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Wang K, He Z, Jin G, Jin S, Du Y, Yuan S, Zhang J. Targeting DNA methyltransferases for cancer therapy. Bioorg Chem 2024; 151:107652. [PMID: 39024804 DOI: 10.1016/j.bioorg.2024.107652] [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: 05/09/2024] [Revised: 06/29/2024] [Accepted: 07/14/2024] [Indexed: 07/20/2024]
Abstract
DNA methyltransferases (DNMTs) play a crucial role in genomic DNA methylation. In mammals, DNMTs regulate the dynamic patterns of DNA methylation in embryonic and adult cells. Abnormal functions of DNMTs are often indicative of cancers, including overall hypomethylation and partial hypermethylation of tumor suppressor genes (TSG), which accelerate the malignancy of tumors, worsen the condition of patients, and significantly exacerbate the difficulty of cancer treatment. Currently, nucleoside DNMT inhibitors such as Azacytidine and Decitabine have been approved by the FDA and EMA for the treatment of acute myeloid leukemia (AML), chronic myelomonocytic leukemia (CMML), and myelodysplastic syndrome (MDS). Therefore, targeting DNMTs is a very promising anti-tumor strategy. This review mainly summarizes the therapeutic effects of DNMT inhibitors on cancers. It aims to provide more possibilities for the treatment of cancers by discovering more DNMT inhibitors with high activity, high selectivity, and good drug-like properties in the future.
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Affiliation(s)
- Kaiyue Wang
- Pharmacy College, Henan University of Chinese Medicine, 450046 Zhengzhou, PR China
| | - Zhangxu He
- Pharmacy College, Henan University of Chinese Medicine, 450046 Zhengzhou, PR China.
| | - Gang Jin
- Pharmacy College, Henan University of Chinese Medicine, 450046 Zhengzhou, PR China
| | - Sasa Jin
- Pharmacy College, Henan University of Chinese Medicine, 450046 Zhengzhou, PR China
| | - Yuanbing Du
- Pharmacy College, Henan University of Chinese Medicine, 450046 Zhengzhou, PR China
| | - Shuo Yuan
- Children's Hospital Affiliated to Zhengzhou University, Henan Children's Hospital, Zhengzhou Children's Hospital, Zhengzhou 450018, PR China.
| | - Jingyu Zhang
- Pharmacy College, Henan University of Chinese Medicine, 450046 Zhengzhou, PR China.
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2
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Kudo G, Hirao T, Harada R, Hirokawa T, Shigeta Y, Yoshino R. Prediction of the binding mechanism of a selective DNA methyltransferase 3A inhibitor by molecular simulation. Sci Rep 2024; 14:13508. [PMID: 38866895 PMCID: PMC11169543 DOI: 10.1038/s41598-024-64236-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2023] [Accepted: 06/06/2024] [Indexed: 06/14/2024] Open
Abstract
DNA methylation is an epigenetic mechanism that introduces a methyl group at the C5 position of cytosine. This reaction is catalyzed by DNA methyltransferases (DNMTs) and is essential for the regulation of gene transcription. The DNMT1 and DNMT3A or -3B family proteins are known targets for the inhibition of DNA hypermethylation in cancer cells. A selective non-nucleoside DNMT3A inhibitor was developed that mimics S-adenosyl-l-methionine and deoxycytidine; however, the mechanism of selectivity is unclear because the inhibitor-protein complex structure determination is absent. Therefore, we performed docking and molecular dynamics simulations to predict the structure of the complex formed by the association between DNMT3A and the selective inhibitor. Our simulations, binding free energy decomposition analysis, structural isoform comparison, and residue scanning showed that Arg688 of DNMT3A is involved in the interaction with this inhibitor, as evidenced by its significant contribution to the binding free energy. The presence of Asn1192 at the corresponding residues in DNMT1 results in a loss of affinity for the inhibitor, suggesting that the interactions mediated by Arg688 in DNMT3A are essential for selectivity. Our findings can be applied in the design of DNMT-selective inhibitors and methylation-specific drug optimization procedures.
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Affiliation(s)
- Genki Kudo
- Physics Department, Graduate School of Pure and Applied Sciences, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki, 305-8571, Japan
| | - Takumi Hirao
- Doctoral Program in Medical Sciences, Graduate School of Comprehensive Human Sciences, University of Tsukuba, Tsukuba, Ibaraki, 305-8575, Japan
- Division of Biomedical Science, Faculty of Medicine, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki, 305-8575, Japan
| | - Ryuhei Harada
- Center for Computational Sciences, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki, 305-8577, Japan
| | - Takatsugu Hirokawa
- Division of Biomedical Science, Faculty of Medicine, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki, 305-8575, Japan
- Transborder Medical Research Center, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki, 305-8575, Japan
| | - Yasuteru Shigeta
- Physics Department, Graduate School of Pure and Applied Sciences, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki, 305-8571, Japan
- Center for Computational Sciences, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki, 305-8577, Japan
| | - Ryunosuke Yoshino
- Division of Biomedical Science, Faculty of Medicine, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki, 305-8575, Japan.
- Transborder Medical Research Center, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki, 305-8575, Japan.
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3
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Luo F, Zhang M, Sun B, Xu C, Yang Y, Zhang Y, Li S, Chen G, Chen C, Li Y, Feng H. LINC00115 promotes chemoresistant breast cancer stem-like cell stemness and metastasis through SETDB1/PLK3/HIF1α signaling. Mol Cancer 2024; 23:60. [PMID: 38520019 PMCID: PMC10958889 DOI: 10.1186/s12943-024-01975-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2024] [Accepted: 02/28/2024] [Indexed: 03/25/2024] Open
Abstract
BACKGROUND Cancer stem-like cell is a key barrier for therapeutic resistance and metastasis in various cancers, including breast cancer, yet the underlying mechanisms are still elusive. Through a genome-wide lncRNA expression profiling, we identified that LINC00115 is robustly upregulated in chemoresistant breast cancer stem-like cells (BCSCs). METHODS LncRNA microarray assay was performed to document abundance changes of lncRNAs in paclitaxel (PTX)-resistant MDA-MB-231 BCSC (ALDH+) and non-BCSC (ALDH-). RNA pull-down and RNA immunoprecipitation (RIP) assays were performed to determine the binding proteins of LINC00115. The clinical significance of the LINC00115 pathway was examined in TNBC metastatic lymph node tissues. The biological function of LINC00115 was investigated through gain- and loss-of-function studies. The molecular mechanism was explored through RNA sequencing, mass spectrometry, and the CRISPR/Cas9-knockout system. The therapeutic potential of LINC00115 was examined through xenograft animal models. RESULTS LINC00115 functions as a scaffold lncRNA to link SETDB1 and PLK3, leading to enhanced SETDB1 methylation of PLK3 at both K106 and K200 in drug-resistant BCSC. PLK3 methylation decreases PLK3 phosphorylation of HIF1α and thereby increases HIF1α stability. HIF1α, in turn, upregulates ALKBH5 to reduce m6A modification of LINC00115, resulting in attenuated degradation of YTHDF2-dependent m6A-modified RNA and enhanced LINC00115 stability. Thus, this positive feedback loop provokes BCSC phenotypes and enhances chemoresistance and metastasis in triple-negative breast cancer. SETDB1 inhibitor TTD-IN with LINC00115 ASO sensitizes PTX-resistant cell response to chemotherapy in a xenograft animal model. Correlative expression of LINC00115, methylation PLK3, SETDB1, and HIF1α are prognostic for clinical triple-negative breast cancers. CONCLUSIONS Our findings uncover LINC00115 as a critical regulator of BCSC and highlight targeting LINC00115 and SETDB1 as a potential therapeutic strategy for chemotherapeutic resistant breast cancer.
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Affiliation(s)
- Fei Luo
- State Key Laboratory of Systems Medicine for Cancer, Renji-Med X Clinical Stem Cell Research Center, Ren Ji Hospital, Shanghai Cancer Institute, Shanghai Jiao Tong University School of Medicine, Shanghai, 200127, China
| | - Mingda Zhang
- State Key Laboratory of Systems Medicine for Cancer, Renji-Med X Clinical Stem Cell Research Center, Ren Ji Hospital, Shanghai Cancer Institute, Shanghai Jiao Tong University School of Medicine, Shanghai, 200127, China
| | - Bowen Sun
- State Key Laboratory of Systems Medicine for Cancer, Renji-Med X Clinical Stem Cell Research Center, Ren Ji Hospital, Shanghai Cancer Institute, Shanghai Jiao Tong University School of Medicine, Shanghai, 200127, China
| | - Chenxin Xu
- State Key Laboratory of Systems Medicine for Cancer, Renji-Med X Clinical Stem Cell Research Center, Ren Ji Hospital, Shanghai Cancer Institute, Shanghai Jiao Tong University School of Medicine, Shanghai, 200127, China
| | - Yi Yang
- Pediatric Translational Medicine Institute, Department of Hematology & Oncology, Committee Key Laboratory of Pediatric Hematology & Oncology, Shanghai Children's Medical Center, Shanghai Jiao Tong University School of Medicine, National Health Committee Key Laboratory of Pediatric Hematology & Oncology, Shanghai, 200127, China
| | - Yingwen Zhang
- State Key Laboratory of Systems Medicine for Cancer, Renji-Med X Clinical Stem Cell Research Center, Ren Ji Hospital, Shanghai Cancer Institute, Shanghai Jiao Tong University School of Medicine, Shanghai, 200127, China
| | - Shanshan Li
- Pediatric Translational Medicine Institute, Department of Hematology & Oncology, Committee Key Laboratory of Pediatric Hematology & Oncology, Shanghai Children's Medical Center, Shanghai Jiao Tong University School of Medicine, National Health Committee Key Laboratory of Pediatric Hematology & Oncology, Shanghai, 200127, China
| | - Guoyu Chen
- State Key Laboratory of Systems Medicine for Cancer, Renji-Med X Clinical Stem Cell Research Center, Ren Ji Hospital, Shanghai Cancer Institute, Shanghai Jiao Tong University School of Medicine, Shanghai, 200127, China
| | - Ceshi Chen
- Academy of Biomedical Engineering, the Third Affiliated Hospital, Kunming Medical University, Kunming, 650500, China.
| | - Yanxin Li
- Pediatric Translational Medicine Institute, Department of Hematology & Oncology, Committee Key Laboratory of Pediatric Hematology & Oncology, Shanghai Children's Medical Center, Shanghai Jiao Tong University School of Medicine, National Health Committee Key Laboratory of Pediatric Hematology & Oncology, Shanghai, 200127, China.
| | - Haizhong Feng
- State Key Laboratory of Systems Medicine for Cancer, Renji-Med X Clinical Stem Cell Research Center, Ren Ji Hospital, Shanghai Cancer Institute, Shanghai Jiao Tong University School of Medicine, Shanghai, 200127, China.
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Yang W, Zhuang J, Li C, Bai C, Cheng G. Insights into the Inhibitory Mechanisms of the Covalent Drugs for DNMT3A. Int J Mol Sci 2023; 24:12652. [PMID: 37628829 PMCID: PMC10454219 DOI: 10.3390/ijms241612652] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2023] [Revised: 08/07/2023] [Accepted: 08/08/2023] [Indexed: 08/27/2023] Open
Abstract
The perturbations of DNA methyltransferase 3 alpha (DNMT3A) may cause uncontrolled gene expression, resulting in cancers and tumors. The DNMT inhibitors Azacytidine (AZA) and Zebularine (ZEB) inhibit the DNMT family with no specificities, and consequently would bring side effects during the treatment. Therefore, it is vital to understand the inhibitory mechanisms in DNMT3A to inform the new inhibitor design for DNMTs. Herein, we carried out molecular dynamics (MD) and quantum mechanics/molecular mechanics (QM/MM) simulations to investigate the inhibitory mechanisms of the AZA and ZEB. The results were compared to the methyl transfer of cytosine. We showed how the AZA might stop the methyl transfer process, whereas the ZEB might be stuck in a methyl-transferred intermediate (IM3). The IM3 state then fails the elimination due to the unique protein dynamics that result in missing the catalytic water chain. Our results brought atomic-level insights into the mechanisms of the two drugs in DNMT3A, which could benefit the new generation of drug design for the DNMTs.
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Affiliation(s)
- Wei Yang
- Warshel Institute for Computational Biology, School of Medicine, The Chinese University of Hong Kong, Shenzhen 518172, China
- National Clinical Research Center for Infectious Diseases, Shenzhen Third People’s Hospital, Shenzhen 518112, China
| | - Jingyuan Zhuang
- Warshel Institute for Computational Biology, School of Medicine, The Chinese University of Hong Kong, Shenzhen 518172, China
| | - Chen Li
- Biomedicine Discovery Institute, Department of Biochemistry and Molecular Biology, Monash University, Melbourne, VIC 3800, Australia;
| | - Chen Bai
- Warshel Institute for Computational Biology, School of Medicine, The Chinese University of Hong Kong, Shenzhen 518172, China
- School of Life and Health Sciences, The Chinese University of Hong Kong, Shenzhen 518172, China
- School of Medicine, The Chinese University of Hong Kong, Shenzhen 518172, China
| | - Guijuan Cheng
- Warshel Institute for Computational Biology, School of Medicine, The Chinese University of Hong Kong, Shenzhen 518172, China
- School of Life and Health Sciences, The Chinese University of Hong Kong, Shenzhen 518172, China
- School of Medicine, The Chinese University of Hong Kong, Shenzhen 518172, China
- Shenzhen Futian Biomedical Innovation R&D Center, The Chinese University of Hong Kong, Shenzhen 518017, China
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5
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Zhang Z, Wang G, Zhong K, Chen Y, Yang N, Lu Q, Yuan B, Wang Z, Li H, Guo L, Zhang R, Wu Z, Zheng M, Zhao S, Tang X, Shao B, Tong A. A drug screening to identify novel combinatorial strategies for boosting cancer immunotherapy efficacy. J Transl Med 2023; 21:23. [PMID: 36635683 PMCID: PMC9838049 DOI: 10.1186/s12967-023-03875-4] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2022] [Accepted: 01/03/2023] [Indexed: 01/14/2023] Open
Abstract
BACKGROUND Chimeric antigen receptor (CAR) T cells and immune checkpoint blockades (ICBs) have made remarkable breakthroughs in cancer treatment, but the efficacy is still limited for solid tumors due to tumor antigen heterogeneity and the tumor immune microenvironment. The restrained treatment efficacy prompted us to seek new potential therapeutic methods. METHODS In this study, we conducted a small molecule compound library screen in a human BC cell line to identify whether certain drugs contribute to CAR T cell killing. Signaling pathways of tumor cells and T cells affected by the screened drugs were predicted via RNA sequencing. Among them, the antitumor activities of JK184 in combination with CAR T cells or ICBs were evaluated in vitro and in vivo. RESULTS We selected three small molecule drugs from a compound library, among which JK184 directly induces tumor cell apoptosis by inhibiting the Hedgehog signaling pathway, modulates B7-H3 CAR T cells to an effector memory phenotype, and promotes B7-H3 CAR T cells cytokine secretion in vitro. In addition, our data suggested that JK184 exerts antitumor activities and strongly synergizes with B7-H3 CAR T cells or ICBs in vivo. Mechanistically, JK184 enhances B7-H3 CAR T cells infiltrating in xenograft mouse models. Moreover, JK184 combined with ICB markedly reshaped the tumor immune microenvironment by increasing effector T cells infiltration and inflammation cytokine secretion, inhibiting the recruitment of MDSCs and the transition of M2-type macrophages in an immunocompetent mouse model. CONCLUSION These data show that JK184 may be a potential adjutant in combination with CAR T cells or ICB therapy.
