIDE TRANSPORTER 3 (ENT3), DNA METHYLTRANSFERASE 1 (MET1) and DECREASE IN DNA METHYLATION 1 (DDM1). Superior resistance of ent3 plants to zebularine indicated that ENT3 is likely necessary for the import of the drug to the cells. Identification of MET1 and DDM1 suggested that zebularine induces DNA damage by interference with the maintenance of CG DNA methylation. The same holds for structurally similar compounds 5-azacytidine and 2-deoxy-5-azacytidine. Based on our genetic and biochemical data, we propose that zebularine induces enzymatic DNA–protein crosslinks (DPCs) of MET1 and zebularine-containing DNA in Arabidopsis, which was confirmed by native chromatin immunoprecipitation experiments. Moreover, zebularine-induced DPCs accumulate preferentially in 45S rDNA chromocenters in a DDM1-dependent manner. These findings open a new avenue for studying genome stability and DPC repair in plants.
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Affiliation(s)
| | | | - Eva Dvořák Tomaštíková
- Institute of Experimental Botany, The Czech Academy of Sciences, Centre of the Region Haná for Biotechnological and Agricultural Research, Šlechtitelů 31, 77900 Olomouc, Czech Republic
| | - Jaroslav Filo
- Institute of Experimental Botany, The Czech Academy of Sciences, Centre of the Region Haná for Biotechnological and Agricultural Research, Šlechtitelů 31, 77900 Olomouc, Czech Republic
| | - Heinrich Bente
- Max Planck Institute for Plant Breeding Research, Carl-von-Linné-Weg 10, 50829 Cologne, Germany
| | - Petr Dvořák
- Department of Botany, Faculty of Science, Palacký University Olomouc, Šlechtitelů 27, 78371 Olomouc, Czech Republic
| | - Miroslav Ovečka
- Department of Cell Biology, Centre of the Region Haná for Biotechnological and Agricultural Research, Faculty of Science, Palacký University Olomouc, Šlechtitelů 27, 78371 Olomouc, Czech Republic
| | - Jozef Šamaj
- Department of Cell Biology, Centre of the Region Haná for Biotechnological and Agricultural Research, Faculty of Science, Palacký University Olomouc, Šlechtitelů 27, 78371 Olomouc, Czech Republic
| | - Ales Pecinka
- To whom correspondence should be addressed. Tel: +420 585 238 709;
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Parker WB, Thottassery JV. 5-Aza-4'-thio-2'-deoxycytidine, a new orally bioavailable non-toxic "best-in-class" DNMT1 depleting agent in clinical development. J Pharmacol Exp Ther 2021; 379:211-222. [PMID: 34503994 DOI: 10.1124/jpet.121.000758] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2021] [Accepted: 09/01/2021] [Indexed: 11/22/2022] Open
Abstract
DNA methyltransferase 1 (DNMT1) is an enzyme that functions as a maintenance methyltransferase during DNA replication, and depletion of this enzyme from cells is considered to be a rational goal in DNA methylation dependent disorders. Two DNMT1 depleting agents aza-dCyd (5-aza-2'-deoxycytidine, decitabine) and aza-Cyd (5-aza-cytidine, azacitidine) are currently used for the treatment of myelodysplastic syndromes and acute myeloid leukemia, and have also been investigated for non-oncology indications such as sickle cell disease. However, these agents have several off-target activities leading to significant toxicities that limit dosing and duration of treatment. Development of more selective inhibitors of DNMT1 could therefore afford treatment for long durations at effective doses. We have discovered that 5-aza-4'-thio-2'-deoxycytidine (aza-T-dCyd) is as effective as aza-dCyd in depleting DNMT1 in mouse tumor models, but with markedly low toxicity. In this review we describe the preclinical studies that led to the development of aza-T-dCyd as a superior DNMT1 depleting agent with respect to aza-dCyd, and will describe its pharmacology, metabolism, and mechanism of action. In an effort to understand why aza-T-dCyd is a more selective DNMT1 depleting agent than aza-dCyd, we will also compare and contrast the activities of these two agents. Significance Statement Aza-T-dCyd is a potent DNMT1 depleting agent. Although similar in structure to decitabine (aza-dCyd) its metabolism and mechanism of action is different than that of aza-dCyd, resulting in less off target activity and less toxicity. The larger therapeutic index of aza-T-dCyd (DNMT1 depletion vs toxicity) in mice suggests that it would be a better clinical candidate to selectively deplete DNMT1 from target cells and determine whether or not depletion of DNMT1 is an effective target for various diseases.
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Epigenetic-Based Therapy-A Prospective Chance for Medulloblastoma Patients' Recovery. Int J Mol Sci 2021; 22:ijms22094925. [PMID: 34066495 PMCID: PMC8124462 DOI: 10.3390/ijms22094925] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2021] [Revised: 04/21/2021] [Accepted: 04/27/2021] [Indexed: 12/25/2022] Open
Abstract
Medulloblastoma (MB) is one of the most frequent and malignant brain tumors in children. The prognosis depends on the advancement of the disease and the patient's age. Current therapies, which include surgery, chemotherapy, and irradiation, despite being quite effective, cause significant side effects that influence the central nervous system's function and cause neurocognitive deficits. Therefore, they substantially lower the quality of life, which is especially severe in a developing organism. Thus, there is a need for new therapies that are less toxic and even more effective. Recently, knowledge about the epigenetic mechanisms that are responsible for medulloblastoma development has increased. Epigenetics is a phenomenon that influences gene expression but can be easily modified by external factors. The best known epigenetic mechanisms are histone modifications, DNA methylation, or noncoding RNAs actions. Epigenetic mechanisms comprehensively explain the complex phenomena of carcinogenesis. At the same time, they seem to be a potential key to treating medulloblastoma with fewer complications than past therapies. This review presents the currently known epigenetic mechanisms that are involved in medulloblastoma pathogenesis and the potential therapies that use epigenetic traits to cure medulloblastoma while maintaining a good quality of life and ensuring a higher median overall survival rate.
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Abstract
DNA methylation is an epigenetic modification that contributes to essential biological processes such as retrotransposon silencing, cell differentiation, genomic imprinting and X-chromosome inactivation. DNA methylation generates a stable epigenetic mark associated with silencing of gene expression. Aberrant DNA methylation is associated with the development of different tumor types. Reversing DNA methylation is a rational strategy to restore gene re-expression and induce cell differentiation in cancer. DNA hypomethylating agents is a class of drugs that demonstrated efficacy in different tumors. In this chapter, the classification of DNA hypomethylating agents, their pharmacodynamics and their potential drawbacks will be discussed.
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Affiliation(s)
- Md Gias Uddin
- Department of Pharmaceutical & Administrative Sciences, School of Pharmacy, University of Charleston, Charleston, WV, United States
| | - Tamer E Fandy
- Department of Pharmaceutical & Administrative Sciences, School of Pharmacy, University of Charleston, Charleston, WV, United States.
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Crabb SJ, Danson S, Catto JWF, Hussain S, Chan D, Dunkley D, Downs N, Marwood E, Day L, Saunders G, Light M, Whitehead A, Ellis D, Sarwar N, Enting D, Birtle A, Johnson B, Huddart R, Griffiths G. Phase I Trial of DNA Methyltransferase Inhibitor Guadecitabine Combined with Cisplatin and Gemcitabine for Solid Malignancies Including Urothelial Carcinoma (SPIRE). Clin Cancer Res 2021; 27:1882-1892. [PMID: 33472913 PMCID: PMC7611191 DOI: 10.1158/1078-0432.ccr-20-3946] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2020] [Revised: 12/22/2020] [Accepted: 01/15/2021] [Indexed: 01/02/2023]
Abstract
PURPOSE Preclinical data indicate that DNA methyltransferase inhibition will circumvent cisplatin resistance in various cancers. PATIENT AND METHODS SPIRE comprised a dose-escalation phase for incurable metastatic solid cancers, followed by a randomized dose expansion phase for neoadjuvant treatment of T2-4a N0 M0 bladder urothelial carcinoma. The primary objective was a recommended phase II dose (RP2D) for guadecitabine combined with gemcitabine and cisplatin. Treatment comprised 21-day gemcitabine and cisplatin cycles (cisplatin 70 mg/m2, i.v., day 8 and gemcitabine 1,000 mg/m2, i.v., days 8 + 15). Guadecitabine was injected subcutaneously on days 1-5, within escalation phase cohorts, and to half of 20 patients in the expansion phase. Registration ID: ISRCTN 16332228. RESULTS Within the escalation phase, dose-limiting toxicities related predominantly to myelosuppression requiring G-CSF prophylaxis from cohort 2 (guadecitabine 20 mg/m2, days 1-5). The most common grade ≥3 adverse events in 17 patients in the dose-escalation phase were neutropenia (76.5%), thrombocytopenia (64.7%), leukopenia (29.4%), and anemia (29.4%). Addition of guadecitabine to gemcitabine and cisplatin in the expansion phase resulted in similar rates of severe hematologic adverse events, similar cisplatin dose intensity, but modestly reduced gemcitabine dose intensity. Radical treatment options after chemotherapy were not compromised. Pharmacodynamics evaluations indicated guadecitabine maximal target effect at the point of cisplatin administration. Pharmacokinetics were consistent with prior data. No treatment-related deaths occurred. CONCLUSIONS The guadecitabine RP2D was 20 mg/m2, days 1-5, in combination with gemcitabine and cisplatin and required GCSF prophylaxis. Gene promoter methylation pharmacodynamics are optimal with this schedule. Addition of guadecitabine to gemcitabine and cisplatin was tolerable, despite some additional myelosuppression, and warrants further investigation to assess efficacy.
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Affiliation(s)
- Simon J Crabb
- Southampton Clinical Trials Unit, University of Southampton, Southampton, England, United Kingdom.
