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Curti L, Rohban S, Bianchi N, Croci O, Andronache A, Barozzi S, Mattioli M, Ricci F, Pastori E, Sberna S, Bellotti S, Accialini A, Ballarino R, Crosetto N, Wade M, Parazzoli D, Campaner S. CDK12 controls transcription at damaged genes and prevents MYC-induced transcription-replication conflicts. Nat Commun 2024; 15:7100. [PMID: 39155303 PMCID: PMC11330984 DOI: 10.1038/s41467-024-51229-5] [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: 11/15/2023] [Accepted: 08/01/2024] [Indexed: 08/20/2024] Open
Abstract
The identification of genes involved in replicative stress is key to understanding cancer evolution and to identify therapeutic targets. Here, we show that CDK12 prevents transcription-replication conflicts (TRCs) and the activation of cytotoxic replicative stress upon deregulation of the MYC oncogene. CDK12 was recruited at damaged genes by PARP-dependent DDR-signaling and elongation-competent RNAPII, to repress transcription. Either loss or chemical inhibition of CDK12 led to DDR-resistant transcription of damaged genes. Loss of CDK12 exacerbated TRCs in MYC-overexpressing cells and led to the accumulation of double-strand DNA breaks, occurring between co-directional early-replicating regions and transcribed genes. Overall, our data demonstrate that CDK12 protects genome integrity by repressing transcription of damaged genes, which is required for proper resolution of DSBs at oncogene-induced TRCs. This provides a rationale that explains both how CDK12 deficiency can promote tandem duplications of early-replicated regions during tumor evolution, and how CDK12 targeting can exacerbate replicative-stress in tumors.
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Affiliation(s)
- Laura Curti
- Center for Genomic Science of IIT, CGS@SEMM (Istituto Italiano di Tecnologia at European School of Molecular Medicine), Fondazione Istituto Italiano di Tecnologia (IIT), 20139, Milan, Italy
| | - Sara Rohban
- Center for Genomic Science of IIT, CGS@SEMM (Istituto Italiano di Tecnologia at European School of Molecular Medicine), Fondazione Istituto Italiano di Tecnologia (IIT), 20139, Milan, Italy
| | - Nicola Bianchi
- Center for Genomic Science of IIT, CGS@SEMM (Istituto Italiano di Tecnologia at European School of Molecular Medicine), Fondazione Istituto Italiano di Tecnologia (IIT), 20139, Milan, Italy
| | - Ottavio Croci
- Center for Genomic Science of IIT, CGS@SEMM (Istituto Italiano di Tecnologia at European School of Molecular Medicine), Fondazione Istituto Italiano di Tecnologia (IIT), 20139, Milan, Italy
| | - Adrian Andronache
- Center for Genomic Science of IIT, CGS@SEMM (Istituto Italiano di Tecnologia at European School of Molecular Medicine), Fondazione Istituto Italiano di Tecnologia (IIT), 20139, Milan, Italy
| | - Sara Barozzi
- IFOM ETS, The AIRC Institute of Molecular Oncology, Milan, Italy
| | - Michela Mattioli
- Center for Genomic Science of IIT, CGS@SEMM (Istituto Italiano di Tecnologia at European School of Molecular Medicine), Fondazione Istituto Italiano di Tecnologia (IIT), 20139, Milan, Italy
| | - Fernanda Ricci
- Center for Genomic Science of IIT, CGS@SEMM (Istituto Italiano di Tecnologia at European School of Molecular Medicine), Fondazione Istituto Italiano di Tecnologia (IIT), 20139, Milan, Italy
| | - Elena Pastori
- Center for Genomic Science of IIT, CGS@SEMM (Istituto Italiano di Tecnologia at European School of Molecular Medicine), Fondazione Istituto Italiano di Tecnologia (IIT), 20139, Milan, Italy
| | - Silvia Sberna
- Center for Genomic Science of IIT, CGS@SEMM (Istituto Italiano di Tecnologia at European School of Molecular Medicine), Fondazione Istituto Italiano di Tecnologia (IIT), 20139, Milan, Italy
| | - Simone Bellotti
- Center for Genomic Science of IIT, CGS@SEMM (Istituto Italiano di Tecnologia at European School of Molecular Medicine), Fondazione Istituto Italiano di Tecnologia (IIT), 20139, Milan, Italy
| | - Anna Accialini
- Center for Genomic Science of IIT, CGS@SEMM (Istituto Italiano di Tecnologia at European School of Molecular Medicine), Fondazione Istituto Italiano di Tecnologia (IIT), 20139, Milan, Italy
| | - Roberto Ballarino
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, SE-17165, Stockholm, Sweden
- Science for Life Laboratory, Tomtebodavägen 23A, SE-17165, Solna, Sweden
- Department of Cell and Molecular Biology, Karolinska Institutet, Stockholm, Sweden
| | - Nicola Crosetto
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, SE-17165, Stockholm, Sweden
- Science for Life Laboratory, Tomtebodavägen 23A, SE-17165, Solna, Sweden
- Human Technopole, Viale Rita Levi-Montalcini 1, 20157, Milan, Italy
| | - Mark Wade
- Center for Genomic Science of IIT, CGS@SEMM (Istituto Italiano di Tecnologia at European School of Molecular Medicine), Fondazione Istituto Italiano di Tecnologia (IIT), 20139, Milan, Italy
- Astex Pharmaceuticals, 436 Cambridge Science Park, CB4 0QA, Cambridge, UK
| | - Dario Parazzoli
- IFOM ETS, The AIRC Institute of Molecular Oncology, Milan, Italy
| | - Stefano Campaner
- Center for Genomic Science of IIT, CGS@SEMM (Istituto Italiano di Tecnologia at European School of Molecular Medicine), Fondazione Istituto Italiano di Tecnologia (IIT), 20139, Milan, Italy.
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2
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Zhang Z, Li Y, Yang J, Li J, Lin X, Liu T, Yang S, Lin J, Xue S, Yu J, Tang C, Li Z, Liu L, Ye Z, Deng Y, Li Z, Chen K, Ding H, Luo C, Lin H. Dual-site molecular glues for enhancing protein-protein interactions of the CDK12-DDB1 complex. Nat Commun 2024; 15:6477. [PMID: 39090085 PMCID: PMC11294606 DOI: 10.1038/s41467-024-50642-0] [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: 01/06/2024] [Accepted: 07/18/2024] [Indexed: 08/04/2024] Open
Abstract
Protein-protein interactions (PPIs) stabilization with molecular glues plays a crucial role in drug discovery, albeit with significant challenges. In this study, we propose a dual-site approach, targeting the PPI region and its dynamic surroundings. We conduct molecular dynamics simulations to identify critical sites on the PPI that stabilize the cyclin-dependent kinase 12 - DNA damage-binding protein 1 (CDK12-DDB1) complex, resulting in further cyclin K degradation. This exploration leads to the creation of LL-K12-18, a dual-site molecular glue, which enhances the glue properties to augment degradation kinetics and efficiency. Notably, LL-K12-18 demonstrates strong inhibition of gene transcription and anti-proliferative effects in tumor cells, showing significant potency improvements in MDA-MB-231 (88-fold) and MDA-MB-468 cells (307-fold) when compared to its precursor compound SR-4835. These findings underscore the potential of dual-site approaches in disrupting CDK12 function and offer a structural insight-based framework for the design of cyclin K molecular glues.
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Affiliation(s)
- Zemin Zhang
- The School of Pharmacy, Fujian Medical University, Fuzhou, China
| | - Yuanqing Li
- School of Chinese Materia Medica, Nanjing University of Chinese Medicine, Nanjing, China
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China
| | - Jie Yang
- Key Laboratory of Microbial Pathogenesis and Interventions of Fujian Province University, the Key Laboratory of Innate Immune Biology of Fujian Province, Biomedical Research Center of South China, College of Life Sciences, Fujian Normal University, Fuzhou, China
| | - Jiacheng Li
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China
| | - Xiongqiang Lin
- The School of Pharmacy, Fujian Medical University, Fuzhou, China
| | - Ting Liu
- The School of Pharmacy, Fujian Medical University, Fuzhou, China
| | - Shiling Yang
- Key Laboratory of Microbial Pathogenesis and Interventions of Fujian Province University, the Key Laboratory of Innate Immune Biology of Fujian Province, Biomedical Research Center of South China, College of Life Sciences, Fujian Normal University, Fuzhou, China
| | - Jin Lin
- The School of Pharmacy, Fujian Medical University, Fuzhou, China
| | - Shengyu Xue
- School of Chinese Materia Medica, Nanjing University of Chinese Medicine, Nanjing, China
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China
| | - Jiamin Yu
- School of Chinese Materia Medica, Nanjing University of Chinese Medicine, Nanjing, China
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China
| | - Cailing Tang
- School of Chinese Materia Medica, Nanjing University of Chinese Medicine, Nanjing, China
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China
| | - Ziteng Li
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Liping Liu
- Zhongshan Institute for Drug Discovery, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Zhongshan, China
| | - Zhengzheng Ye
- School of Pharmaceutical Science and Technology, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Hangzhou, China
| | - Yanan Deng
- School of Pharmaceutical Science and Technology, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Hangzhou, China
| | - Zhihai Li
- School of Pharmaceutical Science and Technology, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Hangzhou, China
| | - Kaixian Chen
- School of Chinese Materia Medica, Nanjing University of Chinese Medicine, Nanjing, China
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Hong Ding
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China.
- State Key Laboratory of Functions and Applications of Medicinal Plants, School of Pharmacy, Guizhou Medical University, Guiyang, China.
| | - Cheng Luo
- The School of Pharmacy, Fujian Medical University, Fuzhou, China.
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China.
- Zhongshan Institute for Drug Discovery, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Zhongshan, China.
- School of Pharmaceutical Science and Technology, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Hangzhou, China.
- State Key Laboratory of Functions and Applications of Medicinal Plants, School of Pharmacy, Guizhou Medical University, Guiyang, China.
| | - Hua Lin
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China.
- Key Laboratory of Microbial Pathogenesis and Interventions of Fujian Province University, the Key Laboratory of Innate Immune Biology of Fujian Province, Biomedical Research Center of South China, College of Life Sciences, Fujian Normal University, Fuzhou, China.
- Zhongshan Institute for Drug Discovery, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Zhongshan, China.
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3
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Nguyen CB, Reimers MA, Perera C, Abida W, Chou J, Feng FY, Antonarakis ES, McKay RR, Pachynski RK, Zhang J, Reichert ZR, Palmbos PL, Caram ME, Vaishampayan UN, Heath EI, Hopkins AC, Cieslik MP, Wu YM, Robinson D, Baladandayuthapani V, Chinnaiyan AM, Alva AS. Evaluating Immune Checkpoint Blockade in Metastatic Castration-Resistant Prostate Cancers with Deleterious CDK12 Alterations in the Phase 2 IMPACT Trial. Clin Cancer Res 2024; 30:3200-3210. [PMID: 38787530 PMCID: PMC11293970 DOI: 10.1158/1078-0432.ccr-24-0400] [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: 02/04/2024] [Revised: 04/08/2024] [Accepted: 05/22/2024] [Indexed: 05/25/2024]
Abstract
PURPOSE CDK12 inactivation in metastatic castration-resistant prostate cancer (mCRPC) may predict immunotherapy responses. This phase 2 trial evaluated the efficacy of immune checkpoint inhibitor (ICI) therapy in patients with CDK12-altered mCRPC. PATIENTS AND METHODS Eligible patients had mCRPC with deleterious CDK12 alterations and any prior therapies except ICI. Cohort A received ipilimumab (1 mg/kg) with nivolumab (3 mg/kg) every 3 weeks for up to four cycles, followed by nivolumab 480 mg every 4 weeks. Cohort C received nivolumab alone 480 mg every 4 weeks. Patients with CDK12-altered nonprostate tumors were enrolled in cohort B and not reported. The primary endpoint was a 50% reduction in PSA (PSA50). Key secondary endpoints included PSA progression-free survival, overall survival, objective response rate, and safety. RESULTS PSA was evaluable in 23 patients in cohort A and 14 in cohort C. Median lines of prior therapy were two in cohorts A and C, including any prior novel hormonal agent (74% and 79%) and chemotherapy (57% and 36%). The PSA50 rate was 9% [95% confidence interval (CI), 1%-28%] in cohort A with two responders; neither had microsatellite instability or a tumor mutational burden >10 mutations/megabase. No PSA50 responses occurred in cohort C. Median PSA progression-free survival was 7.0 months (95% CI, 3.6-11.4) in cohort A and 4.5 months (95% CI, 3.4-13.8) in cohort C. Median overall survival was 9.0 months (95% CI, 6.2-12.3) in cohort A and 13.8 months (95% CI, 3.6-not reached) in cohort C. CONCLUSIONS There was minimal activity with ICI therapy in patients with CDK12-altered mCRPC.
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Affiliation(s)
- Charles B. Nguyen
- Rogel Comprehensive Cancer Center, University of Michigan, Ann Arbor, MI
| | | | - Chamila Perera
- Department of Biostatistics, School of Public Health, University of Michigan, Ann Arbor, MI
| | - Wassim Abida
- Genitourinary Oncology Service, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Jonathan Chou
- Diller Comprehensive Cancer Center, University of California at San Francisco, San Francisco, CA
| | - Felix Y. Feng
- Diller Comprehensive Cancer Center, University of California at San Francisco, San Francisco, CA
| | | | - Rana R. McKay
- Moores Cancer Center, University of California San Diego, San Diego, CA
| | | | | | | | - Phillip L. Palmbos
- Rogel Comprehensive Cancer Center, University of Michigan, Ann Arbor, MI
| | - Megan E.V. Caram
- Rogel Comprehensive Cancer Center, University of Michigan, Ann Arbor, MI
| | | | | | - Alexander C. Hopkins
- Michigan Center for Translational Pathology, Department of Pathology, University of Michigan, Ann Arbor, MI
| | - Marcin P. Cieslik
- Michigan Center for Translational Pathology, Department of Pathology, University of Michigan, Ann Arbor, MI
| | - Yi-Mi Wu
- Michigan Center for Translational Pathology, Department of Pathology, University of Michigan, Ann Arbor, MI
| | - Dan Robinson
- Michigan Center for Translational Pathology, Department of Pathology, University of Michigan, Ann Arbor, MI
| | | | - Arul M. Chinnaiyan
- Michigan Center for Translational Pathology, Department of Pathology, University of Michigan, Ann Arbor, MI
| | - Ajjai S. Alva
- Rogel Comprehensive Cancer Center, University of Michigan, Ann Arbor, MI
- Michigan Center for Translational Pathology, Department of Pathology, University of Michigan, Ann Arbor, MI
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4
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Uboveja A, Aird KM. Interplay between altered metabolism and DNA damage and repair in ovarian cancer. Bioessays 2024; 46:e2300166. [PMID: 38873912 DOI: 10.1002/bies.202300166] [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: 08/31/2023] [Revised: 05/21/2024] [Accepted: 05/22/2024] [Indexed: 06/15/2024]
Abstract
Ovarian cancer is the most lethal gynecological malignancy and is often associated with both DNA repair deficiency and extensive metabolic reprogramming. While still emerging, the interplay between these pathways can affect ovarian cancer phenotypes, including therapeutic resistance to the DNA damaging agents that are standard-of-care for this tumor type. In this review, we will discuss what is currently known about cellular metabolic rewiring in ovarian cancer that may impact DNA damage and repair in addition to highlighting how specific DNA repair proteins also promote metabolic changes. We will also discuss relevant data from other cancers that could be used to inform ovarian cancer therapeutic strategies. Changes in the choice of DNA repair mechanism adopted by ovarian cancer are a major factor in promoting therapeutic resistance. Therefore, the impact of metabolic reprogramming on DNA repair mechanisms in ovarian cancer has major clinical implications for targeted combination therapies for the treatment of this devastating disease.
