1
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Huang Y, Liu W, Zhao C, Shi X, Zhao Q, Jia J, Wang A. Targeting cyclin-dependent kinases: From pocket specificity to drug selectivity. Eur J Med Chem 2024; 275:116547. [PMID: 38852339 DOI: 10.1016/j.ejmech.2024.116547] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2024] [Revised: 05/28/2024] [Accepted: 05/28/2024] [Indexed: 06/11/2024]
Abstract
The development of selective modulators of cyclin-dependent kinases (CDKs), a kinase family with numerous members and functional variations, is a significant preclinical challenge. Recent advancements in crystallography have revealed subtle differences in the highly conserved CDK pockets. Exploiting these differences has proven to be an effective strategy for achieving excellent drug selectivity. While previous reports briefly discussed the structural features that lead to selectivity in individual CDK members, attaining inhibitor selectivity requires consideration of not only the specific structures of the target CDK but also the features of off-target members. In this review, we summarize the structure-activity relationships (SARs) that influence selectivity in CDK drug development and analyze the pocket features that lead to selectivity using molecular-protein binding models. In addition, in recent years, novel CDK modulators have been developed, providing more avenues for achieving selectivity. These cases were also included. We hope that these efforts will assist in the development of novel CDK drugs.
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Affiliation(s)
- Yaoguang Huang
- School of Traditional Chinese Materia Medica, Shenyang Pharmaceutical University, Shenyang, 110016, People's Republic of China
| | - Wenwu Liu
- School of Pharmaceutical Sciences, Tsinghua University, Haidian Dist., Beijing, 100084, People's Republic of China
| | - Changhao Zhao
- Department of Pharmacy, General Hospital of Northern Theater Command, Shenyang, 110840, People's Republic of China
| | - Xiaoyu Shi
- School of Traditional Chinese Materia Medica, Shenyang Pharmaceutical University, Shenyang, 110016, People's Republic of China
| | - Qingchun Zhao
- School of Traditional Chinese Materia Medica, Shenyang Pharmaceutical University, Shenyang, 110016, People's Republic of China; Department of Pharmacy, General Hospital of Northern Theater Command, Shenyang, 110840, People's Republic of China.
| | - Jingming Jia
- School of Traditional Chinese Materia Medica, Shenyang Pharmaceutical University, Shenyang, 110016, People's Republic of China.
| | - Anhua Wang
- School of Traditional Chinese Materia Medica, Shenyang Pharmaceutical University, Shenyang, 110016, People's Republic of China.
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2
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Volegova MP, Brown LE, Banerjee U, Dries R, Sharma B, Kennedy A, Porco JA, George RE. The MYCN 5' UTR as a therapeutic target in neuroblastoma. Cell Rep 2024; 43:114134. [PMID: 38662542 DOI: 10.1016/j.celrep.2024.114134] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2023] [Revised: 02/07/2024] [Accepted: 04/05/2024] [Indexed: 06/01/2024] Open
Abstract
Tumor MYCN amplification is seen in high-risk neuroblastoma, yet direct targeting of this oncogenic transcription factor has been challenging. Here, we take advantage of the dependence of MYCN-amplified neuroblastoma cells on increased protein synthesis to inhibit the activity of eukaryotic translation initiation factor 4A1 (eIF4A1) using an amidino-rocaglate, CMLD012824. Consistent with the role of this RNA helicase in resolving structural barriers in 5' untranslated regions (UTRs), CMLD012824 increased eIF4A1 affinity for polypurine-rich 5' UTRs, including that of the MYCN and associated transcripts with critical roles in cell proliferation. CMLD012824-mediated clamping of eIF4A1 spanned the full lengths of mRNAs, while translational inhibition was mediated through 5' UTR binding in a cap-dependent and -independent manner. Finally, CMLD012824 led to growth inhibition in MYCN-amplified neuroblastoma models without generalized toxicity. Our studies highlight the key role of eIF4A1 in MYCN-amplified neuroblastoma and demonstrate the therapeutic potential of disrupting its function.
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Affiliation(s)
- Marina P Volegova
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Department of Pediatrics, Harvard Medical School, Boston, MA, USA
| | - Lauren E Brown
- Boston University, Center for Molecular Discovery (BU-CMD), Boston, MA, USA; Boston University, Department of Chemistry, Boston, MA, USA
| | - Ushashi Banerjee
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Department of Pediatrics, Harvard Medical School, Boston, MA, USA
| | - Ruben Dries
- Boston University School of Medicine, Computational Biomedicine, Boston, MA, USA
| | - Bandana Sharma
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Alyssa Kennedy
- Boston Children's Cancer and Blood Disorders Center, Pediatric Hematology/Oncology, Boston, MA, USA
| | - John A Porco
- Boston University, Center for Molecular Discovery (BU-CMD), Boston, MA, USA; Boston University, Department of Chemistry, Boston, MA, USA
| | - Rani E George
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Department of Pediatrics, Harvard Medical School, Boston, MA, USA.
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3
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Fansler MM, Mitschka S, Mayr C. Quantifying 3'UTR length from scRNA-seq data reveals changes independent of gene expression. Nat Commun 2024; 15:4050. [PMID: 38744866 PMCID: PMC11094166 DOI: 10.1038/s41467-024-48254-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2023] [Accepted: 04/22/2024] [Indexed: 05/16/2024] Open
Abstract
Although more than half of all genes generate transcripts that differ in 3'UTR length, current analysis pipelines only quantify the amount but not the length of mRNA transcripts. 3'UTR length is determined by 3' end cleavage sites (CS). We map CS in more than 200 primary human and mouse cell types and increase CS annotations relative to the GENCODE database by 40%. Approximately half of all CS are used in few cell types, revealing that most genes only have one or two major 3' ends. We incorporate the CS annotations into a computational pipeline, called scUTRquant, for rapid, accurate, and simultaneous quantification of gene and 3'UTR isoform expression from single-cell RNA sequencing (scRNA-seq) data. When applying scUTRquant to data from 474 cell types and 2134 perturbations, we discover extensive 3'UTR length changes across cell types that are as widespread and coordinately regulated as gene expression changes but affect mostly different genes. Our data indicate that mRNA abundance and mRNA length are two largely independent axes of gene regulation that together determine the amount and spatial organization of protein synthesis.
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Affiliation(s)
- Mervin M Fansler
- Tri-Institutional Training Program in Computational Biology and Medicine, Weill Cornell Graduate College, New York, NY, 10021, USA
- Cancer Biology and Genetics Program, Memorial Sloan Kettering Cancer Center, New York, NY, 10065, USA
| | - Sibylle Mitschka
- Cancer Biology and Genetics Program, Memorial Sloan Kettering Cancer Center, New York, NY, 10065, USA
| | - Christine Mayr
- Tri-Institutional Training Program in Computational Biology and Medicine, Weill Cornell Graduate College, New York, NY, 10021, USA.
- Cancer Biology and Genetics Program, Memorial Sloan Kettering Cancer Center, New York, NY, 10065, USA.
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4
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Ni Z, Ahmed N, Nabeel-Shah S, Guo X, Pu S, Song J, Marcon E, Burke G, Tong AH, Chan K, Ha KH, Blencowe B, Moffat J, Greenblatt J. Identifying human pre-mRNA cleavage and polyadenylation factors by genome-wide CRISPR screens using a dual fluorescence readthrough reporter. Nucleic Acids Res 2024; 52:4483-4501. [PMID: 38587191 PMCID: PMC11077057 DOI: 10.1093/nar/gkae240] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2023] [Revised: 01/29/2024] [Accepted: 04/02/2024] [Indexed: 04/09/2024] Open
Abstract
Messenger RNA precursors (pre-mRNA) generally undergo 3' end processing by cleavage and polyadenylation (CPA), which is specified by a polyadenylation site (PAS) and adjacent RNA sequences and regulated by a large variety of core and auxiliary CPA factors. To date, most of the human CPA factors have been discovered through biochemical and proteomic studies. However, genetic identification of the human CPA factors has been hampered by the lack of a reliable genome-wide screening method. We describe here a dual fluorescence readthrough reporter system with a PAS inserted between two fluorescent reporters. This system enables measurement of the efficiency of 3' end processing in living cells. Using this system in combination with a human genome-wide CRISPR/Cas9 library, we conducted a screen for CPA factors. The screens identified most components of the known core CPA complexes and other known CPA factors. The screens also identified CCNK/CDK12 as a potential core CPA factor, and RPRD1B as a CPA factor that binds RNA and regulates the release of RNA polymerase II at the 3' ends of genes. Thus, this dual fluorescence reporter coupled with CRISPR/Cas9 screens reliably identifies bona fide CPA factors and provides a platform for investigating the requirements for CPA in various contexts.
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Affiliation(s)
- Zuyao Ni
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, 160 College Street, Toronto, ON M5S 3E1, Canada
| | - Nujhat Ahmed
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, 160 College Street, Toronto, ON M5S 3E1, Canada
- Department of Molecular Genetics, University of Toronto, 1 King's College Circle, Toronto, ON M5A 1A8, Canada
| | - Syed Nabeel-Shah
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, 160 College Street, Toronto, ON M5S 3E1, Canada
- Department of Molecular Genetics, University of Toronto, 1 King's College Circle, Toronto, ON M5A 1A8, Canada
| | - Xinghua Guo
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, 160 College Street, Toronto, ON M5S 3E1, Canada
| | - Shuye Pu
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, 160 College Street, Toronto, ON M5S 3E1, Canada
| | - Jingwen Song
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, 160 College Street, Toronto, ON M5S 3E1, Canada
| | - Edyta Marcon
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, 160 College Street, Toronto, ON M5S 3E1, Canada
| | - Giovanni L Burke
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, 160 College Street, Toronto, ON M5S 3E1, Canada
- Department of Molecular Genetics, University of Toronto, 1 King's College Circle, Toronto, ON M5A 1A8, Canada
| | - Amy Hin Yan Tong
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, 160 College Street, Toronto, ON M5S 3E1, Canada
- Department of Molecular Genetics, University of Toronto, 1 King's College Circle, Toronto, ON M5A 1A8, Canada
- Program in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, ON Canada
| | - Katherine Chan
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, 160 College Street, Toronto, ON M5S 3E1, Canada
- Department of Molecular Genetics, University of Toronto, 1 King's College Circle, Toronto, ON M5A 1A8, Canada
- Program in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, ON Canada
| | - Kevin C H Ha
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, 160 College Street, Toronto, ON M5S 3E1, Canada
- Department of Molecular Genetics, University of Toronto, 1 King's College Circle, Toronto, ON M5A 1A8, Canada
| | - Benjamin J Blencowe
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, 160 College Street, Toronto, ON M5S 3E1, Canada
- Department of Molecular Genetics, University of Toronto, 1 King's College Circle, Toronto, ON M5A 1A8, Canada
| | - Jason Moffat
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, 160 College Street, Toronto, ON M5S 3E1, Canada
- Department of Molecular Genetics, University of Toronto, 1 King's College Circle, Toronto, ON M5A 1A8, Canada
- Program in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, ON Canada
- Institute for Biomaterials and Biomedical Engineering, University of Toronto, Toronto, ON Canada
| | - Jack F Greenblatt
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, 160 College Street, Toronto, ON M5S 3E1, Canada
- Department of Molecular Genetics, University of Toronto, 1 King's College Circle, Toronto, ON M5A 1A8, Canada
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5
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Lautert-Dutra W, M Melo C, Chaves LP, Crozier C, P Saggioro F, B Dos Reis R, Bayani J, Bonatto SL, Squire JA. Loss of heterozygosity impacts MHC expression on the immune microenvironment in CDK12-mutated prostate cancer. Mol Cytogenet 2024; 17:11. [PMID: 38704603 PMCID: PMC11070094 DOI: 10.1186/s13039-024-00680-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2024] [Accepted: 04/24/2024] [Indexed: 05/06/2024] Open
Abstract
BACKGROUND In prostate cancer (PCa), well-established biomarkers such as MSI status, TMB high, and PDL1 expression serve as reliable indicators for favorable responses to immunotherapy. Recent studies have suggested a potential association between CDK12 mutations and immunotherapy response; however, the precise mechanisms through which CDK12 mutation may influence immune response remain unclear. A plausible explanation for immune evasion in this subset of CDK12-mutated PCa may be reduced MHC expression. RESULTS Using genomic data of CDK12-mutated PCa from 48 primary and 10 metastatic public domain samples and a retrospective cohort of 53 low-intermediate risk primary PCa, we investigated how variation in the expression of the MHC genes affected associated downstream pathways. We classified the patients based on gene expression quartiles of MHC-related genes and categorized the tumors into "High" and "Low" expression levels. CDK12-mutated tumors with higher MHC-expressed pathways were associated with the immune system and elevated PD-L1, IDO1, and TIM3 expression. Consistent with an inflamed tumor microenvironment (TME) phenotype, digital cytometric analyses identified increased CD8 + T cells, B cells, γδ T cells, and M1 Macrophages in this group. In contrast, CDK12-mutated tumors with lower MHC expression exhibited features consistent with an immune cold TME phenotype and immunoediting. Significantly, low MHC expression was also associated with chromosome 6 loss of heterozygosity (LOH) affecting the entire HLA gene cluster. These LOH events were observed in both major clonal and minor subclonal populations of tumor cells. In our retrospective study of 53 primary PCa cases from this Institute, we found a 4% (2/53) prevalence of CDK12 mutations, with the confirmation of this defect in one tumor through Sanger sequencing. In keeping with our analysis of public domain data this tumor exhibited low MHC expression at the RNA level. More extensive studies will be required to determine whether reduced HLA expression is generally associated with primary tumors or is a specific feature of CDK12 mutated PCa. CONCLUSIONS These data show that analysis of CDK12 alteration, in the context of MHC expression levels, and LOH status may offer improved predictive value for outcomes in this potentially actionable genomic subgroup of PCa. In addition, these findings highlight the need to explore novel therapeutic strategies to enhance MHC expression in CDK12-defective PCa to improve immunotherapy responses.
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Affiliation(s)
- William Lautert-Dutra
- Department of Genetics, Medical School of Ribeirao Preto, University of Sao Paulo - USP, Ribeirão Prêto, SP, 14048-900, Brazil
| | - Camila M Melo
- Department of Genetics, Medical School of Ribeirao Preto, University of Sao Paulo - USP, Ribeirão Prêto, SP, 14048-900, Brazil
| | - Luiz P Chaves
- Department of Genetics, Medical School of Ribeirao Preto, University of Sao Paulo - USP, Ribeirão Prêto, SP, 14048-900, Brazil
| | - Cheryl Crozier
- Diagnostic Development, Ontario Institute for Cancer Research, Toronto, ON, Canada
| | - Fabiano P Saggioro
- Department of Pathology, Ribeirao Preto Medical School, University of Sao Paulo - USP, Ribeirão Prêto, Brazil
| | - Rodolfo B Dos Reis
- Department of Pathology, Ribeirao Preto Medical School, University of Sao Paulo - USP, Ribeirão Prêto, Brazil
- Division of Urology, Department of Surgery and Anatomy, Medical School of Ribeirao Preto, University of Sao Paulo - USP, Ribeirão Prêto, Brazil
| | - Jane Bayani
- Diagnostic Development, Ontario Institute for Cancer Research, Toronto, ON, Canada
- Laboratory Medicine and Pathology, University of Toronto, Toronto, ON, Canada
| | - Sandro L Bonatto
- School of Health and Life Sciences, Pontifical Catholic University of Rio Grande Do Sul - PUCRS, Av. Ipiranga, 668, Porto Alegre, RS, 90619-900, Brazil
| | - Jeremy A Squire
- Department of Genetics, Medical School of Ribeirao Preto, University of Sao Paulo - USP, Ribeirão Prêto, SP, 14048-900, Brazil.
- Department of Pathology and Molecular Medicine, Queen's University, Kingston, ON, K7L3N6, Canada.
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6
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Veth TS, Nouwen LV, Zwaagstra M, Lyoo H, Wierenga KA, Westendorp B, Altelaar MAFM, Berkers C, van Kuppeveld FJM, Heck AJR. Assessment of Kinome-Wide Activity Remodeling upon Picornavirus Infection. Mol Cell Proteomics 2024; 23:100757. [PMID: 38556169 PMCID: PMC11067349 DOI: 10.1016/j.mcpro.2024.100757] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2023] [Revised: 03/16/2024] [Accepted: 03/28/2024] [Indexed: 04/02/2024] Open
Abstract
Picornaviridae represent a large family of single-stranded positive RNA viruses of which different members can infect both humans and animals. These include the enteroviruses (e.g., poliovirus, coxsackievirus, and rhinoviruses) as well as the cardioviruses (e.g., encephalomyocarditis virus). Picornaviruses have evolved to interact with, use, and/or evade cellular host systems to create the optimal environment for replication and spreading. It is known that viruses modify kinase activity during infection, but a proteome-wide overview of the (de)regulation of cellular kinases during picornavirus infection is lacking. To study the kinase activity landscape during picornavirus infection, we here applied dedicated targeted mass spectrometry-based assays covering ∼40% of the human kinome. Our data show that upon infection, kinases of the MAPK pathways become activated (e.g., ERK1/2, RSK1/2, JNK1/2/3, and p38), while kinases involved in regulating the cell cycle (e.g., CDK1/2, GWL, and DYRK3) become inactivated. Additionally, we observed the activation of CHK2, an important kinase involved in the DNA damage response. Using pharmacological kinase inhibitors, we demonstrate that several of these activated kinases are essential for the replication of encephalomyocarditis virus. Altogether, the data provide a quantitative understanding of the regulation of kinome activity induced by picornavirus infection, providing a resource important for developing novel antiviral therapeutic interventions.
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Affiliation(s)
- Tim S Veth
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Utrecht, The Netherlands; Netherlands Proteomics Center, Utrecht, The Netherlands
| | - Lonneke V Nouwen
- Faculty of Veterinary Medicine, Virology Division, Department of Infectious Diseases and Immunology, Utrecht University, Utrecht, The Netherlands
| | - Marleen Zwaagstra
- Faculty of Veterinary Medicine, Virology Division, Department of Infectious Diseases and Immunology, Utrecht University, Utrecht, The Netherlands
| | - Heyrhyoung Lyoo
- Faculty of Veterinary Medicine, Virology Division, Department of Infectious Diseases and Immunology, Utrecht University, Utrecht, The Netherlands
| | - Kathryn A Wierenga
- Faculty of Veterinary Medicine, Division of Cell Biology, Metabolism & Cancer, Department Biomolecular Health Sciences, Utrecht University, Utrecht, The Netherlands
| | - Bart Westendorp
- Faculty of Veterinary Medicine, Division of Cell Biology, Metabolism & Cancer, Department Biomolecular Health Sciences, Utrecht University, Utrecht, The Netherlands
| | - Maarten A F M Altelaar
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Utrecht, The Netherlands; Netherlands Proteomics Center, Utrecht, The Netherlands
| | - Celia Berkers
- Faculty of Veterinary Medicine, Division of Cell Biology, Metabolism & Cancer, Department Biomolecular Health Sciences, Utrecht University, Utrecht, The Netherlands
| | - Frank J M van Kuppeveld
- Faculty of Veterinary Medicine, Virology Division, Department of Infectious Diseases and Immunology, Utrecht University, Utrecht, The Netherlands
| | - Albert J R Heck
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Utrecht, The Netherlands; Netherlands Proteomics Center, Utrecht, The Netherlands.
