1
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Mentzel J, Hildebrand LS, Kuhlmann L, Fietkau R, Distel LV. Effective Radiosensitization of HNSCC Cell Lines by DNA-PKcs Inhibitor AZD7648 and PARP Inhibitors Talazoparib and Niraparib. Int J Mol Sci 2024; 25:5629. [PMID: 38891817 PMCID: PMC11172136 DOI: 10.3390/ijms25115629] [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: 04/30/2024] [Revised: 05/16/2024] [Accepted: 05/19/2024] [Indexed: 06/21/2024] Open
Abstract
(1) Head and neck squamous cell carcinoma (HNSCC) is common, while treatment is difficult, and mortality is high. Kinase inhibitors are promising to enhance the effects of radiotherapy. We compared the effects of the PARP inhibitors talazoparib and niraparib and that of the DNA-PKcs inhibitor AZD7648, combined with ionizing radiation. (2) Seven HNSCC cell lines, including Cal33, CLS-354, Detroit 562, HSC4, RPMI2650 (HPV-negative), UD-SCC-2 and UM-SCC-47 (HPV-positive), and two healthy fibroblast cell lines, SBLF8 and SBLF9, were studied. Flow cytometry was used to analyze apoptosis and necrosis induction (AnnexinV/7AAD) and cell cycle distribution (Hoechst). Cell inactivation was studied by the colony-forming assay. (3) AZD7648 had the strongest effects, radiosensitizing all HNSCC cell lines, almost always in a supra-additive manner. Talazoparib and niraparib were effective in both HPV-positive cell lines but only consistently in one and two HPV-negative cell lines, respectively. Healthy fibroblasts were not affected by any combined treatment in apoptosis and necrosis induction or G2/M-phase arrest. AZD7648 alone was not toxic to healthy fibroblasts, while the combination with ionizing radiation reduced clonogenicity. (4) In conclusion, talazoparib, niraparib and, most potently, AZD7648 could improve radiation therapy in HNSCC. Healthy fibroblasts tolerated AZD7648 alone extremely well, but irradiation-induced effects might occur. Our results justify in vivo studies.
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Affiliation(s)
- Jacob Mentzel
- Department of Radiation Oncology, Universitätsklinikum Erlangen, Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU), 91054 Erlangen, Germany; (J.M.); (L.S.H.); (L.K.); (R.F.)
- Comprehensive Cancer Center Erlangen-Europäische Metropolregion Nürnberg (CCC ER-EMN), 91054 Erlangen, Germany
| | - Laura S. Hildebrand
- Department of Radiation Oncology, Universitätsklinikum Erlangen, Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU), 91054 Erlangen, Germany; (J.M.); (L.S.H.); (L.K.); (R.F.)
- Comprehensive Cancer Center Erlangen-Europäische Metropolregion Nürnberg (CCC ER-EMN), 91054 Erlangen, Germany
| | - Lukas Kuhlmann
- Department of Radiation Oncology, Universitätsklinikum Erlangen, Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU), 91054 Erlangen, Germany; (J.M.); (L.S.H.); (L.K.); (R.F.)
- Comprehensive Cancer Center Erlangen-Europäische Metropolregion Nürnberg (CCC ER-EMN), 91054 Erlangen, Germany
| | - Rainer Fietkau
- Department of Radiation Oncology, Universitätsklinikum Erlangen, Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU), 91054 Erlangen, Germany; (J.M.); (L.S.H.); (L.K.); (R.F.)
- Comprehensive Cancer Center Erlangen-Europäische Metropolregion Nürnberg (CCC ER-EMN), 91054 Erlangen, Germany
| | - Luitpold V. Distel
- Department of Radiation Oncology, Universitätsklinikum Erlangen, Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU), 91054 Erlangen, Germany; (J.M.); (L.S.H.); (L.K.); (R.F.)
- Comprehensive Cancer Center Erlangen-Europäische Metropolregion Nürnberg (CCC ER-EMN), 91054 Erlangen, Germany
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2
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Laroche-Clary A, Josensi C, Derieppe MA, Belhomme S, Vendrely V, Perret R, Cadogan E, Italiano A. Selective DNA-PK Inhibition Enhances Chemotherapy and Ionizing Radiation Activity in Soft-Tissue Sarcomas. Clin Cancer Res 2024; 30:629-637. [PMID: 37982819 DOI: 10.1158/1078-0432.ccr-23-1531] [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: 05/23/2023] [Revised: 07/25/2023] [Accepted: 11/16/2023] [Indexed: 11/21/2023]
Abstract
PURPOSE Patients with advanced soft-tissue sarcomas (STS) exhibit a poor prognosis and have few therapeutic options. DNA-dependent protein kinase (DNA-PK) catalytic subunit is a multifunctional serine-threonine protein kinase that plays a crucial role in DNA double-strand damage repair via nonhomologous end joining. EXPERIMENTAL DESIGN To investigate the therapeutic potential of DNA-PK targeting in STS, we first evaluated the prognostic value of DNA-PK expression in two large cohorts of patients with STS. We then used the potent and selective DNA-PK inhibitor AZD7648 compound to investigate the antitumor effect of the pharmacologic inhibition of DNA-PK in vitro via MTT, apoptosis, cell cycle, and proliferation assays. In vivo studies were performed with patient-derived xenograft models to evaluate the effects of AZD7648 in combination with chemotherapy or ionizing radiation on tumor growth. The mechanisms of sensitivity and resistance to DNA-PK inhibition were investigated by using a genome-wide CRISPR-Cas9 positive screen. RESULTS DNA-PK overexpression is significantly associated with poor prognosis in patients with sarcomas. Selective pharmacologic inhibition of DNA-PK strongly synergizes with radiation- and doxorubicin-based regimen in sarcoma models. By using a genome-wide CRISPR-Cas9 positive screen, we identified genes involved in sensitivity to DNA-PK inhibition. CONCLUSIONS DNA-PK inhibition deserves clinical investigation to improve response to current therapies in patients with sarcoma.
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Affiliation(s)
- Audrey Laroche-Clary
- Sarcoma Unit, Institut Bergonié, Bordeaux, France
- INSERM, U1312, Bordeaux, France
| | - Coralie Josensi
- Sarcoma Unit, Institut Bergonié, Bordeaux, France
- INSERM, U1312, Bordeaux, France
| | | | - Sarah Belhomme
- Department of Radiation Therapy, Institut Bergonié, Bordeaux, France
| | | | - Raul Perret
- Department of Pathology, Institut Bergonié, Bordeaux, France
| | | | - Antoine Italiano
- Sarcoma Unit, Institut Bergonié, Bordeaux, France
- INSERM, U1312, Bordeaux, France
- Faculty of Medicine, University of Bordeaux, Bordeaux, France
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3
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Liu K, Yuan X, Yang T, Deng D, Chen Y, Tang M, Zhang C, Zou Y, Zhang S, Li D, Shi M, Guo Y, Zhou Y, Zhao M, Yang Z, Chen L. Discovery, Optimization, and Evaluation of Potent and Selective DNA-PK Inhibitors in Combination with Chemotherapy or Radiotherapy for the Treatment of Malignancies. J Med Chem 2024; 67:245-271. [PMID: 38117951 DOI: 10.1021/acs.jmedchem.3c01338] [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: 12/22/2023]
Abstract
Given the multifaceted biological functions of DNA-PK encompassing DNA repair pathways and beyond, coupled with the susceptibility of DNA-PK-deficient cells to DNA-damaging agents, significant strides have been made in the pursuit of clinical potential for DNA-PK inhibitors as synergistic adjuncts to chemo- or radiotherapy. Nevertheless, although substantial progress has been made with the discovery of potent inhibitors of DNA-PK, the clinical trial landscape requires even more potent and selective molecules. This necessitates further endeavors to expand the repertoire of clinically accessible DNA-PK inhibitors for the ultimate benefit of patients. Described herein are the obstacles that were encountered and the solutions that were found, which eventually led to the identification of compound 31t. This compound exhibited a remarkable combination of robust potency and exceptional selectivity along with favorable in vivo profiles as substantiated by pharmacokinetic studies in rats and pharmacodynamic assessments in H460, BT474, and A549 xenograft models.