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Affiliation(s)
- Apoorva Uboveja
- Department of Pharmacology & Chemical Biology, UPMC Hillman Cancer Center, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
| | - Katherine M Aird
- Department of Pharmacology & Chemical Biology, UPMC Hillman Cancer Center, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
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Frank S, Persse T, Coleman I, Bankhead A, Li D, De-Sarkar N, Wilson D, Rudoy D, Vashisth M, Galipeau P, Yang M, Hanratty B, Dumpit R, Morrissey C, Corey E, Montgomery RB, Haffner MC, Pritchard C, Vasioukhin V, Ha G, Nelson PS. Molecular consequences of acute versus chronic CDK12 loss in prostate carcinoma nominates distinct therapeutic strategies. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.07.16.603734. [PMID: 39071291 PMCID: PMC11275783 DOI: 10.1101/2024.07.16.603734] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/30/2024]
Abstract
Genomic loss of the transcriptional kinase CDK12 occurs in ~6% of metastatic castration-resistant prostate cancers (mCRPC) and correlates with poor patient outcomes. Prior studies demonstrate that acute CDK12 loss confers a homologous recombination (HR) deficiency (HRd) phenotype via premature intronic polyadenylation (IPA) of key HR pathway genes, including ATM. However, mCRPC patients have not demonstrated benefit from therapies that exploit HRd such as inhibitors of polyADP ribose polymerase (PARP). Based on this discordance, we sought to test the hypothesis that an HRd phenotype is primarily a consequence of acute CDK12 loss and the effect is greatly diminished in prostate cancers adapted to CDK12 loss. Analyses of whole genome sequences (WGS) and RNA sequences (RNAseq) of human mCRPCs determined that tumors with biallelic CDK12 alterations (CDK12 BAL ) lack genomic scar signatures indicative of HRd, despite carrying bi-allelic loss and the appearance of the hallmark tandem-duplicator phenotype (TDP). Experiments confirmed that acute CDK12 inhibition resulted in aberrant polyadenylation and downregulation of long genes (including BRCA1 and BRCA2) but such effects were modest or absent in tumors adapted to chronic CDK12 BAL . One key exception was ATM, which did retain transcript shortening and reduced protein expression in the adapted CDK12 BAL models. However, CDK12 BAL cells demonstrated intact HR as measured by RAD51 foci formation following irradiation. CDK12 BAL cells showed a vulnerability to targeting of CDK13 by sgRNA or CDK12/13 inhibitors and in vivo treatment of prostate cancer xenograft lines showed that tumors with CDK12 BAL responded to the CDK12/13 inhibitor SR4835, while CDK12-intact lines did not. Collectively, these studies show that aberrant polyadenylation and long HR gene downregulation is primarily a consequence of acute CDK12 deficiency, which is largely compensated for in cells that have adapted to CDK12 loss. These results provide an explanation for why PARPi monotherapy has thus far failed to consistently benefit patients with CDK12 alterations, though alternate therapies that target CDK13 or transcription are candidates for future research and testing.
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Affiliation(s)
- Sander Frank
- Division of Human Biology, Fred Hutchinson Cancer Center, Seattle, WA 98119
| | - Thomas Persse
- Divison of Public Health Sciences, Fred Hutchinson Cancer Center, Seattle, WA 98119
| | - Ilsa Coleman
- Division of Human Biology, Fred Hutchinson Cancer Center, Seattle, WA 98119
| | - Armand Bankhead
- Division of Human Biology, Fred Hutchinson Cancer Center, Seattle, WA 98119
| | - Dapei Li
- Division of Human Biology, Fred Hutchinson Cancer Center, Seattle, WA 98119
| | - Navonil De-Sarkar
- Department of Pathology, Medical College of Wisconsin, Milwaukee, WI, 53226
- Research Member, Medical College of Wisconsin Cancer Center, WI-53226
| | - Divin Wilson
- Department of Pathology, Medical College of Wisconsin, Milwaukee, WI, 53226
- Research Member, Medical College of Wisconsin Cancer Center, WI-53226
| | - Dmytro Rudoy
- Division of Human Biology, Fred Hutchinson Cancer Center, Seattle, WA 98119
| | - Manasvita Vashisth
- Divison of Public Health Sciences, Fred Hutchinson Cancer Center, Seattle, WA 98119
| | - Patty Galipeau
- Divison of Public Health Sciences, Fred Hutchinson Cancer Center, Seattle, WA 98119
| | - Michael Yang
- Divison of Public Health Sciences, Fred Hutchinson Cancer Center, Seattle, WA 98119
| | - Brian Hanratty
- Division of Human Biology, Fred Hutchinson Cancer Center, Seattle, WA 98119
| | - Ruth Dumpit
- Division of Human Biology, Fred Hutchinson Cancer Center, Seattle, WA 98119
| | - Colm Morrissey
- Department of Urology, University of Washington, Seattle, WA 98195
| | - Eva Corey
- Department of Urology, University of Washington, Seattle, WA 98195
| | | | - Michael C. Haffner
- Division of Human Biology, Fred Hutchinson Cancer Center, Seattle, WA 98119
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA 98195
| | - Colin Pritchard
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA 98195
| | - Valera Vasioukhin
- Division of Human Biology, Fred Hutchinson Cancer Center, Seattle, WA 98119
| | - Gavin Ha
- Division of Human Biology, Fred Hutchinson Cancer Center, Seattle, WA 98119
- Divison of Public Health Sciences, Fred Hutchinson Cancer Center, Seattle, WA 98119
| | - Peter S. Nelson
- Division of Human Biology, Fred Hutchinson Cancer Center, Seattle, WA 98119
- Divison of Public Health Sciences, Fred Hutchinson Cancer Center, Seattle, WA 98119
- Division of Clinical Research, Fred Hutchinson Cancer Center, Seattle, WA 98119
- Department of Urology, University of Washington, Seattle, WA 98195
- Department of Medicine, University of Washington, Seattle, WA 98195
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA 98195
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6
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Hoshii T, Kikuchi S, Kujirai T, Masuda T, Ito T, Yasuda S, Matsumoto M, Rahmutulla B, Fukuyo M, Murata T, Kurumizaka H, Kaneda A. BOD1L mediates chromatin binding and non-canonical function of H3K4 methyltransferase SETD1A. Nucleic Acids Res 2024:gkae605. [PMID: 38989615 DOI: 10.1093/nar/gkae605] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2024] [Revised: 06/04/2024] [Accepted: 06/28/2024] [Indexed: 07/12/2024] Open
Abstract
The H3K4 methyltransferase SETD1A plays an essential role in both development and cancer. However, essential components involved in SETD1A chromatin binding remain unclear. Here, we discovered that BOD1L exhibits the highest correlated SETD1A co-dependency in human cancer cell lines. BOD1L knockout reduces leukemia cells in vitro and in vivo, and mimics the transcriptional profiles observed in SETD1A knockout cells. The loss of BOD1L immediately reduced SETD1A distribution at transcriptional start sites (TSS), induced transcriptional elongation defect, and increased the RNA polymerase II content at TSS; however, it did not reduce H3K4me3. The Shg1 domain of BOD1L has a DNA binding ability, and a tryptophan residue (W104) in the domain recruits SETD1A to chromatin through the association with SETD1A FLOS domain. In addition, the BOD1L-SETD1A complex associates with transcriptional regulators, including E2Fs. These results reveal that BOD1L mediates chromatin and SETD1A, and regulates the non-canonical function of SETD1A in transcription.
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Affiliation(s)
- Takayuki Hoshii
- Department of Molecular Oncology, Graduate School of Medicine, Chiba University, Chiba-shi, Chiba 260-8670, Japan
| | - Sota Kikuchi
- Department of Molecular Oncology, Graduate School of Medicine, Chiba University, Chiba-shi, Chiba 260-8670, Japan
| | - Tomoya Kujirai
- Laboratory of Chromatin Structure and Function, Institute for Quantitative Biosciences, The University of Tokyo, Bunkyo-ku, Tokyo 113-0032, Japan
| | - Takeshi Masuda
- Institute for Advanced Biosciences, Keio University, Tsuruoka, Yamagata 997-0017, Japan
| | - Tomoko Ito
- Laboratory of Chromatin Structure and Function, Institute for Quantitative Biosciences, The University of Tokyo, Bunkyo-ku, Tokyo 113-0032, Japan
| | - Satoshi Yasuda
- Department of Chemistry, Graduate School of Science, Chiba University, Chiba-shi, Chiba 263-8522, Japan
| | - Makoto Matsumoto
- Department of Molecular Oncology, Graduate School of Medicine, Chiba University, Chiba-shi, Chiba 260-8670, Japan
| | - Bahityar Rahmutulla
- Department of Molecular Oncology, Graduate School of Medicine, Chiba University, Chiba-shi, Chiba 260-8670, Japan
| | - Masaki Fukuyo
- Department of Molecular Oncology, Graduate School of Medicine, Chiba University, Chiba-shi, Chiba 260-8670, Japan
| | - Takeshi Murata
- Department of Chemistry, Graduate School of Science, Chiba University, Chiba-shi, Chiba 263-8522, Japan
| | - Hitoshi Kurumizaka
- Laboratory of Chromatin Structure and Function, Institute for Quantitative Biosciences, The University of Tokyo, Bunkyo-ku, Tokyo 113-0032, Japan
| | - Atsushi Kaneda
- Department of Molecular Oncology, Graduate School of Medicine, Chiba University, Chiba-shi, Chiba 260-8670, Japan
- Health and Disease Omics Center, Chiba University, Chiba-shi, Chiba 260-8670, Japan
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7
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Zhang H, Xing C, Yan B, Lei H, Guan Y, Zhang S, Kang Y, Pang J. Paclitaxel Overload Supramolecular Oxidative Stress Nanoamplifier with a CDK12 Inhibitor for Enhanced Cancer Therapy. Biomacromolecules 2024; 25:3685-3702. [PMID: 38779908 DOI: 10.1021/acs.biomac.4c00260] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/25/2024]
Abstract
Combination therapy has emerged as a promising approach for treating tumors, although there is room for improvement. This study introduced a novel strategy that combined the enhancement of apoptosis, ferroptosis, and DNA damage to improve therapeutic outcomes for prostate cancer. Specifically, we have developed a supramolecular oxidative stress nanoamplifier, which was comprised of β-cyclodextrin, paclitaxel, and ferrocene-poly(ethylene glycol). Paclitaxel within the system disrupted microtubule dynamics, inducing G2/M phase arrest and apoptosis. Concurrently, ferrocene utilized hydrogen peroxide to generate toxic hydroxyl radicals in cells through the Fenton reaction, triggering a cascade of reactive oxygen species expansion, reduction of glutathione levels, lipid peroxidation, and ferroptosis. The increased number of hydroxyl radicals and the inhibitory effect of THZ531 on DNA repair mechanisms exacerbated DNA damage within tumor cells. As expected, the supramolecular nanoparticles demonstrated excellent drug delivery ability to tumor cells or tissues, exhibited favorable biological safety in vivo, and enhanced the killing effect on prostate cancer.
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Affiliation(s)
- Hao Zhang
- Department of Urology, Kidney and Urology Center, Pelvic Floor Disorders Center, The Seventh Affiliated Hospital, Sun Yat-sen University, Shenzhen 518107, P. R. China
- Scientific Research Center, The Seventh Affiliated Hospital, Sun Yat-sen University, Shenzhen 518107, P. R. China
| | - Chengyuan Xing
- Scientific Research Center, The Seventh Affiliated Hospital, Sun Yat-sen University, Shenzhen 518107, P. R. China
| | - Binyuan Yan
- Department of Urology, Kidney and Urology Center, Pelvic Floor Disorders Center, The Seventh Affiliated Hospital, Sun Yat-sen University, Shenzhen 518107, P. R. China
| | - Hanqi Lei
- Department of Urology, Kidney and Urology Center, Pelvic Floor Disorders Center, The Seventh Affiliated Hospital, Sun Yat-sen University, Shenzhen 518107, P. R. China
| | - Yupeng Guan
- Department of Urology, Kidney and Urology Center, Pelvic Floor Disorders Center, The Seventh Affiliated Hospital, Sun Yat-sen University, Shenzhen 518107, P. R. China
- Scientific Research Center, The Seventh Affiliated Hospital, Sun Yat-sen University, Shenzhen 518107, P. R. China
| | - Shiqiang Zhang
- Department of Urology, Kidney and Urology Center, Pelvic Floor Disorders Center, The Seventh Affiliated Hospital, Sun Yat-sen University, Shenzhen 518107, P. R. China
| | - Yang Kang
- Scientific Research Center, The Seventh Affiliated Hospital, Sun Yat-sen University, Shenzhen 518107, P. R. China
| | - Jun Pang
- Department of Urology, Kidney and Urology Center, Pelvic Floor Disorders Center, The Seventh Affiliated Hospital, Sun Yat-sen University, Shenzhen 518107, P. R. China
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8
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Hampl M, Jandová N, Lusková D, Nováková M, Szotkowská T, Čada Š, Procházka J, Kohoutek J, Buchtová M. Early embryogenesis in CHDFIDD mouse model reveals facial clefts and altered cranial neurogenesis. Dis Model Mech 2024; 17:dmm050261. [PMID: 38511331 PMCID: PMC11212636 DOI: 10.1242/dmm.050261] [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: 04/24/2023] [Accepted: 03/12/2024] [Indexed: 03/22/2024] Open
Abstract
CDK13-related disorder, also known as congenital heart defects, dysmorphic facial features and intellectual developmental disorder (CHDFIDD) is associated with mutations in the CDK13 gene encoding transcription-regulating cyclin-dependent kinase 13 (CDK13). Here, we focused on the development of craniofacial structures and analyzed early embryonic stages in CHDFIDD mouse models, with one model comprising a hypomorphic mutation in Cdk13 and exhibiting cleft lip/palate, and another model comprising knockout of Cdk13, featuring a stronger phenotype including midfacial cleft. Cdk13 was found to be physiologically expressed at high levels in the mouse embryonic craniofacial structures, namely in the forebrain, nasal epithelium and maxillary mesenchyme. We also uncovered that Cdk13 deficiency leads to development of hypoplastic branches of the trigeminal nerve including the maxillary branch. Additionally, we detected significant changes in the expression levels of genes involved in neurogenesis (Ache, Dcx, Mef2c, Neurog1, Ntn1, Pou4f1) within the developing palatal shelves. These results, together with changes in the expression pattern of other key face-specific genes (Fgf8, Foxd1, Msx1, Meis2 and Shh) at early stages in Cdk13 mutant embryos, demonstrate a key role of CDK13 in the regulation of craniofacial morphogenesis.