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7
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Alfonso-Gonzalez C, Hilgers V. (Alternative) transcription start sites as regulators of RNA processing. Trends Cell Biol 2024:S0962-8924(24)00033-3. [PMID: 38531762 DOI: 10.1016/j.tcb.2024.02.010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2023] [Revised: 02/20/2024] [Accepted: 02/23/2024] [Indexed: 03/28/2024]
Abstract
Alternative transcription start site usage (ATSS) is a widespread regulatory strategy that enables genes to choose between multiple genomic loci for initiating transcription. This mechanism is tightly controlled during development and is often altered in disease states. In this review, we examine the growing evidence highlighting a role for transcription start sites (TSSs) in the regulation of mRNA isoform selection during and after transcription. We discuss how the choice of transcription initiation sites influences RNA processing and the importance of this crosstalk for cell identity and organism function. We also speculate on possible mechanisms underlying the integration of transcriptional and post-transcriptional processes.
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Affiliation(s)
- Carlos Alfonso-Gonzalez
- Max Planck Institute of Immunobiology and Epigenetics, 79108 Freiburg, Germany; Faculty of Biology, Albert Ludwigs University, 79104 Freiburg, Germany; International Max Planck Research School for Molecular and Cellular Biology (IMPRS- MCB), 79108 Freiburg, Germany
| | - Valérie Hilgers
- Max Planck Institute of Immunobiology and Epigenetics, 79108 Freiburg, Germany.
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8
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Liu X, Chen H, Li Z, Yang X, Jin W, Wang Y, Zheng J, Li L, Xuan C, Yuan J, Yang Y. InPACT: a computational method for accurate characterization of intronic polyadenylation from RNA sequencing data. Nat Commun 2024; 15:2583. [PMID: 38519498 PMCID: PMC10960005 DOI: 10.1038/s41467-024-46875-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2023] [Accepted: 03/12/2024] [Indexed: 03/25/2024] Open
Abstract
Alternative polyadenylation can occur in introns, termed intronic polyadenylation (IPA), has been implicated in diverse biological processes and diseases, as it can produce noncoding transcripts or transcripts with truncated coding regions. However, a reliable method is required to accurately characterize IPA. Here, we propose a computational method called InPACT, which allows for the precise characterization of IPA from conventional RNA-seq data. InPACT successfully identifies numerous previously unannotated IPA transcripts in human cells, many of which are translated, as evidenced by ribosome profiling data. We have demonstrated that InPACT outperforms other methods in terms of IPA identification and quantification. Moreover, InPACT applied to monocyte activation reveals temporally coordinated IPA events. Further application on single-cell RNA-seq data of human fetal bone marrow reveals the expression of several IPA isoforms in a context-specific manner. Therefore, InPACT represents a powerful tool for the accurate characterization of IPA from RNA-seq data.
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Affiliation(s)
- Xiaochuan Liu
- The Province and Ministry Co-sponsored Collaborative Innovation Center for Medical Epigenetics, Tianjin Key Laboratory of Inflammatory Biology, The Second Hospital of Tianjin Medical University, Department of Bioinformatics, School of Basic Medical Sciences, Tianjin Medical University, Tianjin, 300070, China
| | - Hao Chen
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Tianjin Medical University, Tianjin, 300070, China
| | - Zekun Li
- The Province and Ministry Co-sponsored Collaborative Innovation Center for Medical Epigenetics, Tianjin Key Laboratory of Inflammatory Biology, The Second Hospital of Tianjin Medical University, Department of Bioinformatics, School of Basic Medical Sciences, Tianjin Medical University, Tianjin, 300070, China
| | - Xiaoxiao Yang
- The Province and Ministry Co-sponsored Collaborative Innovation Center for Medical Epigenetics, Tianjin Key Laboratory of Inflammatory Biology, The Second Hospital of Tianjin Medical University, Department of Bioinformatics, School of Basic Medical Sciences, Tianjin Medical University, Tianjin, 300070, China
- Department of Pharmacology, School of Basic Medical Sciences, Tianjin Medical University, Tianjin, 300070, China
| | - Wen Jin
- The Province and Ministry Co-sponsored Collaborative Innovation Center for Medical Epigenetics, Tianjin Key Laboratory of Inflammatory Biology, The Second Hospital of Tianjin Medical University, Department of Bioinformatics, School of Basic Medical Sciences, Tianjin Medical University, Tianjin, 300070, China
- Department of Pharmacology, School of Basic Medical Sciences, Tianjin Medical University, Tianjin, 300070, China
| | - Yuting Wang
- The Province and Ministry Co-sponsored Collaborative Innovation Center for Medical Epigenetics, Tianjin Key Laboratory of Inflammatory Biology, The Second Hospital of Tianjin Medical University, Department of Bioinformatics, School of Basic Medical Sciences, Tianjin Medical University, Tianjin, 300070, China
- Department of Pharmacology, School of Basic Medical Sciences, Tianjin Medical University, Tianjin, 300070, China
| | - Jian Zheng
- Department of Immunology, School of Basic Medical Sciences, Tianjin Medical University, Tianjin, 300070, China
| | - Long Li
- Department of Immunology, School of Basic Medical Sciences, Tianjin Medical University, Tianjin, 300070, China
| | - Chenghao Xuan
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Tianjin Medical University, Tianjin, 300070, China.
| | - Jiapei Yuan
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, Institute of Hematology and Blood Diseases Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Tianjin, 300020, China.
- Tianjin Institutes of Health Science, Tianjin, 301600, China.
| | - Yang Yang
- The Province and Ministry Co-sponsored Collaborative Innovation Center for Medical Epigenetics, Tianjin Key Laboratory of Inflammatory Biology, The Second Hospital of Tianjin Medical University, Department of Bioinformatics, School of Basic Medical Sciences, Tianjin Medical University, Tianjin, 300070, China.
- Department of Pharmacology, School of Basic Medical Sciences, Tianjin Medical University, Tianjin, 300070, China.
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9
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Tien JCY, Chang Y, Zhang Y, Chou J, Cheng Y, Wang X, Yang J, Mannan R, Shah P, Wang XM, Todd AJ, Eyunni S, Cheng C, Rebernick RJ, Xiao L, Bao Y, Neiswender J, Brough R, Pettitt SJ, Cao X, Miner SJ, Zhou L, Wu YM, Labanca E, Wang Y, Parolia A, Cieslik M, Robinson DR, Wang Z, Feng FY, Lord CJ, Ding K, Chinnaiyan AM. CDK12 Loss Promotes Prostate Cancer Development While Exposing Vulnerabilities to Paralog-Based Synthetic Lethality. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.03.20.585990. [PMID: 38562774 PMCID: PMC10983964 DOI: 10.1101/2024.03.20.585990] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/04/2024]
Abstract
Biallelic loss of cyclin-dependent kinase 12 (CDK12) defines a unique molecular subtype of metastatic castration-resistant prostate cancer (mCRPC). It remains unclear, however, whether CDK12 loss per se is sufficient to drive prostate cancer development-either alone, or in the context of other genetic alterations-and whether CDK12-mutant tumors exhibit sensitivity to specific pharmacotherapies. Here, we demonstrate that tissue-specific Cdk12 ablation is sufficient to induce preneoplastic lesions and robust T cell infiltration in the mouse prostate. Allograft-based CRISPR screening demonstrated that Cdk12 loss is positively associated with Trp53 inactivation but negatively associated with Pten inactivation-akin to what is observed in human mCRPC. Consistent with this, ablation of Cdk12 in prostate organoids with concurrent Trp53 loss promotes their proliferation and ability to form tumors in mice, while Cdk12 knockout in the Pten-null prostate cancer mouse model abrogates tumor growth. Bigenic Cdk12 and Trp53 loss allografts represent a new syngeneic model for the study of androgen receptor (AR)-positive, luminal prostate cancer. Notably, Cdk12/Trp53 loss prostate tumors are sensitive to immune checkpoint blockade. Cdk12-null organoids (either with or without Trp53 co-ablation) and patient-derived xenografts from tumors with CDK12 inactivation are highly sensitive to inhibition or degradation of its paralog kinase, CDK13. Together, these data identify CDK12 as a bona fide tumor suppressor gene with impact on tumor progression and lends support to paralog-based synthetic lethality as a promising strategy for treating CDK12-mutant mCRPC.
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Affiliation(s)
- Jean Ching-Yi Tien
- Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, MI, USA
- Department of Pathology, University of Michigan, Ann Arbor, MI, USA
| | - Yu Chang
- Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, MI, USA
- Department of Pathology, University of Michigan, Ann Arbor, MI, USA
- These authors contributed equally to this work
| | - Yuping Zhang
- Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, MI, USA
- Department of Pathology, University of Michigan, Ann Arbor, MI, USA
- These authors contributed equally to this work
| | - Jonathan Chou
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, CA, USA
- Division of Hematology/Oncology, Department of Medicine, University of California, San Francisco, CA, USA
- These authors contributed equally to this work
| | - Yunhui Cheng
- Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, MI, USA
- Department of Pathology, University of Michigan, Ann Arbor, MI, USA
- These authors contributed equally to this work
| | - Xiaoju Wang
- Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, MI, USA
- Department of Pathology, University of Michigan, Ann Arbor, MI, USA
| | - Jianzhang Yang
- State Key Laboratory of Chemical Biology, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, Shanghai 200032, People’s Republic of China
- International Cooperative Laboratory of Traditional Chinese Medicine Modernization and Innovative Drug Discovery of Chinese Ministry of Education (MOE), Guangzhou City Key Laboratory of Precision Chemical Drug Development, College of Pharmacy, Jinan University, Guangzhou 511400, People’s Republic of China
| | - Rahul Mannan
- Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, MI, USA
- Department of Pathology, University of Michigan, Ann Arbor, MI, USA
| | - Palak Shah
- Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, MI, USA
- Department of Pathology, University of Michigan, Ann Arbor, MI, USA
| | - Xiao-Ming Wang
- Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, MI, USA
- Department of Pathology, University of Michigan, Ann Arbor, MI, USA
| | - Abigail J. Todd
- Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, MI, USA
- Department of Pathology, University of Michigan, Ann Arbor, MI, USA
| | - Sanjana Eyunni
- Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, MI, USA
- Department of Pathology, University of Michigan, Ann Arbor, MI, USA
| | - Caleb Cheng
- Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, MI, USA
| | - Ryan J. Rebernick
- Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, MI, USA
- Department of Pathology, University of Michigan, Ann Arbor, MI, USA
| | - Lanbo Xiao
- Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, MI, USA
- Department of Pathology, University of Michigan, Ann Arbor, MI, USA
| | - Yi Bao
- Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, MI, USA
- Department of Pathology, University of Michigan, Ann Arbor, MI, USA
| | - James Neiswender
- The CRUK Gene Function Laboratory and Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, London, SW3 6JB, UK
| | - Rachel Brough
- The CRUK Gene Function Laboratory and Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, London, SW3 6JB, UK
| | - Stephen J. Pettitt
- The CRUK Gene Function Laboratory and Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, London, SW3 6JB, UK
| | - Xuhong Cao
- Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, MI, USA
- Department of Pathology, University of Michigan, Ann Arbor, MI, USA
| | - Stephanie J. Miner
- Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, MI, USA
- Department of Pathology, University of Michigan, Ann Arbor, MI, USA
| | - Licheng Zhou
- State Key Laboratory of Chemical Biology, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, Shanghai 200032, People’s Republic of China
- International Cooperative Laboratory of Traditional Chinese Medicine Modernization and Innovative Drug Discovery of Chinese Ministry of Education (MOE), Guangzhou City Key Laboratory of Precision Chemical Drug Development, College of Pharmacy, Jinan University, Guangzhou 511400, People’s Republic of China
| | - Yi-Mi Wu
- Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, MI, USA
- Department of Pathology, University of Michigan, Ann Arbor, MI, USA
| | - Estefania Labanca
- Department of Genitourinary Medical Oncology and David H. Koch Center for Applied Research of Genitourinary Cancer, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Yuzhuo Wang
- Vancouver Prostate Centre, Vancouver General Hospital and Department of Urologic Sciences, University of British Columbia, Vancouver, British Columbia, V6H 3Z6, Canada
| | - Abhijit Parolia
- Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, MI, USA
- Department of Pathology, University of Michigan, Ann Arbor, MI, USA
- Rogel Cancer Center, University of Michigan, Ann Arbor, MI, USA
| | - Marcin Cieslik
- Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, MI, USA
- Department of Pathology, University of Michigan, Ann Arbor, MI, USA
| | - Dan R. Robinson
- Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, MI, USA
- Department of Pathology, University of Michigan, Ann Arbor, MI, USA
| | - Zhen Wang
- State Key Laboratory of Chemical Biology, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, Shanghai 200032, People’s Republic of China
- International Cooperative Laboratory of Traditional Chinese Medicine Modernization and Innovative Drug Discovery of Chinese Ministry of Education (MOE), Guangzhou City Key Laboratory of Precision Chemical Drug Development, College of Pharmacy, Jinan University, Guangzhou 511400, People’s Republic of China
| | - Felix Y. Feng
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, CA, USA
- Division of Hematology/Oncology, Department of Medicine, University of California, San Francisco, CA, USA
- Departments of Radiation Oncology and Urology, University of California, San Francisco, CA, USA
| | - Christopher J. Lord
- The CRUK Gene Function Laboratory and Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, London, SW3 6JB, UK
| | - Ke Ding
- State Key Laboratory of Chemical Biology, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, Shanghai 200032, People’s Republic of China
| | - Arul M. Chinnaiyan
- Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, MI, USA
- Department of Pathology, University of Michigan, Ann Arbor, MI, USA
- Rogel Cancer Center, University of Michigan, Ann Arbor, MI, USA
- Department of Urology, University of Michigan, Ann Arbor, MI, USA
- Howard Hughes Medical Institute, University of Michigan, Ann Arbor, MI, USA
- Lead contact
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10
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Frei K, Schecher S, Daher T, Hörner N, Richter J, Hildebrand U, Schindeldecker M, Witzel HR, Tsaur I, Porubsky S, Gaida MM, Roth W, Tagscherer KE. Inhibition of the Cyclin K-CDK12 complex induces DNA damage and increases the effect of androgen deprivation therapy in prostate cancer. Int J Cancer 2024; 154:1082-1096. [PMID: 37916780 DOI: 10.1002/ijc.34778] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2023] [Revised: 09/07/2023] [Accepted: 10/10/2023] [Indexed: 11/03/2023]
Abstract
Androgen deprivation therapy (ADT) is the mainstay of the current first-line treatment concepts for patients with advanced prostate carcinoma (PCa). However, due to treatment failure and recurrence investigation of new targeted therapeutics is urgently needed. In this study, we investigated the suitability of the Cyclin K-CDK12 complex as a novel therapeutic approach in PCa using the new covalent CDK12/13 inhibitor THZ531. Here we show that THZ531 impairs cellular proliferation, induces apoptosis, and decreases the expression of selected DNA repair genes in PCa cell lines, which is associated with an increasing extent of DNA damage. Furthermore, combination of THZ531 and ADT leads to an increase in these anti-tumoral effects in androgen-sensitive PCa cells. The anti-proliferative and pro-apoptotic activity of THZ531 in combination with ADT was validated in an ex vivo PCa tissue culture model. In a retrospective immunohistochemical analysis of 300 clinical tissue samples we show that Cyclin K (CycK) but not CDK12 expression correlates with a more aggressive type of PCa. In conclusion, this study demonstrates the clinical relevance of the CycK-CDK12 complex as a promising target for combinational therapy with ADT in PCa and its importance as a prognostic biomarker for patients with PCa.
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Affiliation(s)
- Katharina Frei
- Institute of Pathology, University Medical Center of the Johannes Gutenberg University Mainz, Mainz, Germany
| | - Sabrina Schecher
- Institute of Pathology, University Medical Center of the Johannes Gutenberg University Mainz, Mainz, Germany
| | - Tamas Daher
- Institute of Pathology, University Medical Center of the Johannes Gutenberg University Mainz, Mainz, Germany
| | - Nina Hörner
- Institute of Pathology, University Medical Center of the Johannes Gutenberg University Mainz, Mainz, Germany
| | - Jutta Richter
- Institute of Pathology, University Medical Center of the Johannes Gutenberg University Mainz, Mainz, Germany
| | - Ute Hildebrand
- Institute of Pathology, University Medical Center of the Johannes Gutenberg University Mainz, Mainz, Germany
| | - Mario Schindeldecker
- Institute of Pathology, University Medical Center of the Johannes Gutenberg University Mainz, Mainz, Germany
- Tissue Biobank of the University Medical Center of the Johannes Gutenberg University Mainz, Mainz, Germany
| | - Hagen R Witzel
- Institute of Pathology, University Medical Center of the Johannes Gutenberg University Mainz, Mainz, Germany
| | - Igor Tsaur
- Department of Urology and Pediatric Urology, University Medical Center of the Johannes Gutenberg University Mainz, Mainz, Germany
| | - Stefan Porubsky
- Institute of Pathology, University Medical Center of the Johannes Gutenberg University Mainz, Mainz, Germany
| | - Matthias M Gaida
- Institute of Pathology, University Medical Center of the Johannes Gutenberg University Mainz, Mainz, Germany
| | - Wilfried Roth
- Institute of Pathology, University Medical Center of the Johannes Gutenberg University Mainz, Mainz, Germany
| | - Katrin E Tagscherer
- Institute of Pathology, University Medical Center of the Johannes Gutenberg University Mainz, Mainz, Germany
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11
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Akhoundova D, Francica P, Rottenberg S, Rubin MA. DNA Damage Response and Mismatch Repair Gene Defects in Advanced and Metastatic Prostate Cancer. Adv Anat Pathol 2024; 31:61-69. [PMID: 38008971 PMCID: PMC10846598 DOI: 10.1097/pap.0000000000000422] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2023]
Abstract
Alterations in DNA damage response (DDR) and related genes are present in up to 25% of advanced prostate cancers (PCa). Most frequently altered genes are involved in the homologous recombination repair, the Fanconi anemia, and the mismatch repair pathways, and their deficiencies lead to a highly heterogeneous spectrum of DDR-deficient phenotypes. More than half of these alterations concern non- BRCA DDR genes. From a therapeutic perspective, poly-ADP-ribose polymerase inhibitors have demonstrated robust clinical efficacy in tumors with BRCA2 and BRCA1 alterations. Mismatch repair-deficient PCa, and a subset of CDK12-deficient PCa, are vulnerable to immune checkpoint inhibitors. Emerging data point to the efficacy of ATR inhibitors in PCa with ATM deficiencies. Still, therapeutic implications are insufficiently clarified for most of the non- BRCA DDR alterations, and no successful targeted treatment options have been established.