- University Hospital Southampton NHS Foundation Trust, Southampton, England, United Kingdom
- Southampton Experimental Cancer Medicine Centre, University of Southampton, Southampton, England, United Kingdom
| | - Sarah Danson
- Sheffield Experimental Cancer Medicine Centre, Weston Park Hospital, University of Sheffield, Sheffield, England, United Kingdom
| | - James W F Catto
- Academic Urology Unit, University of Sheffield, Sheffield, England, United Kingdom
| | - Syed Hussain
- Sheffield Experimental Cancer Medicine Centre, Weston Park Hospital, University of Sheffield, Sheffield, England, United Kingdom
| | - Danna Chan
- Astex Pharmaceuticals, Inc., Pleasanton, California
| | - Denise Dunkley
- Southampton Clinical Trials Unit, University of Southampton, Southampton, England, United Kingdom
- University Hospital Southampton NHS Foundation Trust, Southampton, England, United Kingdom
- Southampton Experimental Cancer Medicine Centre, University of Southampton, Southampton, England, United Kingdom
| | - Nichola Downs
- Southampton Clinical Trials Unit, University of Southampton, Southampton, England, United Kingdom
- University Hospital Southampton NHS Foundation Trust, Southampton, England, United Kingdom
| | - Ellice Marwood
- Southampton Clinical Trials Unit, University of Southampton, Southampton, England, United Kingdom
- University Hospital Southampton NHS Foundation Trust, Southampton, England, United Kingdom
| | - Laura Day
- Southampton Clinical Trials Unit, University of Southampton, Southampton, England, United Kingdom
- University Hospital Southampton NHS Foundation Trust, Southampton, England, United Kingdom
| | - Geoff Saunders
- Southampton Clinical Trials Unit, University of Southampton, Southampton, England, United Kingdom
- University Hospital Southampton NHS Foundation Trust, Southampton, England, United Kingdom
| | - Michelle Light
- Southampton Clinical Trials Unit, University of Southampton, Southampton, England, United Kingdom
- University Hospital Southampton NHS Foundation Trust, Southampton, England, United Kingdom
| | - Amy Whitehead
- Southampton Clinical Trials Unit, University of Southampton, Southampton, England, United Kingdom
- University Hospital Southampton NHS Foundation Trust, Southampton, England, United Kingdom
| | - Deborah Ellis
- Southampton Clinical Trials Unit, University of Southampton, Southampton, England, United Kingdom
- University Hospital Southampton NHS Foundation Trust, Southampton, England, United Kingdom
| | - Naveed Sarwar
- Department of Oncology, Charing Cross Hospital, London, England, United Kingdom
| | - Deborah Enting
- Department of Oncology, Guy's and St Thomas' NHS Foundation Trust, London, England, United Kingdom
| | - Alison Birtle
- Lancashire Teaching Hospitals NHS Foundation Trust, Preston, England, United Kingdom
| | | | - Robert Huddart
- The Institute of Cancer Research, Sutton, England, United Kingdom
| | - Gareth Griffiths
- Southampton Clinical Trials Unit, University of Southampton, Southampton, England, United Kingdom
- University Hospital Southampton NHS Foundation Trust, Southampton, England, United Kingdom
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12
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Konečná K, Sováková PP, Anteková K, Fajkus J, Fojtová M. Distinct Responses of Arabidopsis Telomeres and Transposable Elements to Zebularine Exposure. Int J Mol Sci 2021; 22:ijms22010468. [PMID: 33466545 PMCID: PMC7796508 DOI: 10.3390/ijms22010468] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2020] [Revised: 12/21/2020] [Accepted: 12/28/2020] [Indexed: 12/17/2022] Open
Abstract
Involvement of epigenetic mechanisms in the regulation of telomeres and transposable elements (TEs), genomic regions with the protective and potentially detrimental function, respectively, has been frequently studied. Here, we analyzed telomere lengths in Arabidopsis thaliana plants of Columbia, Landsberg erecta and Wassilevskija ecotypes exposed repeatedly to the hypomethylation drug zebularine during germination. Shorter telomeres were detected in plants growing from seedlings germinated in the presence of zebularine with a progression in telomeric phenotype across generations, relatively high inter-individual variability, and diverse responses among ecotypes. Interestingly, the extent of telomere shortening in zebularine Columbia and Wassilevskija plants corresponded to the transcriptional activation of TEs, suggesting a correlated response of these genomic elements to the zebularine treatment. Changes in lengths of telomeres and levels of TE transcripts in leaves were not always correlated with a hypomethylation of cytosines located in these regions, indicating a cytosine methylation-independent level of their regulation. These observations, including differences among ecotypes together with distinct dynamics of the reversal of the disruption of telomere homeostasis and TEs transcriptional activation, reflect a complex involvement of epigenetic processes in the regulation of crucial genomic regions. Our results further demonstrate the ability of plant cells to cope with these changes without a critical loss of the genome stability.
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Affiliation(s)
- Klára Konečná
- Mendel Centre for Plant Genomics and Proteomics, Central European Institute for Technology (CEITEC), Masaryk University, Kamenice 5, CZ-62500 Brno, Czech Republic; (K.K.); (P.P.S.); (K.A.); (J.F.)
- Laboratory of Functional Genomics and Proteomics, National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Kotlářská 2, CZ-61137 Brno, Czech Republic
| | - Pavla Polanská Sováková
- Mendel Centre for Plant Genomics and Proteomics, Central European Institute for Technology (CEITEC), Masaryk University, Kamenice 5, CZ-62500 Brno, Czech Republic; (K.K.); (P.P.S.); (K.A.); (J.F.)
- Laboratory of Functional Genomics and Proteomics, National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Kotlářská 2, CZ-61137 Brno, Czech Republic
| | - Karin Anteková
- Mendel Centre for Plant Genomics and Proteomics, Central European Institute for Technology (CEITEC), Masaryk University, Kamenice 5, CZ-62500 Brno, Czech Republic; (K.K.); (P.P.S.); (K.A.); (J.F.)
- Laboratory of Functional Genomics and Proteomics, National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Kotlářská 2, CZ-61137 Brno, Czech Republic
| | - Jiří Fajkus
- Mendel Centre for Plant Genomics and Proteomics, Central European Institute for Technology (CEITEC), Masaryk University, Kamenice 5, CZ-62500 Brno, Czech Republic; (K.K.); (P.P.S.); (K.A.); (J.F.)
- Laboratory of Functional Genomics and Proteomics, National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Kotlářská 2, CZ-61137 Brno, Czech Republic
- Institute of Biophysics, Academy of Sciences of the Czech Republic, Královopolská 135, CZ-61265 Brno, Czech Republic
| | - Miloslava Fojtová
- Mendel Centre for Plant Genomics and Proteomics, Central European Institute for Technology (CEITEC), Masaryk University, Kamenice 5, CZ-62500 Brno, Czech Republic; (K.K.); (P.P.S.); (K.A.); (J.F.)
- Laboratory of Functional Genomics and Proteomics, National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Kotlářská 2, CZ-61137 Brno, Czech Republic
- Institute of Biophysics, Academy of Sciences of the Czech Republic, Královopolská 135, CZ-61265 Brno, Czech Republic
- Correspondence: ; Tel.: +420-54949-8063
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13
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Sanaei M, Kavoosi F. Effect of Zebularine in Comparison to and in Combination with Trichostatin A on CIP/KIP Family (p21Cip1/Waf1/Sdi1, p27Kip1, and p57Kip2), DNMTs (DNMT1, DNMT3a, and DNMT3b), Class I HDACs (HDACs 1, 2, 3) and Class II HDACs (HDACs 4, 5, 6) Gene Expression, Cell Growth Inhibition and Apoptosis Induction in Colon Cancer LS 174T Cell Line. Asian Pac J Cancer Prev 2020; 21:2131-2139. [PMID: 32711442 PMCID: PMC7573409 DOI: 10.31557/apjcp.2020.21.7.2131] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2020] [Indexed: 12/15/2022] Open
Abstract
Background: A pattern of epigenetic modifications and changes, DNA methylation and histone modification, is central to many human cancers. A variety of tumor suppressor genes (TSGs) have been demonstrated to be silenced because of histone deacetylation and DNA hypermethylation in several cancers. Recent in vitro studies have shown that two known mechanisms of epigenetic alteration consisting of methylation and histone deacetylation seem to be the best candidate mechanisms for inactivation of CIP/KIP family (p21Cip1/Waf1/Sdi1, and p27Kip1) in numerous cancers. Numerous investigations have indicated that DNA demethylating and histone deacetylase inhibitors (HDACIs) can restore the CIP/KIP family gene expression. Previously, we evaluated the effect of trichostatin A (TSA) and 5-aza-2′-deoxycytidine (5-AZA-CdR) on hepatocellular carcinoma (HCC). The present study was designed to investigate the effect of zebularine in comparison to and in combination with trichostatin A on p21Cip1/Waf1/Sdi1, p27Kip1, p57Kip2, DNMT1, DNMT3a and DNMT3b, Class I HDACs (HDACs 1, 2, 3) and Class II HDACs (HDACs 4, 5, 6) gene expression, cell growth inhibition and apoptosis induction in colon cancer LS 174T cell line. Materials and Methods: The colon cancer LS 174T cell line was cultured and treated with zebularine and TSA. To determine cell viability, apoptosis, and the relative expression level of the genes, MTT assay, cell apoptosis assay, and qRT-PCR were done respectively. Results: Both compounds significantly inhibited cell growth, and induced apoptosis. Furthermore, both compounds increased p21Cip1/Waf1/Sdi1, p27Kip1, and p57Kip2 significantly. Additionally, zebularine and TSA decreased DNMTs and HDACs gene expression respectively. Conclusion: The zebularine and trichostatin A can reactivate the CIP/KIP family through inhibition of DNMTs and HDACs genes activity.
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Affiliation(s)
- Masumeh Sanaei
- Research Center for Non-Communicable Diseases, Jahrom University of Medical Sciences, Jahrom, Iran
| | - Fraidoon Kavoosi
- Research Center for Non-Communicable Diseases, Jahrom University of Medical Sciences, Jahrom, Iran
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Yu J, Zayas J, Qin B, Wang L. Targeting DNA methylation for treating triple-negative breast cancer. Pharmacogenomics 2019; 20:1151-1157. [PMID: 31755366 PMCID: PMC7026764 DOI: 10.2217/pgs-2019-0078] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2019] [Accepted: 08/23/2019] [Indexed: 12/31/2022] Open
Abstract
Triple-negative breast cancer (TNBC) accounts for 15-20% of all invasive breast cancers and tends to have aggressive histological features and poor clinical outcomes. Unlike, estrogen receptor- or HER2-positive diseases, TNBC patients currently lack the US FDA-approved targeted therapies. DNA methylation is a critical mechanism of epigenetic modification. It is well known that aberrant DNA methylation contributes to the malignant transformation of cells by silencing critical tumor suppressor genes. DNA methyltransferase inhibitors reactivate silenced tumor suppressor genes and result in tumor growth arrest, with therapeutic effects observed in patients with hematologic malignancies. The antitumor effect of these DNA methyltransferase inhibitors has also been explored in solid tumors, especially in TNBC that currently lacks targeted therapies.
