1
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Du TY, Hall SR, Chung F, Kurdyukov S, Crittenden E, Patel K, Dawson CA, Westhorpe AP, Bartlett KE, Rasmussen SA, Moreno CL, Denes CE, Albulescu LO, Marriott AE, Mackay JP, Wilkinson MC, Gutiérrez JM, Casewell NR, Neely GG. Molecular dissection of cobra venom highlights heparinoids as an antidote for spitting cobra envenoming. Sci Transl Med 2024; 16:eadk4802. [PMID: 39018365 DOI: 10.1126/scitranslmed.adk4802] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2023] [Revised: 02/28/2024] [Accepted: 05/31/2024] [Indexed: 07/19/2024]
Abstract
Snakebites affect about 1.8 million people annually. The current standard of care involves antibody-based antivenoms, which can be difficult to access and are generally not effective against local tissue injury, the primary cause of morbidity. Here, we used a pooled whole-genome CRISPR knockout screen to define human genes that, when targeted, modify cell responses to spitting cobra venoms. A large portion of modifying genes that conferred resistance to venom cytotoxicity was found to control proteoglycan biosynthesis, including EXT1, B4GALT7, EXT2, EXTL3, XYLT2, NDST1, and SLC35B2, which we validated independently. This finding suggested heparinoids as possible inhibitors. Heparinoids prevented venom cytotoxicity through binding to three-finger cytotoxins, and the US Food and Drug Administration-approved heparinoid tinzaparin was found to reduce tissue damage in mice when given via a medically relevant route and dose. Overall, our systematic molecular dissection of cobra venom cytotoxicity provides insight into how we can better treat cobra snakebite envenoming.
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Affiliation(s)
- Tian Y Du
- Charles Perkins Centre, Dr. John and Anne Chong Lab for Functional Genomics, and School of Life and Environmental Sciences, University of Sydney, Camperdown, NSW 2006, Australia
| | - Steven R Hall
- Centre for Snakebite Research and Interventions, Department of Tropical Disease Biology, Liverpool School of Tropical Medicine, Pembroke Place, L3 5QA, Liverpool, UK
| | - Felicity Chung
- Charles Perkins Centre, Dr. John and Anne Chong Lab for Functional Genomics, and School of Life and Environmental Sciences, University of Sydney, Camperdown, NSW 2006, Australia
| | - Sergey Kurdyukov
- Charles Perkins Centre, Dr. John and Anne Chong Lab for Functional Genomics, and School of Life and Environmental Sciences, University of Sydney, Camperdown, NSW 2006, Australia
| | - Edouard Crittenden
- Centre for Snakebite Research and Interventions, Department of Tropical Disease Biology, Liverpool School of Tropical Medicine, Pembroke Place, L3 5QA, Liverpool, UK
| | - Karishma Patel
- School of Life and Environmental Sciences, University of Sydney, Sydney, NSW 2008, Australia
| | - Charlotte A Dawson
- Centre for Snakebite Research and Interventions, Department of Tropical Disease Biology, Liverpool School of Tropical Medicine, Pembroke Place, L3 5QA, Liverpool, UK
| | - Adam P Westhorpe
- Centre for Snakebite Research and Interventions, Department of Tropical Disease Biology, Liverpool School of Tropical Medicine, Pembroke Place, L3 5QA, Liverpool, UK
| | - Keirah E Bartlett
- Centre for Snakebite Research and Interventions, Department of Tropical Disease Biology, Liverpool School of Tropical Medicine, Pembroke Place, L3 5QA, Liverpool, UK
| | - Sean A Rasmussen
- Department of Pathology and Laboratory Medicine, Queen Elizabeth II Health Sciences Centre and Dalhousie University, 7th Floor of MacKenzie Building, 5788 University Avenue, Halifax, NS B3H 1V8, Canada
| | - Cesar L Moreno
- Charles Perkins Centre, Dr. John and Anne Chong Lab for Functional Genomics, and School of Life and Environmental Sciences, University of Sydney, Camperdown, NSW 2006, Australia
| | - Christopher E Denes
- Charles Perkins Centre, Dr. John and Anne Chong Lab for Functional Genomics, and School of Life and Environmental Sciences, University of Sydney, Camperdown, NSW 2006, Australia
| | - Laura-Oana Albulescu
- Centre for Snakebite Research and Interventions, Department of Tropical Disease Biology, Liverpool School of Tropical Medicine, Pembroke Place, L3 5QA, Liverpool, UK
| | - Amy E Marriott
- Centre for Snakebite Research and Interventions, Department of Tropical Disease Biology, Liverpool School of Tropical Medicine, Pembroke Place, L3 5QA, Liverpool, UK
| | - Joel P Mackay
- School of Life and Environmental Sciences, University of Sydney, Sydney, NSW 2008, Australia
| | - Mark C Wilkinson
- Centre for Snakebite Research and Interventions, Department of Tropical Disease Biology, Liverpool School of Tropical Medicine, Pembroke Place, L3 5QA, Liverpool, UK
| | - José María Gutiérrez
- Clodomiro Picado Institute, School of Microbiology, University of Costa Rica, P.O. Box 15501, 11501-2060 San José, Costa Rica
| | - Nicholas R Casewell
- Centre for Snakebite Research and Interventions, Department of Tropical Disease Biology, Liverpool School of Tropical Medicine, Pembroke Place, L3 5QA, Liverpool, UK
| | - G Gregory Neely
- Charles Perkins Centre, Dr. John and Anne Chong Lab for Functional Genomics, and School of Life and Environmental Sciences, University of Sydney, Camperdown, NSW 2006, Australia
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2
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Karolak A, Urbaniak K, Monastyrskyi A, Duckett DR, Branciamore S, Stewart PA. Structure-independent machine-learning predictions of the CDK12 interactome. Biophys J 2024:S0006-3495(24)00344-8. [PMID: 38762754 DOI: 10.1016/j.bpj.2024.05.017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2023] [Revised: 04/24/2024] [Accepted: 05/15/2024] [Indexed: 05/20/2024] Open
Abstract
Cyclin-dependent kinase 12 (CDK12) is a critical regulatory protein involved in transcription and DNA repair processes. Dysregulation of CDK12 has been implicated in various diseases, including cancer. Understanding the CDK12 interactome is pivotal for elucidating its functional roles and potential therapeutic targets. Traditional methods for interactome prediction often rely on protein structure information, limiting applicability to CDK12 characterized by partly disordered terminal C region. In this study, we present a structure-independent machine-learning model that utilizes proteins' sequence and functional data to predict the CDK12 interactome. This approach is motivated by the disordered character of the CDK12 C-terminal region mitigating a structure-driven search for binding partners. Our approach incorporates multiple data sources, including protein-protein interaction networks, functional annotations, and sequence-based features, to construct a comprehensive CDK12 interactome prediction model. The ability to predict CDK12 interactions without relying on structural information is a significant advancement, as many potential interaction partners may lack crystallographic data. In conclusion, our structure-independent machine-learning model presents a powerful tool for predicting the CDK12 interactome and holds promise in advancing our understanding of CDK12 biology, identifying potential therapeutic targets, and facilitating precision-medicine approaches for CDK12-associated diseases.
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Affiliation(s)
| | - Konstancja Urbaniak
- Department of Computational and Quantitative Medicine, City of Hope, Duarte, California
| | | | - Derek R Duckett
- Department of Drug Discovery, Moffitt Cancer Center, Tampa, Florida
| | - Sergio Branciamore
- Department of Computational and Quantitative Medicine, City of Hope, Duarte, California
| | - Paul A Stewart
- Department of Biostatistics and Bioinformatics, Moffitt Cancer Center, Tampa, Florida
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3
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Frei K, Schecher S, Daher T, Hörner N, Richter J, Hildebrand U, Schindeldecker M, Witzel HR, Tsaur I, Porubsky S, Gaida MM, Roth W, Tagscherer KE. Inhibition of the Cyclin K-CDK12 complex induces DNA damage and increases the effect of androgen deprivation therapy in prostate cancer. Int J Cancer 2024; 154:1082-1096. [PMID: 37916780 DOI: 10.1002/ijc.34778] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2023] [Revised: 09/07/2023] [Accepted: 10/10/2023] [Indexed: 11/03/2023]
Abstract
Androgen deprivation therapy (ADT) is the mainstay of the current first-line treatment concepts for patients with advanced prostate carcinoma (PCa). However, due to treatment failure and recurrence investigation of new targeted therapeutics is urgently needed. In this study, we investigated the suitability of the Cyclin K-CDK12 complex as a novel therapeutic approach in PCa using the new covalent CDK12/13 inhibitor THZ531. Here we show that THZ531 impairs cellular proliferation, induces apoptosis, and decreases the expression of selected DNA repair genes in PCa cell lines, which is associated with an increasing extent of DNA damage. Furthermore, combination of THZ531 and ADT leads to an increase in these anti-tumoral effects in androgen-sensitive PCa cells. The anti-proliferative and pro-apoptotic activity of THZ531 in combination with ADT was validated in an ex vivo PCa tissue culture model. In a retrospective immunohistochemical analysis of 300 clinical tissue samples we show that Cyclin K (CycK) but not CDK12 expression correlates with a more aggressive type of PCa. In conclusion, this study demonstrates the clinical relevance of the CycK-CDK12 complex as a promising target for combinational therapy with ADT in PCa and its importance as a prognostic biomarker for patients with PCa.
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Affiliation(s)
- Katharina Frei
- Institute of Pathology, University Medical Center of the Johannes Gutenberg University Mainz, Mainz, Germany
| | - Sabrina Schecher
- Institute of Pathology, University Medical Center of the Johannes Gutenberg University Mainz, Mainz, Germany
| | - Tamas Daher
- Institute of Pathology, University Medical Center of the Johannes Gutenberg University Mainz, Mainz, Germany
| | - Nina Hörner
- Institute of Pathology, University Medical Center of the Johannes Gutenberg University Mainz, Mainz, Germany
| | - Jutta Richter
- Institute of Pathology, University Medical Center of the Johannes Gutenberg University Mainz, Mainz, Germany
| | - Ute Hildebrand
- Institute of Pathology, University Medical Center of the Johannes Gutenberg University Mainz, Mainz, Germany
| | - Mario Schindeldecker
- Institute of Pathology, University Medical Center of the Johannes Gutenberg University Mainz, Mainz, Germany
- Tissue Biobank of the University Medical Center of the Johannes Gutenberg University Mainz, Mainz, Germany
| | - Hagen R Witzel
- Institute of Pathology, University Medical Center of the Johannes Gutenberg University Mainz, Mainz, Germany
| | - Igor Tsaur
- Department of Urology and Pediatric Urology, University Medical Center of the Johannes Gutenberg University Mainz, Mainz, Germany
| | - Stefan Porubsky
- Institute of Pathology, University Medical Center of the Johannes Gutenberg University Mainz, Mainz, Germany
| | - Matthias M Gaida
- Institute of Pathology, University Medical Center of the Johannes Gutenberg University Mainz, Mainz, Germany
| | - Wilfried Roth
- Institute of Pathology, University Medical Center of the Johannes Gutenberg University Mainz, Mainz, Germany
| | - Katrin E Tagscherer
- Institute of Pathology, University Medical Center of the Johannes Gutenberg University Mainz, Mainz, Germany
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4
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Yoon H, Rutter JC, Li YD, Ebert BL. Induced protein degradation for therapeutics: past, present, and future. J Clin Invest 2024; 134:e175265. [PMID: 38165043 PMCID: PMC10760958 DOI: 10.1172/jci175265] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2024] Open
Abstract
The concept of induced protein degradation by small molecules has emerged as a promising therapeutic strategy that is particularly effective in targeting proteins previously considered "undruggable." Thalidomide analogs, employed in the treatment of multiple myeloma, stand as prime examples. These compounds serve as molecular glues, redirecting the CRBN E3 ubiquitin ligase to degrade myeloma-dependency factors, IKZF1 and IKZF3. The clinical success of thalidomide analogs demonstrates the therapeutic potential of induced protein degradation. Beyond molecular glue degraders, several additional modalities to trigger protein degradation have been developed and are currently under clinical evaluation. These include heterobifunctional degraders, polymerization-induced degradation, ligand-dependent degradation of nuclear hormone receptors, disruption of protein interactions, and various other strategies. In this Review, we will provide a concise overview of various degradation modalities, their clinical applications, and potential future directions in the field of protein degradation.
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Affiliation(s)
- Hojong Yoon
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts, USA
- Cancer Program, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
| | - Justine C. Rutter
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts, USA
- Cancer Program, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
| | - Yen-Der Li
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts, USA
- Cancer Program, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
| | - Benjamin L. Ebert
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts, USA
- Cancer Program, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
- Howard Hughes Medical Institute, Boston, Massachusetts, USA
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5
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Zhang L, Zhen Y, Feng L, Li Z, Lu Y, Wang G, Ouyang L. Discovery of a novel dual-target inhibitor of CDK12 and PARP1 that induces synthetic lethality for treatment of triple-negative breast cancer. Eur J Med Chem 2023; 259:115648. [PMID: 37478560 DOI: 10.1016/j.ejmech.2023.115648] [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: 06/16/2023] [Revised: 07/07/2023] [Accepted: 07/13/2023] [Indexed: 07/23/2023]
Abstract
Triple negative breast cancer (TNBC) is one of the most aggressive breast tumors, with a high rate of recurrence and metastasis as well as a poor prognosis. Consequently, it is urgent to find new targeted therapeutic strategies and development of corresponding drugs. Previous studies have shown that CDK12 inhibitors in combination with PARP1 inhibitors is able to induce synthetic lethality in TNBC cells. Here, we reported simultaneously inhibition of CDK12 and PARP1 by genetic or pharmacological approaches synergistically inhibited the proliferation of TNBC cells. Then, a series of small molecule inhibitors targeting both CDK12 and PARP1 were designed and synthesized. The new dual-target inhibitor (12e) showed potent inhibitory activity against CDK12 (IC50 = 285 nM) and PARP1 (IC50 = 34 nM), as well as good anti-proliferative effects in TNBC cell lines. Meanwhile, compound 12e showed favorable synergistic anti-tumor efficacy in cells and xenografts by inhibiting DNA damage repair, promoting cell cycle arrest and apoptosis. Taken together, we successfully synthesized the first effective CDK12-PARP1 dual inhibitor, which is expected to be an attractive therapeutic strategy for TNBC.
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Affiliation(s)
- Lan Zhang
- Sichuan Engineering Research Center for Biomimetic Synthesis of Natural Drugs, School of Life Science and Engineering, Southwest Jiaotong University, Chengdu, 610031, China.
| | - Yongqi Zhen
- Sichuan Engineering Research Center for Biomimetic Synthesis of Natural Drugs, School of Life Science and Engineering, Southwest Jiaotong University, Chengdu, 610031, China; Department of Biotherapy, Innovation Center of Nursing Research, Nursing Key Laboratory of Sichuan Province, State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University /West China School of Nursing, Sichuan University, Chengdu, 610041, China
| | - Lu Feng
- Department of Biotherapy, Innovation Center of Nursing Research, Nursing Key Laboratory of Sichuan Province, State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University /West China School of Nursing, Sichuan University, Chengdu, 610041, China
| | - Zhijia Li
- Sichuan Engineering Research Center for Biomimetic Synthesis of Natural Drugs, School of Life Science and Engineering, Southwest Jiaotong University, Chengdu, 610031, China
| | - Yingying Lu
- Sichuan Engineering Research Center for Biomimetic Synthesis of Natural Drugs, School of Life Science and Engineering, Southwest Jiaotong University, Chengdu, 610031, China
| | - Guan Wang
- Department of Biotherapy, Innovation Center of Nursing Research, Nursing Key Laboratory of Sichuan Province, State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University /West China School of Nursing, Sichuan University, Chengdu, 610041, China.
| | - Liang Ouyang
- Department of Biotherapy, Innovation Center of Nursing Research, Nursing Key Laboratory of Sichuan Province, State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University /West China School of Nursing, Sichuan University, Chengdu, 610041, China.
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6
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Yan Z, Du Y, Zhang H, Zheng Y, Lv H, Dong N, He F. Research progress of anticancer drugs targeting CDK12. RSC Med Chem 2023; 14:1629-1644. [PMID: 37731700 PMCID: PMC10507796 DOI: 10.1039/d3md00004d] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2023] [Accepted: 05/17/2023] [Indexed: 09/22/2023] Open
Abstract
Cyclin-dependent kinase 12 (CDK12) is a transcription-associated CDK that plays key roles in transcription, translation, mRNA splicing, the cell cycle, and DNA damage repair. Research has identified that high expression of CDK12 in organs such as the breast, stomach, and uterus can lead to HER2-positive breast cancer, gastric cancer and cervical cancer. Inhibiting high expression of CDK12 suppresses tumor growth and proliferation, suggesting that it is both a biomarker for cancer and a potential target for cancer therapy. CDK12 inhibitors can competitively bind the CDK12 hydrophobic pocket with ATP to avoid CDK12 phosphorylation, blocking subsequent signaling pathways. The development of CDK12 inhibitors is challenging due to the high homology of CDK12 with other CDKs. This review summarizes the research progress of CDK12 inhibitors, their mechanism of action and the structure-activity relationship, providing new insights into the design of CDK12 selective inhibitors.