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Affiliation(s)
- Kongjun Liu
- Laboratory of Natural and Targeted Small Molecule Drugs, State Key Laboratory of Biotherapy and Cancer Center, Collaborative Innovation Center of Biotherapy, West China Hospital of Sichuan University, Chengdu 610041, China
| | - Xue Yuan
- Laboratory of Natural and Targeted Small Molecule Drugs, State Key Laboratory of Biotherapy and Cancer Center, Collaborative Innovation Center of Biotherapy, West China Hospital of Sichuan University, Chengdu 610041, China
| | - Tao Yang
- Laboratory of Natural and Targeted Small Molecule Drugs, State Key Laboratory of Biotherapy and Cancer Center, Collaborative Innovation Center of Biotherapy, West China Hospital of Sichuan University, Chengdu 610041, China
| | - Dexin Deng
- Laboratory of Natural and Targeted Small Molecule Drugs, State Key Laboratory of Biotherapy and Cancer Center, Collaborative Innovation Center of Biotherapy, West China Hospital of Sichuan University, Chengdu 610041, China
| | - Yong Chen
- Laboratory of Natural and Targeted Small Molecule Drugs, State Key Laboratory of Biotherapy and Cancer Center, Collaborative Innovation Center of Biotherapy, West China Hospital of Sichuan University, Chengdu 610041, China
| | - Minghai Tang
- Laboratory of Natural and Targeted Small Molecule Drugs, State Key Laboratory of Biotherapy and Cancer Center, Collaborative Innovation Center of Biotherapy, West China Hospital of Sichuan University, Chengdu 610041, China
| | - Chufeng Zhang
- Laboratory of Natural and Targeted Small Molecule Drugs, State Key Laboratory of Biotherapy and Cancer Center, Collaborative Innovation Center of Biotherapy, West China Hospital of Sichuan University, Chengdu 610041, China
| | - Yurong Zou
- Laboratory of Natural and Targeted Small Molecule Drugs, State Key Laboratory of Biotherapy and Cancer Center, Collaborative Innovation Center of Biotherapy, West China Hospital of Sichuan University, Chengdu 610041, China
| | - Shunjie Zhang
- Laboratory of Natural and Targeted Small Molecule Drugs, State Key Laboratory of Biotherapy and Cancer Center, Collaborative Innovation Center of Biotherapy, West China Hospital of Sichuan University, Chengdu 610041, China
| | - Dan Li
- Laboratory of Natural and Targeted Small Molecule Drugs, State Key Laboratory of Biotherapy and Cancer Center, Collaborative Innovation Center of Biotherapy, West China Hospital of Sichuan University, Chengdu 610041, China
| | - Mingsong Shi
- Laboratory of Natural and Targeted Small Molecule Drugs, State Key Laboratory of Biotherapy and Cancer Center, Collaborative Innovation Center of Biotherapy, West China Hospital of Sichuan University, Chengdu 610041, China
| | - Yong Guo
- Laboratory of Natural and Targeted Small Molecule Drugs, State Key Laboratory of Biotherapy and Cancer Center, Collaborative Innovation Center of Biotherapy, West China Hospital of Sichuan University, Chengdu 610041, China
| | - Yanting Zhou
- Laboratory of Natural and Targeted Small Molecule Drugs, State Key Laboratory of Biotherapy and Cancer Center, Collaborative Innovation Center of Biotherapy, West China Hospital of Sichuan University, Chengdu 610041, China
| | - Min Zhao
- Laboratory of Natural and Targeted Small Molecule Drugs, State Key Laboratory of Biotherapy and Cancer Center, Collaborative Innovation Center of Biotherapy, West China Hospital of Sichuan University, Chengdu 610041, China
| | - Zhuang Yang
- Laboratory of Natural and Targeted Small Molecule Drugs, State Key Laboratory of Biotherapy and Cancer Center, Collaborative Innovation Center of Biotherapy, West China Hospital of Sichuan University, Chengdu 610041, China
| | - Lijuan Chen
- Laboratory of Natural and Targeted Small Molecule Drugs, State Key Laboratory of Biotherapy and Cancer Center, Collaborative Innovation Center of Biotherapy, West China Hospital of Sichuan University, Chengdu 610041, China
- Chengdu Zenitar Biomedical Technology Co., Ltd., Chengdu 610041, China
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4
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Amin H, Zahid S, Hall C, Chaplin AK. Cold snapshots of DNA repair: Cryo-EM structures of DNA-PKcs and NHEJ machinery. PROGRESS IN BIOPHYSICS AND MOLECULAR BIOLOGY 2024; 186:1-13. [PMID: 38036101 DOI: 10.1016/j.pbiomolbio.2023.11.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/23/2023] [Revised: 11/03/2023] [Accepted: 11/24/2023] [Indexed: 12/02/2023]
Abstract
The proteins and protein assemblies involved in DNA repair have been the focus of a multitude of structural studies for the past few decades. Historically, the structures of these protein complexes have been resolved by X-ray crystallography. However, more recently with the advancements in cryo-electron microscopy (cryo-EM) ranging from optimising the methodology for sample preparation to the development of improved electron detectors, the focus has shifted from X-ray crystallography to cryo-EM. This methodological transition has allowed for the structural determination of larger, more complex protein assemblies involved in DNA repair pathways and has subsequently led to a deeper understanding of the mechanisms utilised by these fascinating molecular machines. Here, we review some of the key structural advancements that have been gained in the study of non-homologous end joining (NHEJ) by the use of cryo-EM, with a focus on assemblies composed of DNA-PKcs and Ku70/80 (Ku) and the various methodologies utilised to obtain these structures.
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Affiliation(s)
- Himani Amin
- Leicester Institute for Structural and Chemical Biology, Department of Molecular and Cell Biology, University of Leicester, Leicester, UK
| | - Sayma Zahid
- Leicester Institute for Structural and Chemical Biology, Department of Molecular and Cell Biology, University of Leicester, Leicester, UK
| | - Chloe Hall
- Leicester Institute for Structural and Chemical Biology, Department of Molecular and Cell Biology, University of Leicester, Leicester, UK
| | - Amanda K Chaplin
- Leicester Institute for Structural and Chemical Biology, Department of Molecular and Cell Biology, University of Leicester, Leicester, UK.
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5
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Mladenov E, Mladenova V, Stuschke M, Iliakis G. New Facets of DNA Double Strand Break Repair: Radiation Dose as Key Determinant of HR versus c-NHEJ Engagement. Int J Mol Sci 2023; 24:14956. [PMID: 37834403 PMCID: PMC10573367 DOI: 10.3390/ijms241914956] [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: 08/22/2023] [Revised: 10/01/2023] [Accepted: 10/03/2023] [Indexed: 10/15/2023] Open
Abstract
Radiation therapy is an essential component of present-day cancer management, utilizing ionizing radiation (IR) of different modalities to mitigate cancer progression. IR functions by generating ionizations in cells that induce a plethora of DNA lesions. The most detrimental among them are the DNA double strand breaks (DSBs). In the course of evolution, cells of higher eukaryotes have evolved four major DSB repair pathways: classical non-homologous end joining (c-NHEJ), homologous recombination (HR), alternative end-joining (alt-EJ), and single strand annealing (SSA). These mechanistically distinct repair pathways have different cell cycle- and homology-dependencies but, surprisingly, they operate with widely different fidelity and kinetics and therefore contribute unequally to cell survival and genome maintenance. It is therefore reasonable to anticipate tight regulation and coordination in the engagement of these DSB repair pathway to achieve the maximum possible genomic stability. Here, we provide a state-of-the-art review of the accumulated knowledge on the molecular mechanisms underpinning these repair pathways, with emphasis on c-NHEJ and HR. We discuss factors and processes that have recently come to the fore. We outline mechanisms steering DSB repair pathway choice throughout the cell cycle, and highlight the critical role of DNA end resection in this process. Most importantly, however, we point out the strong preference for HR at low DSB loads, and thus low IR doses, for cells irradiated in the G2-phase of the cell cycle. We further explore the molecular underpinnings of transitions from high fidelity to low fidelity error-prone repair pathways and analyze the coordination and consequences of this transition on cell viability and genomic stability. Finally, we elaborate on how these advances may help in the development of improved cancer treatment protocols in radiation therapy.
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Affiliation(s)
- Emil Mladenov
- Division of Experimental Radiation Biology, Department of Radiation Therapy, University Hospital Essen, University of Duisburg-Essen, 45122 Essen, Germany; (V.M.); (M.S.)
- Institute of Medical Radiation Biology, University Hospital Essen, University of Duisburg-Essen, 45122 Essen, Germany
| | - Veronika Mladenova
- Division of Experimental Radiation Biology, Department of Radiation Therapy, University Hospital Essen, University of Duisburg-Essen, 45122 Essen, Germany; (V.M.); (M.S.)
- Institute of Medical Radiation Biology, University Hospital Essen, University of Duisburg-Essen, 45122 Essen, Germany
| | - Martin Stuschke
- Division of Experimental Radiation Biology, Department of Radiation Therapy, University Hospital Essen, University of Duisburg-Essen, 45122 Essen, Germany; (V.M.); (M.S.)
- German Cancer Consortium (DKTK), Partner Site University Hospital Essen, 45147 Essen, Germany
- German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany
| | - George Iliakis
- Division of Experimental Radiation Biology, Department of Radiation Therapy, University Hospital Essen, University of Duisburg-Essen, 45122 Essen, Germany; (V.M.); (M.S.)
- Institute of Medical Radiation Biology, University Hospital Essen, University of Duisburg-Essen, 45122 Essen, Germany
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6
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Riesenberg S, Kanis P, Macak D, Wollny D, Düsterhöft D, Kowalewski J, Helmbrecht N, Maricic T, Pääbo S. Efficient high-precision homology-directed repair-dependent genome editing by HDRobust. Nat Methods 2023; 20:1388-1399. [PMID: 37474806 PMCID: PMC10482697 DOI: 10.1038/s41592-023-01949-1] [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: 06/21/2022] [Accepted: 06/12/2023] [Indexed: 07/22/2023]
Abstract
Homology-directed repair (HDR), a method for repair of DNA double-stranded breaks can be leveraged for the precise introduction of mutations supplied by synthetic DNA donors, but remains limited by low efficiency and off-target effects. In this study, we report HDRobust, a high-precision method that, via the combined transient inhibition of nonhomologous end joining and microhomology-mediated end joining, resulted in the induction of point mutations by HDR in up to 93% (median 60%, s.e.m. 3) of chromosomes in populations of cells. We found that, using this method, insertions, deletions and rearrangements at the target site, as well as unintended changes at other genomic sites, were largely abolished. We validated this approach for 58 different target sites and showed that it allows efficient correction of pathogenic mutations in cells derived from patients suffering from anemia, sickle cell disease and thrombophilia.
