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Green RA, Khaliullin RN, Zhao Z, Ochoa SD, Hendel JM, Chow TL, Moon H, Biggs RJ, Desai A, Oegema K. Automated profiling of gene function during embryonic development. Cell 2024; 187:3141-3160.e23. [PMID: 38759650 PMCID: PMC11166207 DOI: 10.1016/j.cell.2024.04.012] [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: 05/27/2023] [Revised: 02/10/2024] [Accepted: 04/12/2024] [Indexed: 05/19/2024]
Abstract
Systematic functional profiling of the gene set that directs embryonic development is an important challenge. To tackle this challenge, we used 4D imaging of C. elegans embryogenesis to capture the effects of 500 gene knockdowns and developed an automated approach to compare developmental phenotypes. The automated approach quantifies features-including germ layer cell numbers, tissue position, and tissue shape-to generate temporal curves whose parameterization yields numerical phenotypic signatures. In conjunction with a new similarity metric that operates across phenotypic space, these signatures enabled the generation of ranked lists of genes predicted to have similar functions, accessible in the PhenoBank web portal, for ∼25% of essential development genes. The approach identified new gene and pathway relationships in cell fate specification and morphogenesis and highlighted the utilization of specialized energy generation pathways during embryogenesis. Collectively, the effort establishes the foundation for comprehensive analysis of the gene set that builds a multicellular organism.
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Affiliation(s)
- Rebecca A Green
- Ludwig Institute for Cancer Research, La Jolla, CA 92093, USA; Department of Cell and Developmental Biology, School of Biological Sciences, University of California, San Diego, La Jolla, CA 92093, USA.
| | | | - Zhiling Zhao
- Ludwig Institute for Cancer Research, La Jolla, CA 92093, USA
| | - Stacy D Ochoa
- Ludwig Institute for Cancer Research, La Jolla, CA 92093, USA
| | | | | | - HongKee Moon
- Max Planck Institute of Molecular Cell Biology and Genetics, Pfotenhauerstr. 108, 01307 Dresden, Germany
| | - Ronald J Biggs
- Ludwig Institute for Cancer Research, La Jolla, CA 92093, USA
| | - Arshad Desai
- Ludwig Institute for Cancer Research, La Jolla, CA 92093, USA; Department of Cell and Developmental Biology, School of Biological Sciences, University of California, San Diego, La Jolla, CA 92093, USA; Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA 92093, USA
| | - Karen Oegema
- Ludwig Institute for Cancer Research, La Jolla, CA 92093, USA; Department of Cell and Developmental Biology, School of Biological Sciences, University of California, San Diego, La Jolla, CA 92093, USA; Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA 92093, USA.
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2
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Wang C, Xu L, Du C, Yun H, Wang K, Liu H, Ye M, Fan J, Zhou Y, Cheng H. CDK11 requires a critical activator SAP30BP to regulate pre-mRNA splicing. EMBO J 2023; 42:e114051. [PMID: 38059508 PMCID: PMC10711644 DOI: 10.15252/embj.2023114051] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2023] [Revised: 10/05/2023] [Accepted: 10/06/2023] [Indexed: 12/08/2023] Open
Abstract
CDK11 is an emerging druggable target for cancer therapy due to its prevalent roles in phosphorylating critical transcription and splicing factors and in facilitating cell cycle progression in cancer cells. Like other cyclin-dependent kinases, CDK11 requires its cognate cyclin, cyclin L1 or cyclin L2, for activation. However, little is known about how CDK11 activities might be modulated by other regulators. In this study, we show that CDK11 forms a tight complex with cyclins L1/L2 and SAP30BP, the latter of which is a poorly characterized factor. Acute degradation of SAP30BP mirrors that of CDK11 in causing widespread and strong defects in pre-mRNA splicing. Furthermore, we demonstrate that SAP30BP facilitates CDK11 kinase activities in vitro and in vivo, through ensuring the stabilities and the assembly of cyclins L1/L2 with CDK11. Together, these findings uncover SAP30BP as a critical CDK11 activator that regulates global pre-mRNA splicing.
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Affiliation(s)
- Changshou Wang
- Key Laboratory of RNA Science and Engineering, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell ScienceChinese Academy of Sciences, University of Chinese Academy of SciencesShanghaiChina
| | - Lin Xu
- Key Laboratory of RNA Science and Engineering, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell ScienceChinese Academy of Sciences, University of Chinese Academy of SciencesShanghaiChina
| | - Chen Du
- College of Life Sciences, TaiKang Center for Life and Medical Sciences, RNA Institute, Hubei Key Laboratory of Cell HomeostasisWuhan UniversityWuhanChina§
| | - Hao Yun
- Key Laboratory of RNA Science and Engineering, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell ScienceChinese Academy of Sciences, University of Chinese Academy of SciencesShanghaiChina
| | - Keyun Wang
- CAS Key Laboratory of Separation Sciences for Analytical Chemistry, National Chromatographic R&A Center, Dalian Institute of Chemical PhysicsChinese Academy of SciencesDalianChina
| | - Hui Liu
- Key Laboratory of Systems Health Science of Zhejiang Province, School of Life Science, Hangzhou Institute for Advanced StudyUniversity of Chinese Academy of SciencesHangzhouChina
| | - Mingliang Ye
- CAS Key Laboratory of Separation Sciences for Analytical Chemistry, National Chromatographic R&A Center, Dalian Institute of Chemical PhysicsChinese Academy of SciencesDalianChina
| | - Jing Fan
- Key Laboratory of RNA Science and Engineering, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell ScienceChinese Academy of Sciences, University of Chinese Academy of SciencesShanghaiChina
| | - Yu Zhou
- College of Life Sciences, TaiKang Center for Life and Medical Sciences, RNA Institute, Hubei Key Laboratory of Cell HomeostasisWuhan UniversityWuhanChina§
| | - Hong Cheng
- Key Laboratory of RNA Science and Engineering, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell ScienceChinese Academy of Sciences, University of Chinese Academy of SciencesShanghaiChina
- Key Laboratory of Systems Health Science of Zhejiang Province, School of Life Science, Hangzhou Institute for Advanced StudyUniversity of Chinese Academy of SciencesHangzhouChina
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3
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Wang Z, Himanen SV, Haikala HM, Friedel CC, Vihervaara A, Barborič M. Inhibition of CDK12 elevates cancer cell dependence on P-TEFb by stimulation of RNA polymerase II pause release. Nucleic Acids Res 2023; 51:10970-10991. [PMID: 37811895 PMCID: PMC10639066 DOI: 10.1093/nar/gkad792] [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] [Received: 03/20/2023] [Revised: 09/11/2023] [Accepted: 09/22/2023] [Indexed: 10/10/2023] Open
Abstract
P-TEFb and CDK12 facilitate transcriptional elongation by RNA polymerase II. Given the prominence of both kinases in cancer, gaining a better understanding of their interplay could inform the design of novel anti-cancer strategies. While down-regulation of DNA repair genes in CDK12-targeted cancer cells is being explored therapeutically, little is known about mechanisms and significance of transcriptional induction upon inhibition of CDK12. We show that selective targeting of CDK12 in colon cancer-derived cells activates P-TEFb via its release from the inhibitory 7SK snRNP. In turn, P-TEFb stimulates Pol II pause release at thousands of genes, most of which become newly dependent on P-TEFb. Amongst the induced genes are those stimulated by hallmark pathways in cancer, including p53 and NF-κB. Consequently, CDK12-inhibited cancer cells exhibit hypersensitivity to inhibitors of P-TEFb. While blocking P-TEFb triggers their apoptosis in a p53-dependent manner, it impedes cell proliferation irrespective of p53 by preventing induction of genes downstream of the DNA damage-induced NF-κB signaling. In summary, stimulation of Pol II pause release at the signal-responsive genes underlies the functional dependence of CDK12-inhibited cancer cells on P-TEFb. Our study establishes the mechanistic underpinning for combinatorial targeting of CDK12 with either P-TEFb or the induced oncogenic pathways in cancer.