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Affiliation(s)
- Zongliang Zhang
- grid.412901.f0000 0004 1770 1022State Key Laboratory of Biotherapy and Cancer Center, Research Unit of Gene and Immunotherapy, Chinese Academy of Medical Sciences, Collaborative Innovation Center of Biotherapy, West China Hospital, Sichuan University, Chengdu, 610041 Sichuan Province China
| | - Guoqing Wang
- grid.412901.f0000 0004 1770 1022Department of Neurosurgery, West China Hospital, West China Medical School, Sichuan University, Chengdu, 610041 Sichuan Province China
| | - Kunhong Zhong
- grid.412901.f0000 0004 1770 1022State Key Laboratory of Biotherapy and Cancer Center, Research Unit of Gene and Immunotherapy, Chinese Academy of Medical Sciences, Collaborative Innovation Center of Biotherapy, West China Hospital, Sichuan University, Chengdu, 610041 Sichuan Province China
| | - Yongdong Chen
- grid.412901.f0000 0004 1770 1022State Key Laboratory of Biotherapy and Cancer Center, Research Unit of Gene and Immunotherapy, Chinese Academy of Medical Sciences, Collaborative Innovation Center of Biotherapy, West China Hospital, Sichuan University, Chengdu, 610041 Sichuan Province China
| | - Nian Yang
- grid.412901.f0000 0004 1770 1022State Key Laboratory of Biotherapy and Cancer Center, Research Unit of Gene and Immunotherapy, Chinese Academy of Medical Sciences, Collaborative Innovation Center of Biotherapy, West China Hospital, Sichuan University, Chengdu, 610041 Sichuan Province China
| | - Qizhong Lu
- grid.412901.f0000 0004 1770 1022State Key Laboratory of Biotherapy and Cancer Center, Research Unit of Gene and Immunotherapy, Chinese Academy of Medical Sciences, Collaborative Innovation Center of Biotherapy, West China Hospital, Sichuan University, Chengdu, 610041 Sichuan Province China
| | - Boyang Yuan
- grid.412901.f0000 0004 1770 1022Department of Neurosurgery, West China Hospital, West China Medical School, Sichuan University, Chengdu, 610041 Sichuan Province China
| | - Zeng Wang
- grid.412901.f0000 0004 1770 1022State Key Laboratory of Biotherapy and Cancer Center, Research Unit of Gene and Immunotherapy, Chinese Academy of Medical Sciences, Collaborative Innovation Center of Biotherapy, West China Hospital, Sichuan University, Chengdu, 610041 Sichuan Province China
| | - Hexian Li
- grid.412901.f0000 0004 1770 1022State Key Laboratory of Biotherapy and Cancer Center, Research Unit of Gene and Immunotherapy, Chinese Academy of Medical Sciences, Collaborative Innovation Center of Biotherapy, West China Hospital, Sichuan University, Chengdu, 610041 Sichuan Province China
| | - Liping Guo
- grid.412901.f0000 0004 1770 1022State Key Laboratory of Biotherapy and Cancer Center, Research Unit of Gene and Immunotherapy, Chinese Academy of Medical Sciences, Collaborative Innovation Center of Biotherapy, West China Hospital, Sichuan University, Chengdu, 610041 Sichuan Province China
| | - Ruyuan Zhang
- grid.412901.f0000 0004 1770 1022State Key Laboratory of Biotherapy and Cancer Center, Research Unit of Gene and Immunotherapy, Chinese Academy of Medical Sciences, Collaborative Innovation Center of Biotherapy, West China Hospital, Sichuan University, Chengdu, 610041 Sichuan Province China
| | - Zhiguo Wu
- grid.412901.f0000 0004 1770 1022State Key Laboratory of Biotherapy and Cancer Center, Research Unit of Gene and Immunotherapy, Chinese Academy of Medical Sciences, Collaborative Innovation Center of Biotherapy, West China Hospital, Sichuan University, Chengdu, 610041 Sichuan Province China
| | - Meijun Zheng
- grid.412901.f0000 0004 1770 1022Department of Otolaryngology, Head and Neck Surgery, West China Hospital, West China Medical School, Sichuan University, Chengdu, 610041 Sichuan Province China
| | - Shasha Zhao
- grid.412901.f0000 0004 1770 1022State Key Laboratory of Biotherapy and Cancer Center, Research Unit of Gene and Immunotherapy, Chinese Academy of Medical Sciences, Collaborative Innovation Center of Biotherapy, West China Hospital, Sichuan University, Chengdu, 610041 Sichuan Province China
| | - Xin Tang
- grid.412901.f0000 0004 1770 1022Department of Neurosurgery, West China Hospital, West China Medical School, Sichuan University, Chengdu, 610041 Sichuan Province China
| | - Bin Shao
- grid.412901.f0000 0004 1770 1022State Key Laboratory of Biotherapy and Cancer Center, Research Unit of Gene and Immunotherapy, Chinese Academy of Medical Sciences, Collaborative Innovation Center of Biotherapy, West China Hospital, Sichuan University, Chengdu, 610041 Sichuan Province China ,grid.13291.380000 0001 0807 1581State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, 610041 China
| | - Aiping Tong
- grid.412901.f0000 0004 1770 1022State Key Laboratory of Biotherapy and Cancer Center, Research Unit of Gene and Immunotherapy, Chinese Academy of Medical Sciences, Collaborative Innovation Center of Biotherapy, West China Hospital, Sichuan University, Chengdu, 610041 Sichuan Province China
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Lamiable-Oulaidi F, Harijan RK, Shaffer KJ, Crump DR, Sun Y, Du Q, Gulab SA, Khan AA, Luxenburger A, Woolhouse AD, Sidoli S, Tyler PC, Schramm VL. Synthesis and Characterization of Transition-State Analogue Inhibitors against Human DNA Methyltransferase 1. J Med Chem 2022; 65:5462-5494. [PMID: 35324190 DOI: 10.1021/acs.jmedchem.1c01869] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Hypermethylation of CpG regions by human DNA methyltransferase 1 (DNMT1) silences tumor-suppression genes, and inhibition of DNMT1 can reactivate silenced genes. The 5-azacytidines are approved inhibitors of DNMT1, but their mutagenic mechanism limits their utility. A synthon approach from the analogues of S-adenosylhomocysteine, methionine, and deoxycytidine recapitulated the chemical features of the DNMT1 transition state in the synthesis of 16 chemically stable transition-state mimics. Inhibitors causing both full and partial inhibition of purified DNMT1 were characterized. The inhibitors show modest selectivity for DNMT1 versus DNMT3b. Active-site docking predicts inhibitor interactions with S-adenosyl-l-methionine and deoxycytidine regions of the catalytic site, validated by direct binding analysis. Inhibitor action with purified DNMT1 is not reflected in cultured cells. A partial inhibitor activated cellular DNA methylation, and a full inhibitor had no effect on cellular DNA methylation. These compounds provide chemical access to a new family of noncovalent DNMT chemical scaffolds for use in DNA methyltransferases.
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Affiliation(s)
- Farah Lamiable-Oulaidi
- The Ferrier Research Institute, Victoria University of Wellington, P.O. Box 33436, Petone 5046, New Zealand
| | - Rajesh K Harijan
- Biochemistry Department, Albert Einstein College of Medicine, 1300 Morris Park Avenue, Bronx, New York 10461, United States
| | - Karl J Shaffer
- The Ferrier Research Institute, Victoria University of Wellington, P.O. Box 33436, Petone 5046, New Zealand
| | - Douglas R Crump
- The Ferrier Research Institute, Victoria University of Wellington, P.O. Box 33436, Petone 5046, New Zealand
| | - Yan Sun
- Biochemistry Department, Albert Einstein College of Medicine, 1300 Morris Park Avenue, Bronx, New York 10461, United States
| | - Quan Du
- Biochemistry Department, Albert Einstein College of Medicine, 1300 Morris Park Avenue, Bronx, New York 10461, United States
| | - Shivali A Gulab
- The Ferrier Research Institute, Victoria University of Wellington, P.O. Box 33436, Petone 5046, New Zealand
| | - Ashna A Khan
- The Ferrier Research Institute, Victoria University of Wellington, P.O. Box 33436, Petone 5046, New Zealand
| | - Andreas Luxenburger
- The Ferrier Research Institute, Victoria University of Wellington, P.O. Box 33436, Petone 5046, New Zealand
| | - Anthony D Woolhouse
- The Ferrier Research Institute, Victoria University of Wellington, P.O. Box 33436, Petone 5046, New Zealand
| | - Simone Sidoli
- Biochemistry Department, Albert Einstein College of Medicine, 1300 Morris Park Avenue, Bronx, New York 10461, United States
| | - Peter C Tyler
- The Ferrier Research Institute, Victoria University of Wellington, P.O. Box 33436, Petone 5046, New Zealand
| | - Vern L Schramm
- Biochemistry Department, Albert Einstein College of Medicine, 1300 Morris Park Avenue, Bronx, New York 10461, United States
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7
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He Y, Zheng Z, Liu C, Li W, Zhao L, Nie G, Li H. Inhibiting DNA methylation alleviates cisplatin-induced hearing loss by decreasing oxidative stress-induced mitochondria-dependent apoptosis via the LRP1-PI3K/AKT pathway. Acta Pharm Sin B 2022; 12:1305-1321. [PMID: 35530135 PMCID: PMC9069410 DOI: 10.1016/j.apsb.2021.11.002] [Citation(s) in RCA: 33] [Impact Index Per Article: 16.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2021] [Revised: 10/29/2021] [Accepted: 11/01/2021] [Indexed: 12/15/2022] Open
Abstract
Cisplatin-related ototoxicity is a critical side effect of chemotherapy and can lead to irreversible hearing loss. This study aimed to assess the potential effect of the DNA methyltransferase (DNMT) inhibitor RG108 on cisplatin-induced ototoxicity. Immunohistochemistry, apoptosis assay, and auditory brainstem response (ABR) were employed to determine the impacts of RG108 on cisplatin-induced injury in murine hair cells (HCs) and spiral ganglion neurons (SGNs). Rhodamine 123 and TMRM were utilized for mitochondrial membrane potential (MMP) assessment. Reactive oxygen species (ROS) amounts were evaluated by Cellrox green and Mitosox-red probes. Mitochondrial respiratory function evaluation was performed by determining oxygen consumption rates (OCRs). The results showed that RG108 can markedly reduce cisplatin induced damage in HCs and SGNs, and alleviate apoptotic rate by protecting mitochondrial function through preventing ROS accumulation. Furthermore, RG108 upregulated BCL-2 and downregulated APAF1, BAX, and BAD in HEI-OC1 cells, and triggered the PI3K/AKT pathway. Decreased expression of low-density lipoprotein receptor-related protein 1 (LRP1) and high methylation of the LRP1 promoter were observed after cisplatin treatment. RG108 treatment can increase LRP1 expression and decrease LRP1 promoter methylation. In conclusion, RG108 might represent a new potential agent for preventing hearing loss induced by cisplatin via activating the LRP1-PI3K/AKT pathway.
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Key Words
- 5-mC, 5-methylcytosine
- ABR, auditory brainstem response
- Apoptosis
- Cisplatin
- DNMT
- DNMT, DNA methyltransferase
- EdU, 5-ethynyl-2′-deoxyuridine
- HCs, hair cells
- Hair cell
- IHCs, inner hair cells
- LRP1, low-density lipoprotein receptor-related protein 1
- MMP, mitochondrial membrane potential
- Mitochondrial dysfunction
- OCRs, oxygen consumption rates
- OHCs, outer hair cells
- PI, propidium iodide
- RG108
- ROS
- ROS, reactive oxygen species
- SGNs, spiral ganglion neurons
- Spiral ganglion neurons
- TUNEL, terminal deoxynucleotidyl transferase-mediated dUTP nick-end-labeling
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Mechanisms and Biological Roles of DNA Methyltransferases and DNA Methylation: From Past Achievements to Future Challenges. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2022; 1389:1-19. [DOI: 10.1007/978-3-031-11454-0_1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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9
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Inhibitors of DNA Methylation. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2022; 1389:471-513. [DOI: 10.1007/978-3-031-11454-0_17] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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10
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Z-DNA as a Tool for Nuclease-Free DNA Methyltransferase Assay. Int J Mol Sci 2021; 22:ijms222111990. [PMID: 34769422 PMCID: PMC8585049 DOI: 10.3390/ijms222111990] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2021] [Revised: 10/29/2021] [Accepted: 10/30/2021] [Indexed: 01/16/2023] Open
Abstract
Methylcytosines in mammalian genomes are the main epigenetic molecular codes that switch off the repertoire of genes in cell-type and cell-stage dependent manners. DNA methyltransferases (DMT) are dedicated to managing the status of cytosine methylation. DNA methylation is not only critical in normal development, but it is also implicated in cancers, degeneration, and senescence. Thus, the chemicals to control DMT have been suggested as anticancer drugs by reprogramming the gene expression profile in malignant cells. Here, we report a new optical technique to characterize the activity of DMT and the effect of inhibitors, utilizing the methylation-sensitive B-Z transition of DNA without bisulfite conversion, methylation-sensing proteins, and polymerase chain reaction amplification. With the high sensitivity of single-molecule FRET, this method detects the event of DNA methylation in a single DNA molecule and circumvents the need for amplification steps, permitting direct interpretation. This method also responds to hemi-methylated DNA. Dispensing with methylation-sensitive nucleases, this method preserves the molecular integrity and methylation state of target molecules. Sparing methylation-sensing nucleases and antibodies helps to avoid errors introduced by the antibody’s incomplete specificity or variable activity of nucleases. With this new method, we demonstrated the inhibitory effect of several natural bio-active compounds on DMT. All taken together, our method offers quantitative assays for DMT and DMT-related anticancer drugs.
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11
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Xiao W, Zhou Q, Wen X, Wang R, Liu R, Wang T, Shi J, Hu Y, Hou J. Small-Molecule Inhibitors Overcome Epigenetic Reprogramming for Cancer Therapy. Front Pharmacol 2021; 12:702360. [PMID: 34603017 PMCID: PMC8484527 DOI: 10.3389/fphar.2021.702360] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2021] [Accepted: 08/02/2021] [Indexed: 12/12/2022] Open
Abstract
Cancer treatment is a significant challenge for the global health system, although various pharmacological and therapeutic discoveries have been made. It has been widely established that cancer is associated with epigenetic modification, which is reversible and becomes an attractive target for drug development. Adding chemical groups to the DNA backbone and modifying histone proteins impart distinct characteristics on chromatin architecture. This process is mediated by various enzymes modifying chromatin structures to achieve the diversity of epigenetic space and the intricacy in gene expression files. After decades of effort, epigenetic modification has represented the hallmarks of different cancer types, and the enzymes involved in this process have provided novel targets for antitumor therapy development. Epigenetic drugs show significant effects on both preclinical and clinical studies in which the target development and research offer a promising direction for cancer therapy. Here, we summarize the different types of epigenetic enzymes which target corresponding protein domains, emphasize DNA methylation, histone modifications, and microRNA-mediated cooperation with epigenetic modification, and highlight recent achievements in developing targets for epigenetic inhibitor therapy. This article reviews current anticancer small-molecule inhibitors targeting epigenetic modified enzymes and displays their performances in different stages of clinical trials. Future studies are further needed to address their off-target effects and cytotoxicity to improve their clinical translation.