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Affiliation(s)
- Jia Yu
- Department of Molecular Pharmacology & Experimental Therapeutics, Mayo Clinic, Rochester, MN 55905, USA
| | - Jacqueline Zayas
- Mayo Clinic Graduate School of Biomedical Sciences, Mayo Clinic School of Medicine & The Mayo Clinic Medical Scientist Training Program, Mayo Clinic, Rochester, MN 55905, USA
| | - Bo Qin
- Department of Molecular Pharmacology & Experimental Therapeutics, Mayo Clinic, Rochester, MN 55905, USA
- Department of Oncology, Mayo Clinic, Rochester, MN 55905, USA
| | - Liewei Wang
- Department of Molecular Pharmacology & Experimental Therapeutics, Mayo Clinic, Rochester, MN 55905, USA
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15
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Ribeiro ML, Reyes-Garau D, Armengol M, Fernández-Serrano M, Roué G. Recent Advances in the Targeting of Epigenetic Regulators in B-Cell Non-Hodgkin Lymphoma. Front Genet 2019; 10:986. [PMID: 31681423 PMCID: PMC6807552 DOI: 10.3389/fgene.2019.00986] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2019] [Accepted: 09/17/2019] [Indexed: 12/13/2022] Open
Abstract
In the last 10 years, major advances have been made in the diagnosis and development of selective therapies for several blood cancers, including B-cell non-Hodgkin lymphoma (B-NHL), a heterogeneous group of malignancies arising from the mature B lymphocyte compartment. However, most of these entities remain incurable and current treatments are associated with variable efficacy, several adverse events, and frequent relapses. Thus, new diagnostic paradigms and novel therapeutic options are required to improve the prognosis of patients with B-NHL. With the recent deciphering of the mutational landscapes of B-cell disorders by high-throughput sequencing, it came out that different epigenetic deregulations might drive and/or promote B lymphomagenesis. Consistently, over the last decade, numerous epigenetic drugs (or epidrugs) have emerged in the clinical management of B-NHL patients. In this review, we will present an overview of the most relevant epidrugs tested and/or used so far for the treatment of different subtypes of B-NHL, from first-generation epigenetic therapies like histone acetyl transferases (HDACs) or DNA-methyl transferases (DNMTs) inhibitors to new agents showing selectivity for proteins that are mutated, translocated, and/or overexpressed in these diseases, including EZH2, BET, and PRMT. We will dissect the mechanisms of action of these epigenetic inhibitors, as well as the molecular processes underlying their lack of efficacy in refractory patients. This review will also provide a summary of the latest strategies being employed in preclinical and clinical settings, and will point out the most promising lines of investigation in the field.
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Affiliation(s)
- Marcelo L Ribeiro
- Laboratory of Experimental Hematology, Department of Hematology, Vall d'Hebron Institute of Oncology (VHIO), Vall d'Hebron University Hospital, Autonomous University of Barcelona, Barcelona, Spain.,Laboratory of Immunopharmacology and Molecular Biology, Sao Francisco University Medical School, Braganca Paulista, São Paulo, Brazil
| | - Diana Reyes-Garau
- Laboratory of Experimental Hematology, Department of Hematology, Vall d'Hebron Institute of Oncology (VHIO), Vall d'Hebron University Hospital, Autonomous University of Barcelona, Barcelona, Spain
| | - Marc Armengol
- Laboratory of Experimental Hematology, Department of Hematology, Vall d'Hebron Institute of Oncology (VHIO), Vall d'Hebron University Hospital, Autonomous University of Barcelona, Barcelona, Spain
| | - Miranda Fernández-Serrano
- Laboratory of Experimental Hematology, Department of Hematology, Vall d'Hebron Institute of Oncology (VHIO), Vall d'Hebron University Hospital, Autonomous University of Barcelona, Barcelona, Spain
| | - Gaël Roué
- Laboratory of Experimental Hematology, Department of Hematology, Vall d'Hebron Institute of Oncology (VHIO), Vall d'Hebron University Hospital, Autonomous University of Barcelona, Barcelona, Spain
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Chovanec M, Taza F, Kalra M, Hahn N, Nephew KP, Spinella MJ, Albany C. Incorporating DNA Methyltransferase Inhibitors (DNMTis) in the Treatment of Genitourinary Malignancies: A Systematic Review. Target Oncol 2019; 13:49-60. [PMID: 29230671 DOI: 10.1007/s11523-017-0546-x] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Inhibition of DNA methyltransferases (DNMTs) has emerged as a novel treatment strategy in solid tumors. Aberrant hypermethylation in promoters of critical tumor suppressor genes is the basis for the idea that treatment with hypomethylating agents may lead to the restoration of a "normal" epigenome and produce clinically meaningful therapeutic outcomes. The aim of this review article is to summarize the current state of knowledge of DNMT inhibitors in the treatment of genitourinary malignancies. The efficacy of these agents in genitourinary malignancies was reported in a number of studies and suggests a role of induced DNA hypomethylation in overcoming resistance to conventional cytotoxic treatments. The clinical significance of these findings should be further investigated.
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Affiliation(s)
- Michal Chovanec
- Division of Hematology/Oncology, Indiana University Simon Cancer Center, Indianapolis, IN, USA.
- 2nd Department of Oncology, Faculty of Medicine, Comenius University and National Cancer Institute, Bratislava, Slovakia.
| | - Fadi Taza
- Division of Hematology/Oncology, Indiana University Simon Cancer Center, Indianapolis, IN, USA
| | - Maitri Kalra
- Division of Hematology/Oncology, Indiana University Simon Cancer Center, Indianapolis, IN, USA
| | - Noah Hahn
- The Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Kenneth P Nephew
- Molecular and Cellular Biochemistry Department, Indiana University, Bloomington, IN, USA
| | - Michael J Spinella
- Department of Comparative Biosciences, the University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Costantine Albany
- Division of Hematology/Oncology, Indiana University Simon Cancer Center, Indianapolis, IN, USA
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17
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Sass P, Sosnowski P, Podolak-Popinigis J, Górnikiewicz B, Kamińska J, Deptuła M, Nowicka E, Wardowska A, Ruczyński J, Rekowski P, Rogujski P, Filipowicz N, Mieczkowska A, Peszyńska-Sularz G, Janus Ł, Skowron P, Czupryn A, Mucha P, Piotrowski A, Rodziewicz-Motowidło S, Pikuła M, Sachadyn P. Epigenetic inhibitor zebularine activates ear pinna wound closure in the mouse. EBioMedicine 2019; 46:317-329. [PMID: 31303499 PMCID: PMC6710911 DOI: 10.1016/j.ebiom.2019.07.010] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2019] [Revised: 06/29/2019] [Accepted: 07/03/2019] [Indexed: 12/13/2022] Open
Abstract
BACKGROUND Most studies on regenerative medicine focus on cell-based therapies and transplantations. Small-molecule therapeutics, though proved effective in different medical conditions, have not been extensively investigated in regenerative research. It is known that healing potential decreases with development and developmental changes are driven by epigenetic mechanisms, which suggests epigenetic repression of regenerative capacity. METHODS We applied zebularine, a nucleoside inhibitor of DNA methyltransferases, to stimulate the regenerative response in a model of ear pinna injury in mice. FINDINGS We observed the regeneration of complex tissue that was manifested as improved ear hole repair in mice that received intraperitoneal injections of zebularine. Six weeks after injury, the mean hole area decreased by 83.2 ± 9.4% in zebularine-treated and by 43.6 ± 15.4% in control mice (p < 10-30). Combined delivery of zebularine and retinoic acid potentiated and accelerated this effect, resulting in complete ear hole closure within three weeks after injury. We found a decrease in DNA methylation and transcriptional activation of neurodevelopmental and pluripotency genes in the regenerating tissues. INTERPRETATION This study is the first to demonstrate an effective induction of complex tissue regeneration in adult mammals using zebularine. We showed that the synergistic action of an epigenetic drug (zebularine) and a transcriptional activator (retinoic acid) could be effectively utilized to induce the regenerative response, thus delineating a novel pharmacological strategy for regeneration. The strategy was effective in the model of ear pinna regeneration in mice, but zebularine acts on different cell types, therefore, a similar approach can be tested in other tissues and organs.
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Affiliation(s)
- Piotr Sass
- Laboratory for Regenerative Biotechnology, Gdańsk University of Technology, 80-233 Gdańsk, Poland
| | - Paweł Sosnowski
- Laboratory for Regenerative Biotechnology, Gdańsk University of Technology, 80-233 Gdańsk, Poland
| | | | - Bartosz Górnikiewicz
- Laboratory for Regenerative Biotechnology, Gdańsk University of Technology, 80-233 Gdańsk, Poland
| | - Jolanta Kamińska
- Laboratory for Regenerative Biotechnology, Gdańsk University of Technology, 80-233 Gdańsk, Poland
| | - Milena Deptuła
- Laboratory of Tissue Engineering and Regenerative Medicine, Department of Embryology, Medical University of Gdańsk, 80-211 Gdańsk, Poland
| | - Ewa Nowicka
- Department of Clinical Anatomy, Medical University of Gdańsk, 80-211 Gdańsk, Poland
| | - Anna Wardowska
- Laboratory of Tissue Engineering and Regenerative Medicine, Department of Embryology, Medical University of Gdańsk, 80-211 Gdańsk, Poland
| | - Jarosław Ruczyński
- Department of Molecular Biochemistry, Faculty of Chemistry, University of Gdańsk, Gdańsk, Poland
| | - Piotr Rekowski
- Department of Molecular Biochemistry, Faculty of Chemistry, University of Gdańsk, Gdańsk, Poland
| | - Piotr Rogujski
- Laboratory of Neurobiology, Nencki Institute of Experimental Biology, Polish Academy of Sciences, 02-093 Warsaw, Poland
| | - Natalia Filipowicz
- Faculty of Pharmacy, Medical University of Gdańsk, Gdańsk 80-416, Poland
| | - Alina Mieczkowska
- Faculty of Pharmacy, Medical University of Gdańsk, Gdańsk 80-416, Poland
| | - Grażyna Peszyńska-Sularz
- Tri-City Academic Laboratory Animal Centre, Research and Services Centre, Medical University of Gdańsk, 80-211 Gdańsk, Poland
| | | | - Piotr Skowron
- Department of Molecular Biotechnology, Faculty of Chemistry, University of Gdańsk, 80-308 Gdańsk, Poland
| | - Artur Czupryn
- Laboratory of Neurobiology, Nencki Institute of Experimental Biology, Polish Academy of Sciences, 02-093 Warsaw, Poland
| | - Piotr Mucha
- Department of Molecular Biochemistry, Faculty of Chemistry, University of Gdańsk, Gdańsk, Poland
| | | | | | - Michał Pikuła
- Laboratory of Tissue Engineering and Regenerative Medicine, Department of Embryology, Medical University of Gdańsk, 80-211 Gdańsk, Poland.
| | - Paweł Sachadyn
- Laboratory for Regenerative Biotechnology, Gdańsk University of Technology, 80-233 Gdańsk, Poland.