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Affiliation(s)
- Zhijia Wang
- Department of Biochemistry and Developmental Biology, University of Helsinki, Helsinki FIN-00014, Finland
| | - Samu V Himanen
- Department of Gene Technology, KTH Royal Institute of Technology, Science for Life Laboratory, Stockholm, Sweden
| | - Heidi M Haikala
- Translational Immunology Research Program (TRIMM), Research Programs Unit, Faculty of Medicine, University of Helsinki, Helsinki FIN-00014, Finland
- iCAN Digital Precision Cancer Medicine Flagship, University of Helsinki, Helsinki FIN-00014, Finland
| | - Caroline C Friedel
- Institute of Informatics, Ludwig-Maximilians-Universität München, 80333 Munich, Germany
| | - Anniina Vihervaara
- Department of Gene Technology, KTH Royal Institute of Technology, Science for Life Laboratory, Stockholm, Sweden
| | - Matjaž Barborič
- Department of Biochemistry and Developmental Biology, University of Helsinki, Helsinki FIN-00014, Finland
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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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Cesari E, Ciucci A, Pieraccioli M, Caggiano C, Nero C, Bonvissuto D, Sillano F, Buttarelli M, Piermattei A, Loverro M, Camarda F, Greco V, De Bonis M, Minucci A, Gallo D, Urbani A, Vizzielli G, Scambia G, Sette C. Dual inhibition of CDK12 and CDK13 uncovers actionable vulnerabilities in patient-derived ovarian cancer organoids. J Exp Clin Cancer Res 2023; 42:126. [PMID: 37202753 DOI: 10.1186/s13046-023-02682-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2023] [Accepted: 04/21/2023] [Indexed: 05/20/2023] Open
Abstract
BACKGROUND High grade serous ovarian cancer (HGSOC) is highly lethal, partly due to chemotherapy resistance and limited availability of targeted approaches. Cyclin dependent kinases 12 and 13 (CDK12/13) are promising therapeutic targets in human cancers, including HGSOC. Nevertheless, the effects of their inhibition in HGSOC and the potential synergy with other drugs are poorly known. METHODS We analyzed the effects of the CDK12/13 inhibitor THZ531 in HGSOC cells and patient-derived organoids (PDOs). RNA sequencing and quantitative PCR analyses were performed to identify the genome-wide effects of short-term CDK12/13 inhibition on the transcriptome of HGSOC cells. Viability assays with HGSOC cells and PDOs were performed to assess the efficacy of THZ531 as single agent or in combination with clinically relevant drugs. RESULTS The CDK12 and CDK13 genes are deregulated in HGSOC and their concomitant up-regulation with the oncogene MYC predicts poor prognosis. HGSOC cells and PDOs display high sensitivity to CDK12/13 inhibition, which synergizes with drugs in clinical use for HGSOC. Transcriptome analyses revealed cancer-relevant genes whose expression is repressed by dual CDK12/13 inhibition through impaired splicing. Combined treatment with THZ531 and inhibitors of pathways regulated by these cancer relevant genes (EGFR, RPTOR, ATRIP) exerted synergic effects on HGSOC PDO viability. CONCLUSIONS CDK12 and CDK13 represent valuable therapeutic targets for HGSOC. We uncovered a wide spectrum of CDK12/13 targets as potential therapeutic vulnerabilities for HGSOC. Moreover, our study indicates that CDK12/13 inhibition enhances the efficacy of approved drugs that are already in use for HGSOC or other human cancers.
