1
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Chen W, Chu J, Miao Y, Jiang W, Wang F, Zhang N, Jin J, Cai Y. MOF-mediated acetylation of CDK9 promotes global transcription by modulating P-TEFb complex formation. FEBS J 2024. [PMID: 39250546 DOI: 10.1111/febs.17264] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2024] [Revised: 06/25/2024] [Accepted: 08/22/2024] [Indexed: 09/11/2024]
Abstract
Cyclin-dependent kinase 9 (CDK9), a catalytic subunit of the positive transcription elongation factor b (P-TEFb) complex, is a global transcriptional elongation factor associated with cell proliferation. CDK9 activity is regulated by certain histone acetyltransferases, such as p300, GCN5 and P/CAF. However, the impact of males absent on the first (MOF) (also known as KAT8 or MYST1) on CDK9 activity has not been reported. Therefore, the present study aimed to elucidate the regulatory role of MOF on CDK9. We present evidence from systematic biochemical assays and molecular biology approaches arguing that MOF interacts with and acetylates CDK9 at the lysine 35 (i.e. K35) site, and that this acetyl-group can be removed by histone deacetylase HDAC1. Notably, MOF-mediated acetylation of CDK9 at K35 promotes the formation of the P-TEFb complex through stabilizing CDK9 protein and enhancing its association with cyclin T1, which further increases RNA polymerase II serine 2 residues levels and global transcription. Our study reveals for the first time that MOF promotes global transcription by acetylating CDK9, providing a new strategy for exploring the comprehensive mechanism of the MOF-CDK9 axis in cellular processes.
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Affiliation(s)
- Wenqi Chen
- School of Life Sciences, Jilin University, Changchun, China
| | - Jinmeng Chu
- School of Life Sciences, Jilin University, Changchun, China
| | - Yujuan Miao
- School of Life Sciences, Jilin University, Changchun, China
| | - Wenwen Jiang
- School of Life Sciences, Jilin University, Changchun, China
| | - Fei Wang
- School of Life Sciences, Jilin University, Changchun, China
| | - Na Zhang
- School of Life Sciences, Jilin University, Changchun, China
| | - Jingji Jin
- School of Life Sciences, Jilin University, Changchun, China
| | - Yong Cai
- School of Life Sciences, Jilin University, Changchun, China
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2
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Shao YY, Hsieh MS, Lee YH, Hsu HW, Wo RR, Wang HY, Cheng AL, Hsu CH. Cyclin dependent kinase 9 inhibition reduced programmed death-ligand 1 expression and improved treatment efficacy in hepatocellular carcinoma. Heliyon 2024; 10:e34289. [PMID: 39100490 PMCID: PMC11296019 DOI: 10.1016/j.heliyon.2024.e34289] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2023] [Revised: 07/05/2024] [Accepted: 07/07/2024] [Indexed: 08/06/2024] Open
Abstract
The anti-programmed death-ligand 1 (PD-L1) antibody is a standard therapy for advanced hepatocellular carcinoma (HCC). Tumor expression of PD-L1 can be induced upon stimulus. Because cyclin-dependent kinase 9 (CDK9) inhibition reduces the expression of inducible proteins, we explored the influence of CDK9 inhibition on PD-L1 expression in HCC cells. We found that PD-L1 expression was low in HCC cells; however, IFN-γ treatment increased this expression. CDK9 inhibitors AZD4573 and atuveciclib reduced the IFN-γ induced PD-L1 expression in a dose-dependent manner. CDK9 knockdown yielded similar results, but CDK9 overexpression reversed the influence of the CDK9 inhibitors. In the orthotopic mouse model, mice treated with a CDK9 inhibitor and an anti-PD-L1 antibody had significantly smaller tumors and exhibited longer survival than mice treated with either agent. In conclusion, CDK9 inhibition could reduce the expression of PD-L1 in HCC cells. Using both CDK9 inhibitors and anti-PD-L1 antibodies is more effective than using either agent alone.
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Affiliation(s)
- Yu-Yun Shao
- Graduate Institute of Oncology, National Taiwan University College of Medicine, 1, Sec. 1, Ren'ai Rd., Taipei City, 10051, R.O.C, Taiwan
- Department of Oncology, National Taiwan University Hospital, 7, Chun-Shan S Road, Taipei City, 10002, R.O.C, Taiwan
- Department of Medical Oncology, National Taiwan University Cancer Center, 57, Ln. 155, Sec. 3, Keelung Rd., Taipei City, 106, R.O.C, Taiwan
| | - Min-Shu Hsieh
- Department of Pathology and Graduate Institute of Pathology, National Taiwan University College of Medicine, 1, Sec. 1, Ren'ai Rd., Taipei City, 10051, R.O.C, Taiwan
- Department of Pathology, National Taiwan University Hospital, 7, Chun-Shan S Road, Taipei City, 10002, R.O.C, Taiwan
- Department of Pathology, National Taiwan University Cancer Center, 57, Ln. 155, Sec. 3, Keelung Rd., Taipei City, 106, R.O.C, Taiwan
| | - Yi-Hsuan Lee
- Department of Pathology and Graduate Institute of Pathology, National Taiwan University College of Medicine, 1, Sec. 1, Ren'ai Rd., Taipei City, 10051, R.O.C, Taiwan
- Department of Pathology, National Taiwan University Hospital, 7, Chun-Shan S Road, Taipei City, 10002, R.O.C, Taiwan
| | - Hung-Wei Hsu
- Department of Oncology, National Taiwan University Hospital, 7, Chun-Shan S Road, Taipei City, 10002, R.O.C, Taiwan
| | - Rita Robin Wo
- Department of Oncology, National Taiwan University Hospital, 7, Chun-Shan S Road, Taipei City, 10002, R.O.C, Taiwan
| | - Han-Yu Wang
- Department of Oncology, National Taiwan University Hospital, 7, Chun-Shan S Road, Taipei City, 10002, R.O.C, Taiwan
| | - Ann-Lii Cheng
- Graduate Institute of Oncology, National Taiwan University College of Medicine, 1, Sec. 1, Ren'ai Rd., Taipei City, 10051, R.O.C, Taiwan
- Department of Internal Medicine, National Taiwan University College of Medicine, 1, Sec. 1, Ren'ai Rd., Taipei City, 10051, R.O.C, Taiwan
- Department of Oncology, National Taiwan University Hospital, 7, Chun-Shan S Road, Taipei City, 10002, R.O.C, Taiwan
- Department of Medical Oncology, National Taiwan University Cancer Center, 57, Ln. 155, Sec. 3, Keelung Rd., Taipei City, 106, R.O.C, Taiwan
| | - Chih-Hung Hsu
- Graduate Institute of Oncology, National Taiwan University College of Medicine, 1, Sec. 1, Ren'ai Rd., Taipei City, 10051, R.O.C, Taiwan
- Department of Oncology, National Taiwan University Hospital, 7, Chun-Shan S Road, Taipei City, 10002, R.O.C, Taiwan
- Department of Medical Oncology, National Taiwan University Cancer Center, 57, Ln. 155, Sec. 3, Keelung Rd., Taipei City, 106, R.O.C, Taiwan
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3
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Wang S, Liu F, Li P, Wang JN, Mo Y, Lin B, Mei Y. Potent inhibitors targeting cyclin-dependent kinase 9 discovered via virtual high-throughput screening and absolute binding free energy calculations. Phys Chem Chem Phys 2024; 26:5377-5386. [PMID: 38269624 DOI: 10.1039/d3cp05582e] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2024]
Abstract
Due to the crucial regulatory mechanism of cyclin-dependent kinase 9 (CDK9) in mRNA transcription, the development of kinase inhibitors targeting CDK9 holds promise as a potential treatment strategy for cancer. A structure-based virtual screening approach has been employed for the discovery of potential novel CDK9 inhibitors. First, compounds with kinase inhibitor characteristics were identified from the ZINC15 database via virtual high-throughput screening. Next, the predicted binding modes were optimized by molecular dynamics simulations, followed by precise estimation of binding affinities using absolute binding free energy calculations based on the free energy perturbation scheme. The binding mode of molecule 006 underwent an inward-to-outward flipping, and the new binding mode exhibited binding affinity comparable to the small molecule T6Q in the crystal structure (PDB ID: 4BCF), highlighting the essential role of molecular dynamics simulation in capturing a plausible binding pose bridging docking and absolute binding free energy calculations. Finally, structural modifications based on these findings further enhanced the binding affinity with CDK9. The results revealed that enhancing the molecule's rigidity through ring formation, while maintaining the major interactions, reduced the entropy loss during the binding process and, thus, enhanced binding affinities.
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Affiliation(s)
- Shipeng Wang
- School of Chemistry and Chemical Engineering, Shanghai University of Engineering Science, Shanghai 201620, China.
| | - Fengjiao Liu
- School of Chemistry and Chemical Engineering, Shanghai University of Engineering Science, Shanghai 201620, China.
| | - Pengfei Li
- Single Particle, LLC, 10531 4S Commons Dr 166-629, San Diego, CA 92127, USA
| | - Jia-Ning Wang
- State Key Laboratory of Precision Spectroscopy, School of Physics and Electronic Science, East China Normal University, Shanghai 200241, China
| | - Yan Mo
- State Key Laboratory of Precision Spectroscopy, School of Physics and Electronic Science, East China Normal University, Shanghai 200241, China
- NYU-ECNU Center for Computational Chemistry at NYU Shanghai, Shanghai 200062, China
- Collaborative Innovation Center of Extreme Optics, Shanxi University, Taiyuan, Shanxi 030006, China
| | - Bin Lin
- Wuya College of Innovation, Shenyang Pharmaceutical University, Shenyang 110016, China.
| | - Ye Mei
- State Key Laboratory of Precision Spectroscopy, School of Physics and Electronic Science, East China Normal University, Shanghai 200241, China
- NYU-ECNU Center for Computational Chemistry at NYU Shanghai, Shanghai 200062, China
- Collaborative Innovation Center of Extreme Optics, Shanxi University, Taiyuan, Shanxi 030006, China
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4
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Gomes AR, Varela CL, Pires AS, Tavares-da-Silva EJ, Roleira FMF. Synthetic and natural guanidine derivatives as antitumor and antimicrobial agents: A review. Bioorg Chem 2023; 138:106600. [PMID: 37209561 DOI: 10.1016/j.bioorg.2023.106600] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2023] [Revised: 04/15/2023] [Accepted: 05/05/2023] [Indexed: 05/22/2023]
Abstract
Guanidines are fascinating small nitrogen-rich organic compounds, which have been frequently associated with a wide range of biological activities. This is mainly due to their interesting chemical features. For these reasons, for the past decades, researchers have been synthesizing and evaluating guanidine derivatives. In fact, there are currently on the market several guanidine-bearing drugs. Given the broad panoply of pharmacological activities displayed by guanidine compounds, in this review, we chose to focus on antitumor, antibacterial, antiviral, antifungal, and antiprotozoal activities presented by several natural and synthetic guanidine derivatives, which are undergoing preclinical and clinical studies from January 2010 to January 2023. Moreover, we also present guanidine-containing drugs currently in the market for the treatment of cancer and several infectious diseases. In the preclinical and clinical setting, most of the synthesized and natural guanidine derivatives are being evaluated as antitumor and antibacterial agents. Even though DNA is the most known target of this type of compounds, their cytotoxicity also involves several other different mechanisms, such as interference with bacterial cell membranes, reactive oxygen species (ROS) formation, mitochondrial-mediated apoptosis, mediated-Rac1 inhibition, among others. As for the compounds already used as pharmacological drugs, their main application is in the treatment of different types of cancer, such as breast, lung, prostate, and leukemia. Guanidine-containing drugs are also being used for the treatment of bacterial, antiprotozoal, antiviral infections and, recently, have been proposed for the treatment of COVID-19. To conclude, the guanidine group is a privileged scaffold in drug design. Its remarkable cytotoxic activities, especially in the field of oncology, still make it suitable for a deeper investigation to afford more efficient and target-specific drugs.
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Affiliation(s)
- Ana R Gomes
- Univ Coimbra, CIEPQPF, Faculty of Pharmacy, Laboratory of Pharmaceutical Chemistry, Azinhaga de Santa Comba, Pólo III - Pólo das Ciências da Saúde, 3000-548 Coimbra, Portugal; Univ Coimbra, Coimbra Institute for Clinical and Biomedical Research (iCBR) area of Environment Genetics and Oncobiology (CIMAGO), Institute of Biophysics, Faculty of Medicine, Azinhaga de Santa Comba, Pólo III - Pólo das Ciências da Saúde, 3000-548 Coimbra, Portugal
| | - Carla L Varela
- Clinical Academic Center of Coimbra (CACC), Praceta Professor Mota Pinto, 3004-561 Coimbra, Portugal; Univ Coimbra, Center for Innovative Biomedicine and Biotechnology (CIBB), Rua Larga, 3004-504 Coimbra, Portugal; Univ Coimbra, CIEPQPF, Faculty of Medicine, Azinhaga de Santa Comba, Pólo III - Pólo das Ciências da Saúde, 3000-548 Coimbra, Portugal
| | - Ana S Pires
- Univ Coimbra, Coimbra Institute for Clinical and Biomedical Research (iCBR) area of Environment Genetics and Oncobiology (CIMAGO), Institute of Biophysics, Faculty of Medicine, Azinhaga de Santa Comba, Pólo III - Pólo das Ciências da Saúde, 3000-548 Coimbra, Portugal; Clinical Academic Center of Coimbra (CACC), Praceta Professor Mota Pinto, 3004-561 Coimbra, Portugal; Univ Coimbra, Center for Innovative Biomedicine and Biotechnology (CIBB), Rua Larga, 3004-504 Coimbra, Portugal
| | - Elisiário J Tavares-da-Silva
- Univ Coimbra, CIEPQPF, Faculty of Pharmacy, Laboratory of Pharmaceutical Chemistry, Azinhaga de Santa Comba, Pólo III - Pólo das Ciências da Saúde, 3000-548 Coimbra, Portugal.
| | - Fernanda M F Roleira
- Univ Coimbra, CIEPQPF, Faculty of Pharmacy, Laboratory of Pharmaceutical Chemistry, Azinhaga de Santa Comba, Pólo III - Pólo das Ciências da Saúde, 3000-548 Coimbra, Portugal.
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5
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Plasmodium falciparum CRK5 Is Critical for Male Gametogenesis and Infection of the Mosquito. mBio 2022; 13:e0222722. [PMID: 36154191 PMCID: PMC9600428 DOI: 10.1128/mbio.02227-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Cyclin-dependent kinases (CDKs) and cyclins are critical cell cycle regulators in eukaryotes. In this study, we functionally characterized a CDK-related kinase (CRK5) of the human malaria parasite Plasmodium falciparum. P. falciparum CRK5 (PfCRK5) was expressed in asexual blood stages and sexual gametocyte stages, but showed male gametocyte- specific expression. In contrast to previous findings, we showed that gene deletion Pfcrk5− parasites grew normally as asexual stages and underwent normal gametocytogenesis to stage V gametocytes. However, Pfcrk5− parasites showed a severe defect in male gametogenesis, which was evident by a significant reduction in the emergence of male gametes (exflagellation). This defect caused a severe reduction of parasite transmission to the mosquito. Genetic crosses performed using sex-specific sterile transgenic parasites revealed that Pfcrk5− parasites suffered a defect in male fertility but female gametes were fertile. Taken together, these results demonstrate that PfCRK5 is a critical sexual stage kinase which regulates male gametogenesis and transmission to the mosquito.