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Affiliation(s)
- Zhijia Yan
- School of Chemistry & Chemical Engineering, Qilu University of Technology (Shandong Academy of Sciences) 3501 Da Xue Road Jinan 250353 China
| | - Yongli Du
- School of Chemistry & Chemical Engineering, Qilu University of Technology (Shandong Academy of Sciences) 3501 Da Xue Road Jinan 250353 China
| | - Haibin Zhang
- School of Chemistry & Chemical Engineering, Qilu University of Technology (Shandong Academy of Sciences) 3501 Da Xue Road Jinan 250353 China
| | - Yong Zheng
- School of Chemistry & Chemical Engineering, Qilu University of Technology (Shandong Academy of Sciences) 3501 Da Xue Road Jinan 250353 China
| | - Huiting Lv
- School of Chemistry & Chemical Engineering, Qilu University of Technology (Shandong Academy of Sciences) 3501 Da Xue Road Jinan 250353 China
| | - Ning Dong
- School of Chemistry & Chemical Engineering, Qilu University of Technology (Shandong Academy of Sciences) 3501 Da Xue Road Jinan 250353 China
| | - Fang He
- School of Water Conservancy and Environment, University of Jinan 336 Nanxinzhuang West Road Jinan 250022 China
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7
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Pluta AJ, Studniarek C, Murphy S, Norbury CJ. Cyclin-dependent kinases: Masters of the eukaryotic universe. WILEY INTERDISCIPLINARY REVIEWS. RNA 2023; 15:e1816. [PMID: 37718413 PMCID: PMC10909489 DOI: 10.1002/wrna.1816] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/05/2023] [Revised: 07/21/2023] [Accepted: 08/03/2023] [Indexed: 09/19/2023]
Abstract
A family of structurally related cyclin-dependent protein kinases (CDKs) drives many aspects of eukaryotic cell function. Much of the literature in this area has considered individual members of this family to act primarily either as regulators of the cell cycle, the context in which CDKs were first discovered, or as regulators of transcription. Until recently, CDK7 was the only clear example of a CDK that functions in both processes. However, new data points to several "cell-cycle" CDKs having important roles in transcription and some "transcriptional" CDKs having cell cycle-related targets. For example, novel functions in transcription have been demonstrated for the archetypal cell cycle regulator CDK1. The increasing evidence of the overlap between these two CDK types suggests that they might play a critical role in coordinating the two processes. Here we review the canonical functions of cell-cycle and transcriptional CDKs, and provide an update on how these kinases collaborate to perform important cellular functions. We also provide a brief overview of how dysregulation of CDKs contributes to carcinogenesis, and possible treatment avenues. This article is categorized under: RNA Interactions with Proteins and Other Molecules > RNA-Protein Complexes RNA Processing > 3' End Processing RNA Processing > Splicing Regulation/Alternative Splicing.
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Affiliation(s)
| | | | - Shona Murphy
- Sir William Dunn School of PathologyUniversity of OxfordOxfordUK
| | - Chris J. Norbury
- Sir William Dunn School of PathologyUniversity of OxfordOxfordUK
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8
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Xiao Y, Dong J. Coming of Age: Targeting Cyclin K in Cancers. Cells 2023; 12:2044. [PMID: 37626854 PMCID: PMC10453554 DOI: 10.3390/cells12162044] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2023] [Revised: 08/08/2023] [Accepted: 08/09/2023] [Indexed: 08/27/2023] Open
Abstract
Cyclins and cyclin-dependent kinases (CDKs) play versatile roles in promoting the hallmarks of cancer. Therefore, cyclins and CDKs have been widely studied and targeted in cancer treatment, with four CDK4/6 inhibitors being approved by the FDA and many other inhibitors being examined in clinical trials. The specific purpose of this review is to delineate the role and therapeutic potential of Cyclin K in cancers. Studies have shown that Cyclin K regulates many essential biological processes, including the DNA damage response, mitosis, and pre-replicative complex assembly, and is critical in both cancer cell growth and therapeutic resistance. Importantly, the druggability of Cyclin K has been demonstrated in an increasing number of studies that identify novel opportunities for its use in cancer treatment. This review first introduces the basic features and translational value of human cyclins and CDKs. Next, the discovery, phosphorylation targets, and related functional significance of Cyclin K-CDK12/13 complexes in cancer are detailed. This review then provides a summary of current Cyclin K-associated cancer studies, with an emphasis on the available Cyclin K-targeting drugs. Finally, the current knowledge gaps regarding the potential of Cyclin K in cancers are discussed, along with interesting directions for future investigation.
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Affiliation(s)
| | - Jixin Dong
- Eppley Institute for Research in Cancer and Allied Diseases, Fred and Pamela Buffett Cancer Center, University of Nebraska Medical Center, Omaha, NE 68198, USA;
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9
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Savoy L, Long N, Lee H, Chen R, Allen B, Lin HY, Tognon C, Malhotra SV, Tyner JW, Zhang H. CDK12/13 dual inhibitors are potential therapeutics for acute myeloid leukemia. Br J Haematol 2023; 202:195-198. [PMID: 37182843 PMCID: PMC10330638 DOI: 10.1111/bjh.18843] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2023] [Revised: 04/17/2023] [Accepted: 04/23/2023] [Indexed: 05/16/2023]
Affiliation(s)
- Lindsey Savoy
- Division of Oncological Sciences, Oregon Health & Science University, Knight Cancer Institute, Portland, OR
| | - Nicola Long
- Division of Hematology and Medical Oncology, Oregon Health & Science University, Knight Cancer Institute, Portland, OR
| | - Hyunjung Lee
- Department of Cell, Developmental & Cancer Biology, Oregon Health & Science University, Knight Cancer Institute, Portland, OR
| | - Reid Chen
- Division of Oncological Sciences, Oregon Health & Science University, Knight Cancer Institute, Portland, OR
| | - Basil Allen
- Division of Oncological Sciences, Oregon Health & Science University, Knight Cancer Institute, Portland, OR
| | - Hsin-Yun Lin
- Department of Cell, Developmental & Cancer Biology, Oregon Health & Science University, Knight Cancer Institute, Portland, OR
| | - Cristina Tognon
- Division of Hematology and Medical Oncology, Oregon Health & Science University, Knight Cancer Institute, Portland, OR
| | - Sanjay V. Malhotra
- Center for Experimental Therapeutics, Department of Cell, Developmental & Cancer Biology, Oregon Health & Science University, Knight Cancer Institute, Portland, OR
| | - Jeffrey W. Tyner
- Department of Cell, Developmental & Cancer Biology, Oregon Health & Science University, Knight Cancer Institute, Portland, OR
| | - Haijiao Zhang
- Division of Oncological Sciences, Oregon Health & Science University, Knight Cancer Institute, Portland, OR
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10
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Morison LD, van Reyk O, Forbes E, Rouxel F, Faivre L, Bruinsma F, Vincent M, Jacquemont ML, Dykzeul NL, Geneviève D, Amor DJ, Morgan AT. CDK13-related disorder: a deep characterization of speech and language abilities and addition of 33 novel cases. Eur J Hum Genet 2023; 31:793-804. [PMID: 36599938 PMCID: PMC10325997 DOI: 10.1038/s41431-022-01275-8] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2022] [Revised: 12/01/2022] [Accepted: 12/14/2022] [Indexed: 01/05/2023] Open
Abstract
Speech and language impairments are central features of CDK13-related disorder. While pathogenic CDK13 variants have been associated with childhood apraxia of speech (CAS), a systematic characterisation of communication has not been conducted. Here we examined speech, language, non-verbal communication skills, social behaviour and health and development in 41 individuals with CDK13-related disorder from 10 countries (male = 22, median-age 7 years 1 month, range 1-25 years; 33 novel). Most participants used augmentative and alternative communication (AAC) in early childhood (24/41). CAS was common (14/22). Performance varied widely across intellectual ability, social behaviour and expressive language skills, with participants ranging from within average through to the severely impaired range. Receptive language was significantly stronger than expressive language ability. Social motivation was a relative strength. In terms of a broader health phenotype, a quarter had one or more of: renal, urogenital, musculoskeletal, and cardiac malformations, vision impairment, ear infections and/or sleep disturbance. All had gross and fine motor impairments (41/41). Other conditions included mild-moderate intellectual disability (16/22) and autism (7/41). No genotype-phenotype correlations were found. Recognition of CAS, a rare speech disorder, is required to ensure appropriately targeted therapy. The high prevalence of speech and language impairment underscores the importance of tailored speech therapy, particularly early access to AAC supports.
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Affiliation(s)
- Lottie D Morison
- Speech and Language, Murdoch Children's Research Institute, Melbourne, VIC, Australia
| | - Olivia van Reyk
- Speech and Language, Murdoch Children's Research Institute, Melbourne, VIC, Australia
| | - Elana Forbes
- Speech and Language, Murdoch Children's Research Institute, Melbourne, VIC, Australia
- School of Psychological Sciences, Monash University, Melbourne, VIC, Australia
| | - Flavien Rouxel
- Génétique Clinique, Départment de Génétique Médicale, Maladies Rares et Médecine Personnalisée, CHU Montpellier, Montpellier University, Centre de Référence Anomalies du Développement SOOR, Montpellier, France
| | - Laurence Faivre
- Centre de Référence Anomalies du Développment et Syndromes Malformatifs, FHU TRANSLAD, CHU Dijon, Dijon, France
- Genetics of Developmental Disorders, INSERM - Bourgogne Franche-Comté Univeristy, Dijon, France
| | | | - Marie Vincent
- Service de génétique médicale, CHU Nantes, 9 quai Moncousu, Nantes, France
| | | | - Natalie L Dykzeul
- Lucile Packard Children's Hospital, Stanford Children's Health, Palo Alto, CA, USA
| | - David Geneviève
- Génétique Clinique, Départment de Génétique Médicale, Maladies Rares et Médecine Personnalisée, CHU Montpellier, Montpellier University, Centre de Référence Anomalies du Développement SOOR, Montpellier, France
| | - David J Amor
- Speech and Language, Murdoch Children's Research Institute, Melbourne, VIC, Australia
- Department of Paediatrics, The University of Melbourne, Melbourne, VIC, Australia
- The Royal Children's Hospital, Melbourne, VIC, Australia
| | - Angela T Morgan
- Speech and Language, Murdoch Children's Research Institute, Melbourne, VIC, Australia.
- The Royal Children's Hospital, Melbourne, VIC, Australia.
- Department of Audiology and Speech Pathology, The University of Melbourne, Melbourne, VIC, Australia.
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11
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Wen T, Wang J, Lu R, Tan S, Li P, Yao X, Liu H, Yi Z, Li L, Liu S, Gao P, Qian H, Xie G, Ma F. Development, validation, and evaluation of a deep learning model to screen cyclin-dependent kinase 12 inhibitors in cancers. Eur J Med Chem 2023; 250:115199. [PMID: 36827953 DOI: 10.1016/j.ejmech.2023.115199] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2022] [Revised: 02/07/2023] [Accepted: 02/09/2023] [Indexed: 02/19/2023]
Abstract
Deep learning-based in silico alternatives have been demonstrated to be of significant importance in the acceleration of the drug discovery process and enhancement of success rates. Cyclin-dependent kinase 12 (CDK12) is a transcription-related cyclin-dependent kinase that may act as a biomarker and therapeutic target for cancers. However, currently, there is no high selective CDK12 inhibitor in clinical development and the identification of new specific CDK12 inhibitors has become increasingly challenging due to their similarity with CDK13. In this study, we developed a virtual screening workflow that combines deep learning with virtual screening tools and can be applied rapidly to millions of molecules. We designed a Transformer architecture Drug-Target Interaction (DTI) model with dual-branched self-supervised pre-trained molecular graph models and protein sequence models. Our predictive model produced satisfactory predictions for various targets, including CDK12, with several novel hits. We screened a large compound library consisting of 4.5 million drug-like molecules and recommended a list of potential CDK12 inhibitors for further experimental testing. In kinase assay, compared to the positive CDK12 inhibitor THZ531, the compounds CICAMPA-01, 02, 03 displayed more effective inhibition of CDK12, up to three times as much as THZ531. The compounds CICAMPA-03, 05, 04, 07 showed less inhibition of CDK13 compare to THZ531. In vitro, the IC50 of CICAMPA-01, 04, 05, 06, 09 was less than 3 μM in the HER2 positive CDK12 amplification breast cancer cell line BT-474. Overall, this study provides a highly efficient and end-to-end deep learning protocol, in conjunction with molecular docking, for discovering CDK12 inhibitors in cancers. Additionally, we disclose five novel CDK12 inhibitors. These results may accelerate the discovery of novel chemical-class drugs for cancer treatment.
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Affiliation(s)
- Tingyu Wen
- Department of Medical Oncology, National Cancer Center / National Clinical Research Center for Cancer / Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100021, China
| | - Jun Wang
- Ping An Healthcare Technology, Beijing, 100027, China
| | - Ruiqiang Lu
- Ping An Healthcare Technology, Beijing, 100027, China; College of Chemistry & Chemical Engineering, Lanzhou University, Lanzhou, 730000, Gansu, China
| | - Shuoyan Tan
- Ping An Healthcare Technology, Beijing, 100027, China; College of Chemistry & Chemical Engineering, Lanzhou University, Lanzhou, 730000, Gansu, China
| | - Pengyong Li
- School of Computer Science and Technology, Xidian University, Xi'an, 710126, Shaanxi, China
| | - Xiaojun Yao
- College of Chemistry & Chemical Engineering, Lanzhou University, Lanzhou, 730000, Gansu, China; State Key Laboratory of Quality Research in Chinese Medicines, Macau University of Science and Technology, 999078, Macau
| | - Huanxiang Liu
- Faculty of Applied Science, Macao Polytechnic University, 999078, Macau
| | - Zongbi Yi
- Department of Medical Oncology, National Cancer Center / National Clinical Research Center for Cancer / Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100021, China; Department of Radiation and Medical Oncology, Zhongnan Hospital of Wuhan University, Wuhan, 430071, Hubei, China
| | - Lixi Li
- Department of Medical Oncology, National Cancer Center / National Clinical Research Center for Cancer / Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100021, China
| | - Shuning Liu
- Department of Medical Oncology, National Cancer Center / National Clinical Research Center for Cancer / Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100021, China
| | - Peng Gao
- Ping An Healthcare Technology, Beijing, 100027, China
| | - Haili Qian
- State Key Laboratory of Molecular Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100021, China.
| | - Guotong Xie
- Ping An Healthcare Technology, Beijing, 100027, China; Ping An Health Cloud Company Limited, Beijing, 100027, China; Ping An International Smart City Technology Co., Ltd., Beijing, 100027, China.
| | - Fei Ma
- Department of Medical Oncology, National Cancer Center / National Clinical Research Center for Cancer / Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100021, China.
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12
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Hope I, Endicott JA, Watt JE. Emerging approaches to CDK inhibitor development, a structural perspective. RSC Chem Biol 2023; 4:146-164. [PMID: 36794018 PMCID: PMC9906319 DOI: 10.1039/d2cb00201a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2022] [Accepted: 12/06/2022] [Indexed: 12/15/2022] Open
Abstract
Aberrant activity of the cyclin-dependent kinase family is frequently noted in a number of diseases identifying them as potential targets for drug development. However, current CDK inhibitors lack specificity owing to the high sequence and structural conservation of the ATP binding cleft across family members, highlighting the necessity of finding novel modes of CDK inhibition. The wealth of structural information regarding CDK assemblies and inhibitor complexes derived from X-ray crystallographic studies has been recently complemented through the use of cryo-electron microscopy. These recent advances have provided insights into the functional roles and regulatory mechanisms of CDKs and their interaction partners. This review explores the conformational malleability of the CDK subunit, the importance of SLiM recognition sites in CDK complexes, the progress made in chemically induced CDK degradation and how these studies can contribute to CDK inhibitor design. Additionally, fragment-based drug discovery can be utilised to identify small molecules that bind to allosteric sites on the CDK surface employing interactions which mimic those of native protein-protein interactions. These recent structural advances in CDK inhibitor mechanisms and in chemical probes which do not occupy the orthosteric ATP binding site can provide important insights for targeted CDK therapies.