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Affiliation(s)
- Eleonora Cesari
- Department of Neuroscience, Section of Human Anatomy, Catholic University of the Sacred Heart, 00168, Rome, Italy
- GSTeP Organoids Research Core Facility, IRCCS Fondazione Policlinico A. Gemelli, 00168, Rome, Italy
| | - Alessandra Ciucci
- GSTeP Organoids Research Core Facility, IRCCS Fondazione Policlinico A. Gemelli, 00168, Rome, Italy
- Department of Woman and Child Health and Public Health, Catholic University of the Sacred Heart, 00168, Rome, Italy
| | - Marco Pieraccioli
- Department of Neuroscience, Section of Human Anatomy, Catholic University of the Sacred Heart, 00168, Rome, Italy
- GSTeP Organoids Research Core Facility, IRCCS Fondazione Policlinico A. Gemelli, 00168, Rome, Italy
| | - Cinzia Caggiano
- Department of Neuroscience, Section of Human Anatomy, Catholic University of the Sacred Heart, 00168, Rome, Italy
- GSTeP Organoids Research Core Facility, IRCCS Fondazione Policlinico A. Gemelli, 00168, Rome, Italy
| | - Camilla Nero
- Department of Woman and Child Health and Public Health, Catholic University of the Sacred Heart, 00168, Rome, Italy
- Department of Woman and Child Health and Public Health, Gynecologic Oncology Unit, Fondazione Policlinico Universitario A. Gemelli IRCCS, Largo Francesco Vito 1, 00168, Rome, Italy
| | - Davide Bonvissuto
- Department of Neuroscience, Section of Human Anatomy, Catholic University of the Sacred Heart, 00168, Rome, Italy
| | - Francesca Sillano
- Department of Woman and Child Health and Public Health, Catholic University of the Sacred Heart, 00168, Rome, Italy
| | - Marianna Buttarelli
- Department of Woman and Child Health and Public Health, Catholic University of the Sacred Heart, 00168, Rome, Italy
- Unit of Translational Medicine for Woman and Child Health, IRCCS Fondazione Policlinico Universitario A. Gemelli, 00168, Rome, Italy
| | - Alessia Piermattei
- Department of Woman and Child Health and Public Health, Catholic University of the Sacred Heart, 00168, Rome, Italy
| | - Matteo Loverro
- Department of Woman and Child Health and Public Health, Catholic University of the Sacred Heart, 00168, Rome, Italy
- Department of Woman and Child Health and Public Health, Gynecologic Oncology Unit, Fondazione Policlinico Universitario A. Gemelli IRCCS, Largo Francesco Vito 1, 00168, Rome, Italy
| | - Floriana Camarda
- Department of Woman and Child Health and Public Health, Catholic University of the Sacred Heart, 00168, Rome, Italy
- Department of Woman and Child Health and Public Health, Gynecologic Oncology Unit, Fondazione Policlinico Universitario A. Gemelli IRCCS, Largo Francesco Vito 1, 00168, Rome, Italy
| | - Viviana Greco
- Department of Diagnostic and Laboratory Medicine, Unity of Chemistry, Biochemistry and Clinical Molecular Biology, Fondazione Policlinico Universitario A. Gemelli IRCCS, Rome, Italy
- Department of Basic Biotechnological Sciences, Intensive Care and Perioperative Clinics Research, Catholic University of the Sacred Heart, Università Cattolica del Sacro Cuore, Rome, Italy
| | - Maria De Bonis
- Department of Basic Biotechnological Sciences, Intensive Care and Perioperative Clinics Research, Catholic University of the Sacred Heart, Università Cattolica del Sacro Cuore, Rome, Italy
| | - Angelo Minucci
- Department of Basic Biotechnological Sciences, Intensive Care and Perioperative Clinics Research, Catholic University of the Sacred Heart, Università Cattolica del Sacro Cuore, Rome, Italy
| | - Daniela Gallo
- Department of Woman and Child Health and Public Health, Catholic University of the Sacred Heart, 00168, Rome, Italy
- Unit of Translational Medicine for Woman and Child Health, IRCCS Fondazione Policlinico Universitario A. Gemelli, 00168, Rome, Italy
| | - Andrea Urbani
- Department of Diagnostic and Laboratory Medicine, Unity of Chemistry, Biochemistry and Clinical Molecular Biology, Fondazione Policlinico Universitario A. Gemelli IRCCS, Rome, Italy
- Department of Basic Biotechnological Sciences, Intensive Care and Perioperative Clinics Research, Catholic University of the Sacred Heart, Università Cattolica del Sacro Cuore, Rome, Italy
| | - Giuseppe Vizzielli
- Department of Medical Area (DAME), University of Udine, Udine, Italy
- Clinic of Obstetrics and Gynecology, "Santa Maria Della Misericordia" University Hospital, Azienda Sanitaria Universitaria Friuli Centrale, Udine, Italy
| | - Giovanni Scambia
- Department of Woman and Child Health and Public Health, Catholic University of the Sacred Heart, 00168, Rome, Italy.
- Department of Woman and Child Health and Public Health, Gynecologic Oncology Unit, Fondazione Policlinico Universitario A. Gemelli IRCCS, Largo Francesco Vito 1, 00168, Rome, Italy.
| | - Claudio Sette
- Department of Neuroscience, Section of Human Anatomy, Catholic University of the Sacred Heart, 00168, Rome, Italy.
- GSTeP Organoids Research Core Facility, IRCCS Fondazione Policlinico A. Gemelli, 00168, Rome, Italy.
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Tang R, Liu J, Li S, Zhang J, Yu C, Liu H, Chen F, Lv L, Zhang Q, Yuan K, Shao H. A patent and literature review of CDK12 inhibitors. Expert Opin Ther Pat 2022; 32:1055-1065. [PMID: 36120913 DOI: 10.1080/13543776.2022.2126765] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
Abstract
INTRODUCTION Cyclin-dependent kinase 12 (CDK12) belongs to the CDK family of serine/threonine protein kinases and associates with cyclin K to exert its biological functions, including regulating gene transcription, mRNA processing and translation. Increasing evidences demonstrate the importance of CDK12 in various human cancers, illustrating its potential as both biomarker and therapeutic target. In addition, CDK12 is also a promising target for the treatment of myotonic dystrophy type 1. Efforts have been taken to discover small molecule inhibitors to validate this important therapeutic target. AREAS COVERED This review covers the patented CDK12 inhibitors from 2016 to present, as well as these from peer-reviewed literature. It provides the reader an update of the discovery strategies, chemical structures and molecular profiling of all available CDK12 inhibitors. EXPERT OPINION CDK12 inhibitors with various mechanism of actions have been discovered and it is a great set of tools to evaluate the therapeutic potential of CDK12 in different disease models. CDK12 inhibitors have shown promising results in myotonic dystrophy type 1 mouse model and several preclinical cancer models either as single agent or combination with other anti-cancer agents. Its therapeutic value awaits more rigorous preclinical testing and further clinical investigation.