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6
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Novel CDK9 inhibitor oroxylin A promotes wild-type P53 stability and prevents hepatocellular carcinoma progression by disrupting both MDM2 and SIRT1 signaling. Acta Pharmacol Sin 2022; 43:1033-1045. [PMID: 34188177 DOI: 10.1038/s41401-021-00708-2] [Citation(s) in RCA: 21] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2021] [Accepted: 05/28/2021] [Indexed: 12/21/2022] Open
Abstract
Hepatocellular carcinoma (HCC) is one of the most lethal tumours worldwide. However, the effects of first-line sorafenib treatment in advanced HCC fail to prolong patients' survival due to the highly heterogeneous characteristics of HCC etiology. Cyclin-dependent kinase 9 (CDK9) is an important target in the continuous development of cancer therapy. Here, we demonstrate that CDK9 is closely associated with the progression of HCC and can serve as an HCC therapeutic target by modulating the recovery of wild-type p53 (wt-p53) function. We prove that mouse double minute 2 homologue (MDM2) and Sirtuin 1 (SIRT1) are phosphorylated by CDK9 at Ser166 and Ser47, respectively. Inhibition of CDK9 not only reduces the MDM2-mediated ubiquitination and degradation of wt-p53 but also increases wt-p53 stability by suppressing deacetylase activity of SIRT1. Thus, inhibition of CDK9 promotes the wt-p53 stabilization and prevents HCC progression. However, excessive inhibition by high concentrations of specific CDK9 inhibitors counteracts the promotion of p53 stability and reduces their anti-HCC activity because of extreme general transcription repression. The effects of a novel CDK9 inhibitor named oroxylin A (OA) from Scutellaria baicalensis are explored, with the results indicating that OA shows moderate and controlled inhibition of CDK9 activity and expression, and stabilizes wt-p53 by inhibiting CDK9-regulated MDM2 and SIRT1 signaling. These outcomes indicate the high therapeutic potential of OA against HCC and its low toxicity in normal tissue. This study demonstrates a novel mechanism for the regulation of wt-p53 by CDK9 and indicates that OA is a potential candidate for HCC therapy.
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7
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Syahirah R, Hsu AY, Deng Q. A curious case of cyclin‐dependent kinases in neutrophils. J Leukoc Biol 2022; 111:1057-1068. [PMID: 35188696 PMCID: PMC9035055 DOI: 10.1002/jlb.2ru1021-573r] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2021] [Revised: 01/21/2022] [Accepted: 01/31/2022] [Indexed: 12/11/2022] Open
Abstract
Neutrophils are terminally differentiated, short-lived white blood cells critical for innate immunity. Although cyclin-dependent kinases (CDKs) are typically related to cell cycle progression, increasing evidence has shown that they regulate essential functions of neutrophils. This review highlights the roles of CDKs and their partners, cyclins, in neutrophils, outside of cell cycle regulation. CDK1-10 and several cyclins are expressed in neutrophils, albeit at different levels. Observed phenotypes associated with specific inhibition or genetic loss of CDK2 indicate its role in modulating neutrophil migration. CDK4 and 6 regulate neutrophil extracellular traps (NETs) formation, while CDK5 regulates neutrophil degranulation. CDK7 and 9 are critical in neutrophil apoptosis, contributing to inflammation resolution. In addition to the CDKs that regulate mature neutrophil functions, cyclins are essential in hematopoiesis and granulopoiesis. The pivotal roles of CDKs in neutrophils present an untapped potential in targeting CDKs for treating neutrophil-dominant inflammatory diseases and understanding the regulation of the neutrophil life cycle.
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Affiliation(s)
- Ramizah Syahirah
- Department of Biological Sciences Purdue University West Lafayette Indiana USA
| | - Alan Y. Hsu
- Department of Biological Sciences Purdue University West Lafayette Indiana USA
- Department of Pathology Harvard Medical School Boston Massachusetts USA
- Department of Laboratory Medicine The Stem Cell Program, Boston Children's Hospital Boston Massachusetts USA
| | - Qing Deng
- Department of Biological Sciences Purdue University West Lafayette Indiana USA
- Purdue Institute of Inflammation Immunology and Infectious Disease, Purdue University West Lafayette Indiana USA
- Purdue University Center for Cancer Research, Purdue University West Lafayette Indiana USA
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8
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Ramya Sree PR, Thoppil JE. An overview on breast cancer genetics and recent innovations: Literature survey. Breast Dis 2021; 40:143-154. [PMID: 33867352 DOI: 10.3233/bd-201040] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Breast cancer is one of the leading cancers nowadays. The genetical mechanism behind breast cancer development is an intricate one. In this review, the genetical background of breast cancer, particularly BRCA 1 and BRCA 2 had been included. Moreover, to summarize the genetics of breast cancer, the recent and ongoing preclinical and clinical studies on the treatment of BRCA-associated breast cancer had also been included. A prime knowledge is that the BRCA gene is the basis of breast cancer risk. How it mediates cell proliferation and associated mechanisms are reviewed here. BRCA 1 gene can influence all phases of the cell cycle and regulate cell cycle progression. BRCA 1 gene can also respond to DNA damages and induce responsive mechanisms. The action of the BRCA gene on associated protein has a wide consideration in breast cancer development. Heterogeneity in breast cancer makes them a fascinating and challenging stream to diagnose and treat. Several clinical therapies are available for breast cancer treatments. Chemotherapy, endocrine therapy, radiation therapy and immunotherapy are the milestones in the cancer treatments. Ral binding protein 1 is a promising target for breast cancer treatment and the platinum-based chemotherapies are the other remarkable fields. In immunotherapy, the usage of anti-programmed death (PD)-1 antibody is a new class of cancer immunotherapy that hinders immune effecter inhibition and potentially expanding preexisting anticancer immune responses. Breast cancer genetics and treatment strategies are crucial in escalating survival rates.
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Affiliation(s)
| | - John Ernest Thoppil
- Cell and Molecular Biology Division, Department of Botany, University of Calicut, Kerala, India
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9
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Schnell AP, Kohrt S, Thoma-Kress AK. Latency Reversing Agents: Kick and Kill of HTLV-1? Int J Mol Sci 2021; 22:ijms22115545. [PMID: 34073995 PMCID: PMC8197370 DOI: 10.3390/ijms22115545] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2021] [Revised: 05/19/2021] [Accepted: 05/20/2021] [Indexed: 12/14/2022] Open
Abstract
Human T-cell leukemia virus type 1 (HTLV-1), the cause of adult T-cell leukemia/lymphoma (ATLL), is a retrovirus, which integrates into the host genome and persistently infects CD4+ T-cells. Virus propagation is stimulated by (1) clonal expansion of infected cells and (2) de novo infection. Viral gene expression is induced by the transactivator protein Tax, which recruits host factors like positive transcription elongation factor b (P-TEFb) to the viral promoter. Since HTLV-1 gene expression is repressed in vivo by viral, cellular, and epigenetic mechanisms in late phases of infection, HTLV-1 avoids an efficient CD8+ cytotoxic T-cell (CTL) response directed against the immunodominant viral Tax antigen. Hence, therapeutic strategies using latency reversing agents (LRAs) sought to transiently activate viral gene expression and antigen presentation of Tax to enhance CTL responses towards HTLV-1, and thus, to expose the latent HTLV-1 reservoir to immune destruction. Here, we review strategies that aimed at enhancing Tax expression and Tax-specific CTL responses to interfere with HTLV-1 latency. Further, we provide an overview of LRAs including (1) histone deacetylase inhibitors (HDACi) and (2) activators of P-TEFb, that have mainly been studied in context of human immunodeficiency virus (HIV), but which may also be powerful in the context of HTLV-1.
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10
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Amani J, Gorjizadeh N, Younesi S, Najafi M, Ashrafi AM, Irian S, Gorjizadeh N, Azizian K. Cyclin-dependent kinase inhibitors (CDKIs) and the DNA damage response: The link between signaling pathways and cancer. DNA Repair (Amst) 2021; 102:103103. [PMID: 33812232 DOI: 10.1016/j.dnarep.2021.103103] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2020] [Accepted: 03/16/2021] [Indexed: 02/08/2023]
Abstract
At the cellular level, DNA repair mechanisms are crucial in maintaining both genomic integrity and stability. DNA damage appears to be a central culprit in tumor onset and progression. Cyclin-dependent kinases (CDKs) and their regulatory partners coordinate the cell cycle progression. Aberrant CDK activity has been linked to a variety of cancers through deregulation of cell-cycle control. Besides DNA damaging agents and chromosome instability (CIN), disruptions in the levels of cell cycle regulators including cyclin-dependent kinase inhibitors (CDKIs) would result in unscheduled proliferation and cell division. The INK4 and Cip/Kip (CDK interacting protein/kinase inhibitor protein) family of CDKI proteins are involved in cell cycle regulation, transcription regulation, apoptosis, and cell migration. A thorough understanding of how these CDKIs regulate the DNA damage response through multiple signaling pathways may provide an opportunity to design efficient treatment strategies to inhibit carcinogenesis.
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Affiliation(s)
- Jafar Amani
- Applied Microbiology Research Center, System Biology and Poisonings Institute, Baqiyatallah University of Medical Sciences, Tehran, Iran
| | - Nassim Gorjizadeh
- Cellular and Molecular Biology Research Center, Health Research Institute, Babol University of Medical Sciences, Babol, Iran
| | - Simin Younesi
- School of Health and Biomedical Sciences, RMIT University, Melbourne, Vic., Australia
| | - Mojtaba Najafi
- Department of Genetics, Faculty of Animal Sciences, Gorgan University of Agricultural Sciences and Natural Resources, Golestan, Iran
| | - Arash M Ashrafi
- Cellular and Molecular Biology Research Center, Health Research Institute, Babol University of Medical Sciences, Babol, Iran
| | - Saeed Irian
- Department of Cell and Molecular Biology, Faculty of Biological Sciences, Kharazmi University, Tehran, Iran
| | - Negar Gorjizadeh
- Cellular and Molecular Biology Research Center, Health Research Institute, Babol University of Medical Sciences, Babol, Iran; Department of Cell and Molecular Biology, Faculty of Biological Sciences, Kharazmi University, Tehran, Iran.
| | - Khalil Azizian
- Department of Clinical Microbiology, Sirjan School of Medical Sciences, Sirjan, Iran.
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11
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Shao H, Foley DW, Huang S, Abbas AY, Lam F, Gershkovich P, Bradshaw TD, Pepper C, Fischer PM, Wang S. Structure-based design of highly selective 2,4,5-trisubstituted pyrimidine CDK9 inhibitors as anti-cancer agents. Eur J Med Chem 2021; 214:113244. [PMID: 33581551 DOI: 10.1016/j.ejmech.2021.113244] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2020] [Revised: 01/25/2021] [Accepted: 01/25/2021] [Indexed: 11/17/2022]
Abstract
Cyclin-dependent kinases (CDKs) are a family of Ser/Thr kinases involved in cell cycle and transcriptional regulation. CDK9 regulates transcriptional elongation and this unique property has made it a potential target for several diseases. Due to the conserved ATP binding site, designing selective CDK9 inhibitors has been challenging. Here we report our continued efforts in the optimization of 2,4,5-tri-substituted pyrimidine compounds as potent and selective CDK9 inhibitors. The most selective compound 30m was >100-fold selective for CDK9 over CDK1 and CDK2. These compounds showed broad anti-proliferative activities in various solid tumour cell lines and patient-derived chronic lymphocytic leukaemia (CLL) cells. Decreased phosphorylation of the carboxyl terminal domain (CTD) of RNAPII at Ser-2 and down-regulation of anti-apoptotic protein Mcl-1 were confirmed in both the ovarian cancer model A2780 and patient-derived CLL cells.
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Affiliation(s)
- Hao Shao
- School of Pharmacy and Biodiscovery Institute, University of Nottingham, University Park, Nottingham, NG7 2RD, UK
| | - David W Foley
- School of Pharmacy and Biodiscovery Institute, University of Nottingham, University Park, Nottingham, NG7 2RD, UK
| | - Shiliang Huang
- School of Pharmacy and Biodiscovery Institute, University of Nottingham, University Park, Nottingham, NG7 2RD, UK
| | - Abdullahi Y Abbas
- School of Pharmacy and Biodiscovery Institute, University of Nottingham, University Park, Nottingham, NG7 2RD, UK
| | - Frankie Lam
- Drug Discovery and Development, Clinical and Health Sciences, University of South Australia, Adelaide, SA, 5001, Australia
| | - Pavel Gershkovich
- School of Pharmacy and Biodiscovery Institute, University of Nottingham, University Park, Nottingham, NG7 2RD, UK
| | - Tracey D Bradshaw
- School of Pharmacy and Biodiscovery Institute, University of Nottingham, University Park, Nottingham, NG7 2RD, UK
| | - Chris Pepper
- Brighton and Sussex Medical School, University of Sussex, Brighton, East Sussex, BN1 9PX, UK
| | - Peter M Fischer
- School of Pharmacy and Biodiscovery Institute, University of Nottingham, University Park, Nottingham, NG7 2RD, UK.
| | - Shudong Wang
- School of Pharmacy and Biodiscovery Institute, University of Nottingham, University Park, Nottingham, NG7 2RD, UK; Drug Discovery and Development, Clinical and Health Sciences, University of South Australia, Adelaide, SA, 5001, Australia.
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12
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Zhang Y, Hou J, Shi S, Du J, Liu Y, Huang P, Li Q, Liu L, Hu H, Ji Y, Guo L, Shi Y, Liu Y, Cui H. CSN6 promotes melanoma proliferation and metastasis by controlling the UBR5-mediated ubiquitination and degradation of CDK9. Cell Death Dis 2021; 12:118. [PMID: 33483464 PMCID: PMC7822921 DOI: 10.1038/s41419-021-03398-0] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2020] [Revised: 12/17/2020] [Accepted: 12/28/2020] [Indexed: 12/13/2022]
Abstract
As a critical subunit of the constitutive photomorphogenesis 9 (COP9) signalosome (CSN), CSN6 is upregulated in some human cancers and plays critical roles in tumorigenesis and progression, but its biological functions and molecular mechanisms in melanoma remain unknown. Our study showed that CSN6 expression was upregulated in melanoma patients and cells, and correlated with poor survival in melanoma patients. In melanoma cells, CSN6 knockdown remarkably inhibited cell proliferation, tumorigenicity, migration, and invasion, whereas CSN6 recovery rescued the proliferative and metastatic abilities. Notably, we identified that CSN6 stabilized CDK9 expression by reducing CDK9 ubiquitination levels, thereby activating CDK9-mediated signaling pathways. In addition, our study described a novel CSN6-interacting E3 ligase UBR5, which was negatively regulated by CSN6 and could regulate the ubiquitination and degradation of CDK9 in melanoma cells. Furthermore, in CSN6-knockdown melanoma cells, UBR5 knockdown abrogated the effects caused by CSN6 silencing, suggesting that CSN6 activates the UBR5/CDK9 pathway to promote melanoma cell proliferation and metastasis. Thus, this study illustrates the mechanism by which the CSN6-UBR5-CDK9 axis promotes melanoma development, and demonstrate that CSN6 may be a potential biomarker and anticancer target in melanoma.