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Affiliation(s)
- Stephan Riesenberg
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany.
| | - Philipp Kanis
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Dominik Macak
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Damian Wollny
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Dorothee Düsterhöft
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Johannes Kowalewski
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Nelly Helmbrecht
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Tomislav Maricic
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Svante Pääbo
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
- Human Evolutionary Genomics Unit, Okinawa Institute of Science and Technology, Onna-son, Japan
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7
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Wimberger S, Akrap N, Firth M, Brengdahl J, Engberg S, Schwinn MK, Slater MR, Lundin A, Hsieh PP, Li S, Cerboni S, Sumner J, Bestas B, Schiffthaler B, Magnusson B, Di Castro S, Iyer P, Bohlooly-Y M, Machleidt T, Rees S, Engkvist O, Norris T, Cadogan EB, Forment JV, Šviković S, Akcakaya P, Taheri-Ghahfarokhi A, Maresca M. Simultaneous inhibition of DNA-PK and Polϴ improves integration efficiency and precision of genome editing. Nat Commun 2023; 14:4761. [PMID: 37580318 PMCID: PMC10425386 DOI: 10.1038/s41467-023-40344-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2023] [Accepted: 07/25/2023] [Indexed: 08/16/2023] Open
Abstract
Genome editing, specifically CRISPR/Cas9 technology, has revolutionized biomedical research and offers potential cures for genetic diseases. Despite rapid progress, low efficiency of targeted DNA integration and generation of unintended mutations represent major limitations for genome editing applications caused by the interplay with DNA double-strand break repair pathways. To address this, we conduct a large-scale compound library screen to identify targets for enhancing targeted genome insertions. Our study reveals DNA-dependent protein kinase (DNA-PK) as the most effective target to improve CRISPR/Cas9-mediated insertions, confirming previous findings. We extensively characterize AZD7648, a selective DNA-PK inhibitor, and find it to significantly enhance precise gene editing. We further improve integration efficiency and precision by inhibiting DNA polymerase theta (Polϴ). The combined treatment, named 2iHDR, boosts templated insertions to 80% efficiency with minimal unintended insertions and deletions. Notably, 2iHDR also reduces off-target effects of Cas9, greatly enhancing the fidelity and performance of CRISPR/Cas9 gene editing.
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Affiliation(s)
- Sandra Wimberger
- Genome Engineering, Discovery Sciences, BioPharmaceuticals R&D, AstraZeneca, Gothenburg, Sweden.
- Department of Chemistry & Molecular Biology, University of Gothenburg, Gothenburg, Sweden.
| | - Nina Akrap
- Genome Engineering, Discovery Sciences, BioPharmaceuticals R&D, AstraZeneca, Gothenburg, Sweden
| | - Mike Firth
- Data Sciences & Quantitative Biology, Discovery Sciences, BioPharmaceuticals R&D, AstraZeneca, Cambridge, UK
| | - Johan Brengdahl
- Cell Assay Development, Discovery Sciences, BioPharmaceuticals R&D, AstraZeneca, Gothenburg, Sweden
| | - Susanna Engberg
- Cell Engineering Sweden, Discovery Sciences, BioPharmaceuticals R&D, AstraZeneca, Gothenburg, Sweden
| | | | | | - Anders Lundin
- Translational Genomics, Discovery Sciences, BioPharmaceuticals R&D, AstraZeneca, Gothenburg, Sweden
| | - Pei-Pei Hsieh
- Genome Engineering, Discovery Sciences, BioPharmaceuticals R&D, AstraZeneca, Gothenburg, Sweden
| | - Songyuan Li
- Genome Engineering, Discovery Sciences, BioPharmaceuticals R&D, AstraZeneca, Gothenburg, Sweden
| | - Silvia Cerboni
- Translational Science & Experimental Medicine, Research and Early Development, Respiratory & Immunology (R&I), BioPharmaceuticals R&D, AstraZeneca, Gothenburg, Sweden
| | - Jonathan Sumner
- Cell Immunology, Discovery Sciences, BioPharmaceuticals R&D, AstraZeneca, Cambridge, UK
| | - Burcu Bestas
- Genome Engineering, Discovery Sciences, BioPharmaceuticals R&D, AstraZeneca, Gothenburg, Sweden
| | - Bastian Schiffthaler
- Data Sciences & Quantitative Biology, Discovery Sciences, BioPharmaceuticals R&D, AstraZeneca, Gothenburg, Sweden
| | - Björn Magnusson
- Translational Genomics, Discovery Sciences, BioPharmaceuticals R&D, AstraZeneca, Gothenburg, Sweden
| | - Silvio Di Castro
- Compound Synthesis & Management, Discovery Sciences, BioPharmaceuticals R&D, AstraZeneca, Gothenburg, Sweden
| | - Preeti Iyer
- Molecular AI, Discovery Sciences, BioPharmaceuticals R&D, AstraZeneca, Gothenburg, Sweden
| | - Mohammad Bohlooly-Y
- Translational Genomics, Discovery Sciences, BioPharmaceuticals R&D, AstraZeneca, Gothenburg, Sweden
| | | | - Steve Rees
- Discovery Sciences, BioPharmaceuticals R&D, AstraZeneca, Cambridge, UK
| | - Ola Engkvist
- Molecular AI, Discovery Sciences, BioPharmaceuticals R&D, AstraZeneca, Gothenburg, Sweden
| | - Tyrell Norris
- Cell Engineering Sweden, Discovery Sciences, BioPharmaceuticals R&D, AstraZeneca, Gothenburg, Sweden
| | | | | | - Saša Šviković
- Genome Engineering, Discovery Sciences, BioPharmaceuticals R&D, AstraZeneca, Gothenburg, Sweden
| | - Pinar Akcakaya
- Genome Engineering, Discovery Sciences, BioPharmaceuticals R&D, AstraZeneca, Gothenburg, Sweden
| | - Amir Taheri-Ghahfarokhi
- Genome Engineering, Discovery Sciences, BioPharmaceuticals R&D, AstraZeneca, Gothenburg, Sweden
| | - Marcello Maresca
- Genome Engineering, Discovery Sciences, BioPharmaceuticals R&D, AstraZeneca, Gothenburg, Sweden.
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8
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Dharanipragada P, Zhang X, Liu S, Lomeli SH, Hong A, Wang Y, Yang Z, Lo KZ, Vega-Crespo A, Ribas A, Moschos SJ, Moriceau G, Lo RS. Blocking Genomic Instability Prevents Acquired Resistance to MAPK Inhibitor Therapy in Melanoma. Cancer Discov 2023; 13:880-909. [PMID: 36700848 PMCID: PMC10068459 DOI: 10.1158/2159-8290.cd-22-0787] [Citation(s) in RCA: 17] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2022] [Revised: 11/27/2022] [Accepted: 01/23/2023] [Indexed: 01/27/2023]
Abstract
Blocking cancer genomic instability may prevent tumor diversification and escape from therapies. We show that, after MAPK inhibitor (MAPKi) therapy in patients and mice bearing patient-derived xenografts (PDX), acquired resistant genomes of metastatic cutaneous melanoma specifically amplify resistance-driver, nonhomologous end-joining (NHEJ), and homologous recombination repair (HRR) genes via complex genomic rearrangements (CGR) and extrachromosomal DNAs (ecDNA). Almost all sensitive and acquired-resistant genomes harbor pervasive chromothriptic regions with disproportionately high mutational burdens and significant overlaps with ecDNA and CGR spans. Recurrently, somatic mutations within ecDNA and CGR amplicons enrich for HRR signatures, particularly within acquired resistant tumors. Regardless of sensitivity or resistance, breakpoint-junctional sequence analysis suggests NHEJ as critical to double-stranded DNA break repair underlying CGR and ecDNA formation. In human melanoma cell lines and PDXs, NHEJ targeting by a DNA-PKCS inhibitor prevents/delays acquired MAPKi resistance by reducing the size of ecDNAs and CGRs early on combination treatment. Thus, targeting the causes of genomic instability prevents acquired resistance. SIGNIFICANCE Acquired resistance often results in heterogeneous, redundant survival mechanisms, which challenge strategies aimed at reversing resistance. Acquired-resistant melanomas recurrently evolve resistance-driving and resistance-specific amplicons via ecDNAs and CGRs, thereby nominating chromothripsis-ecDNA-CGR biogenesis as a resistance-preventive target. Specifically, targeting DNA-PKCS/NHEJ prevents resistance by suppressing ecDNA/CGR rearrangements in MAPKi-treated melanomas. This article is highlighted in the In This Issue feature, p. 799.