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Affiliation(s)
- Dilara Akhoundova
- Department for BioMedical Research
- Department of Medical Oncology
- Bern Center for Precision Medicine, Inselspital, University Hospital of Bern, Bern, Switzerland
| | - Paola Francica
- Department for BioMedical Research
- Institute of Animal Pathology, Vetsuisse Faculty, University of Bern
- Bern Center for Precision Medicine, Inselspital, University Hospital of Bern, Bern, Switzerland
| | - Sven Rottenberg
- Department for BioMedical Research
- Institute of Animal Pathology, Vetsuisse Faculty, University of Bern
- Bern Center for Precision Medicine, Inselspital, University Hospital of Bern, Bern, Switzerland
| | - Mark A. Rubin
- Department for BioMedical Research
- Bern Center for Precision Medicine, Inselspital, University Hospital of Bern, Bern, Switzerland
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12
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Mofayezi A, Jadaliha M, Zangeneh FZ, Khoddami V. Poly(A) tale: From A to A; RNA polyadenylation in prokaryotes and eukaryotes. WILEY INTERDISCIPLINARY REVIEWS. RNA 2024; 15:e1837. [PMID: 38485452 DOI: 10.1002/wrna.1837] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/22/2023] [Revised: 02/13/2024] [Accepted: 02/14/2024] [Indexed: 03/19/2024]
Abstract
Most eukaryotic mRNAs and different non-coding RNAs undergo a form of 3' end processing known as polyadenylation. Polyadenylation machinery is present in almost all organisms except few species. In bacteria, the machinery has evolved from PNPase, which adds heteropolymeric tails, to a poly(A)-specific polymerase. Differently, a complex machinery for accurate polyadenylation and several non-canonical poly(A) polymerases are developed in eukaryotes. The role of poly(A) tail has also evolved from serving as a degradative signal to a stabilizing modification that also regulates translation. In this review, we discuss poly(A) tail emergence in prokaryotes and its development into a stable, yet dynamic feature at the 3' end of mRNAs in eukaryotes. We also describe how appearance of novel poly(A) polymerases gives cells flexibility to shape poly(A) tail. We explain how poly(A) tail dynamics help regulate cognate RNA metabolism in a context-dependent manner, such as during oocyte maturation. Finally, we describe specific mRNAs in metazoans that bear stem-loops instead of poly(A) tails. We conclude with how recent discoveries about poly(A) tail can be applied to mRNA technology. This article is categorized under: RNA Evolution and Genomics > RNA and Ribonucleoprotein Evolution RNA Processing > 3' End Processing RNA Turnover and Surveillance > Regulation of RNA Stability.
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Affiliation(s)
- Ahmadreza Mofayezi
- Department of Biotechnology, College of Science, University of Tehran, Tehran, Iran
- ReNAP Therapeutics, Tehran, Iran
| | - Mahdieh Jadaliha
- Department of Biotechnology, College of Science, University of Tehran, Tehran, Iran
| | | | - Vahid Khoddami
- ReNAP Therapeutics, Tehran, Iran
- Pediatric Cell and Gene Therapy Research Center, Children's Medical Center, Tehran University of Medical Sciences, Tehran, Iran
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13
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Wu Z, Zhang W, Chen L, Wang T, Wang X, Shi H, Zhang L, Zhong M, Shi X, Mao X, Chen H, Li Q. CDK12 inhibition upregulates ATG7 triggering autophagy via AKT/FOXO3 pathway and enhances anti-PD-1 efficacy in colorectal cancer. Pharmacol Res 2024; 201:107097. [PMID: 38354870 DOI: 10.1016/j.phrs.2024.107097] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/17/2023] [Revised: 01/31/2024] [Accepted: 02/02/2024] [Indexed: 02/16/2024]
Abstract
As the world's fourth most deadly cancer, colorectal cancer (CRC) still needed the novel therapeutic drugs and target urgently. Although cyclin-dependent kinase 12 (CDK12) has been shown to be implicated in the malignancy of several types of cancer, its functional role and mechanism in CRC remain largely unknown. Here, we found that suppression of CDK12 inhibited tumor growth in CRC by inducing apoptosis. And CDK12 inhibition triggered autophagy by upregulating autophagy related gene 7 (ATG7) expression. Inhibition of autophagy by ATG7 knockdown and chloroquine (CQ) further decreased cell viability induced by CDK12 inhibition. Further mechanism exploration showed that CDK12 interacted with protein kinase B (AKT) regulated autophagy via AKT/forkhead box O3 (AKT/FOXO3) pathway. FOXO3 transcriptionally upregulated ATG7 expression and autophagy when CDK12 inhibition in CRC. Level of CDK12 and p-FOXO3/FOXO3 ratio were correlated with survival in CRC patients. Moreover, CDK12 inhibition improved the efficacy of anti-programmed cell death 1(PD-1) therapy in CRC murine models by enhancing CD8 + T cells infiltration. Thus, our study founded that CDK12 inhibition upregulates ATG7 triggering autophagy via AKT/FOXO3 pathway and enhances anti-PD-1 efficacy in CRC. We revealed the roles of CDK12/FOXO3/ATG7 in regulating CRC progression, suggesting potential biomarkers and therapeutic target for CRC.
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Affiliation(s)
- Zimei Wu
- Department of Pharmacy, Huashan Hospital, Fudan University, Shanghai, China
| | - Wenxin Zhang
- Department of Pharmacy, Huashan Hospital, Fudan University, Shanghai, China
| | - Lu Chen
- Department of Pharmacy, Huashan Hospital, Fudan University, Shanghai, China
| | - Tianxiao Wang
- Department of Pharmacy, Huashan Hospital, Fudan University, Shanghai, China
| | - Xinhai Wang
- Department of Surgery, Huashan Hospital, Fudan University, Shanghai, China
| | - Huanying Shi
- Department of Pharmacy, Huashan Hospital, Fudan University, Shanghai, China
| | - Liudi Zhang
- Department of Pharmacy, Huashan Hospital, Fudan University, Shanghai, China
| | - Mingkang Zhong
- Department of Pharmacy, Huashan Hospital, Fudan University, Shanghai, China
| | - Xiaojin Shi
- Department of Pharmacy, Huashan Hospital, Fudan University, Shanghai, China
| | - Xiang Mao
- Department of Surgery, Huashan Hospital, Fudan University, Shanghai, China.
| | - Haifei Chen
- Department of Pharmacy, Huashan Hospital, Fudan University, Shanghai, China.
| | - Qunyi Li
- Department of Pharmacy, Huashan Hospital, Fudan University, Shanghai, China.
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14
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Wheeler EC, Martin BJE, Doyle WC, Neaher S, Conway CA, Pitton CN, Gorelov RA, Donahue M, Jann JC, Abdel-Wahab O, Taylor J, Seiler M, Buonamici S, Pikman Y, Garcia JS, Belizaire R, Adelman K, Tothova Z. Splicing modulators impair DNA damage response and induce killing of cohesin-mutant MDS and AML. Sci Transl Med 2024; 16:eade2774. [PMID: 38170787 DOI: 10.1126/scitranslmed.ade2774] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2022] [Accepted: 10/08/2023] [Indexed: 01/05/2024]
Abstract
Splicing modulation is a promising treatment strategy pursued to date only in splicing factor-mutant cancers; however, its therapeutic potential is poorly understood outside of this context. Like splicing factors, genes encoding components of the cohesin complex are frequently mutated in cancer, including myelodysplastic syndromes (MDS) and secondary acute myeloid leukemia (AML), where they are associated with poor outcomes. Here, we showed that cohesin mutations are biomarkers of sensitivity to drugs targeting the splicing factor 3B subunit 1 (SF3B1) H3B-8800 and E-7107. We identified drug-induced alterations in splicing, and corresponding reduced gene expression, of a number of DNA repair genes, including BRCA1 and BRCA2, as the mechanism underlying this sensitivity in cell line models, primary patient samples and patient-derived xenograft (PDX) models of AML. We found that DNA damage repair genes are particularly sensitive to exon skipping induced by SF3B1 modulators due to their long length and large number of exons per transcript. Furthermore, we demonstrated that treatment of cohesin-mutant cells with SF3B1 modulators not only resulted in impaired DNA damage response and accumulation of DNA damage, but it sensitized cells to subsequent killing by poly(ADP-ribose) polymerase (PARP) inhibitors and chemotherapy and led to improved overall survival of PDX models of cohesin-mutant AML in vivo. Our findings expand the potential therapeutic benefits of SF3B1 splicing modulators to include cohesin-mutant MDS and AML.
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Affiliation(s)
- Emily C Wheeler
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
- Broad Institute of MIT and Harvard University, Cambridge, MA 02142, USA
| | - Benjamin J E Martin
- Department of Biological Chemistry and Molecular Pharmacology, Blavatnik Institute, Harvard Medical School, Boston, MA 02115, USA
| | - William C Doyle
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
- Broad Institute of MIT and Harvard University, Cambridge, MA 02142, USA
| | - Sofia Neaher
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
- Broad Institute of MIT and Harvard University, Cambridge, MA 02142, USA
| | - Caroline A Conway
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
- Broad Institute of MIT and Harvard University, Cambridge, MA 02142, USA
| | - Caroline N Pitton
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
- Broad Institute of MIT and Harvard University, Cambridge, MA 02142, USA
| | - Rebecca A Gorelov
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
- Broad Institute of MIT and Harvard University, Cambridge, MA 02142, USA
| | - Melanie Donahue
- Broad Institute of MIT and Harvard University, Cambridge, MA 02142, USA
| | - Johann C Jann
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
- Broad Institute of MIT and Harvard University, Cambridge, MA 02142, USA
| | - Omar Abdel-Wahab
- Molecular Pharmacology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY 10021, USA
| | - Justin Taylor
- Division of Hematology, Department of Medicine, Sylvester Comprehensive Cancer Center at the University of Miami Miller School of Medicine, Miami, FL 33136, USA
| | - Michael Seiler
- H3 Biomedicine Inc., 300 Technology Square, Cambridge, MA 02139, USA
| | - Silvia Buonamici
- H3 Biomedicine Inc., 300 Technology Square, Cambridge, MA 02139, USA
| | - Yana Pikman
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Division of Hematology/Oncology, Boston Children's Hospital, Boston, MA 02215 USA
| | - Jacqueline S Garcia
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Roger Belizaire
- Department of Pathology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Karen Adelman
- Broad Institute of MIT and Harvard University, Cambridge, MA 02142, USA
- Department of Biological Chemistry and Molecular Pharmacology, Blavatnik Institute, Harvard Medical School, Boston, MA 02115, USA
- Ludwig Center at Harvard, Harvard Medical School, Boston, MA 02115, USA
| | - Zuzana Tothova
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
- Broad Institute of MIT and Harvard University, Cambridge, MA 02142, USA
- Ludwig Center at Harvard, Harvard Medical School, Boston, MA 02115, USA
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15
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Schmitz M, Kaltheuner IH, Anand K, Düster R, Moecking J, Monastyrskyi A, Duckett DR, Roush WR, Geyer M. The reversible inhibitor SR-4835 binds Cdk12/cyclin K in a noncanonical G-loop conformation. J Biol Chem 2024; 300:105501. [PMID: 38016516 PMCID: PMC10767194 DOI: 10.1016/j.jbc.2023.105501] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2023] [Revised: 10/23/2023] [Accepted: 11/08/2023] [Indexed: 11/30/2023] Open
Abstract
Inhibition of cyclin-dependent kinases (CDKs) has evolved as an emerging anticancer strategy. In addition to the cell cycle-regulating CDKs, the transcriptional kinases Cdk12 and Cdk13 have become the focus of interest as they mediate a variety of functions, including the transition from transcription initiation to elongation and termination, precursor mRNA splicing, and intronic polyadenylation. Here, we determine the crystal structure of the small molecular inhibitor SR-4835 bound to the Cdk12/cyclin K complex at 2.68 Å resolution. The compound's benzimidazole moiety is embedded in a unique hydrogen bond network mediated by the kinase hinge region with flanking hydroxy groups of the Y815 and D819 side chains. Whereas the SR-4835 head group targets the adenine-binding pocket, the kinase's glycine-rich loop is shifted down toward the activation loop. Additionally, the αC-helix adopts an inward conformation, and the phosphorylated T-loop threonine interacts with all three canonical arginines, a hallmark of CDK activation that is altered in Cdk12 and Cdk13. Dose-response inhibition measurements with recombinant CMGC kinases show that SR-4835 is highly specific for Cdk12 and Cdk13 following a 10-fold lower potency for Cdk10. Whereas other CDK-targeting compounds exhibit tighter binding affinities and higher potencies for kinase inhibition, SR-4835 can be considered a selective transcription elongation antagonist. Our results provide the basis for a rational improvement of SR-4835 toward Cdk12 inhibition and a gain in selectivity over other transcription regulating CDKs.
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Affiliation(s)
| | | | - Kanchan Anand
- Institute of Structural Biology, University of Bonn, Bonn, Germany
| | - Robert Düster
- Institute of Structural Biology, University of Bonn, Bonn, Germany
| | - Jonas Moecking
- Institute of Structural Biology, University of Bonn, Bonn, Germany
| | | | - Derek R Duckett
- Department of Drug Discovery, Moffitt Cancer Center, Tampa, Florida, USA
| | - William R Roush
- Department of Chemistry, The Scripps Research Institute, Jupiter, Florida, USA
| | - Matthias Geyer
- Institute of Structural Biology, University of Bonn, Bonn, Germany.
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16
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Zhu S, Xu N, Zeng H. Molecular complexity of intraductal carcinoma of the prostate. Cancer Med 2024; 13:e6939. [PMID: 38379333 PMCID: PMC10879723 DOI: 10.1002/cam4.6939] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2023] [Revised: 11/21/2023] [Accepted: 12/04/2023] [Indexed: 02/22/2024] Open
Abstract
Intraductal carcinoma of the prostate (IDC-P) is an aggressive subtype of prostate cancer characterized by the growth of tumor cells within the prostate ducts. It is often found alongside invasive carcinoma and is associated with poor prognosis. Understanding the molecular mechanisms driving IDC-P is crucial for improved diagnosis, prognosis, and treatment strategies. This review summarizes the molecular characteristics of IDC-P and their prognostic indications, comparing them to conventional prostate acinar adenocarcinoma, to gain insights into its unique behavior and identify potential therapeutic targets.
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Affiliation(s)
- Sha Zhu
- Department of Urology, Institute of Urology, West China HospitalSichuan UniversityChengduChina
| | - Nanwei Xu
- Department of Urology, Institute of Urology, West China HospitalSichuan UniversityChengduChina
| | - Hao Zeng
- Department of Urology, Institute of Urology, West China HospitalSichuan UniversityChengduChina
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17
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Houles T, Boucher J, Lavoie G, MacLeod G, Lin S, Angers S, Roux PP. The CDK12 inhibitor SR-4835 functions as a molecular glue that promotes cyclin K degradation in melanoma. Cell Death Discov 2023; 9:459. [PMID: 38104154 PMCID: PMC10725499 DOI: 10.1038/s41420-023-01754-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2023] [Revised: 11/15/2023] [Accepted: 11/29/2023] [Indexed: 12/19/2023] Open
Abstract
CDK12 is a transcriptional cyclin-dependent kinase (CDK) that interacts with cyclin K to regulate different aspects of gene expression. The CDK12-cyclin K complex phosphorylates several substrates, including RNA polymerase II (Pol II), and thereby regulates transcription elongation, RNA splicing, as well as cleavage and polyadenylation. Because of its implication in cancer, including breast cancer and melanoma, multiple pharmacological inhibitors of CDK12 have been identified to date, including THZ531 and SR-4835. While both CDK12 inhibitors affect Poll II phosphorylation, we found that SR-4835 uniquely promotes cyclin K degradation via the proteasome. Using loss-of-function genetic screening, we found that SR-4835 cytotoxicity depends on a functional CUL4-RBX1-DDB1 ubiquitin ligase complex. Consistent with this, we show that DDB1 is required for cyclin K degradation, and that SR-4835 promotes DDB1 interaction with the CDK12-cyclin K complex. Docking studies and structure-activity relationship analyses of SR-4835 revealed the importance of the benzimidazole side-chain in molecular glue activity. Together, our results indicate that SR-4835 acts as a molecular glue that recruits the CDK12-cyclin K complex to the CUL4-RBX1-DDB1 ubiquitin ligase complex to target cyclin K for degradation.
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Affiliation(s)
- Thibault Houles
- Institute for Research in Immunology and Cancer (IRIC), Université de Montréal, Montreal, QC, Canada.
| | - Jonathan Boucher
- Institute for Research in Immunology and Cancer (IRIC), Université de Montréal, Montreal, QC, Canada
| | - Geneviève Lavoie
- Institute for Research in Immunology and Cancer (IRIC), Université de Montréal, Montreal, QC, Canada
| | - Graham MacLeod
- Donnelly Centre for Cellular & Biomolecular Research, Temerty Faculty of Medicine, University of Toronto, Toronto, ON, Canada
| | - Sichun Lin
- Donnelly Centre for Cellular & Biomolecular Research, Temerty Faculty of Medicine, University of Toronto, Toronto, ON, Canada
| | - Stephane Angers
- Donnelly Centre for Cellular & Biomolecular Research, Temerty Faculty of Medicine, University of Toronto, Toronto, ON, Canada
- Leslie Dan Faculty of Pharmacy, University of Toronto, Toronto, ON, Canada
- Department of Biochemistry, Temerty Faculty of Medicine, University of Toronto, Toronto, ON, Canada
| | - Philippe P Roux
- Institute for Research in Immunology and Cancer (IRIC), Université de Montréal, Montreal, QC, Canada.
- Department of Pathology and Cell Biology, Faculty of Medicine, Université de Montréal, Montreal, QC, Canada.
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18
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Larsen TV, Maansson CT, Daugaard TF, Andresen BS, Sorensen BS, Nielsen AL. Trans-Regulation of Alternative PD-L1 mRNA Processing by CDK12 in Non-Small-Cell Lung Cancer Cells. Cells 2023; 12:2844. [PMID: 38132164 PMCID: PMC10741404 DOI: 10.3390/cells12242844] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2023] [Revised: 11/10/2023] [Accepted: 12/13/2023] [Indexed: 12/23/2023] Open
Abstract
Immunotherapy using checkpoint inhibitors targeting the interaction between PD-1 on T cells and PD-L1 on cancer cells has shown significant results in non-small-cell lung cancer (NSCLC). Not all patients respond to the therapy, and PD-L1 expression heterogeneity is proposed to be one determinant for this. The alternative processing of PD-L1 RNA, which depends on an alternative poly-A site in intron 4, generates a shorter mRNA variant (PD-L1v4) encoding soluble PD-L1 (sPD-L1), relative to the canonical PD-L1v1 mRNA encoding membrane-associated PD-L1 (mPD-L1). This study aimed to identify factors influencing the ratio between these two PD-L1 mRNAs in NSCLC cells. First, we verified the existence of the alternative PD-L1 RNA processing in NSCLC cells, and from in silico analyses, we identified a candidate list of regulatory factors. Examining selected candidates showed that CRISPR/Cas9-generated loss-of-function mutations in CDK12 increased the PD-L1v4/PD-L1v1 mRNA ratio and, accordingly, the sPD-L1/mPD-L1 balance. The CDK12/13 inhibitor THZ531 could also increase the PD-L1v4/PD-L1v1 mRNA ratio and impact the PD-L1 transcriptional response to IFN-γ stimulation. The fact that CDK12 regulates PD-L1 transcript variant formation in NSCLC cells is consistent with CDK12's role in promoting transcriptional elongation over intron-located poly-A sites. This study lays the groundwork for clinical investigations to delineate the implications of the CDK12-mediated balancing of sPD-L1 relative to mPD-L1 for immunotherapeutic responses in NSCLC.