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Affiliation(s)
- Yanli Zhang
- Department of Dermatology, The Third Hospital of Hebei Medical University, 050051, Shijiazhuang, Hebei, China.,State Key Laboratory of Silkworm Genome Biology, Southwest University, 400715, Chongqing, China
| | - Jianbing Hou
- State Key Laboratory of Silkworm Genome Biology, Southwest University, 400715, Chongqing, China.,Cancer center, Medical Research Institute, Southwest University, 400716, Chongqing, China.,Chongqing Engineering and Technology Research Centre for Silk Biomaterials and Regenerative Medicine, 400716, Chongqing, China.,Engineering Research Center for Cancer Biomedical and Translational Medicine, Southwest University, 400716, Chongqing, China
| | - Shaomin Shi
- Department of Dermatology, The Third Hospital of Hebei Medical University, 050051, Shijiazhuang, Hebei, China.,State Key Laboratory of Silkworm Genome Biology, Southwest University, 400715, Chongqing, China
| | - Juan Du
- Department of Dermatology, The Third Hospital of Hebei Medical University, 050051, Shijiazhuang, Hebei, China.,State Key Laboratory of Silkworm Genome Biology, Southwest University, 400715, Chongqing, China
| | - Yudong Liu
- State Key Laboratory of Silkworm Genome Biology, Southwest University, 400715, Chongqing, China.,Cancer center, Medical Research Institute, Southwest University, 400716, Chongqing, China.,Chongqing Engineering and Technology Research Centre for Silk Biomaterials and Regenerative Medicine, 400716, Chongqing, China.,Engineering Research Center for Cancer Biomedical and Translational Medicine, Southwest University, 400716, Chongqing, China
| | - Pan Huang
- State Key Laboratory of Silkworm Genome Biology, Southwest University, 400715, Chongqing, China.,Cancer center, Medical Research Institute, Southwest University, 400716, Chongqing, China.,Chongqing Engineering and Technology Research Centre for Silk Biomaterials and Regenerative Medicine, 400716, Chongqing, China.,Engineering Research Center for Cancer Biomedical and Translational Medicine, Southwest University, 400716, Chongqing, China
| | - Qian Li
- Department of Dermatology, The Third Hospital of Hebei Medical University, 050051, Shijiazhuang, Hebei, China.,State Key Laboratory of Silkworm Genome Biology, Southwest University, 400715, Chongqing, China
| | - Lichao Liu
- Department of Dermatology, The Third Hospital of Hebei Medical University, 050051, Shijiazhuang, Hebei, China.,State Key Laboratory of Silkworm Genome Biology, Southwest University, 400715, Chongqing, China
| | - Huanrong Hu
- Department of Dermatology, The Third Hospital of Hebei Medical University, 050051, Shijiazhuang, Hebei, China.,State Key Laboratory of Silkworm Genome Biology, Southwest University, 400715, Chongqing, China
| | - Yacong Ji
- Department of Dermatology, The Third Hospital of Hebei Medical University, 050051, Shijiazhuang, Hebei, China
| | - Leiyang Guo
- Department of Dermatology, The Third Hospital of Hebei Medical University, 050051, Shijiazhuang, Hebei, China
| | - Yaqiong Shi
- Department of Dermatology, The Third Hospital of Hebei Medical University, 050051, Shijiazhuang, Hebei, China
| | - Yaling Liu
- Department of Dermatology, The Third Hospital of Hebei Medical University, 050051, Shijiazhuang, Hebei, China.
| | - Hongjuan Cui
- State Key Laboratory of Silkworm Genome Biology, Southwest University, 400715, Chongqing, China. .,Cancer center, Medical Research Institute, Southwest University, 400716, Chongqing, China. .,Chongqing Engineering and Technology Research Centre for Silk Biomaterials and Regenerative Medicine, 400716, Chongqing, China. .,Engineering Research Center for Cancer Biomedical and Translational Medicine, Southwest University, 400716, Chongqing, China.
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13
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Juric V, Murphy B. Cyclin-dependent kinase inhibitors in brain cancer: current state and future directions. CANCER DRUG RESISTANCE (ALHAMBRA, CALIF.) 2020; 3:48-62. [PMID: 35582046 PMCID: PMC9094053 DOI: 10.20517/cdr.2019.105] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/05/2019] [Revised: 12/11/2019] [Accepted: 12/20/2019] [Indexed: 12/12/2022]
Abstract
Cyclin-dependent kinases (CDKs) are important regulatory enzymes in the normal physiological processes that drive cell-cycle transitions and regulate transcription. Virtually all cancers harbour genomic alterations that lead to the constitutive activation of CDKs, resulting in the proliferation of cancer cells. CDK inhibitors (CKIs) are currently in clinical use for the treatment of breast cancer, combined with endocrine therapy. In this review, we describe the potential of CKIs for the treatment of cancer with specific focus on glioblastoma (GBM), the most common and aggressive primary brain tumour in adults. Despite intense effort to combat GBM with surgery, radiation and temozolomide chemotherapy, the median survival for patients is 15 months and the majority of patients experience disease recurrence within 6-8 months of treatment onset. Novel therapeutic approaches are urgently needed for both newly diagnosed and recurrent GBM patients. In this review, we summarise the current preclinical and clinical findings emphasising that CKIs could represent an exciting novel approach for GBM treatment.
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Affiliation(s)
- Viktorija Juric
- Department of Physiology and Medical Physics, Royal College of Surgeons in Ireland, Dublin D02, Ireland
| | - Brona Murphy
- Department of Physiology and Medical Physics, Royal College of Surgeons in Ireland, Dublin D02, Ireland
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14
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Tang F, Yang Z, Tan Y, Li Y. Super-enhancer function and its application in cancer targeted therapy. NPJ Precis Oncol 2020; 4:2. [PMID: 32128448 PMCID: PMC7016125 DOI: 10.1038/s41698-020-0108-z] [Citation(s) in RCA: 75] [Impact Index Per Article: 18.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2019] [Accepted: 12/31/2019] [Indexed: 12/12/2022] Open
Abstract
Recently, super-enhancers (SEs) have been identified as a unique type of transcriptional regulation involved in cancer development. SEs exhibit a size, high transcription factor density, and strong binding to the transcriptional machinery compared with typical enhancers. SEs play an essential role in cell growth, differentiation, and disease initiation and progression including tumorigenesis. In particular, cancer-specific SEs have been proven to be key oncogenic drivers types of tumor cells. Furthermore, it has been confirmed that cancer-specific SEs can mediate the dysregulation of signaling pathways and promote cancer cell growth. Additionally, therapeutic strategies directly targeting SE components, for example, by disrupting SE structure or inhibiting SE cofactors, have shown a good curative effect on various cancers.
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Affiliation(s)
- Faqing Tang
- 1Department of Clinical Laboratory, Hunan Cancer Hospital and the Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, 410013 Changsha, China
| | - Zongbei Yang
- 2Department of Clinical Laboratory, Zhuhai People's Hospital & Zhuhai Hospital of Jinan University, 519000 Zhuhai, China
| | - Yuan Tan
- 1Department of Clinical Laboratory, Hunan Cancer Hospital and the Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, 410013 Changsha, China
| | - Yuejin Li
- 1Department of Clinical Laboratory, Hunan Cancer Hospital and the Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, 410013 Changsha, China
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15
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Sorvina A, Shandala T, Wang S, Sharkey DJ, Parkinson-Lawrence E, Selemidis S, Brooks DA. CDKI-73 is a Novel Pharmacological Inhibitor of Rab11 Cargo Delivery and Innate Immune Secretion. Cells 2020; 9:cells9020372. [PMID: 32033486 PMCID: PMC7072129 DOI: 10.3390/cells9020372] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2020] [Revised: 01/31/2020] [Accepted: 02/03/2020] [Indexed: 12/22/2022] Open
Abstract
Innate immunity is critical for host defence against pathogen and environmental challenge and this involves the production and secretion of immune mediators, such as antimicrobial peptides and pro-inflammatory cytokines. However, when dysregulated, innate immunity can contribute to multifactorial diseases, including inflammatory rheumatic disorders, type 2 diabetes, cancer, neurodegenerative and cardiovascular diseases and even septic shock. During an innate immune response, antimicrobial peptides and cytokines are trafficked via Rab11 multivesicular endosomes, and then sorted into Rab11 vesicles for traffic to the plasma membrane and secretion. In this study, a cyclin-dependent kinase inhibitor CDKI-73 was used to determine its effect on the innate immune response, based on previously identified targets for this compound. Our results showed that CDKI-73 inhibited the delivery of Rab11 vesicles to the plasma membrane, resulting in the accumulation of large multivesicular Rab11 endosomes near the cell periphery. In addition to the effect on endosome delivery, CDKI-73 down-regulated the amount of innate immune cargo, including the antimicrobial peptide Drosomycin and pro-inflammatory cytokines interleukin-6 (IL-6) and tumour necrosis factor alpha (TNFα). We concluded that CDKI-73 has the potential to regulate the delivery and secretion of certain innate immune cargo, which could be used to control inflammation.
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Affiliation(s)
- Alexandra Sorvina
- Cell Biology and Disease Research Group, Cancer Research Institute, University of South Australia, Adelaide, SA 5000, Australia (E.P.-L.)
- Correspondence: (A.S.); (D.A.B.)
| | - Tetyana Shandala
- Cell Biology and Disease Research Group, Cancer Research Institute, University of South Australia, Adelaide, SA 5000, Australia (E.P.-L.)
| | - Shudong Wang
- Centre for Drug Discovery and Development, Cancer Research Institute, University of South Australia, Adelaide, SA 5000, Australia;
| | - David J. Sharkey
- Robinson Research Institute, University of Adelaide, Adelaide, SA 5000, Australia;
| | - Emma Parkinson-Lawrence
- Cell Biology and Disease Research Group, Cancer Research Institute, University of South Australia, Adelaide, SA 5000, Australia (E.P.-L.)
| | - Stavros Selemidis
- School of Health and Biomedical Sciences, RMIT University, Bundoora, VIC 3083, Australia;
| | - Douglas A. Brooks
- Cell Biology and Disease Research Group, Cancer Research Institute, University of South Australia, Adelaide, SA 5000, Australia (E.P.-L.)
- Correspondence: (A.S.); (D.A.B.)
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16
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Zhang H, Pandey S, Travers M, Sun H, Morton G, Madzo J, Chung W, Khowsathit J, Perez-Leal O, Barrero CA, Merali C, Okamoto Y, Sato T, Pan J, Garriga J, Bhanu NV, Simithy J, Patel B, Huang J, Raynal NJM, Garcia BA, Jacobson MA, Kadoch C, Merali S, Zhang Y, Childers W, Abou-Gharbia M, Karanicolas J, Baylin SB, Zahnow CA, Jelinek J, Graña X, Issa JPJ. Targeting CDK9 Reactivates Epigenetically Silenced Genes in Cancer. Cell 2018; 175:1244-1258.e26. [PMID: 30454645 PMCID: PMC6247954 DOI: 10.1016/j.cell.2018.09.051] [Citation(s) in RCA: 153] [Impact Index Per Article: 25.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2017] [Revised: 09/19/2018] [Accepted: 09/24/2018] [Indexed: 12/31/2022]
Abstract
Cyclin-dependent kinase 9 (CDK9) promotes transcriptional elongation through RNAPII pause release. We now report that CDK9 is also essential for maintaining gene silencing at heterochromatic loci. Through a live cell drug screen with genetic confirmation, we discovered that CDK9 inhibition reactivates epigenetically silenced genes in cancer, leading to restored tumor suppressor gene expression, cell differentiation, and activation of endogenous retrovirus genes. CDK9 inhibition dephosphorylates the SWI/SNF protein BRG1, which contributes to gene reactivation. By optimization through gene expression, we developed a highly selective CDK9 inhibitor (MC180295, IC50 = 5 nM) that has broad anti-cancer activity in vitro and is effective in in vivo cancer models. Additionally, CDK9 inhibition sensitizes to the immune checkpoint inhibitor α-PD-1 in vivo, making it an excellent target for epigenetic therapy of cancer.
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Affiliation(s)
- Hanghang Zhang
- Fels Institute for Cancer Research, Lewis Katz School of Medicine at Temple University, Philadelphia, PA 19140, USA
| | - Somnath Pandey
- Fels Institute for Cancer Research, Lewis Katz School of Medicine at Temple University, Philadelphia, PA 19140, USA
| | - Meghan Travers
- The Sidney Kimmel Comprehensive Cancer Center at Johns Hopkins, Baltimore, MD 21231, USA
| | - Hongxing Sun
- Fels Institute for Cancer Research, Lewis Katz School of Medicine at Temple University, Philadelphia, PA 19140, USA
| | - George Morton
- Moulder Center for Drug Discovery Research, Temple University School of Pharmacy, Philadelphia, PA 19140, USA
| | - Jozef Madzo
- Fels Institute for Cancer Research, Lewis Katz School of Medicine at Temple University, Philadelphia, PA 19140, USA
| | - Woonbok Chung
- Fels Institute for Cancer Research, Lewis Katz School of Medicine at Temple University, Philadelphia, PA 19140, USA
| | - Jittasak Khowsathit
- Molecular Therapeutics Program, Fox Chase Cancer Center, Philadelphia, PA 19111, USA; Department of Molecular Biosciences, University of Kansas, Lawrence, KS 66045, USA
| | - Oscar Perez-Leal
- Department of Pharmaceutical Sciences, Temple University School of Pharmacy, Philadelphia, PA 19140, USA
| | - Carlos A Barrero
- Department of Pharmaceutical Sciences, Temple University School of Pharmacy, Philadelphia, PA 19140, USA
| | - Carmen Merali
- Department of Pharmaceutical Sciences, Temple University School of Pharmacy, Philadelphia, PA 19140, USA
| | - Yasuyuki Okamoto
- Fels Institute for Cancer Research, Lewis Katz School of Medicine at Temple University, Philadelphia, PA 19140, USA
| | - Takahiro Sato
- Fels Institute for Cancer Research, Lewis Katz School of Medicine at Temple University, Philadelphia, PA 19140, USA
| | - Joshua Pan
- Department of Pediatric Oncology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, MA 02215, USA
| | - Judit Garriga
- Fels Institute for Cancer Research, Lewis Katz School of Medicine at Temple University, Philadelphia, PA 19140, USA
| | - Natarajan V Bhanu
- Epigenetics Institute, Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Johayra Simithy
- Epigenetics Institute, Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Bela Patel
- Fels Institute for Cancer Research, Lewis Katz School of Medicine at Temple University, Philadelphia, PA 19140, USA
| | - Jian Huang
- Fels Institute for Cancer Research, Lewis Katz School of Medicine at Temple University, Philadelphia, PA 19140, USA
| | - Noël J-M Raynal
- Département de pharmacologie et physiologie, Université de Montréal, Montréal, QC H3C 3J7, Canada
| | - Benjamin A Garcia
- Epigenetics Institute, Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Marlene A Jacobson
- Moulder Center for Drug Discovery Research, Temple University School of Pharmacy, Philadelphia, PA 19140, USA
| | - Cigall Kadoch
- Department of Pediatric Oncology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, MA 02215, USA
| | - Salim Merali
- Department of Pharmaceutical Sciences, Temple University School of Pharmacy, Philadelphia, PA 19140, USA
| | - Yi Zhang
- Fels Institute for Cancer Research, Lewis Katz School of Medicine at Temple University, Philadelphia, PA 19140, USA
| | - Wayne Childers
- Moulder Center for Drug Discovery Research, Temple University School of Pharmacy, Philadelphia, PA 19140, USA
| | - Magid Abou-Gharbia
- Moulder Center for Drug Discovery Research, Temple University School of Pharmacy, Philadelphia, PA 19140, USA
| | - John Karanicolas
- Molecular Therapeutics Program, Fox Chase Cancer Center, Philadelphia, PA 19111, USA
| | - Stephen B Baylin
- The Sidney Kimmel Comprehensive Cancer Center at Johns Hopkins, Baltimore, MD 21231, USA
| | - Cynthia A Zahnow
- The Sidney Kimmel Comprehensive Cancer Center at Johns Hopkins, Baltimore, MD 21231, USA
| | - Jaroslav Jelinek
- Fels Institute for Cancer Research, Lewis Katz School of Medicine at Temple University, Philadelphia, PA 19140, USA
| | - Xavier Graña
- Fels Institute for Cancer Research, Lewis Katz School of Medicine at Temple University, Philadelphia, PA 19140, USA
| | - Jean-Pierre J Issa
- Fels Institute for Cancer Research, Lewis Katz School of Medicine at Temple University, Philadelphia, PA 19140, USA.
