51
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Kumar V, Parate S, Thakur G, Lee G, Ro HS, Kim Y, Kim HJ, Kim MO, Lee KW. Identification of CDK7 Inhibitors from Natural Sources Using Pharmacoinformatics and Molecular Dynamics Simulations. Biomedicines 2021; 9:1197. [PMID: 34572383 PMCID: PMC8468199 DOI: 10.3390/biomedicines9091197] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2021] [Revised: 09/03/2021] [Accepted: 09/07/2021] [Indexed: 02/02/2023] Open
Abstract
The cyclin-dependent kinase 7 (CDK7) plays a crucial role in regulating the cell cycle and RNA polymerase-based transcription. Overexpression of this kinase is linked with various cancers in humans due to its dual involvement in cell development. Furthermore, emerging evidence has revealed that inhibiting CDK7 has anti-cancer effects, driving the development of novel and more cost-effective inhibitors with enhanced selectivity for CDK7 over other CDKs. In the present investigation, a pharmacophore-based approach was utilized to identify potential hit compounds against CDK7. The generated pharmacophore models were validated and used as 3D queries to screen 55,578 natural drug-like compounds. The obtained compounds were then subjected to molecular docking and molecular dynamics simulations to predict their binding mode with CDK7. The molecular dynamics simulation trajectories were subsequently used to calculate binding affinity, revealing four hits-ZINC20392430, SN00112175, SN00004718, and SN00262261-having a better binding affinity towards CDK7 than the reference inhibitors (CT7001 and THZ1). The binding mode analysis displayed hydrogen bond interactions with the hinge region residues Met94 and Glu95, DFG motif residue Asp155, ATP-binding site residues Thr96, Asp97, and Gln141, and quintessential residue outside the kinase domain, Cys312 of CDK7. The in silico selectivity of the hits was further checked by docking with CDK2, the close homolog structure of CDK7. Additionally, the detailed pharmacokinetic properties were predicted, revealing that our hits have better properties than established CDK7 inhibitors CT7001 and THZ1. Hence, we argue that proposed hits may be crucial against CDK7-related malignancies.
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Affiliation(s)
- Vikas Kumar
- Department of Bio & Medical Big Data (BK4 Program), Division of Life Sciences, Research Institute of Natural Science (RINS), Gyeongsang National University (GNU), 501 Jinju-daero, Jinju 52828, Korea;
| | - Shraddha Parate
- Plant Molecular Biology and Biotechnology Research Center (PMBBRC), Division of Applied Life Science, Gyeongsang National University (GNU), 501 Jinju-daero, Jinju 52828, Korea; (S.P.); (G.L.)
| | - Gunjan Thakur
- Department of Veterinary Medicine, Institute of Animal Medicine, Gyeongsang National University (GNU), Jinju 52828, Korea;
| | - Gihwan Lee
- Plant Molecular Biology and Biotechnology Research Center (PMBBRC), Division of Applied Life Science, Gyeongsang National University (GNU), 501 Jinju-daero, Jinju 52828, Korea; (S.P.); (G.L.)
| | - Hyeon-Su Ro
- Department of Bio & Medical Big Data (BK4 Program), Research Institute of Life Sciences, Gyeongsang National University (GNU), Jinju 52828, Korea;
| | - Yongseong Kim
- School of Cosmetics and Food Development, Kyungnam University, Masan 631-701, Korea;
| | - Hong Ja Kim
- Division of Life Sciences and Applied Life Science (BK21 Four), Research Institute of Natural Science (RINS), Gyeongsang National University (GNU), 501 Jinju-daero, Jinju 52828, Korea;
| | - Myeong Ok Kim
- Division of Life Sciences and Applied Life Science (BK21 Four), Research Institute of Natural Science (RINS), Gyeongsang National University (GNU), 501 Jinju-daero, Jinju 52828, Korea;
| | - Keun Woo Lee
- Department of Bio & Medical Big Data (BK4 Program), Division of Life Sciences, Research Institute of Natural Science (RINS), Gyeongsang National University (GNU), 501 Jinju-daero, Jinju 52828, Korea;
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52
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Bowry A, Kelly RDW, Petermann E. Hypertranscription and replication stress in cancer. Trends Cancer 2021; 7:863-877. [PMID: 34052137 DOI: 10.1016/j.trecan.2021.04.006] [Citation(s) in RCA: 34] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2021] [Revised: 04/23/2021] [Accepted: 04/30/2021] [Indexed: 12/18/2022]
Abstract
Replication stress results from obstacles to replication fork progression, including ongoing transcription, which can cause transcription-replication conflicts. Oncogenic signaling can promote global increases in transcription activity, also termed hypertranscription. Despite the widely accepted importance of oncogene-induced hypertranscription, its study remains neglected compared with other causes of replication stress and genomic instability in cancer. A growing number of recent studies are reporting that oncogenes, such as RAS, and targeted cancer treatments, such as bromodomain and extraterminal motif (BET) bromodomain inhibitors, increase global transcription, leading to R-loop accumulation, transcription-replication conflicts, and the activation of replication stress responses. Here we discuss our mechanistic understanding of hypertranscription-induced replication stress and the resulting cellular responses, in the context of oncogenes and targeted cancer therapies.
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Affiliation(s)
- Akhil Bowry
- Institute of Cancer and Genomic Sciences, College of Medical and Dental Sciences, University of Birmingham, Birmingham B15 2TT, UK
| | - Richard D W Kelly
- Institute of Cancer and Genomic Sciences, College of Medical and Dental Sciences, University of Birmingham, Birmingham B15 2TT, UK.
| | - Eva Petermann
- Institute of Cancer and Genomic Sciences, College of Medical and Dental Sciences, University of Birmingham, Birmingham B15 2TT, UK.
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53
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Titov IY, Stroylov VS, Rusina P, Svitanko IV. Preliminary modelling as the first stage of targeted organic synthesis. RUSSIAN CHEMICAL REVIEWS 2021. [DOI: 10.1070/rcr5012] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
The review aims to present a classification and applicability analysis of methods for preliminary molecular modelling for targeted organic, catalytic and biocatalytic synthesis. The following three main approaches are considered as a primary classification of the methods: modelling of the target – ligand coordination without structural information on both the target and the resulting complex; calculations based on experimentally obtained structural information about the target; and dynamic simulation of the target – ligand complex and the reaction mechanism with calculation of the free energy of the reaction. The review is meant for synthetic chemists to be used as a guide for building an algorithm for preliminary modelling and synthesis of structures with specified properties.
The bibliography includes 353 references.
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54
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Tantale K, Garcia-Oliver E, Robert MC, L'Hostis A, Yang Y, Tsanov N, Topno R, Gostan T, Kozulic-Pirher A, Basu-Shrivastava M, Mukherjee K, Slaninova V, Andrau JC, Mueller F, Basyuk E, Radulescu O, Bertrand E. Stochastic pausing at latent HIV-1 promoters generates transcriptional bursting. Nat Commun 2021; 12:4503. [PMID: 34301927 PMCID: PMC8302722 DOI: 10.1038/s41467-021-24462-5] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2020] [Accepted: 06/17/2021] [Indexed: 02/06/2023] Open
Abstract
Promoter-proximal pausing of RNA polymerase II is a key process regulating gene expression. In latent HIV-1 cells, it prevents viral transcription and is essential for latency maintenance, while in acutely infected cells the viral factor Tat releases paused polymerase to induce viral expression. Pausing is fundamental for HIV-1, but how it contributes to bursting and stochastic viral reactivation is unclear. Here, we performed single molecule imaging of HIV-1 transcription. We developed a quantitative analysis method that manages multiple time scales from seconds to days and that rapidly fits many models of promoter dynamics. We found that RNA polymerases enter a long-lived pause at latent HIV-1 promoters (>20 minutes), thereby effectively limiting viral transcription. Surprisingly and in contrast to current models, pausing appears stochastic and not obligatory, with only a small fraction of the polymerases undergoing long-lived pausing in absence of Tat. One consequence of stochastic pausing is that HIV-1 transcription occurs in bursts in latent cells, thereby facilitating latency exit and providing a rationale for the stochasticity of viral rebounds.
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Affiliation(s)
- Katjana Tantale
- Institut de Génétique Moléculaire de Montpellier, University of Montpellier, CNRS, Montpellier, France
- Equipe labélisée Ligue Nationale Contre le Cancer, University of Montpellier, CNRS, Montpellier, France
| | - Encar Garcia-Oliver
- Institut de Génétique Moléculaire de Montpellier, University of Montpellier, CNRS, Montpellier, France
| | - Marie-Cécile Robert
- Institut de Génétique Moléculaire de Montpellier, University of Montpellier, CNRS, Montpellier, France
- Equipe labélisée Ligue Nationale Contre le Cancer, University of Montpellier, CNRS, Montpellier, France
- Institut de Génétique Humaine, University of Montpellier, CNRS, Montpellier, France
| | - Adèle L'Hostis
- LPHI, UMR CNRS 5235, University of Montpellier, Montpellier, France
| | - Yueyuxiao Yang
- LPHI, UMR CNRS 5235, University of Montpellier, Montpellier, France
| | - Nikolay Tsanov
- Institut de Génétique Moléculaire de Montpellier, University of Montpellier, CNRS, Montpellier, France
- Equipe labélisée Ligue Nationale Contre le Cancer, University of Montpellier, CNRS, Montpellier, France
| | - Rachel Topno
- Equipe labélisée Ligue Nationale Contre le Cancer, University of Montpellier, CNRS, Montpellier, France
- Institut de Génétique Humaine, University of Montpellier, CNRS, Montpellier, France
- LPHI, UMR CNRS 5235, University of Montpellier, Montpellier, France
| | - Thierry Gostan
- Institut de Génétique Moléculaire de Montpellier, University of Montpellier, CNRS, Montpellier, France
| | - Alja Kozulic-Pirher
- Institut de Génétique Moléculaire de Montpellier, University of Montpellier, CNRS, Montpellier, France
- Equipe labélisée Ligue Nationale Contre le Cancer, University of Montpellier, CNRS, Montpellier, France
| | - Meenakshi Basu-Shrivastava
- Institut de Génétique Moléculaire de Montpellier, University of Montpellier, CNRS, Montpellier, France
- Equipe labélisée Ligue Nationale Contre le Cancer, University of Montpellier, CNRS, Montpellier, France
| | - Kamalika Mukherjee
- Institut de Génétique Moléculaire de Montpellier, University of Montpellier, CNRS, Montpellier, France
- Equipe labélisée Ligue Nationale Contre le Cancer, University of Montpellier, CNRS, Montpellier, France
| | - Vera Slaninova
- Equipe labélisée Ligue Nationale Contre le Cancer, University of Montpellier, CNRS, Montpellier, France
- Institut de Génétique Humaine, University of Montpellier, CNRS, Montpellier, France
| | - Jean-Christophe Andrau
- Institut de Génétique Moléculaire de Montpellier, University of Montpellier, CNRS, Montpellier, France
| | - Florian Mueller
- Unité Imagerie et Modélisation, Institut Pasteur and CNRS UMR 3691, Paris, France
| | - Eugenia Basyuk
- Institut de Génétique Moléculaire de Montpellier, University of Montpellier, CNRS, Montpellier, France.
- Equipe labélisée Ligue Nationale Contre le Cancer, University of Montpellier, CNRS, Montpellier, France.
- Microbiology Fundamental and Pathogenicity CNRS UMR 5234, University of Bordeaux, Bordeaux, France.
| | - Ovidiu Radulescu
- LPHI, UMR CNRS 5235, University of Montpellier, Montpellier, France.
| | - Edouard Bertrand
- Institut de Génétique Moléculaire de Montpellier, University of Montpellier, CNRS, Montpellier, France.
- Equipe labélisée Ligue Nationale Contre le Cancer, University of Montpellier, CNRS, Montpellier, France.
- Institut de Génétique Humaine, University of Montpellier, CNRS, Montpellier, France.
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55
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Berico P, Cigrang M, Davidson G, Braun C, Sandoz J, Legras S, Vokshi BH, Slovic N, Peyresaubes F, Gene Robles CM, Egly JM, Compe E, Davidson I, Coin F. CDK7 and MITF repress a transcription program involved in survival and drug tolerance in melanoma. EMBO Rep 2021; 22:e51683. [PMID: 34296805 DOI: 10.15252/embr.202051683] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2020] [Revised: 06/18/2021] [Accepted: 06/25/2021] [Indexed: 11/09/2022] Open
Abstract
Melanoma cell phenotype switching between differentiated melanocytic and undifferentiated mesenchymal-like states drives metastasis and drug resistance. CDK7 is the serine/threonine kinase of the basal transcription factor TFIIH. We show that dedifferentiation of melanocytic-type melanoma cells into mesenchymal-like cells and acquisition of tolerance to targeted therapies is achieved through chronic inhibition of CDK7. In addition to emergence of a mesenchymal-type signature, we identify a GATA6-dependent gene expression program comprising genes such as AMIGO2 or ABCG2 involved in melanoma survival or targeted drug tolerance, respectively. Mechanistically, we show that CDK7 drives expression of the melanocyte lineage transcription factor MITF that in turn binds to an intronic region of GATA6 to repress its expression in melanocytic-type cells. We show that GATA6 expression is activated in MITF-low melanoma cells of patient-derived xenografts. Taken together, our data show how the poorly characterized repressive function of MITF in melanoma participates in a molecular cascade regulating activation of a transcriptional program involved in survival and drug resistance in melanoma.