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Affiliation(s)
- Trine V. Larsen
- Department of Biomedicine, Aarhus University, 8000 Aarhus, Denmark; (T.V.L.); (C.T.M.); (T.F.D.)
| | - Christoffer T. Maansson
- Department of Biomedicine, Aarhus University, 8000 Aarhus, Denmark; (T.V.L.); (C.T.M.); (T.F.D.)
- Department of Clinical Medicine, Aarhus University, 8200 Aarhus, Denmark;
- Department of Clinical Biochemistry, Aarhus University Hospital, 8200 Aarhus, Denmark
| | - Tina F. Daugaard
- Department of Biomedicine, Aarhus University, 8000 Aarhus, Denmark; (T.V.L.); (C.T.M.); (T.F.D.)
| | - Brage S. Andresen
- Department of Biology and Molecular Biology, Southern University of Denmark, 5230 Odense, Denmark;
| | - Boe S. Sorensen
- Department of Clinical Medicine, Aarhus University, 8200 Aarhus, Denmark;
- Department of Clinical Biochemistry, Aarhus University Hospital, 8200 Aarhus, Denmark
| | - Anders L. Nielsen
- Department of Biomedicine, Aarhus University, 8000 Aarhus, Denmark; (T.V.L.); (C.T.M.); (T.F.D.)
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19
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Shen P, Ye K, Xiang H, Zhang Z, He Q, Zhang X, Cai MC, Chen J, Sun Y, Lin L, Qi C, Zhang M, Cheung LWT, Shi T, Yin X, Li Y, Di W, Zang R, Tan L, Zhuang G. Therapeutic targeting of CPSF3-dependent transcriptional termination in ovarian cancer. SCIENCE ADVANCES 2023; 9:eadj0123. [PMID: 37992178 PMCID: PMC10664987 DOI: 10.1126/sciadv.adj0123] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/01/2023] [Accepted: 10/19/2023] [Indexed: 11/24/2023]
Abstract
Transcriptional dysregulation is a recurring pathogenic hallmark and an emerging therapeutic vulnerability in ovarian cancer. Here, we demonstrated that ovarian cancer exhibited a unique dependency on the regulatory machinery of transcriptional termination, particularly, cleavage and polyadenylation specificity factor (CPSF) complex. Genetic abrogation of multiple CPSF subunits substantially hampered neoplastic cell viability, and we presented evidence that their indispensable roles converged on the endonuclease CPSF3. Mechanistically, CPSF perturbation resulted in lengthened 3'-untranslated regions, diminished intronic polyadenylation and widespread transcriptional readthrough, and consequently suppressed oncogenic pathways. Furthermore, we reported the development of specific CPSF3 inhibitors building upon the benzoxaborole scaffold, which exerted potent antitumor activity. Notably, CPSF3 blockade effectively exacerbated genomic instability by down-regulating DNA damage repair genes and thus acted in synergy with poly(adenosine 5'-diphosphate-ribose) polymerase inhibition. These findings establish CPSF3-dependent transcriptional termination as an exploitable driving mechanism of ovarian cancer and provide a promising class of boron-containing compounds for targeting transcription-addicted human malignancies.
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Affiliation(s)
- Peiye Shen
- State Key Laboratory of Systems Medicine for Cancer, Department of Obstetrics and Gynecology, Shanghai Cancer Institute, Ren Ji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- Shanghai Key Laboratory of Gynecologic Oncology, Ren Ji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Kaiyan Ye
- State Key Laboratory of Systems Medicine for Cancer, Department of Obstetrics and Gynecology, Shanghai Cancer Institute, Ren Ji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- Shanghai Key Laboratory of Gynecologic Oncology, Ren Ji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Huaijiang Xiang
- Interdisciplinary Research Center on Biology and Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, Shanghai, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Zhenfeng Zhang
- State Key Laboratory of Systems Medicine for Cancer, Department of Obstetrics and Gynecology, Shanghai Cancer Institute, Ren Ji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- Shanghai Key Laboratory of Gynecologic Oncology, Ren Ji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Qinyang He
- Interdisciplinary Research Center on Biology and Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, Shanghai, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Xiao Zhang
- Interdisciplinary Research Center on Biology and Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, Shanghai, China
| | - Mei-Chun Cai
- State Key Laboratory of Systems Medicine for Cancer, Department of Obstetrics and Gynecology, Shanghai Cancer Institute, Ren Ji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- Shanghai Key Laboratory of Gynecologic Oncology, Ren Ji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Junfei Chen
- State Key Laboratory of Systems Medicine for Cancer, Department of Obstetrics and Gynecology, Shanghai Cancer Institute, Ren Ji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- Shanghai Key Laboratory of Gynecologic Oncology, Ren Ji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Yunheng Sun
- State Key Laboratory of Systems Medicine for Cancer, Department of Obstetrics and Gynecology, Shanghai Cancer Institute, Ren Ji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- Shanghai Key Laboratory of Gynecologic Oncology, Ren Ji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Lifeng Lin
- Ovarian Cancer Program, Department of Gynecologic Oncology, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Chunting Qi
- Interdisciplinary Research Center on Biology and Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, Shanghai, China
| | - Meiying Zhang
- State Key Laboratory of Systems Medicine for Cancer, Department of Obstetrics and Gynecology, Shanghai Cancer Institute, Ren Ji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- Shanghai Key Laboratory of Gynecologic Oncology, Ren Ji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Lydia W. T. Cheung
- School of Biomedical Sciences, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, China
| | - Tingyan Shi
- Ovarian Cancer Program, Department of Gynecologic Oncology, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Xia Yin
- State Key Laboratory of Systems Medicine for Cancer, Department of Obstetrics and Gynecology, Shanghai Cancer Institute, Ren Ji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- Shanghai Key Laboratory of Gynecologic Oncology, Ren Ji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Ying Li
- Interdisciplinary Research Center on Biology and Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, Shanghai, China
| | - Wen Di
- State Key Laboratory of Systems Medicine for Cancer, Department of Obstetrics and Gynecology, Shanghai Cancer Institute, Ren Ji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- Shanghai Key Laboratory of Gynecologic Oncology, Ren Ji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Rongyu Zang
- Ovarian Cancer Program, Department of Gynecologic Oncology, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Li Tan
- Interdisciplinary Research Center on Biology and Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, Shanghai, China
- State Key Laboratory of Chemical Biology, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, Shanghai, China
| | - Guanglei Zhuang
- State Key Laboratory of Systems Medicine for Cancer, Department of Obstetrics and Gynecology, Shanghai Cancer Institute, Ren Ji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- Shanghai Key Laboratory of Gynecologic Oncology, Ren Ji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
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20
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Aoi Y, Shilatifard A. Transcriptional elongation control in developmental gene expression, aging, and disease. Mol Cell 2023; 83:3972-3999. [PMID: 37922911 DOI: 10.1016/j.molcel.2023.10.004] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2023] [Revised: 09/23/2023] [Accepted: 10/11/2023] [Indexed: 11/07/2023]
Abstract
The elongation stage of transcription by RNA polymerase II (RNA Pol II) is central to the regulation of gene expression in response to developmental and environmental cues in metazoan. Dysregulated transcriptional elongation has been associated with developmental defects as well as disease and aging processes. Decades of genetic and biochemical studies have painstakingly identified and characterized an ensemble of factors that regulate RNA Pol II elongation. This review summarizes recent findings taking advantage of genetic engineering techniques that probe functions of elongation factors in vivo. We propose a revised model of elongation control in this accelerating field by reconciling contradictory results from the earlier biochemical evidence and the recent in vivo studies. We discuss how elongation factors regulate promoter-proximal RNA Pol II pause release, transcriptional elongation rate and processivity, RNA Pol II stability and RNA processing, and how perturbation of these processes is associated with developmental disorders, neurodegenerative disease, cancer, and aging.
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Affiliation(s)
- Yuki Aoi
- Simpson Querrey Institute for Epigenetics, Department of Biochemistry and Molecular Genetics Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
| | - Ali Shilatifard
- Simpson Querrey Institute for Epigenetics, Department of Biochemistry and Molecular Genetics Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA.
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21
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Wang Z, Himanen SV, Haikala HM, Friedel CC, Vihervaara A, Barborič M. Inhibition of CDK12 elevates cancer cell dependence on P-TEFb by stimulation of RNA polymerase II pause release. Nucleic Acids Res 2023; 51:10970-10991. [PMID: 37811895 PMCID: PMC10639066 DOI: 10.1093/nar/gkad792] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2023] [Revised: 09/11/2023] [Accepted: 09/22/2023] [Indexed: 10/10/2023] Open
Abstract
P-TEFb and CDK12 facilitate transcriptional elongation by RNA polymerase II. Given the prominence of both kinases in cancer, gaining a better understanding of their interplay could inform the design of novel anti-cancer strategies. While down-regulation of DNA repair genes in CDK12-targeted cancer cells is being explored therapeutically, little is known about mechanisms and significance of transcriptional induction upon inhibition of CDK12. We show that selective targeting of CDK12 in colon cancer-derived cells activates P-TEFb via its release from the inhibitory 7SK snRNP. In turn, P-TEFb stimulates Pol II pause release at thousands of genes, most of which become newly dependent on P-TEFb. Amongst the induced genes are those stimulated by hallmark pathways in cancer, including p53 and NF-κB. Consequently, CDK12-inhibited cancer cells exhibit hypersensitivity to inhibitors of P-TEFb. While blocking P-TEFb triggers their apoptosis in a p53-dependent manner, it impedes cell proliferation irrespective of p53 by preventing induction of genes downstream of the DNA damage-induced NF-κB signaling. In summary, stimulation of Pol II pause release at the signal-responsive genes underlies the functional dependence of CDK12-inhibited cancer cells on P-TEFb. Our study establishes the mechanistic underpinning for combinatorial targeting of CDK12 with either P-TEFb or the induced oncogenic pathways in cancer.
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Affiliation(s)
- Zhijia Wang
- Department of Biochemistry and Developmental Biology, University of Helsinki, Helsinki FIN-00014, Finland
| | - Samu V Himanen
- Department of Gene Technology, KTH Royal Institute of Technology, Science for Life Laboratory, Stockholm, Sweden
| | - Heidi M Haikala
- Translational Immunology Research Program (TRIMM), Research Programs Unit, Faculty of Medicine, University of Helsinki, Helsinki FIN-00014, Finland
- iCAN Digital Precision Cancer Medicine Flagship, University of Helsinki, Helsinki FIN-00014, Finland
| | - Caroline C Friedel
- Institute of Informatics, Ludwig-Maximilians-Universität München, 80333 Munich, Germany
| | - Anniina Vihervaara
- Department of Gene Technology, KTH Royal Institute of Technology, Science for Life Laboratory, Stockholm, Sweden
| | - Matjaž Barborič
- Department of Biochemistry and Developmental Biology, University of Helsinki, Helsinki FIN-00014, Finland
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22
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Zhang L, Zhen Y, Feng L, Li Z, Lu Y, Wang G, Ouyang L. Discovery of a novel dual-target inhibitor of CDK12 and PARP1 that induces synthetic lethality for treatment of triple-negative breast cancer. Eur J Med Chem 2023; 259:115648. [PMID: 37478560 DOI: 10.1016/j.ejmech.2023.115648] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2023] [Revised: 07/07/2023] [Accepted: 07/13/2023] [Indexed: 07/23/2023]
Abstract
Triple negative breast cancer (TNBC) is one of the most aggressive breast tumors, with a high rate of recurrence and metastasis as well as a poor prognosis. Consequently, it is urgent to find new targeted therapeutic strategies and development of corresponding drugs. Previous studies have shown that CDK12 inhibitors in combination with PARP1 inhibitors is able to induce synthetic lethality in TNBC cells. Here, we reported simultaneously inhibition of CDK12 and PARP1 by genetic or pharmacological approaches synergistically inhibited the proliferation of TNBC cells. Then, a series of small molecule inhibitors targeting both CDK12 and PARP1 were designed and synthesized. The new dual-target inhibitor (12e) showed potent inhibitory activity against CDK12 (IC50 = 285 nM) and PARP1 (IC50 = 34 nM), as well as good anti-proliferative effects in TNBC cell lines. Meanwhile, compound 12e showed favorable synergistic anti-tumor efficacy in cells and xenografts by inhibiting DNA damage repair, promoting cell cycle arrest and apoptosis. Taken together, we successfully synthesized the first effective CDK12-PARP1 dual inhibitor, which is expected to be an attractive therapeutic strategy for TNBC.
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Affiliation(s)
- Lan Zhang
- Sichuan Engineering Research Center for Biomimetic Synthesis of Natural Drugs, School of Life Science and Engineering, Southwest Jiaotong University, Chengdu, 610031, China.
| | - Yongqi Zhen
- Sichuan Engineering Research Center for Biomimetic Synthesis of Natural Drugs, School of Life Science and Engineering, Southwest Jiaotong University, Chengdu, 610031, China; Department of Biotherapy, Innovation Center of Nursing Research, Nursing Key Laboratory of Sichuan Province, State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University /West China School of Nursing, Sichuan University, Chengdu, 610041, China
| | - Lu Feng
- Department of Biotherapy, Innovation Center of Nursing Research, Nursing Key Laboratory of Sichuan Province, State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University /West China School of Nursing, Sichuan University, Chengdu, 610041, China
| | - Zhijia Li
- Sichuan Engineering Research Center for Biomimetic Synthesis of Natural Drugs, School of Life Science and Engineering, Southwest Jiaotong University, Chengdu, 610031, China
| | - Yingying Lu
- Sichuan Engineering Research Center for Biomimetic Synthesis of Natural Drugs, School of Life Science and Engineering, Southwest Jiaotong University, Chengdu, 610031, China
| | - Guan Wang
- Department of Biotherapy, Innovation Center of Nursing Research, Nursing Key Laboratory of Sichuan Province, State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University /West China School of Nursing, Sichuan University, Chengdu, 610041, China.
| | - Liang Ouyang
- Department of Biotherapy, Innovation Center of Nursing Research, Nursing Key Laboratory of Sichuan Province, State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University /West China School of Nursing, Sichuan University, Chengdu, 610041, China.
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23
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Cussenot O, Cancel-Tassin G, Rao SR, Woodcock DJ, Lamb AD, Mills IG, Hamdy FC. Aligning germline and somatic mutations in prostate cancer. Are genetics changing practice? BJU Int 2023; 132:472-484. [PMID: 37410655 DOI: 10.1111/bju.16120] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/08/2023]
Abstract
OBJECTIVE To review the current status of germline and somatic (tumour) genetic testing for prostate cancer (PCa), and its relevance for clinical practice. METHODS A narrative synthesis of various molecular profiles related to their clinical context was carried out. Current guidelines for genetic testing and its feasibility in clinical practice were analysed. We report the main identified genetic sequencing results or functional genomic scores for PCa published in the literature or obtained from the French PROGENE study. RESULTS The molecular alterations observed in PCa are mostly linked to disruption of the androgen receptor (AR) pathway or DNA repair deficiency. The main known germline mutations affect the BReast CAncer gene 2 (BRCA2) and homeobox B13 (HOXB13) genes, whereas AR and tumour protein p53 (TP53) are the genes with most frequent somatic alterations in tumours from men with metastatic PCa. Molecular tests are now available for detecting some of these germline or somatic alterations and sometimes recommended by guidelines, but their utilisation must combine rationality and feasibility. They can guide specific therapies, notably for the management of metastatic disease. Indeed, following androgen deprivation, targeted therapies for PCa currently include poly-(ADP-ribose)-polymerase (PARP) inhibitors, immune checkpoint inhibitors, and prostate-specific membrane antigen (PSMA)-guided radiotherapy. The genetic tests currently approved for targeted therapies remain limited to the detection of BRCA1 and BRCA2 mutation and DNA mismatch repair deficiency, while large panels are recommended for germline analyses, not only for inherited cancer predisposing syndrome, but also for metastatic PCa. CONCLUSIONS Further consensus aligning germline with somatic molecular analysis in metastatic PCa is required, including genomics scars, emergent immunohistochemistry, or functional pre-screen imaging. With rapid advances in knowledge and technology in the field, continuous updating of guidelines to help the clinical management of these individuals, and well-conducted studies to evaluate the benefits of genetic testing are needed.
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Affiliation(s)
- Olivier Cussenot
- Centre de Recherche sur les Pathologies Prostatiques et Urologiques (CeRePP), Paris, France
- GRC 5 Predictive Onco-Urology, Sorbonne University, Paris, France
- Nuffield Department of Surgical Sciences, University of Oxford, Oxford, UK
| | - Geraldine Cancel-Tassin
- Centre de Recherche sur les Pathologies Prostatiques et Urologiques (CeRePP), Paris, France
- GRC 5 Predictive Onco-Urology, Sorbonne University, Paris, France
| | - Srinivasa R Rao
- Nuffield Department of Surgical Sciences, University of Oxford, Oxford, UK
| | - Dan J Woodcock
- Nuffield Department of Surgical Sciences, University of Oxford, Oxford, UK
| | - Alastair D Lamb
- Nuffield Department of Surgical Sciences, University of Oxford, Oxford, UK
| | - Ian G Mills
- Nuffield Department of Surgical Sciences, University of Oxford, Oxford, UK
| | - Freddie C Hamdy
- Nuffield Department of Surgical Sciences, University of Oxford, Oxford, UK
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24
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Ang HX, Sutiman N, Deng XL, Liu A, Cerda-Smith CG, Hutchinson HM, Kim H, Bartelt LC, Chen Q, Barrera A, Lin J, Sheng Z, McDowell IC, Reddy TE, Nicchitta CV, Wood KC. Cooperative regulation of coupled oncoprotein synthesis and stability in triple-negative breast cancer by EGFR and CDK12/13. Proc Natl Acad Sci U S A 2023; 120:e2221448120. [PMID: 37695916 PMCID: PMC10515179 DOI: 10.1073/pnas.2221448120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2023] [Accepted: 07/19/2023] [Indexed: 09/13/2023] Open
Abstract
Evidence has long suggested that epidermal growth factor receptor (EGFR) may play a prominent role in triple-negative breast cancer (TNBC) pathogenesis, but clinical trials of EGFR inhibitors have yielded disappointing results. Using a candidate drug screen, we identified that inhibition of cyclin-dependent kinases 12 and 13 (CDK12/13) dramatically sensitizes diverse models of TNBC to EGFR blockade. This combination therapy drives cell death through the 4E-BP1-dependent suppression of the translation and translation-linked turnover of driver oncoproteins, including MYC. A genome-wide CRISPR/Cas9 screen identified the CCR4-NOT complex as a major determinant of sensitivity to the combination therapy whose loss renders 4E-BP1 unresponsive to drug-induced dephosphorylation, thereby rescuing MYC translational suppression and promoting MYC stability. The central roles of CCR4-NOT and 4E-BP1 in response to the combination therapy were further underscored by the observation of CNOT1 loss and rescue of 4E-BP1 phosphorylation in TNBC cells that naturally evolved therapy resistance. Thus, pharmacological inhibition of CDK12/13 reveals a long-proposed EGFR dependence in TNBC that functions through the cooperative regulation of translation-coupled oncoprotein stability.