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17
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García-Reyes B, Kretz AL, Ruff JP, von Karstedt S, Hillenbrand A, Knippschild U, Henne-Bruns D, Lemke J. The Emerging Role of Cyclin-Dependent Kinases (CDKs) in Pancreatic Ductal Adenocarcinoma. Int J Mol Sci 2018; 19:E3219. [PMID: 30340359 PMCID: PMC6214075 DOI: 10.3390/ijms19103219] [Citation(s) in RCA: 53] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2018] [Revised: 09/27/2018] [Accepted: 10/11/2018] [Indexed: 02/07/2023] Open
Abstract
The family of cyclin-dependent kinases (CDKs) has critical functions in cell cycle regulation and controlling of transcriptional elongation. Moreover, dysregulated CDKs have been linked to cancer initiation and progression. Pharmacological CDK inhibition has recently emerged as a novel and promising approach in cancer therapy. This idea is of particular interest to combat pancreatic ductal adenocarcinoma (PDAC), a cancer entity with a dismal prognosis which is owed mainly to PDAC's resistance to conventional therapies. Here, we review the current knowledge of CDK biology, its role in cancer and the therapeutic potential to target CDKs as a novel treatment strategy for PDAC.
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Affiliation(s)
- Balbina García-Reyes
- Department of General and Visceral Surgery, Ulm University Hospital, Albert-Einstein-Allee 23, 89081 Ulm, Germany.
| | - Anna-Laura Kretz
- Department of General and Visceral Surgery, Ulm University Hospital, Albert-Einstein-Allee 23, 89081 Ulm, Germany.
| | - Jan-Philipp Ruff
- Department of General and Visceral Surgery, Ulm University Hospital, Albert-Einstein-Allee 23, 89081 Ulm, Germany.
| | - Silvia von Karstedt
- Department of Translational Genomics, University Hospital Cologne, Weyertal 115b, 50931 Cologne, Germany.
- Cologne Excellence Cluster on Cellular Stress Response in Aging-Associated Diseases (CECAD), University of Cologne, Joseph-Stelzmann-Straße 26, 50931 Cologne, Germany.
| | - Andreas Hillenbrand
- Department of General and Visceral Surgery, Ulm University Hospital, Albert-Einstein-Allee 23, 89081 Ulm, Germany.
| | - Uwe Knippschild
- Department of General and Visceral Surgery, Ulm University Hospital, Albert-Einstein-Allee 23, 89081 Ulm, Germany.
| | - Doris Henne-Bruns
- Department of General and Visceral Surgery, Ulm University Hospital, Albert-Einstein-Allee 23, 89081 Ulm, Germany.
| | - Johannes Lemke
- Department of General and Visceral Surgery, Ulm University Hospital, Albert-Einstein-Allee 23, 89081 Ulm, Germany.
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18
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Targeting General Transcriptional Machinery as a Therapeutic Strategy for Adult T-Cell Leukemia. Molecules 2018; 23:molecules23051057. [PMID: 29724031 PMCID: PMC6099935 DOI: 10.3390/molecules23051057] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2018] [Revised: 04/27/2018] [Accepted: 04/28/2018] [Indexed: 12/18/2022] Open
Abstract
Cancer cells are highly reliant on certain molecular pathways, which support their survival and proliferation. The fundamental concept of molecularly targeted therapy is to target a protein that is specifically deregulated or overexpressed in cancer cells. However, drug resistance and tumor heterogeneity are major obstacles in the development of specific inhibitors. Additionally, many driver oncogenes exert their oncogenic property via abnormal expression without having genetic mutations. Interestingly, recent accumulating evidence has demonstrated that many critical cancer genes are driven by a unique class of enhancers termed super-enhancers. Genes associated with super-enhancers are relatively more susceptible to the inhibition of general transcriptional machinery compared with genes that are regulated by typical enhancers. Cancer cells are more sensitive to treatment with small-molecule inhibitors of CDK7 or BRD4 than non-transformed cells. These findings proposed a novel strategy to identify functionally important genes as well as novel therapeutic modalities in cancer. This approach would be particularly useful for genetically complicated cancers, such as adult T-cell leukemia (ATL), whereby a large mutational burden is present, but the functional consequences of each mutation have not been well-studied. In this review, we discuss recent findings on super-enhancers, underlying mechanisms, and the efficacy of small-molecule transcriptional inhibitors in ATL.
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19
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Jing L, Tang Y, Xiao Z. Discovery of novel CDK inhibitors via scaffold hopping from CAN508. Bioorg Med Chem Lett 2018; 28:1386-1391. [DOI: 10.1016/j.bmcl.2018.02.054] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2017] [Revised: 02/17/2018] [Accepted: 02/27/2018] [Indexed: 12/21/2022]
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20
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Jing L, Tang Y, Goto M, Lee KH, Xiao Z. SAR study on N2, N4-disubstituted pyrimidine-2,4-diamines as effective CDK2/CDK9 inhibitors and antiproliferative agents. RSC Adv 2018; 8:11871-11885. [PMID: 29682280 PMCID: PMC5890689 DOI: 10.1039/c8ra01440j] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2018] [Accepted: 03/21/2018] [Indexed: 11/25/2022] Open
Abstract
Cyclin-dependent kinases (CDKs) are pivotal kinases in cell cycle transition and gene transcription. A series of N2,N4-diphenylpyrimidine-2,4-diamines were previously identified as potent CDK2/CDK9 inhibitors. To explore the SAR of this structural prototype, twenty-four novel N2,N4-disubstituted pyrimidine-2,4-diamines were designed and synthesized. Among them, twenty-one compounds exhibited potent inhibitory activities against both CDK2/cyclin A and CDK9/cyclin T1 systems, and the most potent CDK2 and CDK9 inhibitors, 3g and 3c, showed IC50 values of 83 nM and 65 nM respectively. Most of these compounds displayed significant inhibition against the tested tumor cell lines in the SRB assay, and in particular, remained active against the triple-negative breast cancer (TNBC) cell line MDA-MB-231. Flow cytometer analysis of compounds 2a, 2d and 3b in MDA-MB-231 cells indicated that these compounds induced cell cycle arrest in G2/M phase. Docking studies on compound 3g were performed, which provided conducive clues for further molecular optimization.
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Affiliation(s)
- Liandong Jing
- Beijing Key Laboratory of Active Substance Discovery and Druggability Evaluation, Institute of Materia Medica, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing 100050, China. Tel: +86-10- 63189228;
| | - Yanbo Tang
- Beijing Key Laboratory of Active Substance Discovery and Druggability Evaluation, Institute of Materia Medica, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing 100050, China. Tel: +86-10- 63189228;
| | - Masuo Goto
- Natural Products Research Laboratories, UNC Eshelman School of Pharmacy, University of North Carolina, Chapel Hill, North Carolina 27599-7568, USA
| | - Kuo-Hsiung Lee
- Natural Products Research Laboratories, UNC Eshelman School of Pharmacy, University of North Carolina, Chapel Hill, North Carolina 27599-7568, USA
- Chinese Medicine Research and Development Center, China Medical University and Hospital, Taichung, Taiwan
| | - Zhiyan Xiao
- Beijing Key Laboratory of Active Substance Discovery and Druggability Evaluation, Institute of Materia Medica, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing 100050, China. Tel: +86-10- 63189228;
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21
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Cdk-related kinase 9 regulates RNA polymerase II mediated transcription in Toxoplasma gondii. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2018; 1861:572-585. [PMID: 29466697 DOI: 10.1016/j.bbagrm.2018.02.004] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/02/2017] [Revised: 01/31/2018] [Accepted: 02/13/2018] [Indexed: 11/20/2022]
Abstract
Cyclin-dependent kinases are an essential part of eukaryotic transcriptional machinery. In Apicomplexan parasites, the role and relevance of the kinases in the multistep process of transcription seeks more attention given the absence of full repertoire of canonical Cdks and cognate cyclin partners. In this study, we functionally characterize T. gondii Cdk-related kinase 9 (TgCrk9) showing maximal homology to eukaryotic Cdk9. An uncanonical cyclin, TgCyclin L, colocalizes with TgCrk9 in the parasite nucleus and co-immunoprecipitate, could activate the kinase in-vitro. We identify two threonines in conserved T-loop domain of TgCrk9 that are important for its activity. The activated TgCrk9 phosphorylates C-terminal domain (CTD) of TgRpb1, the largest subunit of RNA polymerase II highlighting its role in transcription. Selective chemical inhibition of TgCrk9 affected serine 2 phosphorylation in the heptapeptide repeats of TgRpb1-CTD towards 3' end of genes consistent with a possible role in transcription elongation. Interestingly, TgCrk9 kinase activity is regulated by the upstream TgCrk7 based CAK complex. TgCrk9 was found to functionally complement the role of its yeast counterpart Bur1 establishing its role as an important transcriptional kinase. In this study, we provide robust evidence that TgCrk9 is an important part of transcription machinery regulating gene expression in T. gondii.
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22
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Johnson SF, Cruz C, Greifenberg AK, Dust S, Stover DG, Chi D, Primack B, Cao S, Bernhardy AJ, Coulson R, Lazaro JB, Kochupurakkal B, Sun H, Unitt C, Moreau LA, Sarosiek KA, Scaltriti M, Juric D, Baselga J, Richardson AL, Rodig SJ, D'Andrea AD, Balmaña J, Johnson N, Geyer M, Serra V, Lim E, Shapiro GI. CDK12 Inhibition Reverses De Novo and Acquired PARP Inhibitor Resistance in BRCA Wild-Type and Mutated Models of Triple-Negative Breast Cancer. Cell Rep 2017; 17:2367-2381. [PMID: 27880910 DOI: 10.1016/j.celrep.2016.10.077] [Citation(s) in RCA: 195] [Impact Index Per Article: 27.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2016] [Revised: 09/08/2016] [Accepted: 10/23/2016] [Indexed: 02/04/2023] Open
Abstract
Although poly(ADP-ribose) polymerase (PARP) inhibitors are active in homologous recombination (HR)-deficient cancers, their utility is limited by acquired resistance after restoration of HR. Here, we report that dinaciclib, an inhibitor of cyclin-dependent kinases (CDKs) 1, 2, 5, and 9, additionally has potent activity against CDK12, a transcriptional regulator of HR. In BRCA-mutated triple-negative breast cancer (TNBC) cells and patient-derived xenografts (PDXs), dinaciclib ablates restored HR and reverses PARP inhibitor resistance. Additionally, we show that de novo resistance to PARP inhibition in BRCA1-mutated cell lines and a PDX derived from a PARP-inhibitor-naive BRCA1 carrier is mediated by residual HR and is reversed by CDK12 inhibition. Finally, dinaciclib augments the degree of response in a PARP-inhibitor-sensitive model, converting tumor growth inhibition to durable regression. These results highlight the significance of HR disruption as a therapeutic strategy and support the broad use of combined CDK12 and PARP inhibition in TNBC.
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Affiliation(s)
- Shawn F Johnson
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Cristina Cruz
- Experimental Therapeutics Group, Vall d'Hebron Institute of Oncology, 08035 Barcelona, Spain; Medical Oncology Department, Hospital Vall d'Hebron, Vall d'Hebron Institute of Oncology, Universitat Autonoma de Barcelona, 08035 Barcelona, Spain
| | - Ann Katrin Greifenberg
- Department of Structural Immunology, Institute of Innate Immunity, University of Bonn, 53127 Bonn, Germany; Group Physical Biochemistry, Center of Advanced European Studies and Research, 53175 Bonn, Germany
| | - Sofia Dust
- Department of Structural Immunology, Institute of Innate Immunity, University of Bonn, 53127 Bonn, Germany; Group Physical Biochemistry, Center of Advanced European Studies and Research, 53175 Bonn, Germany
| | - Daniel G Stover
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA; Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA
| | - David Chi
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Benjamin Primack
- Department of Radiation Oncology and Center for DNA Damage and Repair, Dana-Farber Cancer Institute and Harvard Medical School, Boston, MA 02215, USA; Department of Pediatric Oncology, Dana-Farber Cancer Institute, Children's Hospital and Harvard Medical School, Boston, MA 02215, USA
| | - Shiliang Cao
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Andrea J Bernhardy
- Developmental Therapeutics Program, Fox Chase Cancer Center, Philadelphia, PA 19111, USA
| | - Rhiannon Coulson
- The Kinghorn Cancer Centre, Garvan Institute of Medical Research, St. Vincent's Health Network, Darlinghurst, NSW 2010, Australia
| | - Jean-Bernard Lazaro
- Department of Radiation Oncology and Center for DNA Damage and Repair, Dana-Farber Cancer Institute and Harvard Medical School, Boston, MA 02215, USA
| | - Bose Kochupurakkal
- Department of Radiation Oncology and Center for DNA Damage and Repair, Dana-Farber Cancer Institute and Harvard Medical School, Boston, MA 02215, USA
| | - Heather Sun
- Department of Pathology, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA
| | - Christine Unitt
- Department of Pathology, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA
| | - Lisa A Moreau
- Department of Radiation Oncology and Center for DNA Damage and Repair, Dana-Farber Cancer Institute and Harvard Medical School, Boston, MA 02215, USA; Department of Pediatric Oncology, Dana-Farber Cancer Institute, Children's Hospital and Harvard Medical School, Boston, MA 02215, USA
| | | | - Maurizio Scaltriti
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Dejan Juric
- Massachusetts General Hospital Cancer Center, Harvard Medical School, Boston, MA 02114, USA; Department of Medicine, Harvard Medical School, Boston, MA 02114, USA
| | - José Baselga
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Andrea L Richardson
- Department of Pathology, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA
| | - Scott J Rodig
- Department of Pathology, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA
| | - Alan D D'Andrea
- Department of Radiation Oncology and Center for DNA Damage and Repair, Dana-Farber Cancer Institute and Harvard Medical School, Boston, MA 02215, USA; Department of Pediatric Oncology, Dana-Farber Cancer Institute, Children's Hospital and Harvard Medical School, Boston, MA 02215, USA
| | - Judith Balmaña
- Medical Oncology Department, Hospital Vall d'Hebron, Vall d'Hebron Institute of Oncology, Universitat Autonoma de Barcelona, 08035 Barcelona, Spain
| | - Neil Johnson
- Developmental Therapeutics Program, Fox Chase Cancer Center, Philadelphia, PA 19111, USA
| | - Matthias Geyer
- Department of Structural Immunology, Institute of Innate Immunity, University of Bonn, 53127 Bonn, Germany; Group Physical Biochemistry, Center of Advanced European Studies and Research, 53175 Bonn, Germany
| | - Violeta Serra
- Experimental Therapeutics Group, Vall d'Hebron Institute of Oncology, 08035 Barcelona, Spain
| | - Elgene Lim
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; The Kinghorn Cancer Centre, Garvan Institute of Medical Research, St. Vincent's Health Network, Darlinghurst, NSW 2010, Australia.
| | - Geoffrey I Shapiro
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA.