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Affiliation(s)
- Pietro Berico
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, Equipe Labélisée Ligue contre le Cancer, Strasbourg, France.,Centre National de la Recherche Scientifique, UMR7104, Illkirch, France.,Institut National de la Santé et de la Recherche Médicale, Illkirch, France.,Université de Strasbourg, Illkirch, France
| | - Max Cigrang
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, Equipe Labélisée Ligue contre le Cancer, Strasbourg, France.,Centre National de la Recherche Scientifique, UMR7104, Illkirch, France.,Institut National de la Santé et de la Recherche Médicale, Illkirch, France.,Université de Strasbourg, Illkirch, France
| | - Guillaume Davidson
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, Equipe Labélisée Ligue contre le Cancer, Strasbourg, France.,Centre National de la Recherche Scientifique, UMR7104, Illkirch, France.,Institut National de la Santé et de la Recherche Médicale, Illkirch, France.,Université de Strasbourg, Illkirch, France
| | - Cathy Braun
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, Equipe Labélisée Ligue contre le Cancer, Strasbourg, France.,Centre National de la Recherche Scientifique, UMR7104, Illkirch, France.,Institut National de la Santé et de la Recherche Médicale, Illkirch, France.,Université de Strasbourg, Illkirch, France
| | - Jeremy Sandoz
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, Equipe Labélisée Ligue contre le Cancer, Strasbourg, France.,Centre National de la Recherche Scientifique, UMR7104, Illkirch, France.,Institut National de la Santé et de la Recherche Médicale, Illkirch, France.,Université de Strasbourg, Illkirch, France
| | - Stephanie Legras
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, Equipe Labélisée Ligue contre le Cancer, Strasbourg, France.,Centre National de la Recherche Scientifique, UMR7104, Illkirch, France.,Institut National de la Santé et de la Recherche Médicale, Illkirch, France.,Université de Strasbourg, Illkirch, France
| | - Bujamin Hektor Vokshi
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, Equipe Labélisée Ligue contre le Cancer, Strasbourg, France.,Centre National de la Recherche Scientifique, UMR7104, Illkirch, France.,Institut National de la Santé et de la Recherche Médicale, Illkirch, France.,Université de Strasbourg, Illkirch, France
| | - Nevena Slovic
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, Equipe Labélisée Ligue contre le Cancer, Strasbourg, France.,Centre National de la Recherche Scientifique, UMR7104, Illkirch, France.,Institut National de la Santé et de la Recherche Médicale, Illkirch, France.,Université de Strasbourg, Illkirch, France
| | - François Peyresaubes
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, Equipe Labélisée Ligue contre le Cancer, Strasbourg, France.,Centre National de la Recherche Scientifique, UMR7104, Illkirch, France.,Institut National de la Santé et de la Recherche Médicale, Illkirch, France.,Université de Strasbourg, Illkirch, France
| | - Carlos Mario Gene Robles
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, Equipe Labélisée Ligue contre le Cancer, Strasbourg, France.,Centre National de la Recherche Scientifique, UMR7104, Illkirch, France.,Institut National de la Santé et de la Recherche Médicale, Illkirch, France.,Université de Strasbourg, Illkirch, France
| | - Jean-Marc Egly
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, Equipe Labélisée Ligue contre le Cancer, Strasbourg, France.,Centre National de la Recherche Scientifique, UMR7104, Illkirch, France.,Institut National de la Santé et de la Recherche Médicale, Illkirch, France.,Université de Strasbourg, Illkirch, France
| | - Emmanuel Compe
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, Equipe Labélisée Ligue contre le Cancer, Strasbourg, France.,Centre National de la Recherche Scientifique, UMR7104, Illkirch, France.,Institut National de la Santé et de la Recherche Médicale, Illkirch, France.,Université de Strasbourg, Illkirch, France
| | - Irwin Davidson
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, Equipe Labélisée Ligue contre le Cancer, Strasbourg, France.,Centre National de la Recherche Scientifique, UMR7104, Illkirch, France.,Institut National de la Santé et de la Recherche Médicale, Illkirch, France.,Université de Strasbourg, Illkirch, France
| | - Frederic Coin
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, Equipe Labélisée Ligue contre le Cancer, Strasbourg, France.,Centre National de la Recherche Scientifique, UMR7104, Illkirch, France.,Institut National de la Santé et de la Recherche Médicale, Illkirch, France.,Université de Strasbourg, Illkirch, France
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56
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Andrade MJ, Van Lonkhuyzen DR, Upton Z, Satyamoorthy K. RPA facilitates rescue of keratinocytes from UVB radiation damage through insulin-like growth factor-I signalling. J Cell Sci 2021; 134:jcs255786. [PMID: 34137442 DOI: 10.1242/jcs.255786] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2020] [Accepted: 05/10/2021] [Indexed: 01/19/2023] Open
Abstract
UVBR-induced photolesions in genomic DNA of keratinocytes impair cellular functions and potentially determine the cell fate post-irradiation. The ability of insulin-like growth factor-I (IGF-I) to rescue epidermal keratinocytes after photodamage via apoptosis prevention and photolesion removal was recently demonstrated using in vitro two-dimensional and three-dimensional skin models. Given the limited knowledge of specific signalling cascades contributing to post-UVBR IGF-I effects, we used inhibitors to investigate the impact of blockade of various signalling mediators on IGF-I photoprotection. IGF-I treatment, in the presence of signalling inhibitors, particularly TDRL-505, which targets replication protein A (RPA), impaired activation of IGF-1R downstream signalling, diminished cyclobutane pyrimidine dimer removal, arrested growth, reduced cell survival and increased apoptosis. Further, the transient partial knockdown of RPA was found to abrogate IGF-I-mediated responses in keratinocytes, ultimately affecting photoprotection and, thereby, establishing that RPA is required for IGF-I function. Our findings thus elucidate the importance of RPA in linking the damage response activation, cell cycle regulation, repair and survival pathways, separately initiated by IGF-I upon UVBR-induced damage. This information is potentially imperative for the development of effective sunburn and photodamage repair strategies. This article has an associated First Person interview with the first author of the paper.
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Affiliation(s)
- Melisa J Andrade
- Department of Cell and Molecular Biology, Manipal School of Life Sciences, Manipal Academy of Higher Education, Manipal, Karnataka 576104, India
- Institute of Health and Biomedical Innovation, School of Biomedical Sciences, Faculty of Health, Queensland University of Technology, Brisbane, Queensland 4059, Australia
| | - Derek R Van Lonkhuyzen
- Institute of Health and Biomedical Innovation, School of Biomedical Sciences, Faculty of Health, Queensland University of Technology, Brisbane, Queensland 4059, Australia
| | - Zee Upton
- Institute of Health and Biomedical Innovation, School of Biomedical Sciences, Faculty of Health, Queensland University of Technology, Brisbane, Queensland 4059, Australia
- Skin Research Institute of Singapore, Agency for Science, Technology and Research, Singapore138648
| | - Kapaettu Satyamoorthy
- Department of Cell and Molecular Biology, Manipal School of Life Sciences, Manipal Academy of Higher Education, Manipal, Karnataka 576104, India
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57
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Lin Y, Xue K, Li Q, Liu Z, Zhu Z, Chen J, Dang E, Wang L, Zhang W, Wang G, Li B. Cyclin-Dependent Kinase 7 Promotes Th17/Th1 Cell Differentiation in Psoriasis by Modulating Glycolytic Metabolism. J Invest Dermatol 2021; 141:2656-2667.e11. [PMID: 34004188 DOI: 10.1016/j.jid.2021.04.018] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2020] [Revised: 04/15/2021] [Accepted: 04/25/2021] [Indexed: 12/20/2022]
Abstract
Excessive activation of CD4+ T cells and T helper type (Th) 17/Th1 cell differentiation are critical events in psoriasis pathogenesis, but the associated molecular mechanism is still unclear. Here, using quantitative proteomics analysis, we found that cyclin-dependent kinase 7 (CDK7) expression was markedly increased in CD4+ T cells from patients with psoriasis compared with healthy controls and was positively correlated with psoriasis severity. Meanwhile, genetic or pharmacological inhibition of CDK7 ameliorated the severity of psoriasis in the imiquimod-induced psoriasis-like mouse model and suppressed CD4+ T-cell activation as well as Th17/Th1 cell differentiation in vivo and in vitro. Furthermore, the CDK7 inhibitor also reduced the enhanced glycolysis of CD4+ T cells from patients with psoriasis. Proinflammatory cytokine IL-23 induced increased CDK7 expression in CD4+ T cells and activated the protein kinase B/mTOR/HIF-1α signaling pathway, enhancing glycolytic metabolism. Correspondingly, CDK7 inhibition significantly impaired IL-23-induced glycolysis via the protein kinase B/mTOR/HIF-1α pathway. In summary, this study shows that CDK7 promotes CD4+ T-cell activation and Th17/Th1 cell differentiation by regulating glycolysis, thus contributing to the pathogenesis of psoriasis. Targeting CDK7 might be a promising immunosuppressive strategy to control skin inflammation mediated by IL-23.
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Affiliation(s)
- Yiting Lin
- Department of Dermatology, Xijing Hospital, Fourth Military Medical University, Xi'an, China
| | - Ke Xue
- Department of Dermatology, Xijing Hospital, Fourth Military Medical University, Xi'an, China; PLA Institute of State Key Laboratory of Cancer Biology, Department of Biopharmaceutics, Fourth Military Medical University, Xi'an, China
| | - Qingyang Li
- Department of Dermatology, Xijing Hospital, Fourth Military Medical University, Xi'an, China
| | - Zhenhua Liu
- Department of Physiology and Pathophysiology, Fourth Military Medical University, Xi'an, China
| | - Zhenlai Zhu
- Department of Dermatology, Xijing Hospital, Fourth Military Medical University, Xi'an, China
| | - Jiaoling Chen
- Department of Dermatology, Xijing Hospital, Fourth Military Medical University, Xi'an, China
| | - Erle Dang
- Department of Dermatology, Xijing Hospital, Fourth Military Medical University, Xi'an, China
| | - Lei Wang
- Department of Dermatology, Xijing Hospital, Fourth Military Medical University, Xi'an, China
| | - Weigang Zhang
- Department of Dermatology, Xijing Hospital, Fourth Military Medical University, Xi'an, China
| | - Gang Wang
- Department of Dermatology, Xijing Hospital, Fourth Military Medical University, Xi'an, China
| | - Bing Li
- Department of Dermatology, Xijing Hospital, Fourth Military Medical University, Xi'an, China.
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58
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Abudureheman T, Xia J, Li MH, Zhou H, Zheng WW, Zhou N, Shi RY, Zhu JM, Yang LT, Chen L, Zheng L, Xue K, Qing K, Duan CW. CDK7 Inhibitor THZ1 Induces the Cell Apoptosis of B-Cell Acute Lymphocytic Leukemia by Perturbing Cellular Metabolism. Front Oncol 2021; 11:663360. [PMID: 33889549 PMCID: PMC8056175 DOI: 10.3389/fonc.2021.663360] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2021] [Accepted: 02/23/2021] [Indexed: 12/14/2022] Open
Abstract
B-cell acute lymphocytic leukemia (B-ALL) is a malignant blood cancer that develops in children and adults and leads to high mortality. THZ1, a covalent cyclin-dependent kinase 7 (CDK7) inhibitor, shows anti-tumor effects in various cancers by inhibiting cell proliferation and inducing apoptosis. However, whether THZ1 has an inhibitory effect on B-ALL cells and the underlying mechanism remains obscure. In this study, we showed that THZ1 arrested the cell cycle of B-ALL cells in vitro in a low concentration, while inducing the apoptosis of B-ALL cells in vitro in a high concentration by activating the apoptotic pathways. In addition, RNA-SEQ results revealed that THZ1 disrupted the cellular metabolic pathways of B-ALL cells. Moreover, THZ1 suppressed the cellular metabolism and blocked the production of cellular metabolic intermediates in B-ALL cells. Mechanistically, THZ1 inhibited the cellular metabolism of B-ALL by downregulating the expression of c-MYC-mediated metabolic enzymes. However, THZ1 treatment enhanced cell apoptosis in over-expressed c-MYC B-ALL cells, which was involved in the upregulation of p53 expression. Collectively, our data demonstrated that CDK7 inhibitor THZ1 induced the apoptosis of B-ALL cells by perturbing c-MYC-mediated cellular metabolism, thereby providing a novel treatment option for B-ALL.
