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Zhu S, Chen Z, Liu C, Duong J, Tran T, Liang Z, Fang X, Ouyang K. The essential role of MED27 in stabilizing the mediator complex for cardiac development and function. Life Sci 2024; 356:123020. [PMID: 39209248 DOI: 10.1016/j.lfs.2024.123020] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2024] [Revised: 08/15/2024] [Accepted: 08/25/2024] [Indexed: 09/04/2024]
Abstract
AIM Transcriptional regulation of gene expression plays a crucial role in orchestrating complex morphogenetic and molecular events during heart development and function. Mediator complex is an essential multi-subunit protein complex that governs gene expression in eukaryotic cells. Although Mediator subunits (MEDs) work integrally in the complex, individual MED component displays specialized functions. MED27, categorized as an Upper Tail subunit, possesses an as-yet-uncharacterized function. In this study, we aimed to investigate the physiological role of MED27 in cardiomyocytes. MATERIALS AND METHODS we generated a Med27 floxed mouse line, which was further used to generate constitutive (cKO) and inducible (icKO) cardiomyocyte-specific Med27 knockout mouse models. Morphological, histological analysis and cardiac physiological studies were performed in Med27 cKO and icKO mutants. Transcriptional profiles were determined by RNA sequencing (RNAseq) analysis. KEY FUNDINGS Ablation of MED27 in developing mouse cardiomyocytes results in embryonic lethality, while its deletion in adult cardiomyocytes leads to heart failure and mortality. Similar to the ablation of another Upper Tail subunit, MED30 in cardiomyocytes, deletion of MED27 leads to decreased protein levels of most MEDs in cardiomyocytes. Interestingly, overexpression of MED30 fails to restore the protein levels of Mediator subunits in MED27-deficient cardiomyocytes, demonstrating that the role of MED27 in maintaining the integrity and stability of the Mediator complex is independent of MED30. SIGNIFICANCE Our results revealed an essential role of MED27 in cardiac development and function by maintaining the stability of the Mediator core.
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Affiliation(s)
- Siting Zhu
- Department of Cardiovascular Surgery, Peking University Shenzhen Hospital, School of Chemical Biology and Biotechnology, State Key Laboratory of Chemical Oncogenomics, Peking University Shenzhen Graduate School, Shenzhen, China; Department of Medicine, University of California San Diego, La Jolla, California, USA
| | - Ze'e Chen
- Department of Cardiovascular Surgery, Peking University Shenzhen Hospital, School of Chemical Biology and Biotechnology, State Key Laboratory of Chemical Oncogenomics, Peking University Shenzhen Graduate School, Shenzhen, China; Department of Medicine, University of California San Diego, La Jolla, California, USA
| | - Canzhao Liu
- Department of Medicine, University of California San Diego, La Jolla, California, USA; Department of Cardiovascular Medicine, Translational Medicine Research Center, Zhujiang Hospital, Southern Medical University, Guangzhou, China
| | - Janelle Duong
- Department of Medicine, University of California San Diego, La Jolla, California, USA
| | - Tiana Tran
- Department of Medicine, University of California San Diego, La Jolla, California, USA
| | - Zhengyu Liang
- Department of Systems Biology, Southern University of Science and Technology, Shenzhen, China
| | - Xi Fang
- Department of Medicine, University of California San Diego, La Jolla, California, USA.
| | - Kunfu Ouyang
- Department of Cardiovascular Surgery, Peking University Shenzhen Hospital, School of Chemical Biology and Biotechnology, State Key Laboratory of Chemical Oncogenomics, Peking University Shenzhen Graduate School, Shenzhen, China.
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Chen M, Li J, Zhang L, Wang L, Cheng C, Ji H, Altilia S, Ding X, Cai G, Altomare D, Shtutman M, Byrum SD, Mackintosh SG, Feoktistov A, Soshnikova N, Mogila VA, Tatarskiy V, Erokhin M, Chetverina D, Prawira A, Ni Y, Urban S, McInnes C, Broude EV, Roninson IB. CDK8 and CDK19: positive regulators of signal-induced transcription and negative regulators of Mediator complex proteins. Nucleic Acids Res 2023; 51:7288-7313. [PMID: 37378433 PMCID: PMC10415139 DOI: 10.1093/nar/gkad538] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2023] [Revised: 06/01/2023] [Accepted: 06/08/2023] [Indexed: 06/29/2023] Open
Abstract
We have conducted a detailed transcriptomic, proteomic and phosphoproteomic analysis of CDK8 and its paralog CDK19, alternative enzymatic components of the kinase module associated with transcriptional Mediator complex and implicated in development and diseases. This analysis was performed using genetic modifications of CDK8 and CDK19, selective CDK8/19 small molecule kinase inhibitors and a potent CDK8/19 PROTAC degrader. CDK8/19 inhibition in cells exposed to serum or to agonists of NFκB or protein kinase C (PKC) reduced the induction of signal-responsive genes, indicating a pleiotropic role of Mediator kinases in signal-induced transcriptional reprogramming. CDK8/19 inhibition under basal conditions initially downregulated a small group of genes, most of which were inducible by serum or PKC stimulation. Prolonged CDK8/19 inhibition or mutagenesis upregulated a larger gene set, along with a post-transcriptional increase in the proteins comprising the core Mediator complex and its kinase module. Regulation of both RNA and protein expression required CDK8/19 kinase activities but both enzymes protected their binding partner cyclin C from proteolytic degradation in a kinase-independent manner. Analysis of isogenic cell populations expressing CDK8, CDK19 or their kinase-inactive mutants revealed that CDK8 and CDK19 have the same qualitative effects on protein phosphorylation and gene expression at the RNA and protein levels, whereas differential effects of CDK8 versus CDK19 knockouts were attributable to quantitative differences in their expression and activity rather than different functions.
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Affiliation(s)
- Mengqian Chen
- Department of Drug Discovery and Biomedical Sciences, College of Pharmacy, University of South Carolina, Columbia, SC 29208, USA
- Senex Biotechnology, Inc. Columbia, SC 29208, USA
| | - Jing Li
- Department of Drug Discovery and Biomedical Sciences, College of Pharmacy, University of South Carolina, Columbia, SC 29208, USA
| | - Li Zhang
- Department of Drug Discovery and Biomedical Sciences, College of Pharmacy, University of South Carolina, Columbia, SC 29208, USA
| | - Lili Wang
- Department of Drug Discovery and Biomedical Sciences, College of Pharmacy, University of South Carolina, Columbia, SC 29208, USA
| | - Chen Cheng
- Department of Drug Discovery and Biomedical Sciences, College of Pharmacy, University of South Carolina, Columbia, SC 29208, USA
| | - Hao Ji
- Department of Drug Discovery and Biomedical Sciences, College of Pharmacy, University of South Carolina, Columbia, SC 29208, USA
| | - Serena Altilia
- Department of Drug Discovery and Biomedical Sciences, College of Pharmacy, University of South Carolina, Columbia, SC 29208, USA
| | - Xiaokai Ding
- Department of Drug Discovery and Biomedical Sciences, College of Pharmacy, University of South Carolina, Columbia, SC 29208, USA
| | - Guoshuai Cai
- Department of Environmental Health Sciences, Arnold School of Public Health, University of South Carolina, Columbia, SC 29208, USA
| | - Diego Altomare
- Department of Drug Discovery and Biomedical Sciences, College of Pharmacy, University of South Carolina, Columbia, SC 29208, USA
| | - Michael Shtutman
- Department of Drug Discovery and Biomedical Sciences, College of Pharmacy, University of South Carolina, Columbia, SC 29208, USA
| | - Stephanie D Byrum
- Department of Biochemistry and Molecular Biology, University of Arkansas for Medical Sciences, Little Rock, AR 72205, USA
| | - Samuel G Mackintosh
- Department of Biochemistry and Molecular Biology, University of Arkansas for Medical Sciences, Little Rock, AR 72205, USA
| | - Alexey Feoktistov
- Institute of Gene Biology, Russian Academy of Sciences, 119334 Moscow, Russian Federation
| | - Nataliya Soshnikova
- Institute of Gene Biology, Russian Academy of Sciences, 119334 Moscow, Russian Federation
| | - Vladislav A Mogila
- Institute of Gene Biology, Russian Academy of Sciences, 119334 Moscow, Russian Federation
| | - Victor Tatarskiy
- Institute of Gene Biology, Russian Academy of Sciences, 119334 Moscow, Russian Federation
| | - Maksim Erokhin
- Institute of Gene Biology, Russian Academy of Sciences, 119334 Moscow, Russian Federation
| | - Darya Chetverina
- Institute of Gene Biology, Russian Academy of Sciences, 119334 Moscow, Russian Federation
| | - Angga Prawira
- Department of Infectious Diseases, University Hospital of Heidelberg, Heidelberg, Germany
| | - Yi Ni
- Department of Infectious Diseases, University Hospital of Heidelberg, Heidelberg, Germany
| | - Stephan Urban
- Department of Infectious Diseases, University Hospital of Heidelberg, Heidelberg, Germany
| | - Campbell McInnes
- Department of Drug Discovery and Biomedical Sciences, College of Pharmacy, University of South Carolina, Columbia, SC 29208, USA
| | - Eugenia V Broude
- Department of Drug Discovery and Biomedical Sciences, College of Pharmacy, University of South Carolina, Columbia, SC 29208, USA
| | - Igor B Roninson
- Department of Drug Discovery and Biomedical Sciences, College of Pharmacy, University of South Carolina, Columbia, SC 29208, USA
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3
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Zabihi M, Lotfi R, Yousefi AM, Bashash D. Cyclins and cyclin-dependent kinases: from biology to tumorigenesis and therapeutic opportunities. J Cancer Res Clin Oncol 2023; 149:1585-1606. [PMID: 35781526 DOI: 10.1007/s00432-022-04135-6] [Citation(s) in RCA: 14] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2022] [Accepted: 06/13/2022] [Indexed: 12/20/2022]
Abstract
The discussion on cell proliferation cannot be continued without taking a look at the cell cycle regulatory machinery. Cyclin-dependent kinases (CDKs), cyclins, and CDK inhibitors (CKIs) are valuable members of this system and their equilibrium guarantees the proper progression of the cell cycle. As expected, any dysregulation in the expression or function of these components can provide a platform for excessive cell proliferation leading to tumorigenesis. The high frequency of CDK abnormalities in human cancers, together with their druggable structure has raised the possibility that perhaps designing a series of inhibitors targeting CDKs might be advantageous for restricting the survival of tumor cells; however, their application has faced a serious concern, since these groups of serine-threonine kinases possess non-canonical functions as well. In the present review, we aimed to take a look at the biology of CDKs and then magnify their contribution to tumorigenesis. Then, by arguing the bright and dark aspects of CDK inhibition in the treatment of human cancers, we intend to reach a consensus on the application of these inhibitors in clinical settings.
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Affiliation(s)
- Mitra Zabihi
- Department of Hematology and Blood Banking, School of Allied Medical Sciences, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Ramin Lotfi
- Clinical Research Development Center, Tohid Hospital, Kurdistan University of Medical Sciences, Sanandaj, Iran
| | - Amir-Mohammad Yousefi
- Department of Hematology and Blood Banking, School of Allied Medical Sciences, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Davood Bashash
- Department of Hematology and Blood Banking, School of Allied Medical Sciences, Shahid Beheshti University of Medical Sciences, Tehran, Iran.
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Donovan MG, Galbraith MD, Espinosa JM. Multi-omics investigation reveals functional specialization of transcriptional cyclin dependent kinases in cancer biology. Sci Rep 2022; 12:22505. [PMID: 36577800 PMCID: PMC9797569 DOI: 10.1038/s41598-022-26860-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2022] [Accepted: 12/21/2022] [Indexed: 12/30/2022] Open
Abstract
Transcriptional addiction is recognized as a valid therapeutic target in cancer, whereby the dependency of cancer cells on oncogenic transcriptional regulators may be pharmacologically exploited. However, a comprehensive understanding of the key factors within the transcriptional machinery that might afford a useful therapeutic window remains elusive. Herein, we present a cross-omics investigation into the functional specialization of the transcriptional cyclin dependent kinases (tCDKs) through analysis of high-content genetic dependency, gene expression, patient survival, and drug response datasets. This analysis revealed specialization among tCDKs in terms of contributions to cancer cell fitness, clinical prognosis, and interaction with oncogenic signaling pathways. CDK7 and CDK9 stand out as the most relevant targets, albeit through distinct mechanisms of oncogenicity and context-dependent contributions to cancer survival and drug sensitivity. Genetic ablation of CDK9, but not CDK7, mimics the effect on cell viability the loss of key components of the transcriptional machinery. Pathway analysis of genetic co-dependency and drug sensitivity data show CDK7 and CDK9 have distinct relationships with major oncogenic signatures, including MYC and E2F targets, oxidative phosphorylation, and the unfolded protein response. Altogether, these results inform the improved design of therapeutic strategies targeting tCDKs in cancer.