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Affiliation(s)
- Wenjing Xiao
- School of Materials Science and Engineering, Southwest Jiaotong University, Chengdu, China.,Department of Pharmacy, The General Hospital of Western Theater Command of PLA, Chengdu, China
| | - Qiaodan Zhou
- Department of Ultrasonic, Sichuan Academy of Medical Sciences and Sichuan Provincial People's Hospital, School of Medicine, University of Electronic Science and Technology of China, Chengdu, China
| | - Xudong Wen
- Department of Gastroenterology and Hepatology, Chengdu First People's Hospital, Chengdu, China
| | - Rui Wang
- Information Department of Medical Security Center, The General Hospital of Western Theater Command of PLA, Chengdu, China
| | - Ruijie Liu
- School of Materials Science and Engineering, Southwest Jiaotong University, Chengdu, China
| | - Tingting Wang
- School of Materials Science and Engineering, Southwest Jiaotong University, Chengdu, China
| | - Jianyou Shi
- Personalized Drug Therapy Key Laboratory of Sichuan Province, Department of Pharmacy, Sichuan Academy of Medical Sciences and Sichuan Provincial People's Hospital, School of Medicine, University of Electronic Science and Technology of China, Chengdu, China
| | - Yonghe Hu
- School of Materials Science and Engineering, Southwest Jiaotong University, Chengdu, China.,Department of Pharmacy, The General Hospital of Western Theater Command of PLA, Chengdu, China
| | - Jun Hou
- School of Materials Science and Engineering, Southwest Jiaotong University, Chengdu, China.,Department of Pharmacy, The General Hospital of Western Theater Command of PLA, Chengdu, China
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12
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Cui G, Wang C, Lin Z, Feng X, Wei M, Miao Z, Sun Z, Wei F. Prognostic and immunological role of Ras-related protein Rap1b in pan-cancer. Bioengineered 2021; 12:4828-4840. [PMID: 34346294 PMCID: PMC8806554 DOI: 10.1080/21655979.2021.1955559] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Ras-related Protein Rap1b, a GTP-binding protein belonging to the proximal RAS, which affects tumor progression through regulating tumor cell proliferation, invasion and participates in the functions of various immune cells. However, the potential roles and mechanisms of Rap1b in tumor progression and immunology remains unclear. In this study, we systematically analyzed the pan-cancer expression and prognostic correlation of Rap1b based on GTEX, CCLE, Oncomine, PrognoScan, Kaplan–Meier plotters and TCGA databases. The potential correlations of Rap1b with immune infiltration were revealed via TIMER and TCGA database. SangerBox database was used to analyzed the correlations between Rap1b expression and immune checkpoint (ICP), tumor mutational burden (TMB), microsatellite instability (MSI), mismatch repairs (MMRs) and DNA methylation. The results indicated that the expression level of Rap1b varies in different tumors. Meanwhile, the expression level of Rap1b strongly correlated with prognosis in patients with tumors, higher expression of Rap1b usually was linked to poor prognosis in different datasets. Rap1b was correlated closely with tumor immunity and interacted with various immune cells in different types of cancers. In addition, there were significant positive correlations between Rap1b expression and ICP, TMB, MSI, MMRs and DNA methylation. In conclusion, the results of pan-cancer analysis showed that the abnormal Rap1b expression was related to poor prognosis and tumor immune infiltration in different cancers. Furthermore, Rap1b gene may be used as a potential biomarker of clinical tumor prognosis.
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Affiliation(s)
- Guoliang Cui
- Department of Gastroenterology, The Second Affiliated Hospital of Nanjing University of Chinese Medicine, Nanjing, China.,Department of Traditional Chinese Medicine, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China.,Institute of Integrated Chinese and Western Medicine, Nanjing Medical University, Nanjing, China
| | - Can Wang
- Department of Gastroenterology, The Second Affiliated Hospital of Nanjing University of Chinese Medicine, Nanjing, China
| | - Zhenyan Lin
- Department of Traditional Chinese Medicine, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China.,Institute of Integrated Chinese and Western Medicine, Nanjing Medical University, Nanjing, China
| | - Xiaoke Feng
- Department of Traditional Chinese Medicine, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China.,Institute of Integrated Chinese and Western Medicine, Nanjing Medical University, Nanjing, China
| | - Muxin Wei
- Department of Traditional Chinese Medicine, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China.,Institute of Integrated Chinese and Western Medicine, Nanjing Medical University, Nanjing, China
| | - Zhengyue Miao
- Department of Traditional Chinese Medicine, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China.,Institute of Integrated Chinese and Western Medicine, Nanjing Medical University, Nanjing, China
| | - Zhiguang Sun
- Department of Gastroenterology, The Second Affiliated Hospital of Nanjing University of Chinese Medicine, Nanjing, China
| | - Fei Wei
- Department of Physiology, School of Medicine & Holistic Integrative Medicine, Nanjing University of Chinese Medicine, Nanjing, China
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13
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Flausino CS, Daniel FI, Modolo F. DNA methylation in oral squamous cell carcinoma: from its role in carcinogenesis to potential inhibitor drugs. Crit Rev Oncol Hematol 2021; 164:103399. [PMID: 34147646 DOI: 10.1016/j.critrevonc.2021.103399] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2020] [Revised: 06/02/2021] [Accepted: 06/04/2021] [Indexed: 02/06/2023] Open
Abstract
DNA methylation is one of epigenetic changes most frequently studied nowadays, together with its relationship with oral carcinogenesis. A group of enzymes is responsible for methylation process, known as DNA methyltransferases (DNMT). Although essential during embryogenesis, DNA methylation pattern alterations, including global hypomethylation or gene promoter hypermethylation, can be respectively associated with chromosomal instability and tumor suppressor gene silencing. Higher expression of DNA methyltransferases is a common finding in oral cancer and may contribute to inactivation of important tumor suppressor genes, influencing development, progression, metastasis, and prognosis of the tumor. To control these alterations, inhibitor drugs have been developed as a way to regulate DNMT overexpression, and they are intended to be associated with ongoing chemo- and radiotherapy in oral cancer treatments. In this article, we aimed to highlight the current knowledge about DNA methylation in oral cancer, including main hyper/hypomethylated genes, DNMT expression and its inhibitor treatments.
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Affiliation(s)
| | - Filipe Ivan Daniel
- Federal University of Santa Catarina, Florianópolis, Santa Catarina, Brazil.
| | - Filipe Modolo
- Federal University of Santa Catarina, Florianópolis, Santa Catarina, Brazil
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14
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Yalcin D, Otu HH. An Unbiased Predictive Model to Detect DNA Methylation Propensity of CpG Islands in the Human Genome. Curr Bioinform 2021. [DOI: 10.2174/1574893615999200724145835] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Background:
Epigenetic repression mechanisms play an important role in gene
regulation, specifically in cancer development. In many cases, a CpG island’s (CGI) susceptibility
or resistance to methylation is shown to be contributed by local DNA sequence features.
Objective:
To develop unbiased machine learning models–individually and combined for different
biological features–that predict the methylation propensity of a CGI.
Methods:
We developed our model consisting of CGI sequence features on a dataset of 75
sequences (28 prone, 47 resistant) representing a genome-wide methylation structure. We tested
our model on two independent datasets that are chromosome (132 sequences) and disease (70
sequences) specific.
Results:
We provided improvements in prediction accuracy over previous models. Our results
indicate that combined features better predict the methylation propensity of a CGI (area under the
curve (AUC) ~0.81). Our global methylation classifier performs well on independent datasets
reaching an AUC of ~0.82 for the complete model and an AUC of ~0.88 for the model using select
sequences that better represent their classes in the training set. We report certain de novo motifs
and transcription factor binding site (TFBS) motifs that are consistently better in separating prone
and resistant CGIs.
Conclusion:
Predictive models for the methylation propensity of CGIs lead to a better
understanding of disease mechanisms and can be used to classify genes based on their tendency to
contain methylation prone CGIs, which may lead to preventative treatment strategies. MATLAB®
and Python™ scripts used for model building, prediction, and downstream analyses are available
at https://github.com/dicleyalcin/methylProp_predictor.
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Affiliation(s)
- Dicle Yalcin
- Department of Electrical and Computer Engineering, University of Nebraska-Lincoln, Lincoln, NE, 68588, United States
| | - Hasan H. Otu
- Department of Electrical and Computer Engineering, University of Nebraska-Lincoln, Lincoln, NE, 68588, United States
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15
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Vural S, Palmisano A, Reinhold WC, Pommier Y, Teicher BA, Krushkal J. Association of expression of epigenetic molecular factors with DNA methylation and sensitivity to chemotherapeutic agents in cancer cell lines. Clin Epigenetics 2021; 13:49. [PMID: 33676569 PMCID: PMC7936435 DOI: 10.1186/s13148-021-01026-4] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2020] [Accepted: 02/10/2021] [Indexed: 12/11/2022] Open
Abstract
BACKGROUND Altered DNA methylation patterns play important roles in cancer development and progression. We examined whether expression levels of genes directly or indirectly involved in DNA methylation and demethylation may be associated with response of cancer cell lines to chemotherapy treatment with a variety of antitumor agents. RESULTS We analyzed 72 genes encoding epigenetic factors directly or indirectly involved in DNA methylation and demethylation processes. We examined association of their pretreatment expression levels with methylation beta-values of individual DNA methylation probes, DNA methylation averaged within gene regions, and average epigenome-wide methylation levels. We analyzed data from 645 cancer cell lines and 23 cancer types from the Cancer Cell Line Encyclopedia and Genomics of Drug Sensitivity in Cancer datasets. We observed numerous correlations between expression of genes encoding epigenetic factors and response to chemotherapeutic agents. Expression of genes encoding a variety of epigenetic factors, including KDM2B, DNMT1, EHMT2, SETDB1, EZH2, APOBEC3G, and other genes, was correlated with response to multiple agents. DNA methylation of numerous target probes and gene regions was associated with expression of multiple genes encoding epigenetic factors, underscoring complex regulation of epigenome methylation by multiple intersecting molecular pathways. The genes whose expression was associated with methylation of multiple epigenome targets encode DNA methyltransferases, TET DNA methylcytosine dioxygenases, the methylated DNA-binding protein ZBTB38, KDM2B, SETDB1, and other molecular factors which are involved in diverse epigenetic processes affecting DNA methylation. While baseline DNA methylation of numerous epigenome targets was correlated with cell line response to antitumor agents, the complex relationships between the overlapping effects of each epigenetic factor on methylation of specific targets and the importance of such influences in tumor response to individual agents require further investigation. CONCLUSIONS Expression of multiple genes encoding epigenetic factors is associated with drug response and with DNA methylation of numerous epigenome targets that may affect response to therapeutic agents. Our findings suggest complex and interconnected pathways regulating DNA methylation in the epigenome, which may both directly and indirectly affect response to chemotherapy.
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Affiliation(s)
- Suleyman Vural
- Biometric Research Program, Division of Cancer Treatment and Diagnosis, National Cancer Institute, 9609 Medical Center Dr., Rockville, MD, 20850, USA
| | - Alida Palmisano
- Biometric Research Program, Division of Cancer Treatment and Diagnosis, National Cancer Institute, 9609 Medical Center Dr., Rockville, MD, 20850, USA
- General Dynamics Information Technology (GDIT), 3150 Fairview Park Drive, Falls Church, VA, 22042, USA
| | - William C Reinhold
- Developmental Therapeutics Branch, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD, 20892, USA
| | - Yves Pommier
- Developmental Therapeutics Branch, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD, 20892, USA
| | - Beverly A Teicher
- Molecular Pharmacology Program, Division of Cancer Treatment and Diagnosis, National Cancer Institute, Bethesda, MD, 20892, USA
| | - Julia Krushkal
- Biometric Research Program, Division of Cancer Treatment and Diagnosis, National Cancer Institute, 9609 Medical Center Dr., Rockville, MD, 20850, USA.
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16
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Synthesis, Cytotoxic Activity, Crystal Structure, DFT Studies and Molecular Docking of 3-Amino-1-(2,5-dichlorophenyl)-8-methoxy-1H-benzo[f]chromene-2-carbonitrile. CRYSTALS 2021. [DOI: 10.3390/cryst11020184] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
The target compound 3-amino-1-(2,5-d ichlorophenyl)-8-methoxy-1H-benzo[f]-chromene-2-carbonitrile (4) was synthesized via a reaction of 6-methoxynaphthalen-2-ol (1), 2,5-dichlorobenzaldehyde (2), and malononitrile (3) in ethanolic piperidine solution under microwave irradiation. The newly synthesized β-enaminonitrile was characterized by FT-IR, 1H NMR, 13C NMR, mass spectroscopy, elemental analysis and X-ray diffraction data. Its cytotoxic activity was evaluated against three different human cancer cell lines MDA-MB-231, A549, and MIA PaCa-2 in comparison to the positive controls etoposide and camptothecin employing the XTT cell viability assay. The analysis of the Hirshfeld surface was utilized to visualize the reliability of the crystal package. The obtained results confirmed that the tested molecule revealed promising cytotoxic activities against the three cancer cell lines. Furthermore, theoretical calculations (DFT) were carried out with the Becke3-Lee-Yang-parr (B3LYP) level using 6-311++G(d,p) basis. The optimization geometry for molecular structures was in agreement with the X-ray structure data. The HOMO-LUMO energy gap of the studied system was discussed. The intermolecular-interactions were studied through analysis of the topological-electron-density(r) using the QTAIM and NCI methods. The novel compound exhibited favorable ADMET properties and its molecular modeling analysis showed strong interaction with DNA methyltransferase 1.
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17
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Liu R, Wu XM, He X, Wang RZ, Yin XY, Zhou F, Ji MH, Shen JC. Contribution of DNA methyltransferases to spared nerve injury induced depression partially through epigenetically repressing Bdnf in hippocampus: Reversal by ketamine. Pharmacol Biochem Behav 2021; 200:173079. [DOI: 10.1016/j.pbb.2020.173079] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/29/2020] [Revised: 11/22/2020] [Accepted: 11/23/2020] [Indexed: 12/31/2022]
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18
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Li S, Li P, Liu W, Shang J, Qiu S, Li X, Liu W, Shi H, Zhou M, Liu H. Danhong Injection Alleviates Cardiac Fibrosis via Preventing the Hypermethylation of Rasal1 and Rassf1 in TAC Mice. OXIDATIVE MEDICINE AND CELLULAR LONGEVITY 2020; 2020:3158108. [PMID: 33456666 PMCID: PMC7787771 DOI: 10.1155/2020/3158108] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/01/2020] [Revised: 12/02/2020] [Accepted: 12/06/2020] [Indexed: 12/11/2022]
Abstract
BACKGROUND/AIM Danhong injection (DHI) is a Chinese patent drug used for relieving cardiovascular diseases. Recent studies have suggested that DNA methylation plays a pivotal role in the maintenance of cardiac fibrosis (CF) in cardiovascular diseases. This study was aimed at identifying the effect and the underlying mechanism of DHI on CF, especially the DNA methylation. METHODS A CF murine model was established by thoracic aortic constriction (TAC). A 28-day daily treatment with or without DHI via intraperitoneal injection was carried out immediately following TAC surgery. The changes in cardiac function, pathology, and fibrosis following TAC were measured by echocardiography and immunostaining. We used methyl-seq analysis to assess the DNA methylation changes in whole genes and identified the methylation changes of two Ras signaling-related genes in TAC mice, including Ras protein activator like-1 (Rasal1) and Ras-association domain family 1 (Rassf1). Next, the methylation status and expression levels of Rasal1 and Rassf1 genes were consolidated by bisulfite sequencing, quantitative reverse transcription polymerase chain reaction (RT-qPCR), and Western blotting, respectively. To determine the underlying molecular mechanism, the expressions of DNA methyltransferases (DNMTs), Tet methylcytosine dioxygenase 3 (TET3), fibrosis-related genes, and the activity of Ras/ERK were measured by RT-qPCR and Western blotting. RESULTS DHI treatment alleviated CF and significantly improved cardiac function on day 28 of TAC. The methyl-seq analysis identified 42,606 differential methylated sites (DMSs), including 19,618 hypermethylated DMSs and 22,988 hypomethylated DMSs between TAC and sham-operated mice. The enrichment analysis of these DMSs suggested that the methylated regulation of Ras signal transduction and focal adhesion-related genes would be involved in the TAC-induced CF development. The results of bisulfite sequencing revealed that the TAC-induced methylation affected the CpG site in both of Rasal1 and Rassf1 genes, and DHI treatment remarkably downregulated the promoter methylation of Rasal1 and Rassf1 in CF hearts. Furthermore, DHI treatment upregulated the expressions of Rasal1 and Rassf1, inhibited the hyperactivity of Ras/ERK, and decreased the expressions of fibrosis-related genes. Notably, we found that DHI treatment markedly downregulated the expression of DNMT3B in CF hearts, while it did not affect the expressions of DNMT1, DNMT3A, and TET3. CONCLUSION Aberrant DNA methylation of Rasal1 and Rassf1 genes was involved in the CF development. DHI treatment alleviated CF, prevented the hypermethylation of Rasal1 and Rassf1, and downregulated DNMT3B expression in CF hearts.