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Affiliation(s)
- Prashanthi Dharanipragada
- Division of Dermatology, Department of Medicine, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, California
| | - Xiao Zhang
- Division of Dermatology, Department of Medicine, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, California
| | - Sixue Liu
- Division of Dermatology, Department of Medicine, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, California
| | - Shirley H. Lomeli
- Division of Dermatology, Department of Medicine, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, California
| | - Aayoung Hong
- Division of Dermatology, Department of Medicine, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, California
| | - Yan Wang
- Division of Dermatology, Department of Medicine, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, California
- Department of Molecular and Medical Pharmacology, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, California
| | - Zhentao Yang
- Division of Dermatology, Department of Medicine, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, California
| | - Kara Z. Lo
- Division of Hematology/Oncology, Department of Medicine, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, California
| | - Agustin Vega-Crespo
- Division of Hematology/Oncology, Department of Medicine, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, California
| | - Antoni Ribas
- Department of Molecular and Medical Pharmacology, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, California
- Division of Hematology/Oncology, Department of Medicine, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, California
- Division of Surgical Oncology, Department of Surgery, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, California
- Jonsson Comprehensive Cancer Center, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, California
| | - Stergios J. Moschos
- Division of Medical Oncology, Department of Medicine, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina
- Lineberger Comprehensive Cancer Center, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina
| | - Gatien Moriceau
- Division of Dermatology, Department of Medicine, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, California
| | - Roger S. Lo
- Division of Dermatology, Department of Medicine, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, California
- Department of Molecular and Medical Pharmacology, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, California
- Jonsson Comprehensive Cancer Center, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, California
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9
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Ray U, Gopinatha VK, Sharma S, Goyary L, Choudhary B, Mantelingu K, Rangappa KS, Raghavan SC. Identification and characterization of mercaptopyrimidine-based small molecules as inhibitors of nonhomologous DNA end joining. FEBS J 2023; 290:796-820. [PMID: 36048168 DOI: 10.1111/febs.16615] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2022] [Revised: 07/21/2022] [Accepted: 08/31/2022] [Indexed: 02/04/2023]
Abstract
Mercaptopyrimidine derivatives are heterocyclic compounds with potent biological activities including antiproliferative, antibacterial, and anti-inflammatory properties. The present study describes the synthesis and characterization of several mercaptopyrimidine derivatives through condensation of 5,6-diamino-2-mercaptopyrimidin-4-ol with various heterocyclic and aromatic aldehydes. Previous studies have shown that SCR7, synthesized from 5,6-diamino-2-mercaptopyrimidin-4-ol, induced cytotoxicity by targeting cancer cells by primarily inhibiting DNA Ligase IV involved in nonhomologous end joining, one of the major DNA double-strand break repair pathways. Inhibition of DNA repair pathways is considered as an important strategy for cancer therapy. Due to limitations of SCR7 in terms of IC50 in cancer cells, here we have designed, synthesized, and characterized potent derivatives of SCR7 using 5,6-diamino-2-mercaptopyrimidin-4-ol as the starting material. Several synthesized imine compounds exhibited significant improvement in inhibition of end joining and cytotoxicity up to 27-fold lower concentrations than SCR7. Among these, two compounds, SCR116 and SCR132, showed increased cancer cell death in a Ligase IV-dependent manner. Treatment with the compounds also led to reduction in V(D)J recombination efficiency, cell cycle arrest at G2/M phase, accumulation of double-strand breaks inside cells, and improved anti-cancer potential when combined with γ-radiation and radiomimetic drugs. Thus, we describe novel inhibitors of NHEJ with higher efficacy and potential, which can be developed as cancer therapeutics.
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Affiliation(s)
- Ujjayinee Ray
- Department of Biochemistry, Indian Institute of Science, Bangalore, India
| | - Vindya K Gopinatha
- Department of Biochemistry, Indian Institute of Science, Bangalore, India.,Department of Studies in Chemistry, University of Mysore, India
| | - Shivangi Sharma
- Department of Biochemistry, Indian Institute of Science, Bangalore, India.,Institute of Bioinformatics and Applied Biotechnology, Electronics City, Bangalore, India
| | - Laijau Goyary
- Department of Biochemistry, Indian Institute of Science, Bangalore, India
| | - Bibha Choudhary
- Institute of Bioinformatics and Applied Biotechnology, Electronics City, Bangalore, India
| | | | - Kanchugarakoppal S Rangappa
- Department of Studies in Chemistry, University of Mysore, India.,Institution of Excellence, Vijnana Bhavana, University of Mysore, India
| | - Sathees C Raghavan
- Department of Biochemistry, Indian Institute of Science, Bangalore, India
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10
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Nasioudis D, George EM, Xu H, Kim H, Simpkins F. Combination DNA Damage Response (DDR) Inhibitors to Overcome Drug Resistance in Ovarian Cancer. Cancer Treat Res 2023; 186:189-206. [PMID: 37978137 DOI: 10.1007/978-3-031-30065-3_11] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2023]
Abstract
The DNA damage response (DDR) results in activation of a series of key target kinases that respond to different DNA damage insults. DDR inhibitors such as PARP inhibitors lead to the accumulation of DNA damage in tumor cells and ultimately apoptosis. However, responses to DDRi monotherapy in the clinic are not durable and resistance ultimately develops. DDRi-DDRi combinations such as PARPi-ATRi, PAPRi-WEE1i and PARPi-AsiDNA can overcome multiple resistance mechanisms to PARP inhibition. In addition, DDRi-DDRi combinations can provide viable treatment options for patients with platinum-resistant disease. In the present chapter we discuss rationale of DDRi-DDRi strategies that capitalize on genomic alterations found in ovarian cancer and other solid tumors and may provide in the near future new treatment options for these patients.
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Affiliation(s)
- Dimitrios Nasioudis
- Division of Gynecologic Oncology, Department of Obstetrics and Gynecology, Perelman School of Medicine, Ovarian Cancer Research Center, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Erin M George
- Division of Gynecologic Oncology, Department of Obstetrics and Gynecology, Perelman School of Medicine, Ovarian Cancer Research Center, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Haineng Xu
- Division of Gynecologic Oncology, Department of Obstetrics and Gynecology, Perelman School of Medicine, Ovarian Cancer Research Center, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Hyoung Kim
- Division of Gynecologic Oncology, Department of Obstetrics and Gynecology, Perelman School of Medicine, Ovarian Cancer Research Center, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Fiona Simpkins
- Division of Gynecologic Oncology, Department of Obstetrics and Gynecology, Perelman School of Medicine, Ovarian Cancer Research Center, University of Pennsylvania, Philadelphia, PA, 19104, USA.
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11
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A rapid multiplex cell-free assay on biochip to evaluate functional aspects of double-strand break repair. Sci Rep 2022; 12:20054. [PMID: 36414637 PMCID: PMC9681732 DOI: 10.1038/s41598-022-23819-0] [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: 02/23/2022] [Accepted: 11/07/2022] [Indexed: 11/24/2022] Open
Abstract
The repair of DNA double-strand breaks (DSBs) involves interdependent molecular pathways, of which the choice is crucial for a cell's fate when facing a damage. Growing evidence points toward the fact that DSB repair capacities correlate with disease aggressiveness, treatment response and treatment-related toxicities in cancer. Scientific and medical communities need more easy-to-use and efficient tools to rapidly estimate DSB repair capacities from a tissue, enable routine-accessible treatment personalization, and hopefully, improve survival. Here, we propose a new functional biochip assay (NEXT-SPOT) that characterizes DSB repair-engaged cellular pathways and provides qualitative and quantitative information on the contribution of several pathways in less than 2 h, from 10 mg of cell lysates. We introduce the NEXT-SPOT technology, detail the molecular characterizations of different repair steps occurring on the biochip, and show examples of DSB repair profiling using three cancer cell lines treated or not with a DSB-inducer (doxorubicin) and/or a DNA repair inhibitor (RAD51 inhibitor; DNA-PK inhibitor; PARP inhibitor). Among others, we demonstrate that NEXT-SPOT can accurately detect decreased activities in strand invasion and end-joining mechanisms following DNA-PK or RAD51 inhibition in DNA-PK-proficient cell lines. This approach offers an all-in-one reliable strategy to consider DSB repair capacities as predictive biomarkers easily translatable to the clinic.
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12
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Vergara X, Schep R, Medema RH, van Steensel B. From fluorescent foci to sequence: Illuminating DNA double strand break repair by high-throughput sequencing technologies. DNA Repair (Amst) 2022; 118:103388. [PMID: 36037787 DOI: 10.1016/j.dnarep.2022.103388] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2022] [Revised: 08/16/2022] [Accepted: 08/17/2022] [Indexed: 11/25/2022]
Abstract
Technologies to study DNA double-strand break (DSB) repair have traditionally mostly relied on fluorescence read-outs, either by microscopy or flow cytometry. The advent of high throughput sequencing (HTS) has created fundamentally new opportunities to study the mechanisms underlying DSB repair. Here, we review the suite of HTS-based assays that are used to study three different aspects of DNA repair: detection of broken ends, protein recruitment and pathway usage. We highlight new opportunities that HTS technology offers towards a better understanding of the DSB repair process.
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Affiliation(s)
- Xabier Vergara
- Division of Gene Regulation, Netherlands Cancer Institute, 1066 CX Amsterdam, the Netherlands; Division of Cell Biology, Netherlands Cancer Institute, 1066 CX Amsterdam, the Netherlands; Oncode Institute, the Netherlands
| | - Ruben Schep
- Division of Gene Regulation, Netherlands Cancer Institute, 1066 CX Amsterdam, the Netherlands; Oncode Institute, the Netherlands
| | - René H Medema
- Division of Cell Biology, Netherlands Cancer Institute, 1066 CX Amsterdam, the Netherlands; Oncode Institute, the Netherlands.
| | - Bas van Steensel
- Division of Gene Regulation, Netherlands Cancer Institute, 1066 CX Amsterdam, the Netherlands; Oncode Institute, the Netherlands; Department of Cell Biology, Erasmus University Medical Centre, the Netherlands.
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13
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Goldberg FW, Ting AKT, Beattie D, Lamont GM, Fallan C, Finlay MRV, Williamson B, Schimpl M, Harmer AR, Adeyemi OB, Nordell P, Cronin AS, Vazquez-Chantada M, Barratt D, Ramos-Montoya A, Cadogan EB, Davies BR. Optimization of hERG and Pharmacokinetic Properties for Basic Dihydro-8 H-purin-8-one Inhibitors of DNA-PK. ACS Med Chem Lett 2022; 13:1295-1301. [PMID: 35978693 PMCID: PMC9377022 DOI: 10.1021/acsmedchemlett.2c00172] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
Abstract
The DNA-PK complex is activated by double-strand DNA breaks and regulates the non-homologous end-joining repair pathway; thus, targeting DNA-PK by inhibiting the DNA-PK catalytic subunit (DNA-PKcs) is potentially a useful therapeutic approach for oncology. A previously reported series of neutral DNA-PKcs inhibitors were modified to incorporate a basic group, with the rationale that increasing the volume of distribution while maintaining good metabolic stability should increase the half-life. However, adding a basic group introduced hERG activity, and basic compounds with modest hERG activity (IC50 = 10-15 μM) prolonged QTc (time from the start of the Q wave to the end of the T wave, corrected by heart rate) in an anaesthetized guinea pig cardiovascular model. Further optimization was necessary, including modulation of pK a, to identify compound 18, which combines low hERG activity (IC50 = 75 μM) with excellent kinome selectivity and favorable pharmacokinetic properties.