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Affiliation(s)
- Micah G Donovan
- Department of Pharmacology, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
- Linda Crnic Institute for Down Syndrome, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Matthew D Galbraith
- Department of Pharmacology, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
- Linda Crnic Institute for Down Syndrome, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Joaquin M Espinosa
- Department of Pharmacology, University of Colorado Anschutz Medical Campus, Aurora, CO, USA.
- Linda Crnic Institute for Down Syndrome, University of Colorado Anschutz Medical Campus, Aurora, CO, USA.
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5
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CDK19 regulates the proliferation of hematopoietic stem cells and acute myeloid leukemia cells by suppressing p53-mediated transcription of p21. Leukemia 2022; 36:956-969. [PMID: 35110726 DOI: 10.1038/s41375-022-01512-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2021] [Revised: 01/07/2022] [Accepted: 01/21/2022] [Indexed: 02/06/2023]
Abstract
The cell cycle progression of hematopoietic stem cells (HSCs) and acute myeloid leukemia (AML) cells is precisely controlled by multiple regulatory factors. However, the underlying mechanisms are not fully understood. Here, we find that cyclin-dependent kinase 19 (CDK19), not its paralogue CDK8, is relatively enriched in mouse HSCs, and its expression is more significantly increased than CDK8 after proliferative stresses. Furthermore, SenexinB (a CDK8/19 inhibitor) treatment impairs the proliferation and self-renewal ability of HSCs. Moreover, overexpression of CDK19 promotes HSC function better than CDK8 overexpression. Using CDK19 knockout mice, we observe that CDK19-/- HSCs exhibit similar phenotypes to those of cells treated with SenexinB. Interestingly, the p53 signaling pathway is significantly activated in HSCs lacking CDK19 expression. Further investigations show that CDK19 can interact with p53 to inhibit p53-mediated transcription of p21 in HSCs and treatment with a specific p53 inhibitor (PFTβ) partially rescues the defects of CDK19-null HSCs. Importantly, SenexinB treatment markedly inhibits the proliferation of AML cells. Collectively, our findings indicate that CDK19 is involved in regulating HSC and AML cell proliferation via the p53-p21 pathway, revealing a new mechanism underlying cell cycle regulation in normal and malignant hematopoietic cells.
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Zarate YA, Uehara T, Abe K, Oginuma M, Harako S, Ishitani S, Lehesjoki AE, Bierhals T, Kloth K, Ehmke N, Horn D, Holtgrewe M, Anderson K, Viskochil D, Edgar-Zarate CL, Sacoto MJG, Schnur RE, Morrow MM, Sanchez-Valle A, Pappas J, Rabin R, Muona M, Anttonen AK, Platzer K, Luppe J, Gburek-Augustat J, Kaname T, Okamoto N, Mizuno S, Kaido Y, Ohkuma Y, Hirose Y, Ishitani T, Kosaki K. CDK19-related disorder results from both loss-of-function and gain-of-function de novo missense variants. Genet Med 2021; 23:1050-1057. [PMID: 33495529 DOI: 10.1038/s41436-020-01091-9] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2020] [Revised: 12/18/2020] [Accepted: 12/22/2020] [Indexed: 11/08/2022] Open
Abstract
PURPOSE To expand the recent description of a new neurodevelopmental syndrome related to alterations in CDK19. METHODS Individuals were identified through international collaboration. Functional studies included autophosphorylation assays for CDK19 Gly28Arg and Tyr32His variants and in vivo zebrafish assays of the CDK19G28R and CDK19Y32H. RESULTS We describe 11 unrelated individuals (age range: 9 months to 14 years) with de novo missense variants mapped to the kinase domain of CDK19, including two recurrent changes at residues Tyr32 and Gly28. In vitro autophosphorylation and substrate phosphorylation assays revealed that kinase activity of protein was lower for p.Gly28Arg and higher for p.Tyr32His substitutions compared with that of the wild-type protein. Injection of CDK19 messenger RNA (mRNA) with either the Tyr32His or the Gly28Arg variants using in vivo zebrafish model significantly increased fraction of embryos with morphological abnormalities. Overall, the phenotype of the now 14 individuals with CDK19-related disorder includes universal developmental delay and facial dysmorphism, hypotonia (79%), seizures (64%), ophthalmologic anomalies (64%), and autism/autistic traits (56%). CONCLUSION CDK19 de novo missense variants are responsible for a novel neurodevelopmental disorder. Both kinase assay and zebrafish experiments showed that the pathogenetic mechanism may be more diverse than previously thought.
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Affiliation(s)
- Yuri A Zarate
- Section of Genetics and Metabolism, University of Arkansas for Medical Sciences, Little Rock, AR, USA.
| | - Tomoko Uehara
- Center for Medical Genetics, Keio University School of Medicine, Tokyo, Japan
| | - Kota Abe
- Department of Homeostatic Regulation, Division of Cellular and Molecular Biology, Research Institute for Microbial Diseases, Osaka University, Suita, Osaka, Japan
| | - Masayuki Oginuma
- Department of Homeostatic Regulation, Division of Cellular and Molecular Biology, Research Institute for Microbial Diseases, Osaka University, Suita, Osaka, Japan
| | - Sora Harako
- Laboratory of Gene Regulation, Graduate School of Medicine and Pharmaceutical Sciences, University of Toyama, Toyama, Japan
| | - Shizuka Ishitani
- Department of Homeostatic Regulation, Division of Cellular and Molecular Biology, Research Institute for Microbial Diseases, Osaka University, Suita, Osaka, Japan
| | | | - Tatjana Bierhals
- Institute of Human Genetics, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Katja Kloth
- Institute of Human Genetics, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Nadja Ehmke
- Institute of Medical and Human Genetics, Charité - Universitätsmedizin Berlin, Berlin, Germany
| | - Denise Horn
- Institute of Medical and Human Genetics, Charité - Universitätsmedizin Berlin, Berlin, Germany
| | - Manuel Holtgrewe
- Charité - Universitätsmedizin Berlin, Berlin, Germany
- Core Unit Bioinformatics - CUBI, Berlin Institute of Health, Berlin, Germany
| | - Katherine Anderson
- Department of Pediatrics, University of Vermont Medical Center, Burlington, VT, USA
| | - David Viskochil
- Division of Medical Genetics, Department of Pediatrics, University of Utah, Salt Lake City, UT, USA
| | | | | | | | | | - Amarilis Sanchez-Valle
- Division of Genetics and Metabolism, Department of Pediatrics, University of South Florida, Tampa, FL, USA
| | - John Pappas
- NYU Grossman School of Medicine, Dept of Pediatrics, Clinical Genetic Services, New York, NY, USA
| | - Rachel Rabin
- NYU Grossman School of Medicine, Dept of Pediatrics, Clinical Genetic Services, New York, NY, USA
| | - Mikko Muona
- Folkhälsan Research Center and University of Helsinki, Helsinki, Finland
- Blueprint Genetics, Helsinki, Finland
| | - Anna-Kaisa Anttonen
- Folkhälsan Research Center and University of Helsinki, Helsinki, Finland
- Department of Genetics, HUS Diagnostic Center, Helsinki University Hospital, Helsinki, Finland
| | - Konrad Platzer
- Institute of Human Genetics, University of Leipzig Medical Center, Leipzig, Germany
| | - Johannes Luppe
- Institute of Human Genetics, University of Leipzig Medical Center, Leipzig, Germany
| | - Janina Gburek-Augustat
- Division of Neuropaediatrics, Hospital for Children and Adolescents, University Leipzig, Leipzig, Germany
| | - Tadashi Kaname
- Department of Genome Medicine, National Center for Child Health and Developemt, Tokyo, Japan
| | - Nobuhiko Okamoto
- Department of Medical Genetics, Osaka Women's and Children's Hospital, Osaka, Japan
| | - Seiji Mizuno
- Department of Clinical Genetics, Central Hospital, Aichi Developmental Disability Center, Aichi, Japan
| | - Yusaku Kaido
- Laboratory of Gene Regulation, Graduate School of Medicine and Pharmaceutical Sciences, University of Toyama, Toyama, Japan
| | - Yoshiaki Ohkuma
- Laboratory of Gene Regulation, Graduate School of Medicine and Pharmaceutical Sciences, University of Toyama, Toyama, Japan
| | - Yutaka Hirose
- Laboratory of Gene Regulation, Graduate School of Medicine and Pharmaceutical Sciences, University of Toyama, Toyama, Japan
| | - Tohru Ishitani
- Department of Homeostatic Regulation, Division of Cellular and Molecular Biology, Research Institute for Microbial Diseases, Osaka University, Suita, Osaka, Japan
| | - Kenjiro Kosaki
- Center for Medical Genetics, Keio University School of Medicine, Tokyo, Japan
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The Inhibition of CDK8/19 Mediator Kinases Prevents the Development of Resistance to EGFR-Targeting Drugs. Cells 2021; 10:cells10010144. [PMID: 33445730 PMCID: PMC7828184 DOI: 10.3390/cells10010144] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2020] [Revised: 01/06/2021] [Accepted: 01/09/2021] [Indexed: 02/07/2023] Open
Abstract
Drug resistance is the main obstacle to achieving cures with both conventional and targeted anticancer drugs. The emergence of acquired drug resistance is initially mediated by non-genetic transcriptional changes, which occur at a much higher frequency than mutations and may involve population-scale transcriptomic adaptation. CDK8/19 kinases, through association with transcriptional Mediator complex, regulate transcriptional reprogramming by co-operating with different signal-responsive transcription factors. Here we tested if CDK8/19 inhibition could prevent adaptation to drugs acting on epidermal growth factor receptor (EGFR/ERBB1/HER1). The development of resistance was analyzed following long-term exposure of BT474 and SKBR3 breast cancer cells to EGFR-targeting small molecules (gefitinib, erlotinib) and of SW48 colon cancer cells to an anti-EGFR monoclonal antibody cetuximab. In all cases, treatment of small cell populations (~105 cells) with a single dose of the drug initially led to growth inhibition that was followed by the resumption of proliferation and development of drug resistance in the adapted populations. However, this adaptation was always prevented by the addition of selective CDK8/19 inhibitors, even though such inhibitors alone had only moderate or no effect on cell growth. These results indicate that combining EGFR-targeting drugs with CDK8/19 inhibitors may delay or prevent the development of tumor resistance to therapy.
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8
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Wu D, Zhang Z, Chen X, Yan Y, Liu X. Angel or Devil ? - CDK8 as the new drug target. Eur J Med Chem 2020; 213:113043. [PMID: 33257171 DOI: 10.1016/j.ejmech.2020.113043] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2020] [Revised: 11/16/2020] [Accepted: 11/17/2020] [Indexed: 12/19/2022]
Abstract
Cyclin-dependent kinase 8 (CDK8) plays an momentous role in transcription regulation by forming kinase module or transcription factor phosphorylation. A large number of evidences have identified CDK8 as an important factor in cancer occurrence and development. In addition, CDK8 also participates in the regulation of cancer cell stress response to radiotherapy and chemotherapy, assists tumor cell invasion, metastasis, and drug resistance. Therefore, CDK8 is regarded as a promising target for cancer therapy. Most studies in recent years supported the role of CDK8 as a carcinogen, however, under certain conditions, CDK8 exists as a tumor suppressor. The functional diversity of CDK8 and its exceptional role in different types of cancer have aroused great interest from scientists but even more controversy during the discovery of CDK8 inhibitors. In addition, CDK8 appears to be an effective target for inflammation diseases and immune system disorders. Therefore, we summarized the research results of CDK8, involving physiological/pathogenic mechanisms and the development status of compounds targeting CDK8, provide a reference for the feasibility evaluation of CDK8 as a therapeutic target, and guidance for researchers who are involved in this field for the first time.