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Affiliation(s)
- Marek Hampl
- Laboratory of Molecular Morphogenesis, Institute of Animal Physiology and Genetics, Czech Academy of Sciences, 60200 Brno, Czech Republic
- Department of Experimental Biology, Faculty of Science, Masaryk University, 60200 Brno, Czech Republic
| | - Nela Jandová
- Laboratory of Molecular Morphogenesis, Institute of Animal Physiology and Genetics, Czech Academy of Sciences, 60200 Brno, Czech Republic
- Department of Experimental Biology, Faculty of Science, Masaryk University, 60200 Brno, Czech Republic
| | - Denisa Lusková
- Laboratory of Molecular Morphogenesis, Institute of Animal Physiology and Genetics, Czech Academy of Sciences, 60200 Brno, Czech Republic
| | - Monika Nováková
- Department of Chemistry and Toxicology, Veterinary Research Institute, 62100 Brno, Czech Republic
| | - Tereza Szotkowská
- Laboratory of Molecular Morphogenesis, Institute of Animal Physiology and Genetics, Czech Academy of Sciences, 60200 Brno, Czech Republic
| | - Štěpán Čada
- Department of Experimental Biology, Faculty of Science, Masaryk University, 60200 Brno, Czech Republic
| | - Jan Procházka
- Laboratory of Transgenic Models of Diseases, Institute of Molecular Genetics, Czech Academy of Sciences, 14220 Prague, Czech Republic
- Czech Centre for Phenogenomics, Institute of Molecular Genetics, Czech Academy of Sciences, 14220 Prague, Czech Republic
| | - Jiri Kohoutek
- Department of Experimental Biology, Faculty of Science, Masaryk University, 60200 Brno, Czech Republic
| | - Marcela Buchtová
- Laboratory of Molecular Morphogenesis, Institute of Animal Physiology and Genetics, Czech Academy of Sciences, 60200 Brno, Czech Republic
- Department of Experimental Biology, Faculty of Science, Masaryk University, 60200 Brno, Czech Republic
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9
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Karolak A, Urbaniak K, Monastyrskyi A, Duckett DR, Branciamore S, Stewart PA. Structure-independent machine-learning predictions of the CDK12 interactome. Biophys J 2024:S0006-3495(24)00344-8. [PMID: 38762754 DOI: 10.1016/j.bpj.2024.05.017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2023] [Revised: 04/24/2024] [Accepted: 05/15/2024] [Indexed: 05/20/2024] Open
Abstract
Cyclin-dependent kinase 12 (CDK12) is a critical regulatory protein involved in transcription and DNA repair processes. Dysregulation of CDK12 has been implicated in various diseases, including cancer. Understanding the CDK12 interactome is pivotal for elucidating its functional roles and potential therapeutic targets. Traditional methods for interactome prediction often rely on protein structure information, limiting applicability to CDK12 characterized by partly disordered terminal C region. In this study, we present a structure-independent machine-learning model that utilizes proteins' sequence and functional data to predict the CDK12 interactome. This approach is motivated by the disordered character of the CDK12 C-terminal region mitigating a structure-driven search for binding partners. Our approach incorporates multiple data sources, including protein-protein interaction networks, functional annotations, and sequence-based features, to construct a comprehensive CDK12 interactome prediction model. The ability to predict CDK12 interactions without relying on structural information is a significant advancement, as many potential interaction partners may lack crystallographic data. In conclusion, our structure-independent machine-learning model presents a powerful tool for predicting the CDK12 interactome and holds promise in advancing our understanding of CDK12 biology, identifying potential therapeutic targets, and facilitating precision-medicine approaches for CDK12-associated diseases.
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Affiliation(s)
| | - Konstancja Urbaniak
- Department of Computational and Quantitative Medicine, City of Hope, Duarte, California
| | | | - Derek R Duckett
- Department of Drug Discovery, Moffitt Cancer Center, Tampa, Florida
| | - Sergio Branciamore
- Department of Computational and Quantitative Medicine, City of Hope, Duarte, California
| | - Paul A Stewart
- Department of Biostatistics and Bioinformatics, Moffitt Cancer Center, Tampa, Florida
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10
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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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11
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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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12
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Fancy NN, Smith AM, Caramello A, Tsartsalis S, Davey K, Muirhead RCJ, McGarry A, Jenkyns MH, Schneegans E, Chau V, Thomas M, Boulger S, Cheung TKD, Adair E, Papageorgopoulou M, Willumsen N, Khozoie C, Gomez-Nicola D, Jackson JS, Matthews PM. Characterisation of premature cell senescence in Alzheimer's disease using single nuclear transcriptomics. Acta Neuropathol 2024; 147:78. [PMID: 38695952 PMCID: PMC11065703 DOI: 10.1007/s00401-024-02727-9] [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: 01/04/2024] [Revised: 03/11/2024] [Accepted: 03/28/2024] [Indexed: 05/05/2024]
Abstract
Aging is associated with cell senescence and is the major risk factor for AD. We characterized premature cell senescence in postmortem brains from non-diseased controls (NDC) and donors with Alzheimer's disease (AD) using imaging mass cytometry (IMC) and single nuclear RNA (snRNA) sequencing (> 200,000 nuclei). We found increases in numbers of glia immunostaining for galactosidase beta (> fourfold) and p16INK4A (up to twofold) with AD relative to NDC. Increased glial expression of genes related to senescence was associated with greater β-amyloid load. Prematurely senescent microglia downregulated phagocytic pathways suggesting reduced capacity for β-amyloid clearance. Gene set enrichment and pseudo-time trajectories described extensive DNA double-strand breaks (DSBs), mitochondrial dysfunction and ER stress associated with increased β-amyloid leading to premature senescence in microglia. We replicated these observations with independent AD snRNA-seq datasets. Our results describe a burden of senescent glia with AD that is sufficiently high to contribute to disease progression. These findings support the hypothesis that microglia are a primary target for senolytic treatments in AD.
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Affiliation(s)
- Nurun N Fancy
- Department of Brain Sciences, Imperial College London, Hammersmith Hospital, Du Cane Road, London, W12 0NN, UK
- UK Dementia Research Institute Centre, Imperial College London, London, UK
| | - Amy M Smith
- Department of Brain Sciences, Imperial College London, Hammersmith Hospital, Du Cane Road, London, W12 0NN, UK
- Centre for Brain Research and Department of Pharmacology and Clinical Pharmacology, University of Auckland, Auckland, New Zealand
- UK Dementia Research Institute Centre, Imperial College London, London, UK
| | - Alessia Caramello
- Department of Brain Sciences, Imperial College London, Hammersmith Hospital, Du Cane Road, London, W12 0NN, UK
- UK Dementia Research Institute Centre, Imperial College London, London, UK
| | - Stergios Tsartsalis
- Department of Brain Sciences, Imperial College London, Hammersmith Hospital, Du Cane Road, London, W12 0NN, UK
- Department of Psychiatry, University of Geneva, Geneva, Switzerland
| | - Karen Davey
- Department of Brain Sciences, Imperial College London, Hammersmith Hospital, Du Cane Road, London, W12 0NN, UK
- UK Dementia Research Institute Centre, Imperial College London, London, UK
- UK Dementia Research Institute Centre, King's College London, London, UK
| | - Robert C J Muirhead
- Department of Brain Sciences, Imperial College London, Hammersmith Hospital, Du Cane Road, London, W12 0NN, UK
- UK Dementia Research Institute Centre, Imperial College London, London, UK
- UK Dementia Research Institute Centre, King's College London, London, UK
| | - Aisling McGarry
- Department of Brain Sciences, Imperial College London, Hammersmith Hospital, Du Cane Road, London, W12 0NN, UK
- UK Dementia Research Institute Centre, Imperial College London, London, UK
- Department of Basic and Clinical Neuroscience, Institute of Psychiatry, Psychology and Neuroscience, King's College London, London, UK
| | - Marion H Jenkyns
- Department of Brain Sciences, Imperial College London, Hammersmith Hospital, Du Cane Road, London, W12 0NN, UK
| | - Eleonore Schneegans
- Department of Brain Sciences, Imperial College London, Hammersmith Hospital, Du Cane Road, London, W12 0NN, UK
- UK Dementia Research Institute Centre, Imperial College London, London, UK
| | - Vicky Chau
- Department of Brain Sciences, Imperial College London, Hammersmith Hospital, Du Cane Road, London, W12 0NN, UK
- UK Dementia Research Institute Centre, Imperial College London, London, UK
| | - Michael Thomas
- Department of Brain Sciences, Imperial College London, Hammersmith Hospital, Du Cane Road, London, W12 0NN, UK
- UK Dementia Research Institute Centre, Imperial College London, London, UK
| | - Sam Boulger
- Department of Brain Sciences, Imperial College London, Hammersmith Hospital, Du Cane Road, London, W12 0NN, UK
- UK Dementia Research Institute Centre, Imperial College London, London, UK
| | - To Ka Dorcas Cheung
- Department of Brain Sciences, Imperial College London, Hammersmith Hospital, Du Cane Road, London, W12 0NN, UK
- UK Dementia Research Institute Centre, Imperial College London, London, UK
| | - Emily Adair
- Department of Brain Sciences, Imperial College London, Hammersmith Hospital, Du Cane Road, London, W12 0NN, UK
- UK Dementia Research Institute Centre, Imperial College London, London, UK
| | - Marianna Papageorgopoulou
- Department of Brain Sciences, Imperial College London, Hammersmith Hospital, Du Cane Road, London, W12 0NN, UK
- UK Dementia Research Institute Centre, Imperial College London, London, UK
| | - Nanet Willumsen
- Department of Brain Sciences, Imperial College London, Hammersmith Hospital, Du Cane Road, London, W12 0NN, UK
- UK Dementia Research Institute Centre, Imperial College London, London, UK
| | - Combiz Khozoie
- Department of Brain Sciences, Imperial College London, Hammersmith Hospital, Du Cane Road, London, W12 0NN, UK
- UK Dementia Research Institute Centre, Imperial College London, London, UK
| | - Diego Gomez-Nicola
- School of Biological Sciences, University of Southampton, Southampton, UK
| | - Johanna S Jackson
- Department of Brain Sciences, Imperial College London, Hammersmith Hospital, Du Cane Road, London, W12 0NN, UK
- UK Dementia Research Institute Centre, Imperial College London, London, UK
| | - Paul M Matthews
- Department of Brain Sciences, Imperial College London, Hammersmith Hospital, Du Cane Road, London, W12 0NN, UK.
- UK Dementia Research Institute Centre, Imperial College London, London, UK.
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13
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Zhang H, Zhou Y, Feng Y, Hou W, Chen Y, Xing Z, Zhang Y, Wei Q, Yin Y, Guo J, Hu H. Cyclin-dependent kinase 12 deficiency reprogrammes cellular metabolism to alleviate ferroptosis potential and promote the progression of castration-resistant prostate cancer. Clin Transl Med 2024; 14:e1678. [PMID: 38736108 PMCID: PMC11089090 DOI: 10.1002/ctm2.1678] [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: 01/31/2024] [Revised: 04/13/2024] [Accepted: 04/17/2024] [Indexed: 05/14/2024] Open
Abstract
BACKGROUND Cyclin-dependent kinase 12 (CDK12)-deficient prostate cancer defines a subtype of castration-resistant prostate cancer (CRPC) with a poor prognosis. Current therapy, including PARP inhibitors, shows minimal treatment efficacy for this subtype of CRPC, and the underlying mechanism remains elusive. METHODS Based on bioinformatics analysis, we evaluated the relationship between CDK12 deficiency and prostate cancer patient's prognosis and treatment resistance. Furthermore, we used CRISPR-Cas9 technology and mass spectrometry-based metabolomic profiling to reveal the metabolic characteristics of CDK12-deficient CRPC. To elucidate the specific mechanisms of CDK12 deficiency-mediated CRPC metabolic reprogramming, we utilized cell RNA-seq profiling and other molecular biology techniques, including cellular reactive oxygen species probes, mitochondrial function assays, ChIP-qPCR and RNA stability analyses, to clarify the role of CDK12 in regulating mitochondrial function and its contribution to ferroptosis. Finally, through in vitro drug sensitivity testing and in vivo experiments in mice, we identified the therapeutic effects of the electron transport chain (ETC) inhibitor IACS-010759 on CDK12-deficient CRPC. RESULTS CDK12-deficient prostate cancers reprogramme cellular energy metabolism to support their aggressive progression. In particular, CDK12 deficiency enhanced the mitochondrial respiratory chain for electronic transfer and ATP synthesis to create a ferroptosis potential in CRPC cells. However, CDK12 deficiency downregulated ACSL4 expression, which counteracts the lipid oxidation stress, leading to the escape of CRPC cells from ferroptosis. Furthermore, targeting the ETC substantially inhibited the proliferation of CDK12-deficient CRPC cells in vitro and in vivo, suggesting a potential new target for the therapy of CDK12-deficient prostate cancer. CONCLUSIONS Our findings show that energy and lipid metabolism in CDK12-deficient CRPC work together to drive CRPC progression and provide a metabolic insight into the worse prognosis of CDK12-deficient prostate cancer patients. KEY POINTS CDK12 deficiency promotes castration-resistant prostate cancer (CRPC) progression by reprogramming cellular metabolism. CDK12 deficiency in CRPC leads to a more active mitochondrial electron transport chain (ETC), ensuring efficient cell energy supply. CDK12 phosphorylates RNA Pol II to ensure the transcription of ACSL4 to regulate ferroptosis. Mitochondrial ETC inhibitors exhibit better selectivity for CDK12-deficient CRPC cells, offering a promising new therapeutic approach for this subtype of CRPC patients.