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Affiliation(s)
| | | | | | | | | | | | | | | | - Alexander R. Harmer
- Clinical
Pharmacology and Safety Sciences, R&D, AstraZeneca, Cambridge CB2 0AA, U.K.
| | - Oladipupo B. Adeyemi
- Clinical
Pharmacology and Safety Sciences, R&D, AstraZeneca, Cambridge CB2 0AA, U.K.
| | - Pär Nordell
- Biopharmaceuticals
R&D, AstraZeneca, 431 50 Gothenburg, Sweden
| | - Anna S. Cronin
- Clinical
Pharmacology and Safety Sciences, R&D, AstraZeneca, Cambridge CB2 0AA, U.K.
| | | | - Derek Barratt
- Discovery
Sciences, R&D, AstraZeneca, Cambridge CB2 0AA, U.K.
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14
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Dylgjeri E, Knudsen KE. DNA-PKcs: A Targetable Protumorigenic Protein Kinase. Cancer Res 2022; 82:523-533. [PMID: 34893509 PMCID: PMC9306356 DOI: 10.1158/0008-5472.can-21-1756] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2021] [Revised: 08/17/2021] [Accepted: 11/10/2021] [Indexed: 01/07/2023]
Abstract
DNA-dependent protein kinase catalytic subunit (DNA-PKcs) is a pleiotropic protein kinase that plays critical roles in cellular processes fundamental to cancer. DNA-PKcs expression and activity are frequently deregulated in multiple hematologic and solid tumors and have been tightly linked to poor outcome. Given the potentially influential role of DNA-PKcs in cancer development and progression, therapeutic targeting of this kinase is being tested in preclinical and clinical settings. This review summarizes the latest advances in the field, providing a comprehensive discussion of DNA-PKcs functions in cancer and an update on the clinical assessment of DNA-PK inhibitors in cancer therapy.
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Affiliation(s)
- Emanuela Dylgjeri
- Department of Cancer Biology, Thomas Jefferson University, Philadelphia, Pennsylvania.,Sidney Kimmel Cancer Center, Thomas Jefferson University, Philadelphia, Pennsylvania
| | - Karen E. Knudsen
- Department of Cancer Biology, Thomas Jefferson University, Philadelphia, Pennsylvania.,Sidney Kimmel Cancer Center, Thomas Jefferson University, Philadelphia, Pennsylvania.,Department of Medical Oncology, Thomas Jefferson University, Philadelphia, Pennsylvania.,Department of Urology, Thomas Jefferson University, Philadelphia, Pennsylvania.,Department of Radiation Oncology, Thomas Jefferson University, Philadelphia, Pennsylvania.,Corresponding Author: Karen E. Knudsen, Thomas Jefferson University, 233 South 10th Street, BLSB 1050, Philadelphia, PA 19107. Phone: 215-503-5692; E-mail:
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15
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Gordhandas SB, Manning-Geist B, Henson C, Iyer G, Gardner GJ, Sonoda Y, Moore KN, Aghajanian C, Chui MH, Grisham RN. Pre-clinical activity of the oral DNA-PK inhibitor, peposertib (M3814), combined with radiation in xenograft models of cervical cancer. Sci Rep 2022; 12:974. [PMID: 35046420 PMCID: PMC8770623 DOI: 10.1038/s41598-021-04618-5] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2021] [Accepted: 12/22/2021] [Indexed: 11/24/2022] Open
Abstract
DNA-dependent protein kinase (DNA-PK) plays a crucial role in repair of DNA double-strand breaks by facilitating non-homologous end-joining. Inhibitors of DNA-PK have the potential to block DNA repair and enhance DNA-damaging agents. Peposertib (M3814) is a DNA-PK inhibitor that has shown preclinical activity in combination with DNA-damaging agents, including ionizing radiation (IR) and topoisomerase II inhibitors. Here we evaluated the activity of peposertib (M3814) in combination with radiation in a mouse xenograft model of HPV-associated cervical cancer. Athymic nude female mice with established tumors derived from HeLa cells injected into the flank were treated with vehicle alone (n = 3), IR alone (n = 4), and peposertib (M38814) in combination with IR (M3814 + IR; n = 4). While IR alone was associated with a trend towards decreased tumor volume compared with untreated, only the M3814 + IR treatment arm was associated with consistent and significant reduction in tumor burden, which correlated with higher levels of γ-H2AX in tumor cells, a marker of double-strand DNA breaks. Our data support further clinical evaluation of the combination of peposertib (M38814) and IR in cervical cancer.
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Affiliation(s)
| | - Beryl Manning-Geist
- Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Christina Henson
- University of Oklahoma Health Sciences Center, Oklahoma City, OK, USA
| | - Gopa Iyer
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA.,Weill Cornell Medical College, New York, NY, USA
| | - Ginger J Gardner
- Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, NY, USA.,Weill Cornell Medical College, New York, NY, USA
| | - Yukio Sonoda
- Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, NY, USA.,Weill Cornell Medical College, New York, NY, USA
| | - Kathleen N Moore
- University of Oklahoma Health Sciences Center, Oklahoma City, OK, USA
| | - Carol Aghajanian
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA.,Weill Cornell Medical College, New York, NY, USA
| | - M Herman Chui
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Rachel N Grisham
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA. .,Weill Cornell Medical College, New York, NY, USA.
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16
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Structural insights into inhibitor regulation of the DNA repair protein DNA-PKcs. Nature 2022; 601:643-648. [PMID: 34987222 PMCID: PMC8791830 DOI: 10.1038/s41586-021-04274-9] [Citation(s) in RCA: 25] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2021] [Accepted: 11/19/2021] [Indexed: 01/29/2023]
Abstract
The DNA-dependent protein kinase catalytic subunit (DNA-PKcs) has a central role in non-homologous end joining, one of the two main pathways that detect and repair DNA double-strand breaks (DSBs) in humans1,2. DNA-PKcs is of great importance in repairing pathological DSBs, making DNA-PKcs inhibitors attractive therapeutic agents for cancer in combination with DSB-inducing radiotherapy and chemotherapy3. Many of the selective inhibitors of DNA-PKcs that have been developed exhibit potential as treatment for various cancers4. Here we report cryo-electron microscopy (cryo-EM) structures of human DNA-PKcs natively purified from HeLa cell nuclear extracts, in complex with adenosine-5′-(γ-thio)-triphosphate (ATPγS) and four inhibitors (wortmannin, NU7441, AZD7648 and M3814), including drug candidates undergoing clinical trials. The structures reveal molecular details of ATP binding at the active site before catalysis and provide insights into the modes of action and specificities of the competitive inhibitors. Of note, binding of the ligands causes movement of the PIKK regulatory domain (PRD), revealing a connection between the p-loop and PRD conformations. Electrophoretic mobility shift assay and cryo-EM studies on the DNA-dependent protein kinase holoenzyme further show that ligand binding does not have a negative allosteric or inhibitory effect on assembly of the holoenzyme complex and that inhibitors function through direct competition with ATP. Overall, the structures described in this study should greatly assist future efforts in rational drug design targeting DNA-PKcs, demonstrating the potential of cryo-EM in structure-guided drug development for large and challenging targets. Cryo-electron microscopy structures of DNA-dependent protein kinase catalytic subunit bound to ATPγS and four inhibitors (wortmannin, NU7441, AZD7648 and M3814) provide molecular details and insights useful for drug design.
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17
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Wu HY, Zheng Y, Laciak AR, Huang NN, Koszelak-Rosenblum M, Flint AJ, Carr G, Zhu G. Structure and Function of SNM1 Family Nucleases. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2022; 1414:1-26. [PMID: 35708844 DOI: 10.1007/5584_2022_724] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/09/2022]
Abstract
Three human nucleases, SNM1A, SNM1B/Apollo, and SNM1C/Artemis, belong to the SNM1 gene family. These nucleases are involved in various cellular functions, including homologous recombination, nonhomologous end-joining, cell cycle regulation, and telomere maintenance. These three proteins share a similar catalytic domain, which is characterized as a fused metallo-β-lactamase and a CPSF-Artemis-SNM1-PSO2 domain. SNM1A and SNM1B/Apollo are exonucleases, whereas SNM1C/Artemis is an endonuclease. This review contains a summary of recent research on SNM1's cellular and biochemical functions, as well as structural biology studies. In addition, protein structure prediction by the artificial intelligence program AlphaFold provides a different view of the proteins' non-catalytic domain features, which may be used in combination with current results from X-ray crystallography and cryo-EM to understand their mechanism more clearly.
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18
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Prados-Carvajal R, Irving E, Lukashchuk N, Forment JV. Preventing and Overcoming Resistance to PARP Inhibitors: A Focus on the Clinical Landscape. Cancers (Basel) 2021; 14:44. [PMID: 35008208 PMCID: PMC8750220 DOI: 10.3390/cancers14010044] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2021] [Revised: 12/17/2021] [Accepted: 12/19/2021] [Indexed: 12/12/2022] Open
Abstract
Poly(ADP-ribose) polymerase (PARP) inhibitors (PARPi) are now a first-line maintenance treatment in ovarian cancer and have been approved in other cancer types, including breast, pancreatic and prostate. Despite their efficacy, and as is the case for other targeted therapies, resistance to PARPi has been reported clinically and is generating a growing patient population of unmet clinical need. Here, we discuss the mechanisms of resistance that have been described in pre-clinical models and focus on those that have been already identified in the clinic, highlighting the key challenges to fully characterise the clinical landscape of PARPi resistance and proposing ways of preventing and overcoming it.