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Hussain A, Verma CK, Chouhan U. Identification of novel inhibitors against Cyclin Dependent Kinase 9/Cyclin T1 complex as: Anti cancer agent. Saudi J Biol Sci 2017; 24:1229-1242. [PMID: 28855816 PMCID: PMC5562455 DOI: 10.1016/j.sjbs.2015.10.003] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2015] [Revised: 10/05/2015] [Accepted: 10/07/2015] [Indexed: 12/20/2022] Open
Abstract
Cell cycle consists of different types of phases, transition from G1, S, G2, M. Inhibition of associated CDKs like CDK9/Cyclin T1 complex, which are indirectly involved in the Cell cycle progression in the form of transcription elongation, reduces diverse diseases such as Cardiac Hypertrophy, Alzheimer’s, Cancer, AIDS and Inflammation. Glide tool of the Schrodinger software has been used for performing Structure Based Virtual Screening and Docking against Drug Bank and MDPI database. The best hits were identified which go and bind in the active site of the target where ATP binds for the activity. The ADMET, MM-GBSA and DFT analysis is also done for the same. Compound 4-{4-[4-(3-aminopropoxy)phenyl]-1H-pyrazol-5-yl}-6-chlorobenzene-1,3-diol (DB08045) was found to be more potent, novel and selective as an inhibitor. Hopefully compound (DB08045) could be used as an anti-cancer agent for the treatment of life-threatening diseases.
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Key Words
- ATP, adenosine triphosphate
- CDK
- CDK9, Cyclin Dependent Kinase 9
- CTD, carboxy terminal domain
- Cancer
- Cell cycle
- DFT, density functional theory
- Drug Bank
- HOMO, high occupied molecular orbital
- LUMO, lowest unoccupied molecular orbital
- MDPI
- MDPI, molecular diversity preservation international
- MW, molecular weight
- P-TEFB, positive transcription elongation factor B
- Potent
- SBVS, structure based virtual screening
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Affiliation(s)
- Afzal Hussain
- Department of Bioinformatics, MANIT, Bhopal, M.P. 462003, India
| | | | - Usha Chouhan
- Department of Bioinformatics, MANIT, Bhopal, M.P. 462003, India
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24
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Paparidis NFDS, Durvale MC, Canduri F. The emerging picture of CDK9/P-TEFb: more than 20 years of advances since PITALRE. MOLECULAR BIOSYSTEMS 2017; 13:246-276. [PMID: 27833949 DOI: 10.1039/c6mb00387g] [Citation(s) in RCA: 49] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
CDK9 is a prominent member of the transcriptional CDKs subfamily, a group of kinases whose function is to control the primary steps of mRNA synthesis and processing by eukaryotic RNA polymerase II. As a cyclin-dependent kinase, CDK9 activation in vivo depends upon its association with T-type cyclins to assemble the positive transcription elongation factor (P-TEFb). Although CDK9/P-TEFb phosphorylates the C-terminal domain of RNAP II in the same positions targeted by CDK7 (TFIIH) and CDK8 (Mediator), the former does not participate in the transcription initiation, but rather plays a unique role by driving the polymerase to productive elongation. In addition to RNAP II CTD, the negative transcription elongation factors DSIF and NELF also represent major CDK9 substrates, whose phosphorylation is required to overcome the proximal pause of the polymerase. CDK9 is recruited to specific genes through proteins that interact with both P-TEFb and distinct elements in DNA, RNA or chromatin, where it modulates the activity of individual RNAP II transcription complexes. The regulation of CDK9 function is an intricate network that includes post-translational modifications (phosphorylation/dephosphorylation and acetylation/deacetylation of key residues) as well as the association of P-TEFb with various proteins that can stimulate or inhibit its kinase activity. Several cases of CDK9 deregulation have been linked to important human diseases, including various types of cancer and also AIDS (due to its essential role in HIV replication). Not only HIV, but also many other human viruses have been shown to depend strongly on CDK9 activity to be transcribed within host cells. This review summarizes the main advances made on CDK9/P-TEFb field in more than 20 years, introducing the structural, functional and genetic aspects that have been elucidated ever since.
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Affiliation(s)
- Nikolas Ferreira Dos Santos Paparidis
- Department of Chemistry and Molecular Physics, Institute of Chemistry of Sao Carlos, Sao Paulo University, Av. Trabalhador Sãocarlense, 400, Zip Code 780, 13560-970, São Carlos-SP, Brazil.
| | - Maxwell Castro Durvale
- Department of Biochemistry, Institute of Chemistry, Sao Paulo University, Av. Prof. Lineu Prestes, 748, 05508-000, Butantã - São Paulo - SP, Brazil
| | - Fernanda Canduri
- Department of Chemistry and Molecular Physics, Institute of Chemistry of Sao Carlos, Sao Paulo University, Av. Trabalhador Sãocarlense, 400, Zip Code 780, 13560-970, São Carlos-SP, Brazil.
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25
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Songock WK, Scott ML, Bodily JM. Regulation of the human papillomavirus type 16 late promoter by transcriptional elongation. Virology 2017; 507:179-191. [PMID: 28448849 DOI: 10.1016/j.virol.2017.04.021] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2016] [Revised: 04/12/2017] [Accepted: 04/19/2017] [Indexed: 01/09/2023]
Abstract
Transcripts from the late promoter of human papillomavirus type 16 (HPV16) are upregulated upon host cell differentiation. Differentiation-dependent transcript regulation is thought to sequester viral antigens in the uppermost epithelial layers, facilitating immune evasion. The mechanisms regulating late promoter upregulation during differentiation are poorly characterized. We show that the late promoter is upregulated at the transcriptional level and that the viral enhancer stimulates promoter activity. Using kinase inhibition and chromatin immunoprecipitation analysis, we show evidence for differentiation-dependent enhancement of transcript elongation. Three factors that promote transcript elongation, cyclin dependent kinase 9 (CDK9), CDK8 (a subunit of the Mediator complex), and bromodomain containing protein 4 (Brd4) are recruited to viral genomes upon differentiation, and each plays a role in promoter activity. These results shed light on the transcriptional processes utilized by HPV16 for proper regulation of gene expression during the viral life cycle.
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Affiliation(s)
- William K Songock
- Department of Microbiology and Immunology, Center for Molecular and Tumor Virology, and Feist-Weiller Cancer Center, Louisiana State University Health Sciences Center, Shreveport, LA, USA
| | - Matthew L Scott
- Department of Microbiology and Immunology, Center for Molecular and Tumor Virology, and Feist-Weiller Cancer Center, Louisiana State University Health Sciences Center, Shreveport, LA, USA
| | - Jason M Bodily
- Department of Microbiology and Immunology, Center for Molecular and Tumor Virology, and Feist-Weiller Cancer Center, Louisiana State University Health Sciences Center, Shreveport, LA, USA.
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26
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Kretz AL, Schaum M, Richter J, Kitzig EF, Engler CC, Leithäuser F, Henne-Bruns D, Knippschild U, Lemke J. CDK9 is a prognostic marker and therapeutic target in pancreatic cancer. Tumour Biol 2017; 39:1010428317694304. [PMID: 28231737 DOI: 10.1177/1010428317694304] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
Despite recent advances in diagnosis and therapy, prognosis of pancreatic cancer still remains very poor. Besides valid prognostic markers, novel therapeutic approaches are urgently needed. The family of cyclin-dependent kinases comprises 20 kinases which contribute to malignancy by promoting proliferation, migration, invasion, and apoptotic resistance of cancer cells. In this work, we investigated the role of CDK9 in pancreatic cancer. Immunohistochemical analysis of CDK9 expression in tumor and normal tissue of pancreatic cancer patients revealed an overexpression of CDK9 in pancreatic cancer tissue. In addition, high CDK9 expression in tumor tissue is associated with significantly shortened survival, especially in well-differentiated tumors. Moreover, the therapeutic potential of selective CDK9 inhibition on pancreatic cancer cells was evaluated by analysis of cell viability, long-term survival, and induction of apoptosis and characterized by western blotting and flow cytometry. Pharmacological CDK9 inhibition by SNS-032 drastically reduced cell viability in pancreatic cancer cells and potently suppressed long-term survival. Analyzing the mechanism of action revealed that CDK9 inhibition induced apoptosis and cell cycle arrest in a time-dependent manner by suppression of anti-apoptotic proteins. Furthermore, CDK9 inhibition potently enhances the therapeutic effect of chemotherapeutics in pancreatic cancer cells. In conclusion, we identified CDK9 as a negative prognostic marker in pancreatic cancer. Furthermore, pharmacological CDK9 inhibition is a novel and promising therapeutic approach for pancreatic cancer.
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Affiliation(s)
- Anna-Laura Kretz
- 1 Department of General and Visceral Surgery, Center for Surgery, Ulm University Hospital, Ulm, Germany
| | - Monika Schaum
- 1 Department of General and Visceral Surgery, Center for Surgery, Ulm University Hospital, Ulm, Germany
| | - Julia Richter
- 1 Department of General and Visceral Surgery, Center for Surgery, Ulm University Hospital, Ulm, Germany
| | - Ella F Kitzig
- 1 Department of General and Visceral Surgery, Center for Surgery, Ulm University Hospital, Ulm, Germany
| | - Christine C Engler
- 1 Department of General and Visceral Surgery, Center for Surgery, Ulm University Hospital, Ulm, Germany
| | - Frank Leithäuser
- 2 Department of Pathology, Ulm University Hospital, Ulm, Germany
| | - Doris Henne-Bruns
- 1 Department of General and Visceral Surgery, Center for Surgery, Ulm University Hospital, Ulm, Germany
| | - Uwe Knippschild
- 1 Department of General and Visceral Surgery, Center for Surgery, Ulm University Hospital, Ulm, Germany
| | - Johannes Lemke
- 1 Department of General and Visceral Surgery, Center for Surgery, Ulm University Hospital, Ulm, Germany
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27
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Liao Y, Feng Y, Shen J, Hornicek FJ, Duan Z. The roles and therapeutic potential of cyclin-dependent kinases (CDKs) in sarcoma. Cancer Metastasis Rev 2017; 35:151-63. [PMID: 26669603 DOI: 10.1007/s10555-015-9601-1] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Uncontrolled proliferation and cell growth is the hallmark of many different malignant diseases, including sarcomas. Cyclin-dependent kinases (CDKs) are members of the serine/threonine protein kinase family and play crucial roles in tumor cell proliferation and growth by controlling cell cycle, transcription, and RNA splicing. In addition, several CDKs influence multiple targets and phosphorylate transcription factors involved in tumorigenesis. There are many examples linking dysregulated activation and expression of CDKs to tumors, and targeting CDKs in tumor cells has become a promising therapeutic strategy. More recently, the Food and Drug Administration (FDA) has approved the CDK4/6 inhibitor palbociclib for treating metastatic breast cancer. In sarcomas, high levels of CDK mRNA and protein expression have been found in most human sarcoma cells and patient tissues. Many studies have demonstrated consistent results in which inhibition of different CDKs decrease sarcoma cell growth and induce apoptosis. Therefore, CDKs comprise an attractive set of targets for novel anti-sarcoma drug development. In this review, we discuss the roles of different members of CDKs in various sarcomas and provide a pre-clinical overview of promising therapeutic potentials of targeting CDKs with a special emphasis on sarcoma.
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Affiliation(s)
- Yunfei Liao
- Department of Orthopaedic Surgery, Sarcoma Biology Laboratory, Massachusetts General Hospital and Harvard Medical School, 55 Fruit Street, Jackson 1115, Boston, MA, 02114, USA.,Wuhan Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, 1277 Jie Fang Avenue, Wuhan, China, 430022
| | - Yong Feng
- Department of Orthopaedic Surgery, Sarcoma Biology Laboratory, Massachusetts General Hospital and Harvard Medical School, 55 Fruit Street, Jackson 1115, Boston, MA, 02114, USA.,Wuhan Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, 1277 Jie Fang Avenue, Wuhan, China, 430022
| | - Jacson Shen
- Department of Orthopaedic Surgery, Sarcoma Biology Laboratory, Massachusetts General Hospital and Harvard Medical School, 55 Fruit Street, Jackson 1115, Boston, MA, 02114, USA
| | - Francis J Hornicek
- Department of Orthopaedic Surgery, Sarcoma Biology Laboratory, Massachusetts General Hospital and Harvard Medical School, 55 Fruit Street, Jackson 1115, Boston, MA, 02114, USA
| | - Zhenfeng Duan
- Department of Orthopaedic Surgery, Sarcoma Biology Laboratory, Massachusetts General Hospital and Harvard Medical School, 55 Fruit Street, Jackson 1115, Boston, MA, 02114, USA.
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28
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Cai Z, Liu Q. Cell Cycle Regulation in Treatment of Breast Cancer. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2017; 1026:251-270. [PMID: 29282688 DOI: 10.1007/978-981-10-6020-5_12] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Cell cycle progression and cell proliferation are under precise and orchestrated control in normal cells. However, uncontrolled cell proliferation caused by aberrant cell cycle progression is a crucial characteristic of cancer. Understanding cell cycle progression and its regulation sheds light on cancer treatment. Agents targeting cell cycle regulators (such as CDKs) have been considered as promising candidates in cancer treatment. Although the first-generation pan-CDK inhibitors failed in clinical trials because of their adverse events and low efficacy, new selective CDK 4/6 inhibitors showed potent efficacy with tolerable safety in preclinical and clinical studies. Here we will review the mechanisms of cell cycle regulation and targeting key cell cycle regulators (such as CDKs) in breast cancer treatment. Particularly, we will discuss the mechanism of CDK inhibitors in disrupting cell cycle progression, the use of selective CDK4/6 inhibitors in treatment of advanced, hormone receptor (HR)-positive postmenopausal breast cancer patients, and other clinical trials that aim to extend the utilization of these agents.
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Affiliation(s)
- Zijie Cai
- Breast Tumor Center, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, 107 Yanjiang West Road, Guangzhou, 510120, Guangdong, China
| | - Qiang Liu
- Breast Tumor Center, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, 107 Yanjiang West Road, Guangzhou, 510120, Guangdong, China.
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29
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Matrone G, Mullins JJ, Tucker CS, Denvir MA. Effects of Cyclin Dependent Kinase 9 inhibition on zebrafish larvae. Cell Cycle 2016; 15:3060-3069. [PMID: 27715402 PMCID: PMC5134698 DOI: 10.1080/15384101.2016.1231283] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
CDK9 is a known regulator of cellular transcription, growth and proliferation. Small molecule inhibitors are currently being developed and assessed in clinical trials as anti-cancer drugs. The zebrafish embryo provides an ideal model to explore the effects of CDK9 inhibition in-vivo. This has not been adequately explored previously at the level of a whole organism. We have compared and contrasted the effects of pharmacological and molecular inhibition of CDK9 on somatic growth, apoptosis and cellular proliferation in zebrafish larvae between 0 to 120 hours post fertilisation (hpf) using flavopiridol, a selective CDK9 antagonist, and CDK9-targeting morpholino. We demonstrate that the inhibition of CDK9 diminishes cellular proliferation and increases apoptosis. Subsequently, it affects somatic growth and development of a number of key embryonic structures including the brain, heart, eye and blood vessels. For the first time, we have localized CDK9 at a subcellular level in whole-mounted larvae. This works shows, at a high-throughput level, that CDK9 clearly plays a fundamental role in early cellular growth and proliferation.
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Affiliation(s)
- Gianfranco Matrone
- a British Heart Foundation Centre for Cardiovascular Science, The Queen's Medical Research Institute, The University of Edinburgh , Edinburgh , UK.,b Department of Cardiovascular Sciences , Methodist Hospital Research Institute , Houston , TX , USA
| | - John J Mullins
- a British Heart Foundation Centre for Cardiovascular Science, The Queen's Medical Research Institute, The University of Edinburgh , Edinburgh , UK
| | - Carl S Tucker
- a British Heart Foundation Centre for Cardiovascular Science, The Queen's Medical Research Institute, The University of Edinburgh , Edinburgh , UK
| | - Martin A Denvir
- a British Heart Foundation Centre for Cardiovascular Science, The Queen's Medical Research Institute, The University of Edinburgh , Edinburgh , UK
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30
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The Smad3/Smad4/CDK9 complex promotes renal fibrosis in mice with unilateral ureteral obstruction. Kidney Int 2015. [DOI: 10.1038/ki.2015.235] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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31
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Super Enhancers in Cancers, Complex Disease, and Developmental Disorders. Genes (Basel) 2015; 6:1183-200. [PMID: 26569311 PMCID: PMC4690034 DOI: 10.3390/genes6041183] [Citation(s) in RCA: 54] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2015] [Revised: 10/24/2015] [Accepted: 10/26/2015] [Indexed: 11/17/2022] Open
Abstract
Recently, unique areas of transcriptional regulation termed super-enhancers have been identified and implicated in human disease. Defined by their magnitude of size, transcription factor density, and binding of transcriptional machinery, super-enhancers have been associated with genes driving cell differentiation. While their functions are not completely understood, it is clear that these regions driving high-level transcription are susceptible to perturbation, and trait-associated single nucleotide polymorphisms (SNPs) occur within super-enhancers of disease-relevant cell types. Here we review evidence for super-enhancer involvement in cancers, complex diseases, and developmental disorders and discuss interactions between super-enhancers and cofactors/chromatin regulators.