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Affiliation(s)
- Ruijun Tang
- Hunan Key Laboratory of Molecular Precision Medicine, Department of Oncology, Central South University, Changsha, Hunan 410008, China.,Center for Clinical Biorepositories and Biospecimen & Department of Neurosurgery, Xiangya Hospital, Central South University, Changsha, Hunan 410008, China
| | - Jing Liu
- Hunan Key Laboratory of Molecular Precision Medicine, Department of Oncology, Central South University, Changsha, Hunan 410008, China
| | - Shuyao Li
- Hunan Key Laboratory of Molecular Precision Medicine, Department of Oncology, Central South University, Changsha, Hunan 410008, China
| | - Junjie Zhang
- Hunan Key Laboratory of Molecular Precision Medicine, Department of Oncology, Central South University, Changsha, Hunan 410008, China
| | - Chunhong Yu
- Hunan Key Laboratory of Molecular Precision Medicine, Department of Oncology, Central South University, Changsha, Hunan 410008, China
| | - Honglu Liu
- Hunan Key Laboratory of Molecular Precision Medicine, Department of Oncology, Central South University, Changsha, Hunan 410008, China
| | - Fang Chen
- Hunan Key Laboratory of Molecular Precision Medicine, Department of Oncology, Central South University, Changsha, Hunan 410008, China
| | - Lu Lv
- Hunan Key Laboratory of Molecular Precision Medicine, Department of Oncology, Central South University, Changsha, Hunan 410008, China
| | - Qian Zhang
- Department of Chemistry, Xi'an Jiaotong-Liverpool University, Suzhou 215123, China
| | - Kai Yuan
- Hunan Key Laboratory of Molecular Precision Medicine, Department of Oncology, Central South University, Changsha, Hunan 410008, China.,Hunan Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, Changsha, Hunan 410008, China.,National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, Hunan 410008, China.,The Biobank of Xiangya Hospital, Central South University, Changsha, Hunan 410008, China.,College of Pharmaceutical Sciences, Southwest University, Chongqing 400716, China
| | - Hao Shao
- Hunan Key Laboratory of Molecular Precision Medicine, Department of Oncology, Central South University, Changsha, Hunan 410008, China
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Hluchý M, Gajdušková P, Ruiz de Los Mozos I, Rájecký M, Kluge M, Berger BT, Slabá Z, Potěšil D, Weiß E, Ule J, Zdráhal Z, Knapp S, Paruch K, Friedel CC, Blazek D. CDK11 regulates pre-mRNA splicing by phosphorylation of SF3B1. Nature 2022; 609:829-834. [PMID: 36104565 DOI: 10.1038/s41586-022-05204-z] [Citation(s) in RCA: 21] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2021] [Accepted: 08/08/2022] [Indexed: 11/09/2022]
Abstract
RNA splicing, the process of intron removal from pre-mRNA, is essential for the regulation of gene expression. It is controlled by the spliceosome, a megadalton RNA-protein complex that assembles de novo on each pre-mRNA intron through an ordered assembly of intermediate complexes1,2. Spliceosome activation is a major control step that requires substantial protein and RNA rearrangements leading to a catalytically active complex1-5. Splicing factor 3B subunit 1 (SF3B1) protein-a subunit of the U2 small nuclear ribonucleoprotein6-is phosphorylated during spliceosome activation7-10, but the kinase that is responsible has not been identified. Here we show that cyclin-dependent kinase 11 (CDK11) associates with SF3B1 and phosphorylates threonine residues at its N terminus during spliceosome activation. The phosphorylation is important for the association between SF3B1 and U5 and U6 snRNAs in the activated spliceosome, termed the Bact complex, and the phosphorylation can be blocked by OTS964, a potent and selective inhibitor of CDK11. Inhibition of CDK11 prevents spliceosomal transition from the precatalytic complex B to the activated complex Bact and leads to widespread intron retention and accumulation of non-functional spliceosomes on pre-mRNAs and chromatin. We demonstrate a central role of CDK11 in spliceosome assembly and splicing regulation and characterize OTS964 as a highly selective CDK11 inhibitor that suppresses spliceosome activation and splicing.
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Affiliation(s)
- Milan Hluchý
- Central European Institute of Technology (CEITEC), Masaryk University, Brno, Czech Republic
| | - 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 Personalized Medicine, NASERTIC, Government of Navarra, Pamplona, Spain
- Center for Applied Medical Research, University of Navarra, Pamplona, Spain
| | - Michal Rájecký
- Central European Institute of Technology (CEITEC), Masaryk University, Brno, Czech Republic
| | - Michael Kluge
- Institut für Informatik, Ludwig-Maximilians-Universität München, München, Germany
| | - Benedict-Tilman Berger
- Structural Genomics Consortium (SGC), Buchmann Institute for Life Sciences (BMLS), Goethe University Frankfurt am Main, Frankfurt am Main, Germany
- Institut für Pharmazeutische Chemie, Goethe University Frankfurt am Main, Frankfurt am Main, Germany
| | - Zuzana Slabá
- Central European Institute of Technology (CEITEC), Masaryk University, Brno, Czech Republic
| | - David Potěšil
- Central European Institute of Technology (CEITEC), Masaryk University, Brno, Czech Republic
| | - Elena Weiß
- Institut für Informatik, Ludwig-Maximilians-Universität München, München, Germany
| | - Jernej Ule
- The Francis Crick Institute, London, UK
- UK Dementia Research Institute, King's College London, London, UK
| | - Zbyněk Zdráhal
- Central European Institute of Technology (CEITEC), Masaryk University, Brno, Czech Republic
| | - Stefan Knapp
- Structural Genomics Consortium (SGC), Buchmann Institute for Life Sciences (BMLS), Goethe University Frankfurt am Main, Frankfurt am Main, Germany
- Institut für Pharmazeutische Chemie, Goethe University Frankfurt am Main, Frankfurt am Main, Germany
| | - Kamil Paruch
- Department of Chemistry, Faculty of Science, Masaryk University, Brno, Czech Republic
- International Clinical Research Center, St Anne's University Hospital in Brno, Brno, Czech Republic
| | - Caroline C Friedel
- Institut für Informatik, Ludwig-Maximilians-Universität München, München, Germany
| | - Dalibor Blazek
- Central European Institute of Technology (CEITEC), Masaryk University, Brno, Czech Republic.
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8
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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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9
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Maijaroen S, Klaynongsruang S, Roytrakul S, Konkchaiyaphum M, Taemaitree L, Jangpromma N. An Integrated Proteomics and Bioinformatics Analysis of the Anticancer Properties of RT2 Antimicrobial Peptide on Human Colon Cancer (Caco-2) Cells. Molecules 2022; 27:molecules27041426. [PMID: 35209215 PMCID: PMC8880037 DOI: 10.3390/molecules27041426] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2021] [Revised: 02/09/2022] [Accepted: 02/18/2022] [Indexed: 12/05/2022] Open
Abstract
New selective, efficacious chemotherapy agents are in demand as traditional drugs display side effects and face growing resistance upon continued administration. To this end, bioactive molecules such as peptides are attracting interest. RT2 is a cationic peptide that was used as an antimicrobial but is being repurposed for targeting cancer. In this work, we investigate the mechanism by which this peptide targets Caco-2 human colon cancer cells, one of the most prevalent and metastatic cancers. Combining label-free proteomics with bioinformatics data, our data explore over 1000 proteins to identify 133 proteins that are downregulated and 79 proteins that are upregulated upon treatment with RT2. These changes occur in a dose-dependent manner and suggest the former group are related to anticancer cell proliferation; the latter group is closely related to apoptosis levels. The mRNA levels of several genes (FGF8, PAPSS2, CDK12, LDHA, PRKCSH, CSE1L, STARD13, TLE3, and OGDHL) were quantified using RT-qPCR and were found to be in agreement with proteomic results. Collectively, the global change in Caco-2 cell protein abundance suggests that RT2 triggers multiple mechanisms, including cell proliferation reduction, apoptosis activation, and alteration of cancerous cell metabolism.