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Affiliation(s)
- Haozhe Zhang
- Department of BiochemistrySchool of MedicineSouthern University of Science and TechnologyShenzhenChina
| | - Yi Zhou
- Department of BiochemistrySchool of MedicineSouthern University of Science and TechnologyShenzhenChina
| | - Yating Feng
- Department of BiochemistrySchool of MedicineSouthern University of Science and TechnologyShenzhenChina
| | - Wenli Hou
- Department of UrologyNanfang Hospital, Southern Medical UniversityGuangzhouChina
| | - Yafei Chen
- Department of BiochemistrySchool of MedicineSouthern University of Science and TechnologyShenzhenChina
| | - Zengzhen Xing
- Department of BiochemistrySchool of MedicineSouthern University of Science and TechnologyShenzhenChina
| | - Yifan Zhang
- Department of UrologyNanfang Hospital, Southern Medical UniversityGuangzhouChina
| | - Qiang Wei
- Department of UrologyNanfang Hospital, Southern Medical UniversityGuangzhouChina
| | - Yu Yin
- Department of PathologyThe First Affiliated Hospital of Anhui Medical UniversityHefeiChina
| | - Ju Guo
- Department of UrologyThe First Affiliated Hospital of Nanchang UniversityNanchangChina
| | - Hailiang Hu
- Department of BiochemistrySchool of MedicineSouthern University of Science and TechnologyShenzhenChina
- Key University Laboratory of Metabolism and Health of GuangdongSouthern University of Science and TechnologyShenzhenChina
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14
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Orhan E, Velazquez C, Tabet I, Fenou L, Rodier G, Orsetti B, Jacot W, Sardet C, Theillet C. CDK inhibition results in pharmacologic BRCAness increasing sensitivity to olaparib in BRCA1-WT and olaparib resistant in Triple Negative Breast Cancer. Cancer Lett 2024; 589:216820. [PMID: 38574883 DOI: 10.1016/j.canlet.2024.216820] [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: 10/06/2023] [Revised: 02/19/2024] [Accepted: 03/15/2024] [Indexed: 04/06/2024]
Abstract
One in three Triple Negative Breast Cancer (TNBC) is Homologous Recombination Deficient (HRD) and susceptible to respond to PARP inhibitor (PARPi), however, resistance resulting from functional HR restoration is frequent. Thus, pharmacologic approaches that induce HRD are of interest. We investigated the effectiveness of CDK-inhibition to induce HRD and increase PARPi sensitivity of TNBC cell lines and PDX models. Two CDK-inhibitors (CDKi), the broad range dinaciclib and the CDK12-specific SR-4835, strongly reduced the expression of key HR genes and impaired HR functionality, as illustrated by BRCA1 and RAD51 nuclear foci obliteration. Consequently, both CDKis showed synergism with olaparib, as well as with cisplatin and gemcitabine, in a range of TNBC cell lines and particularly in olaparib-resistant models. In vivo assays on PDX validated the efficacy of dinaciclib which increased the sensitivity to olaparib of 5/6 models, including two olaparib-resistant and one BRCA1-WT model. However, no olaparib response improvement was observed in vivo with SR-4835. These data support that the implementation of CDK-inhibitors could be effective to sensitize TNBC to olaparib as well as possibly to cisplatin or gemcitabine.
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Affiliation(s)
- Esin Orhan
- Institut de Recherche en Cancérologie de Montpellier, IRCM, U1194, Montpellier University, INSERM, ICM, CNRS, Montpellier, France
| | - Carolina Velazquez
- Institut de Recherche en Cancérologie de Montpellier, IRCM, U1194, Montpellier University, INSERM, ICM, CNRS, Montpellier, France
| | - Imene Tabet
- Institut de Recherche en Cancérologie de Montpellier, IRCM, U1194, Montpellier University, INSERM, ICM, CNRS, Montpellier, France
| | - Lise Fenou
- Institut de Recherche en Cancérologie de Montpellier, IRCM, U1194, Montpellier University, INSERM, ICM, CNRS, Montpellier, France
| | - Geneviève Rodier
- Institut de Recherche en Cancérologie de Montpellier, IRCM, U1194, Montpellier University, INSERM, ICM, CNRS, Montpellier, France
| | - Béatrice Orsetti
- Institut de Recherche en Cancérologie de Montpellier, IRCM, U1194, Montpellier University, INSERM, ICM, CNRS, Montpellier, France
| | - William Jacot
- Institut de Recherche en Cancérologie de Montpellier, IRCM, U1194, Montpellier University, INSERM, ICM, CNRS, Montpellier, France; Oncologie Clinique, Institut Du Cancer de Montpellier, Montpellier, France
| | - Claude Sardet
- Institut de Recherche en Cancérologie de Montpellier, IRCM, U1194, Montpellier University, INSERM, ICM, CNRS, Montpellier, France
| | - Charles Theillet
- Institut de Recherche en Cancérologie de Montpellier, IRCM, U1194, Montpellier University, INSERM, ICM, CNRS, Montpellier, France.
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15
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Du X, Qin W, Yang C, Dai L, San M, Xia Y, Zhou S, Wang M, Wu S, Zhang S, Zhou H, Li F, He F, Tang J, Chen JY, Zhou Y, Xiao R. RBM22 regulates RNA polymerase II 5' pausing, elongation rate, and termination by coordinating 7SK-P-TEFb complex and SPT5. Genome Biol 2024; 25:102. [PMID: 38641822 PMCID: PMC11027413 DOI: 10.1186/s13059-024-03242-6] [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: 11/01/2023] [Accepted: 04/09/2024] [Indexed: 04/21/2024] Open
Abstract
BACKGROUND Splicing factors are vital for the regulation of RNA splicing, but some have also been implicated in regulating transcription. The underlying molecular mechanisms of their involvement in transcriptional processes remain poorly understood. RESULTS Here, we describe a direct role of splicing factor RBM22 in coordinating multiple steps of RNA Polymerase II (RNAPII) transcription in human cells. The RBM22 protein widely occupies the RNAPII-transcribed gene locus in the nucleus. Loss of RBM22 promotes RNAPII pause release, reduces elongation velocity, and provokes transcriptional readthrough genome-wide, coupled with production of transcripts containing sequences from downstream of the gene. RBM22 preferentially binds to the hyperphosphorylated, transcriptionally engaged RNAPII and coordinates its dynamics by regulating the homeostasis of the 7SK-P-TEFb complex and the association between RNAPII and SPT5 at the chromatin level. CONCLUSIONS Our results uncover the multifaceted role of RBM22 in orchestrating the transcriptional program of RNAPII and provide evidence implicating a splicing factor in both RNAPII elongation kinetics and termination control.
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Affiliation(s)
- Xian Du
- Department of Hematology, Medical Research Institute, Frontier Science Center for Immunology and Metabolism, Zhongnan Hospital of Wuhan University, Wuhan University, Wuhan, China
- TaiKang Center for Life and Medical Sciences, Wuhan University, Wuhan, China
| | - Wenying Qin
- Department of Hematology, Medical Research Institute, Frontier Science Center for Immunology and Metabolism, Zhongnan Hospital of Wuhan University, Wuhan University, Wuhan, China
- TaiKang Center for Life and Medical Sciences, Wuhan University, Wuhan, China
| | - Chunyu Yang
- Department of Hematology, Medical Research Institute, Frontier Science Center for Immunology and Metabolism, Zhongnan Hospital of Wuhan University, Wuhan University, Wuhan, China
- TaiKang Center for Life and Medical Sciences, Wuhan University, Wuhan, China
| | - Lin Dai
- Department of Hematology, Medical Research Institute, Frontier Science Center for Immunology and Metabolism, Zhongnan Hospital of Wuhan University, Wuhan University, Wuhan, China
- TaiKang Center for Life and Medical Sciences, Wuhan University, Wuhan, China
| | - Mingkui San
- Department of Hematology, Medical Research Institute, Frontier Science Center for Immunology and Metabolism, Zhongnan Hospital of Wuhan University, Wuhan University, Wuhan, China
- TaiKang Center for Life and Medical Sciences, Wuhan University, Wuhan, China
| | - Yingdan Xia
- Department of Hematology, Medical Research Institute, Frontier Science Center for Immunology and Metabolism, Zhongnan Hospital of Wuhan University, Wuhan University, Wuhan, China
- TaiKang Center for Life and Medical Sciences, Wuhan University, Wuhan, China
| | - Siyu Zhou
- Department of Hematology, Medical Research Institute, Frontier Science Center for Immunology and Metabolism, Zhongnan Hospital of Wuhan University, Wuhan University, Wuhan, China
- TaiKang Center for Life and Medical Sciences, Wuhan University, Wuhan, China
| | - Mengyang Wang
- Department of Hematology, Medical Research Institute, Frontier Science Center for Immunology and Metabolism, Zhongnan Hospital of Wuhan University, Wuhan University, Wuhan, China
- TaiKang Center for Life and Medical Sciences, Wuhan University, Wuhan, China
| | - Shuang Wu
- Department of Hematology, Medical Research Institute, Frontier Science Center for Immunology and Metabolism, Zhongnan Hospital of Wuhan University, Wuhan University, Wuhan, China
- TaiKang Center for Life and Medical Sciences, Wuhan University, Wuhan, China
| | - Shaorui Zhang
- Department of Hematology, Medical Research Institute, Frontier Science Center for Immunology and Metabolism, Zhongnan Hospital of Wuhan University, Wuhan University, Wuhan, China
- TaiKang Center for Life and Medical Sciences, Wuhan University, Wuhan, China
| | - Huiting Zhou
- Department of Hematology, Medical Research Institute, Frontier Science Center for Immunology and Metabolism, Zhongnan Hospital of Wuhan University, Wuhan University, Wuhan, China
- TaiKang Center for Life and Medical Sciences, Wuhan University, Wuhan, China
| | - Fangshu Li
- Department of Hematology, Medical Research Institute, Frontier Science Center for Immunology and Metabolism, Zhongnan Hospital of Wuhan University, Wuhan University, Wuhan, China
- TaiKang Center for Life and Medical Sciences, Wuhan University, Wuhan, China
| | - Fang He
- Department of Hematology, Medical Research Institute, Frontier Science Center for Immunology and Metabolism, Zhongnan Hospital of Wuhan University, Wuhan University, Wuhan, China
- TaiKang Center for Life and Medical Sciences, Wuhan University, Wuhan, China
| | - Jingfeng Tang
- National "111" Center for Cellular Regulation and Molecular Pharmaceutics, School of Life and Health Sciences, Hubei University of Technology, Wuhan, China
| | - Jia-Yu Chen
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Chemistry and Biomedicine Innovation Center, Nanjing University, Nanjing, China
| | - Yu Zhou
- TaiKang Center for Life and Medical Sciences, College of Life Sciences, State Key Laboratory of Virology, Wuhan University, Wuhan, China
| | - Rui Xiao
- Department of Hematology, Medical Research Institute, Frontier Science Center for Immunology and Metabolism, Zhongnan Hospital of Wuhan University, Wuhan University, Wuhan, China.
- TaiKang Center for Life and Medical Sciences, Wuhan University, Wuhan, China.
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16
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Kuzmina A, Sadhu L, Hasanuzzaman M, Fujinaga K, Schwartz JC, Fackler OT, Taube R. Direct and indirect effects of CYTOR lncRNA regulate HIV gene expression. PLoS Pathog 2024; 20:e1012172. [PMID: 38662769 PMCID: PMC11075828 DOI: 10.1371/journal.ppat.1012172] [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: 09/17/2023] [Revised: 05/07/2024] [Accepted: 04/05/2024] [Indexed: 05/08/2024] Open
Abstract
The implementation of antiretroviral therapy (ART) has effectively restricted the transmission of Human Immunodeficiency Virus (HIV) and improved overall clinical outcomes. However, a complete cure for HIV remains out of reach, as the virus persists in a stable pool of infected cell reservoir that is resistant to therapy and thus a main barrier towards complete elimination of viral infection. While the mechanisms by which host proteins govern viral gene expression and latency are well-studied, the emerging regulatory functions of non-coding RNAs (ncRNA) in the context of T cell activation, HIV gene expression and viral latency have not yet been thoroughly explored. Here, we report the identification of the Cytoskeleton Regulator (CYTOR) long non-coding RNA (lncRNA) as an activator of HIV gene expression that is upregulated following T cell stimulation. Functional studies show that CYTOR suppresses viral latency by directly binding to the HIV promoter and associating with the cellular positive transcription elongation factor (P-TEFb) to activate viral gene expression. CYTOR also plays a global role in regulating cellular gene expression, including those involved in controlling actin dynamics. Depletion of CYTOR expression reduces cytoplasmic actin polymerization in response to T cell activation. In addition, treating HIV-infected cells with pharmacological inhibitors of actin polymerization reduces HIV gene expression. We conclude that both direct and indirect effects of CYTOR regulate HIV gene expression.