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18
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The Methylation Status of the Epigenome: Its Emerging Role in the Regulation of Tumor Angiogenesis and Tumor Growth, and Potential for Drug Targeting. Cancers (Basel) 2018; 10:cancers10080268. [PMID: 30103412 PMCID: PMC6115976 DOI: 10.3390/cancers10080268] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2018] [Revised: 07/27/2018] [Accepted: 08/06/2018] [Indexed: 12/13/2022] Open
Abstract
Approximately 50 years ago, Judah Folkman raised the concept of inhibiting tumor angiogenesis for treating solid tumors. The development of anti-angiogenic drugs would decrease or even arrest tumor growth by restricting the delivery of oxygen and nutrient supplies, while at the same time display minimal toxic side effects to healthy tissues. Bevacizumab (Avastin)—a humanized monoclonal anti VEGF-A antibody—is now used as anti-angiogenic drug in several forms of cancers, yet with variable results. Recent years brought significant progresses in our understanding of the role of chromatin remodeling and epigenetic mechanisms in the regulation of angiogenesis and tumorigenesis. Many inhibitors of DNA methylation as well as of histone methylation, have been successfully tested in preclinical studies and some are currently undergoing evaluation in phase I, II or III clinical trials, either as cytostatic molecules—reducing the proliferation of cancerous cells—or as tumor angiogenesis inhibitors. In this review, we will focus on the methylation status of the vascular epigenome, based on the genomic DNA methylation patterns with DNA methylation being mainly transcriptionally repressive, and lysine/arginine histone post-translational modifications which either promote or repress the chromatin transcriptional state. Finally, we discuss the potential use of “epidrugs” in efficient control of tumor growth and tumor angiogenesis.
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19
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Cermakova K, Hodges HC. Next-Generation Drugs and Probes for Chromatin Biology: From Targeted Protein Degradation to Phase Separation. Molecules 2018; 23:molecules23081958. [PMID: 30082609 PMCID: PMC6102721 DOI: 10.3390/molecules23081958] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2018] [Revised: 08/01/2018] [Accepted: 08/01/2018] [Indexed: 12/31/2022] Open
Abstract
Chromatin regulation is a critical aspect of nuclear function. Recent advances have provided detailed information about dynamic three-dimensional organization of chromatin and its regulatory factors. Mechanisms crucial for normal nuclear function and epigenetic control include compartmentalization of biochemical reactions by liquid-phase separated condensates and signal-dependent regulation of protein stability. Synthetic control of these phenomena by small molecules provides deep insight into essential activities such as histone modification, BAF (SWI/SNF) and PBAF remodeling, Polycomb repression, enhancer looping by cohesin and CTCF, as well as many other processes that contribute to transcription. As a result, a complete understanding of the spatiotemporal mechanisms that underlie chromatin regulation increasingly requires the use of fast-acting drugs and chemical probes. Here, we provide a comprehensive review of next-generation chemical biology tools to interrogate the chromatin regulatory landscape, including selective PROTAC E3 ubiquitin ligase degraders, degrons, fluorescent ligands, dimerizers, inhibitors, and other drugs. These small molecules provide important insights into the mechanisms that govern gene regulation, DNA repair, development, and diseases like cancer.
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Affiliation(s)
- Katerina Cermakova
- Department of Molecular & Cellular Biology, Center for Precision Environmental Health, and Dan L Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, TX 77030, USA.
| | - H Courtney Hodges
- Department of Molecular & Cellular Biology, Center for Precision Environmental Health, and Dan L Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, TX 77030, USA.
- Center for Cancer Epigenetics, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA.
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20
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Nucleosidic DNA demethylating epigenetic drugs – A comprehensive review from discovery to clinic. Pharmacol Ther 2018; 188:45-79. [DOI: 10.1016/j.pharmthera.2018.02.006] [Citation(s) in RCA: 68] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
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21
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Takemura Y, Satoh M, Hatanaka K, Kubota S. Zebularine exerts its antiproliferative activity through S phase delay and cell death in human malignant mesothelioma cells. Biosci Biotechnol Biochem 2018; 82:1159-1164. [PMID: 29685095 DOI: 10.1080/09168451.2018.1459466] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
Abstract
Malignant mesothelioma is an asbestos-related aggressive tumor and current therapy remains ineffective. Zebularine as a DNA methyltransferase (DNMT) inhibitor has an anti-tumor effect in several human cancer cells. The aim of the present study was to investigate whether zebularine could induce antiproliferative effect in human malignant mesothelioma cells. Zebularine induced cell growth inhibition in a dose-dependent manner. In addition, zebularine dose-dependently decreased expression of DNMT1 in all malignant mesothelioma cells tested. Cell cycle analysis indicated that zebularine induced S phase delay. Zebularine also induced cell death in malignant mesothelioma cells. In contrast, zebularine did not induce cell growth inhibition and cell death in human normal fibroblast cells. These results suggest that zebularine has a potential for the treatment of malignant mesothelioma by inhibiting cell growth and inducing cell death.
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Affiliation(s)
- Yukitoshi Takemura
- a Institute of Industrial Science , The University of Tokyo , Tokyo , Japan
| | - Motohiko Satoh
- a Institute of Industrial Science , The University of Tokyo , Tokyo , Japan
| | - Kenichi Hatanaka
- a Institute of Industrial Science , The University of Tokyo , Tokyo , Japan
| | - Shunichiro Kubota
- a Institute of Industrial Science , The University of Tokyo , Tokyo , Japan.,b Department of Pharmaceutical Sciences , Teikyo Heisei University , Tokyo , Japan
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22
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Zeng XQ, Wang J, Chen SY. Methylation modification in gastric cancer and approaches to targeted epigenetic therapy (Review). Int J Oncol 2017; 50:1921-1933. [DOI: 10.3892/ijo.2017.3981] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2017] [Accepted: 03/22/2017] [Indexed: 11/06/2022] Open
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23
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Naz A, Cui Y, Collins CJ, Thompson DH, Irudayaraj J. PLGA-PEG nano-delivery system for epigenetic therapy. Biomed Pharmacother 2017; 90:586-597. [PMID: 28407579 DOI: 10.1016/j.biopha.2017.03.093] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2017] [Revised: 03/22/2017] [Accepted: 03/27/2017] [Indexed: 12/31/2022] Open
Abstract
Efficient delivery of cytidine analogues such as Azacitidine (AZA) into solid tumors constitutes a primary challenge in epigenetic therapies. We developed a di-block nano-vector based on poly(lactic-co-glycolic acid) (PLGA) and poly(ethylene glycol) (PEG) for stabilization of the conjugated AZA under physiological conditions. With equimolar drug content, our nano-conjugate could elicit a better anti-proliferative effect over free drug in breast cancer both in vitro and in vivo, through reactivation of p21 and BRCA1 to restrict cell proliferation. In addition, we applied single-molecule fluorescence tools to characterize the intracellular behavior of the AZA-PLGE-PEG nano-micelles at a finer spatiotemporal resolution. Our results suggest that the nano-micelles could effectively enrich in cancer cells and may not be limited by nucleoside transporters. Afterwards, the internalized nano-micelles exhibit pH-dependent release and resistance to active efflux. Altogether, our work describes a delivery strategy for DNA demethylating agents with nanoscale tunability, providing a cost-effective option for pharmaceutics.
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Affiliation(s)
- Asia Naz
- Bindley Bioscience Center and Purdue Center for Cancer Research, Department of Agricultural and Biological Engineering, Purdue University, West Lafayette, IN 47907, USA; Department of Pharmaceutical Chemistry, University of Karachi, Karachi 75270, Pakistan
| | - Yi Cui
- Bindley Bioscience Center and Purdue Center for Cancer Research, Department of Agricultural and Biological Engineering, Purdue University, West Lafayette, IN 47907, USA.
| | | | - David H Thompson
- Department of Chemistry, Purdue University, West Lafayette, IN 47907, USA
| | - Joseph Irudayaraj
- Bindley Bioscience Center and Purdue Center for Cancer Research, Department of Agricultural and Biological Engineering, Purdue University, West Lafayette, IN 47907, USA.
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24
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Andrade AF, Borges KS, Suazo VK, Geron L, Corrêa CAP, Castro-Gamero AM, de Vasconcelos EJR, de Oliveira RS, Neder L, Yunes JA, Dos Santos Aguiar S, Scrideli CA, Tone LG. The DNA methyltransferase inhibitor zebularine exerts antitumor effects and reveals BATF2 as a poor prognostic marker for childhood medulloblastoma. Invest New Drugs 2016; 35:26-36. [PMID: 27785591 DOI: 10.1007/s10637-016-0401-4] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2016] [Accepted: 10/20/2016] [Indexed: 12/11/2022]
Abstract
Medulloblastoma (MB) is the most common solid tumor among pediatric patients and corresponds to 20 % of all pediatric intracranial tumors in this age group. Its treatment currently involves significant side effects. Epigenetic changes such as DNA methylation may contribute to its development and progression. DNA methyltransferase (DNMT) inhibitors have shown promising anticancer effects. The agent Zebularine acts as an inhibitor of DNA methylation and shows low toxicity and high efficacy, being a promising adjuvant agent for anti-cancer chemotherapy. Several studies have reported its effects on different types of tumors; however, there are no studies reporting its effects on MB. We analyzed its potential anticancer effects in four pediatric MB cell lines. The treatment inhibited proliferation and clonogenicity, increased the apoptosis rate and the number of cells in the S phase (p < 0.05), as well as the expression of p53, p21, and Bax, and decreased cyclin A, Survivin and Bcl-2 proteins. In addition, the combination of zebularine with the chemotherapeutic agents vincristine and cisplatin resulted in synergism and antagonism, respectively. Zebularine also modulated the activation of the SHH pathway, reducing SMO and GLI1 levels and one of its targets, PTCH1, without changing SUFU levels. A microarray analysis revealed different pathways modulated by the drug, including the Toll-Like Receptor pathway and high levels of the BATF2 gene. The low expression of this gene was associated with a worse prognosis in MB. Taken together, these data suggest that Zebularine may be a potential drug for further in vivo studies of MB treatment.