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Affiliation(s)
- Rosario Prados-Carvajal
- DDR Biology, Bioscience, Oncology R&D, AstraZeneca, Cambridge CB4 0WG, UK; (R.P.-C.); (E.I.)
| | - Elsa Irving
- DDR Biology, Bioscience, Oncology R&D, AstraZeneca, Cambridge CB4 0WG, UK; (R.P.-C.); (E.I.)
| | - Natalia Lukashchuk
- Translational Medicine, Oncology R&D, AstraZeneca, Cambridge CB4 0WG, UK;
| | - Josep V. Forment
- DDR Biology, Bioscience, Oncology R&D, AstraZeneca, Cambridge CB4 0WG, UK; (R.P.-C.); (E.I.)
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19
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Feng W, Smith CM, Simpson DA, Gupta GP. Targeting Non-homologous and Alternative End Joining Repair to Enhance Cancer Radiosensitivity. Semin Radiat Oncol 2021; 32:29-41. [PMID: 34861993 DOI: 10.1016/j.semradonc.2021.09.007] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Many cancer therapies, including radiotherapy, induce DSBs as the major driving mechanism for inducing cancer cell death. Thus, modulating DSB repair has immense potential for radiosensitization, although such interventions must be carefully designed to be tumor selective to ensure that normal tissue toxicities are not also increased. Here, we review mechanisms of error-prone DSB repair through a highly efficient process called end joining. There are two major pathways of end-joining repair: non-homologous end joining (NHEJ) and alternative end joining (a-EJ), both of which can be selectively upregulated in cancer and thus represent attractive therapeutic targets for radiosensitization. These EJ pathways each have therapeutically targetable pioneer factors - DNA-dependent protein kinase catalytic subunit (DNA-PKcs) for NHEJ and DNA Polymerase Theta (Pol θ) for a-EJ. We summarize the current status of therapeutic targeting of NHEJ and a-EJ to enhance the effects of radiotherapy - focusing on challenges that must be overcome and opportunities that require further exploration. By leveraging preclinical insights into mechanisms of altered DSB repair programs in cancer, selective radiosensitization through NHEJ and/or a-EJ targeting remains a highly attractive avenue for ongoing and future clinical investigation.
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Affiliation(s)
| | - Chelsea M Smith
- Lineberger Comprehensive Cancer Center; Pathobiology and Translational Science Graduate Program
| | | | - Gaorav P Gupta
- Lineberger Comprehensive Cancer Center; Pathobiology and Translational Science Graduate Program; Department of Radiation Oncology; Department of Biochemistry and Biophysics, University of North Carolina, Chapel Hill, NC.
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20
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Radiosensitisation of SCCVII tumours and normal tissues in mice by the DNA-dependent protein kinase inhibitor AZD7648. Radiother Oncol 2021; 166:162-170. [PMID: 34861268 DOI: 10.1016/j.radonc.2021.11.027] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2021] [Revised: 10/18/2021] [Accepted: 11/22/2021] [Indexed: 11/20/2022]
Abstract
BACKGROUND AND PURPOSE Inhibitors of DNA-dependent protein kinase (DNA-PK) are effective radiation sensitisers in preclinical tumours, but little is known about risks of normal tissue radiosensitisation. Here, we evaluate radiosensitisation of head and neck squamous cell carcinoma (HNSCC) cells by DNA-PK inhibitor AZD7648 under oxia and anoxia in vitro, and tumour (SCCVII), oral mucosa and small intestine in mice. MATERIALS AND METHODS Radiosensitisation of human (UT-SCC-54C) and murine (SCCVII) HNSCC cells by AZD7648 under oxia and anoxia was evaluated by clonogenic assay. Radiosensitisation of SCCVII tumours in C3H mice by oral AZD7648 (75 mg/kg) was determined by ex vivo clonogenic assay 3.5 days post-irradiation, with evaluation of normal tissue surrogate endpoints using 5-ethynyl-2'-deoxyuridine to facilitate detection of regenerating crypts in the ileum and repopulating S-phase cells in the ileum and oral mucosa of the same animals. RESULTS AZD7648 potently radiosensitised both cell lines, with similar sensitiser enhancement ratios for 10% survival (SER10) under oxia and anoxia. AZD7648 diffused rapidly through multicellular layers, suggesting rapid equilibration between plasma and hypoxic zones in tumours. SCCVII tumours were radiosensitised by AZD7648 (SER10 2.5). AZD7648 also enhanced radiation-induced body weight loss and suppressed regenerating intestinal crypts and repopulating S-phase cells in the ileum and tongue epithelium with SER values similar to SCCVII tumours. CONCLUSION AZD7648 is a potent radiation sensitiser of both oxic and anoxic tumour cells, but also markedly radiosensitises stem cells in the small intestine and oral mucosa.
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21
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Chen S, Chen D, Liu B, Haisma HJ. Modulating CRISPR/Cas9 genome-editing activity by small molecules. Drug Discov Today 2021; 27:951-966. [PMID: 34823004 DOI: 10.1016/j.drudis.2021.11.018] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2021] [Revised: 10/25/2021] [Accepted: 11/17/2021] [Indexed: 12/12/2022]
Abstract
Clustered regularly interspaced short palindromic repeats/CRISPR-associated protein 9 (CRISPR/Cas9)-mediated genome engineering has become a standard procedure for creating genetic and epigenetic changes of DNA molecules in basic biology, biotechnology, and medicine. However, its versatile applications have been hampered by its overall low precise gene modification efficiency and uncontrollable prolonged Cas9 activity. Therefore, overcoming these problems could broaden the therapeutic use of CRISPR/Cas9-based technologies. Here, we review small molecules with the clinical potential to precisely modulate CRISPR/Cas9-mediated genome-editing activity and discuss their mechanisms of action. Based on these data, we suggest that direct-acting small molecules for Cas9 are more suitable for precisely regulating Cas9 activity. These findings provide useful information for the identification of novel small-molecule enhancers and inhibitors of Cas9 and Cas9-associated endonucleases.
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Affiliation(s)
- Siwei Chen
- Department of Chemical and Pharmaceutical Biology, Groningen Research Institute of Pharmacy, University of Groningen, Groningen 9713 AV, the Netherlands
| | - Deng Chen
- Department of Chemical and Pharmaceutical Biology, Groningen Research Institute of Pharmacy, University of Groningen, Groningen 9713 AV, the Netherlands
| | - Bin Liu
- Department of Chemical and Pharmaceutical Biology, Groningen Research Institute of Pharmacy, University of Groningen, Groningen 9713 AV, the Netherlands; RNA Therapeutics Institute, University of Massachusetts Medical School, Worcester, MA 01605, USA(1)
| | - Hidde J Haisma
- Department of Chemical and Pharmaceutical Biology, Groningen Research Institute of Pharmacy, University of Groningen, Groningen 9713 AV, the Netherlands.
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22
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Arai D, Nakao Y. Efficient biallelic knock-in in mouse embryonic stem cells by in vivo-linearization of donor and transient inhibition of DNA polymerase θ/DNA-PK. Sci Rep 2021; 11:18132. [PMID: 34518609 PMCID: PMC8438075 DOI: 10.1038/s41598-021-97579-8] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2021] [Accepted: 08/24/2021] [Indexed: 01/13/2023] Open
Abstract
CRISPR/Cas9-mediated homology-directed repair (HDR) is used for error-free targeted knock-in of foreign donor DNA. However, the low efficiency of HDR-mediated knock-in hinders establishment of knock-in clones. Double-strand breaks (DSBs) induced by CRISPR/Cas9 are preferentially repaired by non-homologous end joining (NHEJ) or microhomology-mediated end joining (MMEJ) before HDR can occur, thereby preventing HDR-mediated knock-in. NHEJ/MMEJ also cause random integrations, which give rise to false-positive knock-in events, or silently disrupt the genome. In this study, we optimized an HDR-mediated knock-in method for mouse embryonic stem cells (mESCs). We succeeded in improving efficiency of HDR-mediated knock-in of a plasmid donor while almost completely suppressing NHEJ/MMEJ-based integration by combining in vivo-linearization of the donor plasmid, transient knockdown of DNA polymerase θ, and chemical inhibition of DNA-dependent protein kinase (DNA-PK) by M3814. This method also dramatically improved the efficiency of biallelic knock-in; at the Rosa26a locus, 95% of HDR-mediated knock-in clones were biallelic. We designate this method BiPoD (Biallelic knock-in assisted by Pol θ and DNA-PK inhibition). BiPoD achieved simultaneous efficient biallelic knock-in into two loci. BiPoD, therefore, enables rapid and easy establishment of biallelic knock-in mESC lines.