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Affiliation(s)
- Sinai Li
- Beijing Hospital of Traditional Chinese Medicine, Capital Medical University, Beijing 100010, China
- Beijing Institute of Traditional Chinese Medicine, Beijing 100010, China
| | - Ping Li
- Beijing Hospital of Traditional Chinese Medicine, Capital Medical University, Beijing 100010, China
- Beijing Institute of Traditional Chinese Medicine, Beijing 100010, China
| | - Weihong Liu
- Beijing Hospital of Traditional Chinese Medicine, Capital Medical University, Beijing 100010, China
- Beijing Institute of Traditional Chinese Medicine, Beijing 100010, China
| | - Juju Shang
- Beijing Hospital of Traditional Chinese Medicine, Capital Medical University, Beijing 100010, China
| | - Shenglei Qiu
- Beijing Hospital of Traditional Chinese Medicine, Capital Medical University, Beijing 100010, China
| | - Xiang Li
- Beijing Hospital of Traditional Chinese Medicine, Capital Medical University, Beijing 100010, China
| | - Wei Liu
- Beijing Hospital of Traditional Chinese Medicine, Capital Medical University, Beijing 100010, China
| | - Haoyue Shi
- Beijing Hospital of Traditional Chinese Medicine, Capital Medical University, Beijing 100010, China
| | - Mingxue Zhou
- Beijing Hospital of Traditional Chinese Medicine, Capital Medical University, Beijing 100010, China
- Beijing Institute of Traditional Chinese Medicine, Beijing 100010, China
| | - Hongxu Liu
- Beijing Hospital of Traditional Chinese Medicine, Capital Medical University, Beijing 100010, China
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19
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Tomaselli D, Lucidi A, Rotili D, Mai A. Epigenetic polypharmacology: A new frontier for epi-drug discovery. Med Res Rev 2020; 40:190-244. [PMID: 31218726 PMCID: PMC6917854 DOI: 10.1002/med.21600] [Citation(s) in RCA: 62] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2018] [Revised: 05/10/2019] [Accepted: 05/14/2019] [Indexed: 12/11/2022]
Abstract
Recently, despite the great success achieved by the so-called "magic bullets" in the treatment of different diseases through a marked and specific interaction with the target of interest, the pharmacological research is moving toward the development of "molecular network active compounds," embracing the related polypharmacology approach. This strategy was born to overcome the main limitations of the single target therapy leading to a superior therapeutic effect, a decrease of adverse reactions, and a reduction of potential mechanism(s) of drug resistance caused by robustness and redundancy of biological pathways. It has become clear that multifactorial diseases such as cancer, neurological, and inflammatory disorders, may require more complex therapeutic approaches hitting a certain biological system as a whole. Concerning epigenetics, the goal of the multi-epi-target approach consists in the development of small molecules able to simultaneously and (often) reversibly bind different specific epi-targets. To date, two dual histone deacetylase/kinase inhibitors (CUDC-101 and CUDC-907) are in an advanced stage of clinical trials. In the last years, the growing interest in polypharmacology encouraged the publication of high-quality reviews on combination therapy and hybrid molecules. Hence, to update the state-of-the-art of these therapeutic approaches avoiding redundancy, herein we focused only on multiple medication therapies and multitargeting compounds exploiting epigenetic plus nonepigenetic drugs reported in the literature in 2018. In addition, all the multi-epi-target inhibitors known in literature so far, hitting two or more epigenetic targets, have been included.
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Affiliation(s)
- Daniela Tomaselli
- Department of Chemistry and Technologies of Drugs,
“Sapienza” University of Rome, P.le A. Moro 5, 00185 Roma, Italy
| | - Alessia Lucidi
- Department of Chemistry and Technologies of Drugs,
“Sapienza” University of Rome, P.le A. Moro 5, 00185 Roma, Italy
| | - Dante Rotili
- Department of Chemistry and Technologies of Drugs,
“Sapienza” University of Rome, P.le A. Moro 5, 00185 Roma, Italy
| | - Antonello Mai
- Department of Chemistry and Technologies of Drugs,
“Sapienza” University of Rome, P.le A. Moro 5, 00185 Roma, Italy
- Pasteur Institute - Cenci Bolognetti Foundation, Viale
Regina Elena 291, 00161 Roma, Italy
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20
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Synthesis, Antitumor Activity, and Docking Analysis of New Pyrido[3',2':4,5]furo(thieno)[3,2- d]pyrimidin-8-amines. Molecules 2019; 24:molecules24213952. [PMID: 31683699 PMCID: PMC6864781 DOI: 10.3390/molecules24213952] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2019] [Revised: 10/25/2019] [Accepted: 10/29/2019] [Indexed: 12/17/2022] Open
Abstract
Continuing our research in the field of new heterocyclic compounds, herein we report on the synthesis and antitumor activity of new amino derivatives of pyrido[3',2':4,5](furo)thieno[3,2-d]pyrimidines as well as of two new heterocyclic systems: furo[2-e]imidazo[1,2-c]pyrimidine and furo[2,3-e]pyrimido[1,2-c]pyrimidine. Thus, by refluxing the 8-chloro derivatives of pyrido[3',2':4,5]thieno(furo)[3,2-d]pyrimidines with various amines, the relevant pyrido[3',2':4,5]thieno(furo)[3,2-d]pyrimidin-8-amines were obtained. Further, the cyclization of some amines under the action of phosphorus oxychloride led to the formation of new heterorings: imidazo[1,2-c]pyrimidine and pyrimido[1,2-c]pyrimidine. The possible antitumor activity of the newly synthesized compounds was evaluated in vitro. The biological tests evidenced that some of them showed pronounced antitumor activity. A study of the structure-activity relationships revealed that the compound activity depended mostly on the nature of the amine fragments. A docking analysis was also performed for the most active compounds.
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21
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Vucicevic J, Nikolic K, Mitchell JB. Rational Drug Design of Antineoplastic Agents Using 3D-QSAR, Cheminformatic, and Virtual Screening Approaches. Curr Med Chem 2019; 26:3874-3889. [DOI: 10.2174/0929867324666170712115411] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2017] [Revised: 06/06/2017] [Accepted: 06/13/2017] [Indexed: 01/07/2023]
Abstract
Background:Computer-Aided Drug Design has strongly accelerated the development of novel antineoplastic agents by helping in the hit identification, optimization, and evaluation.Results:Computational approaches such as cheminformatic search, virtual screening, pharmacophore modeling, molecular docking and dynamics have been developed and applied to explain the activity of bioactive molecules, design novel agents, increase the success rate of drug research, and decrease the total costs of drug discovery. Similarity, searches and virtual screening are used to identify molecules with an increased probability to interact with drug targets of interest, while the other computational approaches are applied for the design and evaluation of molecules with enhanced activity and improved safety profile.Conclusion:In this review are described the main in silico techniques used in rational drug design of antineoplastic agents and presented optimal combinations of computational methods for design of more efficient antineoplastic drugs.
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Affiliation(s)
- Jelica Vucicevic
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, University of Belgrade, Vojvode Stepe 450, 11000 Belgrade, Serbia
| | - Katarina Nikolic
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, University of Belgrade, Vojvode Stepe 450, 11000 Belgrade, Serbia
| | - John B.O. Mitchell
- EaStCHEM School of Chemistry and Biomedical Sciences Research Complex, University of St Andrews, St Andrews KY16 9ST, United Kingdom
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22
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Evans DM, Fang J, Silvers T, Delosh R, Laudeman J, Ogle C, Reinhart R, Selby M, Bowles L, Connelly J, Harris E, Krushkal J, Rubinstein L, Doroshow JH, Teicher BA. Exposure time versus cytotoxicity for anticancer agents. Cancer Chemother Pharmacol 2019; 84:359-371. [PMID: 31102023 PMCID: PMC8127868 DOI: 10.1007/s00280-019-03863-w] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2019] [Accepted: 05/02/2019] [Indexed: 12/26/2022]
Abstract
PURPOSE Time is a critical factor in drug action. The duration of inhibition of the target or residence time of the drug molecule on the target often guides drug scheduling. METHODS The effects of time on the concentration-dependent cytotoxicity of approved and investigational agents [300 compounds] were examined in the NCI60 cell line panel in 2D at 2, 3, 7 and in 3D 11 days. RESULTS There was a moderate positive linear relationship between data from the 2-day NCI60 screen and the 3-, 7- and 11-day and a strong positive linear relationship between 3-, 7- and 11-day luminescence screen IC50s by Pearson correlation analysis. Cell growth inhibition by agents selective for a specific cell cycle phase plateaued when susceptible cells were growth inhibited or killed. As time increased the depth of cell growth inhibition increased without change in the IC50. DNA interactive agents had decreasing IC50s with increasing exposure time. Epigenetic agents required longer exposure times; several were only cytotoxic after 11 days' exposure. For HDAC inhibitors, time had little or no effect on concentration response. There were potency differences amongst the three BET bromodomain inhibitors tested, and an exposure duration effect. The PARP inhibitors, rucaparib, niraparib, and veliparib reached IC50s < 10 μM in some cell lines after 11 days. CONCLUSIONS The results suggest that variations in compound exposure time may reflect either mechanism of action or compound chemical half-life. The activity of slow-acting compounds may optimally be assessed in spheroid models that can be monitored over prolonged incubation times.
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Affiliation(s)
- David M Evans
- Molecular Pharmacology Group, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, Frederick, MD, 21702, USA
| | - Jianwen Fang
- Biometric Research Program, Division of Cancer Treatment and Diagnosis, National Cancer Institute, Rockville, MD, 20852, USA
| | - Thomas Silvers
- Molecular Pharmacology Group, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, Frederick, MD, 21702, USA
| | - Rene Delosh
- Molecular Pharmacology Group, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, Frederick, MD, 21702, USA
| | - Julie Laudeman
- Molecular Pharmacology Group, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, Frederick, MD, 21702, USA
| | - Chad Ogle
- Molecular Pharmacology Group, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, Frederick, MD, 21702, USA
| | - Russell Reinhart
- Molecular Pharmacology Group, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, Frederick, MD, 21702, USA
| | - Michael Selby
- Molecular Pharmacology Group, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, Frederick, MD, 21702, USA
| | - Lori Bowles
- Molecular Pharmacology Group, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, Frederick, MD, 21702, USA
| | - John Connelly
- Molecular Pharmacology Group, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, Frederick, MD, 21702, USA
| | - Erik Harris
- Molecular Pharmacology Group, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, Frederick, MD, 21702, USA
| | - Julia Krushkal
- Biometric Research Program, Division of Cancer Treatment and Diagnosis, National Cancer Institute, Rockville, MD, 20852, USA
| | - Larry Rubinstein
- Biometric Research Program, Division of Cancer Treatment and Diagnosis, National Cancer Institute, Rockville, MD, 20852, USA
| | - James H Doroshow
- Developmental Therapeutics Program, Division of Cancer Treatment and Diagnosis, National Cancer Institute, Rockville, MD, 20852, USA
| | - Beverly A Teicher
- Developmental Therapeutics Program, Division of Cancer Treatment and Diagnosis, National Cancer Institute, Rockville, MD, 20852, USA.
- Molecular Pharmacology Branch, National Cancer Institute, RM 4-W602, MSC 9735, 9609 Medical Center Drive, Bethesda, MD, 20892, USA.
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23
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Tang RZ, Zhu JJ, Yang FF, Zhang YP, Xie SA, Liu YF, Yao WJ, Pang W, Han LL, Kong W, Wang YX, Zhang T, Zhou J. DNA methyltransferase 1 and Krüppel-like factor 4 axis regulates macrophage inflammation and atherosclerosis. J Mol Cell Cardiol 2019; 128:11-24. [DOI: 10.1016/j.yjmcc.2019.01.009] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/31/2018] [Revised: 12/20/2018] [Accepted: 01/13/2019] [Indexed: 12/17/2022]
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24
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Kuo IY, Huang YL, Lin CY, Lin CH, Chang WL, Lai WW, Wang YC. SOX17 overexpression sensitizes chemoradiation response in esophageal cancer by transcriptional down-regulation of DNA repair and damage response genes. J Biomed Sci 2019; 26:20. [PMID: 30777052 PMCID: PMC6378712 DOI: 10.1186/s12929-019-0510-4] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2018] [Accepted: 02/04/2019] [Indexed: 12/16/2022] Open
Abstract
Background Prognosis of esophageal squamous cell carcinoma (ESCC) patients is poor and the concurrent chemoradiation therapy (CCRT) provided to ESCC patients often failed due to resistance. Therefore, development of biomarkers for predicting CCRT response is immensely important. In this study, we evaluated the predicting value of SRY (sex determining region Y)-box 17 (SOX17) protein during CCRT and its dysregulation of transcriptional targets in CCRT resistance in ESCC. Methods Pyrosequencing methylation, RT-qPCR and immunohistochemistry assays were performed to examine the DNA methylation, mRNA expression and protein expression levels of SOX17 in endoscopic biopsy from a total of 70 ESCC patients received CCRT. Cell proliferation, clonogenic survival and xenograft growth were used to confirm the sensitization of ESCC cell line KYSE510 in response to cisplatin, radiation or CCRT treatment by SOX17 overexpression in vitro and in vivo. Luciferase activity, RT-qPCR and ChIP-qPCR assays were conducted to examine transcription regulation of SOX17 in KYSE510 parental, KYSE510 radio-resistant cells and their derived xenografts. Results High DNA methylation coincided with low mRNA and protein expression levels of SOX17 in pre-treatment endoscopic biopsy from ESCC patients with poor CCRT response. SOX17 protein expression exhibited a good prediction performance in discriminating poor CCRT responders from good responder. Overexpression of SOX17 sensitized KYSE510 radio-resistant cells to cisplatin, radiation or CCRT treatment in cell and xenograft models. Importantly, SOX17 transcriptionally down-regulated DNA repair and damage response-related genes including BRCA1, BRCA2, RAD51, KU80 DNAPK, p21, SIRT1, NFAT5 and REV3L in KYSE510 radio-resistant cells to achieve the sensitization effect to anti-cancer treatment. Low expression of BRCA1, DNAPK, p21, RAD51 and SIRT1 was confirmed in SOX17 sensitized xenograft tissues derived from radio-resistant ESCC cells. Conclusions Our study reveals a novel mechanism by which SOX17 transcriptionally inactivates DNA repair and damage response-related genes to sensitize ESCC cell or xenograft to CCRT treatment. In addition, we establish a proof-of-concept CCRT prediction biomarker using SOX17 immunohistochemical staining in pre-treatment endoscopic biopsies to identify ESCC patients who are at high risk of CCRT failure and need intensive care. Electronic supplementary material The online version of this article (10.1186/s12929-019-0510-4) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- I-Ying Kuo
- Department of Pharmacology, College of Medicine, National Cheng Kung University, No.1, University Road, Tainan, 70101, Taiwan.,Institute of Basic Medical Sciences, College of Medicine, National Cheng Kung University, No.1, University Road, Tainan, 70101, Taiwan
| | - Yu-Lin Huang
- Department of Pharmacology, College of Medicine, National Cheng Kung University, No.1, University Road, Tainan, 70101, Taiwan
| | - Chien-Yu Lin
- Department of Pharmacology, College of Medicine, National Cheng Kung University, No.1, University Road, Tainan, 70101, Taiwan
| | - Chien-Hsun Lin
- Department of Pharmacology, College of Medicine, National Cheng Kung University, No.1, University Road, Tainan, 70101, Taiwan
| | - Wei-Lun Chang
- Department of Internal Medicine, National Cheng Kung University Hospital, College of Medicine, National Cheng Kung University, No.138, Sheng Li Road, Tainan, 704, Taiwan
| | - Wu-Wei Lai
- Department of Surgery, National Cheng Kung University Hospital, College of Medicine, National Cheng Kung University, No.138, Sheng Li Road, Tainan, 704, Taiwan.
| | - Yi-Ching Wang
- Department of Pharmacology, College of Medicine, National Cheng Kung University, No.1, University Road, Tainan, 70101, Taiwan. .,Institute of Basic Medical Sciences, College of Medicine, National Cheng Kung University, No.1, University Road, Tainan, 70101, Taiwan.