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Affiliation(s)
- Dan Wu
- School of Biological Engineering, Hefei Technology College, Hefei, 238000, PR China
| | - Zhaoyan Zhang
- School of Pharmacy, Anhui Province Key Laboratory of Major Autoimmune Diseases, Anhui Institute of Innovative Drugs, Anhui Medical University, Hefei, 230032, PR China
| | - Xing Chen
- School of Pharmacy, Anhui Province Key Laboratory of Major Autoimmune Diseases, Anhui Institute of Innovative Drugs, Anhui Medical University, Hefei, 230032, PR China
| | - Yaoyao Yan
- School of Pharmacy, Anhui Province Key Laboratory of Major Autoimmune Diseases, Anhui Institute of Innovative Drugs, Anhui Medical University, Hefei, 230032, PR China
| | - Xinhua Liu
- School of Pharmacy, Anhui Province Key Laboratory of Major Autoimmune Diseases, Anhui Institute of Innovative Drugs, Anhui Medical University, Hefei, 230032, PR China.
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9
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Lv X, Tian Y, Li S, Cheng K, Huang X, Kong H, Liao C, Xie Z. Discovery and Development of Cyclin-Dependent Kinase 8 Inhibitors. Curr Med Chem 2020; 27:5429-5443. [DOI: 10.2174/0929867326666190402110528] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2018] [Revised: 02/20/2019] [Accepted: 03/20/2019] [Indexed: 12/13/2022]
Abstract
Cyclin-dependent Kinase 8 (CDK8), a member of the CDKs family, has been widely
focused owing to investigations of its critical roles in transcription and oncogenesis in recent years.
Selective inhibition of CDK8 and its paralog CDK19 offers a novel therapeutic strategy for the
treatment of some cancers. Up to now, though many small molecules against CDK8 have been discovered,
most of them are discontinued in the preclinical trials due to the low selectivity and poor
physicochemical properties. This review mainly summarizes the design strategies of selective CDK8
inhibitors having different chemical scaffolds with the aim to improve the inhibitory activity, selectivity,
metabolic stability and solubility. Their corresponding Structure-activity Relationships (SAR)
are also reviewed. On the basis of the discussion in this review, we hope more effective, selective
and drug-like CDK8 inhibitors will be developed and demonstrate therapeutic values in the near
future.
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Affiliation(s)
- Xiao Lv
- School of Food and Biological Engineering, Hefei University of Technology, Hefei, Anhui 230009, China
| | - Yongbing Tian
- School of Food and Biological Engineering, Hefei University of Technology, Hefei, Anhui 230009, China
| | - Shiyu Li
- School of Food and Biological Engineering, Hefei University of Technology, Hefei, Anhui 230009, China
| | - Kai Cheng
- School of Food and Biological Engineering, Hefei University of Technology, Hefei, Anhui 230009, China
| | - Xufeng Huang
- School of Food and Biological Engineering, Hefei University of Technology, Hefei, Anhui 230009, China
| | - Haiyan Kong
- School of Food and Biological Engineering, Hefei University of Technology, Hefei, Anhui 230009, China
| | - Chenzhong Liao
- School of Food and Biological Engineering, Hefei University of Technology, Hefei, Anhui 230009, China
| | - Zhouling Xie
- School of Food and Biological Engineering, Hefei University of Technology, Hefei, Anhui 230009, China
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10
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Hofmann MH, Mani R, Engelhardt H, Impagnatiello MA, Carotta S, Kerenyi M, Lorenzo-Herrero S, Böttcher J, Scharn D, Arnhof H, Zoephel A, Schnitzer R, Gerstberger T, Sanderson MP, Rajgolikar G, Goswami S, Vasu S, Ettmayer P, Gonzalez S, Pearson M, McConnell DB, Kraut N, Muthusamy N, Moll J. Selective and Potent CDK8/19 Inhibitors Enhance NK-Cell Activity and Promote Tumor Surveillance. Mol Cancer Ther 2020; 19:1018-1030. [PMID: 32024684 DOI: 10.1158/1535-7163.mct-19-0789] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2019] [Revised: 12/18/2019] [Accepted: 01/28/2020] [Indexed: 12/14/2022]
Abstract
Natural killer (NK) cells play a pivotal role in controlling cancer. Multiple extracellular receptors and internal signaling nodes tightly regulate NK activation. Cyclin-dependent kinases of the mediator complex (CDK8 and CDK19) were described as a signaling intermediates in NK cells. Here, we report for the first time the development and use of CDK8/19 inhibitors to suppress phosphorylation of STAT1S727 in NK cells and to augment the production of the cytolytic molecules perforin and granzyme B (GZMB). Functionally, this resulted in enhanced NK-cell-mediated lysis of primary leukemia cells. Treatment with the CDK8/19 inhibitor BI-1347 increased the response rate and survival of mice bearing melanoma and breast cancer xenografts. In addition, CDK8/19 inhibition augmented the antitumoral activity of anti-PD-1 antibody and SMAC mimetic therapy, both agents that promote T-cell-mediated antitumor immunity. Treatment with the SMAC mimetic compound BI-8382 resulted in an increased number of NK cells infiltrating EMT6 tumors. Combination of the CDK8/19 inhibitor BI-1347, which augments the amount of degranulation enzymes, with the SMAC mimetic BI-8382 resulted in increased survival of mice carrying the EMT6 breast cancer model. The observed survival benefit was dependent on an intermittent treatment schedule of BI-1347, suggesting the importance of circumventing a hyporesponsive state of NK cells. These results suggest that CDK8/19 inhibitors can be combined with modulators of the adaptive immune system to inhibit the growth of solid tumors, independent of their activity on cancer cells, but rather through promoting NK-cell function.
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Affiliation(s)
| | - Rajeswaran Mani
- Division of Hematology, Department of Internal Medicine, The Ohio State University Comprehensive Cancer Center, Columbus, Ohio
| | | | | | | | - Marc Kerenyi
- Boehringer Ingelheim RCV GmbH & Co KG, Vienna, Austria
| | - Seila Lorenzo-Herrero
- Department of Functional Biology, Universidad de Oviedo, Instituto de Investigación Biosanitaria del Principado de Asturias (IISPA), IUOPA, Oviedo, Spain
| | - Jark Böttcher
- Boehringer Ingelheim RCV GmbH & Co KG, Vienna, Austria
| | - Dirk Scharn
- Boehringer Ingelheim RCV GmbH & Co KG, Vienna, Austria
| | | | | | | | | | | | - Girish Rajgolikar
- Division of Hematology, Department of Internal Medicine, The Ohio State University Comprehensive Cancer Center, Columbus, Ohio
| | - Swagata Goswami
- Division of Hematology, Department of Internal Medicine, The Ohio State University Comprehensive Cancer Center, Columbus, Ohio
| | - Sumithira Vasu
- Division of Hematology, Department of Internal Medicine, The Ohio State University Comprehensive Cancer Center, Columbus, Ohio
| | | | - Segundo Gonzalez
- Department of Functional Biology, Universidad de Oviedo, Instituto de Investigación Biosanitaria del Principado de Asturias (IISPA), IUOPA, Oviedo, Spain
| | - Mark Pearson
- Boehringer Ingelheim RCV GmbH & Co KG, Vienna, Austria
| | | | - Norbert Kraut
- Boehringer Ingelheim RCV GmbH & Co KG, Vienna, Austria
| | - Natarajan Muthusamy
- Division of Hematology, Department of Internal Medicine, The Ohio State University Comprehensive Cancer Center, Columbus, Ohio
| | - Jürgen Moll
- Boehringer Ingelheim RCV GmbH & Co KG, Vienna, Austria
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11
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Calpena E, Hervieu A, Kaserer T, Swagemakers SM, Goos JA, Popoola O, Ortiz-Ruiz MJ, Barbaro-Dieber T, Bownass L, Brilstra EH, Brimble E, Foulds N, Grebe TA, Harder AV, Lees MM, Monaghan KG, Newbury-Ecob RA, Ong KR, Osio D, Reynoso Santos FJ, Ruzhnikov MR, Telegrafi A, van Binsbergen E, van Dooren MF, van der Spek PJ, Blagg J, Twigg SR, Mathijssen IM, Clarke PA, Wilkie AO, Wilkie AOM. De Novo Missense Substitutions in the Gene Encoding CDK8, a Regulator of the Mediator Complex, Cause a Syndromic Developmental Disorder. Am J Hum Genet 2019; 104:709-720. [PMID: 30905399 PMCID: PMC6451695 DOI: 10.1016/j.ajhg.2019.02.006] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2018] [Accepted: 02/04/2019] [Indexed: 12/27/2022] Open
Abstract
The Mediator is an evolutionarily conserved, multi-subunit complex that regulates multiple steps of transcription. Mediator activity is regulated by the reversible association of a four-subunit module comprising CDK8 or CDK19 kinases, together with cyclin C, MED12 or MED12L, and MED13 or MED13L. Mutations in MED12, MED13, and MED13L were previously identified in syndromic developmental disorders with overlapping phenotypes. Here, we report CDK8 mutations (located at 13q12.13) that cause a phenotypically related disorder. Using whole-exome or whole-genome sequencing, and by international collaboration, we identified eight different heterozygous missense CDK8 substitutions, including 10 shown to have arisen de novo, in 12 unrelated subjects; a recurrent mutation, c.185C>T (p.Ser62Leu), was present in five individuals. All predicted substitutions localize to the ATP-binding pocket of the kinase domain. Affected individuals have overlapping phenotypes characterized by hypotonia, mild to moderate intellectual disability, behavioral disorders, and variable facial dysmorphism. Congenital heart disease occurred in six subjects; additional features present in multiple individuals included agenesis of the corpus callosum, ano-rectal malformations, seizures, and hearing or visual impairments. To evaluate the functional impact of the mutations, we measured phosphorylation at STAT1-Ser727, a known CDK8 substrate, in a CDK8 and CDK19 CRISPR double-knockout cell line transfected with wild-type (WT) or mutant CDK8 constructs. These experiments demonstrated a reduction in STAT1 phosphorylation by all mutants, in most cases to a similar extent as in a kinase-dead control. We conclude that missense mutations in CDK8 cause a developmental disorder that has phenotypic similarity to syndromes associated with mutations in other subunits of the Mediator kinase module, indicating probable overlap in pathogenic mechanisms.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | - Andrew O M Wilkie
- Clinical Genetics Group, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford OX3 9DS, UK.
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12
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Abstract
Cryptococcus neoformans is a fungal pathogen that primarily affects severely immunocompromised patients, resulting in 200,000 deaths every year. This yeast occurs in the environment and can establish disease upon inhalation into the lungs of a mammalian host. In this harsh environment it must survive engulfment by host phagocytes, including the oxidative stresses it experiences inside them. To adapt to these challenging conditions, C. neoformans deploys a variety of regulatory proteins to alter gene expression levels and enhance its ability to survive. We have elucidated the role of a protein complex that regulates the cryptococcal response to oxidative stress, survival within phagocytes, and ability to cause disease. These findings are important because they advance our understanding of cryptococcal disease, which we hope will help in the efforts to control this devastating infection. Cryptococcus neoformans kills 200,000 people worldwide each year. After inhalation, this environmental yeast proliferates either extracellularly or within host macrophages. Under conditions of immunocompromise, cryptococci disseminate from the lungs to the brain, causing a deadly meningoencephalitis that is difficult and expensive to treat. Cryptococcal adaptation to the harsh lung environment is a critical first step in its pathogenesis, and consequently a compelling topic of study. This adaptation is mediated by a complex transcriptional program that integrates cellular responses to environmental stimuli. Although several key regulators in this process have been examined, one that remains understudied in C. neoformans is the Mediator complex. In other organisms, this complex promotes transcription of specific genes by increasing assembly of the RNA polymerase II preinitiation complex. We focused on the Kinase Module of Mediator, which consists of cyclin C (Ssn801), cyclin-dependent kinase 8 (Cdk8), Med12, and Med13. This module provides important inhibitory control of Mediator complex assembly and activity. Using transcriptomics, we discovered that Cdk8 and Ssn801 together regulate cryptococcal functions such as the ability to grow on acetate and the response to oxidative stress, both of which were experimentally validated. Deletion of CDK8 yielded altered mitochondrial morphology and the dysregulation of genes involved in oxidation-reduction processes. This strain exhibited increased susceptibility to oxidative stress, resulting in an inability of mutant cells to proliferate within phagocytes, decreased lung burdens, and attenuated virulence in vivo. These findings increase our understanding of cryptococcal adaptation to the host environment and its regulation of oxidative stress resistance and virulence.