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Affiliation(s)
- Tuersunayi Abudureheman
- Key Laboratory of Pediatric Hematology and Oncology Ministry of Health and Pediatric Translational Medicine Institute, Shanghai Children's Medical Center, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Jing Xia
- Key Laboratory of Pediatric Hematology and Oncology Ministry of Health and Pediatric Translational Medicine Institute, Shanghai Children's Medical Center, Shanghai Jiao Tong University School of Medicine, Shanghai, China.,Department of Pathology, The Affiliated Hospital of Youjiang Medical University for Nationalities, Baise, China
| | - Ming-Hao Li
- Key Laboratory of Pediatric Hematology and Oncology Ministry of Health and Pediatric Translational Medicine Institute, Shanghai Children's Medical Center, Shanghai Jiao Tong University School of Medicine, Shanghai, China.,Shanghai Blood Center, Shanghai, China
| | - Hang Zhou
- Key Laboratory of Pediatric Hematology and Oncology Ministry of Health and Pediatric Translational Medicine Institute, Shanghai Children's Medical Center, Shanghai Jiao Tong University School of Medicine, Shanghai, China.,Department of Pharmacology and Chemical Biology, Shanghai Collaborative Innovation Center for Translational Medicine, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Wei-Wei Zheng
- Key Laboratory of Pediatric Hematology and Oncology Ministry of Health and Pediatric Translational Medicine Institute, Shanghai Children's Medical Center, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Neng Zhou
- Key Laboratory of Pediatric Hematology and Oncology Ministry of Health and Pediatric Translational Medicine Institute, Shanghai Children's Medical Center, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Rong-Yi Shi
- Key Laboratory of Pediatric Hematology and Oncology Ministry of Health and Pediatric Translational Medicine Institute, Shanghai Children's Medical Center, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Jian-Min Zhu
- Key Laboratory of Pediatric Hematology and Oncology Ministry of Health and Pediatric Translational Medicine Institute, Shanghai Children's Medical Center, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Li-Ting Yang
- Key Laboratory of Pediatric Hematology and Oncology Ministry of Health and Pediatric Translational Medicine Institute, Shanghai Children's Medical Center, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Li Chen
- Department of Hematology, Institute of Hematology, Changhai Hospital Affiliated to Navy Military Medical University, Shanghai, China
| | - Liang Zheng
- Key Laboratory of Pediatric Hematology and Oncology Ministry of Health and Pediatric Translational Medicine Institute, Shanghai Children's Medical Center, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Kai Xue
- State Key Laboratory of Medical Genomics, National Research Center for Translational Medicine at Shanghai, Shanghai Institute of Hematology, Ruijin Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Kai Qing
- State Key Laboratory of Medical Genomics, National Research Center for Translational Medicine at Shanghai, Shanghai Institute of Hematology, Ruijin Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Cai-Wen Duan
- Key Laboratory of Pediatric Hematology and Oncology Ministry of Health and Pediatric Translational Medicine Institute, Shanghai Children's Medical Center, Shanghai Jiao Tong University School of Medicine, Shanghai, China.,Department of Pathology, The Affiliated Hospital of Youjiang Medical University for Nationalities, Baise, China.,Department of Pharmacology and Chemical Biology, Shanghai Collaborative Innovation Center for Translational Medicine, Shanghai Jiao Tong University School of Medicine, Shanghai, China
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Veo B, Danis E, Pierce A, Wang D, Fosmire S, Sullivan KD, Joshi M, Khanal S, Dahl N, Karam S, Serkova N, Venkataraman S, Vibhakar R. Transcriptional control of DNA repair networks by CDK7 regulates sensitivity to radiation in MYC-driven medulloblastoma. Cell Rep 2021; 35:109013. [PMID: 33910002 DOI: 10.1016/j.celrep.2021.109013] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2020] [Revised: 01/22/2021] [Accepted: 03/29/2021] [Indexed: 12/23/2022] Open
Abstract
MYC-driven medulloblastoma is a major therapeutic challenge due to frequent metastasis and a poor 5-year survival rate. MYC gene amplification results in transcriptional dysregulation, proliferation, and survival of malignant cells. To identify therapeutic targets in MYC-amplified medulloblastoma, we employ a CRISPR-Cas9 essentiality screen targeting 1,140 genes. We identify CDK7 as a mediator of medulloblastoma tumorigenesis. Using chemical inhibitors and genetic depletion, we observe cessation of tumor growth in xenograft mouse models and increases in apoptosis. The results are attributed to repression of a core set of MYC-driven transcriptional programs mediating DNA repair. CDK7 inhibition alters RNA polymerase II (RNA Pol II) and MYC association at DNA repair genes. Blocking CDK7 activity sensitizes cells to ionizing radiation leading to accrual of DNA damage, extending survival and tumor latency in xenograft mouse models. Our studies establish the selective inhibition of MYC-driven medulloblastoma by CDK7 inhibition combined with radiation as a viable therapeutic strategy.
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Affiliation(s)
- Bethany Veo
- Department of Pediatrics, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Etienne Danis
- Department of Pediatrics, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Angela Pierce
- Department of Pediatrics, University of Colorado Anschutz Medical Campus, Aurora, CO, USA; Morgan Adams Foundation Pediatric Brain Tumor Research Program, Children's, Hospital Colorado, Aurora, CO, USA
| | - Dong Wang
- Department of Pediatrics, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Susan Fosmire
- Department of Pediatrics, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | | | | | | | - Nathan Dahl
- Department of Pediatrics, University of Colorado Anschutz Medical Campus, Aurora, CO, USA; Morgan Adams Foundation Pediatric Brain Tumor Research Program, Children's, Hospital Colorado, Aurora, CO, USA
| | - Sana Karam
- Department of Radiation Oncology, University of Colorado Denver, Aurora, CO, USA
| | - Natalie Serkova
- Department of Radiology, University of Colorado Denver, Aurora, CO, USA
| | - Sujatha Venkataraman
- Department of Pediatrics, University of Colorado Anschutz Medical Campus, Aurora, CO, USA; Morgan Adams Foundation Pediatric Brain Tumor Research Program, Children's, Hospital Colorado, Aurora, CO, USA
| | - Rajeev Vibhakar
- Department of Pediatrics, University of Colorado Anschutz Medical Campus, Aurora, CO, USA; Morgan Adams Foundation Pediatric Brain Tumor Research Program, Children's, Hospital Colorado, Aurora, CO, USA; Department of Neurosurgery, University of Colorado Denver, Aurora, CO, USA.
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60
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Peleg Y, Vincentelli R, Collins BM, Chen KE, Livingstone EK, Weeratunga S, Leneva N, Guo Q, Remans K, Perez K, Bjerga GEK, Larsen Ø, Vaněk O, Skořepa O, Jacquemin S, Poterszman A, Kjær S, Christodoulou E, Albeck S, Dym O, Ainbinder E, Unger T, Schuetz A, Matthes S, Bader M, de Marco A, Storici P, Semrau MS, Stolt-Bergner P, Aigner C, Suppmann S, Goldenzweig A, Fleishman SJ. Community-Wide Experimental Evaluation of the PROSS Stability-Design Method. J Mol Biol 2021; 433:166964. [PMID: 33781758 DOI: 10.1016/j.jmb.2021.166964] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2020] [Revised: 03/08/2021] [Accepted: 03/22/2021] [Indexed: 10/21/2022]
Abstract
Recent years have seen a dramatic improvement in protein-design methodology. Nevertheless, most methods demand expert intervention, limiting their widespread adoption. By contrast, the PROSS algorithm for improving protein stability and heterologous expression levels has been successfully applied to a range of challenging enzymes and binding proteins. Here, we benchmark the application of PROSS as a stand-alone tool for protein scientists with no or limited experience in modeling. Twelve laboratories from the Protein Production and Purification Partnership in Europe (P4EU) challenged the PROSS algorithm with 14 unrelated protein targets without support from the PROSS developers. For each target, up to six designs were evaluated for expression levels and in some cases, for thermal stability and activity. In nine targets, designs exhibited increased heterologous expression levels either in prokaryotic and/or eukaryotic expression systems under experimental conditions that were tailored for each target protein. Furthermore, we observed increased thermal stability in nine of ten tested targets. In two prime examples, the human Stem Cell Factor (hSCF) and human Cadherin-Like Domain (CLD12) from the RET receptor, the wild type proteins were not expressible as soluble proteins in E. coli, yet the PROSS designs exhibited high expression levels in E. coli and HEK293 cells, respectively, and improved thermal stability. We conclude that PROSS may improve stability and expressibility in diverse cases, and that improvement typically requires target-specific expression conditions. This study demonstrates the strengths of community-wide efforts to probe the generality of new methods and recommends areas for future research to advance practically useful algorithms for protein science.
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Affiliation(s)
- Yoav Peleg
- Department of Life Sciences Core Facilities (LSCF), Weizmann Institute of Science, Rehovot 7610001, Israel.
| | - Renaud Vincentelli
- Unité Mixte de Recherche (UMR) 7257, Centre National de la Recherche Scientifique (CNRS) Aix-Marseille Université, Architecture et Fonction des Macromolécules Biologiques (AFMB), Marseille, France
| | - Brett M Collins
- The University of Queensland, Institute for Molecular Bioscience, St. Lucia, Queensland 4072, Australia
| | - Kai-En Chen
- The University of Queensland, Institute for Molecular Bioscience, St. Lucia, Queensland 4072, Australia
| | - Emma K Livingstone
- The University of Queensland, Institute for Molecular Bioscience, St. Lucia, Queensland 4072, Australia
| | - Saroja Weeratunga
- The University of Queensland, Institute for Molecular Bioscience, St. Lucia, Queensland 4072, Australia
| | - Natalya Leneva
- The University of Queensland, Institute for Molecular Bioscience, St. Lucia, Queensland 4072, Australia
| | - Qian Guo
- The University of Queensland, Institute for Molecular Bioscience, St. Lucia, Queensland 4072, Australia
| | - Kim Remans
- European Molecular Biology Laboratory (EMBL), Protein Expression and Purification Core Facility, Meyerhofstrasse 1, 69117 Heidelberg, Germany
| | - Kathryn Perez
- European Molecular Biology Laboratory (EMBL), Protein Expression and Purification Core Facility, Meyerhofstrasse 1, 69117 Heidelberg, Germany
| | - Gro E K Bjerga
- NORCE Norwegian Research Centre, Postboks 22 Nygårdstangen, 5038 Bergen, Norway
| | - Øivind Larsen
- NORCE Norwegian Research Centre, Postboks 22 Nygårdstangen, 5038 Bergen, Norway
| | - Ondřej Vaněk
- Department of Biochemistry, Faculty of Science, Charles University, Hlavova 2030/8, 12840 Prague, Czech Republic
| | - Ondřej Skořepa
- Department of Biochemistry, Faculty of Science, Charles University, Hlavova 2030/8, 12840 Prague, Czech Republic
| | - Sophie Jacquemin
- Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), Centre National de la Recherche Scientifique (CNRS), UMR 7104, Institut National de la Santé et de la Recherche Médicale (INSERM), U1258, Université de Strasbourg, France
| | - Arnaud Poterszman
- Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), Centre National de la Recherche Scientifique (CNRS), UMR 7104, Institut National de la Santé et de la Recherche Médicale (INSERM), U1258, Université de Strasbourg, France
| | - Svend Kjær
- Structural Biology Science Technology Platform, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | - Evangelos Christodoulou
- Structural Biology Science Technology Platform, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | - Shira Albeck
- Department of Life Sciences Core Facilities (LSCF), Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Orly Dym
- Department of Life Sciences Core Facilities (LSCF), Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Elena Ainbinder
- Department of Life Sciences Core Facilities (LSCF), Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Tamar Unger
- Department of Life Sciences Core Facilities (LSCF), Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Anja Schuetz
- Max-Delbrück Center for Molecular Medicine (MDC), Robert-Rössle-Straße 10, 13125 Berlin-Buch, Germany
| | - Susann Matthes
- Max-Delbrück Center for Molecular Medicine (MDC), Robert-Rössle-Straße 10, 13125 Berlin-Buch, Germany
| | - Michael Bader
- Max-Delbrück Center for Molecular Medicine (MDC), Robert-Rössle-Straße 10, 13125 Berlin-Buch, Germany; University of Lübeck, Institute for Biology, Ratzeburger Allee 160, 23562 Lübeck, Germany; Charité University Medicine, Charitéplatz 1, 10117 Berlin, Germany; German Center for Cardiovascular Research (DZHK), Partner Site Berlin, Berlin, Germany
| | - Ario de Marco
- Laboratory for Environmental and Life Sciences, University of Nova Gorica, Slovenia
| | - Paola Storici
- Elettra Sincrotrone Trieste - SS 14 - km 163, 5 in Area Science Park, 34149 Basovizza, Trieste, Italy
| | - Marta S Semrau
- Elettra Sincrotrone Trieste - SS 14 - km 163, 5 in Area Science Park, 34149 Basovizza, Trieste, Italy
| | - Peggy Stolt-Bergner
- Vienna Biocenter Core Facilities GmbH, Dr. Bohr-gasse 3, 1030 Vienna, Austria
| | - Christian Aigner
- Vienna Biocenter Core Facilities GmbH, Dr. Bohr-gasse 3, 1030 Vienna, Austria
| | - Sabine Suppmann
- Max-Planck Institute of Biochemistry, Biochemistry Core Facility, Am Klopferspitz 18, 82152 Martinsried, Germany
| | - Adi Goldenzweig
- Department of Biomolecular Sciences, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Sarel J Fleishman
- Department of Biomolecular Sciences, Weizmann Institute of Science, Rehovot 7610001, Israel.