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Affiliation(s)
- Ian Hope
- Translational and Clinical Research Institute, Faculty of Medical Sciences, Newcastle University, Paul O'Gorman Building, Framlington Place Newcastle upon Tyne NE2 4HH UK
| | - Jane A Endicott
- Translational and Clinical Research Institute, Faculty of Medical Sciences, Newcastle University, Paul O'Gorman Building, Framlington Place Newcastle upon Tyne NE2 4HH UK
| | - Jessica E Watt
- Translational and Clinical Research Institute, Faculty of Medical Sciences, Newcastle University, Paul O'Gorman Building, Framlington Place Newcastle upon Tyne NE2 4HH UK
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13
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Wu W, Yu S, Yu X. Transcription-associated cyclin-dependent kinase 12 (CDK12) as a potential target for cancer therapy. Biochim Biophys Acta Rev Cancer 2023; 1878:188842. [PMID: 36460141 DOI: 10.1016/j.bbcan.2022.188842] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2022] [Revised: 11/24/2022] [Accepted: 11/25/2022] [Indexed: 12/05/2022]
Abstract
Cyclin-dependent kinase 12 (CDK12), a transcription-related cyclin dependent kinase (CDK), plays a momentous part in multitudinous biological functions, such as replication, transcription initiation to elongation and termination, precursor mRNA (pre-mRNA) splicing, intron polyadenylation (IPA), and translation. CDK12 can act as a tumour suppressor or oncogene in disparate cellular environments, and its dysregulation likely provokes tumorigenesis. A comprehensive understanding of CDK12 will tremendously facilitate the exploitation of novel tactics for the treatment and precaution of cancer. Currently, CDK12 inhibitors are nonspecific and nonselective, which profoundly hinders the pharmacological target validation and drug exploitation process. Herein, we summarize the newly comprehension of the biological functions of CDK12 with a focus on recently emerged advancements of CDK12-associated therapeutic approaches in cancers.
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Affiliation(s)
- Wence Wu
- Departments of Orthopedics, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China; Department of Etiology and Carcinogenesis, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China; State Key Laboratory of Molecular Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China; Beijing Key Laboratory for Carcinogenesis and Cancer Prevention, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Shengji Yu
- Departments of Orthopedics, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China.
| | - Xiying Yu
- Department of Etiology and Carcinogenesis, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China; State Key Laboratory of Molecular Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China; Beijing Key Laboratory for Carcinogenesis and Cancer Prevention, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China.
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14
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SETD1A regulates transcriptional pause release of heme biosynthesis genes in leukemia. Cell Rep 2022; 41:111727. [PMID: 36450243 PMCID: PMC9771694 DOI: 10.1016/j.celrep.2022.111727] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2022] [Revised: 08/08/2022] [Accepted: 11/03/2022] [Indexed: 12/02/2022] Open
Abstract
Histone methyltransferase SETD1A is critical for acute myeloid leukemia (AML) cell survival, but the molecular mechanism driving SETD1A gene regulation remains elusive. To delineate the role of SETD1A, we utilize a protein degrader technology to induce rapid SETD1A degradation in AML cell lines. SETD1A degradation results in immediate downregulation of transcripts associated with DNA repair and heme biosynthesis pathways. CRISPR-based functional analyses and metabolomics reveal an essential role of SETD1A to maintain mitochondrial respiration in AML cells. These SETD1A targets are enriched in head-to-head (H2H) genes. SETD1A degradation disrupts a non-enzymatic SETD1A domain-dependent cyclin K function, increases the Ser5P RNA polymerase II (RNAPII) at the transcriptional start site (TSS), and induces the promoter-proximal pausing of RNAPII in a strand-specific manner. This study reveals a non-enzymatic role for SETD1A in transcriptional pause release and provides insight into the mechanism of RNAPII pausing and its function in cancer.
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15
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The Green Valley of Drosophila melanogaster Constitutive Heterochromatin: Protein-Coding Genes Involved in Cell Division Control. Cells 2022; 11:cells11193058. [PMID: 36231024 PMCID: PMC9563267 DOI: 10.3390/cells11193058] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2022] [Revised: 09/22/2022] [Accepted: 09/23/2022] [Indexed: 11/25/2022] Open
Abstract
Constitutive heterochromatin represents a significant fraction of eukaryotic genomes (10% in Arabidopsis, 20% in humans, 30% in D. melanogaster, and up to 85% in certain nematodes) and shares similar genetic and molecular properties in animal and plant species. Studies conducted over the last few years on D. melanogaster and other organisms led to the discovery of several functions associated with constitutive heterochromatin. This made it possible to revise the concept that this ubiquitous genomic territory is incompatible with gene expression. The aim of this review is to focus the attention on a group of protein-coding genes resident in D. melanogaster constitutive of heterochromatin, which are implicated in different steps of cell division.
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16
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Silina L, Dufour F, Rapinat A, Reyes C, Gentien D, Maksut F, Radvanyi F, Verrelle P, Bernard-Pierrot I, Mégnin-Chanet F. Tyro3 Targeting as a Radiosensitizing Strategy in Bladder Cancer through Cell Cycle Dysregulation. Int J Mol Sci 2022; 23:ijms23158671. [PMID: 35955805 PMCID: PMC9368768 DOI: 10.3390/ijms23158671] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2022] [Revised: 07/26/2022] [Accepted: 08/01/2022] [Indexed: 12/04/2022] Open
Abstract
Bladder cancer is a common cancer; it is the tenth most common cancer in the world. Around one fourth of all diagnosed patients have muscle-invasive bladder cancer (MIBC), characterized by advanced tumors and which remains a lethal disease. The standard treatment for MIBC is the bladder removal by surgery. However, bladder-preserving alternatives are emerging by combining chemotherapy, radiotherapy and minimal surgery, aiming to increase the patient’s quality of life. The aim of the study was to improve these treatments by investigating a novel approach where in addition to radiotherapy, a receptor, TYRO3, a member of TAM receptor tyrosine kinase family known to be highly expressed on the bladder cancer cells and involved in the control of cell survival is targeted. For this, we evaluated the influence of TYRO3 expression levels on a colony or cell survival assays, DNA damage, γH2AX foci formation, gene expression profiling and cell cycle regulation, after radiation on different bladder cell models. We found that TYRO3 expression impacts the radiation response via the cell cycle dysregulation with noeffets on the DNA repair. Therefore, targeting TYRO3 is a promising sensitization marker that could be clinically employed in future treatments.
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Affiliation(s)
- Linda Silina
- Institut Curie, CNRS, UMR144, Equipe Labellisée Ligue Contre le Cancer, PSL Research University, 75005 Paris, France
- INSERM U 1196/CNRS UMR 9187, Paris-Saclay Research University, 91405 Orsay, France
- Institut Curie, Bat. 112, Rue H. Becquerel, 91405 Orsay, France
| | - Florent Dufour
- Institut Curie, CNRS, UMR144, Equipe Labellisée Ligue Contre le Cancer, PSL Research University, 75005 Paris, France
| | - Audrey Rapinat
- Genomics Platform, Translational Research Department, Research Center, Institut Curie, Paris Sciences et Lettres (PSL) Research University, 75005 Paris, France
| | - Cécile Reyes
- Genomics Platform, Translational Research Department, Research Center, Institut Curie, Paris Sciences et Lettres (PSL) Research University, 75005 Paris, France
| | - David Gentien
- Genomics Platform, Translational Research Department, Research Center, Institut Curie, Paris Sciences et Lettres (PSL) Research University, 75005 Paris, France
| | - Fatlinda Maksut
- INSERM U 1196/CNRS UMR 9187, Paris-Saclay Research University, 91405 Orsay, France
- Institut Curie, Bat. 112, Rue H. Becquerel, 91405 Orsay, France
| | - François Radvanyi
- Institut Curie, CNRS, UMR144, Equipe Labellisée Ligue Contre le Cancer, PSL Research University, 75005 Paris, France
| | - Pierre Verrelle
- INSERM U 1196/CNRS UMR 9187, Paris-Saclay Research University, 91405 Orsay, France
- Institut Curie, Bat. 112, Rue H. Becquerel, 91405 Orsay, France
- Institut Curie-Hospital, Radiation Oncology Department, 75005 Paris, France
- Department of Radiation Oncology, Faculty of Medicine, Clermont Auvergne University, 63000 Clermont-Ferrand, France
| | - Isabelle Bernard-Pierrot
- Institut Curie, CNRS, UMR144, Equipe Labellisée Ligue Contre le Cancer, PSL Research University, 75005 Paris, France
| | - Frédérique Mégnin-Chanet
- INSERM U 1196/CNRS UMR 9187, Paris-Saclay Research University, 91405 Orsay, France
- Institut Curie, Bat. 112, Rue H. Becquerel, 91405 Orsay, France
- Correspondence:
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17
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Lei P, Zhang J, Liao P, Ren C, Wang J, Wang Y. Current progress and novel strategies that target CDK12 for drug discovery. Eur J Med Chem 2022; 240:114603. [PMID: 35868123 DOI: 10.1016/j.ejmech.2022.114603] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2022] [Revised: 07/08/2022] [Accepted: 07/08/2022] [Indexed: 02/05/2023]
Abstract
CDK12 is a cyclin-dependent kinase that plays critical roles in DNA replication, transcription, mRNA splicing, and DNA damage repair. CDK12 genomic changes, including mutation, amplification, deletion, and fusion, lead to various cancers, such as colorectal cancer, gastric cancer, and ovarian cancer. An increasing number of CDK12 inhibitors have been reported since CDK12 was identified as a biomarker and cancer therapeutic target. A major challenge lies in that CDK12 and CDK13 share highly similar sequences, which leads to great difficulties in the development of highly selective CDK12 inhibitors. In recent years, great efforts were made in developing selective CDK12 blockers. Techniques including PROTAC and molecular glue degraders were also applied to facilitate their development. Also, the drug combination strategy of CDK12 small molecule inhibitors were studied. This review discusses the latest studies on CDK12 inhibitors and analyzes their structure-activity relationships, shedding light on their further development.
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Affiliation(s)
- Peng Lei
- Targeted Tracer Research and Development Laboratory, Institute of Respiratory Health, Frontiers Science Center for Disease-related Molecular Network, Joint Research Institution of Altitude Health, National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, Chengdu, 610041, Sichuan, China; State Key Laboratory of Biotherapy and Cancer Center, Department of Respiratory and Critical Care Medicine, West China Hospital, Sichuan University, Chengdu, 610041, Sichuan, China
| | - Jifa Zhang
- Targeted Tracer Research and Development Laboratory, Institute of Respiratory Health, Frontiers Science Center for Disease-related Molecular Network, Joint Research Institution of Altitude Health, National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, Chengdu, 610041, Sichuan, China; State Key Laboratory of Biotherapy and Cancer Center, Department of Respiratory and Critical Care Medicine, West China Hospital, Sichuan University, Chengdu, 610041, Sichuan, China; Tianfu Jincheng Laboratory, Chengdu, 610041, Sichuan, China
| | - Peiyu Liao
- School of Pharmacy, Chengdu Medical College, Chengdu, 610500, Sichuan, China
| | - Changyu Ren
- Department of Pharmacy, Chengdu Fifth People's Hospital, Chengdu, 611130, Sichuan, China
| | - Jiaxing Wang
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Tennessee Health Science Center, Memphis, 38163, Tennessee, United States
| | - Yuxi Wang
- Targeted Tracer Research and Development Laboratory, Institute of Respiratory Health, Frontiers Science Center for Disease-related Molecular Network, Joint Research Institution of Altitude Health, National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, Chengdu, 610041, Sichuan, China; State Key Laboratory of Biotherapy and Cancer Center, Department of Respiratory and Critical Care Medicine, West China Hospital, Sichuan University, Chengdu, 610041, Sichuan, China; Tianfu Jincheng Laboratory, Chengdu, 610041, Sichuan, China.
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18
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Guiro J, Fagbemi M, Tellier M, Zaborowska J, Barker S, Fournier M, Murphy S. CAPTURE of the Human U2 snRNA Genes Expands the Repertoire of Associated Factors. Biomolecules 2022; 12:704. [PMID: 35625631 PMCID: PMC9138887 DOI: 10.3390/biom12050704] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2022] [Revised: 04/29/2022] [Accepted: 05/12/2022] [Indexed: 11/29/2022] Open
Abstract
In order to identify factors involved in transcription of human snRNA genes and 3' end processing of the transcripts, we have carried out CRISPR affinity purification in situ of regulatory elements (CAPTURE), which is deadCas9-mediated pull-down, of the tandemly repeated U2 snRNA genes in human cells. CAPTURE enriched many factors expected to be associated with these human snRNA genes including RNA polymerase II (pol II), Cyclin-Dependent Kinase 7 (CDK7), Negative Elongation Factor (NELF), Suppressor of Ty 5 (SPT5), Mediator 23 (MED23) and several subunits of the Integrator Complex. Suppressor of Ty 6 (SPT6); Cyclin K, the partner of Cyclin-Dependent Kinase 12 (CDK12) and Cyclin-Dependent Kinase 13 (CDK13); and SWI/SNF chromatin remodelling complex-associated SWI/SNF-related, Matrix-associated, Regulator of Chromatin (SMRC) factors were also enriched. Several polyadenylation factors, including Cleavage and Polyadenylation Specificity Factor 1 (CPSF1), Cleavage Stimulation Factors 1 and 2 (CSTF1,and CSTF2) were enriched by U2 gene CAPTURE. We have already shown by chromatin immunoprecipitation (ChIP) that CSTF2-and Pcf11 and Ssu72, which are also polyadenylation factors-are associated with the human U1 and U2 genes. ChIP-seq and ChIP-qPCR confirm the association of SPT6, Cyclin K, and CDK12 with the U2 genes. In addition, knockdown of SPT6 causes loss of subunit 3 of the Integrator Complex (INTS3) from the U2 genes, indicating a functional role in snRNA gene expression. CAPTURE has therefore expanded the repertoire of transcription and RNA processing factors associated with these genes and helped to identify a functional role for SPT6.
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Affiliation(s)
- Joana Guiro
- Sir William Dunn School of Pathology, University of Oxford, Oxford OX1 3RE, UK; (J.G.); (M.F.); (M.T.); (J.Z.); (S.B.)
| | - Mathias Fagbemi
- Sir William Dunn School of Pathology, University of Oxford, Oxford OX1 3RE, UK; (J.G.); (M.F.); (M.T.); (J.Z.); (S.B.)
| | - Michael Tellier
- Sir William Dunn School of Pathology, University of Oxford, Oxford OX1 3RE, UK; (J.G.); (M.F.); (M.T.); (J.Z.); (S.B.)
| | - Justyna Zaborowska
- Sir William Dunn School of Pathology, University of Oxford, Oxford OX1 3RE, UK; (J.G.); (M.F.); (M.T.); (J.Z.); (S.B.)
| | - Stephanie Barker
- Sir William Dunn School of Pathology, University of Oxford, Oxford OX1 3RE, UK; (J.G.); (M.F.); (M.T.); (J.Z.); (S.B.)
| | - Marjorie Fournier
- Advanced Proteomics Facility, Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK;
| | - Shona Murphy
- Sir William Dunn School of Pathology, University of Oxford, Oxford OX1 3RE, UK; (J.G.); (M.F.); (M.T.); (J.Z.); (S.B.)
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19
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Shi Z, Tian L, Qiang T, Li J, Xing Y, Ren X, Liu C, Liang C. From Structure Modification to Drug Launch: A Systematic Review of the Ongoing Development of Cyclin-Dependent Kinase Inhibitors for Multiple Cancer Therapy. J Med Chem 2022; 65:6390-6418. [PMID: 35485642 DOI: 10.1021/acs.jmedchem.1c02064] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Herein, we discuss more than 50 cyclin-dependent kinase (CDK) inhibitors that have been approved or have undergone clinical trials and their therapeutic application in multiple cancers. This review discusses the design strategies, structure-activity relationships, and efficacy performances of these selective or nonselective CDK inhibitors. The theoretical basis of early broad-spectrum CDK inhibitors is similar to the scope of chemotherapy, but because their toxicity is greater than the benefit, there is no clinical therapeutic window. The notion that selective CDK inhibitors have a safer therapeutic potential than pan-CDK inhibitors has been widely recognized during the research process. Four CDK4/6 inhibitors have been approved for the treatment of breast cancer or for prophylactic administration during chemotherapy to protect bone marrow and immune system function. Furthermore, the emerging strategies in the field of CDK inhibitors are summarized briefly, and CDKs continue to be widely pursued as emerging anticancer drug targets for drug discovery.
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Affiliation(s)
- Zhenfeng Shi
- Department of Urology Surgery Center, The People's Hospital of Xinjiang Uyghur Autonomous Region, Urumqi 830002, P. R. China
| | - Lei Tian
- College of Bioresources Chemical and Materials Engineering, Shaanxi University of Science & Technology, Xi'an 710021, P. R. China.,Faculty of Pharmacy, Shaanxi University of Science & Technology, Xi'an 710021, P. R. China
| | - Taotao Qiang
- College of Bioresources Chemical and Materials Engineering, Shaanxi University of Science & Technology, Xi'an 710021, P. R. China
| | - Jingyi Li
- Faculty of Pharmacy, Shaanxi University of Science & Technology, Xi'an 710021, P. R. China
| | - Yue Xing
- Faculty of Pharmacy, Shaanxi University of Science & Technology, Xi'an 710021, P. R. China
| | - Xiaodong Ren
- Medical College, Guizhou University, Guiyang 550025, P. R. China
| | - Chang Liu
- Zhuhai Jinan Selenium Source Nanotechnology Co., Ltd., Zhuhai 519030, P. R. China
| | - Chengyuan Liang
- Faculty of Pharmacy, Shaanxi University of Science & Technology, Xi'an 710021, P. R. China
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20
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Li J, Tiwari M, Chen Y, Luanpitpong S, Sen GL. CDK12 Is Necessary to Promote Epidermal Differentiation Through Transcription Elongation. Stem Cells 2022; 40:435-445. [PMID: 35325240 PMCID: PMC9199850 DOI: 10.1093/stmcls/sxac002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2021] [Accepted: 12/17/2021] [Indexed: 01/30/2023]
Abstract
Proper differentiation of the epidermis is essential to prevent water loss and to protect the body from the outside environment. Perturbations in this process can lead to a variety of skin diseases that impacts 1 in 5 people. While transcription factors that control epidermal differentiation have been well characterized, other aspects of transcription control such as elongation are poorly understood. Here we show that of the two cyclin-dependent kinases (CDK12 and CDK13), that are known to regulate transcription elongation, only CDK12 is necessary for epidermal differentiation. Depletion of CDK12 led to loss of differentiation gene expression and absence of skin barrier formation in regenerated human epidermis. CDK12 binds to genes that code for differentiation promoting transcription factors (GRHL3, KLF4, and OVOL1) and is necessary for their elongation. CDK12 is necessary for elongation by promoting Ser2 phosphorylation on the C-terminal domain of RNA polymerase II and the stabilization of binding of the elongation factor SPT6 to target genes. Our results suggest that control of transcription elongation by CDK12 plays a prominent role in adult cell fate decisions.