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13
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Xi M, Chen T, Wu C, Gao X, Wu Y, Luo X, Du K, Yu L, Cai T, Shen R, Sun H. CDK8 as a therapeutic target for cancers and recent developments in discovery of CDK8 inhibitors. Eur J Med Chem 2018; 164:77-91. [PMID: 30594029 DOI: 10.1016/j.ejmech.2018.11.076] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2018] [Revised: 11/08/2018] [Accepted: 11/09/2018] [Indexed: 02/08/2023]
Abstract
Cyclin-dependent kinases 8 (CDK8) regulates transcriptional process via associating with the mediator complex or phosphorylating transcription factors (TF). Overexpression of CDK8 has been observed in various cancers. It mediates aberrant activation of Wnt/β-catenin signaling pathway, which is initially recognized and best studied in colorectal cancer (CRC). CDK8 acts as an oncogene and represents a potential target for developing novel CDK8 inhibitors in cancer therapeutics. However, other study has revealed its contrary role. The function of CDK8 is context dependent. Even so, a variety of potent and selective CDK8 inhibitors have been discovered after crystal structures were resolved in two states (active or inactive). In this review, we summarize co-crystal structures, biological mechanisms, dysregulation in cancers and recent progress in the field of CDK8 inhibitors, trying to offer an outlook of CDK8 inhibitors in cancer therapy in future.
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Affiliation(s)
- Meiyang Xi
- College of Chemistry and Chemical Engineering, Shaoxing University, Shaoxing, 312000, China
| | - Tingkai Chen
- Department of Medicinal Chemistry, China Pharmaceutical University, Nanjing, 210009, China
| | - Chunlei Wu
- College of Chemistry and Chemical Engineering, Shaoxing University, Shaoxing, 312000, China
| | - Xiaozhong Gao
- College of Chemistry and Chemical Engineering, Shaoxing University, Shaoxing, 312000, China
| | - Yonghua Wu
- College of Chemistry and Chemical Engineering, Shaoxing University, Shaoxing, 312000, China
| | - Xiang Luo
- College of Chemistry and Chemical Engineering, Shaoxing University, Shaoxing, 312000, China
| | - Kui Du
- College of Chemistry and Chemical Engineering, Shaoxing University, Shaoxing, 312000, China
| | - Lemao Yu
- College of Chemistry and Chemical Engineering, Shaoxing University, Shaoxing, 312000, China
| | - Tao Cai
- College of Chemistry and Chemical Engineering, Shaoxing University, Shaoxing, 312000, China
| | - Runpu Shen
- College of Chemistry and Chemical Engineering, Shaoxing University, Shaoxing, 312000, China
| | - Haopeng Sun
- Department of Medicinal Chemistry, China Pharmaceutical University, Nanjing, 210009, China.
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14
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Chen W, Ren X, Chang CEA. Discovery of CDK8/CycC Ligands with a New Virtual Screening Tool. ChemMedChem 2018; 14:107-118. [PMID: 30403831 DOI: 10.1002/cmdc.201800559] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2018] [Revised: 11/02/2018] [Indexed: 12/15/2022]
Abstract
Selective inhibition of cyclin-dependent kinase 8 and cyclin C (CDK8/CycC) has been suggested as a promising strategy for decreasing mitogenic signals in cancer cells with reduced toxicity toward normal cells. We developed a novel virtual screening protocol for drug development and applied it to the discovery of new CDK8/CycC type II ligands, which is likely to achieve long residence time and specificity. We first analyzed the binding thermodynamics of 11 published pyrazolourea ligands using molecular dynamics simulations and a free-energy calculation method, VM2, and extracted the key binding information to assist virtual screening. The urea moiety was found to be the critical structural contributor of the reference ligands. Starting with the urea moiety, we conducted substructure-based searches with our newly developed superposition and single-point energy evaluation method, followed by free-energy calculations, and singled out three purchasable compounds for bioassay testing. The ranking from the experimental results is completely consistent with the predicted rankings. A potent drug-like compound was found to have a Kd value of 42.5 nm, which is similar to those of the most potent reference ligands; this provided a good starting point for further improvement. This study shows that our novel virtual screening protocol is an accurate and efficient tool for drug development.
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Affiliation(s)
- Wei Chen
- Department of Chemistry, University of California, Riverside, CA, 92521, USA.,ChemConsulting LLC, Frederick, MD, 21704, USA.,NanChang Lead Biotech LLC, NanChang, JiangXi, 330096, China
| | - Xiaodong Ren
- Department of Chemistry, University of California, Riverside, CA, 92521, USA
| | - Chia-En A Chang
- Department of Chemistry, University of California, Riverside, CA, 92521, USA
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15
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Using 3D-QSAR and molecular docking insight into inhibitors binding with complex-associated kinases CDK8. J Mol Struct 2018. [DOI: 10.1016/j.molstruc.2018.05.072] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
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16
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Fan Y, Sanyal S, Bruzzone R. Breaking Bad: How Viruses Subvert the Cell Cycle. Front Cell Infect Microbiol 2018; 8:396. [PMID: 30510918 PMCID: PMC6252338 DOI: 10.3389/fcimb.2018.00396] [Citation(s) in RCA: 90] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2018] [Accepted: 10/22/2018] [Indexed: 01/10/2023] Open
Abstract
Interactions between the host and viruses during the course of their co-evolution have not only shaped cellular function and the immune system, but also the counter measures employed by viruses. Relatively small genomes and high replication rates allow viruses to accumulate mutations and continuously present the host with new challenges. It is therefore, no surprise that they either escape detection or modulate host physiology, often by redirecting normal cellular pathways to their own advantage. Viruses utilize a diverse array of strategies and molecular targets to subvert host cellular processes, while evading detection. These include cell-cycle regulation, major histocompatibility complex-restricted antigen presentation, intracellular protein transport, apoptosis, cytokine-mediated signaling, and humoral immune responses. Moreover, viruses routinely manipulate the host cell cycle to create a favorable environment for replication, largely by deregulating cell cycle checkpoints. This review focuses on our current understanding of the molecular aspects of cell cycle regulation that are often targeted by viruses. Further study of their interactions should provide fundamental insights into cell cycle regulation and improve our ability to exploit these viruses.
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Affiliation(s)
- Ying Fan
- HKU-Pasteur Research Pole, LKS Faculty of Medicine, School of Public Health, The University of Hong Kong, Hong Kong, Hong Kong.,MRC Protein Phosphorylation and Ubiquitylation Unit, School of Life Sciences, University of Dundee, Dundee, United Kingdom
| | - Sumana Sanyal
- HKU-Pasteur Research Pole, LKS Faculty of Medicine, School of Public Health, The University of Hong Kong, Hong Kong, Hong Kong.,LKS Faculty of Medicine, School of Biomedical Sciences, The University of Hong Kong, Hong Kong, Hong Kong
| | - Roberto Bruzzone
- HKU-Pasteur Research Pole, LKS Faculty of Medicine, School of Public Health, The University of Hong Kong, Hong Kong, Hong Kong.,Department of Cell Biology and Infection, Institut Pasteur, Paris, France
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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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Cholko T, Chen W, Tang Z, Chang CEA. A molecular dynamics investigation of CDK8/CycC and ligand binding: conformational flexibility and implication in drug discovery. J Comput Aided Mol Des 2018; 32:671-685. [PMID: 29737445 DOI: 10.1007/s10822-018-0120-3] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/25/2017] [Accepted: 05/02/2018] [Indexed: 12/13/2022]
Abstract
Abnormal activity of cyclin-dependent kinase 8 (CDK8) along with its partner protein cyclin C (CycC) is a common feature of many diseases including colorectal cancer. Using molecular dynamics (MD) simulations, this study determined the dynamics of the CDK8-CycC system and we obtained detailed breakdowns of binding energy contributions for four type-I and five type-II CDK8 inhibitors. We revealed system motions and conformational changes that will affect ligand binding, confirmed the essentialness of CycC for inclusion in future computational studies, and provide guidance in development of CDK8 binders. We employed unbiased all-atom MD simulations for 500 ns on twelve CDK8-CycC systems, including apoproteins and protein-ligand complexes, then performed principal component analysis (PCA) and measured the RMSF of key regions to identify protein dynamics. Binding pocket volume analysis identified conformational changes that accompany ligand binding. Next, H-bond analysis, residue-wise interaction calculations, and MM/PBSA were performed to characterize protein-ligand interactions and find the binding energy. We discovered that CycC is vital for maintaining a proper conformation of CDK8 to facilitate ligand binding and that the system exhibits motion that should be carefully considered in future computational work. Surprisingly, we found that motion of the activation loop did not affect ligand binding. Type-I and type-II ligand binding is driven by van der Waals interactions, but electrostatic energy and entropic penalties affect type-II binding as well. Binding of both ligand types affects protein flexibility. Based on this we provide suggestions for development of tighter-binding CDK8 inhibitors and offer insight that can aid future computational studies.
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Affiliation(s)
- Timothy Cholko
- Department of Chemistry, University of California, Riverside, Riverside, CA, 92521, USA
| | - Wei Chen
- Department of Chemistry, University of California, Riverside, Riverside, CA, 92521, USA
| | - Zhiye Tang
- Department of Chemistry, University of California, Riverside, Riverside, CA, 92521, USA
| | - Chia-En A Chang
- Department of Chemistry, University of California, Riverside, Riverside, CA, 92521, USA.
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19
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Park MJ, Shen H, Spaeth JM, Tolvanen JH, Failor C, Knudtson JF, McLaughlin J, Halder SK, Yang Q, Bulun SE, Al-Hendy A, Schenken RS, Aaltonen LA, Boyer TG. Oncogenic exon 2 mutations in Mediator subunit MED12 disrupt allosteric activation of cyclin C-CDK8/19. J Biol Chem 2018; 293:4870-4882. [PMID: 29440396 DOI: 10.1074/jbc.ra118.001725] [Citation(s) in RCA: 43] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2018] [Revised: 01/28/2018] [Indexed: 01/26/2023] Open
Abstract
Somatic mutations in exon 2 of the RNA polymerase II transcriptional Mediator subunit MED12 occur at high frequency in uterine fibroids (UFs) and breast fibroepithelial tumors as well as recurrently, albeit less frequently, in malignant uterine leimyosarcomas, chronic lymphocytic leukemias, and colorectal cancers. Previously, we reported that UF-linked mutations in MED12 disrupt its ability to activate cyclin C (CycC)-dependent kinase 8 (CDK8) in Mediator, implicating impaired Mediator-associated CDK8 activity in the molecular pathogenesis of these clinically significant lesions. Notably, the CDK8 paralog CDK19 is also expressed in myometrium, and both CDK8 and CDK19 assemble into Mediator in a mutually exclusive manner, suggesting that CDK19 activity may also be germane to the pathogenesis of MED12 mutation-induced UFs. However, whether and how UF-linked mutations in MED12 affect CDK19 activation is unknown. Herein, we show that MED12 allosterically activates CDK19 and that UF-linked exon 2 mutations in MED12 disrupt its CDK19 stimulatory activity. Furthermore, we find that within the Mediator kinase module, MED13 directly binds to the MED12 C terminus, thereby suppressing an apparent UF mutation-induced conformational change in MED12 that otherwise disrupts its association with CycC-CDK8/19. Thus, in the presence of MED13, mutant MED12 can bind, but cannot activate, CycC-CDK8/19. These findings indicate that MED12 binding is necessary but not sufficient for CycC-CDK8/19 activation and reveal an additional step in the MED12-dependent activation process, one critically dependent on MED12 residues altered by UF-linked exon 2 mutations. These findings confirm that UF-linked mutations in MED12 disrupt composite Mediator-associated kinase activity and identify CDK8/19 as prospective therapeutic targets in UFs.
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Affiliation(s)
- Min Ju Park
- Departments of Molecular Medicine, San Antonio, Texas 78229
| | - Hailian Shen
- Departments of Molecular Medicine, San Antonio, Texas 78229
| | - Jason M Spaeth
- Departments of Molecular Medicine, San Antonio, Texas 78229
| | - Jaana H Tolvanen
- Genome-Scale Biology Program and Department of Medical Genetics, Haartman Institute, University of Helsinki, Biomedicum, P.O. Box 63 (Haartmaninkatu 8), Helsinki FIN-00014, Finland
| | - Courtney Failor
- Obstetrics and Gynecology, University of Texas Health Science Center at San Antonio, San Antonio, Texas 78229
| | - Jennifer F Knudtson
- Obstetrics and Gynecology, University of Texas Health Science Center at San Antonio, San Antonio, Texas 78229
| | - Jessica McLaughlin
- Obstetrics and Gynecology, University of Texas Health Science Center at San Antonio, San Antonio, Texas 78229
| | - Sunil K Halder
- Department of Obstetrics and Gynecology, Augusta University, Augusta, Georgia 30912
| | - Qiwei Yang
- Department of Obstetrics and Gynecology, Augusta University, Augusta, Georgia 30912
| | - Serdar E Bulun
- Department of Obstetrics and Gynecology, Northwestern University Feinberg School of Medicine, Chicago, Illinois 60611
| | - Ayman Al-Hendy
- Department of Obstetrics and Gynecology, Augusta University, Augusta, Georgia 30912
| | - Robert S Schenken
- Obstetrics and Gynecology, University of Texas Health Science Center at San Antonio, San Antonio, Texas 78229
| | - Lauri A Aaltonen
- Genome-Scale Biology Program and Department of Medical Genetics, Haartman Institute, University of Helsinki, Biomedicum, P.O. Box 63 (Haartmaninkatu 8), Helsinki FIN-00014, Finland
| | - Thomas G Boyer
- Departments of Molecular Medicine, San Antonio, Texas 78229.