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Affiliation(s)
- Surachai Maijaroen
- Department of Biochemistry, Faculty of Science, Khon Kaen University, Khon Kaen 40002, Thailand; (S.M.); (S.K.); (M.K.)
- Protein and Proteomics Research Center for Commercial and Industrial Purposes (ProCCI), Faculty of Science, Khon Kaen University, Khon Kaen 40002, Thailand
| | - Sompong Klaynongsruang
- Department of Biochemistry, Faculty of Science, Khon Kaen University, Khon Kaen 40002, Thailand; (S.M.); (S.K.); (M.K.)
- Protein and Proteomics Research Center for Commercial and Industrial Purposes (ProCCI), Faculty of Science, Khon Kaen University, Khon Kaen 40002, Thailand
| | - Sittiruk Roytrakul
- Functional Ingredients and Food Innovation Research Group, National Center for Genetic Engineering and Biotechnology, National Science and Technology Development Agency, Pathum Thani 12120, Thailand;
| | - Monruedee Konkchaiyaphum
- Department of Biochemistry, Faculty of Science, Khon Kaen University, Khon Kaen 40002, Thailand; (S.M.); (S.K.); (M.K.)
- Protein and Proteomics Research Center for Commercial and Industrial Purposes (ProCCI), Faculty of Science, Khon Kaen University, Khon Kaen 40002, Thailand
| | - Lapatrada Taemaitree
- Department of Integrated Science, Faculty of Science, Khon Kaen University, Khon Kaen 40002, Thailand;
| | - Nisachon Jangpromma
- Protein and Proteomics Research Center for Commercial and Industrial Purposes (ProCCI), Faculty of Science, Khon Kaen University, Khon Kaen 40002, Thailand
- Department of Integrated Science, Faculty of Science, Khon Kaen University, Khon Kaen 40002, Thailand;
- Correspondence:
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10
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Gongora ABL, Marshall CH, Velho PI, Lopes CDH, Marin JF, Camargo AA, Bastos DA, Antonarakis ES. Extreme Responses to a Combination of DNA-Damaging Therapy and Immunotherapy in CDK12-Altered Metastatic Castration-Resistant Prostate Cancer: A Potential Therapeutic Vulnerability. Clin Genitourin Cancer 2021; 20:183-188. [PMID: 35027313 DOI: 10.1016/j.clgc.2021.11.015] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2021] [Accepted: 11/29/2021] [Indexed: 11/29/2022]
Affiliation(s)
| | | | - Pedro Isaacsson Velho
- Department of Oncology, Johns Hopkins School of Medicine, Baltimore, MD; Department of Oncology, Hospital Moinhos de Vento, Porto Alegre, Brazil
| | - Carlos D H Lopes
- Department of Oncology, Hospital Sírio-Libanês, São Paulo, Brazil
| | - José F Marin
- Department of nuclear medicine, Hospital Sírio-Libanês, São Paulo, Brazil
| | | | - Diogo A Bastos
- Department of Oncology, Hospital Sírio-Libanês, São Paulo, Brazil
| | - Emmanuel S Antonarakis
- Department of Medicine, Division of Hematology/Oncology and Transplantation, University of Minnesota, Minneapolis, MN
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11
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Farré X, Molina R, Barteri F, Timmers PRHJ, Joshi PK, Oliva B, Acosta S, Esteve-Altava B, Navarro A, Muntané G. Comparative Analysis of Mammal Genomes Unveils Key Genomic Variability for Human Life Span. Mol Biol Evol 2021; 38:4948-4961. [PMID: 34297086 PMCID: PMC8557403 DOI: 10.1093/molbev/msab219] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
The enormous mammal's lifespan variation is the result of each species' adaptations to their own biological trade-offs and ecological conditions. Comparative genomics have demonstrated that genomic factors underlying both, species lifespans and longevity of individuals, are in part shared across the tree of life. Here, we compared protein-coding regions across the mammalian phylogeny to detect individual amino acid (AA) changes shared by the most long-lived mammals and genes whose rates of protein evolution correlate with longevity. We discovered a total of 2,737 AA in 2,004 genes that distinguish long- and short-lived mammals, significantly more than expected by chance (P = 0.003). These genes belong to pathways involved in regulating lifespan, such as inflammatory response and hemostasis. Among them, a total 1,157 AA showed a significant association with maximum lifespan in a phylogenetic test. Interestingly, most of the detected AA positions do not vary in extant human populations (81.2%) or have allele frequencies below 1% (99.78%). Consequently, almost none of these putatively important variants could have been detected by genome-wide association studies. Additionally, we identified four more genes whose rate of protein evolution correlated with longevity in mammals. Crucially, SNPs located in the detected genes explain a larger fraction of human lifespan heritability than expected, successfully demonstrating for the first time that comparative genomics can be used to enhance interpretation of human genome-wide association studies. Finally, we show that the human longevity-associated proteins are significantly more stable than the orthologous proteins from short-lived mammals, strongly suggesting that general protein stability is linked to increased lifespan.