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Affiliation(s)
- Hazel X Ang
- Department of Pharmacology & Cancer Biology, Duke University School of Medicine, Durham, NC 22710
| | - Natalia Sutiman
- Duke-National University of Singapore Medical School, Singapore 169857, Singapore
| | - Xinyue L Deng
- Department of Pharmacology & Cancer Biology, Duke University School of Medicine, Durham, NC 22710
| | - Annie Liu
- Department of Pharmacology & Cancer Biology, Duke University School of Medicine, Durham, NC 22710
- Department of Surgery, Duke University School of Medicine, Durham, NC 22710
| | - Christian G Cerda-Smith
- Department of Pharmacology & Cancer Biology, Duke University School of Medicine, Durham, NC 22710
| | - Haley M Hutchinson
- Department of Pharmacology & Cancer Biology, Duke University School of Medicine, Durham, NC 22710
| | - Holly Kim
- Department of Pharmacology & Cancer Biology, Duke University School of Medicine, Durham, NC 22710
| | - Luke C Bartelt
- Duke Center for Genomic and Computational Biology, Department of Biostatistics and Bioinformatics, Duke University School of Medicine, Durham, NC 27708
| | - Qiang Chen
- Department of Cell Biology, Duke University School of Medicine, Durham, NC 22710
| | - Alejandro Barrera
- Duke Center for Genomic and Computational Biology, Department of Biostatistics and Bioinformatics, Duke University School of Medicine, Durham, NC 27708
- Department of Biostatistics and Bioinformatics, Duke University School of Medicine, Durham, NC 27708
| | - Jiaxing Lin
- Bioinformatics Shared Resources, Duke Cancer Institute, Duke University Medical Center, Durham, NC 27705
| | - Zhecheng Sheng
- Bioinformatics Shared Resources, Duke Cancer Institute, Duke University Medical Center, Durham, NC 27705
| | - Ian C McDowell
- Duke Center for Genomic and Computational Biology, Department of Biostatistics and Bioinformatics, Duke University School of Medicine, Durham, NC 27708
- Department of Biostatistics and Bioinformatics, Duke University School of Medicine, Durham, NC 27708
| | - Timothy E Reddy
- Duke Center for Genomic and Computational Biology, Department of Biostatistics and Bioinformatics, Duke University School of Medicine, Durham, NC 27708
- Department of Biostatistics and Bioinformatics, Duke University School of Medicine, Durham, NC 27708
| | | | - Kris C Wood
- Department of Pharmacology & Cancer Biology, Duke University School of Medicine, Durham, NC 22710
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25
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Yan Z, Du Y, Zhang H, Zheng Y, Lv H, Dong N, He F. Research progress of anticancer drugs targeting CDK12. RSC Med Chem 2023; 14:1629-1644. [PMID: 37731700 PMCID: PMC10507796 DOI: 10.1039/d3md00004d] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2023] [Accepted: 05/17/2023] [Indexed: 09/22/2023] Open
Abstract
Cyclin-dependent kinase 12 (CDK12) is a transcription-associated CDK that plays key roles in transcription, translation, mRNA splicing, the cell cycle, and DNA damage repair. Research has identified that high expression of CDK12 in organs such as the breast, stomach, and uterus can lead to HER2-positive breast cancer, gastric cancer and cervical cancer. Inhibiting high expression of CDK12 suppresses tumor growth and proliferation, suggesting that it is both a biomarker for cancer and a potential target for cancer therapy. CDK12 inhibitors can competitively bind the CDK12 hydrophobic pocket with ATP to avoid CDK12 phosphorylation, blocking subsequent signaling pathways. The development of CDK12 inhibitors is challenging due to the high homology of CDK12 with other CDKs. This review summarizes the research progress of CDK12 inhibitors, their mechanism of action and the structure-activity relationship, providing new insights into the design of CDK12 selective inhibitors.
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Affiliation(s)
- Zhijia Yan
- School of Chemistry & Chemical Engineering, Qilu University of Technology (Shandong Academy of Sciences) 3501 Da Xue Road Jinan 250353 China
| | - Yongli Du
- School of Chemistry & Chemical Engineering, Qilu University of Technology (Shandong Academy of Sciences) 3501 Da Xue Road Jinan 250353 China
| | - Haibin Zhang
- School of Chemistry & Chemical Engineering, Qilu University of Technology (Shandong Academy of Sciences) 3501 Da Xue Road Jinan 250353 China
| | - Yong Zheng
- School of Chemistry & Chemical Engineering, Qilu University of Technology (Shandong Academy of Sciences) 3501 Da Xue Road Jinan 250353 China
| | - Huiting Lv
- School of Chemistry & Chemical Engineering, Qilu University of Technology (Shandong Academy of Sciences) 3501 Da Xue Road Jinan 250353 China
| | - Ning Dong
- School of Chemistry & Chemical Engineering, Qilu University of Technology (Shandong Academy of Sciences) 3501 Da Xue Road Jinan 250353 China
| | - Fang He
- School of Water Conservancy and Environment, University of Jinan 336 Nanxinzhuang West Road Jinan 250022 China
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26
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Pluta AJ, Studniarek C, Murphy S, Norbury CJ. Cyclin-dependent kinases: Masters of the eukaryotic universe. WILEY INTERDISCIPLINARY REVIEWS. RNA 2023; 15:e1816. [PMID: 37718413 PMCID: PMC10909489 DOI: 10.1002/wrna.1816] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/05/2023] [Revised: 07/21/2023] [Accepted: 08/03/2023] [Indexed: 09/19/2023]
Abstract
A family of structurally related cyclin-dependent protein kinases (CDKs) drives many aspects of eukaryotic cell function. Much of the literature in this area has considered individual members of this family to act primarily either as regulators of the cell cycle, the context in which CDKs were first discovered, or as regulators of transcription. Until recently, CDK7 was the only clear example of a CDK that functions in both processes. However, new data points to several "cell-cycle" CDKs having important roles in transcription and some "transcriptional" CDKs having cell cycle-related targets. For example, novel functions in transcription have been demonstrated for the archetypal cell cycle regulator CDK1. The increasing evidence of the overlap between these two CDK types suggests that they might play a critical role in coordinating the two processes. Here we review the canonical functions of cell-cycle and transcriptional CDKs, and provide an update on how these kinases collaborate to perform important cellular functions. We also provide a brief overview of how dysregulation of CDKs contributes to carcinogenesis, and possible treatment avenues. This article is categorized under: RNA Interactions with Proteins and Other Molecules > RNA-Protein Complexes RNA Processing > 3' End Processing RNA Processing > Splicing Regulation/Alternative Splicing.
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Affiliation(s)
| | | | - Shona Murphy
- Sir William Dunn School of PathologyUniversity of OxfordOxfordUK
| | - Chris J. Norbury
- Sir William Dunn School of PathologyUniversity of OxfordOxfordUK
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Pitolli C, Marini A, Guerra M, Pieraccioli M, Marabitti V, Palluzzi F, Giacò L, Tamburrini G, Cecconi F, Nazio F, Sette C, Pagliarini V. MYC up-regulation confers vulnerability to dual inhibition of CDK12 and CDK13 in high-risk Group 3 medulloblastoma. J Exp Clin Cancer Res 2023; 42:214. [PMID: 37599362 PMCID: PMC10440921 DOI: 10.1186/s13046-023-02790-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2023] [Accepted: 08/09/2023] [Indexed: 08/22/2023] Open
Abstract
BACKGROUND Medulloblastoma (MB) is the most common cerebellar malignancy during childhood. Among MB, MYC-amplified Group 3 tumors display the worst prognosis. MYC is an oncogenic transcription factor currently thought to be undruggable. Nevertheless, targeting MYC-dependent processes (i.e. transcription and RNA processing regulation) represents a promising approach. METHODS We have tested the sensitivity of MYC-driven Group 3 MB cells to a pool of transcription and splicing inhibitors that display a wide spectrum of targets. Among them, we focus on THZ531, an inhibitor of the transcriptional cyclin-dependent kinases (CDK) 12 and 13. High-throughput RNA-sequencing analyses followed by bioinformatics and functional analyses were carried out to elucidate the molecular mechanism(s) underlying the susceptibility of Group 3 MB to CDK12/13 chemical inhibition. Data from International Cancer Genome Consortium (ICGC) and other public databases were mined to evaluate the functional relevance of the cellular pathway/s affected by the treatment with THZ531 in Group 3 MB patients. RESULTS We found that pharmacological inhibition of CDK12/13 is highly selective for MYC-high Group 3 MB cells with respect to MYC-low MB cells. We identified a subset of genes enriched in functional terms related to the DNA damage response (DDR) that are up-regulated in Group 3 MB and repressed by CDK12/13 inhibition. Accordingly, MYC- and CDK12/13-dependent higher expression of DDR genes in Group 3 MB cells limits the toxic effects of endogenous DNA lesions in these cells. More importantly, chemical inhibition of CDK12/13 impaired the DDR and induced irreparable DNA damage exclusively in MYC-high Group 3 MB cells. The augmented sensitivity of MYC-high MB cells to CDK12/13 inhibition relies on the higher elongation rate of the RNA polymerase II in DDR genes. Lastly, combined treatments with THZ531 and DNA damage-inducing agents synergically suppressed viability of MYC-high Group 3 MB cells. CONCLUSIONS Our study demonstrates that CDK12/13 activity represents an exploitable vulnerability in MYC-high Group 3 MB and may pave the ground for new therapeutic approaches for this high-risk brain tumor.
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Affiliation(s)
- Consuelo Pitolli
- Department of Neuroscience, Section of Human Anatomy, Catholic University of the Sacred Heart, 00168, Rome, Italy
| | - Alberto Marini
- Department of Neuroscience, Section of Human Anatomy, Catholic University of the Sacred Heart, 00168, Rome, Italy
- GSTEP-Organoids Research Core Facility, IRCCS Fondazione Policlinico Universitario Agostino Gemelli, 00168, Rome, Italy
| | - Marika Guerra
- Department of Neuroscience, Section of Human Anatomy, Catholic University of the Sacred Heart, 00168, Rome, Italy
| | - Marco Pieraccioli
- Department of Neuroscience, Section of Human Anatomy, Catholic University of the Sacred Heart, 00168, Rome, Italy
- GSTEP-Organoids Research Core Facility, IRCCS Fondazione Policlinico Universitario Agostino Gemelli, 00168, Rome, Italy
| | - Veronica Marabitti
- Department of Pediatric Hemato-Oncology and Cell and Gene Therapy, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy
- Department of Biology, University of Rome Tor Vergata, Rome, Italy
| | - Fernando Palluzzi
- Bioinformatics Research Core Facility, Gemelli Science and Technology Park (GSTeP), IRCCS Fondazione Policlinico Universitario Agostino Gemelli, 00168, Rome, Italy
- Present Address: Integrated Omics Department, Novo Nordisk, 2860, Søborg, Denmark
| | - Luciano Giacò
- Bioinformatics Research Core Facility, Gemelli Science and Technology Park (GSTeP), IRCCS Fondazione Policlinico Universitario Agostino Gemelli, 00168, Rome, Italy
| | - Gianpiero Tamburrini
- Department of Neuroscience, Section of Human Anatomy, Catholic University of the Sacred Heart, 00168, Rome, Italy
- Pediatric Neurosurgery, IRCCS Fondazione Policlinico Universitario Agostino Gemelli, 00168, Rome, Italy
| | - Francesco Cecconi
- Department of Pediatric Hemato-Oncology and Cell and Gene Therapy, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy
- Department of Basic Biotechnological Sciences, Intensive Care and Perioperative Clinics Research, Catholic University of the Sacred Heart, 00168, Rome, Italy
- Unit of Cell Stress and Survival, Danish Cancer Society Research Center, Copenhagen, Denmark
| | - Francesca Nazio
- Department of Pediatric Hemato-Oncology and Cell and Gene Therapy, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy
- Department of Biology, University of Rome Tor Vergata, Rome, Italy
| | - Claudio Sette
- Department of Neuroscience, Section of Human Anatomy, Catholic University of the Sacred Heart, 00168, Rome, Italy.
- GSTEP-Organoids Research Core Facility, IRCCS Fondazione Policlinico Universitario Agostino Gemelli, 00168, Rome, Italy.
| | - Vittoria Pagliarini
- Department of Neuroscience, Section of Human Anatomy, Catholic University of the Sacred Heart, 00168, Rome, Italy.
- GSTEP-Organoids Research Core Facility, IRCCS Fondazione Policlinico Universitario Agostino Gemelli, 00168, Rome, Italy.
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Xiao Y, Dong J. Coming of Age: Targeting Cyclin K in Cancers. Cells 2023; 12:2044. [PMID: 37626854 PMCID: PMC10453554 DOI: 10.3390/cells12162044] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2023] [Revised: 08/08/2023] [Accepted: 08/09/2023] [Indexed: 08/27/2023] Open
Abstract
Cyclins and cyclin-dependent kinases (CDKs) play versatile roles in promoting the hallmarks of cancer. Therefore, cyclins and CDKs have been widely studied and targeted in cancer treatment, with four CDK4/6 inhibitors being approved by the FDA and many other inhibitors being examined in clinical trials. The specific purpose of this review is to delineate the role and therapeutic potential of Cyclin K in cancers. Studies have shown that Cyclin K regulates many essential biological processes, including the DNA damage response, mitosis, and pre-replicative complex assembly, and is critical in both cancer cell growth and therapeutic resistance. Importantly, the druggability of Cyclin K has been demonstrated in an increasing number of studies that identify novel opportunities for its use in cancer treatment. This review first introduces the basic features and translational value of human cyclins and CDKs. Next, the discovery, phosphorylation targets, and related functional significance of Cyclin K-CDK12/13 complexes in cancer are detailed. This review then provides a summary of current Cyclin K-associated cancer studies, with an emphasis on the available Cyclin K-targeting drugs. Finally, the current knowledge gaps regarding the potential of Cyclin K in cancers are discussed, along with interesting directions for future investigation.
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Affiliation(s)
| | - Jixin Dong
- Eppley Institute for Research in Cancer and Allied Diseases, Fred and Pamela Buffett Cancer Center, University of Nebraska Medical Center, Omaha, NE 68198, USA;
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Dilmac S, Ozpolat B. Mechanisms of PARP-Inhibitor-Resistance in BRCA-Mutated Breast Cancer and New Therapeutic Approaches. Cancers (Basel) 2023; 15:3642. [PMID: 37509303 PMCID: PMC10378018 DOI: 10.3390/cancers15143642] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2023] [Revised: 07/10/2023] [Accepted: 07/11/2023] [Indexed: 07/30/2023] Open
Abstract
The recent success of Poly (ADP-ribose) polymerase (PARP) inhibitors has led to the approval of four different PARP inhibitors for the treatment of BRCA1/2-mutant breast and ovarian cancers. About 40-50% of BRCA1/2-mutated patients do not respond to PARP inhibitors due to a preexisting innate or intrinsic resistance; the majority of patients who initially respond to the therapy inevitably develop acquired resistance. However, subsets of patients experience a long-term response (>2 years) to treatment with PARP inhibitors. Poly (ADP-ribose) polymerase 1 (PARP1) is an enzyme that plays an important role in the recognition and repair of DNA damage. PARP inhibitors induce "synthetic lethality" in patients with tumors with a homologous-recombination-deficiency (HRD). Several molecular mechanisms have been identified as causing PARP-inhibitor-resistance. In this review, we focus on the molecular mechanisms underlying the PARP-inhibitor-resistance in BRCA-mutated breast cancer and summarize potential therapeutic strategies to overcome the resistance mechanisms.
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Affiliation(s)
- Sayra Dilmac
- Department of Nanomedicine, Houston Methodist Research Institute, Houston, TX 77030, USA
| | - Bulent Ozpolat
- Department of Nanomedicine, Houston Methodist Research Institute, Houston, TX 77030, USA
- Houston Methodist Neal Cancer Center, Houston, TX 77030, USA
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Grypari IM, Tzelepi V, Gyftopoulos K. DNA Damage Repair Pathways in Prostate Cancer: A Narrative Review of Molecular Mechanisms, Emerging Biomarkers and Therapeutic Targets in Precision Oncology. Int J Mol Sci 2023; 24:11418. [PMID: 37511177 PMCID: PMC10380086 DOI: 10.3390/ijms241411418] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2023] [Revised: 07/09/2023] [Accepted: 07/11/2023] [Indexed: 07/30/2023] Open
Abstract
Prostate cancer (PCa) has a distinct molecular signature, including characteristic chromosomal translocations, gene deletions and defective DNA damage repair mechanisms. One crucial pathway involved is homologous recombination deficiency (HRD) and it is found in almost 20% of metastatic castrate-resistant PCa (mCRPC). Inherited/germline mutations are associated with a hereditary predisposition to early PCa development and aggressive behavior. BRCA2, ATM and CHECK2 are the most frequently HRD-mutated genes. BRCA2-mutated tumors have unfavorable clinical and pathological characteristics, such as intraductal carcinoma. PARP inhibitors, due to the induction of synthetic lethality, have been therapeutically approved for mCRPC with HRD alterations. Mutations are detected in metastatic tissue, while a liquid biopsy is utilized during follow-up, recognizing acquired resistance mechanisms. The mismatch repair (MMR) pathway is another DNA repair mechanism implicated in carcinogenesis, although only 5% of metastatic PCa is affected. It is associated with aggressive disease. PD-1 inhibitors have been used in MMR-deficient tumors; thus, the MMR status should be tested in all metastatic PCa cases. A surrogate marker of defective DNA repair mechanisms is the tumor mutational burden. PDL-1 expression and intratumoral lymphocytes have ambivalent predictive value. Few experimental molecules have been so far proposed as potential biomarkers. Future research may further elucidate the role of DNA damage pathways in PCa, revealing new therapeutic targets and predictive biomarkers.
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Affiliation(s)
- Ioanna-Maria Grypari
- Cytology Department, Aretaieion University Hospital, National Kapodistrian University of Athens, 11528 Athens, Greece
| | - Vasiliki Tzelepi
- Department of Pathology, School of Medicine, University of Patras, 26504 Patras, Greece
| | - Kostis Gyftopoulos
- Department of Anatomy, School of Medicine, University of Patras, 26504 Patras, Greece
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Panzeri V, Pieraccioli M, Cesari E, de la Grange P, Sette C. CDK12/13 promote splicing of proximal introns by enhancing the interaction between RNA polymerase II and the splicing factor SF3B1. Nucleic Acids Res 2023; 51:5512-5526. [PMID: 37026485 PMCID: PMC10287901 DOI: 10.1093/nar/gkad258] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2022] [Revised: 02/17/2023] [Accepted: 03/28/2023] [Indexed: 04/08/2023] Open
Abstract
Transcription-associated cyclin-dependent kinases (CDKs) regulate the transcription cycle through sequential phosphorylation of RNA polymerase II (RNAPII). Herein, we report that dual inhibition of the highly homologous CDK12 and CDK13 impairs splicing of a subset of promoter-proximal introns characterized by weak 3' splice sites located at larger distance from the branchpoint. Nascent transcript analysis indicated that these introns are selectively retained upon pharmacological inhibition of CDK12/13 with respect to downstream introns of the same pre-mRNAs. Retention of these introns was also triggered by pladienolide B (PdB), an inhibitor of the U2 small nucelar ribonucleoprotein (snRNP) factor SF3B1 that recognizes the branchpoint. CDK12/13 activity promotes the interaction of SF3B1 with RNAPII phosphorylated on Ser2, and disruption of this interaction by treatment with the CDK12/13 inhibitor THZ531 impairs the association of SF3B1 with chromatin and its recruitment to the 3' splice site of these introns. Furthermore, by using suboptimal doses of THZ531 and PdB, we describe a synergic effect of these inhibitors on intron retention, cell cycle progression and cancer cell survival. These findings uncover a mechanism by which CDK12/13 couple RNA transcription and processing, and suggest that combined inhibition of these kinases and the spliceosome represents an exploitable anticancer approach.