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20
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Philip S, Kumarasiri M, Teo T, Yu M, Wang S. Cyclin-Dependent Kinase 8: A New Hope in Targeted Cancer Therapy? J Med Chem 2018; 61:5073-5092. [PMID: 29266937 DOI: 10.1021/acs.jmedchem.7b00901] [Citation(s) in RCA: 68] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Cyclin-dependent kinase 8 (CDK8) plays a vital role in regulating transcription either through its association with the Mediator complex or by phosphorylating transcription factors. Myriads of genetic and biochemical studies have established CDK8 as a key oncogenic driver in many cancers. Specifically, CDK8-mediated activation of oncogenic Wnt-β-catenin signaling, transcription of estrogen-inducible genes, and suppression of super enhancer-associated genes contributes to oncogenesis in colorectal, breast, and hematological malignancies, respectively. However, while most research supports the role of CDK8 as an oncogene, other work has raised the possibility of its contrary function. The diverse biological functions of CDK8 and its seemingly context-specific roles in different types of cancers have spurred a great amount of interest and perhaps an even greater amount of controversy in the development of CDK8 inhibitors as potential cancer therapeutic agents. Herein, we review the latest landscape of CDK8 biology and its involvement in carcinogenesis. We dissect current efforts in discovering CDK8 inhibitors and attempt to provide an outlook at the future of CDK8-targeted cancer therapies.
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Affiliation(s)
- Stephen Philip
- 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 5001 , Australia
| | - Malika Kumarasiri
- 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 5001 , Australia
| | - 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 5001 , Australia
| | - Mingfeng Yu
- 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 5001 , Australia
| | - 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 5001 , Australia
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21
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Hall DD, Ponce JM, Chen B, Spitler KM, Alexia A, Oudit GY, Song LS, Grueter CE. Ectopic expression of Cdk8 induces eccentric hypertrophy and heart failure. JCI Insight 2017; 2:92476. [PMID: 28768905 DOI: 10.1172/jci.insight.92476] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2016] [Accepted: 06/20/2017] [Indexed: 11/17/2022] Open
Abstract
Widespread changes in cardiac gene expression occur during heart failure, yet the mechanisms responsible for coordinating these changes remain poorly understood. The Mediator complex represents a nodal point for modulating transcription by bridging chromatin-bound transcription factors with RNA polymerase II activity; it is reversibly regulated by its cyclin-dependent kinase 8 (Cdk8) kinase submodule. Here, we identified increased Cdk8 protein expression in human failing heart explants and determined the consequence of this increase in cardiac-specific Cdk8-expressing mice. Transgenic Cdk8 overexpression resulted in progressive dilated cardiomyopathy, heart failure, and premature lethality. Prior to functional decline, left ventricular cardiomyocytes were dramatically elongated, with disorganized transverse tubules and dysfunctional calcium handling. RNA sequencing results showed that myofilament gene isoforms not typically expressed in adult cardiomyocytes were enriched, while oxidative phosphorylation and fatty acid biosynthesis genes were downregulated. Interestingly, candidate upstream transcription factor expression levels and MAPK signaling pathways thought to determine cardiomyocyte size remained relatively unaffected, suggesting that Cdk8 functions within a novel growth regulatory pathway. Our findings show that manipulating cardiac gene expression through increased Cdk8 levels is detrimental to the heart by establishing a transcriptional program that induces pathological remodeling and eccentric hypertrophy culminating in heart failure.
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Affiliation(s)
- Duane D Hall
- Department of Internal Medicine, Division of Cardiovascular Medicine, Francois M. Abboud Cardiovascular Research Center, Fraternal Order of Eagles Diabetes Research Center, University of Iowa, Iowa City, Iowa, USA
| | - Jessica M Ponce
- Department of Internal Medicine, Division of Cardiovascular Medicine, Francois M. Abboud Cardiovascular Research Center, Fraternal Order of Eagles Diabetes Research Center, University of Iowa, Iowa City, Iowa, USA
| | - Biyi Chen
- Department of Internal Medicine, Division of Cardiovascular Medicine, Francois M. Abboud Cardiovascular Research Center, Fraternal Order of Eagles Diabetes Research Center, University of Iowa, Iowa City, Iowa, USA
| | - Kathryn M Spitler
- Department of Internal Medicine, Division of Cardiovascular Medicine, Francois M. Abboud Cardiovascular Research Center, Fraternal Order of Eagles Diabetes Research Center, University of Iowa, Iowa City, Iowa, USA
| | - Adrianne Alexia
- Department of Internal Medicine, Division of Cardiovascular Medicine, Francois M. Abboud Cardiovascular Research Center, Fraternal Order of Eagles Diabetes Research Center, University of Iowa, Iowa City, Iowa, USA
| | - Gavin Y Oudit
- Department of Medicine, University of Alberta, Edmonton, Alberta, Canada
| | - Long-Sheng Song
- Department of Internal Medicine, Division of Cardiovascular Medicine, Francois M. Abboud Cardiovascular Research Center, Fraternal Order of Eagles Diabetes Research Center, University of Iowa, Iowa City, Iowa, USA
| | - Chad E Grueter
- Department of Internal Medicine, Division of Cardiovascular Medicine, Francois M. Abboud Cardiovascular Research Center, Fraternal Order of Eagles Diabetes Research Center, University of Iowa, Iowa City, Iowa, USA
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22
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Fujimoto J, Hirayama T, Hirata Y, Hikichi Y, Murai S, Hasegawa M, Hasegawa Y, Yonemori K, Hata A, Aoyama K, Cary DR. Studies of CDK 8/19 inhibitors: Discovery of novel and selective CDK8/19 dual inhibitors and elimination of their CYP3A4 time-dependent inhibition potential. Bioorg Med Chem 2017; 25:3018-3033. [DOI: 10.1016/j.bmc.2017.03.049] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2016] [Revised: 02/19/2017] [Accepted: 03/22/2017] [Indexed: 12/13/2022]
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23
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Ono K, Banno H, Okaniwa M, Hirayama T, Iwamura N, Hikichi Y, Murai S, Hasegawa M, Hasegawa Y, Yonemori K, Hata A, Aoyama K, Cary DR. Design and synthesis of selective CDK8/19 dual inhibitors: Discovery of 4,5-dihydrothieno[3′,4′:3,4]benzo[1,2- d ]isothiazole derivatives. Bioorg Med Chem 2017; 25:2336-2350. [DOI: 10.1016/j.bmc.2017.02.038] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2016] [Revised: 02/17/2017] [Accepted: 02/17/2017] [Indexed: 12/29/2022]
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24
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miR-18a counteracts AKT and ERK activation to inhibit the proliferation of pancreatic progenitor cells. Sci Rep 2017; 7:45002. [PMID: 28332553 PMCID: PMC5362961 DOI: 10.1038/srep45002] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2016] [Accepted: 02/17/2017] [Indexed: 12/19/2022] Open
Abstract
Activation of endogenous stem/progenitor cells to repair injured tissues is an ideal option for disease treatment. However, adult pancreatic progenitor cells remain in a quiescent state in vivo. Thus, it is difficult to stimulate proliferation and differentiation in these progenitor cells, and the cause remains elusive. miR-17-92 cluster miRNAs are highly conserved in mammals and are expressed in multiple tissue stem/progenitor cells, but their role in pancreatic progenitor cells are less well known. In the present study, we demonstrate that miR-18a, but not the other members of the miR-17-92 gene cluster, inhibits the proliferation of pancreatic progenitor cells in vitro and ex vivo. miR-18a inhibits proliferation of adult pancreatic progenitor cells through arresting the cell cycle at G1 stage, indicating that miR-18a plays a role in keeping the adult pancreatic progenitor cells in quiescence. miR-18a inhibits pancreatic progenitor proliferation by targeting the gene expressions of connective tissue growth factor (CTGF), neural precursor cell expressed, developmentally down-regulated 9 (Nedd9), and cyclin dependent kinase 19 (CDK19), as well as by suppressing activation of the proliferation-related signaling pathways phosphatidylinositol 3-kinase–protein kinase B (PI3K/AKT) and extracellular signal-regulated kinase (ERK).
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25
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Yamamoto S, Hagihara T, Horiuchi Y, Okui A, Wani S, Yoshida T, Inoue T, Tanaka A, Ito T, Hirose Y, Ohkuma Y. Mediator cyclin-dependent kinases upregulate transcription of inflammatory genes in cooperation with NF-κB and C/EBPβ on stimulation of Toll-like receptor 9. Genes Cells 2017; 22:265-276. [PMID: 28151579 DOI: 10.1111/gtc.12475] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2016] [Accepted: 12/27/2016] [Indexed: 12/17/2022]
Abstract
In eukaryotes, the Mediator complex has important roles in regulation of transcription by RNA polymerase II. Mediator is a large complex with more than 20 subunits that form head, middle, tail and CDK/cyclin modules. Among them, CDK8 and/or CDK19 (CDK8/19), and their counterpart cyclin C, form the CDK/cyclin module together with Mediator subunits MED12 and MED13. Despite evidences of both activation and repression, the precise functional roles of CDK8/19 in transcription are still elusive. Our previous results indicate that CDK8/19 recruits epigenetic regulators to repress immunoresponse genes. Here, this study focused on Toll-like receptors (TLRs), which exert innate immune responses through recognition of pathogen-associated molecular patterns and examined the functional roles of CDK8/19. As a result, CDK8/19 regulated transcription of inflammatory genes on stimulation of TLR9 in myeloma-derived RPMI8226 cells, which led to expression of inflammation-associated genes such as IL8, IL10, PTX3 and CCL2. Mediator subunits CDK8/19 and MED1, inflammation-related transcriptional activator NF-κB and C/EBPβ, and general transcription factors TFIIE and TFIIB colocalized at the promoter regions of these genes under this condition. Our results show that CDK8/19 positively regulates inflammatory gene transcription in cooperation with NF-κB and C/EBPβ on stimulation of TLR9.