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Affiliation(s)
- Xavier Farré
- Department of Experimental and Health Sciences, Institute of Evolutionary Biology (UPF-CSIC), Universitat Pompeu Fabra, Barcelona, Spain
| | - Ruben Molina
- Structural Bioinformatics Lab, Department of Experimental and Health Sciences, Universitat Pompeu Fabra, Barcelona, Spain
| | - Fabio Barteri
- Department of Experimental and Health Sciences, Institute of Evolutionary Biology (UPF-CSIC), Universitat Pompeu Fabra, Barcelona, Spain
| | - Paul R H J Timmers
- MRC Human Genetics Unit, MRC Institute of Genetics & Molecular Medicine, University of Edinburgh, Edinburgh, United Kingdom,Centre for Global Health Research, Usher Institute, University of Edinburgh, Edinburgh, United Kingdom
| | - Peter K Joshi
- Centre for Global Health Research, Usher Institute, University of Edinburgh, Edinburgh, United Kingdom
| | - Baldomero Oliva
- Structural Bioinformatics Lab, Department of Experimental and Health Sciences, Universitat Pompeu Fabra, Barcelona, Spain
| | - Sandra Acosta
- Department of Experimental and Health Sciences, Institute of Evolutionary Biology (UPF-CSIC), Universitat Pompeu Fabra, Barcelona, Spain
| | - Borja Esteve-Altava
- Department of Experimental and Health Sciences, Institute of Evolutionary Biology (UPF-CSIC), Universitat Pompeu Fabra, Barcelona, Spain
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12
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Roosan MR, Mambetsariev I, Pharaon R, Fricke J, Baroz AR, Chao J, Chen C, Nasser MW, Chirravuri-Venkata R, Jain M, Smith L, Yost SE, Reckamp KL, Pillai R, Arvanitis L, Afkhami M, Wang EW, Chung V, Cristea M, Fakih M, Koczywas M, Massarelli E, Mortimer J, Yuan Y, Batra SK, Pal S, Salgia R. Evaluation of Somatic Mutations in Solid Metastatic Pan-Cancer Patients. Cancers (Basel) 2021; 13:2776. [PMID: 34204917 PMCID: PMC8199748 DOI: 10.3390/cancers13112776] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2021] [Revised: 05/27/2021] [Accepted: 05/28/2021] [Indexed: 12/12/2022] Open
Abstract
Metastasis continues to be the primary cause of all cancer-related deaths despite the recent advancements in cancer treatments. To evaluate the role of mutations in overall survival (OS) and treatment outcomes, we analyzed 957 metastatic patients with seven major cancer types who had available molecular testing results with a FoundationOne CDx® panel. The most prevalent genes with somatic mutations were TP53, KRAS, APC, and LRP1B. In this analysis, these genes had mutation frequencies higher than in publicly available datasets. We identified that the somatic mutations were seven mutually exclusive gene pairs and an additional fifty-two co-occurring gene pairs. Mutations in the mutually exclusive gene pair APC and CDKN2A showed an opposite effect on the overall survival. However, patients with CDKN2A mutations showed significantly shorter OS (HR: 1.72, 95% CI: 1.34-2.21, p < 0.001) after adjusting for cancer type, age at diagnosis, and sex. Five-year post metastatic diagnosis survival analysis showed a significant improvement in OS (median survival 28 and 43 months in pre-2015 and post-2015 metastatic diagnosis, respectively, p = 0.00021) based on the year of metastatic diagnosis. Although the use of targeted therapies after metastatic diagnosis prolonged OS, the benefit was not statistically significant. However, longer five-year progression-free survival (PFS) was significantly associated with targeted therapy use (median 10.9 months (CI: 9.7-11.9 months) compared to 9.1 months (CI: 8.1-10.1 months) for non-targeted therapy, respectively, p = 0.0029). Our results provide a clinically relevant overview of the complex molecular landscape and survival mechanisms in metastatic solid cancers.
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Affiliation(s)
- Moom R. Roosan
- School of Pharmacy, Chapman University, Irvine, CA 92618, USA;
| | - Isa Mambetsariev
- Department of Medical Oncology & Therapeutics Research, City of Hope, Duarte, CA 91010, USA; (I.M.); (R.P.); (J.F.); (A.R.B.); (J.C.); (S.E.Y.); (K.L.R.); (E.W.W.); (V.C.); (M.C.); (M.F.); (M.K.); (E.M.); (J.M.); (Y.Y.)
| | - Rebecca Pharaon
- Department of Medical Oncology & Therapeutics Research, City of Hope, Duarte, CA 91010, USA; (I.M.); (R.P.); (J.F.); (A.R.B.); (J.C.); (S.E.Y.); (K.L.R.); (E.W.W.); (V.C.); (M.C.); (M.F.); (M.K.); (E.M.); (J.M.); (Y.Y.)
| | - Jeremy Fricke
- Department of Medical Oncology & Therapeutics Research, City of Hope, Duarte, CA 91010, USA; (I.M.); (R.P.); (J.F.); (A.R.B.); (J.C.); (S.E.Y.); (K.L.R.); (E.W.W.); (V.C.); (M.C.); (M.F.); (M.K.); (E.M.); (J.M.); (Y.Y.)
| | - Angel R. Baroz
- Department of Medical Oncology & Therapeutics Research, City of Hope, Duarte, CA 91010, USA; (I.M.); (R.P.); (J.F.); (A.R.B.); (J.C.); (S.E.Y.); (K.L.R.); (E.W.W.); (V.C.); (M.C.); (M.F.); (M.K.); (E.M.); (J.M.); (Y.Y.)
| | - Joseph Chao
- Department of Medical Oncology & Therapeutics Research, City of Hope, Duarte, CA 91010, USA; (I.M.); (R.P.); (J.F.); (A.R.B.); (J.C.); (S.E.Y.); (K.L.R.); (E.W.W.); (V.C.); (M.C.); (M.F.); (M.K.); (E.M.); (J.M.); (Y.Y.)
| | - Chen Chen
- Applied AI and Data Science, City of Hope, Duarte, CA 91010, USA;
| | - Mohd W. Nasser
- Department of Biochemistry and Molecular Biology, University of Nebraska Medical Center, Omaha, NE 68198, USA; (M.W.N.); (R.C.-V.); (M.J.); (S.K.B.)
| | - Ramakanth Chirravuri-Venkata
- Department of Biochemistry and Molecular Biology, University of Nebraska Medical Center, Omaha, NE 68198, USA; (M.W.N.); (R.C.-V.); (M.J.); (S.K.B.)
| | - Maneesh Jain
- Department of Biochemistry and Molecular Biology, University of Nebraska Medical Center, Omaha, NE 68198, USA; (M.W.N.); (R.C.-V.); (M.J.); (S.K.B.)
| | - Lynette Smith
- Department of Biostatistics, University of Nebraska Medical Center, Omaha, NE 68198, USA;
| | - Susan E. Yost
- Department of Medical Oncology & Therapeutics Research, City of Hope, Duarte, CA 91010, USA; (I.M.); (R.P.); (J.F.); (A.R.B.); (J.C.); (S.E.Y.); (K.L.R.); (E.W.W.); (V.C.); (M.C.); (M.F.); (M.K.); (E.M.); (J.M.); (Y.Y.)
| | - Karen L. Reckamp
- Department of Medical Oncology & Therapeutics Research, City of Hope, Duarte, CA 91010, USA; (I.M.); (R.P.); (J.F.); (A.R.B.); (J.C.); (S.E.Y.); (K.L.R.); (E.W.W.); (V.C.); (M.C.); (M.F.); (M.K.); (E.M.); (J.M.); (Y.Y.)