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25
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AKT methylation by SETDB1 promotes AKT kinase activity and oncogenic functions. Nat Cell Biol 2019; 21:226-237. [PMID: 30692625 PMCID: PMC6377565 DOI: 10.1038/s41556-018-0261-6] [Citation(s) in RCA: 97] [Impact Index Per Article: 19.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2017] [Accepted: 12/10/2018] [Indexed: 12/15/2022]
Abstract
Aberrant activation of Akt disturbs proliferation, survival and metabolic homeostasis of various human cancers. Thus, it is critical to understand upstream signaling pathways governing Akt activation. Here, we report that Akt undergoes SETDB1-mediated lysine-methylation to promote its activation, which is antagonized by the Jumonji-family demethylase, KDM4B. Notably, compared with wild-type mice, mice harboring non-methylated mutant Akt1 not only exhibited reduced body size, but also were less prone to carcinogen-induced skin tumors in part due to reduced Akt activation. Mechanistically, Phosphatidylinositol (3,4,5)-trisphosphate (PIP3) interaction with Akt facilitates its interaction with SETDB1 for subsequent Akt methylation, which in turn sustains Akt phosphorylation. Pathologically, genetic alterations including SETDB1 amplification aberrantly promote Akt methylation to facilitate its activation and oncogenic functions. Thus, Akt methylation is an important step synergizing with PI3K signaling to control Akt activation, suggesting that targeting the SETDB1 signaling could be a potential therapeutic strategy for combatting hyperactive Akt-driven cancers.
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26
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Prognostic and therapeutic significance of phosphorylated STAT3 and protein tyrosine phosphatase-6 in peripheral-T cell lymphoma. Blood Cancer J 2018; 8:110. [PMID: 30420593 PMCID: PMC6232096 DOI: 10.1038/s41408-018-0138-8] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2018] [Revised: 09/12/2018] [Accepted: 09/20/2018] [Indexed: 01/05/2023] Open
Abstract
Peripheral T cell lymphomas (PTCL) is a heterogenous group of non-Hodgkin lymphoma and many patients remain refractory to the frontline therapy. Identifying new prognostic markers and treatment is an unmet need in PTCL. We analyzed phospho-STAT3 (pSTAT3) expression in a cohort of 169 PTCL tumors and show overall 38% positivity with varied distribution among PTCL subtypes with 27% (16/59) in PTCL-NOS; 29% (11/38) in AITL, 57% (13/28) in ALK-negative ALCL, and 93% in ALK-pos ALCL (14/15), respectively. Correlative analysis indicated an adverse correlation between pSTAT3 and overall survival (OS). PTPN6, a tyrosine phosphatase and potential negative regulator of STAT3 activity, was suppressed in 62% of PTCL-NOS, 42% of AITL, 60% ALK-neg ALCL, and 86% of ALK-pos ALCL. Loss of PTPN6 combined with pSTAT3 positivity predicted an infwere considered significantferior OS in PTCL cases. In vitro treatment of TCL lines with azacytidine (aza), a DNA methyltransferase inhibitor (DNMTi), restored PTPN6 expression and decreased pSTAT3. Combining DNMTi with JAK3 inhibitor resulted in synergistic antitumor activity in SUDHL1 cell line. Overall, our results suggest that PTPN6 and activated STAT3 can be developed as prognostic markers, and the combination of DNMTi and JAK3 inhibitors as a novel treatment for patients with PTCL subtypes.
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27
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Mackin SJ, O'Neill KM, Walsh CP. Comparison of DNMT1 inhibitors by methylome profiling identifies unique signature of 5-aza-2'deoxycytidine. Epigenomics 2018; 10:1085-1101. [PMID: 30070602 DOI: 10.2217/epi-2017-0171] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
AIM 5-aza-2'deoxycytidine (Aza) is used to treat myelodysplastic syndrome and is in trials for other cancers. It acts chiefly as a hypomethylating agent inhibiting DNMT1. A lack of understanding of off-target effects in normal cells hinders wider usage. MATERIALS & METHODS We compared treatment of the same normosomic, nontransformed fibroblast cell line with Aza and SMARTpool siRNA against DNMT1. Methylation and transcription were assayed using Illumina 450k and HT12 arrays. RESULTS Both Aza and DNMT1 siRNA caused overall hypomethylation, with siRNA more efficient at demethylating gene bodies. Hypomethylation at the promoters of many histones, and hypermethylation at multiple sites genome wide, were unique to Aza treatment. CONCLUSION Aza had important unique effects and targets compared with DNMT1 inhibition via siRNA.
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Affiliation(s)
- Sarah-Jayne Mackin
- Genomic Medicine Research Group, Centre for Molecular Biosciences, Biomedical Sciences Research Institute, Ulster University, Coleraine, BT52 1SA, UK
| | - Karla M O'Neill
- Genomic Medicine Research Group, Centre for Molecular Biosciences, Biomedical Sciences Research Institute, Ulster University, Coleraine, BT52 1SA, UK.,Current address: The Wellcome-Wolfson Institute for Experimental Medicine, Queen's University Belfast, 97 Lisburn Road, Belfast, BT9 7AE, UK
| | - Colum P Walsh
- Genomic Medicine Research Group, Centre for Molecular Biosciences, Biomedical Sciences Research Institute, Ulster University, Coleraine, BT52 1SA, UK
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28
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Andersen GB, Tost J. A Summary of the Biological Processes, Disease-Associated Changes, and Clinical Applications of DNA Methylation. Methods Mol Biol 2018; 1708:3-30. [PMID: 29224136 DOI: 10.1007/978-1-4939-7481-8_1] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
DNA methylation at cytosines followed by guanines, CpGs, forms one of the multiple layers of epigenetic mechanisms controlling and modulating gene expression through chromatin structure. It closely interacts with histone modifications and chromatin remodeling complexes to form the local genomic and higher-order chromatin landscape. DNA methylation is essential for proper mammalian development, crucial for imprinting and plays a role in maintaining genomic stability. DNA methylation patterns are susceptible to change in response to environmental stimuli such as diet or toxins, whereby the epigenome seems to be most vulnerable during early life. Changes of DNA methylation levels and patterns have been widely studied in several diseases, especially cancer, where interest has focused on biomarkers for early detection of cancer development, accurate diagnosis, and response to treatment, but have also been shown to occur in many other complex diseases. Recent advances in epigenome engineering technologies allow now for the large-scale assessment of the functional relevance of DNA methylation. As a stable nucleic acid-based modification that is technically easy to handle and which can be analyzed with great reproducibility and accuracy by different laboratories, DNA methylation is a promising biomarker for many applications.
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Affiliation(s)
- Gitte Brinch Andersen
- Department of Biomedicine, Aarhus University, Aarhus, Denmark
- Laboratory for Epigenetics & Environment, Centre National de Recherche en Génomique Humaine, CEA-Institut de Biologie Francois Jacob, Bâtiment G2, 2 rue Gaston Crémieux, 91000, Evry, France
| | - Jörg Tost
- Laboratory for Epigenetics & Environment, Centre National de Recherche en Génomique Humaine, CEA-Institut de Biologie Francois Jacob, Bâtiment G2, 2 rue Gaston Crémieux, 91000, Evry, France.
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29
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Lungu C, Pinter S, Broche J, Rathert P, Jeltsch A. Modular fluorescence complementation sensors for live cell detection of epigenetic signals at endogenous genomic sites. Nat Commun 2017; 8:649. [PMID: 28935858 PMCID: PMC5608954 DOI: 10.1038/s41467-017-00457-z] [Citation(s) in RCA: 53] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2017] [Accepted: 06/30/2017] [Indexed: 12/23/2022] Open
Abstract
Investigation of the fundamental role of epigenetic processes requires methods for the locus-specific detection of epigenetic modifications in living cells. Here, we address this urgent demand by developing four modular fluorescence complementation-based epigenetic biosensors for live-cell microscopy applications. These tools combine engineered DNA-binding proteins with domains recognizing defined epigenetic marks, both fused to non-fluorescent fragments of a fluorescent protein. The presence of the epigenetic mark at the target DNA sequence leads to the reconstitution of a functional fluorophore. With this approach, we could for the first time directly detect DNA methylation and histone 3 lysine 9 trimethylation at endogenous genomic sites in live cells and follow dynamic changes in these marks upon drug treatment, induction of epigenetic enzymes and during the cell cycle. We anticipate that this versatile technology will improve our understanding of how specific epigenetic signatures are set, erased and maintained during embryonic development or disease onset.Tools for imaging epigenetic modifications can shed light on the regulation of epigenetic processes. Here, the authors present a fluorescence complementation approach for detection of DNA and histone methylation at endogenous genomic sites allowing following of dynamic changes of these marks by live-cell microscopy.
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Affiliation(s)
- Cristiana Lungu
- Department of Biochemistry, Institute of Biochemistry and Technical Biochemistry, Stuttgart University, Allmandring 31, 70569, Stuttgart, Germany
| | - Sabine Pinter
- Department of Biochemistry, Institute of Biochemistry and Technical Biochemistry, Stuttgart University, Allmandring 31, 70569, Stuttgart, Germany
| | - Julian Broche
- Department of Biochemistry, Institute of Biochemistry and Technical Biochemistry, Stuttgart University, Allmandring 31, 70569, Stuttgart, Germany
| | - Philipp Rathert
- Department of Biochemistry, Institute of Biochemistry and Technical Biochemistry, Stuttgart University, Allmandring 31, 70569, Stuttgart, Germany
| | - Albert Jeltsch
- Department of Biochemistry, Institute of Biochemistry and Technical Biochemistry, Stuttgart University, Allmandring 31, 70569, Stuttgart, Germany.
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30
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Hassanzadeh M, Kasymov R, Mahernia S, Adib M, Emperle M, Dukatz M, Bashtrykov P, Jeltsch A, Amanlou M. Discovery of Novel and Selective DNA Methyltransferase 1 Inhibitors by Pharmacophore and Docking-Based Virtual Screening. ChemistrySelect 2017. [DOI: 10.1002/slct.201701734] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Affiliation(s)
- Malihe Hassanzadeh
- Department of Medicinal Chemistry & Drug Design and Development Research Center; Faculty of Pharmacy; Tehran University of Medical Sciences; 16 Azar Ave. Tehran Iran
| | - Rustem Kasymov
- Department of Biochemistry; Institute of Biochemistry and Technical Biochemistry; University Stuttgart; Allmandring 31 70569 Stuttgart Germany
| | - Shabnam Mahernia
- Department of Medicinal Chemistry & Drug Design and Development Research Center; Faculty of Pharmacy; Tehran University of Medical Sciences; 16 Azar Ave. Tehran Iran
| | - Mehdi Adib
- School of Chemistry; College of Science; University of Tehran; Tehran Iran
| | - Max Emperle
- Department of Biochemistry; Institute of Biochemistry and Technical Biochemistry; University Stuttgart; Allmandring 31 70569 Stuttgart Germany
| | - Michael Dukatz
- Department of Biochemistry; Institute of Biochemistry and Technical Biochemistry; University Stuttgart; Allmandring 31 70569 Stuttgart Germany
| | - Pavel Bashtrykov
- Department of Biochemistry; Institute of Biochemistry and Technical Biochemistry; University Stuttgart; Allmandring 31 70569 Stuttgart Germany
| | - Albert Jeltsch
- Department of Biochemistry; Institute of Biochemistry and Technical Biochemistry; University Stuttgart; Allmandring 31 70569 Stuttgart Germany
| | - Massoud Amanlou
- Department of Medicinal Chemistry & Drug Design and Development Research Center; Faculty of Pharmacy; Tehran University of Medical Sciences; 16 Azar Ave. Tehran Iran
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31
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Little AC, Sulovari A, Danyal K, Heppner DE, Seward DJ, van der Vliet A. Paradoxical roles of dual oxidases in cancer biology. Free Radic Biol Med 2017; 110:117-132. [PMID: 28578013 PMCID: PMC5535817 DOI: 10.1016/j.freeradbiomed.2017.05.024] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/15/2017] [Revised: 05/26/2017] [Accepted: 05/30/2017] [Indexed: 02/06/2023]
Abstract
Dysregulated oxidative metabolism is a well-recognized aspect of cancer biology, and many therapeutic strategies are based on targeting cancers by altering cellular redox pathways. The NADPH oxidases (NOXes) present an important enzymatic source of biological oxidants, and the expression and activation of several NOX isoforms are frequently dysregulated in many cancers. Cell-based studies have demonstrated a role for several NOX isozymes in controlling cell proliferation and/or cell migration, further supporting a potential contributing role for NOX in promoting cancer. While various NOX isoforms are often upregulated in cancers, paradoxical recent findings indicate that dual oxidases (DUOXes), normally prominently expressed in epithelial lineages, are frequently suppressed in epithelial-derived cancers by epigenetic mechanisms, although the functional relevance of such DUOX silencing has remained unclear. This review will briefly summarize our current understanding regarding the importance of reactive oxygen species (ROS) and NOXes in cancer biology, and focus on recent observations indicating the unique and seemingly opposing roles of DUOX enzymes in cancer biology. We will discuss current knowledge regarding the functional properties of DUOX, and recent studies highlighting mechanistic consequences of DUOX1 loss in lung cancer, and its consequences for tumor invasiveness and current anticancer therapy. Finally, we will also discuss potentially unique roles for the DUOX maturation factors. Overall, a better understanding of mechanisms that regulate DUOX and the functional consequences of DUOX silencing in cancer may offer valuable new diagnostic insights and novel therapeutic opportunities.