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61
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Ma H, Dean DC, Wei R, Hornicek FJ, Duan Z. Cyclin-dependent kinase 7 (CDK7) is an emerging prognostic biomarker and therapeutic target in osteosarcoma. Ther Adv Musculoskelet Dis 2021; 13:1759720X21995069. [PMID: 34104229 PMCID: PMC8164556 DOI: 10.1177/1759720x21995069] [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] [Received: 08/11/2020] [Accepted: 11/10/2020] [Indexed: 11/17/2022] Open
Abstract
Background: Overexpression of cyclin-dependent kinase 7 (CDK7) is a well-known pathogenic feature of various malignancies and a sign of a more dismal prognosis. As relatively little is known about CDK7 in osteosarcoma, we elected to evaluate its expression, prognostic value, and function. Methods: We began by analyzing the publicly available data sets on CDK7 expression, including RNA sequencing data from the Therapeutically Applicable Research to Generate Effective Treatments on Osteosarcoma (TARGET-OS) and the Gene Expression database of Normal and Tumor tissues 2 (GENT2). The correlation between patient tissue CDK7 expression and their clinicopathological features and prognosis was assessed via immunohistochemical staining of a unique tissue microarray constructed from osteosarcoma specimens. Furthermore, we analyzed CDK7 expression in osteosarcoma cell lines and tissues by Western blot. CDK7-specific siRNA and a highly-selective CDK7 inhibitor, BS-181, were applied to determine the function of CDK7 on osteosarcoma cell growth and proliferation. In addition, the effect of CDK7 inhibition on clonogenicity was evaluated using a clonogenic assay, and a 3D cell culture model was used to mimic CDK7 effects in an in vivo environment. Results: Our results demonstrate that higher CDK7 expression significantly correlates with recurrence, metastasis, and shorter overall survival in osteosarcoma patients. Therapeutically, we show that CDK7 knockdown with siRNA or selective inhibition with BS-181 decreases proliferation and induces apoptosis of osteosarcoma cells. Conclusion: This study supports CDK7 overexpression as an independent predictor of poor prognosis and promising therapeutic target for osteosarcoma.
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Affiliation(s)
- Hangzhan Ma
- Guangzhou University of Chinese Medicine, Guangzhou, Guangdong, China
| | - Dylan C Dean
- Department of Orthopedic Surgery, David Geffen School of Medicine at UCLA, Los Angeles, CA, USA
| | - Ran Wei
- Department of Orthopedic Surgery, David Geffen School of Medicine at UCLA, Los Angeles, CA, USA
| | - Francis J Hornicek
- Department of Orthopedic Surgery, David Geffen School of Medicine at UCLA, Los Angeles, CA, USA
| | - Zhenfeng Duan
- Department of Orthopedic Surgery, David Geffen School of Medicine at UCLA, 615 Charles E. Young Dr. South, Los Angeles, CA 90095, USA
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62
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Greber BJ, Remis J, Ali S, Nogales E. 2.5 Å-resolution structure of human CDK-activating kinase bound to the clinical inhibitor ICEC0942. Biophys J 2021; 120:677-686. [PMID: 33476598 PMCID: PMC7896097 DOI: 10.1016/j.bpj.2020.12.030] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2020] [Revised: 12/11/2020] [Accepted: 12/21/2020] [Indexed: 12/22/2022] Open
Abstract
The human CDK-activating kinase (CAK), composed of CDK7, cyclin H, and MAT1, is involved in the control of transcription initiation and the cell cycle. Because of these activities, it has been identified as a promising target for cancer chemotherapy. A number of CDK7 inhibitors have entered clinical trials, among them ICEC0942 (also known as CT7001). Structural information can aid in improving the affinity and specificity of such drugs or drug candidates, reducing side effects in patients. Here, we have determined the structure of the human CAK in complex with ICEC0942 at 2.5 Å-resolution using cryogenic electron microscopy. Our structure reveals conformational differences of ICEC0942 compared with previous X-ray crystal structures of the CDK2-bound complex, and highlights the critical ability of cryogenic electron microscopy to resolve structures of drug-bound protein complexes without the need to crystalize the protein target.
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Affiliation(s)
- Basil J Greber
- Division of Structural Biology, The Institute of Cancer Research, London, United Kingdom; California Institute for Quantitative Biosciences (QB3), University of California, Berkeley, Berkeley, California; Molecular Biophysics and Integrative Bio-Imaging Division, Lawrence Berkeley National Laboratory, Berkeley, California.
| | - Jonathan Remis
- California Institute for Quantitative Biosciences (QB3), University of California, Berkeley, Berkeley, California
| | - Simak Ali
- Division of Cancer, Department of Surgery & Cancer, Imperial College London, London, United Kingdom
| | - Eva Nogales
- California Institute for Quantitative Biosciences (QB3), University of California, Berkeley, Berkeley, California; Molecular Biophysics and Integrative Bio-Imaging Division, Lawrence Berkeley National Laboratory, Berkeley, California; Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, California, University of California, Berkeley, Berkeley, California; Howard Hughes Medical Institute, University of California, Berkeley, Berkeley, California
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63
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Zhang H, Zeng L, Liu Q, Jin G, Zhang J, Li Z, Xu Y, Tian H, Deng S, Shi Q, Huang X. CVB3 VP1 interacts with MAT1 to inhibit cell proliferation by interfering with Cdk-activating kinase complex activity in CVB3-induced acute pancreatitis. PLoS Pathog 2021; 17:e1008992. [PMID: 33556114 PMCID: PMC7895353 DOI: 10.1371/journal.ppat.1008992] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2020] [Revised: 02/19/2021] [Accepted: 01/08/2021] [Indexed: 01/09/2023] Open
Abstract
Coxsackievirus B3 (CVB3) belongs to the genus Enterovirus of the family Picornaviridae and can cause acute acinar pancreatitis in adults. However, the molecular mechanisms of pathogenesis underlying CVB3-induced acute pancreatitis have remained unclear. In this study, we discovered that CVB3 capsid protein VP1 inhibited pancreatic cell proliferation and exerted strong cytopathic effects on HPAC cells. Through yeast two-hybrid, co-immunoprecipitation, and confocal microscopy, we show that Menage a trois 1 (MAT1), a subunit of the Cdk-Activating Kinase (CAK) complex involved in cell proliferation and transcription, is a novel interaction protein with CVB3 VP1. Moreover, CVB3 VP1 inhibited MAT1 accumulation and localization, thus interfering with its interaction with CDK7. Furthermore, CVB3 VP1 could suppress CAK complex enzymic phosphorylation activity towards RNA Pol II and CDK4/6, direct substrates of CAK. VP1 also suppresses phosphorylation of retinoblastoma protein (pRb), an indirect CAK substrate, especially at phospho-pRb Ser780 and phospho-pRb Ser807/811 residues, which are associated with cell proliferation. Finally, we present evidence using deletion mutants that the C-terminal domain (VP1-D8, 768-859aa) is the minimal VP1 region required for its interaction with MAT1, and furthermore, VP1-D8 alone was sufficient to arrest cells in G1/S phase as observed during CVB3 infection. Taken together, we demonstrate that CVB3 VP1 can inhibit CAK complex assembly and activity through direct interaction with MAT1, to block MAT1-mediated CAK-CDK4/6-Rb signaling, and ultimately suppress cell proliferation in pancreatic cells. These findings substantially extend our basic understanding of CVB3-mediated pancreatitis, providing strong candidates for strategic therapeutic targeting.
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Affiliation(s)
- Hongxia Zhang
- The First Affiliated Hospital of Nanchang University, Nanchang, China
- Department of Medical Microbiology, School of Medicine, Nanchang University, Nanchang, China
| | - Lingbing Zeng
- The First Affiliated Hospital of Nanchang University, Nanchang, China
| | - Qiong Liu
- Department of Medical Microbiology, School of Medicine, Nanchang University, Nanchang, China
| | - Guilin Jin
- The Affiliated Hospital of JiangXi university of TCM, Nanchang, China
| | - Jieyu Zhang
- Fuzhou Medical School of Nanchang University, Fuzhou, China
| | - Zengbin Li
- Department of Medical Microbiology, School of Medicine, Nanchang University, Nanchang, China
| | - Yilian Xu
- Department of Medical Microbiology, School of Medicine, Nanchang University, Nanchang, China
| | - Huizhen Tian
- Department of Medical Microbiology, School of Medicine, Nanchang University, Nanchang, China
| | - Shanshan Deng
- Department of Medical Microbiology, School of Medicine, Nanchang University, Nanchang, China
| | - Qiaofa Shi
- Department of Medical Microbiology, School of Medicine, Nanchang University, Nanchang, China
| | - Xiaotian Huang
- The First Affiliated Hospital of Nanchang University, Nanchang, China
- Department of Medical Microbiology, School of Medicine, Nanchang University, Nanchang, China
- * E-mail:
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64
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Ge H, Yao Y, Jiang Y, Wu X, Wang Y. Pharmacological inhibition of CDK7 by THZ1 impairs tumor growth in p53-mutated HNSCC. Oral Dis 2021; 28:611-620. [PMID: 33503275 DOI: 10.1111/odi.13783] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2020] [Revised: 11/30/2020] [Accepted: 01/04/2021] [Indexed: 12/22/2022]
Abstract
BACKGROUND Cyclin-dependent kinase 7 (CDK7) has been critically linked to human cancer. However, the roles of CDK7 in head and neck squamous cell carcinoma (HNSCC) remain incompletely known. Here, we sought to dissect the functions of CDK7 underlying HNSCC tumorigenesis and explore whether pharmacological inhibition of CDK7 could induce anti-cancer effects. METHODS CDK7 expression was measured in a panel of HNSCC cell lines with p53 mutation and 20 pairs of HNSCC samples and adjacent non-tumor tissues. Genetic targeting and pharmacological inhibition of CDK7 were conducted to dissect the biological roles of CDK7 in p53-mutated HNSCC cells. An HNSCC xenograft model was developed to determine the therapeutic effects of THZ1 in vivo. Potential genes and pathways responsible for therapeutic effects of THZ1 were identified by genome-wide RNA-sequencing and bioinformatics interrogations. RESULTS CDK7 expression was significantly elevated in cancerous cells and samples as compared with their adjacent non-tumor counterparts. Impaired cell proliferation, migration, and invasion as well increased apoptosis were observed in cells upon CDK7 knockdown or THZ1 exposure. THZ1 administration potently inhibited tumor overgrowth in vivo. Mechanistically, hundreds of genes enriched in cell proliferation, apoptosis, and cancer-related categories were identified to be potentially mediated the therapeutic effects of THZ1 in HNSCC. CONCLUSION Our findings reveal that CDK7 might serve as a novel putative pro-oncogenic gene underlying HNSCC tumorigenesis and therapeutic targeting of CDK7 might be a promising strategy for p53-mutated HNSCC.