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Affiliation(s)
- Seiji Yamamoto
- Laboratory of Gene Regulation, Graduate School of Medicine and Pharmaceutical Sciences, University of Toyama, 2630 Sugitani, Toyama, 930-0194, Japan.,Research and Development Center, Fuso Pharmaceutical Industries, LTD., 2-3-30 Morinomiya, Joto-ku, Osaka, 536-8523, Japan
| | - Tomoko Hagihara
- Research and Development Center, Fuso Pharmaceutical Industries, LTD., 2-3-30 Morinomiya, Joto-ku, Osaka, 536-8523, Japan
| | - Yoshiyuki Horiuchi
- Research and Development Center, Fuso Pharmaceutical Industries, LTD., 2-3-30 Morinomiya, Joto-ku, Osaka, 536-8523, Japan
| | - Akira Okui
- Research and Development Center, Fuso Pharmaceutical Industries, LTD., 2-3-30 Morinomiya, Joto-ku, Osaka, 536-8523, Japan
| | - Shotaro Wani
- Laboratory of Gene Regulation, Graduate School of Medicine and Pharmaceutical Sciences, University of Toyama, 2630 Sugitani, Toyama, 930-0194, Japan
| | - Tokuyuki Yoshida
- Division of Molecular Target and Gene Therapy Products, National Institute of Health Sciences, 1-18-1 Kamiyoga, Setagaya-ku, Tokyo, 153-8501, Japan
| | - Takao Inoue
- Division of Molecular Target and Gene Therapy Products, National Institute of Health Sciences, 1-18-1 Kamiyoga, Setagaya-ku, Tokyo, 153-8501, Japan
| | - Aki Tanaka
- Laboratory of Gene Regulation, Graduate School of Medicine and Pharmaceutical Sciences, University of Toyama, 2630 Sugitani, Toyama, 930-0194, Japan
| | - Takashi Ito
- Department of Biochemistry, Nagasaki University School of Medicine, 1-12-4 Sakamoto, Nagasaki, 852-8523, Japan
| | - Yutaka Hirose
- Laboratory of Gene Regulation, Graduate School of Medicine and Pharmaceutical Sciences, University of Toyama, 2630 Sugitani, Toyama, 930-0194, Japan
| | - Yoshiaki Ohkuma
- Laboratory of Gene Regulation, Graduate School of Medicine and Pharmaceutical Sciences, University of Toyama, 2630 Sugitani, Toyama, 930-0194, Japan.,Department of Biochemistry, Nagasaki University School of Medicine, 1-12-4 Sakamoto, Nagasaki, 852-8523, Japan
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26
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McCurdy SR, Pacal M, Ahmad M, Bremner R. A CDK2 activity signature predicts outcome in CDK2-low cancers. Oncogene 2016; 36:2491-2502. [DOI: 10.1038/onc.2016.409] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2016] [Revised: 08/30/2016] [Accepted: 09/23/2016] [Indexed: 12/21/2022]
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27
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Regulation of metabolism by the Mediator complex. BIOPHYSICS REPORTS 2016; 2:69-77. [PMID: 28018965 PMCID: PMC5138257 DOI: 10.1007/s41048-016-0031-6] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2016] [Accepted: 02/15/2016] [Indexed: 01/11/2023] Open
Abstract
The Mediator complex was originally discovered in yeast, but it is conserved in all eukaryotes. Its best-known function is to regulate RNA polymerase II-dependent gene transcription. Although the mechanisms by which the Mediator complex regulates transcription are often complicated by the context-dependent regulation, this transcription cofactor complex plays a pivotal role in numerous biological pathways. Biochemical, molecular, and physiological studies using cancer cell lines or model organisms have established the current paradigm of the Mediator functions. However, the physiological roles of the mammalian Mediator complex remain poorly defined, but have attracted a great interest in recent years. In this short review, we will summarize some of the reported functions of selective Mediator subunits in the regulation of metabolism. These intriguing findings suggest that the Mediator complex may be an important player in nutrient sensing and energy balance in mammals.
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28
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Czodrowski P, Mallinger A, Wienke D, Esdar C, Pöschke O, Busch M, Rohdich F, Eccles SA, Ortiz-Ruiz MJ, Schneider R, Raynaud FI, Clarke PA, Musil D, Schwarz D, Dale T, Urbahns K, Blagg J, Schiemann K. Structure-Based Optimization of Potent, Selective, and Orally Bioavailable CDK8 Inhibitors Discovered by High-Throughput Screening. J Med Chem 2016; 59:9337-9349. [PMID: 27490956 DOI: 10.1021/acs.jmedchem.6b00597] [Citation(s) in RCA: 74] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
The mediator complex-associated cyclin dependent kinase CDK8 regulates β-catenin-dependent transcription following activation of WNT signaling. Multiple lines of evidence suggest CDK8 may act as an oncogene in the development of colorectal cancer. Here we describe the successful optimization of an imidazo-thiadiazole series of CDK8 inhibitors that was identified in a high-throughput screening campaign and further progressed by structure-based design. In several optimization cycles, we improved the microsomal stability, potency, and kinase selectivity. The initial imidazo-thiadiazole scaffold was replaced by a 3-methyl-1H-pyrazolo[3,4-b]-pyridine which resulted in compound 25 (MSC2530818) that displayed excellent kinase selectivity, biochemical and cellular potency, microsomal stability, and is orally bioavailable. Furthermore, we demonstrated modulation of phospho-STAT1, a pharmacodynamic biomarker of CDK8 activity, and tumor growth inhibition in an APC mutant SW620 human colorectal carcinoma xenograft model after oral administration. Compound 25 demonstrated suitable potency and selectivity to progress into preclinical in vivo efficacy and safety studies.
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Affiliation(s)
- Paul Czodrowski
- Merck KGaA , Frankfurter Strasse 250, Darmstadt, 64293, Germany
| | - Aurélie Mallinger
- Cancer Research UK Cancer Therapeutics Unit at The Institute of Cancer Research , London, SW7 3RP, U.K
| | - Dirk Wienke
- Merck KGaA , Frankfurter Strasse 250, Darmstadt, 64293, Germany
| | - Christina Esdar
- Merck KGaA , Frankfurter Strasse 250, Darmstadt, 64293, Germany
| | - Oliver Pöschke
- Merck KGaA , Frankfurter Strasse 250, Darmstadt, 64293, Germany
| | - Michael Busch
- Merck KGaA , Frankfurter Strasse 250, Darmstadt, 64293, Germany
| | - Felix Rohdich
- Merck KGaA , Frankfurter Strasse 250, Darmstadt, 64293, Germany
| | - Suzanne A Eccles
- Cancer Research UK Cancer Therapeutics Unit at The Institute of Cancer Research , London, SW7 3RP, U.K
| | - Maria-Jesus Ortiz-Ruiz
- Cancer Research UK Cancer Therapeutics Unit at The Institute of Cancer Research , London, SW7 3RP, U.K
| | | | - Florence I Raynaud
- Cancer Research UK Cancer Therapeutics Unit at The Institute of Cancer Research , London, SW7 3RP, U.K
| | - Paul A Clarke
- Cancer Research UK Cancer Therapeutics Unit at The Institute of Cancer Research , London, SW7 3RP, U.K
| | - Djordje Musil
- Merck KGaA , Frankfurter Strasse 250, Darmstadt, 64293, Germany
| | - Daniel Schwarz
- Merck KGaA , Frankfurter Strasse 250, Darmstadt, 64293, Germany
| | - Trevor Dale
- School of Bioscience, Cardiff University , Cardiff, CF10 3AX, U.K
| | - Klaus Urbahns
- Merck KGaA , Frankfurter Strasse 250, Darmstadt, 64293, Germany
| | - Julian Blagg
- Cancer Research UK Cancer Therapeutics Unit at The Institute of Cancer Research , London, SW7 3RP, U.K
| | - Kai Schiemann
- Merck KGaA , Frankfurter Strasse 250, Darmstadt, 64293, Germany
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29
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Kim NH, Livi CB, Yew PR, Boyer TG. Mediator subunit Med12 contributes to the maintenance of neural stem cell identity. BMC DEVELOPMENTAL BIOLOGY 2016; 16:17. [PMID: 27188461 PMCID: PMC4869265 DOI: 10.1186/s12861-016-0114-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/06/2016] [Accepted: 05/08/2016] [Indexed: 12/22/2022]
Abstract
BACKGROUND The RNA polymerase II transcriptional Mediator subunit Med12 is broadly implicated in vertebrate brain development, and genetic variation in human MED12 is associated with X-linked intellectual disability and neuropsychiatric disorders. Although prior studies have begun to elaborate the functional contribution of Med12 within key neurodevelopmental pathways, a more complete description of Med12 function in the developing nervous system, including the specific biological networks and cellular processes under its regulatory influence, remains to be established. Herein, we sought to clarify the global contribution of Med12 to neural stem cell (NSC) biology through unbiased transcriptome profiling of mouse embryonic stem (ES) cell-derived NSCs following RNAi-mediated Med12 depletion. RESULTS A total of 240 genes (177 up, 73 down) were differentially expressed in Med12-knockdown versus control mouse NS-5 (mNS-5) NSCs. Gene set enrichment analysis revealed Med12 to be prominently linked with "cell-to-cell interaction" and "cell cycle" networks, and subsequent functional studies confirmed these associations. Targeted depletion of Med12 led to enhanced NSC adhesion and upregulation of cell adhesion genes, including Syndecan 2 (Sdc2). Concomitant depletion of both Sdc2 and Med12 reversed enhanced cell adhesion triggered by Med12 knockdown alone, confirming that Med12 negatively regulates NSC cell adhesion by suppressing the expression of cell adhesion molecules. Med12-mediated suppression of NSC adhesion is a dynamically regulated process in vitro, enforced in self-renewing NSCs and alleviated during the course of neuronal differentiation. Accordingly, Med12 depletion enhanced adhesion and prolonged survival of mNS-5 NSCs induced to differentiate on gelatin, effects that were bypassed completely by growth on laminin. On the other hand, Med12 depletion in mNS-5 NSCs led to reduced expression of G1/S phase cell cycle regulators and a concordant G1/S phase cell cycle block without evidence of apoptosis, resulting in a severe proliferation defect. CONCLUSIONS Med12 contributes to the maintenance of NSC identity through a functionally bipartite role in suppression and activation of gene expression programs dedicated to cell adhesion and G1/S phase cell cycle progression, respectively. Med12 may thus contribute to the regulatory apparatus that controls the balance between NSC self-renewal and differentiation, with important implications for MED12-linked neurodevelopmental disorders.
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Affiliation(s)
- Nam Hee Kim
- Department of Molecular Medicine and Institute of Biotechnology, The University of Texas Health Science Center at San Antonio, San Antonio, TX, 78229-3900, USA
| | - Carolina B Livi
- Department of Molecular Medicine and Institute of Biotechnology, The University of Texas Health Science Center at San Antonio, San Antonio, TX, 78229-3900, USA
- Agilent Technologies, Portland, OR, 97224-7154, USA
| | - P Renee Yew
- Department of Molecular Medicine and Institute of Biotechnology, The University of Texas Health Science Center at San Antonio, San Antonio, TX, 78229-3900, USA
| | - Thomas G Boyer
- Department of Molecular Medicine and Institute of Biotechnology, The University of Texas Health Science Center at San Antonio, San Antonio, TX, 78229-3900, USA.
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30
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Koehler MFT, Bergeron P, Blackwood EM, Bowman K, Clark KR, Firestein R, Kiefer JR, Maskos K, McCleland ML, Orren L, Salphati L, Schmidt S, Schneider EV, Wu J, Beresini MH. Development of a Potent, Specific CDK8 Kinase Inhibitor Which Phenocopies CDK8/19 Knockout Cells. ACS Med Chem Lett 2016; 7:223-8. [PMID: 26985305 DOI: 10.1021/acsmedchemlett.5b00278] [Citation(s) in RCA: 61] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2015] [Accepted: 01/06/2016] [Indexed: 12/30/2022] Open
Abstract
Beginning with promiscuous COT inhibitors, which were found to inhibit CDK8, a series of 6-aza-benzothiophene containing compounds were developed into potent, selective CDK8 inhibitors. When cocrystallized with CDK8 and cyclin C, these compounds exhibit an unusual binding mode, making a single hydrogen bond to the hinge residue A100, a second to K252, and a key cation-π interaction with R356. Structure-based drug design resulted in tool compounds 13 and 32, which are highly potent, kinase selective, permeable compounds with a free fraction >2% and no measurable efflux. Despite these attractive properties, these compounds exhibit weak antiproliferative activity in the HCT-116 colon cancer cell line. Further examination of the activity of 32 in this cell line revealed that the compound reduced phosphorylation of the known CDK8 substrate STAT1 in a manner identical to a CDK8 knockout clone, illustrating the complex effects of inhibition of CDK8 kinase activity in proliferation in these cells.
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Affiliation(s)
| | | | | | | | | | | | | | - Klaus Maskos
- Proteros Biostructures GmbH, Bunsenstr. 7a, D-82152 Martinsried, Germany
| | | | | | | | | | - Elisabeth V. Schneider
- Proteros Biostructures GmbH, Bunsenstr. 7a, D-82152 Martinsried, Germany
- Max-Planck-Institut für Biochemie, Am Klopferspitz 18a, D-82152 Martinsried, Germany
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31
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Schiemann K, Mallinger A, Wienke D, Esdar C, Poeschke O, Busch M, Rohdich F, Eccles SA, Schneider R, Raynaud FI, Czodrowski P, Musil D, Schwarz D, Urbahns K, Blagg J. Discovery of potent and selective CDK8 inhibitors from an HSP90 pharmacophore. Bioorg Med Chem Lett 2016; 26:1443-51. [DOI: 10.1016/j.bmcl.2016.01.062] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2015] [Revised: 01/18/2016] [Accepted: 01/21/2016] [Indexed: 12/28/2022]
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32
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Mallinger A, Schiemann K, Rink C, Stieber F, Calderini M, Crumpler S, Stubbs M, Adeniji-Popoola O, Poeschke O, Busch M, Czodrowski P, Musil D, Schwarz D, Ortiz-Ruiz MJ, Schneider R, Thai C, Valenti M, de Haven Brandon A, Burke R, Workman P, Dale T, Wienke D, Clarke PA, Esdar C, Raynaud FI, Eccles SA, Rohdich F, Blagg J. Discovery of Potent, Selective, and Orally Bioavailable Small-Molecule Modulators of the Mediator Complex-Associated Kinases CDK8 and CDK19. J Med Chem 2016; 59:1078-101. [PMID: 26796641 PMCID: PMC5362750 DOI: 10.1021/acs.jmedchem.5b01685] [Citation(s) in RCA: 77] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
![]()
The
Mediator complex-associated cyclin-dependent kinase CDK8 has
been implicated in human disease, particularly in colorectal cancer
where it has been reported as a putative oncogene. Here we report
the discovery of 109 (CCT251921), a potent, selective,
and orally bioavailable inhibitor of CDK8 with equipotent affinity
for CDK19. We describe a structure-based design approach leading to
the discovery of a 3,4,5-trisubstituted-2-aminopyridine series and
present the application of physicochemical property analyses to successfully
reduce in vivo metabolic clearance, minimize transporter-mediated
biliary elimination while maintaining acceptable aqueous solubility.