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Affiliation(s)
- Andrew C Little
- Department of Pathology and Laboratory Medicine, Robert Larner, M.D. College of Medicine, University of Vermont, Burlington, VT 05405, United States; Cellular, Molecular, and Biomedical Sciences Graduate Program, University of Vermont, Burlington, VT 05405, United States
| | - Arvis Sulovari
- Cellular, Molecular, and Biomedical Sciences Graduate Program, University of Vermont, Burlington, VT 05405, United States; Department of Microbiology and Molecular Genetics, Robert Larner, M.D. College of Medicine, University of Vermont, Burlington, VT 05405, United States
| | - Karamatullah Danyal
- Department of Pathology and Laboratory Medicine, Robert Larner, M.D. College of Medicine, University of Vermont, Burlington, VT 05405, United States
| | - David E Heppner
- Department of Pathology and Laboratory Medicine, Robert Larner, M.D. College of Medicine, University of Vermont, Burlington, VT 05405, United States
| | - David J Seward
- Department of Pathology and Laboratory Medicine, Robert Larner, M.D. College of Medicine, University of Vermont, Burlington, VT 05405, United States
| | - Albert van der Vliet
- Department of Pathology and Laboratory Medicine, Robert Larner, M.D. College of Medicine, University of Vermont, Burlington, VT 05405, United States; Cellular, Molecular, and Biomedical Sciences Graduate Program, University of Vermont, Burlington, VT 05405, United States.
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32
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Halby L, Menon Y, Rilova E, Pechalrieu D, Masson V, Faux C, Bouhlel MA, David-Cordonnier MH, Novosad N, Aussagues Y, Samson A, Lacroix L, Ausseil F, Fleury L, Guianvarc'h D, Ferroud C, Arimondo PB. Rational Design of Bisubstrate-Type Analogues as Inhibitors of DNA Methyltransferases in Cancer Cells. J Med Chem 2017; 60:4665-4679. [PMID: 28463515 DOI: 10.1021/acs.jmedchem.7b00176] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Aberrant DNA hypermethylation of promoter of tumor suppressor genes is commonly observed in cancer, and its inhibition by small molecules is promising for their reactivation. Here we designed bisubstrate analogues-based inhibitors, by mimicking each substrate, the S-adenosyl-l-methionine and the deoxycytidine, and linking them together. This approach resulted in quinazoline-quinoline derivatives as potent inhibitors of DNMT3A and DNMT1, some showing certain isoform selectivity. We highlighted the importance of (i) the nature and rigidity of the linker between the two moieties for inhibition, as (ii) the presence of the nitrogen on the quinoline group, and (iii) of a hydrophobic group on the quinazoline. The most potent inhibitors induced demethylation of CDKN2A promoter in colon carcinoma HCT116 cells and its reactivation after 7 days of treatment. Furthermore, in a leukemia cell model system, we found a correlation between demethylation of the promoter induced by the treatment, chromatin opening at the promoter, and the reactivation of a reporter gene.
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Affiliation(s)
- Ludovic Halby
- ETaC, Epigenetic Targeting of Cancer, CRDPF, CNRS-Pierre Fabre USR3388 , 3 Avenue H. Curien, 31035 Toulouse cedex 01, France
| | - Yoann Menon
- ETaC, Epigenetic Targeting of Cancer, CRDPF, CNRS-Pierre Fabre USR3388 , 3 Avenue H. Curien, 31035 Toulouse cedex 01, France
| | - Elodie Rilova
- ETaC, Epigenetic Targeting of Cancer, CRDPF, CNRS-Pierre Fabre USR3388 , 3 Avenue H. Curien, 31035 Toulouse cedex 01, France
| | - Dany Pechalrieu
- ETaC, Epigenetic Targeting of Cancer, CRDPF, CNRS-Pierre Fabre USR3388 , 3 Avenue H. Curien, 31035 Toulouse cedex 01, France
| | - Véronique Masson
- ETaC, Epigenetic Targeting of Cancer, CRDPF, CNRS-Pierre Fabre USR3388 , 3 Avenue H. Curien, 31035 Toulouse cedex 01, France
| | - Celine Faux
- ETaC, Epigenetic Targeting of Cancer, CRDPF, CNRS-Pierre Fabre USR3388 , 3 Avenue H. Curien, 31035 Toulouse cedex 01, France
| | - Mohamed Amine Bouhlel
- UMR-S1172-JPARC (Jean-Pierre Aubert Research Center), INSERM, University of Lille, Centre Hospitalier Universitaire de Lille, IRCL , 59045 Lille, France
| | - Marie-Hélène David-Cordonnier
- UMR-S1172-JPARC (Jean-Pierre Aubert Research Center), INSERM, University of Lille, Centre Hospitalier Universitaire de Lille, IRCL , 59045 Lille, France
| | - Natacha Novosad
- ETaC, Epigenetic Targeting of Cancer, CRDPF, CNRS-Pierre Fabre USR3388 , 3 Avenue H. Curien, 31035 Toulouse cedex 01, France
| | - Yannick Aussagues
- ETaC, Epigenetic Targeting of Cancer, CRDPF, CNRS-Pierre Fabre USR3388 , 3 Avenue H. Curien, 31035 Toulouse cedex 01, France
| | - Arnaud Samson
- ETaC, Epigenetic Targeting of Cancer, CRDPF, CNRS-Pierre Fabre USR3388 , 3 Avenue H. Curien, 31035 Toulouse cedex 01, France
| | | | - Fréderic Ausseil
- ETaC, Epigenetic Targeting of Cancer, CRDPF, CNRS-Pierre Fabre USR3388 , 3 Avenue H. Curien, 31035 Toulouse cedex 01, France
| | - Laurence Fleury
- ETaC, Epigenetic Targeting of Cancer, CRDPF, CNRS-Pierre Fabre USR3388 , 3 Avenue H. Curien, 31035 Toulouse cedex 01, France
| | - Dominique Guianvarc'h
- Laboratoire des BioMolécules, UMR 7203, Université Pierre et Marie Curie-Paris 6-ENS-CNRS , 4, place Jussieu, 75252 Paris Cedex 05, France
| | - Clotilde Ferroud
- Laboratoire de Chimie Moléculaire, CMGPCE, EA7341, Conservatoire National des Arts et Métiers , 2 rue Conté, 75003 Paris, France
| | - Paola B Arimondo
- ETaC, Epigenetic Targeting of Cancer, CRDPF, CNRS-Pierre Fabre USR3388 , 3 Avenue H. Curien, 31035 Toulouse cedex 01, France.,Churchill College , CB3 0DS Cambridge, U.K
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Dikmen M. Comparison of the Effects of Curcumin and RG108 on NGF-Induced PC-12 Adh Cell Differentiation and Neurite Outgrowth. J Med Food 2017; 20:376-384. [DOI: 10.1089/jmf.2016.3889] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Affiliation(s)
- Miriş Dikmen
- Department of Pharmacology, Anadolu University, Pharmacy Faculty, Eskişehir, Turkey
- Department of Clinical Pharmacy, Anadolu University, Pharmacy Faculty, Eskişehir, Turkey
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Abstract
Activation of oncogenes or the deactivation of tumor suppressor genes has long been established as the fundamental mechanism leading towards carcinogenesis. Although this age old axiom is vastly accurate, thorough study over the last 15years has given us unprecedented information on the involvement of epigenetic in cancer. Various biochemical pathways that are essential towards tumorigenesis are regulated by the epigenetic phenomenons like remodeling of nucleosome by histone modifications, DNA methylation and miRNA mediated targeting of various genes. Moreover the presence of mutations in the genes controlling the epigenetic players has further strengthened the association of epigenetics in cancer. This merger has opened up newer avenues for targeted anti-cancer drug therapy with numerous pharmaceutical industries focusing on expanding their research and development pipeline with epigenetic drugs. The information provided here elaborates the elementary phenomena of the various epigenetic regulators and discusses their alteration associated with the development of cancer. We also highlight the recent developments in epigenetic drugs combining preclinical and clinical data to signify this evolving field in cancer research.
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Affiliation(s)
- Subhankar Biswas
- Department of Pharmacology, Manipal College of Pharmaceutical Sciences, Manipal University, Manipal 576104, Karnataka, India
| | - C Mallikarjuna Rao
- Department of Pharmacology, Manipal College of Pharmaceutical Sciences, Manipal University, Manipal 576104, Karnataka, India.
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Schiffmann I, Greve G, Jung M, Lübbert M. Epigenetic therapy approaches in non-small cell lung cancer: Update and perspectives. Epigenetics 2016; 11:858-870. [PMID: 27846368 PMCID: PMC5193491 DOI: 10.1080/15592294.2016.1237345] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2016] [Revised: 08/30/2016] [Accepted: 09/12/2016] [Indexed: 10/20/2022] Open
Abstract
Non-small cell lung cancer (NSCLC) still constitutes the most common cancer-related cause of death worldwide. All efforts to introduce suitable treatment options using chemotherapeutics or targeted therapies have, up to this point, failed to exhibit a substantial effect on the 5-year-survival rate. The involvement of epigenetic alterations in the evolution of different cancers has led to the development of epigenetics-based therapies, mainly targeting DNA methyltransferases (DNMTs) and histone-modifying enzymes. So far, their greatest success stories have been registered in hematologic neoplasias. As the effects of epigenetic single agent treatment of solid tumors have been limited, the investigative focus now lies on combination therapies of epigenetically active agents with conventional chemotherapy, immunotherapy, or kinase inhibitors. This review includes a short overview of the most important preclinical approaches as well as an extensive discussion of clinical trials using epigenetic combination therapies in NSCLC, including ongoing trials. Thus, we are providing an overview of what lies ahead in the field of epigenetic combinatory therapies of NSCLC in the coming years.
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Affiliation(s)
- Insa Schiffmann
- Division of Hematology, Oncology and Stem Cell Transplantation, University of Freiburg, Medical Center, Freiburg, Germany
- University of Freiburg, Faculty of Medicine, Freiburg, Germany
| | - Gabriele Greve
- Division of Hematology, Oncology and Stem Cell Transplantation, University of Freiburg, Medical Center, Freiburg, Germany
- University of Freiburg, Faculty of Biology, Freiburg, Germany
| | - Manfred Jung
- University of Freiburg, Institute of Pharmaceutical Sciences, Freiburg, Germany
- German Cancer Consortium (DKTK), Freiburg, Germany
| | - Michael Lübbert
- Division of Hematology, Oncology and Stem Cell Transplantation, University of Freiburg, Medical Center, Freiburg, Germany
- University of Freiburg, Faculty of Medicine, Freiburg, Germany
- German Cancer Consortium (DKTK), Freiburg, Germany
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Megiorni F, Camero S, Ceccarelli S, McDowell HP, Mannarino O, Marampon F, Pizer B, Shukla R, Pizzuti A, Marchese C, Clerico A, Dominici C. DNMT3B in vitro knocking-down is able to reverse embryonal rhabdomyosarcoma cell phenotype through inhibition of proliferation and induction of myogenic differentiation. Oncotarget 2016; 7:79342-79356. [PMID: 27764816 PMCID: PMC5346718 DOI: 10.18632/oncotarget.12688] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2016] [Accepted: 09/29/2016] [Indexed: 01/08/2023] Open
Abstract
Aberrant DNA methylation has been frequently observed in many human cancers, including rhabdomyosarcoma (RMS), the most common soft tissue sarcoma in children. To date, the expression and function of the de novo DNA methyltransferase (DNMT) 3B in RMS have not yet been investigated. Our study show for the first time a significant up-regulation of DNMT3B levels in 14 RMS tumour samples and 4 RMS cell lines in comparison to normal skeletal muscle. Transfection of RD and TE671 cells, two in vitro models of embryonal RMS (ERMS), with a synthetic DNMT3B siRNA decreased cell proliferation by arresting cell cycle at G1 phase, as demonstrated by the reduced expression of Cyclin B1, Cyclin D1 and Cyclin E2, and by the concomitant up-regulation of the checkpoint regulators p21 and p27. DNMT3B depletion also impaired RB phosphorylation status and decreased migratory capacity and clonogenic potential. Interestingly, DNMT3B knock-down was able to commit ERMS cells towards myogenic terminal differentiation, as confirmed by the acquisition of a myogenic-like phenotype and by the increased expression of the myogenic markers MYOD1, Myogenin and MyHC. Finally, inhibition of MEK/ERK signalling by U0126 resulted in a reduction of DNMT3B protein, giving evidence that DNMT3B is a down-stream molecule of this oncogenic pathway.Taken together, our data indicate that altered expression of DNMT3B plays a key role in ERMS development since its silencing is able to reverse cell cancer phenotype by rescuing myogenic program. Epigenetic therapy, by targeting the DNA methylation machinery, may represent a novel therapeutic strategy against RMS.
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Affiliation(s)
- Francesca Megiorni
- Department of Paediatrics and Infantile Neuropsychiatry, Sapienza University of Rome, Rome, Italy
| | - Simona Camero
- Department of Paediatrics and Infantile Neuropsychiatry, Sapienza University of Rome, Rome, Italy
| | - Simona Ceccarelli
- Department of Experimental Medicine, Sapienza University of Rome, Rome, Italy
| | - Heather P. McDowell
- Department of Paediatrics and Infantile Neuropsychiatry, Sapienza University of Rome, Rome, Italy
- Department of Oncology, Alder Hey Children's NHS Foundation Trust, Liverpool, United Kingdom
| | - Olga Mannarino
- Department of Paediatrics and Infantile Neuropsychiatry, Sapienza University of Rome, Rome, Italy
| | - Francesco Marampon
- Department of Biotechnological and Applied Clinical Sciences, University of L'Aquila, L'Aquila, Italy
| | - Barry Pizer
- Department of Oncology, Alder Hey Children's NHS Foundation Trust, Liverpool, United Kingdom
| | - Rajeev Shukla
- Department of Perinatal and Paediatric Pathology, Alder Hey Children's NHS Foundation Trust, Liverpool, United Kingdom
| | - Antonio Pizzuti
- Department of Experimental Medicine, Sapienza University of Rome, Rome, Italy
| | - Cinzia Marchese
- Department of Experimental Medicine, Sapienza University of Rome, Rome, Italy
| | - Anna Clerico
- Department of Paediatrics and Infantile Neuropsychiatry, Sapienza University of Rome, Rome, Italy
| | - Carlo Dominici
- Department of Paediatrics and Infantile Neuropsychiatry, Sapienza University of Rome, Rome, Italy
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Wang XZ, Cheng Y, Wang KL, Liu R, Yang XL, Wen HM, Chai C, Liang JY, Wu H. Peperomin E reactivates silenced tumor suppressor genes in lung cancer cells by inhibition of DNA methyltransferase. Cancer Sci 2016; 107:1506-1519. [PMID: 27501331 PMCID: PMC5084666 DOI: 10.1111/cas.13029] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2016] [Revised: 07/26/2016] [Accepted: 08/01/2016] [Indexed: 12/18/2022] Open
Abstract
Advanced lung cancer has poor prognosis owing to its low sensitivity to current chemotherapy agents. Therefore, discovery of new therapeutic agents is urgently needed. In this study, we investigated the antitumor effects of peperomin E, a secolignan isolated from Peperomia dindygulensis, a frequently used Chinese folk medicine for lung cancer treatment. The results indicate that peperomin E has antiproliferative effects, promoting apoptosis and cell cycle arrest in non‐small‐cell lung cancer (NSCLC) cell lines in a dose‐dependent manner, while showing lower toxicity against normal human lung epidermal cells. Peperomin E inhibited tumor growth in A549 xenograft BALB/c nude mice without significant secondary adverse effects, indicating that it may be safely used to treat NSCLC. Furthermore, the mechanisms underlying the anticancer effects of peperomin E have been investigated. Using an in silico target fishing method, we observed that peperomin E directly interacts with the active domain of DNA methyltransferase 1 (DNMT1), potentially affecting its genome methylation activity. Subsequent experiments verified that peperomin E decreased DNMT1 activity and expression, thereby decreasing global methylation and reactivating the epigenetically silenced tumor suppressor genes including RASSF1A,APC,RUNX3, and p16INK4, which in turn activates their mediated pro‐apoptotic and cell cycle regulatory signaling pathways in lung cancer cells. The observations herein report for the first time that peperomin E is a potential chemotherapeutic agent for NSCLC. The anticancer effects of peperomin E may be partly attributable to its ability to demethylate and reactivate methylation‐silenced tumor suppressor genes through direct inhibition of the activity and expression of DNMT1.