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32
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Matrone G, Wilson KS, Maqsood S, Mullins JJ, Tucker CS, Denvir MA. CDK9 and its repressor LARP7 modulate cardiomyocyte proliferation and response to injury in the zebrafish heart. J Cell Sci 2015; 128:4560-71. [PMID: 26542022 PMCID: PMC4696495 DOI: 10.1242/jcs.175018] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2015] [Accepted: 10/29/2015] [Indexed: 12/12/2022] Open
Abstract
Cyclin dependent kinase (Cdk)9 acts through the positive transcription elongation factor-b (P-TEFb) complex to activate and expand transcription through RNA polymerase II. It has also been shown to regulate cardiomyocyte hypertrophy, with recent evidence linking it to cardiomyocyte proliferation. We hypothesised that modification of CDK9 activity could both impair and enhance the cardiac response to injury by modifying cardiomyocyte proliferation. Cdk9 expression and activity were inhibited in the zebrafish (Danio rerio) embryo. We show that dephosphorylation of residue Ser2 on the C-terminal domain of RNA polymerase II is associated with impaired cardiac structure and function, and cardiomyocyte proliferation and also results in impaired functional recovery following cardiac laser injury. In contrast, de-repression of Cdk9 activity, through knockdown of La-related protein (Larp7) increases phosphorylation of Ser2 in RNA polymerase II and increases cardiomyocyte proliferation. Larp7 knockdown rescued the structural and functional phenotype associated with knockdown of Cdk9. The balance of Cdk9 and Larp7 plays a key role in cardiomyocyte proliferation and response to injury. Larp7 represents a potentially novel therapeutic target to promote cardiomyocyte proliferation and recovery from injury. Summary: The balance of CDK9 and LARP7 plays a key role in cardiomyocyte proliferation and response to injury. LARP7 represents a potentially novel therapeutic target in promoting recovery from injury.
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Affiliation(s)
- Gianfranco Matrone
- British Heart Foundation Centre for Cardiovascular Science, The Queen's Medical Research Institute, The University of Edinburgh, Edinburgh EH16 4TJ, UK Center for Cardiovascular Regeneration, Department of Cardiovascular Sciences, Methodist Hospital Research Institute, Houston, TX 77030, USA
| | - Kathryn S Wilson
- British Heart Foundation Centre for Cardiovascular Science, The Queen's Medical Research Institute, The University of Edinburgh, Edinburgh EH16 4TJ, UK
| | - Sana Maqsood
- British Heart Foundation Centre for Cardiovascular Science, The Queen's Medical Research Institute, The University of Edinburgh, Edinburgh EH16 4TJ, UK
| | - John J Mullins
- British Heart Foundation Centre for Cardiovascular Science, The Queen's Medical Research Institute, The University of Edinburgh, Edinburgh EH16 4TJ, UK
| | - Carl S Tucker
- British Heart Foundation Centre for Cardiovascular Science, The Queen's Medical Research Institute, The University of Edinburgh, Edinburgh EH16 4TJ, UK
| | - Martin A Denvir
- British Heart Foundation Centre for Cardiovascular Science, The Queen's Medical Research Institute, The University of Edinburgh, Edinburgh EH16 4TJ, UK
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33
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Dupont CA, Dardalhon-Cuménal D, Kyba M, Brock HW, Randsholt NB, Peronnet F. Drosophila Cyclin G and epigenetic maintenance of gene expression during development. Epigenetics Chromatin 2015; 8:18. [PMID: 25995770 PMCID: PMC4438588 DOI: 10.1186/s13072-015-0008-6] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2014] [Accepted: 04/01/2015] [Indexed: 12/31/2022] Open
Abstract
Background Cyclins and cyclin-dependent kinases (CDKs) are essential for cell cycle regulation and are functionally associated with proteins involved in epigenetic maintenance of transcriptional patterns in various developmental or cellular contexts. Epigenetic maintenance of transcription patterns, notably of Hox genes, requires the conserved Polycomb-group (PcG), Trithorax-group (TrxG), and Enhancer of Trithorax and Polycomb (ETP) proteins, particularly well studied in Drosophila. These proteins form large multimeric complexes that bind chromatin and appose or recognize histone post-translational modifications. PcG genes act as repressors, counteracted by trxG genes that maintain gene activation, while ETPs interact with both, behaving alternatively as repressors or activators. Drosophila Cyclin G negatively regulates cell growth and cell cycle progression, binds and co-localizes with the ETP Corto on chromatin, and participates with Corto in Abdominal-B Hox gene regulation. Here, we address further implications of Cyclin G in epigenetic maintenance of gene expression. Results We show that Cyclin G physically interacts and extensively co-localizes on chromatin with the conserved ETP Additional sex combs (ASX), belonging to the repressive PR-DUB complex that participates in H2A deubiquitination and Hox gene silencing. Furthermore, Cyclin G mainly co-localizes with RNA polymerase II phosphorylated on serine 2 that is specific to productive transcription. CycG interacts with Asx, PcG, and trxG genes in Hox gene maintenance, and behaves as a PcG gene. These interactions correlate with modified ectopic Hox protein domains in imaginal discs, consistent with a role for Cyclin G in PcG-mediated Hox gene repression. Conclusions We show here that Drosophila CycG is a Polycomb-group gene enhancer, acting in epigenetic maintenance of the Hox genes Sex combs reduced (Scr) and Ultrabithorax (Ubx). However, our data suggest that Cyclin G acts alternatively as a transcriptional activator or repressor depending on the developmental stage, the tissue or the target gene. Interestingly, since Cyclin G interacts with several CDKs, Cyclin G binding to the ETPs ASX or Corto suggests that their activity could depend on Cyclin G-mediated phosphorylation. We discuss whether Cyclin G fine-tunes transcription by controlling H2A ubiquitination and transcriptional elongation via interaction with the ASX subunit of PR-DUB. Electronic supplementary material The online version of this article (doi:10.1186/s13072-015-0008-6) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Camille A Dupont
- Sorbonne Universités, UPMC Univ Paris 06, Institut de Biologie Paris-Seine (IBPS), UMR 7622, Developmental Biology, 9, quai Saint-Bernard, F-75005 Paris, France ; CNRS, IBPS, UMR 7622, Developmental Biology, 9, quai Saint-Bernard, F-75005 Paris, France
| | - Delphine Dardalhon-Cuménal
- Sorbonne Universités, UPMC Univ Paris 06, Institut de Biologie Paris-Seine (IBPS), UMR 7622, Developmental Biology, 9, quai Saint-Bernard, F-75005 Paris, France ; CNRS, IBPS, UMR 7622, Developmental Biology, 9, quai Saint-Bernard, F-75005 Paris, France
| | - Michael Kyba
- Lillehei Heart Institute and Department of Pediatrics, University of Minnesota, 2231 6th Street SE, Minneapolis, MN 55455 USA
| | - Hugh W Brock
- Department of Zoology, University of British Columbia, 6270 University Boulevard, V6T 1Z4 Vancouver, BC Canada
| | - Neel B Randsholt
- Sorbonne Universités, UPMC Univ Paris 06, Institut de Biologie Paris-Seine (IBPS), UMR 7622, Developmental Biology, 9, quai Saint-Bernard, F-75005 Paris, France ; CNRS, IBPS, UMR 7622, Developmental Biology, 9, quai Saint-Bernard, F-75005 Paris, France
| | - Frédérique Peronnet
- Sorbonne Universités, UPMC Univ Paris 06, Institut de Biologie Paris-Seine (IBPS), UMR 7622, Developmental Biology, 9, quai Saint-Bernard, F-75005 Paris, France ; CNRS, IBPS, UMR 7622, Developmental Biology, 9, quai Saint-Bernard, F-75005 Paris, France
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Ctk1 function is necessary for full translation initiation activity in Saccharomyces cerevisiae. EUKARYOTIC CELL 2014; 14:86-95. [PMID: 25416238 DOI: 10.1128/ec.00106-14] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Translation is a fundamental and highly regulated cellular process. Previously, we reported that the kinase and transcription elongation factor Ctk1 increases fidelity during translation elongation in Saccharomyces cerevisiae. Here, we show that loss of Ctk1 function also affects the initiation step of translation. Translation active extracts from Ctk1-depleted cells show impaired translation activity of capped mRNA, but not mRNA reporters containing the cricket paralysis virus (CrPV) internal ribosome entry site (IRES). Furthermore, the formation of 80S initiation complexes is decreased, which is probably due to reduced subunit joining. In addition, we determined the changes in the phosphorylation pattern of a ribosome enriched fraction after depletion of Ctk1. Thus, we provide a catalogue of phosphoproteomic changes dependent on Ctk1. Taken together, our data suggest a stimulatory function of Ctk1 in 80S formation during translation initiation.
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Chipumuro E, Marco E, Christensen CL, Kwiatkowski N, Zhang T, Hatheway CM, Abraham BJ, Sharma B, Yeung C, Altabef A, Perez-Atayde A, Wong KK, Yuan GC, Gray NS, Young RA, George RE. CDK7 inhibition suppresses super-enhancer-linked oncogenic transcription in MYCN-driven cancer. Cell 2014; 159:1126-1139. [PMID: 25416950 DOI: 10.1016/j.cell.2014.10.024] [Citation(s) in RCA: 460] [Impact Index Per Article: 46.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2014] [Revised: 08/18/2014] [Accepted: 09/24/2014] [Indexed: 02/06/2023]
Abstract
The MYC oncoproteins are thought to stimulate tumor cell growth and proliferation through amplification of gene transcription, a mechanism that has thwarted most efforts to inhibit MYC function as potential cancer therapy. Using a covalent inhibitor of cyclin-dependent kinase 7 (CDK7) to disrupt the transcription of amplified MYCN in neuroblastoma cells, we demonstrate downregulation of the oncoprotein with consequent massive suppression of MYCN-driven global transcriptional amplification. This response translated to significant tumor regression in a mouse model of high-risk neuroblastoma, without the introduction of systemic toxicity. The striking treatment selectivity of MYCN-overexpressing cells correlated with preferential downregulation of super-enhancer-associated genes, including MYCN and other known oncogenic drivers in neuroblastoma. These results indicate that CDK7 inhibition, by selectively targeting the mechanisms that promote global transcriptional amplification in tumor cells, may be useful therapy for cancers that are driven by MYC family oncoproteins.
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Affiliation(s)
- Edmond Chipumuro
- Department of Pediatric Hematology/Oncology, Dana-Farber Cancer Institute and Boston Children's Hospital, Boston, MA 02215, USA; Department of Pediatrics, Harvard Medical School, Boston, MA 02115, USA
| | - Eugenio Marco
- Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Harvard School of Public Health, Boston, MA 02115, USA
| | | | - Nicholas Kwiatkowski
- Whitehead Institute for Biomedical Research and Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Tinghu Zhang
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA
| | - Clark M Hatheway
- Department of Pediatric Hematology/Oncology, Dana-Farber Cancer Institute and Boston Children's Hospital, Boston, MA 02215, USA
| | - Brian J Abraham
- Whitehead Institute for Biomedical Research and Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Bandana Sharma
- Department of Pediatric Hematology/Oncology, Dana-Farber Cancer Institute and Boston Children's Hospital, Boston, MA 02215, USA
| | - Caleb Yeung
- Department of Pediatric Hematology/Oncology, Dana-Farber Cancer Institute and Boston Children's Hospital, Boston, MA 02215, USA; Department of Pediatrics, Harvard Medical School, Boston, MA 02115, USA
| | - Abigail Altabef
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | | | - Kwok-Kin Wong
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Guo-Cheng Yuan
- Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Harvard School of Public Health, Boston, MA 02115, USA
| | - Nathanael S Gray
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA
| | - Richard A Young
- Whitehead Institute for Biomedical Research and Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Rani E George
- Department of Pediatric Hematology/Oncology, Dana-Farber Cancer Institute and Boston Children's Hospital, Boston, MA 02215, USA; Department of Pediatrics, Harvard Medical School, Boston, MA 02115, USA.
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Chipumuro E, Marco E, Christensen CL, Kwiatkowski N, Zhang T, Hatheway CM, Abraham BJ, Sharma B, Yeung C, Altabef A, Perez-Atayde A, Wong KK, Yuan GC, Gray NS, Young RA, George RE. CDK7 inhibition suppresses super-enhancer-linked oncogenic transcription in MYCN-driven cancer. Cell 2014. [PMID: 25416950 DOI: 10.1016/j.cell.2014.10.024,] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
The MYC oncoproteins are thought to stimulate tumor cell growth and proliferation through amplification of gene transcription, a mechanism that has thwarted most efforts to inhibit MYC function as potential cancer therapy. Using a covalent inhibitor of cyclin-dependent kinase 7 (CDK7) to disrupt the transcription of amplified MYCN in neuroblastoma cells, we demonstrate downregulation of the oncoprotein with consequent massive suppression of MYCN-driven global transcriptional amplification. This response translated to significant tumor regression in a mouse model of high-risk neuroblastoma, without the introduction of systemic toxicity. The striking treatment selectivity of MYCN-overexpressing cells correlated with preferential downregulation of super-enhancer-associated genes, including MYCN and other known oncogenic drivers in neuroblastoma. These results indicate that CDK7 inhibition, by selectively targeting the mechanisms that promote global transcriptional amplification in tumor cells, may be useful therapy for cancers that are driven by MYC family oncoproteins.
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Affiliation(s)
- Edmond Chipumuro
- Department of Pediatric Hematology/Oncology, Dana-Farber Cancer Institute and Boston Children's Hospital, Boston, MA 02215, USA; Department of Pediatrics, Harvard Medical School, Boston, MA 02115, USA
| | - Eugenio Marco
- Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Harvard School of Public Health, Boston, MA 02115, USA
| | | | - Nicholas Kwiatkowski
- Whitehead Institute for Biomedical Research and Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Tinghu Zhang
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA
| | - Clark M Hatheway
- Department of Pediatric Hematology/Oncology, Dana-Farber Cancer Institute and Boston Children's Hospital, Boston, MA 02215, USA
| | - Brian J Abraham
- Whitehead Institute for Biomedical Research and Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Bandana Sharma
- Department of Pediatric Hematology/Oncology, Dana-Farber Cancer Institute and Boston Children's Hospital, Boston, MA 02215, USA
| | - Caleb Yeung
- Department of Pediatric Hematology/Oncology, Dana-Farber Cancer Institute and Boston Children's Hospital, Boston, MA 02215, USA; Department of Pediatrics, Harvard Medical School, Boston, MA 02115, USA
| | - Abigail Altabef
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | | | - Kwok-Kin Wong
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Guo-Cheng Yuan
- Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Harvard School of Public Health, Boston, MA 02115, USA
| | - Nathanael S Gray
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA
| | - Richard A Young
- Whitehead Institute for Biomedical Research and Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Rani E George
- Department of Pediatric Hematology/Oncology, Dana-Farber Cancer Institute and Boston Children's Hospital, Boston, MA 02215, USA; Department of Pediatrics, Harvard Medical School, Boston, MA 02115, USA.