Compound 109 affords the optimal compromise of in vitro
biochemical, pharmacokinetic, and physicochemical properties and is
suitable for progression to animal models of cancer.
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Affiliation(s)
- Aurélie Mallinger
- Cancer Research UK Cancer Therapeutics Unit at The Institute of Cancer Research, London, SW7 3RP, U.K
| | | | - Christian Rink
- Cancer Research UK Cancer Therapeutics Unit at The Institute of Cancer Research, London, SW7 3RP, U.K
| | | | | | - Simon Crumpler
- Cancer Research UK Cancer Therapeutics Unit at The Institute of Cancer Research, London, SW7 3RP, U.K
| | - Mark Stubbs
- Cancer Research UK Cancer Therapeutics Unit at The Institute of Cancer Research, London, SW7 3RP, U.K
| | - Olajumoke Adeniji-Popoola
- Cancer Research UK Cancer Therapeutics Unit at The Institute of Cancer Research, London, SW7 3RP, U.K
| | | | | | | | | | | | - Maria-Jesus Ortiz-Ruiz
- Cancer Research UK Cancer Therapeutics Unit at The Institute of Cancer Research, London, SW7 3RP, U.K
| | | | - Ching Thai
- Cancer Research UK Cancer Therapeutics Unit at The Institute of Cancer Research, London, SW7 3RP, U.K
| | - Melanie Valenti
- Cancer Research UK Cancer Therapeutics Unit at The Institute of Cancer Research, London, SW7 3RP, U.K
| | - Alexis de Haven Brandon
- Cancer Research UK Cancer Therapeutics Unit at The Institute of Cancer Research, London, SW7 3RP, U.K
| | - Rosemary Burke
- Cancer Research UK Cancer Therapeutics Unit at The Institute of Cancer Research, London, SW7 3RP, U.K
| | - Paul Workman
- Cancer Research UK Cancer Therapeutics Unit at The Institute of Cancer Research, London, SW7 3RP, U.K
| | - Trevor Dale
- School of Bioscience, Cardiff University , Cardiff, CF10 3AX, U.K
| | | | - Paul A Clarke
- Cancer Research UK Cancer Therapeutics Unit at The Institute of Cancer Research, London, SW7 3RP, U.K
| | | | - Florence I Raynaud
- Cancer Research UK Cancer Therapeutics Unit at The Institute of Cancer Research, London, SW7 3RP, U.K
| | - Suzanne A Eccles
- Cancer Research UK Cancer Therapeutics Unit at The Institute of Cancer Research, London, SW7 3RP, U.K
| | | | - Julian Blagg
- Cancer Research UK Cancer Therapeutics Unit at The Institute of Cancer Research, London, SW7 3RP, U.K
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33
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Clark AD, Oldenbroek M, Boyer TG. Mediator kinase module and human tumorigenesis. Crit Rev Biochem Mol Biol 2015; 50:393-426. [PMID: 26182352 DOI: 10.3109/10409238.2015.1064854] [Citation(s) in RCA: 59] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Mediator is a conserved multi-subunit signal processor through which regulatory informatiosn conveyed by gene-specific transcription factors is transduced to RNA Polymerase II (Pol II). In humans, MED13, MED12, CDK8 and Cyclin C (CycC) comprise a four-subunit "kinase" module that exists in variable association with a 26-subunit Mediator core. Genetic and biochemical studies have established the Mediator kinase module as a major ingress of developmental and oncogenic signaling through Mediator, and much of its function in signal-dependent gene regulation derives from its resident CDK8 kinase activity. For example, CDK8-targeted substrate phosphorylation impacts transcription factor half-life, Pol II activity and chromatin chemistry and functional status. Recent structural and biochemical studies have revealed a precise network of physical and functional subunit interactions required for proper kinase module activity. Accordingly, pathologic change in this activity through altered expression or mutation of constituent kinase module subunits can have profound consequences for altered signaling and tumor formation. Herein, we review the structural organization, biological function and oncogenic potential of the Mediator kinase module. We focus principally on tumor-associated alterations in kinase module subunits for which mechanistic relationships as opposed to strictly correlative associations are established. These considerations point to an emerging picture of the Mediator kinase module as an oncogenic unit, one in which pathogenic activation/deactivation through component change drives tumor formation through perturbation of signal-dependent gene regulation. It follows that therapeutic strategies to combat CDK8-driven tumors will involve targeted modulation of CDK8 activity or pharmacologic manipulation of dysregulated CDK8-dependent signaling pathways.
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Affiliation(s)
- Alison D Clark
- a Department of Molecular Medicine , Institute of Biotechnology, University of Texas Health Science Center at San Antonio , San Antonio , TX , USA
| | - Marieke Oldenbroek
- a Department of Molecular Medicine , Institute of Biotechnology, University of Texas Health Science Center at San Antonio , San Antonio , TX , USA
| | - Thomas G Boyer
- a Department of Molecular Medicine , Institute of Biotechnology, University of Texas Health Science Center at San Antonio , San Antonio , TX , USA
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34
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Rzymski T, Mikula M, Wiklik K, Brzózka K. CDK8 kinase--An emerging target in targeted cancer therapy. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2015; 1854:1617-29. [PMID: 26006748 DOI: 10.1016/j.bbapap.2015.05.011] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/18/2015] [Revised: 05/15/2015] [Accepted: 05/16/2015] [Indexed: 12/31/2022]
Abstract
Cyclin-dependent kinase (CDK) inhibitors have been developed as potential anticancer therapeutics and several nonselective compounds are currently in advanced clinical trials. This review is focused on the key biological roles of CDK8 kinase, which provide a proof-of-principle for continued efforts toward effective cancer treatment, targeting activity of this CDK family member. Among currently identified kinase inhibitors, several displayed significant selectivity for CDK8 and notably the effectiveness in targeting cancer specific gene expression programs. Structural features of CDK8 and available ligands were discussed from a perspective of the rational drug design process. Current state of the art confirms that further development of CDK8 inhibitors will translate into targeted therapies in oncology. This article is part of a Special Issue entitled:Inhibitors of Protein Kinases.
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Affiliation(s)
| | - Michał Mikula
- Maria Sklodowska-Curie Memorial Cancer Center and Institute of Oncology, Warsaw, Poland
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35
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Fukasawa R, Iida S, Tsutsui T, Hirose Y, Ohkuma Y. Mediator complex cooperatively regulates transcription of retinoic acid target genes with Polycomb Repressive Complex 2 during neuronal differentiation. J Biochem 2015; 158:373-84. [PMID: 26002960 DOI: 10.1093/jb/mvv055] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2015] [Accepted: 04/07/2015] [Indexed: 02/05/2023] Open
Abstract
The Mediator complex (Mediator) plays key roles in transcription and functions as the nexus for integration of various transcriptional signals. Previously, we screened for Mediator cyclin-dependent kinase (CDK)-interacting factors and identified three proteins related to chromatin regulation. One of them, SUZ12 is required for both stability and activity of Polycomb Repressive Complex 2 (PRC2). PRC2 primarily suppresses gene expression through histone H3 lysine 27 trimethylation, resulting in stem cell maintenance and differentiation; perturbation of this process leads to oncogenesis. Recent work showed that Mediator contributes to the embryonic stem cell state through DNA loop formation, which is strongly associated with chromatin architecture; however, it remains unclear how Mediator regulates gene expression in cooperation with chromatin regulators (i.e. writers, readers and remodelers). We found that Mediator CDKs interact directly with the PRC2 subunit EZH2, as well as SUZ12. Known PRC2 target genes were deregulated by Mediator CDK knockdown during neuronal differentiation, and both Mediator and PRC2 complexes co-occupied the promoters of developmental genes regulated by retinoic acid. Our results provide a mechanistic link between Mediator and PRC2 during neuronal differentiation.
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Affiliation(s)
- Rikiya Fukasawa
- Laboratory of Gene Regulation, Graduate School of Medicine and Pharmaceutical Sciences, University of Toyama, 2630 Sugitani, Toyama 930-0194, Japan
| | - Satoshi Iida
- Laboratory of Gene Regulation, Graduate School of Medicine and Pharmaceutical Sciences, University of Toyama, 2630 Sugitani, Toyama 930-0194, Japan
| | - Taiki Tsutsui
- Laboratory of Gene Regulation, Graduate School of Medicine and Pharmaceutical Sciences, University of Toyama, 2630 Sugitani, Toyama 930-0194, Japan; Department of Cellular and Molecular Medicine, UCSD School of Medicine, 9500 Gilman Drive, La Jolla, California 92093, USA; and
| | - Yutaka Hirose
- Laboratory of Gene Regulation, Graduate School of Medicine and Pharmaceutical Sciences, University of Toyama, 2630 Sugitani, Toyama 930-0194, Japan
| | - Yoshiaki Ohkuma
- Laboratory of Gene Regulation, Graduate School of Medicine and Pharmaceutical Sciences, University of Toyama, 2630 Sugitani, Toyama 930-0194, Japan; Department of Biochemistry, Nagasaki University School of Medicine, 1-12-4 Sakamoto, Nagasaki 852-8523, Japan
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Broude EV, Győrffy B, Chumanevich AA, Chen M, McDermott MSJ, Shtutman M, Catroppo JF, Roninson IB. Expression of CDK8 and CDK8-interacting Genes as Potential Biomarkers in Breast Cancer. Curr Cancer Drug Targets 2015; 15:739-49. [PMID: 26452386 PMCID: PMC4755306 DOI: 10.2174/156800961508151001105814] [Citation(s) in RCA: 56] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2015] [Revised: 06/28/2015] [Accepted: 06/28/2015] [Indexed: 12/18/2022]
Abstract
CDK8 and its paralog CDK19, in complex with CCNC, MED12 and MED13, are transcriptional regulators that mediate several carcinogenic pathways and the chemotherapy-induced tumor-supporting paracrine network. Following up on our previous observation that CDK8, CDK19 and CCNC RNA expression is associated with shorter relapse-free survival (RFS) in breast cancer, we now found by immunohistochemical analysis that CDK8/19 protein is overexpressed in invasive ductal carcinomas relative to non-malignant mammary tissues. Meta-analysis of transcriptomic data revealed that higher CDK8 expression is associated with shorter RFS in all molecular subtypes of breast cancer. These correlations were much stronger in patients who underwent systemic adjuvant therapy, suggesting that CDK8 impacts the failure of systemic therapy. The same associations were found for CDK19, CCNC and MED13. In contrast, MED12 showed the opposite association with a longer RFS. The expression levels of CDK8 in breast cancer samples were directly correlated with the expression of MYC, as well as CDK19, CCNC and MED13 but inversely correlated with MED12. CDK8, CDK19 and CCNC expression was strongly increased and MED12 expression was decreased in tumors with mutant p53. Gene amplification is the most frequent type of genetic alterations of CDK8, CDK19, CCNC and MED13 in breast cancers (9.7% of which have amplified MED13), whereas point mutations are more common in MED12. These results suggest that the expression of CDK8 and its interactive genes has a profound impact on the response to adjuvant therapy in breast cancer in accordance with the role of CDK8 in chemotherapy-induced tumor-supporting paracrine activities.
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Affiliation(s)
- Eugenia V Broude
- Department of Drug Discovery and Biomedical Sciences, South Carolina College of Pharmacy, University of South Carolina, 715 Sumter St. Coker Life Science Building, Room 713C, Columbia, SC 29208, USA.