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Affiliation(s)
- Alona Kuzmina
- The Shraga Segal Department of Microbiology Immunology and Genetics, Faculty of Health Sciences, Ben-Gurion University of the Negev, Israel
| | - Lopamudra Sadhu
- Department of Infectious Diseases, Heidelberg University, Medical Faculty Heidelberg, Integrative Virology, Center for Integrative Infectious Disease Research (CIID), Heidelberg, Germany
| | - Md Hasanuzzaman
- Department of Infectious Diseases, Heidelberg University, Medical Faculty Heidelberg, Integrative Virology, Center for Integrative Infectious Disease Research (CIID), Heidelberg, Germany
| | - Koh Fujinaga
- Department of Medicine, University of California, San Francisco, San Francisco, California, United States of America
| | - Jacob C. Schwartz
- Department of Pharmacology, University of Arizona College of Medicine, Tucson, Arizona, United States of America
| | - Oliver T. Fackler
- Department of Infectious Diseases, Heidelberg University, Medical Faculty Heidelberg, Integrative Virology, Center for Integrative Infectious Disease Research (CIID), Heidelberg, Germany
- German Center for Infection Research, DZIF, Partner Site Heidelberg, Heidelberg. Germany
| | - Ran Taube
- The Shraga Segal Department of Microbiology Immunology and Genetics, Faculty of Health Sciences, Ben-Gurion University of the Negev, Israel
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17
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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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18
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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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19
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Xing H, Yau C. Bayesian inference for identifying tumour-specific cancer dependencies through integration of ex-vivo drug response assays and drug-protein profiling. BMC Bioinformatics 2024; 25:104. [PMID: 38459430 PMCID: PMC10921766 DOI: 10.1186/s12859-024-05682-0] [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: 11/23/2023] [Accepted: 01/29/2024] [Indexed: 03/10/2024] Open
Abstract
The identification of tumor-specific molecular dependencies is essential for the development of effective cancer therapies. Genetic and chemical perturbations are powerful tools for discovering these dependencies. Even though chemical perturbations can be applied to primary cancer samples at large scale, the interpretation of experiment outcomes is often complicated by the fact that one chemical compound can affect multiple proteins. To overcome this challenge, Batzilla et al. (PLoS Comput Biol 18(8): e1010438, 2022) proposed DepInfeR, a regularized multi-response regression model designed to identify and estimate specific molecular dependencies of individual cancers from their ex-vivo drug sensitivity profiles. Inspired by their work, we propose a Bayesian extension to DepInfeR. Our proposed approach offers several advantages over DepInfeR, including e.g. the ability to handle missing values in both protein-drug affinity and drug sensitivity profiles without the need for data pre-processing steps such as imputation. Moreover, our approach uses Gaussian Processes to capture more complex molecular dependency structures, and provides probabilistic statements about whether a protein in the protein-drug affinity profiles is informative to the drug sensitivity profiles. Simulation studies demonstrate that our proposed approach achieves better prediction accuracy, and is able to discover unreported dependency structures.
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Affiliation(s)
- Hanwen Xing
- Nuffield Department of Women's and Reproductive Health, University of Oxford, Oxford, UK
| | - Christopher Yau
- Nuffield Department of Women's and Reproductive Health, University of Oxford, Oxford, UK.
- Health Data Research UK, London, UK.
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20
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Li Y, Gong J, Sun Q, Vong EG, Cheng X, Wang B, Yuan Y, Jin L, Gamazon ER, Zhou D, Lai M, Zhang D. Alternative polyadenylation quantitative trait methylation mapping in human cancers provides clues into the molecular mechanisms of APA. Am J Hum Genet 2024; 111:562-583. [PMID: 38367620 PMCID: PMC10940021 DOI: 10.1016/j.ajhg.2024.01.010] [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: 09/12/2023] [Revised: 01/19/2024] [Accepted: 01/22/2024] [Indexed: 02/19/2024] Open
Abstract
Genetic variants are involved in the orchestration of alternative polyadenylation (APA) events, while the role of DNA methylation in regulating APA remains unclear. We generated a comprehensive atlas of APA quantitative trait methylation sites (apaQTMs) across 21 different types of cancer (1,612 to 60,219 acting in cis and 4,448 to 142,349 in trans). Potential causal apaQTMs in non-cancer samples were also identified. Mechanistically, we observed a strong enrichment of cis-apaQTMs near polyadenylation sites (PASs) and both cis- and trans-apaQTMs in proximity to transcription factor (TF) binding regions. Through the integration of ChIP-signals and RNA-seq data from cell lines, we have identified several regulators of APA events, acting either directly or indirectly, implicating novel functions of some important genes, such as TCF7L2, which is known for its involvement in type 2 diabetes and cancers. Furthermore, we have identified a vast number of QTMs that share the same putative causal CpG sites with five different cancer types, underscoring the roles of QTMs, including apaQTMs, in the process of tumorigenesis. DNA methylation is extensively involved in the regulation of APA events in human cancers. In an attempt to elucidate the potential underlying molecular mechanisms of APA by DNA methylation, our study paves the way for subsequent experimental validations into the intricate biological functions of DNA methylation in APA regulation and the pathogenesis of human cancers. To present a comprehensive catalog of apaQTM patterns, we introduce the Pancan-apaQTM database, available at https://pancan-apaqtm-zju.shinyapps.io/pancanaQTM/.
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Affiliation(s)
- Yige Li
- Department of Pathology, and Department of Medical Oncology of the Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang Province, China; Department of Pathology, Key Laboratory of Disease Proteomics of Zhejiang Province, School of Medicine, Zhejiang University, Hangzhou, Zhejiang Province, China; Department of Pathology, the Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang Province, China
| | - Jingwen Gong
- Department of Pathology, and Department of Medical Oncology of the Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang Province, China; Department of Pathology, Key Laboratory of Disease Proteomics of Zhejiang Province, School of Medicine, Zhejiang University, Hangzhou, Zhejiang Province, China; Alibaba-Zhejiang University Joint Research Center of Future Digital Healthcare, Hangzhou, Zhejiang Province, China
| | - Qingrong Sun
- Department of Pathology, Key Laboratory of Disease Proteomics of Zhejiang Province, School of Medicine, Zhejiang University, Hangzhou, Zhejiang Province, China; Alibaba-Zhejiang University Joint Research Center of Future Digital Healthcare, Hangzhou, Zhejiang Province, China; Liangzhu Laboratory, Zhejiang University Medical Center, 1369 West Wenyi Road, Hangzhou, Zhejiang Province, China; College of Information Science and Technology, ZheJiang Shuren University, Hangzhou 310015, ZheJiang, China
| | - Eu Gene Vong
- Department of Pathology, Key Laboratory of Disease Proteomics of Zhejiang Province, School of Medicine, Zhejiang University, Hangzhou, Zhejiang Province, China; Department of Biochemistry and Genetics, Zhejiang University School of Medicine, Hangzhou, Zhejiang Province, China; The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang Province, China
| | - Xiaoqing Cheng
- Department of Pathology, Sir Run Run Shaw Hospital, School of Medicine, Zhejiang University, Hangzhou, Zhejiang Province, China
| | - Binghong Wang
- Sir Run Run Shaw Hospital, School of Medicine, Zhejiang University, Hangzhou, Zhejiang Province, China
| | - Ying Yuan
- Department of Medical Oncology, the Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang Province, China; Cancer Institute (Key Laboratory of Cancer Prevention and Intervention, Chinese National Ministry of Education), the Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang Province, China
| | - Li Jin
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Human Phenome Institute, Zhangjiang Fudan International Innovation Center, Fudan University, Shanghai, China; Research Unit of Dissecting the Population Genetics and Developing New Technologies for Treatment and Prevention of Skin Phenotypes and Dermatological Diseases (2019RU058), Chinese Academy of Medical Sciences, Shanghai, China
| | - Eric R Gamazon
- Division of Genetic Medicine, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA; Data Science Institute, Vanderbilt University Medical Center, Nashville, TN, USA; Vanderbilt Genetics Institute, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Dan Zhou
- Vanderbilt Genetics Institute, Vanderbilt University Medical Center, Nashville, TN, USA; School of Public Health and the Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Maode Lai
- Department of Pathology, Key Laboratory of Disease Proteomics of Zhejiang Province, School of Medicine, Zhejiang University, Hangzhou, Zhejiang Province, China; Alibaba-Zhejiang University Joint Research Center of Future Digital Healthcare, Hangzhou, Zhejiang Province, China; Department of Pathology, Research Unit of Intelligence Classification of Tumor Pathology and Precision Therapy, Chinese Academy of Medical Sciences (2019RU042), Key Laboratory of Disease Proteomics of Zhejiang Province, Zhejiang University School of Medicine, Hangzhou, Zhejiang Province, China.
| | - Dandan Zhang
- Department of Pathology, and Department of Medical Oncology of the Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang Province, China; Department of Pathology, Key Laboratory of Disease Proteomics of Zhejiang Province, School of Medicine, Zhejiang University, Hangzhou, Zhejiang Province, China; Alibaba-Zhejiang University Joint Research Center of Future Digital Healthcare, Hangzhou, Zhejiang Province, China; Department of Pathology, Research Unit of Intelligence Classification of Tumor Pathology and Precision Therapy, Chinese Academy of Medical Sciences (2019RU042), Key Laboratory of Disease Proteomics of Zhejiang Province, Zhejiang University School of Medicine, Hangzhou, Zhejiang Province, China.
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21
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Horvath RM, Brumme ZL, Sadowski I. Small molecule inhibitors of transcriptional cyclin-dependent kinases impose HIV-1 latency, presenting "block and lock" treatment strategies. Antimicrob Agents Chemother 2024; 68:e0107223. [PMID: 38319085 PMCID: PMC10923280 DOI: 10.1128/aac.01072-23] [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: 08/17/2023] [Accepted: 01/09/2024] [Indexed: 02/07/2024] Open
Abstract
Current antiretroviral therapy for HIV-1 infection does not represent a cure for infection as viral rebound inevitably occurs following discontinuation of treatment. The "block and lock" therapeutic strategy is intended to enforce proviral latency and durably suppress viremic reemergence in the absence of other intervention. The transcription-associated cyclin-dependent protein kinases (tCDKs) are required for expression from the 5´ HIV-1 long-terminal repeat, but the therapeutic potential of inhibiting these kinases for enforcing HIV-1 latency has not been characterized. Here, we expanded previous observations to directly compare the effect of highly selective small molecule inhibitors of CDK7 (YKL-5-124), CDK9 (LDC000067), and CDK8/19 (Senexin A), and found each of these prevented HIV-1 provirus expression at concentrations that did not cause cell toxicity. Inhibition of CDK7 caused cell cycle arrest, whereas CDK9 and CDK8/19 inhibitors did not, and could be continuously administered to establish proviral latency. Upon discontinuation of drug administration, HIV immediately rebounded in cells that had been treated with the CDK9 inhibitor, while proviral latency persisted for several days in cells that had been treated with CDK8/19 inhibitors. These results identify the mediator kinases CDK8/CDK19 as potential "block and lock" targets for therapeutic suppression of HIV-1 provirus expression.
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Affiliation(s)
- Riley M. Horvath
- Department of Biochemistry and Molecular Biology Molecular Epigenetics Group, LSI, University of British Columbia, Vancouver, British Columbia, Canada
| | - Zabrina L. Brumme
- Faculty of Health Sciences, Simon Fraser University, Burnaby, British Columbia, Canada
- British Columbia Centre for Excellence in HIV/AIDS, Vancouver, British Columbia, Canada
| | - Ivan Sadowski
- Department of Biochemistry and Molecular Biology Molecular Epigenetics Group, LSI, University of British Columbia, Vancouver, British Columbia, Canada
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22
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Li Q, Zhu G, Zhang L, Zeng B, Cai T, Wu J, Wei B, Xie Z, He L, Tang W, Lin X, Lu H, Wu F, Huang J, Hu H, Liu N, Fan S. Mutational landscape of head and neck cancer and cervical cancer in Chinese and Western population. Head Neck 2024; 46:528-540. [PMID: 38111234 DOI: 10.1002/hed.27603] [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: 04/29/2023] [Revised: 11/12/2023] [Accepted: 12/05/2023] [Indexed: 12/20/2023] Open
Abstract
BACKGROUND We aimed to unbiasedly map the genetic mutation profile of HNSC and CESC associated with HPV status in the Chinese population (SYSU-cohort) and compare them with Western population (TCGA-cohort). METHODS Fifty-one HNSC patients (SYSU-HNSC) and 38 CESC patients (SYSU-CESC) were enrolled in this study. Genomic alterations were examined, and the profile was produced using the YuanSuTM450 gene panel (OrigiMed, Shanghai, China). The altered genes were inferred and compared to Western patients from TCGA cohorts. RESULTS Compared to the TCGA-HNSC cohort, FGFR3 mutation was identified as a novel target in SYSU-HNSC with therapeutic potential. Compared to the TCGA-CESC cohort, some epigenetic regulation-associated genes were frequently mutated in SYSU-CESC cohort (KMT2C, KMT2D, KDM5C, KMT2A). CONCLUSION In summary, our study provides unbiased insights into the genetic landscape of HNSC and CESC in the Chinese population and highlights potential novel therapeutic targets that may benefit Chinese patients.
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Affiliation(s)
- Qunxing Li
- Department of Oral and Maxillofacial Surgery, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, China
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Sun Yat-sen Memorial Hospital, Guangzhou, China
| | - Genhai Zhu
- Department of Gynecology, Hainan General Hospital, Haikou, China
| | - Lizao Zhang
- Department of Oral and Maxillofacial Surgery, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, China
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Sun Yat-sen Memorial Hospital, Guangzhou, China
| | - Binghui Zeng
- Guanghua School of Stomatology, Hospital of Stomatology, Guangdong Provincial Key Laboratory of Stomatology, Sun Yat-sen University, Guangzhou, China
| | - Tingting Cai
- Department of Oral and Maxillofacial Surgery, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, China
| | - Jiaying Wu
- Department of Oral and Maxillofacial Surgery, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, China
| | - Bin Wei
- Department of Oral and Maxillofacial Surgery, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, China
| | - Zhijun Xie
- Department of Oral and Maxillofacial Surgery, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, China
| | - Lile He
- Department of Cardiovascular Surgery, The Second Xiangya Hospital, Central South University, Changsha, China
| | - Wenbing Tang
- Department of Stomatology, Guangdong Agriculture and Reclamation Central Hospital, Zhanjiang, China
| | - Xinyu Lin
- Department of Oral and Maxillofacial Surgery, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, China
| | - Huaiwu Lu
- Department of Gynecologic Oncology, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, China
| | - Fan Wu
- Department of Oral and Maxillofacial Surgery, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, China
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Sun Yat-sen Memorial Hospital, Guangzhou, China
| | | | - Huijun Hu
- Department of Radiology, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, China
| | - Niu Liu
- Department of Oral and Maxillofacial Surgery, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, China
| | - Song Fan
- Department of Oral and Maxillofacial Surgery, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, China
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Sun Yat-sen Memorial Hospital, Guangzhou, China
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23
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Zhang YL, Tang TT, Ni WJ, Li ZT, Jiang LYZ, Wang Y, Zhou X, Cao JY, Yin Q, Jiang W, Zhao YJ, Gan WH, Zhang AQ, Li ZL, Wen Y, Lv LL, Liu BC, Wang B. Tubule-specific cyclin-dependent kinase 12 knockdown potentiates kidney injury through transcriptional elongation defects. Int J Biol Sci 2024; 20:1669-1687. [PMID: 38481813 PMCID: PMC10929189 DOI: 10.7150/ijbs.90872] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2023] [Accepted: 01/17/2024] [Indexed: 07/18/2024] Open
Abstract
Direct tubular injury caused by several medications, especially chemotherapeutic drugs, is a common cause of AKI. Inhibition or loss of cyclin-dependent kinase 12 (CDK12) triggers a transcriptional elongation defect that results in deficiencies in DNA damage repair, producing genomic instability in a variety of cancers. Notably, 10-25% of individuals developed AKI after treatment with a CDK12 inhibitor, and the potential mechanism is not well understood. Here, we found that CDK12 was downregulated in the renal tubular epithelial cells in both patients with AKI and murine AKI models. Moreover, tubular cell-specific knockdown of CDK12 in mice enhanced cisplatin-induced AKI through promotion of genome instability, apoptosis, and proliferative inhibition, whereas CDK12 overexpression protected against AKI. Using the single molecule real-time (SMRT) platform on the kidneys of CDK12RTEC+/- mice, we found that CDK12 knockdown targeted Fgf1 and Cast through transcriptional elongation defects, thereby enhancing genome instability and apoptosis. Overall, these data demonstrated that CDK12 knockdown could potentiate the development of AKI by altering the transcriptional elongation defect of the Fgf1 and Cast genes, and more attention should be given to patients treated with CDK12 inhibitors to prevent AKI.