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Affiliation(s)
- Jingting Li
- Institute of Precision Medicine, Department of Burns, The First Affiliated Hospital, Sun Yat-Sen University, Guangzhou, Guangdong, China
| | - Manisha Tiwari
- Department of Dermatology and Department of Cellular and Molecular Medicine, UCSD Stem Cell Program, University of California, San Diego, La Jolla, CA, USA
| | - Yifang Chen
- Department of Dermatology and Department of Cellular and Molecular Medicine, UCSD Stem Cell Program, University of California, San Diego, La Jolla, CA, USA
| | - Sudjit Luanpitpong
- Siriraj Center of Excellence for Stem Cell Research, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkoknoi, Bangkok, Thailand
| | - George L Sen
- Department of Dermatology and Department of Cellular and Molecular Medicine, UCSD Stem Cell Program, University of California, San Diego, La Jolla, CA, USA
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21
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Cui X, Wu X, Wang H, Zhang S, Wang W, Jing X. Genetic of preimplantation diagnosis of dysmorphic facial features and intellectual developmental disorder (CHDFIDD) without congenital heart defects. Mol Genet Genomic Med 2022; 10:e1863. [PMID: 35034425 PMCID: PMC8830809 DOI: 10.1002/mgg3.1863] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2021] [Revised: 12/15/2021] [Accepted: 12/17/2021] [Indexed: 11/28/2022] Open
Abstract
Background Cyclin‐dependent kinase 13 plays a critical role in the regulation of gene transcription. Recent evidence suggests that heterozygous variants in CDK13 are associated with a syndromic form of mental deficiency and developmental delay, which is inherited in an autosomal dominant manner. Methods A mentally retarded mother (33‐year‐old) and son (10‐year‐old boy) in our hospital with CDK13 variant (c.2149 (exon 4) G>A. p.Gly717Arg) were detected by whole‐exome sequencing (WES). All published CDK13 variant syndrome cases as of November 11, 2021, were searched, and their clinical information was recorded and summarized. Results We studied two patients in a Chinese family with a heterozygous constitutional CDK13 variant (c.2149 (exon 4) G>A. p.Gly717Arg), exhibiting the classical characteristics of dysmorphic facial features and intellectual developmental disorder (CHDFIDD, OMIM # 617360), without congenital heart defects. This is the first reported case of an adult patient with a CDK13 variant that gave birth to the next generation with the same variant. Preimplantation genetic testing for monogenic disease (PGT‐M) was performed for the proband and her husband with full informed consent and successfully blocked the inheritance of the disease. Conclusion Our study is of great significance for molecular diagnosis and genetic counseling of patients with CDHFIDD and extends the variant spectrum of CDK13.
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Affiliation(s)
- Xiangrong Cui
- Reproductive Medicine Center, Children's Hospital of Shanxi and Women Health Center of Shanxi, Affiliated of Shanxi Medical University, Taiyuan, China
| | - Xueqing Wu
- Reproductive Medicine Center, Children's Hospital of Shanxi and Women Health Center of Shanxi, Affiliated of Shanxi Medical University, Taiyuan, China
| | - Hongwei Wang
- Department of Hematology, 2nd Hospital of Shanxi Medical University, Taiyuan, China
| | - Sanyuan Zhang
- Department of Gynecology, First Hospital of Shanxi Medical University, Taiyuan, China
| | - Wei Wang
- Chigene Translational Medicine Research Center, Beijing, China
| | - Xuan Jing
- Clinical Laboratory, Shanxi Prov. People's Hospital, Affiliated of Shanxi Medical University, Taiyuan, China
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22
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Liu Y, Fu L, Wu J, Liu M, Wang G, Liu B, Zhang L. Transcriptional cyclin-dependent kinases: Potential drug targets in cancer therapy. Eur J Med Chem 2021; 229:114056. [PMID: 34942431 DOI: 10.1016/j.ejmech.2021.114056] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2021] [Revised: 12/14/2021] [Accepted: 12/14/2021] [Indexed: 02/08/2023]
Abstract
In the wake of the development of the concept of cell cycle and its limiting points, cyclin-dependent kinases (CDKs) are considered to play a central role in regulating cell cycle progression. Recent studies have strongly demonstrated that CDKs also has multiple functions, especially in response to extracellular and intracellular signals by interfering with transcriptional events. Consequently, how to inhibit their function has been a hot research topic. It is worth noting that the key role of CDKs in regulating transcription has been explored in recent years, but its related pharmacological targets are less developed, and most inhibitors have not entered the clinical stage. Accordingly, this perspective focus on the biological functions of transcription related CDKs and their complexes, some key upstream and downstream signals, and inhibitors for cancer treatment in recent years. In addition, some corresponding combined treatment strategies will provide a more novel perspective for future cancer remedy.
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Affiliation(s)
- Yi Liu
- Sichuan Engineering Research Center for Biomimetic Synthesis of Natural Drugs, School of Life Science and Engineering, Southwest Jiaotong University, 610031, Chengdu, China
| | - Leilei Fu
- Sichuan Engineering Research Center for Biomimetic Synthesis of Natural Drugs, School of Life Science and Engineering, Southwest Jiaotong University, 610031, Chengdu, China
| | - Junhao Wu
- Department of Otolaryngology, Head and Neck Surgery, West China Hospital, Sichuan University, Chengdu, China
| | - Ming Liu
- Department of Orthopedics, West China Hospital, Sichuan University, Chengdu, 610041, China.
| | - Guan Wang
- State Key Laboratory of Biotherapy and Cancer Center, Innovation Center of Nursing Research, Nursing Key Laboratory of Sichuan Province, West China Hospital, and Collaborative Innovation Center of Biotherapy, Sichuan University, Chengdu, 610041, China.
| | - Bo Liu
- State Key Laboratory of Biotherapy and Cancer Center, Innovation Center of Nursing Research, Nursing Key Laboratory of Sichuan Province, West China Hospital, and Collaborative Innovation Center of Biotherapy, Sichuan University, Chengdu, 610041, China
| | - Lan Zhang
- Sichuan Engineering Research Center for Biomimetic Synthesis of Natural Drugs, School of Life Science and Engineering, Southwest Jiaotong University, 610031, Chengdu, China.
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23
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Disrupting the Molecular Pathway in Myotonic Dystrophy. Int J Mol Sci 2021; 22:ijms222413225. [PMID: 34948025 PMCID: PMC8708683 DOI: 10.3390/ijms222413225] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2021] [Revised: 12/03/2021] [Accepted: 12/06/2021] [Indexed: 01/26/2023] Open
Abstract
Myotonic dystrophy is the most common muscular dystrophy in adults. It consists of two forms: type 1 (DM1) and type 2 (DM2). DM1 is associated with a trinucleotide repeat expansion mutation, which is transcribed but not translated into protein. The mutant RNA remains in the nucleus, which leads to a series of downstream abnormalities. DM1 is widely considered to be an RNA-based disorder. Thus, we consider three areas of the RNA pathway that may offer targeting opportunities to disrupt the production, stability, and degradation of the mutant RNA.
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24
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Mandal R, Becker S, Strebhardt K. Targeting CDK9 for Anti-Cancer Therapeutics. Cancers (Basel) 2021; 13:2181. [PMID: 34062779 PMCID: PMC8124690 DOI: 10.3390/cancers13092181] [Citation(s) in RCA: 50] [Impact Index Per Article: 16.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2021] [Revised: 04/28/2021] [Accepted: 04/29/2021] [Indexed: 12/23/2022] Open
Abstract
Cyclin Dependent Kinase 9 (CDK9) is one of the most important transcription regulatory members of the CDK family. In conjunction with its main cyclin partner-Cyclin T1, it forms the Positive Transcription Elongation Factor b (P-TEFb) whose primary function in eukaryotic cells is to mediate the positive transcription elongation of nascent mRNA strands, by phosphorylating the S2 residues of the YSPTSPS tandem repeats at the C-terminus domain (CTD) of RNA Polymerase II (RNAP II). To aid in this process, P-TEFb also simultaneously phosphorylates and inactivates a number of negative transcription regulators like 5,6-dichloro-1-β-D-ribofuranosylbenzimidazole (DRB) Sensitivity-Inducing Factor (DSIF) and Negative Elongation Factor (NELF). Significantly enhanced activity of CDK9 is observed in multiple cancer types, which is universally associated with significantly shortened Overall Survival (OS) of the patients. In these cancer types, CDK9 regulates a plethora of cellular functions including proliferation, survival, cell cycle regulation, DNA damage repair and metastasis. Due to the extremely critical role of CDK9 in cancer cells, inhibiting its functions has been the subject of intense research, resulting the development of multiple, increasingly specific small-molecule inhibitors, some of which are presently in clinical trials. The search for newer generation CDK9 inhibitors with higher specificity and lower potential toxicities and suitable combination therapies continues. In fact, the Phase I clinical trials of the latest, highly specific CDK9 inhibitor BAY1251152, against different solid tumors have shown good anti-tumor and on-target activities and pharmacokinetics, combined with manageable safety profile while the phase I and II clinical trials of another inhibitor AT-7519 have been undertaken or are undergoing. To enhance the effectiveness and target diversity and reduce potential drug-resistance, the future of CDK9 inhibition would likely involve combining CDK9 inhibitors with inhibitors like those against BRD4, SEC, MYC, MCL-1 and HSP90.
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Affiliation(s)
- Ranadip Mandal
- Department of Gynecology and Obstetrics, Johann Wolfgang Goethe University, Theodor-Stern-Kai 7, 60590 Frankfurt am Main, Germany; (R.M.); (S.B.)
| | - Sven Becker
- Department of Gynecology and Obstetrics, Johann Wolfgang Goethe University, Theodor-Stern-Kai 7, 60590 Frankfurt am Main, Germany; (R.M.); (S.B.)
| | - Klaus Strebhardt
- Department of Gynecology and Obstetrics, Johann Wolfgang Goethe University, Theodor-Stern-Kai 7, 60590 Frankfurt am Main, Germany; (R.M.); (S.B.)
- German Cancer Consortium (DKTK), 69120 Heidelberg, Germany
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25
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Jiang B, Jiang J, Kaltheuner IH, Iniguez AB, Anand K, Ferguson FM, Ficarro SB, Seong BKA, Greifenberg AK, Dust S, Kwiatkowski NP, Marto JA, Stegmaier K, Zhang T, Geyer M, Gray NS. Structure-activity relationship study of THZ531 derivatives enables the discovery of BSJ-01-175 as a dual CDK12/13 covalent inhibitor with efficacy in Ewing sarcoma. Eur J Med Chem 2021; 221:113481. [PMID: 33945934 DOI: 10.1016/j.ejmech.2021.113481] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2021] [Revised: 04/13/2021] [Accepted: 04/14/2021] [Indexed: 12/22/2022]
Abstract
Development of inhibitors targeting CDK12/13 is of increasing interest as a potential therapy for cancers as these compounds inhibit transcription of DNA damage response (DDR) genes. We previously described THZ531, a covalent inhibitor with selectivity for CDK12/13. In order to elucidate structure-activity relationship (SAR), we have undertaken a medicinal chemistry campaign and established a focused library of THZ531 analogs. Among these analogs, BSJ-01-175 demonstrates exquisite selectivity, potent inhibition of RNA polymerase II phosphorylation, and downregulation of CDK12-targeted genes in cancer cells. A 3.0 Å co-crystal structure with CDK12/CycK provides a structural rational for selective targeting of Cys1039 located in a C-terminal extension from the kinase domain. With moderate pharmacokinetic properties, BSJ-01-175 exhibits efficacy against an Ewing sarcoma tumor growth in a patient-derived xenograft (PDX) mouse model following 10 mg/kg once a day, intraperitoneal administration. Taken together, BSJ-01-175 represents the first selective CDK12/13 covalent inhibitor with in vivo efficacy reported to date.
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Affiliation(s)
- Baishan Jiang
- Department of Cancer Biology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, 02115, USA; Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, 02115, USA
| | - Jie Jiang
- Department of Cancer Biology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, 02115, USA; Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, 02115, USA
| | - Ines H Kaltheuner
- Institute of Structural Biology, University of Bonn, Venusberg-Campus 1, 53127, Bonn, Germany
| | - Amanda Balboni Iniguez
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, 02115, USA; The Broad Institute, Cambridge, MA, 02142, USA
| | - Kanchan Anand
- Institute of Structural Biology, University of Bonn, Venusberg-Campus 1, 53127, Bonn, Germany
| | - Fleur M Ferguson
- Department of Cancer Biology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, 02115, USA; Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, 02115, USA
| | - Scott B Ficarro
- Department of Cancer Biology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, 02115, USA; Blais Proteomics Center, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, 02215, USA
| | - Bo Kyung Alex Seong
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, 02115, USA; The Broad Institute, Cambridge, MA, 02142, USA
| | - Ann Katrin Greifenberg
- Institute of Structural Biology, University of Bonn, Venusberg-Campus 1, 53127, Bonn, Germany
| | - Sofia Dust
- Institute of Structural Biology, University of Bonn, Venusberg-Campus 1, 53127, Bonn, Germany
| | - Nicholas P Kwiatkowski
- Department of Cancer Biology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, 02115, USA; Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, 02115, USA
| | - Jarrod A Marto
- Department of Cancer Biology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, 02115, USA; Blais Proteomics Center, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, 02215, USA
| | - Kimberly Stegmaier
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, 02115, USA; The Broad Institute, Cambridge, MA, 02142, USA
| | - Tinghu Zhang
- Department of Cancer Biology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, 02115, USA; Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, 02115, USA
| | - Matthias Geyer
- Institute of Structural Biology, University of Bonn, Venusberg-Campus 1, 53127, Bonn, Germany
| | - Nathanael S Gray
- Department of Cancer Biology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, 02115, USA; Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, 02115, USA.
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26
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Dodge MJ, MacNeil KM, Tessier TM, Weinberg JB, Mymryk JS. Emerging antiviral therapeutics for human adenovirus infection: Recent developments and novel strategies. Antiviral Res 2021; 188:105034. [PMID: 33577808 DOI: 10.1016/j.antiviral.2021.105034] [Citation(s) in RCA: 37] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2020] [Revised: 02/04/2021] [Accepted: 02/05/2021] [Indexed: 12/11/2022]
Abstract
Human adenoviruses (HAdV) are ubiquitous human pathogens that cause a significant burden of respiratory, ocular, and gastrointestinal illnesses. Although HAdV infections are generally self-limiting, pediatric and immunocompromised individuals are at particular risk for developing severe disease. Currently, no approved antiviral therapies specific to HAdV exist. Recent outbreaks underscore the need for effective antiviral agents to treat life-threatening infections. In this review we will focus on recent developments in search of potential therapeutic agents for controlling HAdV infections, with a focus on those targeting post-entry stages of the virus replicative cycle.
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Affiliation(s)
- Mackenzie J Dodge
- Department of Microbiology and Immunology, The University of Western Ontario, London, ON, Canada
| | - Katelyn M MacNeil
- Department of Microbiology and Immunology, The University of Western Ontario, London, ON, Canada
| | - Tanner M Tessier
- Department of Microbiology and Immunology, The University of Western Ontario, London, ON, Canada
| | - Jason B Weinberg
- Department of Pediatrics, University of Michigan, Ann Arbor, MI, USA; Department of Microbiology and Immunology, University of Michigan, Ann Arbor, MI, USA
| | - Joe S Mymryk
- Department of Microbiology and Immunology, The University of Western Ontario, London, ON, Canada; Department of Otolaryngology, Head & Neck Surgery, The University of Western Ontario, London, ON, Canada; Department of Oncology, The University of Western Ontario, London, ON, Canada; London Regional Cancer Program, Lawson Health Research Institute, London, ON, Canada.