- Cedars-Sinai Medical Center, Department of Medicine, Division of Medical Oncology, Los Angeles, CA 90048, USA
| | - Raju Pillai
- Department of Pathology, City of Hope, Duarte, CA 91010, USA; (R.P.); (L.A.); (M.A.)
| | - Leonidas Arvanitis
- Department of Pathology, City of Hope, Duarte, CA 91010, USA; (R.P.); (L.A.); (M.A.)
| | - Michelle Afkhami
- Department of Pathology, City of Hope, Duarte, CA 91010, USA; (R.P.); (L.A.); (M.A.)
| | - Edward W. Wang
- Department of Medical Oncology & Therapeutics Research, City of Hope, Duarte, CA 91010, USA; (I.M.); (R.P.); (J.F.); (A.R.B.); (J.C.); (S.E.Y.); (K.L.R.); (E.W.W.); (V.C.); (M.C.); (M.F.); (M.K.); (E.M.); (J.M.); (Y.Y.)
| | - Vincent Chung
- Department of Medical Oncology & Therapeutics Research, City of Hope, Duarte, CA 91010, USA; (I.M.); (R.P.); (J.F.); (A.R.B.); (J.C.); (S.E.Y.); (K.L.R.); (E.W.W.); (V.C.); (M.C.); (M.F.); (M.K.); (E.M.); (J.M.); (Y.Y.)
| | - Mihaela Cristea
- Department of Medical Oncology & Therapeutics Research, City of Hope, Duarte, CA 91010, USA; (I.M.); (R.P.); (J.F.); (A.R.B.); (J.C.); (S.E.Y.); (K.L.R.); (E.W.W.); (V.C.); (M.C.); (M.F.); (M.K.); (E.M.); (J.M.); (Y.Y.)
| | - Marwan Fakih
- Department of Medical Oncology & Therapeutics Research, City of Hope, Duarte, CA 91010, USA; (I.M.); (R.P.); (J.F.); (A.R.B.); (J.C.); (S.E.Y.); (K.L.R.); (E.W.W.); (V.C.); (M.C.); (M.F.); (M.K.); (E.M.); (J.M.); (Y.Y.)
| | - Marianna Koczywas
- Department of Medical Oncology & Therapeutics Research, City of Hope, Duarte, CA 91010, USA; (I.M.); (R.P.); (J.F.); (A.R.B.); (J.C.); (S.E.Y.); (K.L.R.); (E.W.W.); (V.C.); (M.C.); (M.F.); (M.K.); (E.M.); (J.M.); (Y.Y.)
| | - Erminia Massarelli
- Department of Medical Oncology & Therapeutics Research, City of Hope, Duarte, CA 91010, USA; (I.M.); (R.P.); (J.F.); (A.R.B.); (J.C.); (S.E.Y.); (K.L.R.); (E.W.W.); (V.C.); (M.C.); (M.F.); (M.K.); (E.M.); (J.M.); (Y.Y.)
| | - Joanne Mortimer
- Department of Medical Oncology & Therapeutics Research, City of Hope, Duarte, CA 91010, USA; (I.M.); (R.P.); (J.F.); (A.R.B.); (J.C.); (S.E.Y.); (K.L.R.); (E.W.W.); (V.C.); (M.C.); (M.F.); (M.K.); (E.M.); (J.M.); (Y.Y.)
| | - Yuan Yuan
- Department of Medical Oncology & Therapeutics Research, City of Hope, Duarte, CA 91010, USA; (I.M.); (R.P.); (J.F.); (A.R.B.); (J.C.); (S.E.Y.); (K.L.R.); (E.W.W.); (V.C.); (M.C.); (M.F.); (M.K.); (E.M.); (J.M.); (Y.Y.)
| | - Surinder K. Batra
- Department of Biochemistry and Molecular Biology, University of Nebraska Medical Center, Omaha, NE 68198, USA; (M.W.N.); (R.C.-V.); (M.J.); (S.K.B.)
| | - Sumanta Pal
- Department of Medical Oncology & Therapeutics Research, City of Hope, Duarte, CA 91010, USA; (I.M.); (R.P.); (J.F.); (A.R.B.); (J.C.); (S.E.Y.); (K.L.R.); (E.W.W.); (V.C.); (M.C.); (M.F.); (M.K.); (E.M.); (J.M.); (Y.Y.)
| | - Ravi Salgia
- Department of Medical Oncology & Therapeutics Research, City of Hope, Duarte, CA 91010, USA; (I.M.); (R.P.); (J.F.); (A.R.B.); (J.C.); (S.E.Y.); (K.L.R.); (E.W.W.); (V.C.); (M.C.); (M.F.); (M.K.); (E.M.); (J.M.); (Y.Y.)
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13
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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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14
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Risdon EN, Chau CH, Price DK, Sartor O, Figg WD. PARP Inhibitors and Prostate Cancer: To Infinity and Beyond BRCA. Oncologist 2021; 26:e115-e129. [PMID: 32790034 PMCID: PMC7794174 DOI: 10.1634/theoncologist.2020-0697] [Citation(s) in RCA: 49] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2020] [Accepted: 08/04/2020] [Indexed: 12/18/2022] Open
Abstract
The U.S. Food and Drug Administration recently approved two poly-adenosine diphosphate-ribose polymerase (PARP) inhibitors, olaparib and rucaparib, for treatment of biomarker-positive metastatic castrate resistant prostate cancer. The benefits of PARP inhibition have been well characterized in patients who have BRCA1 and BRCA2 mutations in several forms of cancer. BRCA1 and BRCA2 occupy key roles in DNA damage repair, which is comprised of several different pathways with numerous participants. Patients with mutations in other key genes within the DNA damage repair pathway may also respond to treatment with PARP inhibitors, and identification of these alterations could significantly increase the percentage of patients that may benefit from PARP inhibition. This review focuses on the potential for synthetically lethal interactions between PARP inhibitors and non-BRCA DNA damage repair genes. IMPLICATIONS FOR PRACTICE: The treatment potential of PARP inhibition has been well characterized in patients with BRCA1 and BRCA2 mutations, but there is compelling evidence for expanding the use of PARP inhibitors to mutations of other non-BRCA DNA damage repair (DDR) genes. This could increase the percentage of patients that may benefit from treatment with PARP inhibitors alone or in combination with other therapies. Understanding the significance of PARP inhibitor-sensitizing alterations in other common non-BRCA DDR genes will help guide clinical decisions to provide targeted treatment options to a wider population of patients.