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Affiliation(s)
- Han Ge
- Jiangsu Key Laboratory of Oral Disease, Nanjing Medical University, Jiangsu, China PRC.,Department of Oral and Maxillofacial Surgery, Affiliated Hospital of Stomatology, Nanjing Medical University, Nanjing, China PRC
| | - Yuan Yao
- Jiangsu Key Laboratory of Oral Disease, Nanjing Medical University, Jiangsu, China PRC.,Department of Oral and Maxillofacial Surgery, Affiliated Hospital of Stomatology, Nanjing Medical University, Nanjing, China PRC
| | - Yue Jiang
- Jiangsu Key Laboratory of Oral Disease, Nanjing Medical University, Jiangsu, China PRC.,Department of Oral and Maxillofacial Surgery, Affiliated Hospital of Stomatology, Nanjing Medical University, Nanjing, China PRC
| | - Xiang Wu
- Jiangsu Key Laboratory of Oral Disease, Nanjing Medical University, Jiangsu, China PRC.,Department of Oral Pathology, Affiliated Hospital of Stomatology, Nanjing Medical University, Nanjing, China PRC
| | - Yanling Wang
- Jiangsu Key Laboratory of Oral Disease, Nanjing Medical University, Jiangsu, China PRC.,Department of Oral and Maxillofacial Surgery, Affiliated Hospital of Stomatology, Nanjing Medical University, Nanjing, China PRC
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65
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Liang H, Du J, Elhassan RM, Hou X, Fang H. Recent progress in development of cyclin-dependent kinase 7 inhibitors for cancer therapy. Expert Opin Investig Drugs 2021; 30:61-76. [PMID: 33183110 DOI: 10.1080/13543784.2021.1850693] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Introduction: Cyclin-dependent kinase 7 (CDK7) is a part of the CDK-activating kinase family (CAK) which has a key role in the cell cycle and transcriptional regulation. Several lines of evidence suggest that CDK7 is a promising therapeutic target for cancer. CDK7 selective inhibitors such as SY-5609 and CT7001 are in clinical development. Areas covered: We explore the biology of CDK7 and its role in cancer and follow this with an evaluation of the preclinical and clinical progress of CDK7 inhibitors, and their potential in the clinic. We searched PubMed and ClinicalTrials to identify relevant data from the database inception to 14 October 2020. Expert opinion: CDK7 inhibitors are next generation therapeutics for cancer. However, there are still challenges which include selectively, side effects, and drug resistance. Nevertheless, with ongoing clinical development of these inhibitors and greater analysis of their target, CDK7 inhibitors will become a promising approach for treatment of cancer in the near future.
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Affiliation(s)
- Hanzhi Liang
- Department of Medicinal Chemistry and Key Laboratory of Chemical Biology of Natural Products (MOE), School of Pharmaceutical Sciences, Cheeloo College of Medicine, Shandong University , Jinan, Shandong, China
| | - Jintong Du
- Shandong Cancer Hospital and Institute, Shandong First Medical University , Jinan, Shandong, China
| | - Reham M Elhassan
- Department of Medicinal Chemistry and Key Laboratory of Chemical Biology of Natural Products (MOE), School of Pharmaceutical Sciences, Cheeloo College of Medicine, Shandong University , Jinan, Shandong, China
| | - Xuben Hou
- Department of Medicinal Chemistry and Key Laboratory of Chemical Biology of Natural Products (MOE), School of Pharmaceutical Sciences, Cheeloo College of Medicine, Shandong University , Jinan, Shandong, China
| | - Hao Fang
- Department of Medicinal Chemistry and Key Laboratory of Chemical Biology of Natural Products (MOE), School of Pharmaceutical Sciences, Cheeloo College of Medicine, Shandong University , Jinan, Shandong, China
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66
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Asangani I, Blair IA, Van Duyne G, Hilser VJ, Moiseenkova-Bell V, Plymate S, Sprenger C, Wand AJ, Penning TM. Using biochemistry and biophysics to extinguish androgen receptor signaling in prostate cancer. J Biol Chem 2021; 296:100240. [PMID: 33384381 PMCID: PMC7949100 DOI: 10.1074/jbc.rev120.012411] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2020] [Revised: 12/19/2020] [Accepted: 12/31/2020] [Indexed: 12/12/2022] Open
Abstract
Castration resistant prostate cancer (CRPC) continues to be androgen receptor (AR) driven. Inhibition of AR signaling in CRPC could be advanced using state-of-the-art biophysical and biochemical techniques. Structural characterization of AR and its complexes by cryo-electron microscopy would advance the development of N-terminal domain (NTD) and ligand-binding domain (LBD) antagonists. The structural basis of AR function is unlikely to be determined by any single structure due to the intrinsic disorder of its NTD, which not only interacts with coregulators but likely accounts for the constitutive activity of AR-splice variants (SV), which lack the LBD and emerge in CRPC. Using different AR constructs lacking the LBD, their effects on protein folding, DNA binding, and transcriptional activity could reveal how interdomain coupling explains the activity of AR-SVs. The AR also interacts with coregulators that promote chromatin looping. Elucidating the mechanisms involved can identify vulnerabilities to treat CRPC, which do not involve targeting the AR. Phosphorylation of the AR coactivator MED-1 by CDK7 is one mechanism that can be blocked by the use of CDK7 inhibitors. CRPC gains resistance to AR signaling inhibitors (ARSI). Drug resistance may involve AR-SVs, but their role requires their reliable quantification by SILAC-mass spectrometry during disease progression. ARSI drug resistance also occurs by intratumoral androgen biosynthesis catalyzed by AKR1C3 (type 5 17β-hydroxysteroid dehydrogenase), which is unique in that its acts as a coactivator of AR. Novel bifunctional inhibitors that competitively inhibit AKR1C3 and block its coactivator function could be developed using reverse-micelle NMR and fragment-based drug discovery.
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Affiliation(s)
- Irfan Asangani
- Department Cancer Biology, Perelman School of Medicine University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Ian A Blair
- Department Systems Pharmacology & Translational Therapeutics, Perelman School of Medicine University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Gregory Van Duyne
- Department of Biochemistry & Biophysics, Perelman School of Medicine University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Vincent J Hilser
- Department of Biology, Johns Hopkins University, Baltimore, Maryland, USA
| | - Vera Moiseenkova-Bell
- Department Systems Pharmacology & Translational Therapeutics, Perelman School of Medicine University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Stephen Plymate
- Division of Gerontology & Geriatric Medicine, Department of Medicine, University of Washington, and GRECC, Seattle, Washington, USA
| | - Cynthia Sprenger
- Division of Gerontology & Geriatric Medicine, Department of Medicine, University of Washington, and GRECC, Seattle, Washington, USA
| | - A Joshua Wand
- Department of Biochemistry & Biophysics, Texas A&M University, College Station, Texas, USA
| | - Trevor M Penning
- Department Systems Pharmacology & Translational Therapeutics, Perelman School of Medicine University of Pennsylvania, Philadelphia, Pennsylvania, USA.
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Tatum NJ, Endicott JA. Chatterboxes: the structural and functional diversity of cyclins. Semin Cell Dev Biol 2020; 107:4-20. [PMID: 32414682 DOI: 10.1016/j.semcdb.2020.04.021] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2020] [Revised: 04/28/2020] [Accepted: 04/29/2020] [Indexed: 12/16/2022]
Abstract
Proteins of the cyclin family have divergent sequences and execute diverse roles within the cell while sharing a common fold: the cyclin box domain. Structural studies of cyclins have played a key role in our characterization and understanding of cellular processes that they control, though to date only ten of the 29 CDK-activating cyclins have been structurally characterized by X-ray crystallography or cryo-electron microscopy with or without their cognate kinases. In this review, we survey the available structures of human cyclins, highlighting their molecular features in the context of their cellular roles. We pay particular attention to how cyclin activity is regulated through fine control of degradation motif recognition and ubiquitination. Finally, we discuss the emergent roles of cyclins independent of their roles as cyclin-dependent protein kinase activators, demonstrating the cyclin box domain to be a versatile and generalized scaffolding domain for protein-protein interactions across the cellular machinery.
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Affiliation(s)
- Natalie J Tatum
- Cancer Research UK Newcastle Drug Discovery Unit, Newcastle Centre for Cancer, Translational and Clinical Research Institute, Newcastle University, Newcastle upon Tyne NE2 4HH, United Kingdom
| | - Jane A Endicott
- Cancer Research UK Newcastle Drug Discovery Unit, Newcastle Centre for Cancer, Translational and Clinical Research Institute, Newcastle University, Newcastle upon Tyne NE2 4HH, United Kingdom.
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68
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Lin D, Lin X, He T, Xie G. Gambogic Acid Inhibits the Progression of Gastric Cancer via circRNA_ASAP2/miR-33a-5p/CDK7 Axis. Cancer Manag Res 2020; 12:9221-9233. [PMID: 33061613 PMCID: PMC7532043 DOI: 10.2147/cmar.s269768] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2020] [Accepted: 08/27/2020] [Indexed: 12/31/2022] Open
Abstract
Background Gastric cancer (GC) is a major cancer-related mortality disease. Gambogic acid (GA) has been investigated to inhibit cancer progression. In the present study, the molecular mechanism of GA in regulating GC progression was studied. Methods The expression levels of circular RNA ASAP2 (circ_ASAP2), miR-33a-5p and cyclin-dependent kinases 7 (CDK7) were detected by quantitative real-time polymerase reaction (qRT-PCR). CDK7 protein level was evaluated by Western blot. Cell colony formation assay, 3-(4,5-Dimethylthazol-2-yl)-2,5-diphenyltetrazolium bromide (MTT) assay, transwell assay and flow cytometry analysis were employed to reveal the functional effects among circ_ASAP2, miR-33a-5p and CDK7 on GA-induced GC progression. Mechanistically, the binding relationship between miR-33a-5p and circ_ASAP2 or CDK7 was predicted with starBase v3.0 online database and verified by dual-luciferase reporter assay. In vivo tumor formation assay was used to explain the impacts of GA treatment on GC growth in vivo. Results Circ_ASAP2 and CDK7 expression were downregulated in GA-induced GC cells compared with GC cells. MiR-33a-5p expression was upregulated in GA-induced GC cells relative to GC cells. The protein expression level of CDK7 was lower in GA-induced GC cells than that in GC cells. Further, circ_ASAP2 overexpression decreased GA-induced inhibition effects on cell proliferation, migration and invasion and GA-induced promotion effect on cell apoptosis in both AGS and HGC-27 cells, whereas this phenomenon was reversed by miR-33a-5p. In addition, circ_ASAP2 functioned as a sponge of miR-33a-5p and miR-33a-5p was associated with CDK7. Furthermore, GA treatment inhibited GC growth in vivo. Conclusion Circ_ASAP2 overexpression promoted cell proliferation, migration and invasion, whereas inhibited cell apoptosis by upregulating CDK7 expression through binding to miR-33a-5p in GA-induced GC cells. This study provided a theoretical basis in GC treatment with GA.
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Affiliation(s)
- Dan Lin
- Department of Oncology, Yueyang Hospital of Integrated Traditional Chinese and Western Medicine, Shanghai University of Traditional Chinese Medicine, Shanghai, People's Republic of China
| | - Xiaoyang Lin
- Department of Integrated TCM and Western Medicine, The First People's Hospital of Wenling, Wenling, Zhejiang, People's Republic of China
| | - Tianlin He
- Department of Oncology, Yueyang Hospital of Integrated Traditional Chinese and Western Medicine, Shanghai University of Traditional Chinese Medicine, Shanghai, People's Republic of China
| | - Guoqun Xie
- Department of Oncology, Yueyang Hospital of Integrated Traditional Chinese and Western Medicine, Shanghai University of Traditional Chinese Medicine, Shanghai, People's Republic of China
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A review on kinases phosphorylating the carboxyl-terminal domain of RNA polymerase II-Biological functions and inhibitors. Bioorg Chem 2020; 104:104318. [PMID: 33142427 DOI: 10.1016/j.bioorg.2020.104318] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2020] [Revised: 08/18/2020] [Accepted: 09/23/2020] [Indexed: 12/14/2022]
Abstract
RNA polymerase II (RNA Pol II) plays a major role in gene transcription for eukaryote. One of the major modes of regulation in eukaryotes is the phosphorylation of the carboxyl-terminal domain (CTD) of RNA Pol II. The current study found that the phosphorylation of Ser2, Ser5, Ser7, Thr4 and Tyr1 among the heptapeptide repeats of CTD plays a key role in the transcription process. We therefore review the biological functions and inhibitors of kinases that phosphorylate these amino acid residues including transcriptional cyclin-dependent protein kinases (CDKs), bromodomain-containing protein 4 (BRD4), Polo-like kinases 3 (Plk3) and Abelson murine leukemia viral oncogene 1 and 2 (c-Abl1/2).