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HEXIM1 plays a critical role in the inhibition of the androgen receptor by anti-androgens. Biochem J 2014; 462:315-27. [PMID: 24844355 DOI: 10.1042/bj20140174] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
We show that HEXIM1 (hexamethylene bis-acetamide inducible 1) functions as an AR (androgen receptor) co-repressor as it physically interacts with the AR and is required for the ability of anti-androgens to inhibit androgen-induced target gene expression and cell proliferation. Oncomine™ database and IHC (immunohistochemistry) analyses of human prostate tissues revealed that expression of HEXIM1 mRNA and protein are down-regulated during the development and progression of prostate cancer. Enforced down-regulation of HEXIM1 in parental hormone-dependent LNCaP cells results in resistance to the inhibitory action of anti-androgens. Conversely, ectopic expression of HEXIM1 in the CRPC (castration-resistant prostate cancer) cell line, C4-2, enhances their sensitivity to the repressive effects of the anti-androgen bicalutamide. Novel insight into the mechanistic basis for HEXIM1 inhibition of AR activity is provided by the present studies showing that HEXIM1 induces expression of the histone demethylase KDM5B (lysine-specific demethylase 5B) and inhibits histone methylation, resulting in the inhibition of FOXA1 (forkhead box A1) licensing activity. This is a new mechanism of action attributed to HEXIM1, and distinct from what has been reported so far to be involved in HEXIM1 regulation of other nuclear hormone receptors, including the oestrogen receptor.
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Houzé S, Hoang NT, Lozach O, Le Bras J, Meijer L, Galons H, Demange L. Several human cyclin-dependent kinase inhibitors, structurally related to roscovitine, are new anti-malarial agents. Molecules 2014; 19:15237-57. [PMID: 25251193 PMCID: PMC6271241 DOI: 10.3390/molecules190915237] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2014] [Revised: 09/08/2014] [Accepted: 09/11/2014] [Indexed: 11/16/2022] Open
Abstract
In Africa, malaria kills one child each minute. It is also responsible for about one million deaths worldwide each year. Plasmodium falciparum, is the protozoan responsible for the most lethal form of the disease, with resistance developing against the available anti-malarial drugs. Among newly proposed anti-malaria targets, are the P. falciparum cyclin-dependent kinases (PfCDKs). There are involved in different stages of the protozoan growth and development but share high sequence homology with human cyclin-dependent kinases (CDKs). We previously reported the synthesis of CDKs inhibitors that are structurally-related to (R)-roscovitine, a 2,6,9-trisubstituted purine, and they showed activity against neuronal diseases and cancers. In this report, we describe the synthesis and the characterization of new CDK inhibitors, active in reducing the in vitro growth of P. falciparum (3D7 and 7G8 strains). Six compounds are more potent inhibitors than roscovitine, and three exhibited IC50 values close to 1 µM for both 3D7 and 7G8 strains. Although, such molecules do inhibit P. falciparum growth, they require further studies to improve their selectivity for PfCDKs.
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Affiliation(s)
- Sandrine Houzé
- Laboratoire de Parasitologie, CNR du Paludisme, AP-HP, Hôpital Bichat & UMR 216 IRD, Université Paris Descartes, Sorbonne Paris Cité, UFR des Sciences Pharmaceutiques, 4 avenue de l'Observatoire, Paris 75006, France.
| | - Nha-Thu Hoang
- Laboratoire de Chimie et Biochimie Pharmacologiques et Toxicologiques (LCBPT), UMR 8601 CNRS, Université Paris Descartes, Sorbonne Paris Cité, UFR Biomédicale des Saints Pères, 45 rue des Saints-Pères, Paris 75270, France.
| | - Olivier Lozach
- Protein Phosphorylation and Human Diseases Group, CNRS, USR 3151, Station biologique, Roscoff 29680, France.
| | - Jacques Le Bras
- Laboratoire de Parasitologie, CNR du Paludisme, AP-HP, Hôpital Bichat & UMR 216 IRD, Université Paris Descartes, Sorbonne Paris Cité, UFR des Sciences Pharmaceutiques, 4 avenue de l'Observatoire, Paris 75006, France.
| | - Laurent Meijer
- Protein Phosphorylation and Human Diseases Group, CNRS, USR 3151, Station biologique, Roscoff 29680, France.
| | - Hervé Galons
- ManRos Therapeutics, Hôtel de Recherche, Centre de Perharidy, Roscoff 29680, France.
| | - Luc Demange
- Laboratoire de Chimie et Biochimie Pharmacologiques et Toxicologiques (LCBPT), UMR 8601 CNRS, Université Paris Descartes, Sorbonne Paris Cité, UFR Biomédicale des Saints Pères, 45 rue des Saints-Pères, Paris 75270, France.
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Šmerdová L, Svobodová J, Kabátková M, Kohoutek J, Blažek D, Machala M, Vondráček J. Upregulation of CYP1B1 expression by inflammatory cytokines is mediated by the p38 MAP kinase signal transduction pathway. Carcinogenesis 2014; 35:2534-43. [DOI: 10.1093/carcin/bgu190] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023] Open
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Lam F, Abbas AY, Shao H, Teo T, Adams J, Li P, Bradshaw TD, Fischer PM, Walsby E, Pepper C, Chen Y, Ding J, Wang S. Targeting RNA transcription and translation in ovarian cancer cells with pharmacological inhibitor CDKI-73. Oncotarget 2014; 5:7691-704. [PMID: 25277198 PMCID: PMC4202154 DOI: 10.18632/oncotarget.2296] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2014] [Accepted: 07/31/2014] [Indexed: 01/09/2023] Open
Abstract
Dysregulation of cellular transcription and translation is a fundamental hallmark of cancer. As CDK9 and Mnks play pivotal roles in the regulation of RNA transcription and protein synthesis, respectively, they are important targets for drug development. We herein report the cellular mechanism of a novel CDK9 inhibitor CDKI-73 in an ovarian cancer cell line (A2780). We also used shRNA-mediated CDK9 knockdown to investigate the importance of CDK9 in the maintenance of A2780 cells. This study revealed that CDKI-73 rapidly inhibited cellular CDK9 kinase activity and down-regulated the RNAPII phosphorylation. This subsequently caused a decrease in the eIF4E phosphorylation by blocking Mnk1 kinase activity. Consistently, CDK9 shRNA was also found to down-regulate the Mnk1 expression. Both CDKI-73 and CDK9 shRNA decreased anti-apoptotic proteins Mcl-1 and Bcl-2 and induced apoptosis. The study confirmed that CDK9 is required for cell survival and that ovarian cancer may be susceptible to CDK9 inhibition strategy. The data also implied a role of CDK9 in eIF4E-mediated translational control, suggesting that CDK9 may have important implication in the Mnk-eIF4E axis, the key determinants of PI3K/Akt/mTOR- and Ras/Raf/MAPK-mediated tumorigenic activity. As such, CDK9 inhibitor drug candidate CDKI-73 should have a major impact on these pathways in human cancers.
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Affiliation(s)
- Frankie Lam
- Centre for Drug Discovery and Development, Sansom Institute for Health Research and School of Pharmacy and Medical Sciences, University of South Australia, Adelaide, South Australia, Australia
| | - Abdullahi Y. Abbas
- School of Pharmacy and Centre for Biomolecular Sciences, University of Nottingham, University Park, Nottingham, United Kingdom
| | - Hao Shao
- School of Pharmacy and Centre for Biomolecular Sciences, University of Nottingham, University Park, Nottingham, United Kingdom
| | - Theodosia Teo
- Centre for Drug Discovery and Development, Sansom Institute for Health Research and School of Pharmacy and Medical Sciences, University of South Australia, Adelaide, South Australia, Australia
| | - Julian Adams
- Centre for Drug Discovery and Development, Sansom Institute for Health Research and School of Pharmacy and Medical Sciences, University of South Australia, Adelaide, South Australia, Australia
| | - Peng Li
- Centre for Drug Discovery and Development, Sansom Institute for Health Research and School of Pharmacy and Medical Sciences, University of South Australia, Adelaide, South Australia, Australia
| | - Tracey D. Bradshaw
- School of Pharmacy and Centre for Biomolecular Sciences, University of Nottingham, University Park, Nottingham, United Kingdom
| | - Peter M. Fischer
- School of Pharmacy and Centre for Biomolecular Sciences, University of Nottingham, University Park, Nottingham, United Kingdom
| | - Elisabeth Walsby
- Cardiff CLL Research Group, Institute of Cancer and Genetics, School of Medicine, Cardiff University, Health Park, Cardiff, United Kingdom
| | - Chris Pepper
- Cardiff CLL Research Group, Institute of Cancer and Genetics, School of Medicine, Cardiff University, Health Park, Cardiff, United Kingdom
| | - Yi Chen
- Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, People's Republic of China
| | - Jian Ding
- Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, People's Republic of China
| | - Shudong Wang
- Centre for Drug Discovery and Development, Sansom Institute for Health Research and School of Pharmacy and Medical Sciences, University of South Australia, Adelaide, South Australia, Australia
- School of Pharmacy and Centre for Biomolecular Sciences, University of Nottingham, University Park, Nottingham, United Kingdom
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Albert TK, Rigault C, Eickhoff J, Baumgart K, Antrecht C, Klebl B, Mittler G, Meisterernst M. Characterization of molecular and cellular functions of the cyclin-dependent kinase CDK9 using a novel specific inhibitor. Br J Pharmacol 2014; 171:55-68. [PMID: 24102143 DOI: 10.1111/bph.12408] [Citation(s) in RCA: 92] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2013] [Revised: 07/22/2013] [Accepted: 08/11/2013] [Indexed: 01/07/2023] Open
Abstract
BACKGROUND AND PURPOSE The cyclin-dependent kinase CDK9 is an important therapeutic target but currently available inhibitors exhibit low specificity and/or narrow therapeutic windows. Here we have used a new highly specific CDK9 inhibitor, LDC000067 to interrogate gene control mechanisms mediated by CDK9. EXPERIMENTAL APPROACH The selectivity of LDC000067 was established in functional kinase assays. Functions of CDK9 in gene expression were assessed with in vitro transcription experiments, single gene analyses and genome-wide expression profiling. Cultures of mouse embryonic stem cells, HeLa cells, several cancer cell lines, along with cells from patients with acute myelogenous leukaemia were also used to investigate cellular responses to LDC000067. KEY RESULTS The selectivity of LDC000067 for CDK9 over other CDKs exceeded that of the known inhibitors flavopiridol and DRB. LDC000067 inhibited in vitro transcription in an ATP-competitive and dose-dependent manner. Gene expression profiling of cells treated with LDC000067 demonstrated a selective reduction of short-lived mRNAs, including important regulators of proliferation and apoptosis. Analysis of de novo RNA synthesis suggested a wide ranging positive role of CDK9. At the molecular and cellular level, LDC000067 reproduced effects characteristic of CDK9 inhibition such as enhanced pausing of RNA polymerase II on genes and, most importantly, induction of apoptosis in cancer cells. CONCLUSIONS AND IMPLICATIONS Our study provides a framework for the mechanistic understanding of cellular responses to CDK9 inhibition. LDC000067 represents a promising lead for the development of clinically useful, highly specific CDK9 inhibitors.
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Affiliation(s)
- T K Albert
- Institute of Molecular Tumor Biology (IMTB), Faculty of Medicine, Westfalian Wilhelms University Muenster (WWU), Muenster, Germany
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Burlein C, Bahnck C, Bhatt T, Murphy D, Lemaire P, Carroll S, Miller MD, Lai MT. Development of a sensitive amplified luminescent proximity homogeneous assay to monitor the interactions between pTEFb and Tat. Anal Biochem 2014; 465:164-71. [PMID: 25132562 DOI: 10.1016/j.ab.2014.08.007] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2014] [Revised: 08/03/2014] [Accepted: 08/06/2014] [Indexed: 12/31/2022]
Abstract
The viral transactivator protein (Tat) plays an essential role in the replication of human immunodeficiency type 1 virus (HIV-1) by recruiting the host positive transcription elongation factor (pTEFb) to the RNA polymerase II transcription machinery to enable an efficient HIV-1 RNA elongation process. Blockade of the interaction between Tat and pTEFb represents a novel strategy for developing a new class of antiviral agents. In this study, we developed a homogeneous assay in AlphaLISA (amplified luminescent proximity homogeneous assay) format using His-tagged pTEFb and biotinylated Tat to monitor the interaction between Tat and pTEFb. On optimizing the assay conditions, the signal-to-background ratio was found to be greater than 10-fold. The assay was validated with untagged Tat and peptides known to compete with Tat for pTEFb binding. The Z' of the assay is greater than 0.5, indicating that the assay is robust and can be easily adapted to a high-throughput screening format. Furthermore, the affinity between Tat and pTEFb was determined to be approximately 20 pM, and only 7% of purified Tat was found to be active in forming tertiary complex with pTEFb. Development of this assay should facilitate the discovery of a new class of antiviral agents providing HIV-1 patients with broader treatment choices.
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Affiliation(s)
- Christine Burlein
- Department of In Vitro Pharmacology, Merck Research Laboratories, West Point, PA 19486, USA
| | - Carolyn Bahnck
- Department of In Vitro Pharmacology, Merck Research Laboratories, West Point, PA 19486, USA
| | - Triveni Bhatt
- Department of In Vitro Pharmacology, Merck Research Laboratories, West Point, PA 19486, USA
| | - Dennis Murphy
- Department of In Vitro Pharmacology, Merck Research Laboratories, West Point, PA 19486, USA
| | - Peter Lemaire
- Department of In Vitro Pharmacology, Merck Research Laboratories, West Point, PA 19486, USA
| | - Steve Carroll
- Department of In Vitro Pharmacology, Merck Research Laboratories, West Point, PA 19486, USA
| | - Michael D Miller
- Antiviral Research, Merck Research Laboratories, West Point, PA 19486, USA
| | - Ming-Tain Lai
- Antiviral Research, Merck Research Laboratories, West Point, PA 19486, USA.
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Han Y, Zhan Y, Hou G, Li L. Cyclin-dependent kinase 9 may as a novel target in downregulating the atherosclerosis inflammation (Review). Biomed Rep 2014; 2:775-779. [PMID: 25279144 DOI: 10.3892/br.2014.322] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2014] [Accepted: 07/17/2014] [Indexed: 01/05/2023] Open
Abstract
Inflammation is a key component of atherosclerosis. Genes coding for inflammatory or anti-inflammatory molecules are considered good candidates for estimating the risk of developing atherosclerosis. Cyclin-dependent kinase 9 (CDK9), the kinase of positive transcription elongation factor b (P-TEFb), is crucial in the cell cycle and apoptosis. Previous studies have focused on its inhibition of immune cells for the resolution of inflammation. Considering the effects of inflammation in the pathogenicity of atherosclerosis, decreasing inflammation through the inhibition of CDK9 may be useful for the prognosis of atherosclerosis. The aim of this review was to examine whether inhibition of the CDK9 monocyte may affect the process of inflammation by acting on the cytokine secretion and interacting with endothelial cells (ECs). Thus, CDK9 may be a novel target for the diagnosis and therapy of atherosclerosis.