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Kikuchi Y, Umemura H, Nishitani S, Iida S, Fukasawa R, Hayashi H, Hirose Y, Tanaka A, Sugasawa K, Ohkuma Y. Human mediator MED17 subunit plays essential roles in gene regulation by associating with the transcription and DNA repair machineries. Genes Cells 2014; 20:191-202. [DOI: 10.1111/gtc.12210] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2014] [Accepted: 11/02/2014] [Indexed: 01/22/2023]
Affiliation(s)
- Yuko Kikuchi
- Laboratory of Gene Regulation; Graduate School of Medicine and Pharmaceutical Sciences; University of Toyama; Toyama Japan
| | - Hiroyasu Umemura
- Laboratory of Gene Regulation; Graduate School of Medicine and Pharmaceutical Sciences; University of Toyama; Toyama Japan
| | - Saori Nishitani
- Laboratory of Gene Regulation; Graduate School of Medicine and Pharmaceutical Sciences; University of Toyama; Toyama Japan
| | - Satoshi Iida
- Laboratory of Gene Regulation; Graduate School of Medicine and Pharmaceutical Sciences; University of Toyama; Toyama Japan
| | - Rikiya Fukasawa
- Laboratory of Gene Regulation; Graduate School of Medicine and Pharmaceutical Sciences; University of Toyama; Toyama Japan
| | - Hiroto Hayashi
- Laboratory of Gene Regulation; Graduate School of Medicine and Pharmaceutical Sciences; University of Toyama; Toyama Japan
| | - Yutaka Hirose
- Laboratory of Gene Regulation; Graduate School of Medicine and Pharmaceutical Sciences; University of Toyama; Toyama Japan
| | - Aki Tanaka
- Laboratory of Gene Regulation; Graduate School of Medicine and Pharmaceutical Sciences; University of Toyama; Toyama Japan
| | - Kaoru Sugasawa
- Biosignal Research Center; Organization of Advanced Science and Technology; Kobe University; Kobe Japan
| | - Yoshiaki Ohkuma
- Laboratory of Gene Regulation; Graduate School of Medicine and Pharmaceutical Sciences; University of Toyama; Toyama Japan
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Kumafuji M, Umemura H, Furumoto T, Fukasawa R, Tanaka A, Ohkuma Y. Mediator MED18 subunit plays a negative role in transcription via the CDK/cyclin module. Genes Cells 2014; 19:582-93. [PMID: 24840924 DOI: 10.1111/gtc.12155] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2014] [Accepted: 04/02/2014] [Indexed: 01/24/2023]
Abstract
The Mediator complex (Mediator) is conserved among eukaryotes and is comprised of head, middle, tail and CDK/cyclin modules. The head module has received the most attention because its interaction with RNA polymerase II (Pol II) and the general transcription factors TFIIH and TBP facilitates phosphorylation of the carboxy-terminal domain (CTD) of the largest subunit of Pol II. We studied the human head module subunit hMED18 to elucidate how Mediator is involved in both transcriptional activation and repression. siRNA-mediated hMED18 depletion augmented transcription, indicating that hMED18 functions in transcriptional repression. Treatment of cells with two histone deacetylase (HDAC) inhibitors, the HDAC inhibitor trichostatin A (TSA) and the SIRT inhibitor nicotinamide showed that this repression was not caused by those HDAC activities. A screen for hMED18-target genes showed that the promoters for cap RNA methyltransferase RNMT-activating mini protein (RAM/FAM103A1) and divalent metal transporter 1 (DMT1/SLC11A2) genes were bound by hMED18. Depletion of hMED18 showed hMED18 and the middle module subunit hMED1 were lost from the promoters of those genes, whereas the CDK/cyclin module subunit hCDK8 remained bound. This indicates a novel transcriptional repression mechanism of hMED18 mediated by hCDK8 and further a novel positive role of free CDK/cyclin module in transcriptional activation. [Correction added on 12 June 2014, after first online publication: SLC11A2 amended from SCL11A2.].
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Affiliation(s)
- Masayuki Kumafuji
- Laboratory of Gene Regulation, Graduate School of Medicine and Pharmaceutical Sciences, University of Toyama, Toyama, Japan
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Kuuluvainen E, Hakala H, Havula E, Sahal Estimé M, Rämet M, Hietakangas V, Mäkelä TP. Cyclin-dependent kinase 8 module expression profiling reveals requirement of mediator subunits 12 and 13 for transcription of Serpent-dependent innate immunity genes in Drosophila. J Biol Chem 2014; 289:16252-61. [PMID: 24778181 DOI: 10.1074/jbc.m113.541904] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
The Cdk8 (cyclin-dependent kinase 8) module of Mediator integrates regulatory cues from transcription factors to RNA polymerase II. It consists of four subunits where Med12 and Med13 link Cdk8 and cyclin C (CycC) to core Mediator. Here we have investigated the contributions of the Cdk8 module subunits to transcriptional regulation using RNA interference in Drosophila cells. Genome-wide expression profiling demonstrated separation of Cdk8-CycC and Med12-Med13 profiles. However, transcriptional regulation by Cdk8-CycC was dependent on Med12-Med13. This observation also revealed that Cdk8-CycC and Med12-Med13 often have opposite transcriptional effects. Interestingly, Med12 and Med13 profiles overlapped significantly with that of the GATA factor Serpent. Accordingly, mutational analyses indicated that GATA sites are required for Med12-Med13 regulation of Serpent-dependent genes. Med12 and Med13 were also found to be required for Serpent-activated innate immunity genes in defense to bacterial infection. The results reveal a novel role for the Cdk8 module in Serpent-dependent transcription and innate immunity.
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Affiliation(s)
- Emilia Kuuluvainen
- From the Institute of Biotechnology, University of Helsinki, P. O. Box 56, 00014 Helsinki
| | - Heini Hakala
- From the Institute of Biotechnology, University of Helsinki, P. O. Box 56, 00014 Helsinki
| | - Essi Havula
- From the Institute of Biotechnology, University of Helsinki, P. O. Box 56, 00014 Helsinki, the Department of Biosciences, University of Helsinki, P. O. Box 65, 00014 Helsinki
| | - Michelle Sahal Estimé
- From the Institute of Biotechnology, University of Helsinki, P. O. Box 56, 00014 Helsinki
| | - Mika Rämet
- the Institute of Biomedical Technology, and BioMediTech, University of Tampere, 33014 Tampere, the Department of Pediatrics, Tampere University Hospital, 22521 Tampere, the Department of Pediatrics, Institute of Clinical Medicine, and Medical Research Center Oulu, University of Oulu, 90014 Oulu, and the Department of Children and Adolescents, Oulu University Hospital, 90029 Oulu, Finland
| | - Ville Hietakangas
- From the Institute of Biotechnology, University of Helsinki, P. O. Box 56, 00014 Helsinki, the Department of Biosciences, University of Helsinki, P. O. Box 65, 00014 Helsinki
| | - Tomi P Mäkelä
- From the Institute of Biotechnology, University of Helsinki, P. O. Box 56, 00014 Helsinki,
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Abstract
The Mediator complex is a multi-subunit assembly that appears to be required for regulating expression of most RNA polymerase II (pol II) transcripts, which include protein-coding and most non-coding RNA genes. Mediator and pol II function within the pre-initiation complex (PIC), which consists of Mediator, pol II, TFIIA, TFIIB, TFIID, TFIIE, TFIIF and TFIIH and is approximately 4.0 MDa in size. Mediator serves as a central scaffold within the PIC and helps regulate pol II activity in ways that remain poorly understood. Mediator is also generally targeted by sequence-specific, DNA-binding transcription factors (TFs) that work to control gene expression programs in response to developmental or environmental cues. At a basic level, Mediator functions by relaying signals from TFs directly to the pol II enzyme, thereby facilitating TF-dependent regulation of gene expression. Thus, Mediator is essential for converting biological inputs (communicated by TFs) to physiological responses (via changes in gene expression). In this review, we summarize an expansive body of research on the Mediator complex, with an emphasis on yeast and mammalian complexes. We focus on the basics that underlie Mediator function, such as its structure and subunit composition, and describe its broad regulatory influence on gene expression, ranging from chromatin architecture to transcription initiation and elongation, to mRNA processing. We also describe factors that influence Mediator structure and activity, including TFs, non-coding RNAs and the CDK8 module.
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Affiliation(s)
- Zachary C Poss
- Department of Chemistry and Biochemistry, University of Colorado , Boulder, CO , USA
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Tsutsui T, Fukasawa R, Shinmyouzu K, Nakagawa R, Tobe K, Tanaka A, Ohkuma Y. Mediator complex recruits epigenetic regulators via its two cyclin-dependent kinase subunits to repress transcription of immune response genes. J Biol Chem 2013; 288:20955-20965. [PMID: 23749998 DOI: 10.1074/jbc.m113.486746] [Citation(s) in RCA: 58] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
The Mediator complex (Mediator) plays pivotal roles in activating transcription by RNA polymerase II, but relatively little is known about its roles in repression. Here, we identified the histone arginine methyltransferase PRMT5 and WD repeat protein 77/methylosome protein 50 (WDR77/MEP50) as Mediator cyclin-dependent kinase (CDK)-interacting proteins and studied the roles of PRMT5 in the transcriptional regulation of CCAAT enhancer-binding protein (C/EBP) β target genes. First, we purified CDK8- and CDK19-containing complexes from HeLa nuclear extracts and subjected these purified complexes to mass spectrometric analyses. These experiments revealed that two Mediator CDKs, CDK8 and CDK19, individually interact with PRMT5 and WDR77, and their interactions with PRMT5 cause transcriptional repression of C/EBPβ target genes by regulating symmetric dimethylation of histone H4 arginine 3 (H4R3me2s) in the promoter regions of those genes. Furthermore, the recruitment of the DNA methyltransferase DNMT3A correlated with H4R3 dimethylation potentially leading to DNA methylation at the promoter proximal region and tight inhibition of preinitiation complex formation. In vertebrates, C/EBPβ regulates many genes involved in immune responses and cell differentiation. These findings shed light on the molecular mechanisms of the repressive roles of Mediator CDKs in transcription of C/EBPβ target genes and might provide clues that enable future studies of the functional associations between Mediators and epigenetic regulation.
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Affiliation(s)
- Taiki Tsutsui
- From the Laboratory of Gene Regulation, Graduate School of Medicine and Pharmaceutical Sciences, and
| | - Rikiya Fukasawa
- From the Laboratory of Gene Regulation, Graduate School of Medicine and Pharmaceutical Sciences, and
| | - Kaori Shinmyouzu
- the Mass Spectrometry Analysis Unit, RIKEN Center for Developmental Biology, 2-2-3 Minatojima-minamimachi, Chuo-ku, Kobe 650-0047, Japan
| | - Reiko Nakagawa
- the Mass Spectrometry Analysis Unit, RIKEN Center for Developmental Biology, 2-2-3 Minatojima-minamimachi, Chuo-ku, Kobe 650-0047, Japan
| | - Kazuyuki Tobe
- the First Department of Internal Medicine, University of Toyama, 2630 Sugitani, Toyama 930-0194, Japan and
| | - Aki Tanaka
- From the Laboratory of Gene Regulation, Graduate School of Medicine and Pharmaceutical Sciences, and
| | - Yoshiaki Ohkuma
- From the Laboratory of Gene Regulation, Graduate School of Medicine and Pharmaceutical Sciences, and.
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Cyclin-dependent kinase 8 mediates chemotherapy-induced tumor-promoting paracrine activities. Proc Natl Acad Sci U S A 2012; 109:13799-804. [PMID: 22869755 DOI: 10.1073/pnas.1206906109] [Citation(s) in RCA: 133] [Impact Index Per Article: 11.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Conventional chemotherapy not only kills tumor cells but also changes gene expression in treatment-damaged tissues, inducing production of multiple tumor-supporting secreted factors. This secretory phenotype was found here to be mediated in part by a damage-inducible cell-cycle inhibitor p21 (CDKN1A). We developed small-molecule compounds that inhibit damage-induced transcription downstream of p21. These compounds were identified as selective inhibitors of a transcription-regulating kinase CDK8 and its isoform CDK19. Remarkably, p21 was found to bind to CDK8 and stimulate its kinase activity. p21 and CDK8 also cooperate in the formation of internucleolar bodies, where both proteins accumulate. A CDK8 inhibitor suppresses damage-induced tumor-promoting paracrine activities of tumor cells and normal fibroblasts and reverses the increase in tumor engraftment and serum mitogenic activity in mice pretreated with a chemotherapeutic drug. The inhibitor also increases the efficacy of chemotherapy against xenografts formed by tumor cell/fibroblast mixtures. Microarray data analysis revealed striking correlations between CDK8 expression and poor survival in breast and ovarian cancers. CDK8 inhibition offers a promising approach to increasing the efficacy of cancer chemotherapy.
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