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70
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Klener P. Mantle cell lymphoma: insights into therapeutic targets at the preclinical level. Expert Opin Ther Targets 2020; 24:1029-1045. [PMID: 32842810 DOI: 10.1080/14728222.2020.1813718] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Abstract
INTRODUCTION Mantle cell lymphoma (MCL) is a chronically relapsing B-cell non-Hodgkin lymphoma characterized by recurrent molecular-cytogenetic aberrations that lead to deregulation of DNA damage response, cell cycle progression, epigenetics, apoptosis, proliferation, and motility. In the last 10 years, clinical approval of several innovative drugs dramatically changed the landscape of treatment options in the relapsed/refractory (R/R) MCL, which translated into significantly improved survival parameters. AREAS COVERED Here, up-to-date knowledge on the biology of MCL together with currently approved and clinically tested frontline and salvage therapies are reviewed. In addition, novel therapeutic targets in MCL based on the scientific reports published in Pubmed are discussed. EXPERT OPINION Bruton tyrosine-kinase inhibitors, NFkappaB inhibitors, BCL2 inhibitors, and immunomodulary agents in combination with monoclonal antibodies and genotoxic drugs have the potential to induce long-term remissions in majority of newly diagnosed MCL patients. Several other classes of anti-tumor drugs including phosphoinositole-3-kinase, cyclin-dependent kinase or DNA damage response kinase inhibitors have demonstrated promising anti-lymphoma efficacy in R/R MCL. Most importantly, adoptive immunotherapy with genetically modified T-cells carrying chimeric antigen receptor represents a potentially curative treatment approach even in the patients with chemotherapy and ibrutinib-refractory disease.
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Affiliation(s)
- Pavel Klener
- First Department of Internal Medicine- Hematology, University General Hospital and First Faculty of Medicine, Charles University , Prague, Czech Republic.,Institute of Pathological Physiology, First Faculty of Medicine, Charles University , Prague, Czech Republic
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71
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Thanindratarn P, Dean DC, Feng W, Wei R, Nelson SD, Hornicek FJ, Duan Z. Cyclin-dependent kinase 12 (CDK12) in chordoma: prognostic and therapeutic value. EUROPEAN SPINE JOURNAL : OFFICIAL PUBLICATION OF THE EUROPEAN SPINE SOCIETY, THE EUROPEAN SPINAL DEFORMITY SOCIETY, AND THE EUROPEAN SECTION OF THE CERVICAL SPINE RESEARCH SOCIETY 2020; 29:3214-3228. [PMID: 32691223 DOI: 10.1007/s00586-020-06543-z] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/08/2020] [Accepted: 07/14/2020] [Indexed: 01/22/2023]
Abstract
PURPOSE To determine the cyclin-dependent kinase 12 (CDK12) expression in chordoma patient tissues and cell lines, its correlation with oncologic outcomes, and its function in chordoma cell proliferation. METHODS A chordoma tissue microarray was constructed from fifty-six patient specimens and examined by immunohistochemistry to measure CDK12 expression and its correlation to patient clinical characteristics and survival. CDK12 expression in chordoma cell lines and patient tissues was evaluated via western blot. CDK12 specific small interfering RNA (siRNA) was applied to determine whether its inhibition attenuated chordoma cell growth and proliferation. RESULTS CDK12 was expressed in the majority of chordoma specimens, with notably higher expression in patients with recurrent or metastatic disease. High CDK12 expression was an independent prognostic predictor for shorter overall and progression-free survival in chordoma by univariate and multivariate analysis. Western blot analysis revealed that CDK12 was also highly expressed in chordoma cell lines, with CDK12 specific small interfering RNA (siRNA) mediated knockdown decreasing proliferation and inducing apoptosis. Mechanistically, inhibition of CDK12 decreased phosphorylation of RNA polymerase II (RNAP II) and the anti-apoptotic proteins Survivin and Mcl-1. CONCLUSION High expression of CDK12 is an independent predictor of poor prognosis in chordoma. Inhibition of CDK12 significantly decreased chordoma cell proliferation and induced apoptosis. Our results support CDK12 as a novel prognostic biomarker and therapeutic target in chordoma.
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Affiliation(s)
- Pichaya Thanindratarn
- Department of Orthopaedic Surgery, Sarcoma Biology Laboratory, David Geffen School of Medicine, University of California, Los Angeles, 615 Charles E. Young. Dr. South, Los Angeles, CA, 90095, USA.,Department of Orthopedic Surgery, Chulabhorn Hospital, HRH Princess Chulabhorn College of Medical Science, Chulabhorn Royal Academy, Bangkok, Thailand
| | - Dylan C Dean
- Department of Orthopaedic Surgery, Sarcoma Biology Laboratory, David Geffen School of Medicine, University of California, Los Angeles, 615 Charles E. Young. Dr. South, Los Angeles, CA, 90095, USA
| | - Wenlong Feng
- Department of Orthopaedic Surgery, Sarcoma Biology Laboratory, David Geffen School of Medicine, University of California, Los Angeles, 615 Charles E. Young. Dr. South, Los Angeles, CA, 90095, USA.,Department of Obstetrics and Gynecology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, China
| | - Ran Wei
- Department of Orthopaedic Surgery, Sarcoma Biology Laboratory, David Geffen School of Medicine, University of California, Los Angeles, 615 Charles E. Young. Dr. South, Los Angeles, CA, 90095, USA.,Musculoskeletal Tumor Center, Beijing Key Laboratory of Musculoskeletal Tumor, Peking University People's Hospital, Beijing, China
| | - Scott D Nelson
- Department of Pathology, University of California, Los Angeles, CA, USA
| | - Francis J Hornicek
- Department of Orthopaedic Surgery, Sarcoma Biology Laboratory, David Geffen School of Medicine, University of California, Los Angeles, 615 Charles E. Young. Dr. South, Los Angeles, CA, 90095, USA
| | - Zhenfeng Duan
- Department of Orthopaedic Surgery, Sarcoma Biology Laboratory, David Geffen School of Medicine, University of California, Los Angeles, 615 Charles E. Young. Dr. South, Los Angeles, CA, 90095, USA.
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Rusina PV, Titov IY, Panova MV, Stroylov VS, Abdyusheva YR, Murlatova EY, Svitanko IV, Novikov FN. Modeling of novel CDK7 inhibitors activity by molecular dynamics and free energy perturbation methods. MENDELEEV COMMUNICATIONS 2020. [DOI: 10.1016/j.mencom.2020.07.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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73
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Uriostegui-Arcos M, Aguayo-Ortiz R, Valencia-Morales MDP, Melchy-Pérez E, Rosenstein Y, Dominguez L, Zurita M. Disruption of TFIIH activities generates a stress gene expression response and reveals possible new targets against cancer. Open Biol 2020; 10:200050. [PMID: 32543350 PMCID: PMC7333893 DOI: 10.1098/rsob.200050] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2020] [Accepted: 05/10/2020] [Indexed: 12/13/2022] Open
Abstract
Disruption of the enzymatic activities of the transcription factor TFIIH by the small molecules Triptolide (TPL) or THZ1 could be used against cancer. Here, we used the MCF10A-ErSrc oncogenesis model to compare the effect of TFIIH inhibitors between transformed cells and their progenitors. We report that tumour cells exhibited highly increased sensitivity to TPL or THZ1 and that the combination of both had a synergic effect. TPL affects the interaction between XPB and p52, causing a reduction in the levels of XPB, p52 and p8, but not other TFIIH subunits. RNA-Seq and RNAPII-ChIP-Seq experiments showed that although the levels of many transcripts were reduced, the levels of a significant number were increased after TPL treatment, with maintained or increased RNAPII promoter occupancy. A significant number of these genes encode for factors that have been related to tumour growth and metastasis, suggesting that transformed cells might rapidly develop resistance to TPL/THZ inhibitors. Some of these genes were also overexpressed in response to THZ1, of which depletion enhances the toxicity of TPL, and are possible new targets against cancer.
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Affiliation(s)
- Maritere Uriostegui-Arcos
- Departamento de Genética del Desarrollo y Fisiología Molecular, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca Morelos 62250, Mexico
| | - Rodrigo Aguayo-Ortiz
- Departamento de Fisicoquímica, Facultad de Química, Universidad Nacional Autónoma de México, Mexico City 04510, Mexico
- Center for Arrhythmia Research, Department of Internal Medicine, Division of Cardiovascular Medicine, University of Michigan, Ann Arbor, MI 48109, USA
| | - María del Pilar Valencia-Morales
- Departamento de Genética del Desarrollo y Fisiología Molecular, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca Morelos 62250, Mexico
| | - Erika Melchy-Pérez
- Departamento de Biomedicina Molecular y Bioprocesos, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca Morelos 62250, Mexico
| | - Yvonne Rosenstein
- Departamento de Biomedicina Molecular y Bioprocesos, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca Morelos 62250, Mexico
| | - Laura Dominguez
- Departamento de Fisicoquímica, Facultad de Química, Universidad Nacional Autónoma de México, Mexico City 04510, Mexico
| | - Mario Zurita
- Departamento de Genética del Desarrollo y Fisiología Molecular, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca Morelos 62250, Mexico
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Loyer P, Trembley JH. Roles of CDK/Cyclin complexes in transcription and pre-mRNA splicing: Cyclins L and CDK11 at the cross-roads of cell cycle and regulation of gene expression. Semin Cell Dev Biol 2020; 107:36-45. [PMID: 32446654 DOI: 10.1016/j.semcdb.2020.04.016] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2020] [Revised: 04/22/2020] [Accepted: 04/24/2020] [Indexed: 12/18/2022]
Abstract
Cyclin Dependent Kinases (CDKs) represent a large family of serine/threonine protein kinases that become active upon binding to a Cyclin regulatory partner. CDK/cyclin complexes recently identified, as well as "canonical" CDK/Cyclin complexes regulating cell cycle, are implicated in the regulation of gene expression via the phosphorylation of key components of the transcription and pre-mRNA processing machineries. In this review, we summarize the role of CDK/cyclin-dependent phosphorylation in the regulation of transcription and RNA splicing and highlight recent findings that indicate the involvement of CDK11/cyclin L complexes at the cross-roads of cell cycle, transcription and RNA splicing. Finally, we discuss the potential of CDK11 and Cyclins L as therapeutic targets in cancer.
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Affiliation(s)
- Pascal Loyer
- INSERM, INRAE, Univ Rennes, NuMeCan, Nutrition Metabolisms and Cancer, Rennes, France.
| | - Janeen H Trembley
- Research Service, Minneapolis VA Health Care System, Minneapolis, MN 55417, USA; Department of Laboratory Medicine and Pathology, University of Minnesota, Minneapolis, MN 55455, USA; Masonic Cancer Center, University of Minnesota, Minneapolis, MN 55455, USA.
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75
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Fan Z, Devlin JR, Hogg SJ, Doyle MA, Harrison PF, Todorovski I, Cluse LA, Knight DA, Sandow JJ, Gregory G, Fox A, Beilharz TH, Kwiatkowski N, Scott NE, Vidakovic AT, Kelly GP, Svejstrup JQ, Geyer M, Gray NS, Vervoort SJ, Johnstone RW. CDK13 cooperates with CDK12 to control global RNA polymerase II processivity. SCIENCE ADVANCES 2020; 6:eaaz5041. [PMID: 32917631 PMCID: PMC7190357 DOI: 10.1126/sciadv.aaz5041] [Citation(s) in RCA: 69] [Impact Index Per Article: 17.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/17/2019] [Accepted: 02/10/2020] [Indexed: 05/04/2023]
Abstract
The RNA polymerase II (POLII)-driven transcription cycle is tightly regulated at distinct checkpoints by cyclin-dependent kinases (CDKs) and their cognate cyclins. The molecular events underpinning transcriptional elongation, processivity, and the CDK-cyclin pair(s) involved remain poorly understood. Using CRISPR-Cas9 homology-directed repair, we generated analog-sensitive kinase variants of CDK12 and CDK13 to probe their individual and shared biological and molecular roles. Single inhibition of CDK12 or CDK13 induced transcriptional responses associated with cellular growth signaling pathways and/or DNA damage, with minimal effects on cell viability. In contrast, dual kinase inhibition potently induced cell death, which was associated with extensive genome-wide transcriptional changes including widespread use of alternative 3' polyadenylation sites. At the molecular level, dual kinase inhibition resulted in the loss of POLII CTD phosphorylation and greatly reduced POLII elongation rates and processivity. These data define substantial redundancy between CDK12 and CDK13 and identify both as fundamental regulators of global POLII processivity and transcription elongation.