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Affiliation(s)
- Yeming Han
- Key Laboratory of Cardiovascular Remodeling and Function Research, Chinese Ministry of Education and Chinese Ministry of Public Health, Qilu Hospital, Shandong University, Jinan, Shandong 250012, P.R. China
| | - Yang Zhan
- Institute of Experimental Nuclear Medicine, School of Medicine, Shandong University, Jinan, Shandong 250012, P.R. China
| | - Guihua Hou
- Institute of Experimental Nuclear Medicine, School of Medicine, Shandong University, Jinan, Shandong 250012, P.R. China
| | - Li Li
- Key Laboratory of Cardiovascular Remodeling and Function Research, Chinese Ministry of Education and Chinese Ministry of Public Health, Qilu Hospital, Shandong University, Jinan, Shandong 250012, P.R. China
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Garriga J, Graña X. CDK9 inhibition strategy defines distinct sets of target genes. BMC Res Notes 2014; 7:301. [PMID: 24886624 PMCID: PMC4045923 DOI: 10.1186/1756-0500-7-301] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2013] [Accepted: 05/08/2014] [Indexed: 12/02/2022] Open
Abstract
Background CDK9 is the catalytic subunit of the Positive Transcription Elongation Factor b (P-TEFb), which phosphorylates the CTD of RNAPII and negative elongation factors enabling for productive elongation after initiation. CDK9 associates with T-type cyclins and cyclin K and its activity is tightly regulated in cells at different levels. CDK9 is also the catalytic subunit of TAK (Tat activating Kinase), essential for HIV1 replication. Because of CDK9′s potential as a therapeutic target in AIDS, cancer, inflammation, and cardiomyophathy it is important to understand the consequences of CDK9 inhibition. A previous gene expression profiling study performed with human glioblastoma T98G cells in which CDK9 activity was inhibited either with a dominant negative mutant form of CDK9 (dnCDK9) or the pharmacological inhibitor Flavopiridol unveiled striking differences in gene expression effects. In the present report we extended these studies by (1) using both immortalized normal human fibroblasts and primary human astrocytes, (2) eliminating potential experimental variability due to transduction methodology and (3) also modulating CDK9 activity with siRNA. Findings Striking differences in the effects on gene expression resulting from the strategy used to inhibit CDK9 activity (dnCDK9 or FVP) remain even when potential variability due to viral transduction is eliminated. siRNA mediated CDK9 knockdown in human fibroblasts and astrocytes efficiently reduced CDK9 expression and led to potent changes in gene expression that exhibit little correlation with the effects of dnCDK9 or FVP. Interestingly, HEXIM1 a validated CDK9 target gene, was found to be potently downregulated by dnCDK9, FVP and siCDK9, but the cluster of genes with expression profiles similar to HEXIM1 was small. Finally, cluster analysis of all treatments revealed higher correlation between treatments than cell type origin. Conclusion The nature of the strategy used to inhibit CDK9 profoundly affects the patterns of gene expression resulting from CDK9 inhibition. These results suggest multiple variables that affect outcome, including kinetics of inhibition, potency, off-target effects, and selectivity issues. This is particularly important when considering CDK9 as a potential target for therapeutic intervention.
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Affiliation(s)
| | - Xavier Graña
- Fels Institute for Cancer Research and Molecular Biology, AHP bldg,, room 308, 3307 North Broad St,, Philadelphia, PA 19140, USA.
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Cao L, Chen F, Yang X, Xu W, Xie J, Yu L. Phylogenetic analysis of CDK and cyclin proteins in premetazoan lineages. BMC Evol Biol 2014; 14:10. [PMID: 24433236 PMCID: PMC3923393 DOI: 10.1186/1471-2148-14-10] [Citation(s) in RCA: 91] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2013] [Accepted: 01/02/2014] [Indexed: 12/21/2022] Open
Abstract
Background The molecular history of animal evolution from single-celled ancestors remains a major question in biology, and little is known regarding the evolution of cell cycle regulation during animal emergence. In this study, we conducted a comprehensive evolutionary analysis of CDK and cyclin proteins in metazoans and their unicellular relatives. Results Our analysis divided the CDK family into eight subfamilies. Seven subfamilies (CDK1/2/3, CDK5, CDK7, CDK 20, CDK8/19, CDK9, and CDK10/11) are conserved in metazoans and fungi, with the remaining subfamily, CDK4/6, found only in eumetazoans. With respect to cyclins, cyclin C, H, L, Y subfamilies, and cyclin K and T as a whole subfamily, are generally conserved in animal, fungi, and amoeba Dictyostelium discoideum. In contrast, cyclin subfamilies B, A, E, and D, which are cell cycle-related, have distinct evolutionary histories. The cyclin B subfamily is generally conserved in D. discoideum, fungi, and animals, whereas cyclin A and E subfamilies are both present in animals and their unicellular relatives such as choanoflagellate Monosiga brevicollis and filasterean Capsaspora owczarzaki, but are absent in fungi and D. discoideum. Although absent in fungi and D. discoideum, cyclin D subfamily orthologs can be found in the early-emerging, non-opisthokont apusozoan Thecamonas trahens. Within opisthokonta, the cyclin D subfamily is conserved only in eumetazoans, and is absent in fungi, choanoflagellates, and the basal metazoan Amphimedon queenslandica. Conclusions Our data indicate that the CDK4/6 subfamily and eumetazoans emerged simultaneously, with the evolutionary conservation of the cyclin D subfamily also tightly linked with eumetazoan appearance. Establishment of the CDK4/6-cyclin D complex may have been the key step in the evolution of cell cycle control during eumetazoan emergence.
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Affiliation(s)
- Lihuan Cao
- State Key Laboratory of Genetic Engineering, Institute of Genetics, School of Life Sciences, Fudan University, Shanghai 200433, PR China.
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Alexander A, Keyomarsi K. Exploiting Cell Cycle Pathways in Cancer Therapy: New (and Old) Targets and Potential Strategies. NUCLEAR SIGNALING PATHWAYS AND TARGETING TRANSCRIPTION IN CANCER 2014. [DOI: 10.1007/978-1-4614-8039-6_14] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
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47
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Gojo I, Sadowska M, Walker A, Feldman EJ, Iyer SP, Baer MR, Sausville EA, Lapidus RG, Zhang D, Zhu Y, Jou YM, Poon J, Small K, Bannerji R. Clinical and laboratory studies of the novel cyclin-dependent kinase inhibitor dinaciclib (SCH 727965) in acute leukemias. Cancer Chemother Pharmacol 2013; 72:897-908. [PMID: 23949430 PMCID: PMC3784060 DOI: 10.1007/s00280-013-2249-z] [Citation(s) in RCA: 66] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2013] [Accepted: 07/26/2013] [Indexed: 01/19/2023]
Abstract
Purpose Dinaciclib inhibits cyclin-dependent kinases 1, 2, 5, and 9 with a better therapeutic index than flavopiridol in preclinical studies. This study assessed the activity of dinaciclib in acute leukemia both in the clinic and in vitro. Methods Adults with relapsed/refractory acute myeloid leukemia (n = 14) and acute lymphoid leukemia (n = 6) were treated with dinaciclib 50 mg/m2 given as a 2-h infusion every 21 days. Results Most patients had dramatic but transient reduction in circulating blasts; however, no remissions were achieved on this schedule. The most common toxicities were gastrointestinal, fatigue, transaminitis, and clinical and laboratory manifestations of tumor lysis syndrome, including one patient who died of acute renal failure. Dinaciclib pharmacokinetics showed rapid (2 h) achievement of maximum concentration and a short elimination/distribution phase. Pharmacodynamic studies demonstrated in vivo inhibition of Mcl-1 expression and induction of PARP cleavage in patients’ peripheral blood mononuclear cells 4 h after dinaciclib infusion, but the effects were lost by 24 h and did not correlate with clinical outcome. Correlative in vitro studies showed that prolonged exposures to dinaciclib, at clinically attainable concentrations, result in improved leukemia cell kill. Conclusions While dinaciclib given as a 2-h bolus did not exhibit durable clinical activity, pharmacokinetic and pharmacodynamic data support the exploration of prolonged infusion schedules in future trials in patients with acute leukemias. Electronic supplementary material The online version of this article (doi:10.1007/s00280-013-2249-z) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Ivana Gojo
- Division of Hematology/Oncology, Marlene and Stewart Greenebaum Cancer Center, University of Maryland, Baltimore, MD, USA,
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Deregulations in the cyclin-dependent kinase-9-related pathway in cancer: implications for drug discovery and development. ISRN ONCOLOGY 2013; 2013:305371. [PMID: 23840966 PMCID: PMC3690251 DOI: 10.1155/2013/305371] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/23/2013] [Accepted: 05/19/2013] [Indexed: 12/21/2022]
Abstract
The CDK9-related pathway is an important regulator of mammalian cell biology and is also involved in the replication cycle of several viruses, including the human immunodeficiency virus type 1. CDK9 is present in two isoforms termed CDK9-42 and CDK9-55 that bind noncovalently type T cyclins and cyclin K. This association forms a heterodimer, where CDK9 carries the enzymatic site and the cyclin partner functions as a regulatory subunit. This heterodimer is the main component of the positive transcription elongation factor b, which stabilizes RNA elongation via phosphorylation of the RNA pol II carboxyl terminal domain. Abnormal activities in the CDK9-related pathway were observed in human malignancies and cardiac hypertrophies. Thus, the elucidation of the CDK9 pathway deregulations may provide useful insights into the pathogenesis and progression of human malignancies, cardiac hypertrophy, AIDS and other viral-related maladies. These studies may lead to the improvement of kinase inhibitors for the treatment of the previously mentioned pathological conditions. This review describes the CDK9-related pathway deregulations in malignancies and the development of kinase inhibitors in cancer therapy, which can be classified into three categories: antagonists that block the ATP binding site of the catalytic domain, allosteric inhibitors, and small molecules that disrupt protein-protein interactions.
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Shao H, Shi S, Huang S, Hole A, Abbas AY, Baumli S, Liu X, Lam F, Foley D, Fischer PM, Noble M, Endicott JA, Pepper C, Wang S. Substituted 4-(thiazol-5-yl)-2-(phenylamino)pyrimidines are highly active CDK9 inhibitors: synthesis, X-ray crystal structures, structure-activity relationship, and anticancer activities. J Med Chem 2013; 56:640-59. [PMID: 23301767 PMCID: PMC3579313 DOI: 10.1021/jm301475f] [Citation(s) in RCA: 101] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Cancer cells often have a high demand for antiapoptotic proteins in order to resist programmed cell death. CDK9 inhibition selectively targets survival proteins and reinstates apoptosis in cancer cells. We designed a series of 4-thiazol-2-anilinopyrimidine derivatives with functional groups attached to the C5-position of the pyrimidine or to the C4-thiazol moiety and investigated their effects on CDK9 potency and selectivity. One of the most selective compounds, 12u inhibits CDK9 with IC(50) = 7 nM and shows over 80-fold selectivity for CDK9 versus CDK2. X-ray crystal structures of 12u bound to CDK9 and CDK2 provide insights into the binding modes. This work, together with crystal structures of selected inhibitors in complex with both enzymes described in a companion paper, (34) provides a rationale for the observed SAR. 12u demonstrates potent anticancer activity against primary chronic lymphocytic leukemia cells with a therapeutic window 31- and 107-fold over those of normal B- and T-cells.
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Affiliation(s)
- Hao Shao
- School of Pharmacy and Centre
for Biomolecular Sciences, University of Nottingham, University Park, Nottingham NG7 2RD, U.K
| | - Shenhua Shi
- School of Pharmacy and Centre
for Biomolecular Sciences, University of Nottingham, University Park, Nottingham NG7 2RD, U.K
| | - Shiliang Huang
- School of Pharmacy and Centre
for Biomolecular Sciences, University of Nottingham, University Park, Nottingham NG7 2RD, U.K
| | - Alison
J. Hole
- Department of Biochemistry, University of Oxford, Oxford OX1 3QU, U.K
| | - Abdullahi Y. Abbas
- School of Pharmacy and Centre
for Biomolecular Sciences, University of Nottingham, University Park, Nottingham NG7 2RD, U.K
| | - Sonja Baumli
- Department of Biochemistry, University of Oxford, Oxford OX1 3QU, U.K
| | - Xiangrui Liu
- School of Pharmacy and Centre
for Biomolecular Sciences, University of Nottingham, University Park, Nottingham NG7 2RD, U.K
| | - Frankie Lam
- School of Pharmacy and Centre
for Biomolecular Sciences, University of Nottingham, University Park, Nottingham NG7 2RD, U.K
- Shool of Pharmacy and Medical
Sciences, University of South Australia, Adelaide, SA 5001, Australia
| | - David
W. Foley
- School of Pharmacy and Centre
for Biomolecular Sciences, University of Nottingham, University Park, Nottingham NG7 2RD, U.K
| | - Peter M. Fischer
- School of Pharmacy and Centre
for Biomolecular Sciences, University of Nottingham, University Park, Nottingham NG7 2RD, U.K
| | - Martin Noble
- Department of Biochemistry, University of Oxford, Oxford OX1 3QU, U.K
- Northern Institute for Cancer
Research, Medical School, Newcastle University, Newcastle upon Tyne NE2 4HH, U.K
| | - Jane A. Endicott
- Department of Biochemistry, University of Oxford, Oxford OX1 3QU, U.K
- Northern Institute for Cancer
Research, Medical School, Newcastle University, Newcastle upon Tyne NE2 4HH, U.K
| | - Chris Pepper
- Institute of Cancer and Genetics,
School of Medicine, Cardiff University,
Heath Park, Cardiff CF14 4XN, U.K
| | - Shudong Wang
- School of Pharmacy and Centre
for Biomolecular Sciences, University of Nottingham, University Park, Nottingham NG7 2RD, U.K
- Shool of Pharmacy and Medical
Sciences, University of South Australia, Adelaide, SA 5001, Australia
- Phone: +61883022372. E-mail:
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50
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Torres-Guzmán R, Chu S, Velasco JA, Lallena MJ. Multiparametric Cell-Based Assay for the Evaluation of Transcription Inhibition by High-Content Imaging. ACTA ACUST UNITED AC 2013; 18:556-66. [DOI: 10.1177/1087057112472539] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
Loss of normal cell cycle regulation is a hallmark of human cancer. Cyclin-dependent kinases (CDKs) are key regulators of the cell cycle and have been actively pursued as promising therapeutic targets. Likewise, members of the CDK family are functionally related to transcriptional modulation, a molecular pathway suitable for therapeutic intervention. We used a set of 2500 compounds in the U2OS cell line to evaluate its effect in the cell division process. Interestingly, out of this analysis, we identified a subpopulation of compounds that are able to inhibit RNA polymerase activity, thus interfering with gene transcription processes. After this finding, we developed, validated, and fully automated a multiparameter high-content imaging (HCI) assay to measure phosphorylation of the RNA polymerase II carboxyl terminal domain (pCTD). Simultaneously, we measured both the DNA content and cell proliferation index in the treated cells. The linear regression analysis comparing the IC50 for pCTD and the 4N EC50 for DNA content or IC50 for cell proliferation showed an excellent agreement ( r2 = 0.84 and r2 = 0.94, respectively). Our results confirm that this method allows discriminating between cell cycle and transcription inhibition and confirms HCI as a powerful technology for the identification of compounds with an effective and selective pathway phenotype.
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Affiliation(s)
- Raquel Torres-Guzmán
- Translational Sciences & Technologies, Lilly Research Laboratories, Eli Lilly & Company, Lilly Research Laboratories, Alcobendas, Madrid, Spain
| | - Shaoyou Chu
- Translational Sciences & Technologies, Lilly Research Laboratories, Eli Lilly & Company, Lilly Research Laboratories, Indianapolis, IN, USA
| | - Juan A. Velasco
- Translational Sciences & Technologies, Lilly Research Laboratories, Eli Lilly & Company, Lilly Research Laboratories, Alcobendas, Madrid, Spain
| | - María José Lallena
- Translational Sciences & Technologies, Lilly Research Laboratories, Eli Lilly & Company, Lilly Research Laboratories, Alcobendas, Madrid, Spain
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