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Affiliation(s)
- Augusto Faria Andrade
- Department of Genetics, Ribeirão Preto Medical School, University of São Paulo (USP), Avenida Bandeirantes 3900, 14048-900, Ribeirão Preto, SP, Brazil.
| | - Kleiton Silva Borges
- Department of Pediatrics - Ribeirão Preto Medical School, University of São Paulo (USP), São Paulo, Brazil
| | - Veridiana Kiill Suazo
- Department of Pediatrics - Ribeirão Preto Medical School, University of São Paulo (USP), São Paulo, Brazil
| | - Lenisa Geron
- Department of Genetics, Ribeirão Preto Medical School, University of São Paulo (USP), Avenida Bandeirantes 3900, 14048-900, Ribeirão Preto, SP, Brazil
| | | | | | | | | | - Luciano Neder
- Department of Pathology, Ribeirão Preto Medical School, USP, São Paulo, Brazil
| | | | | | - Carlos Alberto Scrideli
- Department of Pediatrics - Ribeirão Preto Medical School, University of São Paulo (USP), São Paulo, Brazil
| | - Luiz Gonzaga Tone
- Department of Genetics, Ribeirão Preto Medical School, University of São Paulo (USP), Avenida Bandeirantes 3900, 14048-900, Ribeirão Preto, SP, Brazil.,Department of Pediatrics - Ribeirão Preto Medical School, University of São Paulo (USP), São Paulo, Brazil
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25
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A Comparative Analysis of 5-Azacytidine- and Zebularine-Induced DNA Demethylation. G3-GENES GENOMES GENETICS 2016; 6:2773-80. [PMID: 27402357 PMCID: PMC5015934 DOI: 10.1534/g3.116.030262] [Citation(s) in RCA: 57] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
The nonmethylable cytosine analogs, 5-azacytidine and zebularine, are widely used to inhibit DNA methyltransferase activity and reduce genomic DNA methylation. In this study, whole-genome bisulfite sequencing is used to construct maps of DNA methylation with single base pair resolution in Arabidopsis thaliana seedlings treated with each demethylating agent. We find that both inhibitor treatments result in nearly indistinguishable patterns of genome-wide DNA methylation and that 5-azacytidine had a slightly greater demethylating effect at higher concentrations across the genome. Transcriptome analyses revealed a substantial number of upregulated genes, with an overrepresentation of transposable element genes, in particular CACTA-like elements. This demonstrates that chemical demethylating agents have a disproportionately large effect on loci that are otherwise silenced by DNA methylation.
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26
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Ma X, Wang Q, Wang Y, Ma J, Wu N, Ni S, Luo T, Zhuang L, Chu C, Cho SW, Tsujimoto H, Qi Z. Chromosome aberrations induced by zebularine in triticale. Genome 2016; 59:485-92. [DOI: 10.1139/gen-2016-0047] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Chromosome engineering is an important approach for generating wheat germplasm. Efficient development of chromosome aberrations will facilitate the introgression and application of alien genes in wheat. In this study, zebularine, a DNA methylation transferase inhibitor, was successfully used to induce chromosome aberrations in the octoploid triticale cultivar Jinghui#1. Dry seeds were soaked in zebularine solutions (250, 500, and 750 μmol/L) for 24 h, and the 500 μmol/L treatment was tested in three additional treatment times, i.e., 12, 36, and 48 h. All treatments induced aberrations involving wheat and rye chromosomes. Of the 920 cells observed in 67 M1 plants, 340 (37.0%) carried 817 aberrations with an average of 0.89 aberrations per cell (range: 0–12). The aberrations included probable deletions, telosomes and acentric fragments (49.0%), large segmental translocations (28.9%), small segmental translocations (17.1%), intercalary translocations (2.6%), long chromosomes that could carry more than one centromere (2.0%), and ring chromosomes (0.5%). Of 510 M2 plants analyzed, 110 (21.6%) were found to carry stable aberrations. Such aberrations included 79 with varied rye chromosome numbers, 7 with wheat and rye chromosome translocations, 15 with possible rye telosomes/deletions, and 9 with complex aberrations involving variation in rye chromosome number and wheat–rye translocations. These indicated that aberrations induced by zebularine can be steadily transmitted, suggesting that zebularine is a new efficient agent for chromosome manipulation.
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Affiliation(s)
- Xuhui Ma
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, JCIC-MCP, Nanjing Agricultural University, Nanjing 210095, China
| | - Qing Wang
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, JCIC-MCP, Nanjing Agricultural University, Nanjing 210095, China
| | - Yanzhi Wang
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, JCIC-MCP, Nanjing Agricultural University, Nanjing 210095, China
| | - Jieyun Ma
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, JCIC-MCP, Nanjing Agricultural University, Nanjing 210095, China
| | - Nan Wu
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, JCIC-MCP, Nanjing Agricultural University, Nanjing 210095, China
| | - Shuang Ni
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, JCIC-MCP, Nanjing Agricultural University, Nanjing 210095, China
| | - Tengxiao Luo
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, JCIC-MCP, Nanjing Agricultural University, Nanjing 210095, China
| | - Lifang Zhuang
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, JCIC-MCP, Nanjing Agricultural University, Nanjing 210095, China
| | - Chenggen Chu
- Monsanto Company, 21120 Hwy 30, Filer, ID 83328, USA
| | - Seong-Woo Cho
- Crop Breeding Research Division, National Institute of Crop Science, RDA, Wanju-gun, Jeollabuk-do, 55365, South Korea
| | - Hisashi Tsujimoto
- Arid Land Research Center, Tottori University, Hamasaka, Tottori 680-0001, Japan
| | - Zengjun Qi
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, JCIC-MCP, Nanjing Agricultural University, Nanjing 210095, China
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27
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Dnmts and Tet target memory-associated genes after appetitive olfactory training in honey bees. Sci Rep 2015; 5:16223. [PMID: 26531238 PMCID: PMC4632027 DOI: 10.1038/srep16223] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2015] [Accepted: 10/08/2015] [Indexed: 11/09/2022] Open
Abstract
DNA methylation and demethylation are epigenetic mechanisms involved in memory formation. In honey bees DNA methyltransferase (Dnmt) function is necessary for long-term memory to be stimulus specific (i.e. to reduce generalization). So far, however, it remains elusive which genes are targeted and what the time-course of DNA methylation is during memory formation. Here, we analyse how DNA methylation affects memory retention, gene expression, and differential methylation in stimulus-specific olfactory long-term memory formation. Out of 30 memory-associated genes investigated here, 9 were upregulated following Dnmt inhibition in trained bees. These included Dnmt3 suggesting a negative feedback loop for DNA methylation. Within these genes also the DNA methylation pattern changed during the first 24 hours after training. Interestingly, this was accompanied by sequential activation of the DNA methylation machinery (i.e. Dnmts and Tet). In sum, memory formation involves a temporally complex epigenetic regulation of memory-associated genes that facilitates stimulus specific long-term memory in the honey bee.
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28
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Fulkerson CM, Dhawan D, Jones DR, Marquez VE, Jones PA, Wang Z, Wu Q, Klaunig JE, Fourez LM, Bonney PL, Knapp DW. Pharmacokinetics and toxicity of the novel oral demethylating agent zebularine in laboratory and tumor bearing dogs. Vet Comp Oncol 2015; 15:226-236. [PMID: 26178438 DOI: 10.1111/vco.12159] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2014] [Revised: 05/07/2015] [Accepted: 05/07/2015] [Indexed: 12/31/2022]
Abstract
The purpose of this study was to determine the plasma pharmacokinetics (PK) and toxicity of zebularine, an oral cytidine analog with demethylating activity, in dogs. Plasma zebularine concentrations were determined by HPLC-MS/MS following an oral zebularine dose of 8 or 4 mg kg-1 . Plasma zebularine clearance was constant. Mean maximum concentration (Cmax ) was 23 ± 4.8 and 8.6 ± 1.4 µM following 8 and 4 mg kg-1 , respectively. Mean half-life was 5.7 ± 0.84 and 7.1 ± 2.1 following 8 and 4 mg kg-1 , respectively. A single 8 mg kg-1 dose was well tolerated. Daily 4 mg kg-1 treatment in three laboratory dogs resulted in grade 4 neutropenia (n = 3), grade 1 anorexia (n = 2) and grade 1 or 2 dermatologic changes (n = 2). All adverse events resolved with supportive care. A 4 mg kg-1 dose every 21 days was well tolerated. A follow-up dose escalation study is in progress with a lower starting dose.