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Affiliation(s)
- Emily N. Risdon
- Genitourinary Malignancies Branch, Center for Cancer Research, National Cancer Institute, National Institutes of HealthBethesdaMarylandUSA
| | - Cindy H. Chau
- Genitourinary Malignancies Branch, Center for Cancer Research, National Cancer Institute, National Institutes of HealthBethesdaMarylandUSA
| | - Douglas K. Price
- Genitourinary Malignancies Branch, Center for Cancer Research, National Cancer Institute, National Institutes of HealthBethesdaMarylandUSA
| | | | - William D. Figg
- Genitourinary Malignancies Branch, Center for Cancer Research, National Cancer Institute, National Institutes of HealthBethesdaMarylandUSA
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15
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Tsang B, Pritišanac I, Scherer SW, Moses AM, Forman-Kay JD. Phase Separation as a Missing Mechanism for Interpretation of Disease Mutations. Cell 2020; 183:1742-1756. [DOI: 10.1016/j.cell.2020.11.050] [Citation(s) in RCA: 69] [Impact Index Per Article: 17.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2020] [Revised: 11/04/2020] [Accepted: 11/25/2020] [Indexed: 02/08/2023]
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16
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Štětková M, Growková K, Fojtík P, Valčíková B, Palušová V, Verlande A, Jorda R, Kryštof V, Hejret V, Alexiou P, Rotrekl V, Uldrijan S. CDK9 activity is critical for maintaining MDM4 overexpression in tumor cells. Cell Death Dis 2020; 11:754. [PMID: 32934219 PMCID: PMC7494941 DOI: 10.1038/s41419-020-02971-3] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2020] [Revised: 08/19/2020] [Accepted: 08/27/2020] [Indexed: 12/31/2022]
Abstract
The identification of the essential role of cyclin-dependent kinases (CDKs) in the control of cell division has prompted the development of small-molecule CDK inhibitors as anticancer drugs. For many of these compounds, the precise mechanism of action in individual tumor types remains unclear as they simultaneously target different classes of CDKs - enzymes controlling the cell cycle progression as well as CDKs involved in the regulation of transcription. CDK inhibitors are also capable of activating p53 tumor suppressor in tumor cells retaining wild-type p53 gene by modulating MDM2 levels and activity. In the current study, we link, for the first time, CDK activity to the overexpression of the MDM4 (MDMX) oncogene in cancer cells. Small-molecule drugs targeting the CDK9 kinase, dinaciclib, flavopiridol, roscovitine, AT-7519, SNS-032, and DRB, diminished MDM4 levels and activated p53 in A375 melanoma and MCF7 breast carcinoma cells with only a limited effect on MDM2. These results suggest that MDM4, rather than MDM2, could be the primary transcriptional target of pharmacological CDK inhibitors in the p53 pathway. CDK9 inhibitor atuveciclib downregulated MDM4 and enhanced p53 activity induced by nutlin-3a, an inhibitor of p53-MDM2 interaction, and synergized with nutlin-3a in killing A375 melanoma cells. Furthermore, we found that human pluripotent stem cell lines express significant levels of MDM4, which are also maintained by CDK9 activity. In summary, we show that CDK9 activity is essential for the maintenance of high levels of MDM4 in human cells, and drugs targeting CDK9 might restore p53 tumor suppressor function in malignancies overexpressing MDM4.
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Affiliation(s)
- Monika Štětková
- Faculty of Medicine, Department of Biology, Masaryk University, Kamenice 5, 625 00, Brno, Czech Republic
| | - Kateřina Growková
- Faculty of Medicine, Department of Biology, Masaryk University, Kamenice 5, 625 00, Brno, Czech Republic
| | - Petr Fojtík
- Faculty of Medicine, Department of Biology, Masaryk University, Kamenice 5, 625 00, Brno, Czech Republic
- International Clinical Research Center, St. Anne's University Hospital, Pekařská 53, 656 91, Brno, Czech Republic
| | - Barbora Valčíková
- Faculty of Medicine, Department of Biology, Masaryk University, Kamenice 5, 625 00, Brno, Czech Republic
- International Clinical Research Center, St. Anne's University Hospital, Pekařská 53, 656 91, Brno, Czech Republic
| | - Veronika Palušová
- Faculty of Medicine, Department of Biology, Masaryk University, Kamenice 5, 625 00, Brno, Czech Republic
- International Clinical Research Center, St. Anne's University Hospital, Pekařská 53, 656 91, Brno, Czech Republic
| | - Amandine Verlande
- Faculty of Medicine, Department of Biology, Masaryk University, Kamenice 5, 625 00, Brno, Czech Republic
- International Clinical Research Center, St. Anne's University Hospital, Pekařská 53, 656 91, Brno, Czech Republic
| | - Radek Jorda
- Laboratory of Growth Regulators, Palacký University and Institute of Experimental Botany, The Czech Academy of Sciences, Šlechtitelů 27, 783 71, Olomouc, Czech Republic
- Faculty of Medicine and Dentistry, Institute of Molecular and Translational Medicine, Palacký University, Hněvotínská 5, 779 00, Olomouc, Czech Republic
| | - Vladimír Kryštof
- Laboratory of Growth Regulators, Palacký University and Institute of Experimental Botany, The Czech Academy of Sciences, Šlechtitelů 27, 783 71, Olomouc, Czech Republic
- Faculty of Medicine and Dentistry, Institute of Molecular and Translational Medicine, Palacký University, Hněvotínská 5, 779 00, Olomouc, Czech Republic
| | - Václav Hejret
- Central European Institute of Technology (CEITEC), Masaryk University, Kamenice 5, 625 00, Brno, Czech Republic
| | - Panagiotis Alexiou
- Central European Institute of Technology (CEITEC), Masaryk University, Kamenice 5, 625 00, Brno, Czech Republic
| | - Vladimír Rotrekl
- Faculty of Medicine, Department of Biology, Masaryk University, Kamenice 5, 625 00, Brno, Czech Republic
- International Clinical Research Center, St. Anne's University Hospital, Pekařská 53, 656 91, Brno, Czech Republic
| | - Stjepan Uldrijan
- Faculty of Medicine, Department of Biology, Masaryk University, Kamenice 5, 625 00, Brno, Czech Republic.
- International Clinical Research Center, St. Anne's University Hospital, Pekařská 53, 656 91, Brno, Czech Republic.
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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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