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27
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The promise and current status of CDK12/13 inhibition for the treatment of cancer. Future Med Chem 2020; 13:117-141. [PMID: 33295810 DOI: 10.4155/fmc-2020-0240] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
CDK12 and CDK13 are Ser/Thr protein kinases that regulate transcription and co-transcriptional processes. Genetic silencing of CDK12 is associated with genomic instability in a variety of cancers, including difficult-to-treat breast, ovarian, colorectal, brain and pancreatic cancers, and is synthetic lethal with PARP, MYC or EWS/FLI inhibition. CDK13 is amplified in hepatocellular carcinoma. Consequently, selective CDK12/13 inhibitors constitute powerful research tools as well as promising anti-cancer therapeutics, either alone or in combination therapy. Herein the authors discuss the role of CDK12 and CDK13 in normal and cancer cells, describe their utility as a biomarker and therapeutic target, review the medicinal chemistry optimization of existing CDK12/13 inhibitors and outline strategies for the rational design of CDK12/13 selective inhibitors.
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28
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Yao G, Tang J, Yang X, Zhao Y, Zhou R, Meng R, Zhang S, Dong X, Zhang T, Yang K, Wu G, Xu S. Cyclin K interacts with β-catenin to induce Cyclin D1 expression and facilitates tumorigenesis and radioresistance in lung cancer. Am J Cancer Res 2020; 10:11144-11158. [PMID: 33042275 PMCID: PMC7532664 DOI: 10.7150/thno.42578] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2019] [Accepted: 08/24/2020] [Indexed: 12/16/2022] Open
Abstract
Rationale: Radioresistance remains the major cause of local relapse and distant metastasis in lung cancer. However, the underlying molecular mechanisms remain poorly defined. This study aimed to investigate the role and regulatory mechanism of Cyclin K in lung cancer radioresistance. Methods: Expression levels of Cyclin K were measured by immunohistochemistry in human lung cancer tissues and adjacent normal lung tissues. Cell growth and proliferation, neutral comet and foci formation assays, G2/M checkpoint and a xenograft mouse model were used for functional analyses. Gene expression was examined by RNA sequencing and quantitative real-time PCR. Protein-protein interaction was assessed by immunoprecipitation and GST pull-down assays. Results: We report that Cyclin K is frequently overexpressed and correlates with poor prognosis in lung cancer patients. Functionally, we demonstrate that Cyclin K depletion results in reduced proliferation, defective G2/M checkpoint and enhanced radiosensitivity in lung cancer. Mechanistically, we reveal that Cyclin K interacts with and promotes the stabilization of β-catenin protein, thereby upregulating the expression of Cyclin D1. More importantly, we show that Cyclin D1 is the major effector that mediates the biological functions of Cyclin K in lung cancer. Conclusions: These findings suggest that Cyclin K positively modulates the β-catenin/Cyclin D1 axis to promote tumorigenesis and radioresistance in lung cancer, indicating that Cyclin K may represent a novel attractive biomarker for lung cancer radiotherapy.
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29
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Liang S, Hu L, Wu Z, Chen Z, Liu S, Xu X, Qian A. CDK12: A Potent Target and Biomarker for Human Cancer Therapy. Cells 2020; 9:E1483. [PMID: 32570740 PMCID: PMC7349380 DOI: 10.3390/cells9061483] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2020] [Revised: 06/07/2020] [Accepted: 06/10/2020] [Indexed: 01/01/2023] Open
Abstract
Cyclin-dependent kinases (CDKs) are a group of serine/threonine protein kinases and play crucial roles in various cellular processes by regulating cell cycle and gene transcription. Cyclin-dependent kinase 12 (CDK12) is an important transcription-associated CDK. It shows versatile roles in regulating gene transcription, RNA splicing, translation, DNA damage response (DDR), cell cycle progression and cell proliferation. Recently, increasing evidence demonstrates the important role of CDK12 in various human cancers, illustrating it as both a biomarker of cancer and a potential target for cancer therapy. Here, we summarize the current knowledge of CDK12, and review the research advances of CDK12's biological functions, especially its role in human cancers and as a potential target and biomarker for cancer therapy.
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Affiliation(s)
- Shujing Liang
- Laboratory for Bone Metabolism, Xi’an Key Laboratory of Special Medicine and Health Engineering, Northwestern Polytechnical University, Xi’an 710072, China; (S.L.); (L.H.); (Z.W.); (Z.C.); (S.L.); (X.X.)
- Key Laboratory for Space Biosciences and Biotechnology, Research Center for Special Medicine and Health Systems Engineering, Northwestern Polytechnical University, Xi’an 710072, China
- NPU-UAB Joint Laboratory for Bone Metabolism, School of Life Sciences, Northwestern Polytechnical University, Xi’an 710072, China
| | - Lifang Hu
- Laboratory for Bone Metabolism, Xi’an Key Laboratory of Special Medicine and Health Engineering, Northwestern Polytechnical University, Xi’an 710072, China; (S.L.); (L.H.); (Z.W.); (Z.C.); (S.L.); (X.X.)
- Key Laboratory for Space Biosciences and Biotechnology, Research Center for Special Medicine and Health Systems Engineering, Northwestern Polytechnical University, Xi’an 710072, China
- NPU-UAB Joint Laboratory for Bone Metabolism, School of Life Sciences, Northwestern Polytechnical University, Xi’an 710072, China
| | - Zixiang Wu
- Laboratory for Bone Metabolism, Xi’an Key Laboratory of Special Medicine and Health Engineering, Northwestern Polytechnical University, Xi’an 710072, China; (S.L.); (L.H.); (Z.W.); (Z.C.); (S.L.); (X.X.)
- Key Laboratory for Space Biosciences and Biotechnology, Research Center for Special Medicine and Health Systems Engineering, Northwestern Polytechnical University, Xi’an 710072, China
- NPU-UAB Joint Laboratory for Bone Metabolism, School of Life Sciences, Northwestern Polytechnical University, Xi’an 710072, China
| | - Zhihao Chen
- Laboratory for Bone Metabolism, Xi’an Key Laboratory of Special Medicine and Health Engineering, Northwestern Polytechnical University, Xi’an 710072, China; (S.L.); (L.H.); (Z.W.); (Z.C.); (S.L.); (X.X.)
- Key Laboratory for Space Biosciences and Biotechnology, Research Center for Special Medicine and Health Systems Engineering, Northwestern Polytechnical University, Xi’an 710072, China
- NPU-UAB Joint Laboratory for Bone Metabolism, School of Life Sciences, Northwestern Polytechnical University, Xi’an 710072, China
| | - Shuyu Liu
- Laboratory for Bone Metabolism, Xi’an Key Laboratory of Special Medicine and Health Engineering, Northwestern Polytechnical University, Xi’an 710072, China; (S.L.); (L.H.); (Z.W.); (Z.C.); (S.L.); (X.X.)
- Key Laboratory for Space Biosciences and Biotechnology, Research Center for Special Medicine and Health Systems Engineering, Northwestern Polytechnical University, Xi’an 710072, China
- NPU-UAB Joint Laboratory for Bone Metabolism, School of Life Sciences, Northwestern Polytechnical University, Xi’an 710072, China
| | - Xia Xu
- Laboratory for Bone Metabolism, Xi’an Key Laboratory of Special Medicine and Health Engineering, Northwestern Polytechnical University, Xi’an 710072, China; (S.L.); (L.H.); (Z.W.); (Z.C.); (S.L.); (X.X.)
- Key Laboratory for Space Biosciences and Biotechnology, Research Center for Special Medicine and Health Systems Engineering, Northwestern Polytechnical University, Xi’an 710072, China
- NPU-UAB Joint Laboratory for Bone Metabolism, School of Life Sciences, Northwestern Polytechnical University, Xi’an 710072, China
| | - Airong Qian
- Laboratory for Bone Metabolism, Xi’an Key Laboratory of Special Medicine and Health Engineering, Northwestern Polytechnical University, Xi’an 710072, China; (S.L.); (L.H.); (Z.W.); (Z.C.); (S.L.); (X.X.)
- Key Laboratory for Space Biosciences and Biotechnology, Research Center for Special Medicine and Health Systems Engineering, Northwestern Polytechnical University, Xi’an 710072, China
- NPU-UAB Joint Laboratory for Bone Metabolism, School of Life Sciences, Northwestern Polytechnical University, Xi’an 710072, China
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30
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Lyons DE, McMahon S, Ott M. A combinatorial view of old and new RNA polymerase II modifications. Transcription 2020; 11:66-82. [PMID: 32401151 DOI: 10.1080/21541264.2020.1762468] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
The production of mRNA is a dynamic process that is highly regulated by reversible post-translational modifications of the C-terminal domain (CTD) of RNA polymerase II. The CTD is a highly repetitive domain consisting mostly of the consensus heptad sequence Tyr1-Ser2-Pro3-Thr4-Ser5-Pro6-Ser7. Phosphorylation of serine residues within this repeat sequence is well studied, but modifications of all residues have been described. Here, we focus on integrating newly identified and lesser-studied CTD post-translational modifications into the existing framework. We also review the growing body of work demonstrating crosstalk between different CTD modifications and the functional consequences of such crosstalk on the dynamics of transcriptional regulation.
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Affiliation(s)
- Danielle E Lyons
- Gladstone Institute of Virology and Immunology, San Francisco, CA, USA
| | - Sarah McMahon
- Gladstone Institute of Virology and Immunology, San Francisco, CA, USA.,Department of Medicine, University of California, San Francisco , San Francisco, CA, USA
| | - Melanie Ott
- Gladstone Institute of Virology and Immunology, San Francisco, CA, USA.,Department of Medicine, University of California, San Francisco , San Francisco, CA, USA
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31
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Therapeutic Targeting of the General RNA Polymerase II Transcription Machinery. Int J Mol Sci 2020; 21:ijms21093354. [PMID: 32397434 PMCID: PMC7246882 DOI: 10.3390/ijms21093354] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2020] [Revised: 05/06/2020] [Accepted: 05/07/2020] [Indexed: 12/27/2022] Open
Abstract
Inhibitors targeting the general RNA polymerase II (RNAPII) transcription machinery are candidate therapeutics in cancer and other complex diseases. Here, we review the molecular targets and mechanisms of action of these compounds, framing them within the steps of RNAPII transcription. We discuss the effects of transcription inhibitors in vitro and in cellular models (with an emphasis on cancer), as well as their efficacy in preclinical and clinical studies. We also discuss the rationale for inhibiting broadly acting transcriptional regulators or RNAPII itself in complex diseases.
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32
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Gajdušková P, Ruiz de Los Mozos I, Rájecký M, Hluchý M, Ule J, Blazek D. CDK11 is required for transcription of replication-dependent histone genes. Nat Struct Mol Biol 2020; 27:500-510. [PMID: 32367068 PMCID: PMC7116321 DOI: 10.1038/s41594-020-0406-8] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2019] [Accepted: 03/05/2020] [Indexed: 01/13/2023]
Abstract
Replication-dependent histones (RDH) are required for packaging of newly synthetized DNA into nucleosomes during S-phase when their expression is highly upregulated. However, the mechanisms of this upregulation in metazoan cells remain poorly understood. Using iCLIP and ChIP-seq, we found that human cyclin-dependent kinase 11 (CDK11) associates with RNA and chromatin of RDH genes primarily in the S-phase. Moreover, its N-terminal region binds FLASH, RDH-specific 3´end processing factor, which keeps the kinase on the chromatin. CDK11 phosphorylates serine 2 (Ser2) of the C-terminal domain (CTD) of RNA polymerase II (RNAPII), which is initiated at the middle of RDH genes and is required for further RNAPII elongation and 3´end processing. CDK11 depletion leads to decreased number of cells in S-phase, likely due to the function of CDK11 in RDH gene expression. Thus, the reliance of RDH expression on CDK11 could explain why CDK11 is essential for growth of many cancers.
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Affiliation(s)
- Pavla Gajdušková
- Central European Institute of Technology (CEITEC), Masaryk University, Brno, Czech Republic
| | - Igor Ruiz de Los Mozos
- The Francis Crick Institute, London, UK.,Department of Neuromuscular Disease, Institute of Neurology, University College London, London, UK
| | - Michal Rájecký
- Central European Institute of Technology (CEITEC), Masaryk University, Brno, Czech Republic
| | - Milan Hluchý
- Central European Institute of Technology (CEITEC), Masaryk University, Brno, Czech Republic
| | - Jernej Ule
- The Francis Crick Institute, London, UK.,Department of Neuromuscular Disease, Institute of Neurology, University College London, London, UK
| | - Dalibor Blazek
- Central European Institute of Technology (CEITEC), Masaryk University, Brno, Czech Republic.
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33
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Bai N, Xia F, Wang W, Lei Y, Bo J, Li X. CDK12 promotes papillary thyroid cancer progression through regulating the c-myc/β-catenin pathway. J Cancer 2020; 11:4308-4315. [PMID: 32489449 PMCID: PMC7255385 DOI: 10.7150/jca.42849] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2019] [Accepted: 03/29/2020] [Indexed: 12/14/2022] Open
Abstract
Background: CDK12 is a potential therapeutic target in papillary thyroid cancer that regulates the c-myc/β-catenin pathway. Objective: We aimed to explore the specific mechanism of CDK12 in papillary thyroid cancer and provide a new target of cancer therapy. Methods: RT-qPCR was used to determine the CDK12 mRNA expression level. An IHC assay was performed to detect the tissue expression of CDK12. Then, we downregulated CDK12 expression in the thyroid cancer cell lines TPC-1-shCDK12 and KAT-5-shCDK12. CCK8 assays, colony formation assays, and animal xenograft models were used to evaluate the effect of CDK12 on tumorigenesis. Transwell assays and in vivo metastasis models were used to observe whether CDK12 can promote cancer metastasis. Western blotting further confirmed the mechanism of CDK12 in papillary thyroid cancer through the c-myc/β-catenin pathway. Results: Upregulated CDK12 expression in papillary thyroid cancer promoted papillary thyroid cancer carcinogenesis in vivo, and in vitro CDK12 strengthened papillary thyroid cancer (PTC) cell migration and tumor metastasis. CDK12 promoted tumor progression by regulating c-myc/β-catenin pathway activation. Conclusions: CDK12 affects the c-myc/β-catenin pathway to stimulate papillary thyroid cancer proliferation and metastasis. Inhibiting CDK12 might be a new method in papillary thyroid cancer therapy.
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Affiliation(s)
- Ning Bai
- Department of General Surgery, Xiangya Hospital, Central South University, Changsha, China
| | - Fada Xia
- Department of General Surgery, Xiangya Hospital, Central South University, Changsha, China
| | - Wenlong Wang
- Department of General Surgery, Xiangya Hospital, Central South University, Changsha, China
| | - Yao Lei
- Department of General Surgery, Xiangya Hospital, Central South University, Changsha, China
| | - Jiang Bo
- Department of General Surgery, Xiangya Hospital, Central South University, Changsha, China
| | - Xinying Li
- Department of General Surgery, Xiangya Hospital, Central South University, Changsha, China
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Ding L, Cao J, Lin W, Chen H, Xiong X, Ao H, Yu M, Lin J, Cui Q. The Roles of Cyclin-Dependent Kinases in Cell-Cycle Progression and Therapeutic Strategies in Human Breast Cancer. Int J Mol Sci 2020; 21:ijms21061960. [PMID: 32183020 PMCID: PMC7139603 DOI: 10.3390/ijms21061960] [Citation(s) in RCA: 250] [Impact Index Per Article: 62.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2019] [Revised: 02/23/2020] [Accepted: 02/24/2020] [Indexed: 12/12/2022] Open
Abstract
Cyclin-dependent kinases (CDKs) are serine/threonine kinases whose catalytic activities are regulated by interactions with cyclins and CDK inhibitors (CKIs). CDKs are key regulatory enzymes involved in cell proliferation through regulating cell-cycle checkpoints and transcriptional events in response to extracellular and intracellular signals. Not surprisingly, the dysregulation of CDKs is a hallmark of cancers, and inhibition of specific members is considered an attractive target in cancer therapy. In breast cancer (BC), dual CDK4/6 inhibitors, palbociclib, ribociclib, and abemaciclib, combined with other agents, were approved by the Food and Drug Administration (FDA) recently for the treatment of hormone receptor positive (HR+) advanced or metastatic breast cancer (A/MBC), as well as other sub-types of breast cancer. Furthermore, ongoing studies identified more selective CDK inhibitors as promising clinical targets. In this review, we focus on the roles of CDKs in driving cell-cycle progression, cell-cycle checkpoints, and transcriptional regulation, a highlight of dysregulated CDK activation in BC. We also discuss the most relevant CDK inhibitors currently in clinical BC trials, with special emphasis on CDK4/6 inhibitors used for the treatment of estrogen receptor-positive (ER+)/human epidermal growth factor 2-negative (HER2−) M/ABC patients, as well as more emerging precise therapeutic strategies, such as combination therapies and microRNA (miRNA) therapy.
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Affiliation(s)
- Lei Ding
- Lab of Biochemistry & Molecular Biology, School of Life Sciences, Yunnan University, Kunming 650091, China; (L.D.); (J.C.); (W.L.); (H.C.); (X.X.); (H.A.); (M.Y.); (J.L.)
- Key Lab of Molecular Cancer Biology, Yunnan Education Department, Kunming 650091, China
| | - Jiaqi Cao
- Lab of Biochemistry & Molecular Biology, School of Life Sciences, Yunnan University, Kunming 650091, China; (L.D.); (J.C.); (W.L.); (H.C.); (X.X.); (H.A.); (M.Y.); (J.L.)