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Affiliation(s)
- C M Fulkerson
- Department of Veterinary Clinical Sciences, Purdue University College of Veterinary Medicine, West Lafayette, IN, USA
| | - D Dhawan
- Department of Veterinary Clinical Sciences, Purdue University College of Veterinary Medicine, West Lafayette, IN, USA
| | - D R Jones
- Division of Clinical Pharmacology, Indiana University School of Medicine, Indianapolis, IN, USA
| | - V E Marquez
- Center for Cancer Research, Chemical Biology Laboratory, National Cancer Institute, Frederick, MD, USA
| | - P A Jones
- Van Adel Research Institute, Grand Rapids, MI, USA
| | - Z Wang
- Department of Environmental Health, School of Public Health, Indiana University, Bloomington, IN, USA
| | - Q Wu
- Department of Environmental Health, School of Public Health, Indiana University, Bloomington, IN, USA
| | - J E Klaunig
- Department of Environmental Health, School of Public Health, Indiana University, Bloomington, IN, USA
| | - L M Fourez
- Department of Veterinary Clinical Sciences, Purdue University College of Veterinary Medicine, West Lafayette, IN, USA
| | - P L Bonney
- Department of Veterinary Clinical Sciences, Purdue University College of Veterinary Medicine, West Lafayette, IN, USA
| | - D W Knapp
- Department of Veterinary Clinical Sciences, Purdue University College of Veterinary Medicine, West Lafayette, IN, USA.,Purdue University Center for Cancer Research, West Lafayette, IN, USA
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29
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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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30
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Bapiro TE, Frese KK, Courtin A, Bramhall JL, Madhu B, Cook N, Neesse A, Griffiths JR, Tuveson DA, Jodrell DI, Richards FM. Gemcitabine diphosphate choline is a major metabolite linked to the Kennedy pathway in pancreatic cancer models in vivo. Br J Cancer 2014; 111:318-25. [PMID: 24874484 PMCID: PMC4102943 DOI: 10.1038/bjc.2014.288] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Revised: 04/15/2014] [Accepted: 04/30/2014] [Indexed: 01/03/2023] Open
Abstract
BACKGROUND The modest benefits of gemcitabine (dFdC) therapy in patients with pancreatic ductal adenocarcinoma (PDAC) are well documented, with drug delivery and metabolic lability cited as important contributing factors. We have used a mouse model of PDAC: KRAS(G12D); p53(R172H); pdx-Cre (KPC) that recapitulates the human disease to study dFdC intra-tumoural metabolism. METHODS LC-MS/MS and NMR were used to measure drug and physiological analytes. Cytotoxicity was assessed by the Sulphorhodamine B assay. RESULTS In KPC tumour tissue, we identified a new, Kennedy pathway-linked dFdC metabolite (gemcitabine diphosphate choline (GdPC)) present at equimolar amounts to its precursor, the accepted active metabolite gemcitabine triphosphate (dFdCTP). Utilising additional subcutaneous PDAC tumour models, we demonstrated an inverse correlation between GdPC/dFdCTP ratios and cytidine triphosphate (CTP). In tumour homogenates in vitro, CTP inhibited GdPC formation from dFdCTP, indicating competition between CTP and dFdCTP for CTP:phosphocholine cytidylyltransferase (CCT). As the structure of GdPC precludes entry into cells, potential cytotoxicity was assessed by stimulating CCT activity using linoleate in KPC cells in vitro, leading to increased GdPC concentration and synergistic growth inhibition after dFdC addition. CONCLUSIONS GdPC is an important element of the intra-tumoural dFdC metabolic pathway in vivo.
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Affiliation(s)
- T E Bapiro
- Cancer Research UK Cambridge Institute, University of Cambridge, Li Ka Shing Centre, Box 278, Robinson Way, Cambridge CB2 0RE, UK
| | - K K Frese
- Cancer Research UK Cambridge Institute, University of Cambridge, Li Ka Shing Centre, Box 278, Robinson Way, Cambridge CB2 0RE, UK
| | - A Courtin
- Cancer Research UK Cambridge Institute, University of Cambridge, Li Ka Shing Centre, Box 278, Robinson Way, Cambridge CB2 0RE, UK
| | - J L Bramhall
- Cancer Research UK Cambridge Institute, University of Cambridge, Li Ka Shing Centre, Box 278, Robinson Way, Cambridge CB2 0RE, UK
| | - B Madhu
- Cancer Research UK Cambridge Institute, University of Cambridge, Li Ka Shing Centre, Box 278, Robinson Way, Cambridge CB2 0RE, UK
| | - N Cook
- Cancer Research UK Cambridge Institute, University of Cambridge, Li Ka Shing Centre, Box 278, Robinson Way, Cambridge CB2 0RE, UK
| | - A Neesse
- Cancer Research UK Cambridge Institute, University of Cambridge, Li Ka Shing Centre, Box 278, Robinson Way, Cambridge CB2 0RE, UK
| | - J R Griffiths
- Cancer Research UK Cambridge Institute, University of Cambridge, Li Ka Shing Centre, Box 278, Robinson Way, Cambridge CB2 0RE, UK
| | - D A Tuveson
- Cold Spring Harbor Laboratory, 1 Bungtown Road, Cold Spring Harbor, NY 11724, USA
| | - D I Jodrell
- Cancer Research UK Cambridge Institute, University of Cambridge, Li Ka Shing Centre, Box 278, Robinson Way, Cambridge CB2 0RE, UK
| | - F M Richards
- Cancer Research UK Cambridge Institute, University of Cambridge, Li Ka Shing Centre, Box 278, Robinson Way, Cambridge CB2 0RE, UK
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31
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NAPSO TINA, FARES FUAD. Zebularine induces prolonged apoptosis effects via the caspase-3/PARP pathway in head and neck cancer cells. Int J Oncol 2014; 44:1971-9. [DOI: 10.3892/ijo.2014.2386] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2013] [Accepted: 11/18/2013] [Indexed: 11/05/2022] Open
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32
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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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Flis S, Gnyszka A, Flis K. DNA methyltransferase inhibitors improve the effect of chemotherapeutic agents in SW48 and HT-29 colorectal cancer cells. PLoS One 2014; 9:e92305. [PMID: 24676085 PMCID: PMC3967992 DOI: 10.1371/journal.pone.0092305] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2013] [Accepted: 02/20/2014] [Indexed: 11/29/2022] Open
Abstract
DNA methylation is an epigenetic phenomenon known to play an important role in the development and progression of human cancer. Enzyme responsible for this process is DNA methyltransferase 1 (DNMT1) that maintains an altered methylation pattern by copying it from parent to daughter DNA strands after replication. Aberrant methylation of the promoter regions of genes critical for normal cellular functions is potentially reversible. Therefore, inactivation of DNMT1 seems to be a valuable target for the development of cancer therapies. Currently, the most popular DNMT inhibitors (DNMTi) are cytidine analogues like 5-azacytidine, 5-aza-2′-deoxycytidine (decitabine) and pyrimidin-2-one ribonucleoside (zebularine). In colorectal cancer, epigenetic modifications play an essential role at each step of carcinogenesis. Therefore, we have addressed the hypothesis that DNA methyltransferase inhibitors may potentiate inhibitory effects of classical chemotherapeutic agents, such as oxaliplatin and 5-fluorouracil (5-FU), commonly used in colorectal cancer therapy. Here, our report shows that DNMTi can have positive interactions with standard chemotherapeutics in colorectal cancer treatment. Using pharmacological models for the drug-drug interaction analysis, we have revealed that the combination of decitabine with 5-FU or oxaliplatin shows the most attractive interaction (synergism), whereas the effect of zebularine in combinations with chemotherapeutics is moderate and may be depended on genetic/epigenetic background of a cell line or secondary drug used in combination. Our results suggest that DNMTi administered in combination with standard chemotherapeutics might improve the treatment of patients with colorectal cancers.
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Affiliation(s)
- Sylwia Flis
- Department of Pharmacology, National Medicines Institute, Warsaw, Poland
- * E-mail:
| | - Agnieszka Gnyszka
- Department of Pharmacology, National Medicines Institute, Warsaw, Poland
| | - Krzysztof Flis
- Department of Genetics, Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warsaw, Poland
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Tsai CT, Yang PM, Chern TR, Chuang SH, Lin JH, Klemm L, Müschen M, Chen CC. AID downregulation is a novel function of the DNMT inhibitor 5-aza-deoxycytidine. Oncotarget 2014; 5:211-23. [PMID: 24457556 PMCID: PMC3960202 DOI: 10.18632/oncotarget.1319] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2013] [Accepted: 11/23/2013] [Indexed: 11/25/2022] Open
Abstract
Activation-induced cytidine deaminase (AID) was originally identified as an inducer of somatic hypermutation (SHM) and class switch recombination (CSR) in immunoglobulin genes. However, AID can also cause mutations in host genes and contribute to cancer progression and drug resistance. In this study, molecular docking showed the interaction of free 5-aza-CdR and Zebularine (Zeb) with AID. However, only 5-aza-CdR-incorporated ssDNA bound to the active site of AID and inhibited AID expression through proteasomal degradation. 5-aza-CdR demonstrated cytotoxicity against AID-positive and -negative hematopoietic cancer cells. In contrast, Zeb exhibited a cytotoxic effect only in AID-negative cells due to its inability to inhibit AID expression. This differential effect might be due to the DNMT1 stabilization induced by AID, thus restricting the ability of Zeb to deplete DNMT1 and induce tumor suppressor genes (TSGs), such as p21, in AID-positive cells. Moreover, the in vivo anticancer effect of 5-aza-CdR but not Zeb in AID-positive hematopoietic cancer cells was demonstrated. The study not only displays the association of AID and DNMT1 and identifies a novel biological function of AID, but also provides novel information regarding the use of DNMT inhibitors to treat AID-positive hematopoietic cancers.
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Affiliation(s)
- Chiou-Tsun Tsai
- Department of Pharmacology, College of Medicine, National Taiwan University, Taipei, Taiwan
| | - Pei-Ming Yang
- Department of Pharmacology, College of Medicine, National Taiwan University, Taipei, Taiwan
| | - Ting-Rong Chern
- Department of Pharmacology, College of Medicine, National Taiwan University, Taipei, Taiwan
| | - Shu-Hui Chuang
- Department of Pharmacology, College of Medicine, National Taiwan University, Taipei, Taiwan
| | - Jung-Hsin Lin
- School of Pharmacy, College of Medicine, National Taiwan University, Taipei, Taiwan
- Research Center for Applied Sciences, Academia Sinica, Taipei, Taiwan
- Institute of Biomedical Science, Academia Sinica, Taipei, Taiwan
| | - Lars Klemm
- Department of Laboratory Medicine, University of California San Francisco, San Francisco, California
| | - Markus Müschen
- Department of Laboratory Medicine, University of California San Francisco, San Francisco, California
| | - Ching-Chow Chen
- Department of Pharmacology, College of Medicine, National Taiwan University, Taipei, Taiwan
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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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36
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Zebularine inhibits tumorigenesis and stemness of colorectal cancer via p53-dependent endoplasmic reticulum stress. Sci Rep 2013; 3:3219. [PMID: 24225777 PMCID: PMC3827606 DOI: 10.1038/srep03219] [Citation(s) in RCA: 53] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2013] [Accepted: 10/24/2013] [Indexed: 12/11/2022] Open
Abstract
Aberrant DNA hypermethylation is frequently found in tumor cells and inhibition of DNA methylation is an effective anticancer strategy. In this study, the therapeutic effect of DNA methyltransferase (DNMT) inhibitor zebularine (Zeb) on colorectal cancer (CRC) was investigated. Zeb exhibited anticancer activity in cell cultures, tumor xenografts and mouse colitis-associated CRC model. It stabilizes p53 through ribosomal protein S7 (RPS7)/MDM2 pathways and DNA damage. Zeb-induced cell death was dependent on p53. Microarray analysis revealed that genes related to endoplasmic reticulum (ER) stress and unfolded protein response (UPR) were affected by Zeb. Zeb induced p53-dependent ER stress and autophagy. Pro-survival markers of ER stress/UPR (GRP78) and autophagy (p62) were increased in tumor tissues of CRC patients, AOM/DSS-induced CRC mice and HCT116-derived colonospheres. Zeb downregulates GRP78 and p62, and upregulates a pro-apoptotic CHOP. Our results reveal a novel mechanism for the anticancer activity of Zeb.