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Affiliation(s)
- Zheng Fan
- The Peter MacCallum Cancer Centre, Melbourne, 3000 VIC, Australia
- The Sir Peter MacCallum Department of Oncology, University of Melbourne, Parkville, 3052 VIC, Australia
| | - Jennifer R Devlin
- The Peter MacCallum Cancer Centre, Melbourne, 3000 VIC, Australia
- The Sir Peter MacCallum Department of Oncology, University of Melbourne, Parkville, 3052 VIC, Australia
| | - Simon J Hogg
- The Peter MacCallum Cancer Centre, Melbourne, 3000 VIC, Australia
| | - Maria A Doyle
- The Peter MacCallum Cancer Centre, Melbourne, 3000 VIC, Australia
- The Sir Peter MacCallum Department of Oncology, University of Melbourne, Parkville, 3052 VIC, Australia
| | - Paul F Harrison
- Monash Biomedicine Discovery Institute, Monash University, Clayton, 3800 VIC, Australia
- Monash Bioinformatics Platform, Monash University, Clayton, 3800 VIC, Australia
| | - Izabela Todorovski
- The Peter MacCallum Cancer Centre, Melbourne, 3000 VIC, Australia
- The Sir Peter MacCallum Department of Oncology, University of Melbourne, Parkville, 3052 VIC, Australia
| | - Leonie A Cluse
- The Peter MacCallum Cancer Centre, Melbourne, 3000 VIC, Australia
| | - Deborah A Knight
- The Peter MacCallum Cancer Centre, Melbourne, 3000 VIC, Australia
| | - Jarrod J Sandow
- Walter and Eliza Hall Institute of Medical Research, Parkville, 3052 VIC, Australia
- Department of Medical Biology, University of Melbourne, Melbourne, 3052 VIC, Australia
| | - Gareth Gregory
- The Peter MacCallum Cancer Centre, Melbourne, 3000 VIC, Australia
| | - Andrew Fox
- The Peter MacCallum Cancer Centre, Melbourne, 3000 VIC, Australia
| | - Traude H Beilharz
- Monash Biomedicine Discovery Institute, Monash University, Clayton, 3800 VIC, Australia
| | - Nicholas Kwiatkowski
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, USA
| | - Nichollas E Scott
- Department of Microbiology and Immunology, Peter Doherty Institute, University of Melbourne, Parkville, 3052 VIC, Australia
| | | | - Gavin P Kelly
- Bioinformatics and Biostatistics, The Francis Crick Institute, London NW1 1AT, UK
| | - Jesper Q Svejstrup
- Mechanisms of Transcription Laboratory, The Francis Crick Institute, London NW1 1AT, UK
| | - Matthias Geyer
- Institute of Structural Biology, University of Bonn, Sigmund-Freud-Strasse 25, 53127 Bonn, Germany
| | - Nathanael S Gray
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, USA
| | - Stephin J Vervoort
- The Peter MacCallum Cancer Centre, Melbourne, 3000 VIC, Australia.
- The Sir Peter MacCallum Department of Oncology, University of Melbourne, Parkville, 3052 VIC, Australia
| | - Ricky W Johnstone
- The Peter MacCallum Cancer Centre, Melbourne, 3000 VIC, Australia.
- The Sir Peter MacCallum Department of Oncology, University of Melbourne, Parkville, 3052 VIC, Australia
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Kohlmeyer JL, Gordon DJ, Tanas MR, Monga V, Dodd RD, Quelle DE. CDKs in Sarcoma: Mediators of Disease and Emerging Therapeutic Targets. Int J Mol Sci 2020; 21:E3018. [PMID: 32344731 PMCID: PMC7215455 DOI: 10.3390/ijms21083018] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2020] [Revised: 04/20/2020] [Accepted: 04/22/2020] [Indexed: 12/13/2022] Open
Abstract
Sarcomas represent one of the most challenging tumor types to treat due to their diverse nature and our incomplete understanding of their underlying biology. Recent work suggests cyclin-dependent kinase (CDK) pathway activation is a powerful driver of sarcomagenesis. CDK proteins participate in numerous cellular processes required for normal cell function, but their dysregulation is a hallmark of many pathologies including cancer. The contributions and significance of aberrant CDK activity to sarcoma development, however, is only partly understood. Here, we describe what is known about CDK-related alterations in the most common subtypes of sarcoma and highlight areas that warrant further investigation. As disruptions in CDK pathways appear in most, if not all, subtypes of sarcoma, we discuss the history and value of pharmacologically targeting CDKs to combat these tumors. The goals of this review are to (1) assess the prevalence and importance of CDK pathway alterations in sarcomas, (2) highlight the gap in knowledge for certain CDKs in these tumors, and (3) provide insight into studies focused on CDK inhibition for sarcoma treatment. Overall, growing evidence demonstrates a crucial role for activated CDKs in sarcoma development and as important targets for sarcoma therapy.
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Affiliation(s)
- Jordan L Kohlmeyer
- Molecular Medicine Graduate Program, Carver College of Medicine, University of Iowa, Iowa City, IA 52242, USA;
- The Department of Neuroscience and Pharmacology, Carver College of Medicine, University of Iowa, 2-570 Bowen Science Bldg., Iowa City, IA 52242, USA
| | - David J Gordon
- The Department of Pediatrics, Carver College of Medicine, University of Iowa, Iowa City, IA 52242, USA;
| | - Munir R Tanas
- The Department of Pathology, Carver College of Medicine, University of Iowa, Iowa City, IA 52242, USA;
| | - Varun Monga
- The Department of Internal Medicine, Carver College of Medicine, University of Iowa, Iowa City, IA 52242, USA; (V.M.); (R.D.D.)
| | - Rebecca D Dodd
- The Department of Internal Medicine, Carver College of Medicine, University of Iowa, Iowa City, IA 52242, USA; (V.M.); (R.D.D.)
| | - Dawn E Quelle
- Molecular Medicine Graduate Program, Carver College of Medicine, University of Iowa, Iowa City, IA 52242, USA;
- The Department of Neuroscience and Pharmacology, Carver College of Medicine, University of Iowa, 2-570 Bowen Science Bldg., Iowa City, IA 52242, USA
- The Department of Pathology, Carver College of Medicine, University of Iowa, Iowa City, IA 52242, USA;
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Attia YM, Shouman SA, Salama SA, Ivan C, Elsayed AM, Amero P, Rodriguez-Aguayo C, Lopez-Berestein G. Blockade of CDK7 Reverses Endocrine Therapy Resistance in Breast Cancer. Int J Mol Sci 2020; 21:ijms21082974. [PMID: 32340192 PMCID: PMC7215326 DOI: 10.3390/ijms21082974] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2020] [Revised: 04/15/2020] [Accepted: 04/18/2020] [Indexed: 12/19/2022] Open
Abstract
Cyclin-dependent kinase (CDK)-7 inhibitors are emerging as promising drugs for the treatment of different types of cancer that show chemotherapy resistance. Evaluation of the effects of CDK7 inhibitor, THZ1, alone and combined with tamoxifen is of paramount importance. Thus, in the current work, we assessed the effects of THZ1 and/or tamoxifen in two estrogen receptor-positive (ER+) breast cancer cell lines (MCF7) and its tamoxifen resistant counterpart (LCC2) in vitro and in xenograft mouse models of breast cancer. Furthermore, we evaluated the expression of CDK7 in clinical samples from breast cancer patients. Cell viability, apoptosis, and genes involved in cell cycle regulation and tamoxifen resistance were determined. Tumor volume and weight, proliferation marker (Ki67), angiogenic marker (CD31), and apoptotic markers were assayed. Bioinformatic data indicated CDK7 expression was associated with negative prognosis, enhanced pro-oncogenic pathways, and decreased response to tamoxifen. Treatment with THZ1 enhanced tamoxifen-induced cytotoxicity, while it inhibited genes involved in tumor progression in MCF-7 and LCC2 cells. In vivo, THZ1 boosted the effect of tamoxifen on tumor weight and tumor volume, reduced Ki67 and CD31 expression, and increased apoptotic cell death. Our findings identify CDK7 as a possible therapeutic target for breast cancer whether it is sensitive or resistant to tamoxifen therapy.
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Affiliation(s)
- Yasmin M. Attia
- Pharmacology Unit, Cancer Biology Department, National Cancer Institute, Cairo University, Kasr Al Eini Street, Fom El Khalig, Cairo 11796, Egypt; (Y.M.A.); (S.A.S.)
- Department of Experimental Therapeutics, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA; (C.I.); (A.M.E.); (P.A.); (C.R.-A.); (G.L.-B.)
| | - Samia A. Shouman
- Pharmacology Unit, Cancer Biology Department, National Cancer Institute, Cairo University, Kasr Al Eini Street, Fom El Khalig, Cairo 11796, Egypt; (Y.M.A.); (S.A.S.)
| | - Salama A. Salama
- Pharmacology & Toxicology Department, Al-Azhar University, Cairo 11675, Egypt
- Correspondence: ; Tel.: +20-109-550-8894
| | - Cristina Ivan
- Department of Experimental Therapeutics, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA; (C.I.); (A.M.E.); (P.A.); (C.R.-A.); (G.L.-B.)
- Center for RNA Interference and Non-Coding RNA, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Abdelrahman M. Elsayed
- Department of Experimental Therapeutics, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA; (C.I.); (A.M.E.); (P.A.); (C.R.-A.); (G.L.-B.)
- Pharmacology & Toxicology Department, Al-Azhar University, Cairo 11675, Egypt
| | - Paola Amero
- Department of Experimental Therapeutics, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA; (C.I.); (A.M.E.); (P.A.); (C.R.-A.); (G.L.-B.)
| | - Cristian Rodriguez-Aguayo
- Department of Experimental Therapeutics, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA; (C.I.); (A.M.E.); (P.A.); (C.R.-A.); (G.L.-B.)
- Center for RNA Interference and Non-Coding RNA, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Gabriel Lopez-Berestein
- Department of Experimental Therapeutics, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA; (C.I.); (A.M.E.); (P.A.); (C.R.-A.); (G.L.-B.)
- Center for RNA Interference and Non-Coding RNA, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
- Department of Cancer Biology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
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Abstract
This Outlook discusses Cho et al.’s finding showing that CDK7 directly phosphorylates YAP/TAZ/Yki in the nucleus, protecting them from ubiquitination and degradation, in a manner independent of the Hippo cascade and from CDK7 basal transcriptional effects. Inhibition of CDK7 is a promising strategy for cancer therapy. CDK7 so far has been understood mainly in the context of Pol II-driven transcription. However, how are the roles of CDK7 in the “basal” transcriptional machinery reconciled with the function of CDK7 as inducer of specific transcriptional programs in tumor cells? In this issue of Genes & Development, Cho and colleagues (pp. 53–71) advance in this direction, demonstrating that attenuation of CDK7 fosters the oncogenic activity of the YAP/TAZ/Yki coactivators. CDK7 directly phosphorylates YAP/TAZ/Yki in the nucleus, protecting them from ubiquitination and degradation, in a manner independent from the Hippo cascade and independent from CDK7 basal transcriptional functions.
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Affiliation(s)
- Stefano Piccolo
- Department of Molecular Medicine, University of Padua School of Medicine, 35121 Padua, Italy; IFOM, The FIRC Institute of Molecular Oncology, 35121 Padua, Italy
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79
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Diab S, Yu M, Wang S. CDK7 Inhibitors in Cancer Therapy: The Sweet Smell of Success? J Med Chem 2020; 63:7458-7474. [DOI: 10.1021/acs.jmedchem.9b01985] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Affiliation(s)
- Sarah Diab
- School of Pharmacy, Lebanese American University, P.O. Box 36, Byblos, Lebanon
| | - Mingfeng Yu
- Drug Discovery and Development, University of South Australia Cancer Research Institute, Adelaide, SA 5000, Australia
| | - Shudong Wang
- Drug Discovery and Development, University of South Australia Cancer Research Institute, Adelaide, SA 5000, Australia
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80
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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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81
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Zurita M, Murillo-Maldonado JM. Drosophila as a Model Organism to Understand the Effects during Development of TFIIH-Related Human Diseases. Int J Mol Sci 2020; 21:ijms21020630. [PMID: 31963603 PMCID: PMC7013941 DOI: 10.3390/ijms21020630] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2019] [Revised: 12/02/2019] [Accepted: 12/02/2019] [Indexed: 12/20/2022] Open
Abstract
Human mutations in the transcription and nucleotide excision repair (NER) factor TFIIH are linked with three human syndromes: xeroderma pigmentosum (XP), trichothiodystrophy (TTD) and Cockayne syndrome (CS). In particular, different mutations in the XPB, XPD and p8 subunits of TFIIH may cause one or a combination of these syndromes, and some of these mutations are also related to cancer. The participation of TFIIH in NER and transcription makes it difficult to interpret the different manifestations observed in patients, particularly since some of these phenotypes may be related to problems during development. TFIIH is present in all eukaryotic cells, and its functions in transcription and DNA repair are conserved. Therefore, Drosophila has been a useful model organism for the interpretation of different phenotypes during development as well as the understanding of the dynamics of this complex. Interestingly, phenotypes similar to those observed in humans caused by mutations in the TFIIH subunits are present in mutant flies, allowing the study of TFIIH in different developmental processes. Furthermore, studies performed in Drosophila of mutations in different subunits of TFIIH that have not been linked to any human diseases, probably because they are more deleterious, have revealed its roles in differentiation and cell death. In this review, different achievements made through studies in the fly to understand the functions of TFIIH during development and its relationship with human diseases are analysed and discussed.