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Affiliation(s)
- Yi-Lin Zhang
- Institute of Nephrology, Zhong Da Hospital, Southeast University School of Medicine, Nanjing, Jiangsu, China
| | - Tao-Tao Tang
- Institute of Nephrology, Zhong Da Hospital, Southeast University School of Medicine, Nanjing, Jiangsu, China
| | - Wei-Jie Ni
- Institute of Nephrology, Zhong Da Hospital, Southeast University School of Medicine, Nanjing, Jiangsu, China
| | - Zhong-Tang Li
- Nanjing University of Traditional Chinese Medicine, Nanjing, Jiangsu, China
| | - Liang-Yun-Zi Jiang
- Institute of Nephrology, Zhong Da Hospital, Southeast University School of Medicine, Nanjing, Jiangsu, China
| | - Yao Wang
- Department of Nephrology, The Affiliated Hospital of Yangzhou University, Yangzhou University, Yangzhou, Jiangsu, China
| | - Xuan Zhou
- Shanghai OE Biotech Co., Ltd., Shanghai, China
| | - Jing-Yuan Cao
- Institute of Nephrology, The Affiliated Taizhou People's Hospital of Nanjing Medical University, Taizhou School of Clinical Medicine, Nanjing Medical University, Nanjing, Jinagsu, China
| | - Qing Yin
- Institute of Nephrology, Zhong Da Hospital, Southeast University School of Medicine, Nanjing, Jiangsu, China
| | - Wei Jiang
- Institute of Nephrology, Zhong Da Hospital, Southeast University School of Medicine, Nanjing, Jiangsu, China
| | - Ya-Jie Zhao
- Department of Pediatric Nephrology, the Second Affiliated Hospital of Nanjing Medical University, Nanjing, Jiangsu, China
| | - Wei-Hua Gan
- Department of Pediatric Nephrology, the Second Affiliated Hospital of Nanjing Medical University, Nanjing, Jiangsu, China
| | - Ai-Qing Zhang
- Department of Pediatric Nephrology, the Second Affiliated Hospital of Nanjing Medical University, Nanjing, Jiangsu, China
| | - Zuo-Lin Li
- Institute of Nephrology, Zhong Da Hospital, Southeast University School of Medicine, Nanjing, Jiangsu, China
| | - Yi Wen
- Institute of Nephrology, Zhong Da Hospital, Southeast University School of Medicine, Nanjing, Jiangsu, China
| | - Lin-Li Lv
- Institute of Nephrology, Zhong Da Hospital, Southeast University School of Medicine, Nanjing, Jiangsu, China
| | - Bi-Cheng Liu
- Institute of Nephrology, Zhong Da Hospital, Southeast University School of Medicine, Nanjing, Jiangsu, China
| | - Bin Wang
- Institute of Nephrology, Zhong Da Hospital, Southeast University School of Medicine, Nanjing, Jiangsu, China
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24
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O'Malley DE, Raspin K, Melton PE, Burdon KP, Dickinson JL, FitzGerald LM. Acquired copy number variation in prostate tumours: a review of common somatic copy number alterations, how they are formed and their clinical utility. Br J Cancer 2024; 130:347-357. [PMID: 37945750 PMCID: PMC10844642 DOI: 10.1038/s41416-023-02485-7] [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: 12/05/2022] [Revised: 10/23/2023] [Accepted: 10/27/2023] [Indexed: 11/12/2023] Open
Abstract
Prostate cancer is one of the most commonly diagnosed cancers in men and unfortunately, disease will progress in up to a third of patients despite primary treatment. Currently, there is a significant lack of prognostic tests that accurately predict disease course; however, the acquisition of somatic chromosomal variation in the form of DNA copy number variants may help understand disease progression. Notably, studies have found that a higher burden of somatic copy number alterations (SCNA) correlates with more aggressive disease, recurrence after surgery and metastasis. Here we will review the literature surrounding SCNA formation, including the roles of key tumour suppressors and oncogenes (PTEN, BRCA2, NKX3.1, ERG and AR), and their potential to inform diagnostic and prognostic clinical testing to improve predictive value. Ultimately, SCNAs, or inherited germline alterations that predispose to SCNAs, could have significant clinical utility in diagnostic and prognostic tests, in addition to guiding therapeutic selection.
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Affiliation(s)
- Dannielle E O'Malley
- Menzies Institute for Medical Research, University of Tasmania, 17 Liverpool Street, Hobart, TAS, 7000, Australia
| | - Kelsie Raspin
- Menzies Institute for Medical Research, University of Tasmania, 17 Liverpool Street, Hobart, TAS, 7000, Australia
| | - Phillip E Melton
- Menzies Institute for Medical Research, University of Tasmania, 17 Liverpool Street, Hobart, TAS, 7000, Australia
- School of Population and Global Health, The University of Western Australia, Crawley, WA, Australia
| | - Kathryn P Burdon
- Menzies Institute for Medical Research, University of Tasmania, 17 Liverpool Street, Hobart, TAS, 7000, Australia
| | - Joanne L Dickinson
- Menzies Institute for Medical Research, University of Tasmania, 17 Liverpool Street, Hobart, TAS, 7000, Australia
| | - Liesel M FitzGerald
- Menzies Institute for Medical Research, University of Tasmania, 17 Liverpool Street, Hobart, TAS, 7000, Australia.
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25
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Zheng M, Zhang XY, Chen W, Xia F, Yang H, Yuan K, Yang P. Molecules inducing specific cyclin-dependent kinase degradation and their possible use in cancer therapy. Future Med Chem 2024; 16:369-388. [PMID: 38288571 DOI: 10.4155/fmc-2023-0259] [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: 09/01/2023] [Accepted: 01/12/2024] [Indexed: 02/07/2024] Open
Abstract
Cyclin-dependent kinases (CDKs) play an important role in the regulation of cell proliferation, and many CDK inhibitors were developed. However, pan-CDK inhibitors failed to be approved due to intolerant toxicity or low efficacy and the use of selective CDK4/6 inhibitors is limited by resistance. Protein degraders have the potential to increase selectivity, efficacy and overcome resistance, which provides a novel strategy for regulating CDKs. In this review, we summarized the function of CDKs in regulating the cell cycle and transcription, and introduced the representative CDK inhibitors. Then we made a detailed introduction about four types of CDKs degraders, including their action mechanisms, research status and application prospects, which could help the development of novel CDKs degraders.
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Affiliation(s)
- Mingming Zheng
- State Key Laboratory of Natural Medicines and Jiangsu Key Laboratory of Drug Design and Optimization, China Pharmaceutical University, Nanjing, 210009, China
- Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, Nanjing, 211198, China
| | - Xiao-Yu Zhang
- State Key Laboratory of Natural Medicines and Jiangsu Key Laboratory of Drug Design and Optimization, China Pharmaceutical University, Nanjing, 210009, China
- Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, Nanjing, 211198, China
| | - Weijiao Chen
- State Key Laboratory of Natural Medicines and Jiangsu Key Laboratory of Drug Design and Optimization, China Pharmaceutical University, Nanjing, 210009, China
- Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, Nanjing, 211198, China
| | - Fei Xia
- State Key Laboratory of Natural Medicines and Jiangsu Key Laboratory of Drug Design and Optimization, China Pharmaceutical University, Nanjing, 210009, China
- Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, Nanjing, 211198, China
| | - Huanaoyu Yang
- State Key Laboratory of Natural Medicines and Jiangsu Key Laboratory of Drug Design and Optimization, China Pharmaceutical University, Nanjing, 210009, China
- Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, Nanjing, 211198, China
| | - Kai Yuan
- State Key Laboratory of Natural Medicines and Jiangsu Key Laboratory of Drug Design and Optimization, China Pharmaceutical University, Nanjing, 210009, China
- Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, Nanjing, 211198, China
| | - Peng Yang
- State Key Laboratory of Natural Medicines and Jiangsu Key Laboratory of Drug Design and Optimization, China Pharmaceutical University, Nanjing, 210009, China
- Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, Nanjing, 211198, China
- Institute of Innovative Drug Discovery and Development, China Pharmaceutical University, Nanjing, 211198, China
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26
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Dunn LEM, Birkenheuer CH, Baines JD. A Revision of Herpes Simplex Virus Type 1 Transcription: First, Repress; Then, Express. Microorganisms 2024; 12:262. [PMID: 38399666 PMCID: PMC10892140 DOI: 10.3390/microorganisms12020262] [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: 12/15/2023] [Revised: 01/22/2024] [Accepted: 01/24/2024] [Indexed: 02/25/2024] Open
Abstract
The herpes virus genome bears more than 80 strong transcriptional promoters. Upon entry into the host cell nucleus, these genes are transcribed in an orderly manner, producing five immediate-early (IE) gene products, including ICP0, ICP4, and ICP22, while non-IE genes are mostly silent. The IE gene products are necessary for the transcription of temporal classes following sequentially as early, leaky late, and true late. A recent analysis using precision nuclear run-on followed by deep sequencing (PRO-seq) has revealed an important step preceding all HSV-1 transcription. Specifically, the immediate-early proteins ICP4 and ICP0 enter the cell with the incoming genome to help preclude the nascent antisense, intergenic, and sense transcription of all viral genes. VP16, which is also delivered into the nucleus upon entry, almost immediately reverses this repression on IE genes. The resulting de novo expression of ICP4 and ICP22 further repress antisense, intergenic, and early and late viral gene transcription through different mechanisms before the sequential de-repression of these gene classes later in infection. This early repression, termed transient immediate-early protein-mediated repression (TIEMR), precludes unproductive, antisense, intergenic, and late gene transcription early in infection to ensure the efficient and orderly progression of the viral cascade.
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Affiliation(s)
- Laura E M Dunn
- Baker Institute for Animal Health, Department of Microbiology and Immunology, Cornell University, Ithaca, NY 14850, USA
| | - Claire H Birkenheuer
- Baker Institute for Animal Health, Department of Microbiology and Immunology, Cornell University, Ithaca, NY 14850, USA
| | - Joel D Baines
- Baker Institute for Animal Health, Department of Microbiology and Immunology, Cornell University, Ithaca, NY 14850, USA
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27
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Khamidullina AI, Abramenko YE, Bruter AV, Tatarskiy VV. Key Proteins of Replication Stress Response and Cell Cycle Control as Cancer Therapy Targets. Int J Mol Sci 2024; 25:1263. [PMID: 38279263 PMCID: PMC10816012 DOI: 10.3390/ijms25021263] [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: 12/07/2023] [Revised: 01/14/2024] [Accepted: 01/17/2024] [Indexed: 01/28/2024] Open
Abstract
Replication stress (RS) is a characteristic state of cancer cells as they tend to exchange precision of replication for fast proliferation and increased genomic instability. To overcome the consequences of improper replication control, malignant cells frequently inactivate parts of their DNA damage response (DDR) pathways (the ATM-CHK2-p53 pathway), while relying on other pathways which help to maintain replication fork stability (ATR-CHK1). This creates a dependency on the remaining DDR pathways, vulnerability to further destabilization of replication and synthetic lethality of DDR inhibitors with common oncogenic alterations such as mutations of TP53, RB1, ATM, amplifications of MYC, CCNE1 and others. The response to RS is normally limited by coordination of cell cycle, transcription and replication. Inhibition of WEE1 and PKMYT1 kinases, which prevent unscheduled mitosis entry, leads to fragility of under-replicated sites. Recent evidence also shows that inhibition of Cyclin-dependent kinases (CDKs), such as CDK4/6, CDK2, CDK8/19 and CDK12/13 can contribute to RS through disruption of DNA repair and replication control. Here, we review the main causes of RS in cancers as well as main therapeutic targets-ATR, CHK1, PARP and their inhibitors.
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Affiliation(s)
- Alvina I. Khamidullina
- Laboratory of Molecular Oncobiology, Institute of Gene Biology, Russian Academy of Sciences, 34/5 Vavilov Street, 119334 Moscow, Russia; (A.I.K.); (Y.E.A.)
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Institute of Gene Biology, Russian Academy of Sciences, 34/5 Vavilov Street, 119334 Moscow, Russia
| | - Yaroslav E. Abramenko
- Laboratory of Molecular Oncobiology, Institute of Gene Biology, Russian Academy of Sciences, 34/5 Vavilov Street, 119334 Moscow, Russia; (A.I.K.); (Y.E.A.)
| | - Alexandra V. Bruter
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Institute of Gene Biology, Russian Academy of Sciences, 34/5 Vavilov Street, 119334 Moscow, Russia
| | - Victor V. Tatarskiy
- Laboratory of Molecular Oncobiology, Institute of Gene Biology, Russian Academy of Sciences, 34/5 Vavilov Street, 119334 Moscow, Russia; (A.I.K.); (Y.E.A.)