- Key Lab of Molecular Cancer Biology, Yunnan Education Department, Kunming 650091, China
| | - Wen Lin
- Lab of Biochemistry & Molecular Biology, School of Life Sciences, Yunnan University, Kunming 650091, China; (L.D.); (J.C.); (W.L.); (H.C.); (X.X.); (H.A.); (M.Y.); (J.L.)
- Key Lab of Molecular Cancer Biology, Yunnan Education Department, Kunming 650091, China
| | - Hongjian Chen
- Lab of Biochemistry & Molecular Biology, School of Life Sciences, Yunnan University, Kunming 650091, China; (L.D.); (J.C.); (W.L.); (H.C.); (X.X.); (H.A.); (M.Y.); (J.L.)
- Key Lab of Molecular Cancer Biology, Yunnan Education Department, Kunming 650091, China
| | - Xianhui Xiong
- Lab of Biochemistry & Molecular Biology, School of Life Sciences, Yunnan University, Kunming 650091, China; (L.D.); (J.C.); (W.L.); (H.C.); (X.X.); (H.A.); (M.Y.); (J.L.)
- Key Lab of Molecular Cancer Biology, Yunnan Education Department, Kunming 650091, China
| | - Hongshun Ao
- Lab of Biochemistry & Molecular Biology, School of Life Sciences, Yunnan University, Kunming 650091, China; (L.D.); (J.C.); (W.L.); (H.C.); (X.X.); (H.A.); (M.Y.); (J.L.)
- Key Lab of Molecular Cancer Biology, Yunnan Education Department, Kunming 650091, China
| | - Min Yu
- Lab of Biochemistry & Molecular Biology, School of Life Sciences, Yunnan University, Kunming 650091, China; (L.D.); (J.C.); (W.L.); (H.C.); (X.X.); (H.A.); (M.Y.); (J.L.)
- Key Lab of Molecular Cancer Biology, Yunnan Education Department, Kunming 650091, China
| | - Jie Lin
- Lab of Biochemistry & Molecular Biology, School of Life Sciences, Yunnan University, Kunming 650091, China; (L.D.); (J.C.); (W.L.); (H.C.); (X.X.); (H.A.); (M.Y.); (J.L.)
- Key Lab of Molecular Cancer Biology, Yunnan Education Department, Kunming 650091, China
| | - Qinghua Cui
- Lab of Biochemistry & Molecular Biology, School of Life Sciences, Yunnan University, Kunming 650091, China; (L.D.); (J.C.); (W.L.); (H.C.); (X.X.); (H.A.); (M.Y.); (J.L.)
- Key Lab of Molecular Cancer Biology, Yunnan Education Department, Kunming 650091, China
- Correspondence:
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Pilarova K, Herudek J, Blazek D. CDK12: cellular functions and therapeutic potential of versatile player in cancer. NAR Cancer 2020; 2:zcaa003. [PMID: 34316683 PMCID: PMC8210036 DOI: 10.1093/narcan/zcaa003] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2020] [Revised: 02/14/2020] [Accepted: 02/20/2020] [Indexed: 12/16/2022] Open
Abstract
Cyclin-dependent kinase 12 (CDK12) phosphorylates the C-terminal domain of RNA polymerase II and is needed for the optimal transcription elongation and translation of a subset of human protein-coding genes. The kinase has a pleiotropic effect on the maintenance of genome stability, and its inactivation in prostate and ovarian tumours results in focal tandem duplications, a CDK12-unique genome instability phenotype. CDK12 aberrations were found in many other malignancies and have the potential to be used as biomarkers for therapeutic intervention. Moreover, the inhibition of CDK12 emerges as a promising strategy for treatment in several types of cancers. In this review, we summarize mechanisms that CDK12 utilizes for the regulation of gene expression and discuss how the perturbation of CDK12-sensitive genes contributes to the disruption of cell cycle progression and the onset of genome instability. Furthermore, we describe tumour-suppressive and oncogenic functions of CDK12 and its potential as a biomarker and inhibition target in anti-tumour treatments.
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Affiliation(s)
- Kveta Pilarova
- Central European Institute of Technology (CEITEC), Masaryk University, 62500 Brno, Czech Republic
| | - Jan Herudek
- Central European Institute of Technology (CEITEC), Masaryk University, 62500 Brno, Czech Republic
| | - Dalibor Blazek
- Central European Institute of Technology (CEITEC), Masaryk University, 62500 Brno, Czech Republic
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36
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Chou J, Quigley DA, Robinson TM, Feng FY, Ashworth A. Transcription-Associated Cyclin-Dependent Kinases as Targets and Biomarkers for Cancer Therapy. Cancer Discov 2020; 10:351-370. [DOI: 10.1158/2159-8290.cd-19-0528] [Citation(s) in RCA: 105] [Impact Index Per Article: 26.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2019] [Revised: 09/29/2019] [Accepted: 11/04/2019] [Indexed: 11/16/2022]
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37
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Shen S, Dean DC, Yu Z, Duan Z. Role of cyclin-dependent kinases (CDKs) in hepatocellular carcinoma: Therapeutic potential of targeting the CDK signaling pathway. Hepatol Res 2019; 49:1097-1108. [PMID: 31009153 DOI: 10.1111/hepr.13353] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/20/2018] [Revised: 02/23/2019] [Accepted: 03/28/2019] [Indexed: 12/12/2022]
Abstract
Liver cancer is the fourth leading cause of cancer related mortality in the world, with hepatocellular carcinoma (HCC) representing the most common primary subtype. Two-thirds of HCC patients have advanced disease when diagnosed, and for these patients, treatment strategies remain limited. In addition, there is a high incidence of tumor recurrence after surgical resection with the current treatment regimens. The development of novel and more effective agents is required. Cyclin-dependent kinases (CDKs) constitute a family of 21 different protein kinases involved in regulating cell proliferation, apoptosis, and drug resistance, and are evaluated in preclinical and clinical trials as chemotherapeutics. To summarize and discuss the therapeutic potential of targeting CDKs in HCC, recent published articles identified from PubMed were comprehensively reviewed. The key words included hepatocellular carcinoma, cyclin-dependent kinases, and CDK inhibitors. This review focuses on the emerging evidence from studies describing the genetic and functional aspects of CDKs in HCC. We also present an overview of CDK inhibitors that have shown efficacy in laboratory studies of HCC. Although many of the studies assessing CDK-targeting therapies in HCC are at the preclinical stage, there is significant evidence that CDK inhibitors used alone or in combination with established chemotherapy drugs could have significant applications in HCC.
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Affiliation(s)
- Shen Shen
- Precision Medicine Center, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China.,Sarcoma Biology Laboratory, Department of Orthopedic Surgery, David Geffen School of Medicine at University of Los Angeles, Los Angeles, CA, USA
| | - Dylan C Dean
- Sarcoma Biology Laboratory, Department of Orthopedic Surgery, David Geffen School of Medicine at University of Los Angeles, Los Angeles, CA, USA
| | - Zujiang Yu
- Precision Medicine Center, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Zhenfeng Duan
- Precision Medicine Center, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China.,Sarcoma Biology Laboratory, Department of Orthopedic Surgery, David Geffen School of Medicine at University of Los Angeles, Los Angeles, CA, USA
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38
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van den Akker WMR, Brummelman I, Martis LM, Timmermans RN, Pfundt R, Kleefstra T, Willemsen MH, Gerkes EH, Herkert JC, van Essen AJ, Rump P, Vansenne F, Terhal PA, van Haelst MM, Cristian I, Turner CE, Cho MT, Begtrup A, Willaert R, Fassi E, van Gassen KLI, Stegmann APA, de Vries BBA, Schuurs-Hoeijmakers JHM. De novo variants in CDK13 associated with syndromic ID/DD: Molecular and clinical delineation of 15 individuals and a further review. Clin Genet 2019; 93:1000-1007. [PMID: 29393965 DOI: 10.1111/cge.13225] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2017] [Revised: 01/03/2018] [Accepted: 01/24/2018] [Indexed: 01/06/2023]
Abstract
De novo variants in the gene encoding cyclin-dependent kinase 13 (CDK13) have been associated with congenital heart defects and intellectual disability (ID). Here, we present the clinical assessment of 15 individuals and report novel de novo missense variants within the kinase domain of CDK13. Furthermore, we describe 2 nonsense variants and a recurrent frame-shift variant. We demonstrate the synthesis of 2 aberrant CDK13 transcripts in lymphoblastoid cells from an individual with a splice-site variant. Clinical characteristics of the individuals include mild to severe ID, developmental delay, behavioral problems, (neonatal) hypotonia and a variety of facial dysmorphism. Congenital heart defects were present in 2 individuals of the current cohort, but in at least 42% of all known individuals. An overview of all published cases is provided and does not demonstrate an obvious genotype-phenotype correlation, although 2 individuals harboring a stop codons at the end of the kinase domain might have a milder phenotype. Overall, there seems not to be a clinically recognizable facial appearance. The variability in the phenotypes impedes an à vue diagnosis of this syndrome and therefore genome-wide or gene-panel driven genetic testing is needed. Based on this overview, we provide suggestions for clinical work-up and management of this recently described ID syndrome.
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Affiliation(s)
- W M R van den Akker
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands
| | - I Brummelman
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands
| | - L M Martis
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands
| | - R N Timmermans
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands
| | - R Pfundt
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands
| | - T Kleefstra
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands
| | - M H Willemsen
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands
| | - E H Gerkes
- Department of Genetics, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
| | - J C Herkert
- Department of Genetics, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
| | - A J van Essen
- Department of Genetics, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
| | - P Rump
- Department of Genetics, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
| | - F Vansenne
- Department of Genetics, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
| | - P A Terhal
- Department of Genetics, University Medical Centre Utrecht, Utrecht, The Netherlands
| | - M M van Haelst
- Department of Genetics, University Medical Centre Utrecht, Utrecht, The Netherlands.,Department of Clinical Genetics, AMC/VUmc, Amsterdam, The Netherlands
| | - I Cristian
- Division of Genetics and Metabolism, Department of Pediatrics, Nemours Children's Hospital Orlando, Orlando, Florida
| | - C E Turner
- Department of Genetics, Walter Reed National Military Medical Center, Bethesda, Maryland
| | - M T Cho
- GeneDx, Gaithersburg, Maryland
| | | | | | - E Fassi
- Division of Genetics and Genomic Medicine, Department of Pediatrics, Washington University School of Medicine, St Louis, Missouri
| | - K L I van Gassen
- Department of Genetics, University Medical Centre Utrecht, Utrecht, The Netherlands
| | - A P A Stegmann
- Department of Human Genetics, Maastricht University Hospital, Maastricht, The Netherlands
| | - B B A de Vries
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands
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Chirackal Manavalan AP, Pilarova K, Kluge M, Bartholomeeusen K, Rajecky M, Oppelt J, Khirsariya P, Paruch K, Krejci L, Friedel CC, Blazek D. CDK12 controls G1/S progression by regulating RNAPII processivity at core DNA replication genes. EMBO Rep 2019; 20:e47592. [PMID: 31347271 PMCID: PMC6727028 DOI: 10.15252/embr.201847592] [Citation(s) in RCA: 54] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2018] [Revised: 06/09/2019] [Accepted: 06/24/2019] [Indexed: 12/31/2022] Open
Abstract
CDK12 is a kinase associated with elongating RNA polymerase II (RNAPII) and is frequently mutated in cancer. CDK12 depletion reduces the expression of homologous recombination (HR) DNA repair genes, but comprehensive insight into its target genes and cellular processes is lacking. We use a chemical genetic approach to inhibit analog-sensitive CDK12, and find that CDK12 kinase activity is required for transcription of core DNA replication genes and thus for G1/S progression. RNA-seq and ChIP-seq reveal that CDK12 inhibition triggers an RNAPII processivity defect characterized by a loss of mapped reads from 3'ends of predominantly long, poly(A)-signal-rich genes. CDK12 inhibition does not globally reduce levels of RNAPII-Ser2 phosphorylation. However, individual CDK12-dependent genes show a shift of P-Ser2 peaks into the gene body approximately to the positions where RNAPII occupancy and transcription were lost. Thus, CDK12 catalytic activity represents a novel link between regulation of transcription and cell cycle progression. We propose that DNA replication and HR DNA repair defects as a consequence of CDK12 inactivation underlie the genome instability phenotype observed in many cancers.
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Affiliation(s)
| | - Kveta Pilarova
- Central European Institute of Technology (CEITEC)Masaryk UniversityBrnoCzech Republic
| | - Michael Kluge
- Institut für InformatikLudwig‐Maximilians‐Universität MünchenMünchenGermany
| | - Koen Bartholomeeusen
- Central European Institute of Technology (CEITEC)Masaryk UniversityBrnoCzech Republic
- Present address:
Department of Biomedical SciencesInstitute of Tropical MedicineAntwerpBelgium
| | - Michal Rajecky
- Central European Institute of Technology (CEITEC)Masaryk UniversityBrnoCzech Republic
| | - Jan Oppelt
- Central European Institute of Technology (CEITEC)Masaryk UniversityBrnoCzech Republic
| | - Prashant Khirsariya
- Department of ChemistryCZ OpenscreenFaculty of ScienceMasaryk UniversityBrnoCzech Republic
- Center of Biomolecular and Cellular EngineeringInternational Clinical Research CenterSt. Anne's University HospitalBrnoCzech Republic
| | - Kamil Paruch
- Department of ChemistryCZ OpenscreenFaculty of ScienceMasaryk UniversityBrnoCzech Republic
- Center of Biomolecular and Cellular EngineeringInternational Clinical Research CenterSt. Anne's University HospitalBrnoCzech Republic
| | - Lumir Krejci
- Center of Biomolecular and Cellular EngineeringInternational Clinical Research CenterSt. Anne's University HospitalBrnoCzech Republic
- Department of BiologyMasaryk UniversityBrnoCzech Republic
- National Centre for Biomolecular ResearchMasaryk UniversityBrnoCzech Republic
| | - Caroline C Friedel
- Institut für InformatikLudwig‐Maximilians‐Universität MünchenMünchenGermany
| | - Dalibor Blazek
- Central European Institute of Technology (CEITEC)Masaryk UniversityBrnoCzech Republic
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Nováková M, Hampl M, Vrábel D, Procházka J, Petrezselyová S, Procházková M, Sedláček R, Kavková M, Zikmund T, Kaiser J, Juan HC, Fann MJ, Buchtová M, Kohoutek J. Mouse Model of Congenital Heart Defects, Dysmorphic Facial Features and Intellectual Developmental Disorders as a Result of Non-functional CDK13. Front Cell Dev Biol 2019; 7:155. [PMID: 31440507 PMCID: PMC6694211 DOI: 10.3389/fcell.2019.00155] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2019] [Accepted: 07/23/2019] [Indexed: 12/16/2022] Open
Abstract
Congenital heart defects, dysmorphic facial features and intellectual developmental disorders (CHDFIDD) syndrome in humans was recently associated with mutation in CDK13 gene. In order to assess the loss of function of Cdk13 during mouse development, we employed gene trap knock-out (KO) allele in Cdk13 gene. Embryonic lethality of Cdk13-deficient animals was observed by the embryonic day (E) 16.5, while live embryos were observed on E15.5. At this stage, improper development of multiple organs has been documented, partly resembling defects observed in patients with mutated CDK13. In particular, overall developmental delay, incomplete secondary palate formation with variability in severity among Cdk13-deficient animals or complete midline deficiency, kidney failure accompanied by congenital heart defects were detected. Based on further analyses, the lethality at this stage is a result of heart failure most likely due to multiple heart defects followed by insufficient blood circulation resulting in multiple organs dysfunctions. Thus, Cdk13 KO mice might be a very useful model for further studies focused on delineating signaling circuits and molecular mechanisms underlying CHDFIDD caused by mutation in CDK13 gene.