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82
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Tibes R, Bogenberger JM. Transcriptional Silencing of MCL-1 Through Cyclin-Dependent Kinase Inhibition in Acute Myeloid Leukemia. Front Oncol 2019; 9:1205. [PMID: 31921615 PMCID: PMC6920180 DOI: 10.3389/fonc.2019.01205] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2019] [Accepted: 10/23/2019] [Indexed: 12/13/2022] Open
Abstract
Acute myeloid leukemia (AML) is the most common adult acute leukemia. Survival remains poor, despite decades of scientific advances. Cytotoxic induction chemotherapy regimens are standard-of-care for most patients. Many investigations have highlighted the genomic heterogeneity of AML, and several new targeted therapeutic options have recently been approved. Additional novel therapies are showing promising clinical results and may rapidly transform the therapeutic landscape of AML. Despite the emerging clinical success of B-cell lymphoma (BCL)-2 targeting in AML and a large body of preclinical data supporting myeloid leukemia cell (MCL)-1 as an attractive therapeutic target for AML, MCL-1 targeting remains relatively unexplored, although novel MCL-1 inhibitors are under clinical investigation. Inhibitors of cyclin-dependent kinases (CDKs) involved in the regulation of transcription, CDK9 in particular, are being investigated in AML as a strategy to target MCL-1 indirectly. In this article, we review the basis for CDK inhibition in oncology with a focus on relevant preclinical mechanism-of-action studies of CDK9 inhibitors in the context of their therapeutic potential specifically in AML.
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Affiliation(s)
- Raoul Tibes
- NYU School of Medicine & Perlmutter Cancer Center, NYU Langone Health, New York, NY, United States
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83
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A high-throughput screen identifies that CDK7 activates glucose consumption in lung cancer cells. Nat Commun 2019; 10:5444. [PMID: 31784510 PMCID: PMC6884612 DOI: 10.1038/s41467-019-13334-8] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2019] [Accepted: 11/04/2019] [Indexed: 02/06/2023] Open
Abstract
Elevated glucose consumption is fundamental to cancer, but selectively targeting this pathway is challenging. We develop a high-throughput assay for measuring glucose consumption and use it to screen non-small-cell lung cancer cell lines against bioactive small molecules. We identify Milciclib that blocks glucose consumption in H460 and H1975, but not in HCC827 or A549 cells, by decreasing SLC2A1 (GLUT1) mRNA and protein levels and by inhibiting glucose transport. Milciclib blocks glucose consumption by targeting cyclin-dependent kinase 7 (CDK7) similar to other CDK7 inhibitors including THZ1 and LDC4297. Enhanced PIK3CA signaling leads to CDK7 phosphorylation, which promotes RNA Polymerase II phosphorylation and transcription. Milciclib, THZ1, and LDC4297 lead to a reduction in RNA Polymerase II phosphorylation on the SLC2A1 promoter. These data indicate that our high-throughput assay can identify compounds that regulate glucose consumption and that CDK7 is a key regulator of glucose consumption in cells with an activated PI3K pathway. Many cancer cells have increased glucose consumption compared to normal cells, a feature that can be exploited therapeutically. Here, the authors carry out a chemical screen and identify compounds that selectively blocks glucose metabolism in non-small-cell lung cancer cell lines.
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84
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Hu Z, Ghosh A, Stolze SC, Horváth M, Bai B, Schaefer S, Zündorf S, Liu S, Harzen A, Hajheidari M, Sarnowski TJ, Nakagami H, Koncz Z, Koncz C. Gene modification by fast-track recombineering for cellular localization and isolation of components of plant protein complexes. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2019; 100:411-429. [PMID: 31276249 PMCID: PMC6852550 DOI: 10.1111/tpj.14450] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/29/2019] [Revised: 06/14/2019] [Accepted: 06/26/2019] [Indexed: 05/04/2023]
Abstract
To accelerate the isolation of plant protein complexes and study cellular localization and interaction of their components, an improved recombineering protocol is described for simple and fast site-directed modification of plant genes in bacterial artificial chromosomes (BACs). Coding sequences of fluorescent and affinity tags were inserted into genes and transferred together with flanking genomic sequences of desired size by recombination into Agrobacterium plant transformation vectors using three steps of E. coli transformation with PCR-amplified DNA fragments. Application of fast-track recombineering is illustrated by the simultaneous labelling of CYCLIN-DEPENDENT KINASE D (CDKD) and CYCLIN H (CYCH) subunits of kinase module of TFIIH general transcription factor and the CDKD-activating CDKF;1 kinase with green fluorescent protein (GFP) and mCherry (green and red fluorescent protein) tags, and a PIPL (His18 -StrepII-HA) epitope. Functionality of modified CDKF;1 gene constructs is verified by complementation of corresponding T-DNA insertion mutation. Interaction of CYCH with all three known CDKD homologues is confirmed by their co-localization and co-immunoprecipitation. Affinity purification and mass spectrometry analyses of CDKD;2, CYCH, and DNA-replication-coupled HISTONE H3.1 validate their association with conserved TFIIH subunits and components of CHROMATIN ASSEMBLY FACTOR 1, respectively. The results document that simple modification of plant gene products with suitable tags by fast-track recombineering is well suited to promote a wide range of protein interaction and proteomics studies.
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Affiliation(s)
- Zhoubo Hu
- Max‐Planck Institute for Plant Breeding ResearchCarl‐von‐Linné‐Weg 10D‐50829CologneGermany
| | - Ajit Ghosh
- Max‐Planck Institute for Plant Breeding ResearchCarl‐von‐Linné‐Weg 10D‐50829CologneGermany
- Department of Biochemistry and Molecular BiologyShahjalal University of Science and TechnologySylhet3114, Bangladesh
| | - Sara C. Stolze
- Max‐Planck Institute for Plant Breeding ResearchCarl‐von‐Linné‐Weg 10D‐50829CologneGermany
| | - Mihály Horváth
- Max‐Planck Institute for Plant Breeding ResearchCarl‐von‐Linné‐Weg 10D‐50829CologneGermany
| | - Bing Bai
- Max‐Planck Institute for Plant Breeding ResearchCarl‐von‐Linné‐Weg 10D‐50829CologneGermany
| | - Sabine Schaefer
- Max‐Planck Institute for Plant Breeding ResearchCarl‐von‐Linné‐Weg 10D‐50829CologneGermany
| | - Simone Zündorf
- Max‐Planck Institute for Plant Breeding ResearchCarl‐von‐Linné‐Weg 10D‐50829CologneGermany
| | - Shanda Liu
- Max‐Planck Institute for Plant Breeding ResearchCarl‐von‐Linné‐Weg 10D‐50829CologneGermany
| | - Anne Harzen
- Max‐Planck Institute for Plant Breeding ResearchCarl‐von‐Linné‐Weg 10D‐50829CologneGermany
| | - Mohsen Hajheidari
- Max‐Planck Institute for Plant Breeding ResearchCarl‐von‐Linné‐Weg 10D‐50829CologneGermany
- Botanical InstituteCologne Biocenter, Cluster of Excellence on Plant Sciences, University of CologneD‐50674CologneGermany
| | - Tomasz J. Sarnowski
- Max‐Planck Institute for Plant Breeding ResearchCarl‐von‐Linné‐Weg 10D‐50829CologneGermany
- Institute of Biochemistry and BiophysicsPolish Academy of SciencesPawińskiego 5A02‐106WarsawPoland
| | - Hirofumi Nakagami
- Max‐Planck Institute for Plant Breeding ResearchCarl‐von‐Linné‐Weg 10D‐50829CologneGermany
| | - Zsuzsa Koncz
- Max‐Planck Institute for Plant Breeding ResearchCarl‐von‐Linné‐Weg 10D‐50829CologneGermany
| | - Csaba Koncz
- Max‐Planck Institute for Plant Breeding ResearchCarl‐von‐Linné‐Weg 10D‐50829CologneGermany
- Institute of Plant BiologyBiological Research Center of Hungarian Academy of SciencesTemesvári krt. 62H‐6726SzegedHungary
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85
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Li BB, Wang B, Zhu CM, Tang D, Pang J, Zhao J, Sun CH, Qiu MJ, Qian ZR. Cyclin-dependent kinase 7 inhibitor THZ1 in cancer therapy. Chronic Dis Transl Med 2019; 5:155-169. [PMID: 31891127 PMCID: PMC6926117 DOI: 10.1016/j.cdtm.2019.08.006] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2019] [Indexed: 12/11/2022] Open
Abstract
Current cancer therapies have encountered adverse response due to poor therapeutic efficiency, severe side effects and acquired resistance to multiple drugs. Thus, there are urgent needs for finding new cancer-targeted pharmacological strategies. In this review, we summarized the current understanding with THZ1, a covalent inhibitor of cyclin-dependent kinase 7 (CDK7), which demonstrated promising anti-tumor activity against different cancer types. By introducing the anti-tumor behaviors and the potential targets for different cancers, this review aims to provide more effective approaches to CDK7 inhibitor-based therapeutic agents and deeper insight into the diverse tumor proliferation mechanisms.
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Affiliation(s)
- Bin-Bin Li
- School of Biological Sciences, Nanyang Technological University, Singapore 639798, Singapore
- Scientific Research Center, The Seventh Affiliated Hospital, Sun Yat-sen University, Shenzhen, Guangdong 518107, China
| | - Bo Wang
- Scientific Research Center, The Seventh Affiliated Hospital, Sun Yat-sen University, Shenzhen, Guangdong 518107, China
| | - Cheng-Ming Zhu
- Scientific Research Center, The Seventh Affiliated Hospital, Sun Yat-sen University, Shenzhen, Guangdong 518107, China
| | - Di Tang
- Scientific Research Center, The Seventh Affiliated Hospital, Sun Yat-sen University, Shenzhen, Guangdong 518107, China
| | - Jun Pang
- Scientific Research Center, The Seventh Affiliated Hospital, Sun Yat-sen University, Shenzhen, Guangdong 518107, China
| | - Jing Zhao
- Scientific Research Center, The Seventh Affiliated Hospital, Sun Yat-sen University, Shenzhen, Guangdong 518107, China
| | - Chun-Hui Sun
- Scientific Research Center, The Seventh Affiliated Hospital, Sun Yat-sen University, Shenzhen, Guangdong 518107, China
- Equipe Communication Intercellulaire et Infections Microbiennes, Centre de Recherche Interdisciplinaire en Biologie (CIRB), College de France, Paris 75005, France
| | - Miao-Juan Qiu
- Scientific Research Center, The Seventh Affiliated Hospital, Sun Yat-sen University, Shenzhen, Guangdong 518107, China
| | - Zhi-Rong Qian
- Scientific Research Center, The Seventh Affiliated Hospital, Sun Yat-sen University, Shenzhen, Guangdong 518107, China
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86
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Affiliation(s)
- Joaquin M Espinosa
- a Linda Crnic Institute for Down Syndrome & Department of Pharmacology , University of Colorado Anschutz Medical Campus , Aurora , Colorado , U.S.A
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87
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Greber BJ, Nogales E. The Structures of Eukaryotic Transcription Pre-initiation Complexes and Their Functional Implications. Subcell Biochem 2019; 93:143-192. [PMID: 31939151 DOI: 10.1007/978-3-030-28151-9_5] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Transcription is a highly regulated process that supplies living cells with coding and non-coding RNA molecules. Failure to properly regulate transcription is associated with human pathologies, including cancers. RNA polymerase II is the enzyme complex that synthesizes messenger RNAs that are then translated into proteins. In spite of its complexity, RNA polymerase requires a plethora of general transcription factors to be recruited to the transcription start site as part of a large transcription pre-initiation complex, and to help it gain access to the transcribed strand of the DNA. This chapter reviews the structure and function of these eukaryotic transcription pre-initiation complexes, with a particular emphasis on two of its constituents, the multisubunit complexes TFIID and TFIIH. We also compare the overall architecture of the RNA polymerase II pre-initiation complex with those of RNA polymerases I and III, involved in transcription of ribosomal RNA and non-coding RNAs such as tRNAs and snRNAs, and discuss the general, conserved features that are applicable to all eukaryotic RNA polymerase systems.
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Affiliation(s)
- Basil J Greber
- California Institute for Quantitative Biosciences (QB3), University of California, Berkeley, CA, 94720, USA.
- Molecular Biophysics and Integrative Bio-Imaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA.
| | - Eva Nogales
- California Institute for Quantitative Biosciences (QB3), University of California, Berkeley, CA, 94720, USA
- Molecular Biophysics and Integrative Bio-Imaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
- Howard Hughes Medical Institute, University of California, Berkeley, CA, 94720, USA
- Department of Molecular and Cell Biology, University of California, Berkeley, CA, 94720, USA
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