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Affiliation(s)
- Valentina Panzeri
- Department of Neuroscience, Section of Human Anatomy, Catholic University of the Sacred Heart, Rome, Italy
| | - Marco Pieraccioli
- Department of Neuroscience, Section of Human Anatomy, Catholic University of the Sacred Heart, Rome, Italy
- Gemelli Science and Technology Park (GSTeP)-Organoids Research Core Facility, Fondazione Policlinico Agostino Gemelli IRCCS, Rome, Italy
| | - Eleonora Cesari
- Department of Neuroscience, Section of Human Anatomy, Catholic University of the Sacred Heart, Rome, Italy
- Gemelli Science and Technology Park (GSTeP)-Organoids Research Core Facility, Fondazione Policlinico Agostino Gemelli IRCCS, Rome, Italy
| | | | - Claudio Sette
- Department of Neuroscience, Section of Human Anatomy, Catholic University of the Sacred Heart, Rome, Italy
- Gemelli Science and Technology Park (GSTeP)-Organoids Research Core Facility, Fondazione Policlinico Agostino Gemelli IRCCS, Rome, Italy
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Araki S, Ohori M, Yugami M. Targeting pre-mRNA splicing in cancers: roles, inhibitors, and therapeutic opportunities. Front Oncol 2023; 13:1152087. [PMID: 37342192 PMCID: PMC10277747 DOI: 10.3389/fonc.2023.1152087] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2023] [Accepted: 05/09/2023] [Indexed: 06/22/2023] Open
Abstract
Accumulating evidence has indicated that pre-mRNA splicing plays critical roles in a variety of physiological processes, including development of multiple diseases. In particular, alternative splicing is profoundly involved in cancer progression through abnormal expression or mutation of splicing factors. Small-molecule splicing modulators have recently attracted considerable attention as a novel class of cancer therapeutics, and several splicing modulators are currently being developed for the treatment of patients with various cancers and are in the clinical trial stage. Novel molecular mechanisms modulating alternative splicing have proven to be effective for treating cancer cells resistant to conventional anticancer drugs. Furthermore, molecular mechanism-based combination strategies and patient stratification strategies for cancer treatment targeting pre-mRNA splicing must be considered for cancer therapy in the future. This review summarizes recent progress in the relationship between druggable splicing-related molecules and cancer, highlights small-molecule splicing modulators, and discusses future perspectives of splicing modulation for personalized and combination therapies in cancer treatment.
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Cesari E, Ciucci A, Pieraccioli M, Caggiano C, Nero C, Bonvissuto D, Sillano F, Buttarelli M, Piermattei A, Loverro M, Camarda F, Greco V, De Bonis M, Minucci A, Gallo D, Urbani A, Vizzielli G, Scambia G, Sette C. Dual inhibition of CDK12 and CDK13 uncovers actionable vulnerabilities in patient-derived ovarian cancer organoids. J Exp Clin Cancer Res 2023; 42:126. [PMID: 37202753 DOI: 10.1186/s13046-023-02682-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2023] [Accepted: 04/21/2023] [Indexed: 05/20/2023] Open
Abstract
BACKGROUND High grade serous ovarian cancer (HGSOC) is highly lethal, partly due to chemotherapy resistance and limited availability of targeted approaches. Cyclin dependent kinases 12 and 13 (CDK12/13) are promising therapeutic targets in human cancers, including HGSOC. Nevertheless, the effects of their inhibition in HGSOC and the potential synergy with other drugs are poorly known. METHODS We analyzed the effects of the CDK12/13 inhibitor THZ531 in HGSOC cells and patient-derived organoids (PDOs). RNA sequencing and quantitative PCR analyses were performed to identify the genome-wide effects of short-term CDK12/13 inhibition on the transcriptome of HGSOC cells. Viability assays with HGSOC cells and PDOs were performed to assess the efficacy of THZ531 as single agent or in combination with clinically relevant drugs. RESULTS The CDK12 and CDK13 genes are deregulated in HGSOC and their concomitant up-regulation with the oncogene MYC predicts poor prognosis. HGSOC cells and PDOs display high sensitivity to CDK12/13 inhibition, which synergizes with drugs in clinical use for HGSOC. Transcriptome analyses revealed cancer-relevant genes whose expression is repressed by dual CDK12/13 inhibition through impaired splicing. Combined treatment with THZ531 and inhibitors of pathways regulated by these cancer relevant genes (EGFR, RPTOR, ATRIP) exerted synergic effects on HGSOC PDO viability. CONCLUSIONS CDK12 and CDK13 represent valuable therapeutic targets for HGSOC. We uncovered a wide spectrum of CDK12/13 targets as potential therapeutic vulnerabilities for HGSOC. Moreover, our study indicates that CDK12/13 inhibition enhances the efficacy of approved drugs that are already in use for HGSOC or other human cancers.
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Affiliation(s)
- Eleonora Cesari
- Department of Neuroscience, Section of Human Anatomy, Catholic University of the Sacred Heart, 00168, Rome, Italy
- GSTeP Organoids Research Core Facility, IRCCS Fondazione Policlinico A. Gemelli, 00168, Rome, Italy
| | - Alessandra Ciucci
- GSTeP Organoids Research Core Facility, IRCCS Fondazione Policlinico A. Gemelli, 00168, Rome, Italy
- Department of Woman and Child Health and Public Health, Catholic University of the Sacred Heart, 00168, Rome, Italy
| | - Marco Pieraccioli
- Department of Neuroscience, Section of Human Anatomy, Catholic University of the Sacred Heart, 00168, Rome, Italy
- GSTeP Organoids Research Core Facility, IRCCS Fondazione Policlinico A. Gemelli, 00168, Rome, Italy
| | - Cinzia Caggiano
- Department of Neuroscience, Section of Human Anatomy, Catholic University of the Sacred Heart, 00168, Rome, Italy
- GSTeP Organoids Research Core Facility, IRCCS Fondazione Policlinico A. Gemelli, 00168, Rome, Italy
| | - Camilla Nero
- Department of Woman and Child Health and Public Health, Catholic University of the Sacred Heart, 00168, Rome, Italy
- Department of Woman and Child Health and Public Health, Gynecologic Oncology Unit, Fondazione Policlinico Universitario A. Gemelli IRCCS, Largo Francesco Vito 1, 00168, Rome, Italy
| | - Davide Bonvissuto
- Department of Neuroscience, Section of Human Anatomy, Catholic University of the Sacred Heart, 00168, Rome, Italy
| | - Francesca Sillano
- Department of Woman and Child Health and Public Health, Catholic University of the Sacred Heart, 00168, Rome, Italy
| | - Marianna Buttarelli
- Department of Woman and Child Health and Public Health, Catholic University of the Sacred Heart, 00168, Rome, Italy
- Unit of Translational Medicine for Woman and Child Health, IRCCS Fondazione Policlinico Universitario A. Gemelli, 00168, Rome, Italy
| | - Alessia Piermattei
- Department of Woman and Child Health and Public Health, Catholic University of the Sacred Heart, 00168, Rome, Italy
| | - Matteo Loverro
- Department of Woman and Child Health and Public Health, Catholic University of the Sacred Heart, 00168, Rome, Italy
- Department of Woman and Child Health and Public Health, Gynecologic Oncology Unit, Fondazione Policlinico Universitario A. Gemelli IRCCS, Largo Francesco Vito 1, 00168, Rome, Italy
| | - Floriana Camarda
- Department of Woman and Child Health and Public Health, Catholic University of the Sacred Heart, 00168, Rome, Italy
- Department of Woman and Child Health and Public Health, Gynecologic Oncology Unit, Fondazione Policlinico Universitario A. Gemelli IRCCS, Largo Francesco Vito 1, 00168, Rome, Italy
| | - Viviana Greco
- Department of Diagnostic and Laboratory Medicine, Unity of Chemistry, Biochemistry and Clinical Molecular Biology, Fondazione Policlinico Universitario A. Gemelli IRCCS, Rome, Italy
- Department of Basic Biotechnological Sciences, Intensive Care and Perioperative Clinics Research, Catholic University of the Sacred Heart, Università Cattolica del Sacro Cuore, Rome, Italy
| | - Maria De Bonis
- Department of Basic Biotechnological Sciences, Intensive Care and Perioperative Clinics Research, Catholic University of the Sacred Heart, Università Cattolica del Sacro Cuore, Rome, Italy
| | - Angelo Minucci
- Department of Basic Biotechnological Sciences, Intensive Care and Perioperative Clinics Research, Catholic University of the Sacred Heart, Università Cattolica del Sacro Cuore, Rome, Italy
| | - Daniela Gallo
- Department of Woman and Child Health and Public Health, Catholic University of the Sacred Heart, 00168, Rome, Italy
- Unit of Translational Medicine for Woman and Child Health, IRCCS Fondazione Policlinico Universitario A. Gemelli, 00168, Rome, Italy
| | - Andrea Urbani
- Department of Diagnostic and Laboratory Medicine, Unity of Chemistry, Biochemistry and Clinical Molecular Biology, Fondazione Policlinico Universitario A. Gemelli IRCCS, Rome, Italy
- Department of Basic Biotechnological Sciences, Intensive Care and Perioperative Clinics Research, Catholic University of the Sacred Heart, Università Cattolica del Sacro Cuore, Rome, Italy
| | - Giuseppe Vizzielli
- Department of Medical Area (DAME), University of Udine, Udine, Italy
- Clinic of Obstetrics and Gynecology, "Santa Maria Della Misericordia" University Hospital, Azienda Sanitaria Universitaria Friuli Centrale, Udine, Italy
| | - Giovanni Scambia
- Department of Woman and Child Health and Public Health, Catholic University of the Sacred Heart, 00168, Rome, Italy.
- Department of Woman and Child Health and Public Health, Gynecologic Oncology Unit, Fondazione Policlinico Universitario A. Gemelli IRCCS, Largo Francesco Vito 1, 00168, Rome, Italy.
| | - Claudio Sette
- Department of Neuroscience, Section of Human Anatomy, Catholic University of the Sacred Heart, 00168, Rome, Italy.
- GSTeP Organoids Research Core Facility, IRCCS Fondazione Policlinico A. Gemelli, 00168, Rome, Italy.
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Ford K, Munson BP, Fong SH, Panwala R, Chu WK, Rainaldi J, Plongthongkum N, Arunachalam V, Kostrowicki J, Meluzzi D, Kreisberg JF, Jensen-Pergakes K, VanArsdale T, Paul T, Tamayo P, Zhang K, Bienkowska J, Mali P, Ideker T. Multimodal perturbation analyses of cyclin-dependent kinases reveal a network of synthetic lethalities associated with cell-cycle regulation and transcriptional regulation. Sci Rep 2023; 13:7678. [PMID: 37169829 PMCID: PMC10175263 DOI: 10.1038/s41598-023-33329-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2022] [Accepted: 04/11/2023] [Indexed: 05/13/2023] Open
Abstract
Cell-cycle control is accomplished by cyclin-dependent kinases (CDKs), motivating extensive research into CDK targeting small-molecule drugs as cancer therapeutics. Here we use combinatorial CRISPR/Cas9 perturbations to uncover an extensive network of functional interdependencies among CDKs and related factors, identifying 43 synthetic-lethal and 12 synergistic interactions. We dissect CDK perturbations using single-cell RNAseq, for which we develop a novel computational framework to precisely quantify cell-cycle effects and diverse cell states orchestrated by specific CDKs. While pairwise disruption of CDK4/6 is synthetic-lethal, only CDK6 is required for normal cell-cycle progression and transcriptional activation. Multiple CDKs (CDK1/7/9/12) are synthetic-lethal in combination with PRMT5, independent of cell-cycle control. In-depth analysis of mRNA expression and splicing patterns provides multiple lines of evidence that the CDK-PRMT5 dependency is due to aberrant transcriptional regulation resulting in premature termination. These inter-dependencies translate to drug-drug synergies, with therapeutic implications in cancer and other diseases.
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Affiliation(s)
- Kyle Ford
- Department of Bioengineering, University of California San Diego, La Jolla, CA, 92093, USA
| | - Brenton P Munson
- Department of Bioengineering, University of California San Diego, La Jolla, CA, 92093, USA
- Department of Medicine, University of California San Diego, La Jolla, CA, 92093, USA
| | - Samson H Fong
- Department of Bioengineering, University of California San Diego, La Jolla, CA, 92093, USA
- Department of Medicine, University of California San Diego, La Jolla, CA, 92093, USA
| | - Rebecca Panwala
- Department of Bioengineering, University of California San Diego, La Jolla, CA, 92093, USA
| | - Wai Keung Chu
- Department of Bioengineering, University of California San Diego, La Jolla, CA, 92093, USA
| | - Joseph Rainaldi
- Department of Bioengineering, University of California San Diego, La Jolla, CA, 92093, USA
- Biomedical Sciences Program, University of California San Diego, La Jolla, CA, 92093, USA
| | - Nongluk Plongthongkum
- Department of Bioengineering, University of California San Diego, La Jolla, CA, 92093, USA
| | | | | | - Dario Meluzzi
- Department of Medicine, University of California San Diego, La Jolla, CA, 92093, USA
| | - Jason F Kreisberg
- Department of Medicine, University of California San Diego, La Jolla, CA, 92093, USA
| | | | - Todd VanArsdale
- Pfizer Inc, 10555 Science Center Drive, San Diego, CA, 92121, USA
| | - Thomas Paul
- Pfizer Inc, 10555 Science Center Drive, San Diego, CA, 92121, USA
| | - Pablo Tamayo
- Department of Medicine, University of California San Diego, La Jolla, CA, 92093, USA
| | - Kun Zhang
- Department of Bioengineering, University of California San Diego, La Jolla, CA, 92093, USA
| | | | - Prashant Mali
- Department of Bioengineering, University of California San Diego, La Jolla, CA, 92093, USA.
| | - Trey Ideker
- Department of Bioengineering, University of California San Diego, La Jolla, CA, 92093, USA.
- Department of Medicine, University of California San Diego, La Jolla, CA, 92093, USA.
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35
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van der Noord VE, van der Stel W, Louwerens G, Verhoeven D, Kuiken HJ, Lieftink C, Grandits M, Ecker GF, Beijersbergen RL, Bouwman P, Le Dévédec SE, van de Water B. Systematic screening identifies ABCG2 as critical factor underlying synergy of kinase inhibitors with transcriptional CDK inhibitors. Breast Cancer Res 2023; 25:51. [PMID: 37147730 PMCID: PMC10161439 DOI: 10.1186/s13058-023-01648-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2023] [Accepted: 04/07/2023] [Indexed: 05/07/2023] Open
Abstract
BACKGROUND Triple-negative breast cancer (TNBC) is a subtype of breast cancer with limited treatment options and poor clinical prognosis. Inhibitors of transcriptional CDKs are currently under thorough investigation for application in the treatment of multiple cancer types, including breast cancer. These studies have raised interest in combining these inhibitors, including CDK12/13 inhibitor THZ531, with a variety of other anti-cancer agents. However, the full scope of these potential synergistic interactions of transcriptional CDK inhibitors with kinase inhibitors has not been systematically investigated. Moreover, the mechanisms behind these previously described synergistic interactions remain largely elusive. METHODS Kinase inhibitor combination screenings were performed to identify kinase inhibitors that synergize with CDK7 inhibitor THZ1 and CDK12/13 inhibitor THZ531 in TNBC cell lines. CRISPR-Cas9 knockout screening and transcriptomic evaluation of resistant versus sensitive cell lines were performed to identify genes critical for THZ531 resistance. RNA sequencing analysis after treatment with individual and combined synergistic treatments was performed to gain further insights into the mechanism of this synergy. Kinase inhibitor screening in combination with visualization of ABCG2-substrate pheophorbide A was used to identify kinase inhibitors that inhibit ABCG2. Multiple transcriptional CDK inhibitors were evaluated to extend the significance of the found mechanism to other transcriptional CDK inhibitors. RESULTS We show that a very high number of tyrosine kinase inhibitors synergize with the CDK12/13 inhibitor THZ531. Yet, we identified the multidrug transporter ABCG2 as key determinant of THZ531 resistance in TNBC cells. Mechanistically, we demonstrate that most synergistic kinase inhibitors block ABCG2 function, thereby sensitizing cells to transcriptional CDK inhibitors, including THZ531. Accordingly, these kinase inhibitors potentiate the effects of THZ531, disrupting gene expression and increasing intronic polyadenylation. CONCLUSION Overall, this study demonstrates the critical role of ABCG2 in limiting the efficacy of transcriptional CDK inhibitors and identifies multiple kinase inhibitors that disrupt ABCG2 transporter function and thereby synergize with these CDK inhibitors. These findings therefore further facilitate the development of new (combination) therapies targeting transcriptional CDKs and highlight the importance of evaluating the role of ABC transporters in synergistic drug-drug interactions in general.
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Affiliation(s)
- Vera E van der Noord
- Division of Drug Discovery and Safety, Leiden Academic Centre for Drug Research, Leiden University, Einsteinweg 55, 2333 CC, Leiden, The Netherlands
| | - Wanda van der Stel
- Division of Drug Discovery and Safety, Leiden Academic Centre for Drug Research, Leiden University, Einsteinweg 55, 2333 CC, Leiden, The Netherlands
| | - Gijs Louwerens
- Division of Drug Discovery and Safety, Leiden Academic Centre for Drug Research, Leiden University, Einsteinweg 55, 2333 CC, Leiden, The Netherlands
| | - Danielle Verhoeven
- Division of Drug Discovery and Safety, Leiden Academic Centre for Drug Research, Leiden University, Einsteinweg 55, 2333 CC, Leiden, The Netherlands
| | - Hendrik J Kuiken
- Division of Molecular Carcinogenesis, The NKI Robotics and Screening Center, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Cor Lieftink
- Division of Molecular Carcinogenesis, The NKI Robotics and Screening Center, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Melanie Grandits
- Department of Pharmaceutical Sciences, University of Vienna, Vienna, Austria
| | - Gerhard F Ecker
- Department of Pharmaceutical Sciences, University of Vienna, Vienna, Austria
| | - Roderick L Beijersbergen
- Division of Molecular Carcinogenesis, The NKI Robotics and Screening Center, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Peter Bouwman
- Division of Drug Discovery and Safety, Leiden Academic Centre for Drug Research, Leiden University, Einsteinweg 55, 2333 CC, Leiden, The Netherlands
| | - Sylvia E Le Dévédec
- Division of Drug Discovery and Safety, Leiden Academic Centre for Drug Research, Leiden University, Einsteinweg 55, 2333 CC, Leiden, The Netherlands
| | - Bob van de Water
- Division of Drug Discovery and Safety, Leiden Academic Centre for Drug Research, Leiden University, Einsteinweg 55, 2333 CC, Leiden, The Netherlands.