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Affiliation(s)
- Xin-Zhi Wang
- College of Pharmacy, Nanjing University of Chinese Medicine, Nanjing, China
| | - Ying Cheng
- College of Pharmacy, Nanjing University of Chinese Medicine, Nanjing, China
| | - Kui-Long Wang
- College of Pharmacy, Nanjing University of Chinese Medicine, Nanjing, China
| | - Rui Liu
- College of Pharmacy, Nanjing University of Chinese Medicine, Nanjing, China
| | - Xiao-Lin Yang
- College of Pharmacy, Nanjing University of Chinese Medicine, Nanjing, China
| | - Hong-Mei Wen
- College of Pharmacy, Nanjing University of Chinese Medicine, Nanjing, China
| | - Chuan Chai
- College of Pharmacy, Nanjing University of Chinese Medicine, Nanjing, China
| | - Jing-Yu Liang
- Department of Natural Medicinal Chemistry, China Pharmaceutical University, Nanjing, China
| | - Hao Wu
- College of Pharmacy, Nanjing University of Chinese Medicine, Nanjing, China.
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Aldawsari FS, Aguayo-Ortiz R, Kapilashrami K, Yoo J, Luo M, Medina-Franco JL, Velázquez-Martínez CA. Resveratrol-salicylate derivatives as selective DNMT3 inhibitors and anticancer agents. J Enzyme Inhib Med Chem 2016; 31:695-703. [PMID: 26118420 PMCID: PMC4828318 DOI: 10.3109/14756366.2015.1058256] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2015] [Accepted: 05/22/2015] [Indexed: 12/30/2022] Open
Abstract
Resveratrol is a natural polyphenol with plethora of biological activities. Resveratrol has previously shown to decrease DNA-methyltransferase (DNMT) enzymes expression and to reactivate silenced tumor suppressor genes. Currently, it seems that no resveratrol analogs have been developed as DNMT inhibitors. Recently, we reported the synthesis of resveratrol-salicylate derivatives and by examining the chemical structure of these analogs, we proposed that these compounds could exhibit DNMT inhibition especially that they resembled NSC 14778, a compound we previously identified as a DNMT inhibitor by virtual screening. Indeed, using in vitro DNMT inhibition assay, some of the resveratrol-salicylate analogs we screened in this work that showed selective inhibition against DNMT3 enzymes which were greater than resveratrol. A molecular docking study revealed key binding interactions with DNMT3A and DNMT3B enzymes. In addition, the most active analog, 10 showed considerable cytotoxicity against three human cancer cells; HT-29, HepG2 and SK-BR-3, which was greater than resveratrol. Further studies are needed to understand the anticancer mechanisms of these derivatives.
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Affiliation(s)
- Fahad S. Aldawsari
- Faculty of Pharmacy and Pharmaceutical Sciences, University of Alberta, Edmonton, Alberta, Canada
| | - Rodrigo Aguayo-Ortiz
- Facultad de Química, Departamento de Farmacia, Universidad Nacional Autónoma de México, México City, México
| | - Kanishk Kapilashrami
- Molecular Pharmacology and Chemistry Program, Memorial Sloan-Kettering Cancer Center, New York, N.Y., USA
| | - Jakyung Yoo
- Life Science Research Institute, Daewoong Pharmaceutical Co., Ltd, Pogok-Eup, Republic of Korea
| | - Minkui Luo
- Molecular Pharmacology and Chemistry Program, Memorial Sloan-Kettering Cancer Center, New York, N.Y., USA
| | - José L. Medina-Franco
- Facultad de Química, Departamento de Farmacia, Universidad Nacional Autónoma de México, México City, México
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Brenner C, Luciani J, Bizet M, Ndlovu M, Josseaux E, Dedeurwaerder S, Calonne E, Putmans P, Cartron PF, Defrance M, Fuks F, Deplus R. The interplay between the lysine demethylase KDM1A and DNA methyltransferases in cancer cells is cell cycle dependent. Oncotarget 2016; 7:58939-58952. [PMID: 27449289 PMCID: PMC5312287 DOI: 10.18632/oncotarget.10624] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2016] [Accepted: 07/06/2016] [Indexed: 12/12/2022] Open
Abstract
DNA methylation and histone modifications are key epigenetic regulators of gene expression, and tight connections are known between the two. DNA methyltransferases are upregulated in several tumors and aberrant DNA methylation profiles are a cancer hallmark. On the other hand, histone demethylases are upregulated in cancer cells. Previous work on ES cells has shown that the lysine demethylase KDM1A binds to DNMT1, thereby affecting DNA methylation. In cancer cells, the occurrence of this interaction has not been explored. Here we demonstrate in several tumor cell lines an interaction between KDM1A and both DNMT1 and DNMT3B. Intriguingly and in contrast to what is observed in ES cells, KDM1A depletion in cancer cells was found not to trigger any reduction in the DNMT1 or DNMT3B protein level or any change in DNA methylation. In the S-phase, furthermore, KDM1A and DNMT1 were found, to co-localize within the heterochromatin. Using P-LISA, we revealed substantially increased binding of KDM1A to DNMT1 during the S-phase. Together, our findings propose a mechanistic link between KDM1A and DNA methyltransferases in cancer cells and suggest that the KDM1A/DNMT1 interaction may play a role during replication. Our work also strengthens the idea that DNMTs can exert functions unrelated to act on DNA methylation.
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Affiliation(s)
- Carmen Brenner
- Laboratory of Cancer Epigenetics, Faculty of Medicine, ULB-Cancer Research Centre (U-CRC), Université Libre de Bruxelles, 1070 Brussels, Belgium
| | - Judith Luciani
- Laboratory of Cancer Epigenetics, Faculty of Medicine, ULB-Cancer Research Centre (U-CRC), Université Libre de Bruxelles, 1070 Brussels, Belgium
| | - Martin Bizet
- Laboratory of Cancer Epigenetics, Faculty of Medicine, ULB-Cancer Research Centre (U-CRC), Université Libre de Bruxelles, 1070 Brussels, Belgium
| | - Matladi Ndlovu
- Laboratory of Cancer Epigenetics, Faculty of Medicine, ULB-Cancer Research Centre (U-CRC), Université Libre de Bruxelles, 1070 Brussels, Belgium
| | - Eleonore Josseaux
- Laboratory of Cancer Epigenetics, Faculty of Medicine, ULB-Cancer Research Centre (U-CRC), Université Libre de Bruxelles, 1070 Brussels, Belgium
| | - Sarah Dedeurwaerder
- Laboratory of Cancer Epigenetics, Faculty of Medicine, ULB-Cancer Research Centre (U-CRC), Université Libre de Bruxelles, 1070 Brussels, Belgium
| | - Emilie Calonne
- Laboratory of Cancer Epigenetics, Faculty of Medicine, ULB-Cancer Research Centre (U-CRC), Université Libre de Bruxelles, 1070 Brussels, Belgium
| | - Pascale Putmans
- Laboratory of Cancer Epigenetics, Faculty of Medicine, ULB-Cancer Research Centre (U-CRC), Université Libre de Bruxelles, 1070 Brussels, Belgium
| | - Pierre-Francois Cartron
- Centre de Recherche en Cancérologie Nantes-Angers, INSERM, U892, Equipe Apoptose et Progression Tumorale, BP7021, 44007 Nantes, France
- Département de Recherche en Cancérologie, Faculté de Médecine, Université de Nantes, IFR26, F-4400, Nantes, France
- LaBCT, Institut de Cancérologie de l'Ouest, 44805 Nantes, Saint Herblain Cedex, France
| | - Matthieu Defrance
- Laboratory of Cancer Epigenetics, Faculty of Medicine, ULB-Cancer Research Centre (U-CRC), Université Libre de Bruxelles, 1070 Brussels, Belgium
| | - François Fuks
- Laboratory of Cancer Epigenetics, Faculty of Medicine, ULB-Cancer Research Centre (U-CRC), Université Libre de Bruxelles, 1070 Brussels, Belgium
| | - Rachel Deplus
- Laboratory of Cancer Epigenetics, Faculty of Medicine, ULB-Cancer Research Centre (U-CRC), Université Libre de Bruxelles, 1070 Brussels, Belgium
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40
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Cheray M, Pacaud R, Nadaradjane A, Oliver L, Vallette FM, Cartron PF. Specific Inhibition of DNMT3A/ISGF3γ Interaction Increases the Temozolomide Efficiency to Reduce Tumor Growth. Am J Cancer Res 2016; 6:1988-1999. [PMID: 27698935 PMCID: PMC5039338 DOI: 10.7150/thno.9150] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2015] [Accepted: 07/16/2015] [Indexed: 11/28/2022] Open
Abstract
DNA methylation is a fundamental feature of genomes and is a candidate for pharmacological manipulation that might have important therapeutic advantage. Thus, DNA methyltransferases (DNMTs) appear to be ideal targets for drug intervention. By focusing on interactions existing between DNMT3A and DNMT3A-binding protein (D3A-BP), our work identifies the DNMT3A/ISGF3γ interaction such as a biomarker whose the presence level is associated with a poor survival prognosis and with a poor prognosis of response to the conventional chemotherapeutic treatment of glioblastoma multiforme (radiation plus temozolomide). Our data also demonstrates that the disruption of DNMT3A/ISGF3γ interactions increases the efficiency of chemotherapeutic treatment on established tumors in mice. Thus, our data opens a promising and innovative alternative to the development of specific DNMT inhibitors.
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41
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Liu H, Liu Z, Du J, He J, Lin P, Amini B, Starbuck MW, Novane N, Shah JJ, Davis RE, Hou J, Gagel RF, Yang J. Thymidine phosphorylase exerts complex effects on bone resorption and formation in myeloma. Sci Transl Med 2016; 8:353ra113. [PMID: 27559096 PMCID: PMC5109917 DOI: 10.1126/scitranslmed.aad8949] [Citation(s) in RCA: 52] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2015] [Accepted: 07/26/2016] [Indexed: 11/02/2022]
Abstract
Myelomatous bone disease is characterized by the development of lytic bone lesions and a concomitant reduction in bone formation, leading to chronic bone pain and fractures. To understand the underlying mechanism, we investigated the contribution of myeloma-expressed thymidine phosphorylase (TP) to bone lesions. In osteoblast progenitors, TP up-regulated the methylation of RUNX2 and osterix, leading to decreased bone formation. In osteoclast progenitors, TP up-regulated the methylation of IRF8 and thereby enhanced expression of NFATc1 (nuclear factor of activated T cells, cytoplasmic 1 protein), leading to increased bone resorption. TP reversibly catalyzes thymidine into thymine and 2-deoxy-d-ribose (2DDR). Myeloma-secreted 2DDR bound to integrin αVβ3/α5β1 in the progenitors, activated PI3K (phosphoinositide 3-kinase)/Akt signaling, and increased DNMT3A (DNA methyltransferase 3A) expression, resulting in hypermethylation of RUNX2, osterix, and IRF8 This study elucidates an important mechanism for myeloma-induced bone lesions, suggesting that targeting TP may be a viable approach to healing resorbed bone in patients. Because TP overexpression is common in bone-metastatic tumors, our findings could have additional mechanistic implications.
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Affiliation(s)
- Huan Liu
- Department of Lymphoma and Myeloma, Division of Cancer Medicine, Center for Cancer Immunology Research, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Zhiqiang Liu
- Department of Lymphoma and Myeloma, Division of Cancer Medicine, Center for Cancer Immunology Research, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Juan Du
- Department of Hematology, The Myeloma and Lymphoma Center, Changzheng Hospital, The Second Military Medical University, Shanghai 200003, China
| | - Jin He
- Department of Lymphoma and Myeloma, Division of Cancer Medicine, Center for Cancer Immunology Research, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Pei Lin
- Department of Hematopathology, Division of Pathology and Laboratory Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Behrang Amini
- Department of Diagnostic Radiology, Division of Diagnostic Imaging, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Michael W Starbuck
- Department of Genitourinary Medical Oncology, Division of Cancer Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Nora Novane
- Department of Genitourinary Medical Oncology, Division of Cancer Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Jatin J Shah
- Department of Lymphoma and Myeloma, Division of Cancer Medicine, Center for Cancer Immunology Research, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Richard E Davis
- Department of Lymphoma and Myeloma, Division of Cancer Medicine, Center for Cancer Immunology Research, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Jian Hou
- Department of Hematology, The Myeloma and Lymphoma Center, Changzheng Hospital, The Second Military Medical University, Shanghai 200003, China
| | - Robert F Gagel
- Department of Endocrine Neoplasia and Hormonal Disorders, Division of Internal Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Jing Yang
- Department of Lymphoma and Myeloma, Division of Cancer Medicine, Center for Cancer Immunology Research, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA.
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Xu P, Hu G, Luo C, Liang Z. DNA methyltransferase inhibitors: an updated patent review (2012-2015). Expert Opin Ther Pat 2016; 26:1017-30. [PMID: 27376512 DOI: 10.1080/13543776.2016.1209488] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
INTRODUCTION DNA methyltransferases (DNMTs), important enzymes involved in epigenetic regulation of gene expression, represent promising targets in cancer therapy. DNMT inhibitors (DNMTi), which can modulate the aberrant DNA methylation pattern in a reversible way via inhibiting DNMT activity, have attracted significant attention in recent years. AREAS COVERED This review outlines the newly patented inhibitors targeting DNMTs, mainly incorporating small molecular inhibitors and oligonucleotide derivatives. The chemical structures, biological activity, and the encouraging clinical research in progress are delineated in detail. EXPERT OPINION Two drugs, azacitidine and decitabine, have evidently shown efficacy in hematologic malignancies, yet do not work well on solid tumors, have low specificity, substantial toxicity, and poor bioavailability. With the rapid advancement in systems biology, drug combinations, such as DNMTi, in conjugation with histone deacetylase inhibitors (HDACi) or immunotherapy, probably serve as an efficient way of implementing epigenetic therapy. Meanwhile, the resolved autoinhibitory structures of DNMTs afford a novel strategy for targeting the protein-protein interface involved in the autoinhi-bitory interactions. The molecular mechanism underlying the conformational transitions would also shed new light on the design of allosteric inhibitors. Both strategies would produce inhibitors with more selectivity compared to nucleotide derivatives.