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Institute of Gene Biology, Russian Academy of Sciences, 34/5 Vavilov Street, 119334 Moscow, Russia
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28
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Kuchukulla RR, Hwang I, Kim SH, Kye Y, Park N, Cha H, Moon S, Chung HW, Lee C, Kong G, Hur W. Identification of a novel potent CDK inhibitor degrading cyclinK with a superb activity to reverse trastuzumab-resistance in HER2-positive breast cancer in vivo. Eur J Med Chem 2024; 264:116014. [PMID: 38061230 DOI: 10.1016/j.ejmech.2023.116014] [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: 09/21/2023] [Revised: 11/19/2023] [Accepted: 11/26/2023] [Indexed: 12/30/2023]
Abstract
CDK12 is overexpressed in HER2-positive breast cancers and promotes tumorigenesis and trastuzumab resistance. Thus CDK12 is a good therapeutic target for the HER2-positive breast tumors resistant to trastuzumab. We previously reported a novel purine-based CDK inhibitor with an ability to degrade cyclinK. Herein, we further explored and synthesized new derivatives, and identified a new potent pan-CDK inhibitor degrading cyclinK (32e). Compound 32e potently inhibited CDK12/cyclinK with IC50 = 3 nM, and suppressed the growth of the both trastuzumab-sensitive and trastuzumab-resistant HER2-positive breast cancer cell lines (GI50's = 9-21 nM), which is superior to a potent, clinical pan-CDK inhibitor dinaciclib. Moreover, 32e (10, 20 mg/kg, ip, twice a week) showed a dose-dependent inhibition of tumor growth and a more dramatic anti-cancer effect than dinaciclib in mouse in vivo orthotopic breast cancer model of trastuzumab-resistant HCC1954 cells. Kinome-wide inhibition profiling revealed that 32e at 1 μM exhibits a decent selectivity toward CDK-family kinases including CDK12 over other wildtype protein kinases. Quantitative global proteomic analysis of 32e-treated HCC1954 cells demonstrated that 32e also showed a decent selectivity in degrading cyclinK over other cyclins. Compound 32e could be developed as a drug for intractable trastuzumab-resistant HER2-positive breast cancers. Our current study would provide a useful insight in designing potent cyclinK degraders.
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Affiliation(s)
- Ratnakar Reddy Kuchukulla
- HY-KIST Bioconvergence, Hanyang University, 222 Wangsimniro, Seongdong-gu, Seoul, 04763, Republic of Korea
| | - Injeoung Hwang
- HY-KIST Bioconvergence, Hanyang University, 222 Wangsimniro, Seongdong-gu, Seoul, 04763, Republic of Korea; Medicinal Materials Research Center, Korea Institute of Science and Technology (KIST), 5 Hwarangro 14 gil, Seongbuk-gu, Seoul, 02792, Republic of Korea
| | - Suhn Hyung Kim
- Medicinal Materials Research Center, Korea Institute of Science and Technology (KIST), 5 Hwarangro 14 gil, Seongbuk-gu, Seoul, 02792, Republic of Korea
| | - Younghyeon Kye
- HY-KIST Bioconvergence, Hanyang University, 222 Wangsimniro, Seongdong-gu, Seoul, 04763, Republic of Korea
| | - Narae Park
- Chemical & Biological Integrative Research Center, Korea Institute of Science and Technology (KIST), 5 Hwarangro 14 gil, Seongbuk-gu, Seoul, 02792, Republic of Korea; KHU-KIST Department of Converging Science and Technology, Kyung Hee University, 26 Kyungheedaero, Dongdaemun-gu, Seoul, 02447, Republic of Korea
| | - Heary Cha
- HY-KIST Bioconvergence, Hanyang University, 222 Wangsimniro, Seongdong-gu, Seoul, 04763, Republic of Korea
| | - Sojeong Moon
- HY-KIST Bioconvergence, Hanyang University, 222 Wangsimniro, Seongdong-gu, Seoul, 04763, Republic of Korea
| | - Hwan Won Chung
- Computational Science Research Center, Korea Institute of Science and Technology (KIST), 5 Hwarangro 14 gil, Seongbuk-gu, Seoul, 02792, Republic of Korea
| | - Cheolju Lee
- Chemical & Biological Integrative Research Center, Korea Institute of Science and Technology (KIST), 5 Hwarangro 14 gil, Seongbuk-gu, Seoul, 02792, Republic of Korea
| | - Gu Kong
- HY-KIST Bioconvergence, Hanyang University, 222 Wangsimniro, Seongdong-gu, Seoul, 04763, Republic of Korea; Medicinal Materials Research Center, Korea Institute of Science and Technology (KIST), 5 Hwarangro 14 gil, Seongbuk-gu, Seoul, 02792, Republic of Korea; Department of Pathology, Hanyang University College of Medicine, 222 Wangsimniro, Seongdong-gu, Seoul, 04763, Republic of Korea.
| | - Wooyoung Hur
- HY-KIST Bioconvergence, Hanyang University, 222 Wangsimniro, Seongdong-gu, Seoul, 04763, Republic of Korea; Medicinal Materials Research Center, Korea Institute of Science and Technology (KIST), 5 Hwarangro 14 gil, Seongbuk-gu, Seoul, 02792, Republic of Korea.
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29
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Yang Y, Badura ML, O’Leary PC, Delavan HM, Robinson TM, Egusa EA, Zhong X, Swinderman JT, Li H, Zhang M, Kim M, Ashworth A, Feng FY, Chou J, Yang L. Large tandem duplications in cancer result from transcription and DNA replication collisions. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2024:2023.05.17.23290140. [PMID: 38260434 PMCID: PMC10802642 DOI: 10.1101/2023.05.17.23290140] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/24/2024]
Abstract
Despite the abundance of somatic structural variations (SVs) in cancer, the underlying molecular mechanisms of their formation remain unclear. Here, we use 6,193 whole-genome sequenced tumors to study the contributions of transcription and DNA replication collisions to genome instability. After deconvoluting robust SV signatures in three independent pan-cancer cohorts, we detect transcription-dependent replicated-strand bias, the expected footprint of transcription-replication collision (TRC), in large tandem duplications (TDs). Large TDs are abundant in female-enriched, upper gastrointestinal tract and prostate cancers. They are associated with poor patient survival and mutations in TP53, CDK12, and SPOP. Upon inactivating CDK12, cells display significantly more TRCs, R-loops, and large TDs. Inhibition of G2/M checkpoint proteins, such as WEE1, CHK1, and ATR, selectively inhibits the growth of cells deficient in CDK12. Our data suggest that large TDs in cancer form due to TRCs, and their presence can be used as a biomarker for prognosis and treatment.
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Affiliation(s)
- Yang Yang
- Ben May Department for Cancer Research, University of Chicago, Chicago, IL, USA
| | - Michelle L. Badura
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, CA, USA
- Departments of Radiation Oncology and Urology, University of California, San Francisco, CA, USA
| | - Patrick C. O’Leary
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, CA, USA
| | - Henry M. Delavan
- 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
| | - Troy M. Robinson
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, CA, USA
- Departments of Radiation Oncology and Urology, University of California, San Francisco, CA, USA
| | - Emily A. Egusa
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, CA, USA
- Departments of Radiation Oncology and Urology, University of California, San Francisco, CA, USA
| | - Xiaoming Zhong
- Ben May Department for Cancer Research, University of Chicago, Chicago, IL, USA
| | - Jason T. Swinderman
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, CA, USA
- Departments of Radiation Oncology and Urology, University of California, San Francisco, CA, USA
| | - Haolong Li
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, CA, USA
- Departments of Radiation Oncology and Urology, University of California, San Francisco, CA, USA
| | - Meng Zhang
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, CA, USA
- Departments of Radiation Oncology and Urology, University of California, San Francisco, CA, USA
| | - Minkyu Kim
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, CA, USA
- Department of Cellular Molecular Pharmacology, University of California San Francisco, San Francisco, CA, USA
| | - Alan Ashworth
- 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
| | - Felix Y. Feng
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, CA, USA
- Departments of Radiation Oncology and Urology, University of California, San Francisco, CA, USA
- Division of Hematology/Oncology, Department of Medicine, University of California, San Francisco, CA, USA
| | - 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
| | - Lixing Yang
- Ben May Department for Cancer Research, University of Chicago, Chicago, IL, USA
- Department of Human Genetics, University of Chicago, Chicago, IL, USA
- University of Chicago Comprehensive Cancer Center, Chicago, IL, USA
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30
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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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31
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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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32
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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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33
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Dai W, Wang H, Zhan Y, Li N, Li F, Wang J, Yan H, Zhang Y, Wang J, Wu L, Liu H, Fan Y, Tao Y, Mo X, Yang JJ, Sun K, Chen G, Yu Y. CCNK Gene Deficiency Influences Neural Progenitor Cells Via Wnt5a Signaling in CCNK-Related Syndrome. Ann Neurol 2023; 94:1136-1154. [PMID: 37597256 DOI: 10.1002/ana.26766] [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: 02/13/2023] [Revised: 08/07/2023] [Accepted: 08/11/2023] [Indexed: 08/21/2023]
Abstract
OBJECTIVE Rare variants of CCNK (cyclin K) give rise to a syndrome with intellectual disability. The purpose of this study was to describe the genotype-phenotype spectrum of CCNK-related syndrome and the underlying molecular mechanisms of pathogenesis. METHODS We identified a number of de novo CCNK variants in unrelated patients. We generated patient-induced pluripotent stem cells (iPSCs) and neural progenitor cells (NPCs) as disease models. In addition, we constructed NPC-specific Ccnk knockout (KO) mice and performed molecular and morphological analyses. RESULTS We identified 2 new patients harboring CCNK missense variants and followed-up 3 previous reported patients, which constitute the largest patient population analysis of the disease. We demonstrate that both the patient-derived NPC models and the Ccnk KO mouse displayed deficient NPC proliferation and enhanced apoptotic cell death. RNA sequencing analyses of these NPC models uncovered transcriptomic signatures unique to CCNK-related syndrome, revealing significant changes in genes, including WNT5A, critical for progenitor proliferation and cell death. Further, to confirm WNT5A's role, we conducted rescue experiments using NPC and mouse models. We found that a Wnt5a inhibitor significantly increased proliferation and reduced apoptosis in NPCs derived from patients with CCNK-related syndrome and NPCs in the developing cortex of Ccnk KO mice. INTERPRETATION We discussed the genotype-phenotype relationship of CCNK-related syndrome. Importantly, we demonstrated that CCNK plays critical roles in NPC proliferation and NPC apoptosis in vivo and in vitro. Together, our study highlights that Wnt5a may serve as a promising therapeutic target for the disease intervention. ANN NEUROL 2023;94:1136-1154.
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Affiliation(s)
- Weiqian Dai
- Department of Pediatric Endocrinology and Genetics, Xinhua Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai Institute for Pediatric Research, Shanghai, China
| | - He Wang
- Department of Anesthesiology, Pain and Perioperative Medicine, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Yongkun Zhan
- Department of Pediatric Endocrinology and Genetics, Xinhua Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai Institute for Pediatric Research, Shanghai, China
| | - Nan Li
- Department of Pediatric Endocrinology and Genetics, Xinhua Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai Institute for Pediatric Research, Shanghai, China
| | - Fei Li
- Department of Developmental and Behavioral Pediatrics, Department of Child Primary Care, Brain and Behavioral Research Unit of Shanghai Institute for Pediatric Research and MOE-Shanghai Key Laboratory for Children's Environmental Health, Xinhua Hospital, School of Medicine, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Jingmin Wang
- Departmentof Pediatrics, Peking University First Hospital, Beijing, China
| | - Huifang Yan
- Departmentof Pediatrics, Peking University First Hospital, Beijing, China
| | - Yu Zhang
- Departmentof Pediatrics, Peking University First Hospital, Beijing, China
| | - Junyu Wang
- Departmentof Pediatrics, Peking University First Hospital, Beijing, China
| | - Lingqian Wu
- State Key Laboratory of Medical Genetics, Central South University, Changsha, China
| | - Huili Liu
- Department of Pediatric Endocrinology and Genetics, Xinhua Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai Institute for Pediatric Research, Shanghai, China
| | - Yanjie Fan
- Department of Pediatric Endocrinology and Genetics, Xinhua Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai Institute for Pediatric Research, Shanghai, China
| | - Yue Tao
- Pediatric Translational Medicine Institute, Shanghai Children's Medical Center, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Xi Mo
- Pediatric Translational Medicine Institute, Shanghai Children's Medical Center, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Jian-Jun Yang
- Department of Anesthesiology, Pain and Perioperative Medicine, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Kun Sun
- Department of Pediatric Cardiovascular, Center of Clinical Genetics, Xinhua Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Guiquan Chen
- MOE Key Laboratory of Model Animal for Disease Study, Model Animal Research Center, Medical School, Nanjing University, Nanjing, China
| | - Yongguo Yu
- Department of Pediatric Endocrinology and Genetics, Xinhua Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai Institute for Pediatric Research, Shanghai, China
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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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35
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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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36
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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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37
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Davoudi F, Moradi A, Becker TM, Lock JG, Abbey B, Fontanarosa D, Haworth A, Clements J, Ecker RC, Batra J. Genomic and Phenotypic Biomarkers for Precision Medicine Guidance in Advanced Prostate Cancer. Curr Treat Options Oncol 2023; 24:1451-1471. [PMID: 37561382 PMCID: PMC10547634 DOI: 10.1007/s11864-023-01121-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/21/2023] [Indexed: 08/11/2023]
Abstract
OPINION STATEMENT Prostate cancer (PCa) is the second most diagnosed malignant neoplasm and is one of the leading causes of cancer-related death in men worldwide. Despite significant advances in screening and treatment of PCa, given the heterogeneity of this disease, optimal personalized therapeutic strategies remain limited. However, emerging predictive and prognostic biomarkers based on individual patient profiles in combination with computer-assisted diagnostics have the potential to guide precision medicine, where patients may benefit from therapeutic approaches optimally suited to their disease. Also, the integration of genotypic and phenotypic diagnostic methods is supporting better informed treatment decisions. Focusing on advanced PCa, this review discusses polygenic risk scores for screening of PCa and common genomic aberrations in androgen receptor (AR), PTEN-PI3K-AKT, and DNA damage response (DDR) pathways, considering clinical implications for diagnosis, prognosis, and treatment prediction. Furthermore, we evaluate liquid biopsy, protein biomarkers such as serum testosterone levels, SLFN11 expression, total alkaline phosphatase (tALP), neutrophil-to-lymphocyte ratio (NLR), tissue biopsy, and advanced imaging tools, summarizing current phenotypic biomarkers and envisaging more effective utilization of diagnostic and prognostic biomarkers in advanced PCa. We conclude that prognostic and treatment predictive biomarker discovery can improve the management of patients, especially in metastatic stages of advanced PCa. This will result in decreased mortality and enhanced quality of life and help design a personalized treatment regimen.