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36
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Zhang G, Lan B, Zhang X, Lin M, Liu Y, Chen J, Guo F. AR-A014418 regulates intronic polyadenylation and transcription of PD-L1 through inhibiting CDK12 and CDK13 in tumor cells. J Immunother Cancer 2023; 11:jitc-2022-006483. [PMID: 37164450 PMCID: PMC10174041 DOI: 10.1136/jitc-2022-006483] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/30/2023] [Indexed: 05/12/2023] Open
Abstract
BACKGROUND Immune checkpoint molecules, especially programmed death 1 (PD-1) and its ligand, programmed death ligand 1 (PD-L1), protect tumor cells from T cell-mediated killing. Immune checkpoint inhibitors, designed to restore the antitumor immunosurveillance, have exhibited significant clinical benefits for patients with certain cancer types. Nevertheless, the relatively low response rate and acquisition of resistance greatly limit their clinical applications. A deeper understanding of the regulatory mechanisms of PD-L1 protein expression and activity will help to develop more effective therapeutic strategies. METHODS The effects of AR-A014418 and THZ531 on PD-L1 expression were detected by western blot, reverse transcription-quantitative polymerase chain reaction (RT-qPCR) and flow cytometry. In vitro kinase assays with recombinant proteins were performed to confirm that AR-A014418 functioned as a CDK12 and CDK13 dual inhibitor. The roles of CDK12 and CDK13 in intronic polyadenylation (IPA) and transcription of PD-L1 were determined via RNA interference or protein overexpression. T-cell cytotoxicity assays were used to validate the activation of antitumor immunity by AR-A014418 and THZ531. RESULTS AR-A014418 inhibits CDK12 to enhance the IPA, and inhibits CDK13 to repress the transcription of PD-L1. IPA generates a secreted PD-L1 isoform (PD-L1-v4). The extent of IPA was not enough to reduce full-length PD-L1 expression obviously. Only the superposition of enhancing IPA and repressing transcription (dual inhibition of CDK12 and CDK13) dramatically suppresses full-length PD-L1 induction by interferon-γ. AR-A014418 and THZ531 could potentiate T-cell cytotoxicity against tumor cells. CONCLUSIONS Our work identifies a new regulatory pathway for PD-L1 expression and discovers CDK12 and CDK13 as promising drug targets for immune modulation and combined therapeutic strategies.
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Affiliation(s)
- Ganggang Zhang
- Key Laboratory of Systems Biomedicine (Ministry of Education), Shanghai Center for Systems Biomedicine, Shanghai Jiao Tong University, Shanghai, China
| | - Bin Lan
- Fujian Provincial Key Laboratory of Tumor Biotherapy, Clinical Oncology School of Fujian Medical University, Fujian Cancer Hospital, Fuzhou, Fujian, China
| | - Xin Zhang
- Key Laboratory of Systems Biomedicine (Ministry of Education), Shanghai Center for Systems Biomedicine, Shanghai Jiao Tong University, Shanghai, China
| | - Mengyao Lin
- Key Laboratory of Systems Biomedicine (Ministry of Education), Shanghai Center for Systems Biomedicine, Shanghai Jiao Tong University, Shanghai, China
| | - Yi Liu
- Department of Radiation Oncology, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Junsong Chen
- Key Laboratory of Systems Biomedicine (Ministry of Education), Shanghai Center for Systems Biomedicine, Shanghai Jiao Tong University, Shanghai, China
| | - Fang Guo
- Key Laboratory of Systems Biomedicine (Ministry of Education), Shanghai Center for Systems Biomedicine, Shanghai Jiao Tong University, Shanghai, China
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37
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Insco ML, Abraham BJ, Dubbury SJ, Kaltheuner IH, Dust S, Wu C, Chen KY, Liu D, Bellaousov S, Cox AM, Martin BJ, Zhang T, Ludwig CG, Fabo T, Modhurima R, Esgdaille DE, Henriques T, Brown KM, Chanock SJ, Geyer M, Adelman K, Sharp PA, Young RA, Boutz PL, Zon LI. Oncogenic CDK13 mutations impede nuclear RNA surveillance. Science 2023; 380:eabn7625. [PMID: 37079685 PMCID: PMC10184553 DOI: 10.1126/science.abn7625] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2021] [Accepted: 02/27/2023] [Indexed: 04/22/2023]
Abstract
RNA surveillance pathways detect and degrade defective transcripts to ensure RNA fidelity. We found that disrupted nuclear RNA surveillance is oncogenic. Cyclin-dependent kinase 13 (CDK13) is mutated in melanoma, and patient-mutated CDK13 accelerates zebrafish melanoma. CDK13 mutation causes aberrant RNA stabilization. CDK13 is required for ZC3H14 phosphorylation, which is necessary and sufficient to promote nuclear RNA degradation. Mutant CDK13 fails to activate nuclear RNA surveillance, causing aberrant protein-coding transcripts to be stabilized and translated. Forced aberrant RNA expression accelerates melanoma in zebrafish. We found recurrent mutations in genes encoding nuclear RNA surveillance components in many malignancies, establishing nuclear RNA surveillance as a tumor-suppressive pathway. Activating nuclear RNA surveillance is crucial to avoid accumulation of aberrant RNAs and their ensuing consequences in development and disease.
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Affiliation(s)
- Megan L. Insco
- Stem Cell Program and Division of Hematology/Oncology, Boston Children’s Hospital, Howard Hughes Medical Institute, Boston, MA, 02115, USA
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, 02115, USA
| | - Brian J. Abraham
- Department of Computational Biology, St. Jude Children’s Research Hospital, Memphis, TN, 38105, USA
| | - Sara J. Dubbury
- The David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
| | - Ines H. Kaltheuner
- Institute of Structural Biology, University of Bonn, Bonn, 53127, Germany
| | - Sofia Dust
- Institute of Structural Biology, University of Bonn, Bonn, 53127, Germany
| | - Constance Wu
- Stem Cell Program and Division of Hematology/Oncology, Boston Children’s Hospital, Howard Hughes Medical Institute, Boston, MA, 02115, USA
| | - Kevin Y. Chen
- Stem Cell Program and Division of Hematology/Oncology, Boston Children’s Hospital, Howard Hughes Medical Institute, Boston, MA, 02115, USA
| | - David Liu
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, 02115, USA
| | - Stanislav Bellaousov
- University of Rochester School of Medicine and Dentistry, Rochester, NY, 14642, USA
| | - Anna M. Cox
- Stem Cell Program and Division of Hematology/Oncology, Boston Children’s Hospital, Howard Hughes Medical Institute, Boston, MA, 02115, USA
| | - Benjamin J.E. Martin
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, 02115, USA
| | - Tongwu Zhang
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, MD, 20850, USA
| | - Calvin G. Ludwig
- Stem Cell Program and Division of Hematology/Oncology, Boston Children’s Hospital, Howard Hughes Medical Institute, Boston, MA, 02115, USA
| | - Tania Fabo
- Stem Cell Program and Division of Hematology/Oncology, Boston Children’s Hospital, Howard Hughes Medical Institute, Boston, MA, 02115, USA
| | - Rodsy Modhurima
- Stem Cell Program and Division of Hematology/Oncology, Boston Children’s Hospital, Howard Hughes Medical Institute, Boston, MA, 02115, USA
| | - Dakarai E. Esgdaille
- University of Rochester School of Medicine and Dentistry, Rochester, NY, 14642, USA
| | - Telmo Henriques
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, 02115, USA
| | - Kevin M. Brown
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, MD, 20850, USA
| | - Stephen J. Chanock
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, MD, 20850, USA
| | - Matthias Geyer
- Institute of Structural Biology, University of Bonn, Bonn, 53127, Germany
| | - Karen Adelman
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, 02115, USA
| | - Phillip A. Sharp
- The David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
| | - Richard A. Young
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
- Whitehead Institute for Biomedical Research, Massachusetts Institute of Technology, Cambridge, MA, 02142, USA
| | - Paul L. Boutz
- University of Rochester School of Medicine and Dentistry, Rochester, NY, 14642, USA
- Center for RNA Biology, University of Rochester, Rochester, NY, 14642, USA
- Center for Biomedical Informatics, University of Rochester, Rochester, NY, 14642, USA
| | - Leonard I. Zon
- Stem Cell Program and Division of Hematology/Oncology, Boston Children’s Hospital, Howard Hughes Medical Institute, Boston, MA, 02115, USA
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38
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Fisher RP. Tumor suppression by RNA surveillance. Science 2023; 380:240-241. [PMID: 37079669 DOI: 10.1126/science.adh4051] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/22/2023]
Abstract
A cyclin-dependent kinase triggers degradation of prematurely terminated RNAs.
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Affiliation(s)
- Robert P Fisher
- Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
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39
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Mimoso CA, Adelman K. U1 snRNP increases RNA Pol II elongation rate to enable synthesis of long genes. Mol Cell 2023; 83:1264-1279.e10. [PMID: 36965480 PMCID: PMC10135401 DOI: 10.1016/j.molcel.2023.03.002] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2022] [Revised: 02/06/2023] [Accepted: 02/28/2023] [Indexed: 03/27/2023]
Abstract
The expansion of introns within mammalian genomes poses a challenge for the production of full-length messenger RNAs (mRNAs), with increasing evidence that these long AT-rich sequences present obstacles to transcription. Here, we investigate RNA polymerase II (RNAPII) elongation at high resolution in mammalian cells and demonstrate that RNAPII transcribes faster across introns. Moreover, we find that this acceleration requires the association of U1 snRNP (U1) with the elongation complex at 5' splice sites. The role of U1 to stimulate elongation rate through introns reduces the frequency of both premature termination and transcriptional arrest, thereby dramatically increasing RNA production. We further show that changes in RNAPII elongation rate due to AT content and U1 binding explain previous reports of pausing or termination at splice junctions and the edge of CpG islands. We propose that U1-mediated acceleration of elongation has evolved to mitigate the risks that long AT-rich introns pose to transcript completion.
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Affiliation(s)
- Claudia A Mimoso
- Department of Biological Chemistry and Molecular Pharmacology, Blavatnik Institute, Harvard Medical School, Boston, MA 02115, USA
| | - Karen Adelman
- Department of Biological Chemistry and Molecular Pharmacology, Blavatnik Institute, Harvard Medical School, Boston, MA 02115, USA; Ludwig Center at Harvard, Boston, MA 02115, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA.
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40
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Maity TK, Kim EY, Cultraro CM, Venugopalan A, Khare L, Poddutoori R, Marappan S, Syed SD, Telford WG, Samajdar S, Ramachandra M, Guha U. Novel CDK12/13 Inhibitors AU-15506 and AU-16770 Are Potent Anti-Cancer Agents in EGFR Mutant Lung Adenocarcinoma with and without Osimertinib Resistance. Cancers (Basel) 2023; 15:cancers15082263. [PMID: 37190191 DOI: 10.3390/cancers15082263] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2023] [Accepted: 04/07/2023] [Indexed: 05/17/2023] Open
Abstract
Osimertinib is a third-generation epidermal growth factor receptor and tyrosine kinase inhibitor (EGFR-TKI) approved for the treatment of lung adenocarcinoma patients harboring EGFR mutations. However, acquired resistance to this targeted therapy is inevitable, leading to disease relapse within a few years. Therefore, understanding the molecular mechanisms of osimertinib resistance and identifying novel targets to overcome such resistance are unmet needs of cancer patients. Here, we investigated the efficacy of two novel CDK12/13 inhibitors, AU-15506 and AU-16770, in osimertinib-resistant EGFR mutant lung adenocarcinoma cells in culture and xenograft models in vivo. We demonstrate that these drugs, either alone or in combination with osimertinib, are potent inhibitors of osimertinib-resistant as well as -sensitive lung adenocarcinoma cells in culture. Interestingly, only the CDK12/13 inhibitor in combination with osimertinib, although not as monotherapy, suppresses the growth of resistant tumors in xenograft models in vivo. Taken together, the results of this study suggest that inhibition of CDK12/13 in combination with osimertinib has the potential to overcome osimertinib resistance in EGFR mutant lung adenocarcinoma patients.
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Affiliation(s)
- Tapan K Maity
- Thoracic and GI Malignancies Branch, CCR, NCI, NIH, Bethesda, MD 20892, USA
| | - Eun Young Kim
- Thoracic and GI Malignancies Branch, CCR, NCI, NIH, Bethesda, MD 20892, USA
| | | | | | - Leena Khare
- Aurigene Discovery Technologies Ltd., Bangalore 560100, India
| | | | | | - Samiulla D Syed
- Aurigene Discovery Technologies Ltd., Bangalore 560100, India
| | - William G Telford
- Experimental Transplantation & Immunotherapy Branch, CCR, NCI, NIH, Bethesda, MD 20892, USA
| | | | | | - Udayan Guha
- Thoracic and GI Malignancies Branch, CCR, NCI, NIH, Bethesda, MD 20892, USA
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41
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Alternative Polyadenylation Is a Novel Strategy for the Regulation of Gene Expression in Response to Stresses in Plants. Int J Mol Sci 2023; 24:ijms24054727. [PMID: 36902157 PMCID: PMC10003127 DOI: 10.3390/ijms24054727] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2022] [Revised: 02/13/2023] [Accepted: 02/17/2023] [Indexed: 03/05/2023] Open
Abstract
Precursor message RNA requires processing to generate mature RNA. Cleavage and polyadenylation at the 3'-end in the maturation of mRNA is one of key processing steps in eukaryotes. The polyadenylation (poly(A)) tail of mRNA is an essential feature that is required to mediate its nuclear export, stability, translation efficiency, and subcellular localization. Most genes have at least two mRNA isoforms via alternative splicing (AS) or alternative polyadenylation (APA), which increases the diversity of transcriptome and proteome. However, most previous studies have focused on the role of alternative splicing on the regulation of gene expression. In this review, we summarize the recent advances concerning APA in the regulation of gene expression and in response to stresses in plants. We also discuss the mechanisms for the regulation of APA for plants in the adaptation to stress responses, and suggest that APA is a novel strategy for the adaptation to environmental changes and response to stresses in plants.
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42
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Wang Z, Mačáková M, Bugai A, Kuznetsov SG, Hassinen A, Lenasi T, Potdar S, Friedel CC, Barborič M. P-TEFb promotes cell survival upon p53 activation by suppressing intrinsic apoptosis pathway. Nucleic Acids Res 2023; 51:1687-1706. [PMID: 36727434 PMCID: PMC9976905 DOI: 10.1093/nar/gkad001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2022] [Revised: 12/27/2022] [Accepted: 01/03/2023] [Indexed: 02/03/2023] Open
Abstract
Positive transcription elongation factor b (P-TEFb) is the crucial player in RNA polymerase II (Pol II) pause release that has emerged as a promising target in cancer. Because single-agent therapy may fail to deliver durable clinical response, targeting of P-TEFb shall benefit when deployed as a combination therapy. We screened a comprehensive oncology library and identified clinically relevant antimetabolites and Mouse double minute 2 homolog (MDM2) inhibitors as top compounds eliciting p53-dependent death of colorectal cancer cells in synergy with selective inhibitors of P-TEFb. While the targeting of P-TEFb augments apoptosis by anti-metabolite 5-fluorouracil, it switches the fate of cancer cells by the non-genotoxic MDM2 inhibitor Nutlin-3a from cell-cycle arrest to apoptosis. Mechanistically, the fate switching is enabled by the induction of p53-dependent pro-apoptotic genes and repression of P-TEFb-dependent pro-survival genes of the PI3K-AKT signaling cascade, which stimulates caspase 9 and intrinsic apoptosis pathway in BAX/BAK-dependent manner. Finally, combination treatments trigger apoptosis of cancer cell spheroids. Together, co-targeting of P-TEFb and suppressors of intrinsic apoptosis could become a viable strategy to eliminate cancer cells.
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Affiliation(s)
- Zhijia Wang
- Department of Biochemistry and Developmental Biology, University of Helsinki, Helsinki FIN-00014, Finland
| | - Monika Mačáková
- Department of Biochemistry and Developmental Biology, University of Helsinki, Helsinki FIN-00014, Finland
| | - Andrii Bugai
- Department of Biochemistry and Developmental Biology, University of Helsinki, Helsinki FIN-00014, Finland.,Department of Molecular Biology and Genetics, Aarhus University, 8000 Aarhus C, Denmark
| | - Sergey G Kuznetsov
- High-Throughput Biomedicine Unit (HTB), Institute for Molecular Medicine Finland (FIMM), University of Helsinki, Helsinki FIN-00014, Finland
| | - Antti Hassinen
- High Content Imaging and Analysis Unit (HCA), Institute for Molecular Medicine Finland (FIMM), University of Helsinki, Helsinki FIN-00014, Finland
| | - Tina Lenasi
- Department of Biochemistry and Developmental Biology, University of Helsinki, Helsinki FIN-00014, Finland
| | - Swapnil Potdar
- High-Throughput Biomedicine Unit (HTB), Institute for Molecular Medicine Finland (FIMM), University of Helsinki, Helsinki FIN-00014, Finland
| | - Caroline C Friedel
- Institute for Informatics, Ludwig-Maximilians-Universität München, 80333 Munich, Germany
| | - Matjaž Barborič
- Department of Biochemistry and Developmental Biology, University of Helsinki, Helsinki FIN-00014, Finland
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Hope I, Endicott JA, Watt JE. Emerging approaches to CDK inhibitor development, a structural perspective. RSC Chem Biol 2023; 4:146-164. [PMID: 36794018 PMCID: PMC9906319 DOI: 10.1039/d2cb00201a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2022] [Accepted: 12/06/2022] [Indexed: 12/15/2022] Open
Abstract
Aberrant activity of the cyclin-dependent kinase family is frequently noted in a number of diseases identifying them as potential targets for drug development. However, current CDK inhibitors lack specificity owing to the high sequence and structural conservation of the ATP binding cleft across family members, highlighting the necessity of finding novel modes of CDK inhibition. The wealth of structural information regarding CDK assemblies and inhibitor complexes derived from X-ray crystallographic studies has been recently complemented through the use of cryo-electron microscopy. These recent advances have provided insights into the functional roles and regulatory mechanisms of CDKs and their interaction partners. This review explores the conformational malleability of the CDK subunit, the importance of SLiM recognition sites in CDK complexes, the progress made in chemically induced CDK degradation and how these studies can contribute to CDK inhibitor design. Additionally, fragment-based drug discovery can be utilised to identify small molecules that bind to allosteric sites on the CDK surface employing interactions which mimic those of native protein-protein interactions. These recent structural advances in CDK inhibitor mechanisms and in chemical probes which do not occupy the orthosteric ATP binding site can provide important insights for targeted CDK therapies.