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Affiliation(s)
- Pan Xu
- a Center for Systems Biology , Soochow University , Jiangsu , China.,b Shanghai Institute of Materia Medica, State Key Laboratory of Drug Research , Chinese Academy of Sciences , Shanghai , China
| | - Guang Hu
- a Center for Systems Biology , Soochow University , Jiangsu , China
| | - Cheng Luo
- b Shanghai Institute of Materia Medica, State Key Laboratory of Drug Research , Chinese Academy of Sciences , Shanghai , China
| | - Zhongjie Liang
- a Center for Systems Biology , Soochow University , Jiangsu , China
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Garella D, Atlante S, Borretto E, Cocco M, Giorgis M, Costale A, Stevanato L, Miglio G, Cencioni C, Fernández-de Gortari E, Medina-Franco JL, Spallotta F, Gaetano C, Bertinaria M. Design and synthesis of N-benzoyl amino acid derivatives as DNA methylation inhibitors. Chem Biol Drug Des 2016; 88:664-676. [PMID: 27225604 DOI: 10.1111/cbdd.12794] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2016] [Revised: 05/02/2016] [Accepted: 05/14/2016] [Indexed: 12/11/2022]
Abstract
The inhibition of human DNA Methyl Transferases (DNMT) is a novel promising approach to address the epigenetic dysregulation of gene expression in different diseases. Inspired by the validated virtual screening hit NSC137546, a series of N-benzoyl amino acid analogues was synthesized and obtained compounds were assessed for their ability to inhibit DNMT-dependent DNA methylation in vitro. The biological screening allowed the definition of a set of preliminary structure-activity relationships and the identification of compounds promising for further development. Among the synthesized compounds, L-glutamic acid derivatives 22, 23, and 24 showed the highest ability to prevent DNA methylation in a total cell lysate. Compound 22 inhibited DNMT1 and DNMT3A activity in a concentration-dependent manner in the micromolar range. In addition, compound 22 proved to be stable in human serum and it was thus selected as a starting point for further biological studies.
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Affiliation(s)
- Davide Garella
- Dipartimento di Scienza e Tecnologia del Farmaco, Università degli Studi di Torino, Torino, Italy.
| | - Sandra Atlante
- Division of Cardiovascular Epigenetics, Department of Cardiology, Goethe University, Frankfurt am Main, Germany
| | - Emily Borretto
- Dipartimento di Scienza e Tecnologia del Farmaco, Università degli Studi di Torino, Torino, Italy
| | - Mattia Cocco
- Dipartimento di Scienza e Tecnologia del Farmaco, Università degli Studi di Torino, Torino, Italy
| | - Marta Giorgis
- Dipartimento di Scienza e Tecnologia del Farmaco, Università degli Studi di Torino, Torino, Italy
| | - Annalisa Costale
- Dipartimento di Scienza e Tecnologia del Farmaco, Università degli Studi di Torino, Torino, Italy
| | - Livio Stevanato
- Dipartimento di Scienza e Tecnologia del Farmaco, Università degli Studi di Torino, Torino, Italy
| | - Gianluca Miglio
- Dipartimento di Scienza e Tecnologia del Farmaco, Università degli Studi di Torino, Torino, Italy
| | - Chiara Cencioni
- Division of Cardiovascular Epigenetics, Department of Cardiology, Goethe University, Frankfurt am Main, Germany
| | - Eli Fernández-de Gortari
- Facultad de Química , Departamento de Farmacia, Universidad Nacional Autónoma de México, Mexico City, México
| | - José L Medina-Franco
- Facultad de Química , Departamento de Farmacia, Universidad Nacional Autónoma de México, Mexico City, México
| | - Francesco Spallotta
- Division of Cardiovascular Epigenetics, Department of Cardiology, Goethe University, Frankfurt am Main, Germany
| | - Carlo Gaetano
- Division of Cardiovascular Epigenetics, Department of Cardiology, Goethe University, Frankfurt am Main, Germany.
| | - Massimo Bertinaria
- Dipartimento di Scienza e Tecnologia del Farmaco, Università degli Studi di Torino, Torino, Italy
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Krushkal J, Zhao Y, Hose C, Monks A, Doroshow JH, Simon R. Concerted changes in transcriptional regulation of genes involved in DNA methylation, demethylation, and folate-mediated one-carbon metabolism pathways in the NCI-60 cancer cell line panel in response to cancer drug treatment. Clin Epigenetics 2016; 8:73. [PMID: 27347216 PMCID: PMC4919895 DOI: 10.1186/s13148-016-0240-3] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2016] [Accepted: 06/15/2016] [Indexed: 02/06/2023] Open
Abstract
BACKGROUND Aberrant patterns of DNA methylation are abundant in cancer, and epigenetic pathways are increasingly being targeted in cancer drug treatment. Genetic components of the folate-mediated one-carbon metabolism pathway can affect DNA methylation and other vital cell functions, including DNA synthesis, amino acid biosynthesis, and cell growth. RESULTS We used a bioinformatics tool, the Transcriptional Pharmacology Workbench, to analyze temporal changes in gene expression among epigenetic regulators of DNA methylation and demethylation, and one-carbon metabolism genes in response to cancer drug treatment. We analyzed gene expression information from the NCI-60 cancer cell line panel after treatment with five antitumor agents, 5-azacytidine, doxorubicin, vorinostat, paclitaxel, and cisplatin. Each antitumor agent elicited concerted changes in gene expression of multiple pathway components across the cell lines. Expression changes of FOLR2, SMUG1, GART, GADD45A, MBD1, MTR, MTHFD1, and CTH were significantly correlated with chemosensitivity to some of the agents. Among many genes with concerted expression response to individual antitumor agents were genes encoding DNA methyltransferases DNMT1, DNMT3A, and DNMT3B, epigenetic and DNA repair factors MGMT, GADD45A, and MBD1, and one-carbon metabolism pathway members MTHFD1, TYMS, DHFR, MTR, MAT2A, SLC19A1, ATIC, and GART. CONCLUSIONS These transcriptional changes are likely to influence vital cellular functions of DNA methylation and demethylation, cellular growth, DNA biosynthesis, and DNA repair, and some of them may contribute to cytotoxic and apoptotic action of the drugs. This concerted molecular response was observed in a time-dependent manner, which may provide future guidelines for temporal selection of genetic drug targets for combination drug therapy treatment regimens.
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Affiliation(s)
- Julia Krushkal
- />Biometric Research Program, Division of Cancer Treatment and Diagnosis, National Cancer Institute, 9609 Medical Center Dr., Rockville, MD 20850 USA
| | - Yingdong Zhao
- />Biometric Research Program, Division of Cancer Treatment and Diagnosis, National Cancer Institute, 9609 Medical Center Dr., Rockville, MD 20850 USA
| | - Curtis Hose
- />Molecular Pharmacology Group, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, Frederick, MD 21702 USA
| | - Anne Monks
- />Molecular Pharmacology Group, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, Frederick, MD 21702 USA
| | - James H. Doroshow
- />Division of Cancer Treatment and Diagnosis, National Cancer Institute, Bethesda, MD 20892 USA
| | - Richard Simon
- />Biometric Research Program, Division of Cancer Treatment and Diagnosis, National Cancer Institute, 9609 Medical Center Dr., Rockville, MD 20850 USA
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Knothe C, Shiratori H, Resch E, Ultsch A, Geisslinger G, Doehring A, Lötsch J. Disagreement between two common biomarkers of global DNA methylation. Clin Epigenetics 2016; 8:60. [PMID: 27222668 PMCID: PMC4877994 DOI: 10.1186/s13148-016-0227-0] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2016] [Accepted: 05/10/2016] [Indexed: 12/30/2022] Open
Abstract
BACKGROUND The quantification of global DNA methylation has been established in epigenetic screening. As more practicable alternatives to the HPLC-based gold standard, the methylation analysis of CpG islands in repeatable elements (LINE-1) and the luminometric methylation assay (LUMA) of overall 5-methylcytosine content in "CCGG" recognition sites are most widely used. Both methods are applied as virtually equivalent, despite the hints that their results only partly agree. This triggered the present agreement assessments. RESULTS Three different human cell types (cultured MCF7 and SHSY5Y cell lines treated with different chemical modulators of DNA methylation and whole blood drawn from pain patients and healthy volunteers) were submitted to the global DNA methylation assays employing LINE-1 or LUMA-based pyrosequencing measurements. The agreement between the two bioassays was assessed using generally accepted approaches to the statistics for laboratory method comparison studies. Although global DNA methylation levels measured by the two methods correlated, five different lines of statistical evidence consistently rejected the assumption of complete agreement. Specifically, a bias was observed between the two methods. In addition, both the magnitude and direction of bias were tissue-dependent. Interassay differences could be grouped based on Bayesian statistics, and these groups allowed in turn to re-identify the originating tissue. CONCLUSIONS Although providing partly correlated measurements of DNA methylation, interchangeability of the quantitative results obtained with LINE-1 and LUMA was jeopardized by a consistent bias between the results. Moreover, the present analyses strongly indicate a tissue specificity of the differences between the two methods.
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Affiliation(s)
- Claudia Knothe
- />Institute of Clinical Pharmacology, Goethe University, Theodor-Stern-Kai 7, 60590 Frankfurt am Main, Germany
| | - Hiromi Shiratori
- />Project Group Translational Medicine and Pharmacology TMP, Fraunhofer Institute for Molecular Biology and Applied Ecology IME, Theodor-Stern-Kai 7, 60590 Frankfurt am Main, Germany
| | - Eduard Resch
- />Project Group Translational Medicine and Pharmacology TMP, Fraunhofer Institute for Molecular Biology and Applied Ecology IME, Theodor-Stern-Kai 7, 60590 Frankfurt am Main, Germany
| | - Alfred Ultsch
- />DataBionics Research Group, University of Marburg, Hans-Meerwein-Straße, 35032 Marburg, Germany
| | - Gerd Geisslinger
- />Institute of Clinical Pharmacology, Goethe University, Theodor-Stern-Kai 7, 60590 Frankfurt am Main, Germany
- />Project Group Translational Medicine and Pharmacology TMP, Fraunhofer Institute for Molecular Biology and Applied Ecology IME, Theodor-Stern-Kai 7, 60590 Frankfurt am Main, Germany
| | - Alexandra Doehring
- />Institute of Clinical Pharmacology, Goethe University, Theodor-Stern-Kai 7, 60590 Frankfurt am Main, Germany
| | - Jörn Lötsch
- />Institute of Clinical Pharmacology, Goethe University, Theodor-Stern-Kai 7, 60590 Frankfurt am Main, Germany
- />Project Group Translational Medicine and Pharmacology TMP, Fraunhofer Institute for Molecular Biology and Applied Ecology IME, Theodor-Stern-Kai 7, 60590 Frankfurt am Main, Germany
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Aranda J, Zinovjev K, Świderek K, Roca M, Tuñón I. Unraveling the Reaction Mechanism of Enzymatic C5-Cytosine Methylation of DNA. A Combined Molecular Dynamics and QM/MM Study of Wild Type and Gln119 Variant. ACS Catal 2016. [DOI: 10.1021/acscatal.6b00394] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Affiliation(s)
- Juan Aranda
- Departament
de Quı́mica Fı́sica, Universitat de València, 46100 Burjassot, Spain
| | - Kirill Zinovjev
- Departament
de Quı́mica Fı́sica, Universitat de València, 46100 Burjassot, Spain
| | - Katarzyna Świderek
- Departament
de Quı́mica Fı́sica, Universitat de València, 46100 Burjassot, Spain
- Institute
of Applied Radiation Chemistry, Lodz University of Technology, 90-924 Lodz, Poland
| | - Maite Roca
- Departament
de Quı́mica Fı́sica, Universitat de València, 46100 Burjassot, Spain
| | - Iñaki Tuñón
- Departament
de Quı́mica Fı́sica, Universitat de València, 46100 Burjassot, Spain
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Kazanets A, Shorstova T, Hilmi K, Marques M, Witcher M. Epigenetic silencing of tumor suppressor genes: Paradigms, puzzles, and potential. BIOCHIMICA ET BIOPHYSICA ACTA 2016; 1865:275-88. [PMID: 27085853 DOI: 10.1016/j.bbcan.2016.04.001] [Citation(s) in RCA: 91] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/05/2016] [Accepted: 04/08/2016] [Indexed: 12/20/2022]
Abstract
Cancer constitutes a set of diseases with heterogeneous molecular pathologies. However, there are a number of universal aberrations common to all cancers, one of these being the epigenetic silencing of tumor suppressor genes (TSGs). The silencing of TSGs is thought to be an early, driving event in the oncogenic process. With this in consideration, great efforts have been made to develop small molecules aimed at the restoration of TSGs in order to limit tumor cell proliferation and survival. However, the molecular forces that drive the broad epigenetic reprogramming and transcriptional repression of these genes remain ill-defined. Undoubtedly, understanding the molecular underpinnings of transcriptionally silenced TSGs will aid us in our ability to reactivate these key anti-cancer targets. Here, we describe what we consider to be the five most logical molecular mechanisms that may account for this widely observed phenomenon: 1) ablation of transcription factor binding, 2) overexpression of DNA methyltransferases, 3) disruption of CTCF binding, 4) elevation of EZH2 activity, 5) aberrant expression of long non-coding RNAs. The strengths and weaknesses of each proposed mechanism is highlighted, followed by an overview of clinical efforts to target these processes.
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Affiliation(s)
- Anna Kazanets
- The Lady Davis Institute of the Jewish General Hospital, Department of Oncology, McGill University, Montreal, Canada.
| | - Tatiana Shorstova
- The Lady Davis Institute of the Jewish General Hospital, Department of Oncology, McGill University, Montreal, Canada.
| | - Khalid Hilmi
- The Lady Davis Institute of the Jewish General Hospital, Department of Oncology, McGill University, Montreal, Canada.
| | - Maud Marques
- The Lady Davis Institute of the Jewish General Hospital, Department of Oncology, McGill University, Montreal, Canada.
| | - Michael Witcher
- The Lady Davis Institute of the Jewish General Hospital, Department of Oncology, McGill University, Montreal, Canada.
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Identification and optimization of hydrazone-gallate derivatives as specific inhibitors of DNA methyltransferase 3A. Future Med Chem 2016; 8:373-80. [PMID: 26976348 DOI: 10.4155/fmc.15.192] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
DNA methylation is the most studied epigenetic event. Since the methylation profile of the genome is widely modified in cancer cells, DNA methyltransferases are the target of new anticancer therapies. Nucleosidic inhibitors suffer from toxicity and chemical stability, while non-nucleosidic inhibitors lack potency. Here, we found a novel DNMT inhibitor scaffold by enzymatic screening and structure-activity relationship studies. The optimization studies led to an inhibitor containing three fragments: a gallate frame, a hydrazone linker and a benzothiazole moiety. Interestingly, the compound inhibits DNMT3A with micromolar potency (EC50 = 1.6 μM) and does not inhibit DNMT1; this DNMT3A selectivity is supported by a docking study. Finally, the compound reactivates a reporter gene in leukemia KG-1 cells.
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49
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Ganesan A. Multitarget Drugs: an Epigenetic Epiphany. ChemMedChem 2016; 11:1227-41. [PMID: 26891251 DOI: 10.1002/cmdc.201500394] [Citation(s) in RCA: 59] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2015] [Revised: 01/28/2016] [Indexed: 12/22/2022]
Abstract
Epigenetics refers to changes in a biological phenotype that are not due to an underlying change in genotype. In eukaryotes, epigenetics involves a set of chemical modifications of the DNA and the histone proteins in nucleosomes. These dynamic changes are carried out by enzymes and modulate protein-protein and protein-nucleic acid interactions to determine whether specific genes are expressed or silenced. Both the epigenetic enzymes and recognition domains are currently important drug discovery targets, particularly for the treatment of cancer. This review summarizes the progress of epigenetic targets that have reached a clinical stage: DNA methyltransferases, histone deacetylases, lysine methyltransferases, lysine demethylases, and bromodomains; this is followed by a comprehensive survey of multitarget drugs that have included an epigenetic target as one of their mechanisms of action.
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Affiliation(s)
- A Ganesan
- School of Pharmacy, University of East Anglia, Norwich Research Park, Norwich, NR4 7TJ, UK.
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Jurkowska RZ, Jeltsch A. Mechanisms and Biological Roles of DNA Methyltransferases and DNA Methylation: From Past Achievements to Future Challenges. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2016; 945:1-17. [DOI: 10.1007/978-3-319-43624-1_1] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
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