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Affiliation(s)
- Monika Nováková
- Department of Chemistry and Toxicology, Veterinary Research Institute, Brno, Czechia
| | - Marek Hampl
- Laboratory of Molecular Morphogenesis, Institute of Animal Physiology and Genetics, Czech Academy of Sciences, Brno, Czechia.,Department of Experimental Biology, Faculty of Science, Masaryk University, Brno, Czechia
| | - Dávid Vrábel
- Department of Chemistry and Toxicology, Veterinary Research Institute, Brno, Czechia
| | - Jan Procházka
- Laboratory of Transgenic Models of Diseases, Institute of Molecular Genetics, Czech Academy of Sciences, Prague, Czechia.,Czech Centre for Phenogenomics, Institute of Molecular Genetics, Czech Academy of Sciences, Prague, Czechia
| | - Silvia Petrezselyová
- Laboratory of Transgenic Models of Diseases, Institute of Molecular Genetics, Czech Academy of Sciences, Prague, Czechia.,Czech Centre for Phenogenomics, Institute of Molecular Genetics, Czech Academy of Sciences, Prague, Czechia
| | - Michaela Procházková
- Laboratory of Transgenic Models of Diseases, Institute of Molecular Genetics, Czech Academy of Sciences, Prague, Czechia.,Czech Centre for Phenogenomics, Institute of Molecular Genetics, Czech Academy of Sciences, Prague, Czechia
| | - Radislav Sedláček
- Laboratory of Transgenic Models of Diseases, Institute of Molecular Genetics, Czech Academy of Sciences, Prague, Czechia.,Czech Centre for Phenogenomics, Institute of Molecular Genetics, Czech Academy of Sciences, Prague, Czechia
| | - Michaela Kavková
- Central European Institute of Technology, Brno University of Technology, Brno, Czechia
| | - Tomáš Zikmund
- Central European Institute of Technology, Brno University of Technology, Brno, Czechia
| | - Jozef Kaiser
- Central European Institute of Technology, Brno University of Technology, Brno, Czechia
| | - Hsien-Chia Juan
- Department of Life Sciences, Institute of Genome Sciences, National Yang-Ming University, Taipei, Taiwan
| | - Ming-Ji Fann
- Department of Life Sciences, Institute of Genome Sciences, National Yang-Ming University, Taipei, Taiwan
| | - Marcela Buchtová
- Laboratory of Molecular Morphogenesis, Institute of Animal Physiology and Genetics, Czech Academy of Sciences, Brno, Czechia.,Department of Experimental Biology, Faculty of Science, Masaryk University, Brno, Czechia
| | - Jiří Kohoutek
- Department of Chemistry and Toxicology, Veterinary Research Institute, Brno, Czechia
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Wood DJ, Endicott JA. Structural insights into the functional diversity of the CDK-cyclin family. Open Biol 2019; 8:rsob.180112. [PMID: 30185601 PMCID: PMC6170502 DOI: 10.1098/rsob.180112] [Citation(s) in RCA: 141] [Impact Index Per Article: 28.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2018] [Accepted: 08/10/2018] [Indexed: 12/17/2022] Open
Abstract
Since their characterization as conserved modules that regulate progression through the eukaryotic cell cycle, cyclin-dependent protein kinases (CDKs) in higher eukaryotic cells are now also emerging as significant regulators of transcription, metabolism and cell differentiation. The cyclins, though originally characterized as CDK partners, also have CDK-independent roles that include the regulation of DNA damage repair and transcriptional programmes that direct cell differentiation, apoptosis and metabolic flux. This review compares the structures of the members of the CDK and cyclin families determined by X-ray crystallography, and considers what mechanistic insights they provide to guide functional studies and distinguish CDK- and cyclin-specific activities. Aberrant CDK activity is a hallmark of a number of diseases, and structural studies can provide important insights to identify novel routes to therapy.
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Affiliation(s)
- Daniel J Wood
- Newcastle Cancer Centre, Northern Institute for Cancer Research, Medical School, Newcastle University, Paul O'Gorman Building, Framlington Place, Newcastle upon Tyne NE2 4HH, UK
| | - Jane A Endicott
- Newcastle Cancer Centre, Northern Institute for Cancer Research, Medical School, Newcastle University, Paul O'Gorman Building, Framlington Place, Newcastle upon Tyne NE2 4HH, UK
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42
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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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43
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Ito M, Tanaka T, Toita A, Uchiyama N, Kokubo H, Morishita N, Klein MG, Zou H, Murakami M, Kondo M, Sameshima T, Araki S, Endo S, Kawamoto T, Morin GB, Aparicio SA, Nakanishi A, Maezaki H, Imaeda Y. Discovery of 3-Benzyl-1-( trans-4-((5-cyanopyridin-2-yl)amino)cyclohexyl)-1-arylurea Derivatives as Novel and Selective Cyclin-Dependent Kinase 12 (CDK12) Inhibitors. J Med Chem 2018; 61:7710-7728. [PMID: 30067358 DOI: 10.1021/acs.jmedchem.8b00683] [Citation(s) in RCA: 37] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Cyclin-dependent kinase 12 (CDK12) plays a key role in the coordination of transcription with elongation and mRNA processing. CDK12 mutations found in tumors and CDK12 inhibition sensitize cancer cells to DNA-damaging reagents and DNA-repair inhibitors. This suggests that CDK12 inhibitors are potential therapeutics for cancer that may cause synthetic lethality. Here, we report the discovery of 3-benzyl-1-( trans-4-((5-cyanopyridin-2-yl)amino)cyclohexyl)-1-arylurea derivatives as novel and selective CDK12 inhibitors. Structure-activity relationship studies of a HTS hit, structure-based drug design, and conformation-oriented design using the Cambridge Structural Database afforded the optimized compound 2, which exhibited not only potent CDK12 (and CDK13) inhibitory activity and excellent selectivity but also good physicochemical properties. Furthermore, 2 inhibited the phosphorylation of Ser2 in the C-terminal domain of RNA polymerase II and induced growth inhibition in SK-BR-3 cells. Therefore, 2 represents an excellent chemical probe for functional studies of CDK12 and could be a promising lead compound for drug discovery.
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Affiliation(s)
- Masahiro Ito
- Pharmaceutical Research Division , Takeda Pharmaceutical Company Limited , 26-1, Muraoka-Higashi 2-chome , Fujisawa , Kanagawa 251-8555 , Japan
| | - Toshio Tanaka
- Pharmaceutical Research Division , Takeda Pharmaceutical Company Limited , 26-1, Muraoka-Higashi 2-chome , Fujisawa , Kanagawa 251-8555 , Japan
| | - Akinori Toita
- Pharmaceutical Research Division , Takeda Pharmaceutical Company Limited , 26-1, Muraoka-Higashi 2-chome , Fujisawa , Kanagawa 251-8555 , Japan
| | - Noriko Uchiyama
- Pharmaceutical Research Division , Takeda Pharmaceutical Company Limited , 26-1, Muraoka-Higashi 2-chome , Fujisawa , Kanagawa 251-8555 , Japan
| | - Hironori Kokubo
- Pharmaceutical Research Division , Takeda Pharmaceutical Company Limited , 26-1, Muraoka-Higashi 2-chome , Fujisawa , Kanagawa 251-8555 , Japan
| | - Nao Morishita
- Pharmaceutical Research Division , Takeda Pharmaceutical Company Limited , 26-1, Muraoka-Higashi 2-chome , Fujisawa , Kanagawa 251-8555 , Japan
| | - Michael G Klein
- Department of Structural Biology , Takeda California Inc. , 10410 Science Center Drive , San Diego , California 92121 , United States
| | - Hua Zou
- Department of Structural Biology , Takeda California Inc. , 10410 Science Center Drive , San Diego , California 92121 , United States
| | - Morio Murakami
- Pharmaceutical Research Division , Takeda Pharmaceutical Company Limited , 26-1, Muraoka-Higashi 2-chome , Fujisawa , Kanagawa 251-8555 , Japan
| | - Mitsuyo Kondo
- Pharmaceutical Research Division , Takeda Pharmaceutical Company Limited , 26-1, Muraoka-Higashi 2-chome , Fujisawa , Kanagawa 251-8555 , Japan
| | - Tomoya Sameshima
- Pharmaceutical Research Division , Takeda Pharmaceutical Company Limited , 26-1, Muraoka-Higashi 2-chome , Fujisawa , Kanagawa 251-8555 , Japan
| | - Shinsuke Araki
- Pharmaceutical Research Division , Takeda Pharmaceutical Company Limited , 26-1, Muraoka-Higashi 2-chome , Fujisawa , Kanagawa 251-8555 , Japan
| | - Satoshi Endo
- Pharmaceutical Research Division , Takeda Pharmaceutical Company Limited , 26-1, Muraoka-Higashi 2-chome , Fujisawa , Kanagawa 251-8555 , Japan
| | - Tomohiro Kawamoto
- Pharmaceutical Research Division , Takeda Pharmaceutical Company Limited , 26-1, Muraoka-Higashi 2-chome , Fujisawa , Kanagawa 251-8555 , Japan
| | - Gregg B Morin
- Genome Sciences Centre , British Columbia Cancer Agency , 675 West 10th Avenue , Vancouver , British Columbia V5Z 1L3 , Canada.,Department of Medical Genetics , University of British Columbia , Vancouver , British Columbia V6H 3N1 , Canada
| | - Samuel A Aparicio
- Department of Molecular Oncology , British Columbia Cancer Agency , 675 West 10th Avenue , Vancouver , British Columbia V5Z 1L3 , Canada
| | - Atsushi Nakanishi
- Pharmaceutical Research Division , Takeda Pharmaceutical Company Limited , 26-1, Muraoka-Higashi 2-chome , Fujisawa , Kanagawa 251-8555 , Japan
| | - Hironobu Maezaki
- Pharmaceutical Research Division , Takeda Pharmaceutical Company Limited , 26-1, Muraoka-Higashi 2-chome , Fujisawa , Kanagawa 251-8555 , Japan
| | - Yasuhiro Imaeda
- Pharmaceutical Research Division , Takeda Pharmaceutical Company Limited , 26-1, Muraoka-Higashi 2-chome , Fujisawa , Kanagawa 251-8555 , Japan
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44
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Johannes JW, Denz CR, Su N, Wu A, Impastato AC, Mlynarski S, Varnes JG, Prince DB, Cidado J, Gao N, Haddrick M, Jones NH, Li S, Li X, Liu Y, Nguyen TB, O'Connell N, Rivers E, Robbins DW, Tomlinson R, Yao T, Zhu X, Ferguson AD, Lamb ML, Manchester JI, Guichard S. Structure-Based Design of Selective Noncovalent CDK12 Inhibitors. ChemMedChem 2018; 13:231-235. [PMID: 29266803 DOI: 10.1002/cmdc.201700695] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2017] [Revised: 12/13/2017] [Indexed: 12/21/2022]
Abstract
Cyclin-dependent kinase (CDK) 12 knockdown via siRNA decreases the transcription of DNA-damage-response genes and sensitizes BRCA wild-type cells to poly(ADP-ribose) polymerase (PARP) inhibition. To recapitulate this effect with a small molecule, we sought a potent, selective CDK12 inhibitor. Crystal structures and modeling informed hybridization between dinaciclib and SR-3029, resulting in lead compound 5 [(S)-2-(1-(6-(((6,7-difluoro-1H-benzo[d]imidazol-2-yl)methyl)amino)-9-ethyl-9H-purin-2-yl)piperidin-2-yl)ethan-1-ol]. Further structure-guided optimization delivered a series of selective CDK12 inhibitors, including compound 7 [(S)-2-(1-(6-(((6,7-difluoro-1H-benzo[d]imidazol-2-yl)methyl)amino)-9-isopropyl-9H-purin-2-yl)piperidin-2-yl)ethan-1-ol]. Profiling of this compound across CDK9, 7, 2, and 1 at high ATP concentration, single-point kinase panel screening against 352 targets at 0.1 μm, and proteomics via kinase affinity matrix technology demonstrated the selectivity. This series of compounds inhibits phosphorylation of Ser2 on the C-terminal repeat domain of RNA polymerase II, consistent with CDK12 inhibition. These selective compounds were also acutely toxic to OV90 as well as THP1 cells.
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Affiliation(s)
| | | | - Nancy Su
- Discovery Sciences, IMED Biotech Unit, AstraZeneca, Boston, MA, USA
| | - Allan Wu
- Discovery Sciences, IMED Biotech Unit, AstraZeneca, Boston, MA, USA
| | - Anna C Impastato
- Discovery Sciences, IMED Biotech Unit, AstraZeneca, Boston, MA, USA
| | | | | | - D Bryan Prince
- Discovery Sciences, IMED Biotech Unit, AstraZeneca, Boston, MA, USA
| | - Justin Cidado
- Oncology, IMED Biotech Unit, AstraZeneca, Boston, MA, USA
| | - Ning Gao
- Discovery Sciences, IMED Biotech Unit, AstraZeneca, Boston, MA, USA
| | - Malcolm Haddrick
- Discovery Sciences, IMED Biotech Unit, AstraZeneca Pharmaceuticals LP, Alderley Park, Macclesfield, SK10 4TG, UK
| | - Natalie H Jones
- Discovery Sciences, IMED Biotech Unit, AstraZeneca, Boston, MA, USA
| | - Shaobin Li
- Pharmaron Beijing Co. Ltd., 6 Taihe Road BDA, Beijing, 100176, P.R. China
| | - Xiuwei Li
- Pharmaron Beijing Co. Ltd., 6 Taihe Road BDA, Beijing, 100176, P.R. China
| | - Yang Liu
- Pharmaron Beijing Co. Ltd., 6 Taihe Road BDA, Beijing, 100176, P.R. China
| | - Toan B Nguyen
- Discovery Sciences, IMED Biotech Unit, AstraZeneca, Boston, MA, USA
| | | | - Emma Rivers
- Discovery Sciences, IMED Biotech Unit, AstraZeneca Pharmaceuticals LP, Unit 310 Darwin Building, Cambridge, CB4 0WG, UK
| | | | - Ronald Tomlinson
- Discovery Sciences, IMED Biotech Unit, AstraZeneca, Boston, MA, USA
| | - Tieguang Yao
- Pharmaron Beijing Co. Ltd., 6 Taihe Road BDA, Beijing, 100176, P.R. China
| | - Xiahui Zhu
- Discovery Sciences, IMED Biotech Unit, AstraZeneca, Boston, MA, USA
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45
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Uehara T, Takenouchi T, Kosaki R, Kurosawa K, Mizuno S, Kosaki K. Redefining the phenotypic spectrum of de novo heterozygous CDK13 variants: Three patients without cardiac defects. Eur J Med Genet 2017; 61:243-247. [PMID: 29222009 DOI: 10.1016/j.ejmg.2017.12.004] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2017] [Revised: 11/08/2017] [Accepted: 12/04/2017] [Indexed: 11/16/2022]
Abstract
Recently, 7 patients with de novo constitutional non-synonymous mutations in the CDK13 gene were ascertained through a trio exome analysis of a large cohort of 610 patients with congenital cardiac diseases. Despite another report describing 9 additional patients, the clinical spectrum of this condition has yet to be defined. Herein, we report 3 patients with heterozygous constitutional CDK13 mutations, who were ascertained through exome analysis of children with intellectual disability and minor anomalies, who lacked cardiac anomalies. Two patients had a c.2149G > A, p.Gly717Arg mutation, and one had a c.2525A > G, p. Asn842Ser mutation. A review of the previously described patients and those described herein has enabled the following points to be clarified. First, congenital heart diseases are not an essential feature (13/19). Second, nasal features may help syndromic recognition (14/16). Third, widely spaced and peg-shaped teeth may represent a previously unappreciated diagnostic clue for this newly identified syndrome. Here, we show that p.Gly717Arg represents a hotspot in addition to p.Asn842Ser. We suggest that this CDK13-related disorder may represent a clinically recognizable syndrome.
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Affiliation(s)
- Tomoko Uehara
- Center for Medical Genetics, Keio University School of Medicine, Tokyo, Japan
| | - Toshiki Takenouchi
- Department of Pediatrics, Keio University School of Medicine, Tokyo, Japan
| | - Rika Kosaki
- Division of Medical Genetics, National Center for Child Health and Development, Tokyo, Japan
| | - Kenji Kurosawa
- Division of Medical Genetics, Kanagawa Children's Medical Center, Yokohama, Japan
| | - Seiji Mizuno
- Department of Pediatrics, Central Hospital, Aichi Human Service Center, Aichi, Japan
| | - Kenjiro Kosaki
- Center for Medical Genetics, Keio University School of Medicine, Tokyo, Japan.
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46
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Paculová H, Kramara J, Šimečková Š, Fedr R, Souček K, Hylse O, Paruch K, Svoboda M, Mistrík M, Kohoutek J. BRCA1 or CDK12 loss sensitizes cells to CHK1 inhibitors. Tumour Biol 2017; 39:1010428317727479. [PMID: 29025359 DOI: 10.1177/1010428317727479] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
A broad spectrum of tumors develop resistance to classic chemotherapy, necessitating the discovery of new therapies. One successful strategy exploits the synthetic lethality between poly(ADP-ribose) polymerase 1/2 proteins and DNA damage response genes, including BRCA1, a factor involved in homologous recombination-mediated DNA repair, and CDK12, a transcriptional kinase known to regulate the expression of DDR genes. CHK1 inhibitors have been shown to enhance the anti-cancer effect of DNA-damaging compounds. Since loss of BRCA1 increases replication stress and leads to DNA damage, we tested a hypothesis that CDK12- or BRCA1-depleted cells rely extensively on S-phase-related CHK1 functions for survival. The silencing of BRCA1 or CDK12 sensitized tumor cells to CHK1 inhibitors in vitro and in vivo. BRCA1 downregulation combined with CHK1 inhibition induced excessive amounts of DNA damage, resulting in an inability to complete the S-phase. Therefore, we suggest CHK1 inhibition as a strategy for targeting BRCA1- or CDK12-deficient tumors.