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Advances in the development of nucleoside and nucleotide analogues for cancer and viral diseases. Nat Rev Drug Discov 2013; 12:447-64. [PMID: 23722347 DOI: 10.1038/nrd4010] [Citation(s) in RCA: 804] [Impact Index Per Article: 73.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Nucleoside analogues have been in clinical use for almost 50 years and have become cornerstones of treatment for patients with cancer or viral infections. The approval of several additional drugs over the past decade demonstrates that this family still possesses strong potential. Here, we review new nucleoside analogues and associated compounds that are currently in preclinical or clinical development for the treatment of cancer and viral infections, and that aim to provide increased response rates and reduced side effects. We also highlight the different approaches used in the development of these drugs and the potential of personalized therapy.
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Ahmadi M, Ranjbaran H, Amiri MM, Nozari J, Mirzajani MR, Azadbakht M, Hosseinimehr SJ. Epidemiologic and socioeconomic status of bladder cancer in Mazandaran Province, northern Iran. Asian Pac J Cancer Prev 2013; 13:5053-6. [PMID: 23244109 DOI: 10.7314/apjcp.2012.13.10.5053] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Bladder cancer is one the most common malignancies of the genitourinary tract. The present study aimed to assess the epidemiology, of bladder cancer in Mazandaran, a large province in northern Iran as high-incidence cancer area, during a 2-year period. METHODS The data for this study were obtained from the population-based cancer registry of the Vice-Chancellory for Health Affairs of Mazandaran University of Medical Sciences and Mazandaran hospitals between March 1, 2010 and March 1, 2011. Demographic data, including sex, age, residency and symptoms were investigated through careful review of medical records. Using a questionnaire protocol, several variables were assessed for these cases such as smoking, history of opium, vegetable consumption habits, and history of other cancers. RESULTS A total of 112 cases were analyzed, 98 (87.5%) in men and 14 (12.5%) in women (mean age of 68.0 ± 14.6 years). Urban and rural residence were 60.7% and 39.3%. Tobacco and opium use were found in 45.5% and 21.4% of patients, respectively. Approximately 60% consumed vegetables an average of fewer than one time per day. Hematuria was the first symptom in these cases which were mainly diagnosed as having bladder cancer by ultrasonography. CONCLUSION The results showed that bladder cancer tends to be found in the elderly and the male to female ratio is high. Macroscopic hematuria is a very important symptom for indicating probably urothelial tumor that should be followed up patients with transabdominal ultrasonography as a routine modality.
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Affiliation(s)
- Mohammad Ahmadi
- Deputy of Health Affairs, Mazandaran University of Medical Sciences, Sari, Iran
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39
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Advances in the development of nucleoside and nucleotide analogues for cancer and viral diseases. NATURE REVIEWS. DRUG DISCOVERY 2013. [PMID: 23722347 DOI: 10.1038/nrd4010]] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Nucleoside analogues have been in clinical use for almost 50 years and have become cornerstones of treatment for patients with cancer or viral infections. The approval of several additional drugs over the past decade demonstrates that this family still possesses strong potential. Here, we review new nucleoside analogues and associated compounds that are currently in preclinical or clinical development for the treatment of cancer and viral infections, and that aim to provide increased response rates and reduced side effects. We also highlight the different approaches used in the development of these drugs and the potential of personalized therapy.
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40
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Nakamura K, Aizawa K, Nakabayashi K, Kato N, Yamauchi J, Hata K, Tanoue A. DNA methyltransferase inhibitor zebularine inhibits human hepatic carcinoma cells proliferation and induces apoptosis. PLoS One 2013; 8:e54036. [PMID: 23320119 PMCID: PMC3540068 DOI: 10.1371/journal.pone.0054036] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2012] [Accepted: 12/07/2012] [Indexed: 12/21/2022] Open
Abstract
Hepatocellular carcinoma is one of the most common cancers worldwide. During tumorigenesis, tumor suppressor and cancer-related genes are commonly silenced by aberrant DNA methylation in their promoter regions. Zebularine (1-(β-(D)-ribofuranosyl)-1,2-dihydropyrimidin-2-one) acts as an inhibitor of DNA methylation and exhibits chemical stability and minimal cytotoxicity both in vitro and in vivo. In this study, we explore the effect and possible mechanism of action of zebularine on hepatocellular carcinoma cell line HepG2. We demonstrate that zebularine exhibits antitumor activity on HepG2 cells by inhibiting cell proliferation and inducing apoptosis, however, it has little effect on DNA methylation in HepG2 cells. On the other hand, zebularine treatment downregulated CDK2 and the phosphorylation of retinoblastoma protein (Rb), and upregulated p21(WAF/CIP1) and p53. We also found that zebularine treatment upregulated the phosphorylation of p44/42 mitogen-activated protein kinase (MAPK). These results suggest that the p44/42 MAPK pathway plays a role in zebularine-induced cell-cycle arrest by regulating the activity of p21(WAF/CIP1) and Rb. Furthermore, although the proapoptotic protein Bax levels were not affected, the antiapoptotic protein Bcl-2 level was downregulated with zebularine treatment. In addition, the data in the present study indicate that inhibition of the double-stranded RNA-dependent protein kinase (PKR) is involved in inducing apoptosis with zebularine. These results suggest a novel mechanism of zebularine-induced cell growth arrest and apoptosis via a DNA methylation-independent pathway in hepatocellular carcinoma.
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Affiliation(s)
- Kazuaki Nakamura
- Department of Pharmacology, National Research Institute for Child Health and Development, Tokyo, Japan.
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Savickiene J, Treigyte G, Borutinskaite VV, Navakauskiene R. Antileukemic activity of combined epigenetic agents, DNMT inhibitors zebularine and RG108 with HDAC inhibitors, against promyelocytic leukemia HL-60 cells. Cell Mol Biol Lett 2012; 17:501-25. [PMID: 22820861 PMCID: PMC6275587 DOI: 10.2478/s11658-012-0024-5] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2011] [Accepted: 07/12/2012] [Indexed: 12/12/2022] Open
Abstract
DNMT inhibitors are promising new drugs for cancer therapies. In this study, we have observed the antileukemic action of two diverse DNMT inhibitors, the nucleoside agent zebularine and the non-nucleoside agent RG108, in human promyelocytic leukemia (PML) HL-60 cells. Zebularine but not RG108 caused dose- and time-dependent cell growth inhibition and induction of apoptosis. However, co-treatment with either drug at a non-toxic dose and all trans retinoic acid (RA) reinforced differentiation to granulocytes, while 24 or 48 h-pretreatment with zebularine or RG108 followed by RA alone or in the presence of HDAC inhibitors (sodium phenyl butyrate or BML-210) significantly accelerated and enhanced cell maturation to granulocytes. This occurs in parallel with the expression of a surface biomarker, CD11b, and early changes in histone H4 acetylation and histone H3K4me3 methylation. The application of both drugs to HL-60 cells in continuous or sequential fashion decreased DNMT1 expression, and induced E-cadherin promoter demethylation and reactivation at both the mRNA and the protein levels in association with the induction of granulocytic differentiation. The results confirmed the utility of zebularine and RG108 in combinations with RA and HDAC inhibitors to reinforce differentiation effects in promyelocytic leukemia.
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Affiliation(s)
- Jurate Savickiene
- Department of Molecular Cell Biology, Institute of Biochemistry, Vilnius University, Mokslininkų 12, Vilnius, LT 08662 Lithuania
| | - Grazina Treigyte
- Department of Molecular Cell Biology, Institute of Biochemistry, Vilnius University, Mokslininkų 12, Vilnius, LT 08662 Lithuania
| | - Veronika-Viktorija Borutinskaite
- Department of Molecular Cell Biology, Institute of Biochemistry, Vilnius University, Mokslininkų 12, Vilnius, LT 08662 Lithuania
| | - Ruta Navakauskiene
- Department of Molecular Cell Biology, Institute of Biochemistry, Vilnius University, Mokslininkų 12, Vilnius, LT 08662 Lithuania
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42
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Zebularine inhibits the growth of HeLa cervical cancer cells via cell cycle arrest and caspase-dependent apoptosis. Mol Biol Rep 2012; 39:9723-31. [PMID: 22718513 DOI: 10.1007/s11033-012-1837-z] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2012] [Accepted: 06/10/2012] [Indexed: 10/28/2022]
Abstract
Zebularine (Zeb) as a DNA methyltrasferase (DNMT) inhibitor has various cellular effects such as cell growth inhibition and apoptosis. In the present study, we evaluated the effects of Zeb on the growth and death of HeLa cervical cancer cells. Zeb inhibited the growth of HeLa cells with an IC(50) of approximately 130 μM at 72 h in a dose-dependent manner. DNA flow cytometric analysis indicated that Zeb induced an S phase arrest of the cell cycle, which was accompanied by the increased levels of cdk2 and cyclin A proteins. This agent also induced apoptosis, which was accompanied by the loss of mitochondrial membrane potential (Ψ(m)), PARP-1 cleavage and the activation of caspase-3, -8 and -9. All of the tested caspase inhibitors significantly rescued some cells from Zeb-induced HeLa cell death. In relation to reactive oxygen species (ROS) and glutathione (GSH) levels, O (2) (•-) level was significantly increased in 100 μM Zeb-treated HeLa cells and caspase inhibitors reduced O (2) (•-) level in these cells. Zeb induced GSH depletion in HeLa cells, which was attenuated by caspase inhibitors. In conclusion, this is the first report that Zeb inhibited the growth of HeLa cells via cell cycle arrest and apoptosis.