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Affiliation(s)
- Daisuke Arai
- School of Advanced Science and Engineering, Waseda University, 3-4-1 Okubo, Shinjuku-ku, Tokyo, 169-8555, Japan.
| | - Yoichi Nakao
- School of Advanced Science and Engineering, Waseda University, 3-4-1 Okubo, Shinjuku-ku, Tokyo, 169-8555, Japan
- Research Institute for Science and Engineering, Waseda University, 3-4-1 Okubo, Shinjuku-ku, Tokyo, 169-8555, Japan
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23
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Tan KT, Yeh CN, Chang YC, Cheng JH, Fang WL, Yeh YC, Wang YC, Hsu DSS, Wu CE, Lai JI, Chang PMH, Chen MH, Lu ML, Chen SJ, Chao Y, Hsiao M, Chen MH. PRKDC: new biomarker and drug target for checkpoint blockade immunotherapy. J Immunother Cancer 2021; 8:jitc-2019-000485. [PMID: 32238472 PMCID: PMC7174075 DOI: 10.1136/jitc-2019-000485] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/03/2020] [Indexed: 12/25/2022] Open
Abstract
Background Immunological checkpoint blockade is effective in treating various malignancies. Identifying predictive biomarkers to assist patient selection for immunotherapy has become a priority in both clinical and research settings. Methods Mutations in patients who responded to immunotherapy were identified through next-generation sequencing. Relationships among protein kinase, DNA-activated, catalytic polypeptide (PRKDC) mutations, mutation load and microsatellite instability (MSI) were analyzed using datasets from The Cancer Genome Atlas. These relationships were validated by conducting an in vitro study and by using tissue samples from 34 patients with gastric cancer. The CT26 animal model was used to evaluate the role of PRKDC as a predictive biomarker and the efficacy of the DNA-PK inhibitor. Results From the published literature, we found that among patients whose tumors harbored PRKDC mutations, 75%, 53.8%, and 50% of those with lung cancer, melanoma, and renal cell carcinoma, respectively, responded to immunotherapy. Most of these mutations were truncating and located in functional domains or in a destabilizing PRKDC protein structure. Additional analysis showed that a PRKDC mutation was significantly associated with a high mutation load in cervical cancer, colon adenocarcinoma, head and neck squamous cell carcinoma, lung adenocarcinoma, gastric adenocarcinoma and endometrial cancer. Patients with gastric cancer or colon cancer harboring PRKDC mutations were also highly associated with MSI-high status. Finally, we found that knockout PRKDC or DNA-PK inhibitor (PRKDC encodes the catalytic subunit of DNA-dependent protein kinase) enhanced the efficacy of the anti-programmed cell death protein one pathway monoclonal antibody in the CT26 animal model. Conclusions PRKDC is not only a predictive biomarker but also a drug target for immune checkpoint inhibitors.
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Affiliation(s)
| | - Chun-Nan Yeh
- Department of Surgery, Liver Research Center, Chang Gung Memorial Hospital, Chang Gung University, Taoyuan, Taiwan
| | - Yu-Chan Chang
- Genomics Research Center, Academia Sinica, Taipei, Taiwan
| | | | - Wen-Liang Fang
- Department of Surgery, Taipei Veterans General Hospital, Taipei, Taiwan.,School of Medicine, National Yang-Ming University, Taipei, Taiwan
| | - Yi-Chen Yeh
- School of Medicine, National Yang-Ming University, Taipei, Taiwan.,Department of Pathology, Taipei Veterans General Hospital, Taipei, Taiwan
| | - Yu-Chao Wang
- Institute of Biomedical Informatics, National Yang-Ming University, Taipei, Taiwan.,Preventive Medicine Research Center, National Yang-Ming University, Taipei, Taiwan
| | | | - Chiao-En Wu
- Department of Surgery, Liver Research Center, Chang Gung Memorial Hospital, Chang Gung University, Taoyuan, Taiwan
| | - Jiun-I Lai
- School of Medicine, National Yang-Ming University, Taipei, Taiwan.,Center of Immuno-Oncology, Department of Oncology, Taipei Veterans General Hospital, Taipei, Taiwan
| | - Peter Mu-Hsin Chang
- School of Medicine, National Yang-Ming University, Taipei, Taiwan.,Center of Immuno-Oncology, Department of Oncology, Taipei Veterans General Hospital, Taipei, Taiwan
| | - Ming-Han Chen
- School of Medicine, National Yang-Ming University, Taipei, Taiwan
| | - Meng-Lun Lu
- Center of Immuno-Oncology, Department of Oncology, Taipei Veterans General Hospital, Taipei, Taiwan
| | | | - Yee Chao
- School of Medicine, National Yang-Ming University, Taipei, Taiwan.,Center of Immuno-Oncology, Department of Oncology, Taipei Veterans General Hospital, Taipei, Taiwan
| | - Michael Hsiao
- Genomics Research Center, Academia Sinica, Taipei, Taiwan
| | - Ming-Huang Chen
- School of Medicine, National Yang-Ming University, Taipei, Taiwan .,Center of Immuno-Oncology, Department of Oncology, Taipei Veterans General Hospital, Taipei, Taiwan
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24
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Raimundo L, Calheiros J, Saraiva L. Exploiting DNA Damage Repair in Precision Cancer Therapy: BRCA1 as a Prime Therapeutic Target. Cancers (Basel) 2021; 13:cancers13143438. [PMID: 34298653 PMCID: PMC8303227 DOI: 10.3390/cancers13143438] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2021] [Revised: 06/21/2021] [Accepted: 07/07/2021] [Indexed: 12/24/2022] Open
Abstract
Simple Summary Chemical inhibition of central DNA damage repair (DDR) proteins has become a promising approach in precision cancer therapy. In particular, BRCA1 and its DDR-associated proteins constitute important targets for developing DNA repair inhibiting drugs. This review provides relevant insights on DDR biology and pharmacology, aiming to boost the development of more effective DDR targeted therapies. Abstract Precision medicine aims to identify specific molecular alterations, such as driver mutations, allowing tailored and effective anticancer therapies. Poly(ADP)-ribose polymerase inhibitors (PARPi) are the prototypical example of targeted therapy, exploiting the inability of cancer cells to repair DNA damage. Following the concept of synthetic lethality, PARPi have gained great relevance, particularly in BRCA1 dysfunctional cancer cells. In fact, BRCA1 mutations culminate in DNA repair defects that can render cancer cells more vulnerable to therapy. However, the efficacy of these drugs has been greatly affected by the occurrence of resistance due to multi-connected DNA repair pathways that may compensate for each other. Hence, the search for additional effective agents targeting DNA damage repair (DDR) is of crucial importance. In this context, BRCA1 has assumed a central role in developing drugs aimed at inhibiting DNA repair activity. Collectively, this review provides an in-depth understanding of the biology and regulatory mechanisms of DDR pathways, highlighting the potential of DDR-associated molecules, particularly BRCA1 and its interconnected partners, in precision cancer medicine. It also affords an overview about what we have achieved and a reflection on how much remains to be done in this field, further addressing encouraging clues for the advance of DDR targeted therapy.
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25
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Ray U, Raghavan SC. Understanding the DNA double-strand break repair and its therapeutic implications. DNA Repair (Amst) 2021; 106:103177. [PMID: 34325086 DOI: 10.1016/j.dnarep.2021.103177] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2021] [Revised: 06/25/2021] [Accepted: 07/07/2021] [Indexed: 10/20/2022]
Abstract
Repair of DNA double-strand breaks (DSBs) and its regulation are tightly integrated inside cells. Homologous recombination, nonhomologous end joining and microhomology mediated end joining are three major DSB repair pathways in mammalian cells. Targeting proteins associated with these repair pathways using small molecule inhibitors can prove effective in tumors, especially those with deregulated repair. Sensitization of cancer to current age therapy including radio and chemotherapy, using small molecule inhibitors is promising and warrant further development. Although several are under clinical trial, till date no repair inhibitor is approved for commercial use in cancer patients, with the exception of PARP inhibitors targeting single-strand break repair. Based on molecular profiling of repair proteins, better prognostic and therapeutic output can be achieved in patients. In the present review, we highlight the different mechanisms of DSB repair, chromatin dynamics to provide repair accessibility and modulation of inhibitors in association with molecular profiling and current gold standard treatment modalities for cancer.
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Affiliation(s)
- Ujjayinee Ray
- Department of Biochemistry, Indian Institute of Science, Bangalore 560012, India
| | - Sathees C Raghavan
- Department of Biochemistry, Indian Institute of Science, Bangalore 560012, India.
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26
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Hognon C, Monari A. Staring at the Naked Goddess: Unraveling the Structure and Reactivity of Artemis Endonuclease Interacting with a DNA Double Strand. Molecules 2021; 26:molecules26133986. [PMID: 34210101 PMCID: PMC8271620 DOI: 10.3390/molecules26133986] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2021] [Revised: 06/23/2021] [Accepted: 06/26/2021] [Indexed: 11/16/2022] Open
Abstract
Artemis is an endonuclease responsible for breaking hairpin DNA strands during immune system adaptation and maturation as well as the processing of potentially toxic DNA lesions. Thus, Artemis may be an important target in the development of anticancer therapy, both for the sensitization of radiotherapy and for immunotherapy. Despite its importance, its structure has been resolved only recently, and important questions concerning the arrangement of its active center, the interaction with the DNA substrate, and the catalytic mechanism remain unanswered. In this contribution, by performing extensive molecular dynamic simulations, both classically and at the hybrid quantum mechanics/molecular mechanics level, we evidenced the stable interaction modes of Artemis with a model DNA strand. We also analyzed the catalytic cycle providing the free energy profile and key transition states for the DNA cleavage reaction.
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27
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Druggable binding sites in the multicomponent assemblies that characterise DNA double-strand-break repair through non-homologous end joining. Essays Biochem 2021; 64:791-806. [PMID: 32579168 PMCID: PMC7588668 DOI: 10.1042/ebc20190092] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2020] [Revised: 05/19/2020] [Accepted: 05/21/2020] [Indexed: 02/07/2023]
Abstract
Non-homologous end joining (NHEJ) is one of the two principal damage repair pathways for DNA double-strand breaks in cells. In this review, we give a brief overview of the system including a discussion of the effects of deregulation of NHEJ components in carcinogenesis and resistance to cancer therapy. We then discuss the relevance of targeting NHEJ components pharmacologically as a potential cancer therapy and review previous approaches to orthosteric regulation of NHEJ factors. Given the limited success of previous investigations to develop inhibitors against individual components, we give a brief discussion of the recent advances in computational and structural biology that allow us to explore different targets, with a particular focus on modulating protein-protein interaction interfaces. We illustrate this discussion with three examples showcasing some current approaches to developing protein-protein interaction inhibitors to modulate the assembly of NHEJ multiprotein complexes in space and time.