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Affiliation(s)
- Fatemeh Davoudi
- School of Biomedical Sciences, Faculty of Health, Queensland University of Technology, Brisbane, 4059 Australia
- Department of Medical Genetics, School of Medicine, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran
| | - Afshin Moradi
- School of Biomedical Sciences, Faculty of Health, Queensland University of Technology, Brisbane, 4059 Australia
- Centre for Genomics and Personalised Health, Queensland University of Technology, Brisbane, 4059 Australia
- Translational Research Institute, Queensland University of Technology, Brisbane, 4102 Australia
| | - Therese M. Becker
- Ingham Institute for Applied Medical Research, University of Western Sydney and University of New South Wales, Liverpool, 2170 Australia
| | - John G. Lock
- Ingham Institute for Applied Medical Research, University of Western Sydney and University of New South Wales, Liverpool, 2170 Australia
- School of Biomedical Sciences, Faculty of Medicine and Health, University of New South Wales, Sydney, 2052 Australia
| | - Brian Abbey
- Department of Mathematical and Physical Sciences, School of Computing Engineering and Mathematical Sciences, La Trobe Institute for Molecular Sciences, La Trobe University, Bundoora, VIC Australia
| | - Davide Fontanarosa
- School of Clinical Sciences, Queensland University of Technology, Gardens Point Campus, 2 George St, Brisbane, QLD 4000 Australia
- Centre for Biomedical Technologies (CBT), Queensland University of Technology, Brisbane, QLD 4000 Australia
| | - Annette Haworth
- Institute of Medical Physics, School of Physics, University of Sydney, Camperdown, NSW 2006 Australia
| | - Judith Clements
- School of Biomedical Sciences, Faculty of Health, Queensland University of Technology, Brisbane, 4059 Australia
- Translational Research Institute, Queensland University of Technology, Brisbane, 4102 Australia
| | - Rupert C. Ecker
- School of Biomedical Sciences, Faculty of Health, Queensland University of Technology, Brisbane, 4059 Australia
- Translational Research Institute, Queensland University of Technology, Brisbane, 4102 Australia
- TissueGnostics GmbH, EU 1020 Vienna, Austria
| | - Jyotsna Batra
- School of Biomedical Sciences, Faculty of Health, Queensland University of Technology, Brisbane, 4059 Australia
- Centre for Genomics and Personalised Health, Queensland University of Technology, Brisbane, 4059 Australia
- Translational Research Institute, Queensland University of Technology, Brisbane, 4102 Australia
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38
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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, NC22710
| | - Natalia Sutiman
- Duke-National University of Singapore Medical School,Singapore169857, Singapore
| | - Xinyue L. Deng
- Department of Pharmacology & Cancer Biology, Duke University School of Medicine, Durham, NC22710
| | - Annie Liu
- Department of Pharmacology & Cancer Biology, Duke University School of Medicine, Durham, NC22710
- Department of Surgery, Duke University School of Medicine, Durham, NC22710
| | - Christian G. Cerda-Smith
- Department of Pharmacology & Cancer Biology, Duke University School of Medicine, Durham, NC22710
| | - Haley M. Hutchinson
- Department of Pharmacology & Cancer Biology, Duke University School of Medicine, Durham, NC22710
| | - Holly Kim
- Department of Pharmacology & Cancer Biology, Duke University School of Medicine, Durham, NC22710
| | - Luke C. Bartelt
- Duke Center for Genomic and Computational Biology, Department of Biostatistics and Bioinformatics, Duke University School of Medicine, Durham, NC27708
| | - Qiang Chen
- Department of Cell Biology, Duke University School of Medicine, Durham, NC22710
| | - Alejandro Barrera
- Duke Center for Genomic and Computational Biology, Department of Biostatistics and Bioinformatics, Duke University School of Medicine, Durham, NC27708
- Department of Biostatistics and Bioinformatics, Duke University School of Medicine, Durham, NC27708
| | - Jiaxing Lin
- Bioinformatics Shared Resources, Duke Cancer Institute, Duke University Medical Center, Durham, NC27705
| | - Zhecheng Sheng
- Bioinformatics Shared Resources, Duke Cancer Institute, Duke University Medical Center, Durham, NC27705
| | - Ian C. McDowell
- Duke Center for Genomic and Computational Biology, Department of Biostatistics and Bioinformatics, Duke University School of Medicine, Durham, NC27708
- Department of Biostatistics and Bioinformatics, Duke University School of Medicine, Durham, NC27708
| | - Timothy E. Reddy
- Duke Center for Genomic and Computational Biology, Department of Biostatistics and Bioinformatics, Duke University School of Medicine, Durham, NC27708
- Department of Biostatistics and Bioinformatics, Duke University School of Medicine, Durham, NC27708
| | | | - Kris C. Wood
- Department of Pharmacology & Cancer Biology, Duke University School of Medicine, Durham, NC22710
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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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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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Sarkar GC, Rautela U, Goyala A, Datta S, Anand N, Singh A, Singh P, Chamoli M, Mukhopadhyay A. DNA damage signals from somatic uterine tissue arrest oogenesis through activated DAF-16. Development 2023; 150:dev201472. [PMID: 37577954 DOI: 10.1242/dev.201472] [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: 11/24/2022] [Accepted: 07/21/2023] [Indexed: 08/15/2023]
Abstract
Germ line integrity is crucial for progeny fitness. Organisms deploy the DNA damage response (DDR) signaling to protect the germ line from genotoxic stress, facilitating the cell-cycle arrest of germ cells and DNA repair or their apoptosis. Cell-autonomous regulation of germ line quality in response to DNA damage is well studied; however, how quality is enforced cell non-autonomously on sensing somatic DNA damage is less known. Using Caenorhabditis elegans, we show that DDR disruption, only in the uterus, when insulin/IGF-1 signaling (IIS) is low, arrests oogenesis in the pachytene stage of meiosis I, in a FOXO/DAF-16 transcription factor-dependent manner. Without FOXO/DAF-16, germ cells of the IIS mutant escape the arrest to produce poor-quality oocytes, showing that the transcription factor imposes strict quality control during low IIS. Activated FOXO/DAF-16 senses DDR perturbations during low IIS to lower ERK/MPK-1 signaling below a threshold to promote germ line arrest. Altogether, we elucidate a new surveillance role for activated FOXO/DAF-16 that ensures optimal germ cell quality and progeny fitness in response to somatic DNA damage.
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Affiliation(s)
- Gautam Chandra Sarkar
- Molecular Aging Laboratory, National Institute of Immunology, Aruna Asaf Ali Marg, New Delhi 110067, India
| | - Umanshi Rautela
- Molecular Aging Laboratory, National Institute of Immunology, Aruna Asaf Ali Marg, New Delhi 110067, India
| | - Anita Goyala
- Molecular Aging Laboratory, National Institute of Immunology, Aruna Asaf Ali Marg, New Delhi 110067, India
| | - Sudeshna Datta
- Molecular Aging Laboratory, National Institute of Immunology, Aruna Asaf Ali Marg, New Delhi 110067, India
| | - Nikhita Anand
- Molecular Aging Laboratory, National Institute of Immunology, Aruna Asaf Ali Marg, New Delhi 110067, India
| | - Anupama Singh
- Molecular Aging Laboratory, National Institute of Immunology, Aruna Asaf Ali Marg, New Delhi 110067, India
| | - Prachi Singh
- Molecular Aging Laboratory, National Institute of Immunology, Aruna Asaf Ali Marg, New Delhi 110067, India
| | - Manish Chamoli
- Molecular Aging Laboratory, National Institute of Immunology, Aruna Asaf Ali Marg, New Delhi 110067, India
| | - Arnab Mukhopadhyay
- Molecular Aging Laboratory, National Institute of Immunology, Aruna Asaf Ali Marg, New Delhi 110067, India
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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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Lin S, Jiang Q, Huang X, Xu J, Wu L, Liu Y. Synthesis of Novel Dual Target Inhibitors of CDK12 and PARP1 and Their Antitumor Activities in HER2-Positive Breast Cancers. ACS OMEGA 2023; 8:25574-25581. [PMID: 37483237 PMCID: PMC10357520 DOI: 10.1021/acsomega.3c02912] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/15/2023] [Accepted: 06/23/2023] [Indexed: 07/25/2023]
Abstract
Several anti-human epidermal growth factor receptor 2 (HER2) treatments have improved the landscape of HER2-positive breast cancer (BC) over the past few years; due to the heterogeneity of the disease itself, the drug resistance mechanisms and relapse are still the main issue in HER2-positive BC. Here, we intended to target simultaneous inhibition of both poly ADP-ribose polymerase 1 (PARP1) and cyclin-dependent kinase 12 (CDK12) that have had an impact on this disease up to their implementation in clinical practice. We successfully screened PARP1 inhibitors (PARPis) containing bicyclic tetrahydropyridine pyrimidines with antitumor activity. Most synthesized compounds with various alcohols were more effective at killing tumor cells than olaparib (ola), especially in HER2-positive cancer cells. Among them, compound 9 showed potent inhibitory effects on PARP1 enzymatic activity and the PAR protein level; moreover, the expression of CDK12 was inhibited by compound 9. Overall, compound 9 exhibited a significant antitumor effect by inhibiting DNA damage repair in tumors.
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Affiliation(s)
- Shanshan Lin
- Department
of Pharmacy, The Second Affiliated Hospital
of Fujian Medical University, Quanzhou 362046, P. R. China
- Department
of Pharmacology, School of Pharmacy, Fujian
Medical University (FMU), Fuzhou 350108, P. R. China
| | - Qingna Jiang
- Department
of Pharmacology, School of Pharmacy, Fujian
Medical University (FMU), Fuzhou 350108, P. R. China
| | - Xiuwang Huang
- Department
of Public Technology Service Center, Fujian
Medical University (FMU), Fuzhou 350108, P. R. China
| | - Jianhua Xu
- Department
of Pharmacology, School of Pharmacy, Fujian
Medical University (FMU), Fuzhou 350108, P. R. China
| | - Lixian Wu
- Department
of Pharmacology, School of Pharmacy, Fujian
Medical University (FMU), Fuzhou 350108, P. R. China
- Fujian
Key Laboratory of Natural Medicine Pharmacology, Fujian Medical University (FMU), Fuzhou 350108, PR China
| | - Yang Liu
- Fujian
Key Laboratory of Natural Medicine Pharmacology, Fujian Medical University (FMU), Fuzhou 350108, PR China
- Department
of Medicinal Chemistry, School of Pharmacy, Fujian Medical University (FMU), Fuzhou 350108, PR China
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Lagarde H, Lallias D, Patrice P, Dehaullon A, Prchal M, François Y, D'Ambrosio J, Segret E, Acin-Perez A, Cachelou F, Haffray P, Dupont-Nivet M, Phocas F. Genetic architecture of acute hyperthermia resistance in juvenile rainbow trout (Oncorhynchus mykiss) and genetic correlations with production traits. Genet Sel Evol 2023; 55:39. [PMID: 37308823 DOI: 10.1186/s12711-023-00811-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2022] [Accepted: 05/11/2023] [Indexed: 06/14/2023] Open
Abstract
BACKGROUND Selective breeding is a promising solution to reduce the vulnerability of fish farms to heat waves, which are predicted to increase in intensity and frequency. However, limited information about the genetic architecture of acute hyperthermia resistance in fish is available. Two batches of sibs from a rainbow trout commercial line were produced: the first (N = 1382) was phenotyped for acute hyperthermia resistance at nine months of age and the second (N = 1506) was phenotyped for main production traits (growth, body length, muscle fat content and carcass yield) at 20 months of age. Fish were genotyped on a 57 K single nucleotide polymorphism (SNP) array and their genotypes were imputed to high-density based on the parent's genotypes from a 665 K SNP array. RESULTS The heritability estimate of resistance to acute hyperthermia was 0.29 ± 0.05, confirming the potential of selective breeding for this trait. Since genetic correlations of acute hyperthermia resistance with the main production traits near harvest age were all close to zero, selecting for acute hyperthermia resistance should not impact the main production traits, and vice-versa. A genome-wide association study revealed that resistance to acute hyperthermia is a highly polygenic trait, with six quantitative trait loci (QTL) detected, but explaining less than 5% of the genetic variance. Two of these QTL, including the most significant one, may explain differences in acute hyperthermia resistance across INRAE isogenic lines of rainbow trout. Differences in mean acute hyperthermia resistance phenotypes between homozygotes at the most significant SNP was 69% of the phenotypic standard deviation, showing promising potential for marker-assisted selection. We identified 89 candidate genes within the QTL regions, among which the most convincing functional candidates are dnajc7, hsp70b, nkiras2, cdk12, phb, fkbp10, ddx5, cygb1, enpp7, pdhx and acly. CONCLUSIONS This study provides valuable insight into the genetic architecture of acute hyperthermia resistance in juvenile rainbow trout. We show that the selection potential for this trait is substantial and selection for this trait should not be too detrimental to improvement of other traits of interest. Identified functional candidate genes provide new knowledge on the physiological mechanisms involved in acute hyperthermia resistance, such as protein chaperoning, oxidative stress response, homeostasis maintenance and cell survival.
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Affiliation(s)
- Henri Lagarde
- Université Paris-Saclay, INRAE, AgroParisTech, GABI, 78350, Jouy-en-Josas, France
| | - Delphine Lallias
- Université Paris-Saclay, INRAE, AgroParisTech, GABI, 78350, Jouy-en-Josas, France
| | - Pierre Patrice
- SYSAAF, French Poultry, Aquaculture and Insect Breeders Association, 35042, Rennes, France
| | - Audrey Dehaullon
- Université Paris-Saclay, INRAE, AgroParisTech, GABI, 78350, Jouy-en-Josas, France
| | - Martin Prchal
- Faculty of Fisheries and Protection of Waters, South Bohemian Research Center of Aquaculture and Biodiversity of Hydrocenoses, University of South Bohemia in České Budějovice, Zátiší 728/II, 389 25, Vodňany, Czech Republic
| | - Yoannah François
- SYSAAF, French Poultry, Aquaculture and Insect Breeders Association, 35042, Rennes, France
| | - Jonathan D'Ambrosio
- SYSAAF, French Poultry, Aquaculture and Insect Breeders Association, 35042, Rennes, France
| | - Emilien Segret
- Viviers de Sarrance, Pisciculture Labedan, 64490, Sarrance, France
| | - Ana Acin-Perez
- Viviers de Sarrance, Pisciculture Labedan, 64490, Sarrance, France
| | | | - Pierrick Haffray
- SYSAAF, French Poultry, Aquaculture and Insect Breeders Association, 35042, Rennes, France
| | | | - Florence Phocas
- Université Paris-Saclay, INRAE, AgroParisTech, GABI, 78350, Jouy-en-Josas, France.
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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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48
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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: 3] [Impact Index Per Article: 3.0] [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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49
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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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50
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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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