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43
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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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Horvat T, Mužinić A, Barišić D, Bosnar MH, Zoldoš V. Epigenetic modulation of the HeLa cell membrane N-glycome. Biochim Biophys Acta Gen Subj 2011; 1820:1412-9. [PMID: 22192783 DOI: 10.1016/j.bbagen.2011.12.007] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2011] [Revised: 12/05/2011] [Accepted: 12/05/2011] [Indexed: 12/31/2022]
Abstract
BACKGROUND Epigenetic changes play a role in all major events during tumorigenesis and changes in glycan structures are hallmarks of virtually every cancer. Also, proper N-glycosylation of membrane receptors is important in cell to cell and cell-environment communication. To study how modulation of epigenetic information can affect N-glycan expression we analyzed effects of epigenetic inhibitors on HeLa cell membrane N-glycome. METHODS HeLa cells were treated with DNA methylation (zebularin and 5-aza-2-deoxycytidine) and histone deacetylation (trichostatin A and Na-butyrate) inhibitors. The effects on HeLa cell membrane N-glycome were analyzed by hydrophilic interaction high performance liquid chromatography (HILIC). RESULTS Each of the four epigenetic inhibitors induced changes in the expression of HeLa cell membrane N-glycans that were seen either as an increase or a decrease of individual glycans in the total N-glycome. Compared to DNA methylation inhibitors, histone deacetylation inhibitors showed more moderate changes, probably due to their higher gene target selectivity. CONCLUSIONS The results clearly show that composition of HeLa cell membrane N-glycome can be specifically altered by epigenetic inhibitors. GENERAL SIGNIFICANCE Glycans on the cell membrane are essential elements of tumor cell's metastatic potential and are also an entry point for nearly all pathogenic microorganisms. Since epigenetic inhibitors used in this work are registered drugs, our results provide a new line of research in the application of these drugs as anticancer and antimicrobial agents. This article is part of a Special Issue entitled Glycoproteomics.
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Affiliation(s)
- Tomislav Horvat
- University of Zagreb, Faculty of Science, Horvatovac 102a, Zagreb, Croatia
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45
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Lim SP, Neilsen P, Kumar R, Abell A, Callen DF. The Application of Delivery Systems for DNA Methyltransferase Inhibitors. BioDrugs 2011; 25:227-42. [DOI: 10.2165/11592770-000000000-00000] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
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46
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Alva AS, Hahn NM, Aparicio AM, Singal R, Yellapragada S, Sonpavde G. Hypomethylating agents for urologic cancers. Future Oncol 2011; 7:447-63. [PMID: 21417907 DOI: 10.2217/fon.11.9] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
Silencing of tumor suppressor genes by promoter-region methylation as an epigenetic mechanism of gene regulation is increasingly recognized as beneficial in cancer. Initially developed as cytotoxic high-dose therapies, azacitidine and decitabine are now being reinvestigated in lower-dose cancer treatment regimens with a different paradigm - hypomethylation. Recent evidence for benefit in myelodysplastic syndromes and acute myeloid leukemias has renewed interest in hypomethylation as a therapeutic option in epithelial cancers. In this article, we describe the mechanistic aspects of DNA methylation, which alters gene expression, and review the evidence for hypomethylation as a therapeutic option in urologic cancers. Potential correlative studies that may assist in developing tailored therapy with hypomethylating agents are reviewed. Given that the population with urologic cancers is typically elderly with multiple comorbidities, the excellent tolerability of lower-dose hypomethylating agents provides a high therapeutic index and rational development is warranted, bearing in mind that the cytostatic and delayed activity present challenges in the choice of appropriate trial end points.
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Affiliation(s)
- Ajjai S Alva
- Baylor College of Medicine & Michael E DeBakey VA Medical Center, Houston, TX 77030, USA
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47
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Yoo J, Medina-Franco JL. Homology modeling, docking and structure-based pharmacophore of inhibitors of DNA methyltransferase. J Comput Aided Mol Des 2011; 25:555-67. [DOI: 10.1007/s10822-011-9441-1] [Citation(s) in RCA: 64] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2011] [Accepted: 05/30/2011] [Indexed: 11/28/2022]
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Matoušová M, Votruba I, Otmar M, Tloušťová E, Günterová J, Mertlíková-Kaiserová H. 2´-deoxy-5,6-dihydro-5-azacytidine - a less toxic alternative of 2´-deoxy-5-azacytidine: a comparative study of hypomethylating potential. Epigenetics 2011; 6:769-76. [PMID: 21566456 DOI: 10.4161/epi.6.6.16215] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
Restoration of transcriptionally silenced genes by means of methyltransferases inhibitors plays a crucial role in the current therapy of myelodysplastic syndromes and certain types of leukemias. A comparative study of hypomethylating activities of a series of 5-azacytidine nucleosides: 5-azacytidine (AC), 2'-deoxy-5-azacytidine (DAC) and its α-anomer (α-DAC), 5,6-dihydro-5-azacytidine (DHAC), 2'-deoxy-5,6-dihydro-5-azacytidine (DHDAC, KP-1212) and its α-anomer (α-DHDAC), and of a 2-pyrimidone ribonucleoside (zebularine) was conducted. Methylation-specific PCR was employed to detect the efficiency of individual agents on cyclin-dependent kinase inhibitor 2B and thrombospondin-1 hypermethylated gene loci. Overall changes in DNA methylation level were quantified by direct estimation of 5-methyl-2'-deoxycytidine-5'-monophosphate by HPLC using digested genomic DNA. Flow cytometric analysis of cell cycle progression and apoptotic markers was used to determine cytotoxicity of the compounds. mRNA expression was measured using qRT-PCR. 2'-deoxy-5,6-dihydro-5-azacytidine was found to be less cytotoxic and more stable than 2'-deoxy-5-azacytidine at the doses that induce comparable DNA hypomethylation and gene reactivation. This makes it a valuable tool for epigenetic research and worth further investigations to elucidate its possible therapeutic potential.
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Affiliation(s)
- Marika Matoušová
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, v.v.i.; Gilead Sciences and IOCB Research Center, Prague, Czech Republic
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Meador JA, Su Y, Ravanat JL, Balajee AS. DNA-dependent protein kinase (DNA-PK)-deficient human glioblastoma cells are preferentially sensitized by Zebularine. Carcinogenesis 2009; 31:184-91. [PMID: 19933707 DOI: 10.1093/carcin/bgp284] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
Brain tumor cells respond poorly to radiotherapy and chemotherapy due to inherently efficient anti-apoptotic and DNA repair mechanisms. This necessitates the development of new strategies for brain cancer therapy. Here, we report that the DNA-demethylating agent Zebularine preferentially sensitizes the killing of human glioblastomas deficient in DNA-dependent protein kinase (DNA-PK). In contrast to DNA-PK-proficient human glioblastoma cells (MO59K), cytotoxicity assay with increasing Zebularine concentrations up to 300 microM resulted in a specific elevation of cell killing in DNA-PK-deficient MO59J cells. Further, an elevated frequency of polyploid cells observed in MO59J cells after Zebularine treatment pointed out a deficiency in mitotic checkpoint control. Existence of mitotic checkpoint deficiency in MO59J cells was confirmed by the abnormal centrosome number observed in Zebularine-treated MO59J cells. Although depletion of DNA methyltransferase 1 by Zebularine occurred at similar levels in both cell lines, MO59J cells displayed increased extent of DNA demethylation detected both at the gene promoter-specific level and at the genome overall level. Consistent with increased sensitivity, deoxy-Zebularine adduct level in the genomic DNA was 3- to 6-fold higher in MO59J than in MO59K cells. Elevated micronuclei frequency observed after Zebularine treatment in MO59J cells indicates the impairment of DNA repair response in MO59J cells. Collectively, our study suggests that DNA-PK is the major determining factor for cellular response to Zebularine.
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Affiliation(s)
- Jarah A Meador
- Center for Radiological Research, Department of Radiation Oncology, Columbia University Medical Center, New York, NY 10032, USA
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50
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van Bemmel DM, Brank AS, Eritja R, Marquez VE, Christman JK. DNA (Cytosine-C5) methyltransferase inhibition by oligodeoxyribonucleotides containing 2-(1H)-pyrimidinone (zebularine aglycon) at the enzymatic target site. Biochem Pharmacol 2009; 78:633-41. [PMID: 19467223 DOI: 10.1016/j.bcp.2009.05.017] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2009] [Revised: 05/15/2009] [Accepted: 05/15/2009] [Indexed: 11/16/2022]
Abstract
Aberrant cytosine methylation in promoter regions leads to gene silencing associated with cancer progression. A number of DNA methyltransferase inhibitors are known to reactivate silenced genes; including 5-azacytidine and 2-(1H)-pyrimidinone riboside (zebularine). Zebularine is a more stable, less cytotoxic inhibitor compared to 5-azacytidine. To determine the mechanistic basis for this difference, we carried out a detailed comparisons of the interaction between purified DNA methyltransferases and oligodeoxyribonucleotides (ODNs) containing either 5-azacytosine or 2-(1H)-pyrimidinone in place of the cytosine targeted for methylation. When incorporated into small ODNs, the rate of C5 DNA methyltransferase inhibition by both nucleosides is essentially identical. However, the stability and reversibility of the enzyme complex in the absence and presence of cofactor differs. 5-Azacytosine ODNs form complexes with C5 DNA methyltransferases that are irreversible when the 5-azacytosine ring is intact. ODNs containing 2-(1H)-pyrimidinone at the enzymatic target site are competitive inhibitors of both prokaryotic and mammalian DNA C5 methyltransferases. We determined that the ternary complexes between the enzymes, 2-(1H)-pyrimidinone inhibitor, and the cofactor S-adenosyl methionine are maintained through the formation of a reversible covalent interaction. The differing stability and reversibility of the covalent bonds may partially account for the observed differences in cytotoxicity between zebularine and 5-azacytidine inhibitors.
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Affiliation(s)
- Dana M van Bemmel
- Department of Biochemistry and Molecular Biology, Omaha, NE 68198-5870, USA.
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