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Affiliation(s)
- Hana Paculová
- 1 Department of Chemistry and Toxicology, Veterinary Research Institute, Brno, Czech Republic
| | - Juraj Kramara
- 2 Institute of Molecular and Translational Medicine, Faculty of Medicine and Dentistry, Palacky University, Olomouc, Czech Republic
| | - Šárka Šimečková
- 3 Institute of Biophysics of the Czech Academy of Sciences, Brno,Czech Republic.,4 Department of Experimental Biology, Faculty of Science, Masaryk University, Brno, Czech Republic
| | - Radek Fedr
- 3 Institute of Biophysics of the Czech Academy of Sciences, Brno,Czech Republic.,5 International Clinical Research Center, St. Anne's University Hospital, Brno, Czech Republic
| | - Karel Souček
- 3 Institute of Biophysics of the Czech Academy of Sciences, Brno,Czech Republic.,4 Department of Experimental Biology, Faculty of Science, Masaryk University, Brno, Czech Republic.,5 International Clinical Research Center, St. Anne's University Hospital, Brno, Czech Republic
| | - Ondřej Hylse
- 5 International Clinical Research Center, St. Anne's University Hospital, Brno, Czech Republic.,6 Department of Chemistry, CZ Openscreen, Faculty of Science, Masaryk University, Brno, Czech Republic
| | - Kamil Paruch
- 5 International Clinical Research Center, St. Anne's University Hospital, Brno, Czech Republic.,6 Department of Chemistry, CZ Openscreen, Faculty of Science, Masaryk University, Brno, Czech Republic
| | - Marek Svoboda
- 7 Department of Comprehensive Cancer Care, Masaryk Memorial Cancer Institute, Brno, Czech Republic
| | - Martin Mistrík
- 2 Institute of Molecular and Translational Medicine, Faculty of Medicine and Dentistry, Palacky University, Olomouc, Czech Republic
| | - Jiří Kohoutek
- 1 Department of Chemistry and Toxicology, Veterinary Research Institute, Brno, Czech Republic
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47
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Bostwick BL, McLean S, Posey JE, Streff HE, Gripp KW, Blesson A, Powell-Hamilton N, Tusi J, Stevenson DA, Farrelly E, Hudgins L, Yang Y, Xia F, Wang X, Liu P, Walkiewicz M, McGuire M, Grange DK, Andrews MV, Hummel M, Madan-Khetarpal S, Infante E, Coban-Akdemir Z, Miszalski-Jamka K, Jefferies JL, Rosenfeld JA, Emrick L, Nugent KM, Lupski JR, Belmont JW, Lee B, Lalani SR. Phenotypic and molecular characterisation of CDK13-related congenital heart defects, dysmorphic facial features and intellectual developmental disorders. Genome Med 2017; 9:73. [PMID: 28807008 PMCID: PMC5557075 DOI: 10.1186/s13073-017-0463-8] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2017] [Accepted: 07/24/2017] [Indexed: 12/21/2022] Open
Abstract
Background De novo missense variants in CDK13 have been described as the cause of syndromic congenital heart defects in seven individuals ascertained from a large congenital cardiovascular malformations cohort. We aimed to further define the phenotypic and molecular spectrum of this newly described disorder. Methods To minimise ascertainment bias, we recruited nine additional individuals with CDK13 pathogenic variants from clinical and research exome laboratory sequencing cohorts. Each individual underwent dysmorphology exam and comprehensive medical history review. Results We demonstrate greater than expected phenotypic heterogeneity, including 33% (3/9) of individuals without structural heart disease on echocardiogram. There was a high penetrance for a unique constellation of facial dysmorphism and global developmental delay, as well as less frequently seen renal and sacral anomalies. Two individuals had novel CDK13 variants (p.Asn842Asp, p.Lys734Glu), while the remaining seven unrelated individuals had a recurrent, previously published p.Asn842Ser variant. Summary of all variants published to date demonstrates apparent restriction of pathogenic variants to the protein kinase domain with clustering in the ATP and magnesium binding sites. Conclusions Here we provide detailed phenotypic and molecular characterisation of individuals with pathogenic variants in CDK13 and propose management guidelines based upon the estimated prevalence of anomalies identified. Electronic supplementary material The online version of this article (doi:10.1186/s13073-017-0463-8) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Bret L Bostwick
- Department of Molecular and Human Genetics, Baylor College of Medicine, 6701 Fannin St, Suite 1560, Houston, TX, 77030, USA.
| | - Scott McLean
- Department of Molecular and Human Genetics, Baylor College of Medicine, 6701 Fannin St, Suite 1560, Houston, TX, 77030, USA.,Department of Pediatrics, Baylor College of Medicine, San Antonio, TX, 78207, USA
| | - Jennifer E Posey
- Department of Molecular and Human Genetics, Baylor College of Medicine, 6701 Fannin St, Suite 1560, Houston, TX, 77030, USA
| | - Haley E Streff
- Department of Molecular and Human Genetics, Baylor College of Medicine, 6701 Fannin St, Suite 1560, Houston, TX, 77030, USA
| | - Karen W Gripp
- Division of Medical Genetics, A.I. duPont Hospital for Children/Nemours, Wilmington, DE, USA
| | - Alyssa Blesson
- Division of Medical Genetics, A.I. duPont Hospital for Children/Nemours, Wilmington, DE, USA
| | - Nina Powell-Hamilton
- Division of Medical Genetics, A.I. duPont Hospital for Children/Nemours, Wilmington, DE, USA
| | - Jessica Tusi
- Division of Medical Genetics, A.I. duPont Hospital for Children/Nemours, Wilmington, DE, USA
| | - David A Stevenson
- Division of Medical Genetics, Stanford University School of Medicine, Stanford, CA, USA
| | - Ellyn Farrelly
- Division of Medical Genetics, Stanford University School of Medicine, Stanford, CA, USA
| | - Louanne Hudgins
- Division of Medical Genetics, Stanford University School of Medicine, Stanford, CA, USA
| | - Yaping Yang
- Department of Molecular and Human Genetics, Baylor College of Medicine, 6701 Fannin St, Suite 1560, Houston, TX, 77030, USA.,Baylor Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Fan Xia
- Department of Molecular and Human Genetics, Baylor College of Medicine, 6701 Fannin St, Suite 1560, Houston, TX, 77030, USA.,Baylor Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Xia Wang
- Department of Molecular and Human Genetics, Baylor College of Medicine, 6701 Fannin St, Suite 1560, Houston, TX, 77030, USA.,Baylor Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Pengfei Liu
- Department of Molecular and Human Genetics, Baylor College of Medicine, 6701 Fannin St, Suite 1560, Houston, TX, 77030, USA.,Baylor Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Magdalena Walkiewicz
- Department of Molecular and Human Genetics, Baylor College of Medicine, 6701 Fannin St, Suite 1560, Houston, TX, 77030, USA.,Baylor Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Marianne McGuire
- Department of Molecular and Human Genetics, Baylor College of Medicine, 6701 Fannin St, Suite 1560, Houston, TX, 77030, USA
| | - Dorothy K Grange
- Division of Genetics and Genomic Medicine, Department of Pediatrics, Washington University School of Medicine, St. Louis, MO, USA
| | - Marisa V Andrews
- Division of Genetics and Genomic Medicine, Department of Pediatrics, Washington University School of Medicine, St. Louis, MO, USA
| | - Marybeth Hummel
- Department of Pediatrics, Section of Medical Genetics, West Virginia University Health Sciences Center, Morgantown, WV, USA
| | | | - Elena Infante
- Children's Hospital of Pittsburgh of UPMC, University of Pittsburgh, Pittsburgh, PA, USA
| | - Zeynep Coban-Akdemir
- Department of Molecular and Human Genetics, Baylor College of Medicine, 6701 Fannin St, Suite 1560, Houston, TX, 77030, USA
| | - Karol Miszalski-Jamka
- Division of Magnetic Resonance Imaging, Silesian Center for Heart Disease, Zabrze, Poland
| | - John L Jefferies
- The Heart Institute, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
| | | | - Jill A Rosenfeld
- Department of Molecular and Human Genetics, Baylor College of Medicine, 6701 Fannin St, Suite 1560, Houston, TX, 77030, USA
| | - Lisa Emrick
- Department of Molecular and Human Genetics, Baylor College of Medicine, 6701 Fannin St, Suite 1560, Houston, TX, 77030, USA
| | - Kimberly M Nugent
- Department of Molecular and Human Genetics, Baylor College of Medicine, 6701 Fannin St, Suite 1560, Houston, TX, 77030, USA.,Department of Pediatrics, Baylor College of Medicine, San Antonio, TX, 78207, USA
| | - James R Lupski
- Department of Molecular and Human Genetics, Baylor College of Medicine, 6701 Fannin St, Suite 1560, Houston, TX, 77030, USA.,Texas Children's Hospital, Houston, TX, 77030, USA.,Department of Pediatrics, Baylor College of Medicine, Houston, TX, 77030, USA.,Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, 77030, USA
| | - John W Belmont
- Department of Molecular and Human Genetics, Baylor College of Medicine, 6701 Fannin St, Suite 1560, Houston, TX, 77030, USA
| | - Brendan Lee
- Department of Molecular and Human Genetics, Baylor College of Medicine, 6701 Fannin St, Suite 1560, Houston, TX, 77030, USA
| | - Seema R Lalani
- Department of Molecular and Human Genetics, Baylor College of Medicine, 6701 Fannin St, Suite 1560, Houston, TX, 77030, USA
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48
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Paparidis NFDS, Durvale MC, Canduri F. The emerging picture of CDK9/P-TEFb: more than 20 years of advances since PITALRE. MOLECULAR BIOSYSTEMS 2017; 13:246-276. [PMID: 27833949 DOI: 10.1039/c6mb00387g] [Citation(s) in RCA: 49] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
CDK9 is a prominent member of the transcriptional CDKs subfamily, a group of kinases whose function is to control the primary steps of mRNA synthesis and processing by eukaryotic RNA polymerase II. As a cyclin-dependent kinase, CDK9 activation in vivo depends upon its association with T-type cyclins to assemble the positive transcription elongation factor (P-TEFb). Although CDK9/P-TEFb phosphorylates the C-terminal domain of RNAP II in the same positions targeted by CDK7 (TFIIH) and CDK8 (Mediator), the former does not participate in the transcription initiation, but rather plays a unique role by driving the polymerase to productive elongation. In addition to RNAP II CTD, the negative transcription elongation factors DSIF and NELF also represent major CDK9 substrates, whose phosphorylation is required to overcome the proximal pause of the polymerase. CDK9 is recruited to specific genes through proteins that interact with both P-TEFb and distinct elements in DNA, RNA or chromatin, where it modulates the activity of individual RNAP II transcription complexes. The regulation of CDK9 function is an intricate network that includes post-translational modifications (phosphorylation/dephosphorylation and acetylation/deacetylation of key residues) as well as the association of P-TEFb with various proteins that can stimulate or inhibit its kinase activity. Several cases of CDK9 deregulation have been linked to important human diseases, including various types of cancer and also AIDS (due to its essential role in HIV replication). Not only HIV, but also many other human viruses have been shown to depend strongly on CDK9 activity to be transcribed within host cells. This review summarizes the main advances made on CDK9/P-TEFb field in more than 20 years, introducing the structural, functional and genetic aspects that have been elucidated ever since.
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Affiliation(s)
- Nikolas Ferreira Dos Santos Paparidis
- Department of Chemistry and Molecular Physics, Institute of Chemistry of Sao Carlos, Sao Paulo University, Av. Trabalhador Sãocarlense, 400, Zip Code 780, 13560-970, São Carlos-SP, Brazil.
| | - Maxwell Castro Durvale
- Department of Biochemistry, Institute of Chemistry, Sao Paulo University, Av. Prof. Lineu Prestes, 748, 05508-000, Butantã - São Paulo - SP, Brazil
| | - Fernanda Canduri
- Department of Chemistry and Molecular Physics, Institute of Chemistry of Sao Carlos, Sao Paulo University, Av. Trabalhador Sãocarlense, 400, Zip Code 780, 13560-970, São Carlos-SP, Brazil.
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49
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Schecher S, Walter B, Falkenstein M, Macher-Goeppinger S, Stenzel P, Krümpelmann K, Hadaschik B, Perner S, Kristiansen G, Duensing S, Roth W, Tagscherer KE. Cyclin K dependent regulation of Aurora B affects apoptosis and proliferation by induction of mitotic catastrophe in prostate cancer. Int J Cancer 2017; 141:1643-1653. [PMID: 28670704 DOI: 10.1002/ijc.30864] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2017] [Revised: 05/30/2017] [Accepted: 06/12/2017] [Indexed: 12/11/2022]
Abstract
Cyclin K plays a critical role in transcriptional regulation as well as cell development. However, the role of Cyclin K in prostate cancer is unknown. Here, we describe the impact of Cyclin K on prostate cancer cells and examine the clinical relevance of Cyclin K as a biomarker for patients with prostate cancer. We show that Cyclin K depletion in prostate cancer cells induces apoptosis and inhibits proliferation accompanied by an accumulation of cells in the G2/M phase. Moreover, knockdown of Cyclin K causes mitotic catastrophe displayed by multinucleation and spindle multipolarity. Furthermore, we demonstrate a Cyclin K dependent regulation of the mitotic kinase Aurora B and provide evidence for an Aurora B dependent induction of mitotic catastrophe. In addition, we show that Cyclin K expression is associated with poor biochemical recurrence-free survival in patients with prostate cancer treated with an adjuvant therapy. In conclusion, targeting Cyclin K represents a novel, promising anti-cancer strategy to induce cell cycle arrest and apoptotic cell death through induction of mitotic catastrophe in prostate cancer cells. Moreover, our results indicate that Cyclin K is a putative predictive biomarker for clinical outcome and therapy response for patients with prostate cancer.
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Affiliation(s)
- Sabrina Schecher
- Molecular Tumor-Pathology, German Cancer Research Center (DKFZ), Heidelberg, Germany.,Institute of Pathology, University of Heidelberg, Heidelberg, Germany.,Institute of Pathology, University Medical Center Mainz, Mainz, Germany
| | - Britta Walter
- Institute of Pathology, University of Heidelberg, Heidelberg, Germany
| | - Michael Falkenstein
- Molecular Urooncology, Department of Urology, University of Heidelberg, Heidelberg, Germany
| | - Stephan Macher-Goeppinger
- Molecular Tumor-Pathology, German Cancer Research Center (DKFZ), Heidelberg, Germany.,Institute of Pathology, University of Heidelberg, Heidelberg, Germany.,Institute of Pathology, University Medical Center Mainz, Mainz, Germany
| | - Philipp Stenzel
- Institute of Pathology, University Medical Center Mainz, Mainz, Germany
| | | | - Boris Hadaschik
- Department of Urology, Essen University Hospital, Essen, Germany.,Department of Urology, University of Heidelberg, Heidelberg, Germany
| | - Sven Perner
- Pathology of the University Medical Center Schleswig-Holstein, Campus Luebeck and the Research Center Borstel, Leibniz Center for Medicine and Biosciences, 23538 Luebeck and 23845 Borstel, Germany
| | | | - Stefan Duensing
- Molecular Urooncology, Department of Urology, University of Heidelberg, Heidelberg, Germany
| | - Wilfried Roth
- Molecular Tumor-Pathology, German Cancer Research Center (DKFZ), Heidelberg, Germany.,Institute of Pathology, University of Heidelberg, Heidelberg, Germany.,Institute of Pathology, University Medical Center Mainz, Mainz, Germany
| | - Katrin E Tagscherer
- Molecular Tumor-Pathology, German Cancer Research Center (DKFZ), Heidelberg, Germany.,Institute of Pathology, University of Heidelberg, Heidelberg, Germany.,Institute of Pathology, University Medical Center Mainz, Mainz, Germany
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50
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Songock WK, Scott ML, Bodily JM. Regulation of the human papillomavirus type 16 late promoter by transcriptional elongation. Virology 2017; 507:179-191. [PMID: 28448849 DOI: 10.1016/j.virol.2017.04.021] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2016] [Revised: 04/12/2017] [Accepted: 04/19/2017] [Indexed: 01/09/2023]
Abstract
Transcripts from the late promoter of human papillomavirus type 16 (HPV16) are upregulated upon host cell differentiation. Differentiation-dependent transcript regulation is thought to sequester viral antigens in the uppermost epithelial layers, facilitating immune evasion. The mechanisms regulating late promoter upregulation during differentiation are poorly characterized. We show that the late promoter is upregulated at the transcriptional level and that the viral enhancer stimulates promoter activity. Using kinase inhibition and chromatin immunoprecipitation analysis, we show evidence for differentiation-dependent enhancement of transcript elongation. Three factors that promote transcript elongation, cyclin dependent kinase 9 (CDK9), CDK8 (a subunit of the Mediator complex), and bromodomain containing protein 4 (Brd4) are recruited to viral genomes upon differentiation, and each plays a role in promoter activity. These results shed light on the transcriptional processes utilized by HPV16 for proper regulation of gene expression during the viral life cycle.
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Affiliation(s)
- William K Songock
- Department of Microbiology and Immunology, Center for Molecular and Tumor Virology, and Feist-Weiller Cancer Center, Louisiana State University Health Sciences Center, Shreveport, LA, USA
| | - Matthew L Scott
- Department of Microbiology and Immunology, Center for Molecular and Tumor Virology, and Feist-Weiller Cancer Center, Louisiana State University Health Sciences Center, Shreveport, LA, USA
| | - Jason M Bodily
- Department of Microbiology and Immunology, Center for Molecular and Tumor Virology, and Feist-Weiller Cancer Center, Louisiana State University Health Sciences Center, Shreveport, LA, USA.
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