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Affiliation(s)
- Ian Hope
- Translational and Clinical Research Institute, Faculty of Medical Sciences, Newcastle University, Paul O'Gorman Building, Framlington Place Newcastle upon Tyne NE2 4HH UK
| | - Jane A Endicott
- Translational and Clinical Research Institute, Faculty of Medical Sciences, Newcastle University, Paul O'Gorman Building, Framlington Place Newcastle upon Tyne NE2 4HH UK
| | - Jessica E Watt
- Translational and Clinical Research Institute, Faculty of Medical Sciences, Newcastle University, Paul O'Gorman Building, Framlington Place Newcastle upon Tyne NE2 4HH UK
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44
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Wu W, Yu S, Yu X. Transcription-associated cyclin-dependent kinase 12 (CDK12) as a potential target for cancer therapy. Biochim Biophys Acta Rev Cancer 2023; 1878:188842. [PMID: 36460141 DOI: 10.1016/j.bbcan.2022.188842] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2022] [Revised: 11/24/2022] [Accepted: 11/25/2022] [Indexed: 12/05/2022]
Abstract
Cyclin-dependent kinase 12 (CDK12), a transcription-related cyclin dependent kinase (CDK), plays a momentous part in multitudinous biological functions, such as replication, transcription initiation to elongation and termination, precursor mRNA (pre-mRNA) splicing, intron polyadenylation (IPA), and translation. CDK12 can act as a tumour suppressor or oncogene in disparate cellular environments, and its dysregulation likely provokes tumorigenesis. A comprehensive understanding of CDK12 will tremendously facilitate the exploitation of novel tactics for the treatment and precaution of cancer. Currently, CDK12 inhibitors are nonspecific and nonselective, which profoundly hinders the pharmacological target validation and drug exploitation process. Herein, we summarize the newly comprehension of the biological functions of CDK12 with a focus on recently emerged advancements of CDK12-associated therapeutic approaches in cancers.
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Affiliation(s)
- Wence Wu
- Departments of Orthopedics, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China; Department of Etiology and Carcinogenesis, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China; State Key Laboratory of Molecular Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China; Beijing Key Laboratory for Carcinogenesis and Cancer Prevention, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Shengji Yu
- Departments of Orthopedics, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China.
| | - Xiying Yu
- Department of Etiology and Carcinogenesis, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China; State Key Laboratory of Molecular Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China; Beijing Key Laboratory for Carcinogenesis and Cancer Prevention, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China.
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45
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The PNUTS-PP1 complex acts as an intrinsic barrier to herpesvirus KSHV gene expression and replication. Nat Commun 2022; 13:7447. [PMID: 36460671 PMCID: PMC9718767 DOI: 10.1038/s41467-022-35268-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2022] [Accepted: 11/24/2022] [Indexed: 12/03/2022] Open
Abstract
Control of RNA Polymerase II (pol II) elongation is a critical component of gene expression in mammalian cells. The PNUTS-PP1 complex controls elongation rates, slowing pol II after polyadenylation sites to promote termination. The Kaposi's sarcoma-associated herpesvirus (KSHV) co-opts pol II to express its genes, but little is known about its regulation of pol II elongation. We identified PNUTS as a suppressor of a KSHV reporter gene in a genome-wide CRISPR screen. PNUTS depletion enhances global KSHV gene expression and overall viral replication. Mechanistically, PNUTS requires PP1 interaction, binds viral RNAs downstream of polyadenylation sites, and restricts transcription readthrough of viral genes. Surprisingly, PNUTS also represses productive elongation at the 5´ ends of the KSHV reporter and the KSHV T1.4 RNA. From these data, we conclude that PNUTS' activity constitutes an intrinsic barrier to KSHV replication likely by suppressing pol II elongation at promoter-proximal regions.
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46
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Mitschka S, Mayr C. Context-specific regulation and function of mRNA alternative polyadenylation. Nat Rev Mol Cell Biol 2022; 23:779-796. [PMID: 35798852 PMCID: PMC9261900 DOI: 10.1038/s41580-022-00507-5] [Citation(s) in RCA: 84] [Impact Index Per Article: 42.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/02/2022] [Indexed: 02/08/2023]
Abstract
Alternative cleavage and polyadenylation (APA) is a widespread mechanism to generate mRNA isoforms with alternative 3' untranslated regions (UTRs). The expression of alternative 3' UTR isoforms is highly cell type specific and is further controlled in a gene-specific manner by environmental cues. In this Review, we discuss how the dynamic, fine-grained regulation of APA is accomplished by several mechanisms, including cis-regulatory elements in RNA and DNA and factors that control transcription, pre-mRNA cleavage and post-transcriptional processes. Furthermore, signalling pathways modulate the activity of these factors and integrate APA into gene regulatory programmes. Dysregulation of APA can reprogramme the outcome of signalling pathways and thus can control cellular responses to environmental changes. In addition to the regulation of protein abundance, APA has emerged as a major regulator of mRNA localization and the spatial organization of protein synthesis. This role enables the regulation of protein function through the addition of post-translational modifications or the formation of protein-protein interactions. We further discuss recent transformative advances in single-cell RNA sequencing and CRISPR-Cas technologies, which enable the mapping and functional characterization of alternative 3' UTRs in any biological context. Finally, we discuss new APA-based RNA therapeutics, including compounds that target APA in cancer and therapeutic genome editing of degenerative diseases.
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Affiliation(s)
- Sibylle Mitschka
- Cancer Biology and Genetics Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Christine Mayr
- Cancer Biology and Genetics Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA.
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Houles T, Lavoie G, Nourreddine S, Cheung W, Vaillancourt-Jean É, Guérin CM, Bouttier M, Grondin B, Lin S, Saba-El-Leil MK, Angers S, Meloche S, Roux PP. CDK12 is hyperactivated and a synthetic-lethal target in BRAF-mutated melanoma. Nat Commun 2022; 13:6457. [PMID: 36309522 PMCID: PMC9617877 DOI: 10.1038/s41467-022-34179-8] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2021] [Accepted: 10/13/2022] [Indexed: 12/25/2022] Open
Abstract
Melanoma is the deadliest form of skin cancer and considered intrinsically resistant to chemotherapy. Nearly all melanomas harbor mutations that activate the RAS/mitogen-activated protein kinase (MAPK) pathway, which contributes to drug resistance via poorly described mechanisms. Herein we show that the RAS/MAPK pathway regulates the activity of cyclin-dependent kinase 12 (CDK12), which is a transcriptional CDK required for genomic stability. We find that melanoma cells harbor constitutively high CDK12 activity, and that its inhibition decreases the expression of long genes containing multiple exons, including many genes involved in DNA repair. Conversely, our results show that CDK12 inhibition promotes the expression of short genes with few exons, including many growth-promoting genes regulated by the AP-1 and NF-κB transcription factors. Inhibition of these pathways strongly synergize with CDK12 inhibitors to suppress melanoma growth, suggesting promising drug combinations for more effective melanoma treatment.
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Affiliation(s)
- Thibault Houles
- grid.14848.310000 0001 2292 3357Institute for Research in Immunology and Cancer (IRIC), Université de Montréal, Montreal, 2950, Chemin de la Polytechnique, Montréal, QC H3T 1J4 Canada
| | - Geneviève Lavoie
- grid.14848.310000 0001 2292 3357Institute for Research in Immunology and Cancer (IRIC), Université de Montréal, Montreal, 2950, Chemin de la Polytechnique, Montréal, QC H3T 1J4 Canada
| | - Sami Nourreddine
- grid.14848.310000 0001 2292 3357Institute for Research in Immunology and Cancer (IRIC), Université de Montréal, Montreal, 2950, Chemin de la Polytechnique, Montréal, QC H3T 1J4 Canada ,grid.266100.30000 0001 2107 4242Present Address: Department of Bioengineering, University of California, San Diego, San Diego, CA USA
| | - Winnie Cheung
- grid.14848.310000 0001 2292 3357Institute for Research in Immunology and Cancer (IRIC), Université de Montréal, Montreal, 2950, Chemin de la Polytechnique, Montréal, QC H3T 1J4 Canada
| | - Éric Vaillancourt-Jean
- grid.14848.310000 0001 2292 3357Institute for Research in Immunology and Cancer (IRIC), Université de Montréal, Montreal, 2950, Chemin de la Polytechnique, Montréal, QC H3T 1J4 Canada
| | - Célia M. Guérin
- grid.14848.310000 0001 2292 3357Institute for Research in Immunology and Cancer (IRIC), Université de Montréal, Montreal, 2950, Chemin de la Polytechnique, Montréal, QC H3T 1J4 Canada
| | - Mathieu Bouttier
- grid.14848.310000 0001 2292 3357Institute for Research in Immunology and Cancer (IRIC), Université de Montréal, Montreal, 2950, Chemin de la Polytechnique, Montréal, QC H3T 1J4 Canada
| | - Benoit Grondin
- grid.14848.310000 0001 2292 3357Institute for Research in Immunology and Cancer (IRIC), Université de Montréal, Montreal, 2950, Chemin de la Polytechnique, Montréal, QC H3T 1J4 Canada ,grid.38678.320000 0001 2181 0211Present Address: Department of Biological Sciences, Université du Québec à Montréal, Montreal, QC Canada
| | - Sichun Lin
- grid.17063.330000 0001 2157 2938Donnelly Centre for Cellular & Biomolecular Research, Temerty Faculty of Medicine, University of Toronto, Toronto, ON Canada
| | - Marc K. Saba-El-Leil
- grid.14848.310000 0001 2292 3357Institute for Research in Immunology and Cancer (IRIC), Université de Montréal, Montreal, 2950, Chemin de la Polytechnique, Montréal, QC H3T 1J4 Canada
| | - Stephane Angers
- grid.17063.330000 0001 2157 2938Donnelly Centre for Cellular & Biomolecular Research, Temerty Faculty of Medicine, University of Toronto, Toronto, ON Canada ,grid.17063.330000 0001 2157 2938Leslie Dan Faculty of Pharmacy, University of Toronto, Toronto, ON Canada ,grid.17063.330000 0001 2157 2938Department of Biochemistry, Temerty Faculty of Medicine, University of Toronto, Toronto, ON Canada
| | - Sylvain Meloche
- grid.14848.310000 0001 2292 3357Institute for Research in Immunology and Cancer (IRIC), Université de Montréal, Montreal, 2950, Chemin de la Polytechnique, Montréal, QC H3T 1J4 Canada ,grid.14848.310000 0001 2292 3357Department of Pharmacology and Physiology, Faculty of Medicine, Université de Montréal, Montreal, QC Canada
| | - Philippe P. Roux
- grid.14848.310000 0001 2292 3357Institute for Research in Immunology and Cancer (IRIC), Université de Montréal, Montreal, 2950, Chemin de la Polytechnique, Montréal, QC H3T 1J4 Canada ,grid.14848.310000 0001 2292 3357Department of Pathology and Cell Biology, Faculty of Medicine, Université de Montréal, Montreal, QC Canada
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Wang B, Wang Y, Wen Y, Zhang YL, Ni WJ, Tang TT, Cao JY, Yin Q, Jiang W, Yin D, Li ZL, Lv LL, Liu BC. Tubular-specific CDK12 knockout causes a defect in urine concentration due to premature cleavage of the slc12a1 gene. Mol Ther 2022; 30:3300-3312. [PMID: 35581939 PMCID: PMC9552909 DOI: 10.1016/j.ymthe.2022.05.012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2021] [Revised: 04/21/2022] [Accepted: 05/11/2022] [Indexed: 11/27/2022] Open
Abstract
Cyclin-dependent kinase 12 (CDK12) plays a critical role in regulating gene transcription. CDK12 inhibition is a potential anticancer therapeutic strategy. However, several clinical trials have shown that CDK inhibitors might cause renal dysfunction and electrolyte disorders. CDK12 is abundant in renal tubular epithelial cells (RTECs), but the exact role of CDK12 in renal physiology remains unclear. Genetic knockout of CDK12 in mouse RTECs causes polydipsia, polyuria, and hydronephrosis. This phenotype is caused by defects in water reabsorption that are the result of reduced Na-K-2Cl cotransporter 2 (NKCC2) levels in the kidney. In addition, CKD12 knockout causes an increase in Slc12a1 (which encodes NKCC2) intronic polyadenylation events, which results in Slc12a1 truncated transcript production and NKCC2 downregulation. These findings provide novel insight into CDK12 being necessary for maintaining renal homeostasis by regulating NKCC2 transcription, which explains the critical water and electrolyte disturbance that occurs during the application of CDK12 inhibitors for cancer treatment. Therefore, there are safety concerns about the clinical use of these new anticancer drugs.
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Affiliation(s)
- Bin Wang
- Institute of Nephrology, Zhong da Hospital, Southeast University School of Medicine, No. 87, Dingjiaqiao Road, Gulou District, Nanjing, Jiangsu Province, China
| | - Yao Wang
- Nanjing Medical University, Nanjing, Jiangsu, China; Department of Nephrology, The Affiliated Hospital of Yangzhou University, Yangzhou University, Yangzhou, Jiangsu, China
| | - Yi Wen
- Institute of Nephrology, Zhong da Hospital, Southeast University School of Medicine, No. 87, Dingjiaqiao Road, Gulou District, Nanjing, Jiangsu Province, China.
| | - Yi-Lin Zhang
- Institute of Nephrology, Zhong da Hospital, Southeast University School of Medicine, No. 87, Dingjiaqiao Road, Gulou District, Nanjing, Jiangsu Province, China
| | - Wei-Jie Ni
- Institute of Nephrology, Zhong da Hospital, Southeast University School of Medicine, No. 87, Dingjiaqiao Road, Gulou District, Nanjing, Jiangsu Province, China
| | - Tao-Tao Tang
- Institute of Nephrology, Zhong da Hospital, Southeast University School of Medicine, No. 87, Dingjiaqiao Road, Gulou District, Nanjing, Jiangsu Province, China
| | - Jing-Yuan Cao
- Institute of Nephrology, Zhong da Hospital, Southeast University School of Medicine, No. 87, Dingjiaqiao Road, Gulou District, Nanjing, Jiangsu Province, China
| | - Qing Yin
- Institute of Nephrology, Zhong da Hospital, Southeast University School of Medicine, No. 87, Dingjiaqiao Road, Gulou District, Nanjing, Jiangsu Province, China
| | - Wei Jiang
- Institute of Nephrology, Zhong da Hospital, Southeast University School of Medicine, No. 87, Dingjiaqiao Road, Gulou District, Nanjing, Jiangsu Province, China
| | - Di Yin
- Institute of Nephrology, Zhong da Hospital, Southeast University School of Medicine, No. 87, Dingjiaqiao Road, Gulou District, Nanjing, Jiangsu Province, China
| | - Zuo-Lin Li
- Institute of Nephrology, Zhong da Hospital, Southeast University School of Medicine, No. 87, Dingjiaqiao Road, Gulou District, Nanjing, Jiangsu Province, China
| | - Lin-Li Lv
- Institute of Nephrology, Zhong da Hospital, Southeast University School of Medicine, No. 87, Dingjiaqiao Road, Gulou District, Nanjing, Jiangsu Province, China
| | - Bi-Cheng Liu
- Institute of Nephrology, Zhong da Hospital, Southeast University School of Medicine, No. 87, Dingjiaqiao Road, Gulou District, Nanjing, Jiangsu Province, China; Nanjing Medical University, Nanjing, Jiangsu, China.
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49
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Dai W, Wu J, Peng X, Hou W, Huang H, Cheng Q, Liu Z, Luyten W, Schoofs L, Zhou J, Liu S. CDK12 orchestrates super-enhancer-associated CCDC137 transcription to direct hepatic metastasis in colorectal cancer. Clin Transl Med 2022; 12:e1087. [PMID: 36254394 PMCID: PMC9577262 DOI: 10.1002/ctm2.1087] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2022] [Revised: 09/22/2022] [Accepted: 09/29/2022] [Indexed: 02/06/2023] Open
Abstract
BACKGROUND Hepatic metastasis is the primary and direct cause of death in individuals with colorectal cancer (CRC) attribute to lack of effective therapeutic targets. The present study aimed to identify potential druggable candidate targets for patients with liver metastatic CRC. METHODS The transcriptional profiles of super-enhancers (SEs) in primary and liver metastatic CRC were evaluated in publicly accessible CRC datasets. Immunohistochemistry of human CRC tissues was conducted to determine the expression level of CDK12. Cellular proliferation, survival and stemness were examined upon CDK12 inhibition by shCDK12 or a selective CDK12 inhibitor named SR-4835 with multiple in vitro and in vivo assays. RNA sequencing and bioinformatics analyses were carried out to investigate the mechanisms of CDK12 inhibition in CRC cells. RESULTS We identified CDK12 as a driver gene for direct hepatic metastasis in CRC. Suppression of CDK12 led to robust inhibition of proliferation, survival and stemness. Mechanistically, CDK12 intervention preferentially repressed the transcription of SE-associated genes. Integration of the SE landscape and RNA sequencing, BCL2L1 and CCDC137 were identified as SE-associated oncogenic genes to strengthen the abilities of cellular survival, proliferation and stemness, eventually increasing liver metastasis of CRC. CONCLUSIONS Our data highlight the potential of CDK12 and SE-associated oncogenic transcripts as therapeutic targets for patients with liver metastatic CRC.
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Affiliation(s)
- Wei Dai
- School of PharmacyGannan Medical UniversityGanzhouJiangxiChina
| | - Junhong Wu
- School of PharmacyGannan Medical UniversityGanzhouJiangxiChina
| | - Xiaopeng Peng
- School of PharmacyGannan Medical UniversityGanzhouJiangxiChina
| | - Wen Hou
- School of PharmacyGannan Medical UniversityGanzhouJiangxiChina
| | - Hao Huang
- School of PharmacyGannan Medical UniversityGanzhouJiangxiChina
| | - Qilai Cheng
- School of PharmacyGannan Medical UniversityGanzhouJiangxiChina
| | - Zhiping Liu
- Center for ImmunologyGannan Medical UniversityGanzhouJiangxiChina
| | | | | | - Jingfeng Zhou
- Department of Hematology and OncologyInternational Cancer CenterShenzhen Key LaboratoryShenzhen University General HospitalShenzhen University Clinical Medical AcademyShenzhen University Health Science CenterShenzhenChina
| | - Shenglan Liu
- School of PharmacyGannan Medical UniversityGanzhouJiangxiChina
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50
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Clopper KC, Taatjes DJ. Chemical inhibitors of transcription-associated kinases. Curr Opin Chem Biol 2022; 70:102186. [PMID: 35926294 PMCID: PMC10676000 DOI: 10.1016/j.cbpa.2022.102186] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2022] [Revised: 06/20/2022] [Accepted: 06/22/2022] [Indexed: 11/18/2022]
Abstract
Transcription by RNA polymerase II (pol II) is regulated by kinases. In recent years, many selective and potent inhibitors of pol II transcription-associated kinases have been developed, and these molecules have advanced understanding of kinase function in mammalian cells. Here, we focus on chemical inhibitors of the transcription-associated kinases CDK7, CDK8, CDK9, CDK12, CDK13, and CDK19. We provide a brief overview of the function of these kinases and common activation mechanisms. We then highlight the advantages of kinase inhibitors compared with other basic research methods, and describe the caveats associated with non-selective compounds (e.g. flavopiridol). We conclude with strategies and recommendations for implementation of chemical inhibitors for experimental analysis of transcription-associated kinases.
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Affiliation(s)
- Kevin C Clopper
- Dept. of Biochemistry, University of Colorado, Boulder, CO, USA
| | - Dylan J Taatjes
- Dept. of Biochemistry, University of Colorado, Boulder, CO, USA.
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