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28
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Bosch-Guiteras N, Uroda T, Guillen-Ramirez HA, Riedo R, Gazdhar A, Esposito R, Pulido-Quetglas C, Zimmer Y, Medová M, Johnson R. Enhancing CRISPR deletion via pharmacological delay of DNA-PKcs. Genome Res 2021; 31:461-471. [PMID: 33574136 PMCID: PMC7919447 DOI: 10.1101/gr.265736.120] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2020] [Accepted: 01/15/2021] [Indexed: 12/15/2022]
Abstract
CRISPR-Cas9 deletion (CRISPR-del) is the leading approach for eliminating DNA from mammalian cells and underpins a variety of genome-editing applications. Target DNA, defined by a pair of double-strand breaks (DSBs), is removed during nonhomologous end-joining (NHEJ). However, the low efficiency of CRISPR-del results in laborious experiments and false-negative results. By using an endogenous reporter system, we show that repression of the DNA-dependent protein kinase catalytic subunit (DNA-PKcs)—an early step in NHEJ—yields substantial increases in DNA deletion. This is observed across diverse cell lines, gene delivery methods, commercial inhibitors, and guide RNAs, including those that otherwise display negligible activity. We further show that DNA-PKcs inhibition can be used to boost the sensitivity of pooled functional screens and detect true-positive hits that would otherwise be overlooked. Thus, delaying the kinetics of NHEJ relative to DSB formation is a simple and effective means of enhancing CRISPR-deletion.
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Affiliation(s)
- Núria Bosch-Guiteras
- Department of Medical Oncology, Inselspital, Bern University Hospital, University of Bern, 3010 Bern, Switzerland.,Department for BioMedical Research, University of Bern, 3008 Bern, Switzerland.,Graduate School of Cellular and Biomedical Sciences, University of Bern, 3012 Bern, Switzerland
| | - Tina Uroda
- Department of Medical Oncology, Inselspital, Bern University Hospital, University of Bern, 3010 Bern, Switzerland.,Department for BioMedical Research, University of Bern, 3008 Bern, Switzerland
| | - Hugo A Guillen-Ramirez
- Department of Medical Oncology, Inselspital, Bern University Hospital, University of Bern, 3010 Bern, Switzerland.,Department for BioMedical Research, University of Bern, 3008 Bern, Switzerland
| | - Rahel Riedo
- Department for BioMedical Research, University of Bern, 3008 Bern, Switzerland.,Department of Radiation Oncology, Inselspital, Bern University Hospital, University of Bern, 3010 Bern, Switzerland
| | - Amiq Gazdhar
- Department for BioMedical Research, University of Bern, 3008 Bern, Switzerland.,Department of Pulmonary Medicine, University Hospital Bern, University of Bern, 3008 Bern, Switzerland
| | - Roberta Esposito
- Department of Medical Oncology, Inselspital, Bern University Hospital, University of Bern, 3010 Bern, Switzerland.,Department for BioMedical Research, University of Bern, 3008 Bern, Switzerland
| | - Carlos Pulido-Quetglas
- Department of Medical Oncology, Inselspital, Bern University Hospital, University of Bern, 3010 Bern, Switzerland.,Department for BioMedical Research, University of Bern, 3008 Bern, Switzerland.,Graduate School of Cellular and Biomedical Sciences, University of Bern, 3012 Bern, Switzerland
| | - Yitzhak Zimmer
- Department for BioMedical Research, University of Bern, 3008 Bern, Switzerland.,Department of Radiation Oncology, Inselspital, Bern University Hospital, University of Bern, 3010 Bern, Switzerland
| | - Michaela Medová
- Department for BioMedical Research, University of Bern, 3008 Bern, Switzerland.,Department of Radiation Oncology, Inselspital, Bern University Hospital, University of Bern, 3010 Bern, Switzerland
| | - Rory Johnson
- Department of Medical Oncology, Inselspital, Bern University Hospital, University of Bern, 3010 Bern, Switzerland.,Department for BioMedical Research, University of Bern, 3008 Bern, Switzerland.,School of Biology and Environmental Science, University College Dublin, Dublin D04 V1W8, Ireland.,Conway Institute for Biomolecular and Biomedical Research, University College Dublin, Dublin D04 V1W8, Ireland
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29
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Hu S, Hui Z, Lirussi F, Garrido C, Ye XY, Xie T. Small molecule DNA-PK inhibitors as potential cancer therapy: a patent review (2010-present). Expert Opin Ther Pat 2021; 31:435-452. [PMID: 33347360 DOI: 10.1080/13543776.2021.1866540] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
Abstract
Introduction: DNA-dependent protein kinase (DNA-PK) plays a crucial role in the repair of DSBs via non-homologous end joining (NHEJ). Several DNA-PK inhibitors are being investigated for potential anticancer treatment in clinical trials.Area covered: This review aims to give an overview of patents published since 2010 by analyzing the patent space and structure features of scaffolds used in those patents. It also discusses the recent clinical developments and provides perspectives on future challenges and directions in this field.Expert opinion: As a key component of the DNA damage response (DDR) pathway, DNA-PK appears to be a viable drug target for anticancer therapy. The clinical investigation of a DNA-PK inhibitor employs both a monotherapy and a combination strategy. In the combination strategy, a DNA-PK inhibitor is typically combined with a DSB inducer, radiation, a chemotherapy agent, or a PARP inhibitor, etc. Patent analyses suggest that diverse structures comprising different scaffolds from mono-heteroaryl to bicyclic heteroaryl to tricyclic heteroaryl are capable to achieve good DNA-PK inhibitory activity and good DNA-PK selectivity over other closely related enzymes. Several DNA-PK inhibitors are currently being evaluated in clinics, with the hope to get approval in the near future.
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Affiliation(s)
- Suwen Hu
- College of Pharmacy, School of Medicine, Hangzhou Normal University, Hangzhou, Zhejiang Province, Zhejiang, People's Republic of China.,Engineering Laboratory of Development and Application of Traditional Chinese Medicine from Zhejiang Province, Zhejiang Province, People's Republic of China.,;cCollaborative Innovation Center of Chinese Medicines from Zhejiang Province, Zhejiang Province, People's Republic of China.,;dKey Laboratory of Elemene Class Anti-Cancer Chinese Medicine of Zhejiang Province, Hangzhou, Zhejiang Province, People's Republic of China.,;eHangzhou Huadong Medicine Group, Pharmaceutical Research Institute Co. Ltd, Hanzhou City, Zhejiang Province, People's Republic of China
| | - Zi Hui
- College of Pharmacy, School of Medicine, Hangzhou Normal University, Hangzhou, Zhejiang Province, Zhejiang, People's Republic of China.,Engineering Laboratory of Development and Application of Traditional Chinese Medicine from Zhejiang Province, Zhejiang Province, People's Republic of China.,;cCollaborative Innovation Center of Chinese Medicines from Zhejiang Province, Zhejiang Province, People's Republic of China.,;Key Laboratory of Elemene Class Anti-Cancer Chinese Medicine of Zhejiang Province, Hangzhou, Zhejiang Province, People's Republic of China
| | - Frédéric Lirussi
- ;fINSERM, U1231, Label LipSTIC, and Ligue Nationale Contre Le Cancer, Dijon, France.,;gUniversité De Bourgogne-Franche Comté, I-SITE, France.,;hDepartment of Pharmacology-Toxicology & Metabolomics, University hospital of Besançon (CHU), 2 Boulevard Fleming, 25030 BESANCON, France
| | - Carmen Garrido
- ;INSERM, U1231, Label LipSTIC, and Ligue Nationale Contre Le Cancer, Dijon, France.,;Université De Bourgogne-Franche Comté, I-SITE, France.,;iAnti-cancer Center George-François Leclerc, CGFL, Dijon, France
| | - Xiang-Yang Ye
- College of Pharmacy, School of Medicine, Hangzhou Normal University, Hangzhou, Zhejiang Province, Zhejiang, People's Republic of China.,Engineering Laboratory of Development and Application of Traditional Chinese Medicine from Zhejiang Province, Zhejiang Province, People's Republic of China.,;cCollaborative Innovation Center of Chinese Medicines from Zhejiang Province, Zhejiang Province, People's Republic of China.,;Key Laboratory of Elemene Class Anti-Cancer Chinese Medicine of Zhejiang Province, Hangzhou, Zhejiang Province, People's Republic of China
| | - Tian Xie
- College of Pharmacy, School of Medicine, Hangzhou Normal University, Hangzhou, Zhejiang Province, Zhejiang, People's Republic of China.,Engineering Laboratory of Development and Application of Traditional Chinese Medicine from Zhejiang Province, Zhejiang Province, People's Republic of China.,;cCollaborative Innovation Center of Chinese Medicines from Zhejiang Province, Zhejiang Province, People's Republic of China.,;Key Laboratory of Elemene Class Anti-Cancer Chinese Medicine of Zhejiang Province, Hangzhou, Zhejiang Province, People's Republic of China
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30
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Inhibitors of DNA double-strand break repair at the crossroads of cancer therapy and genome editing. Biochem Pharmacol 2020; 182:114195. [DOI: 10.1016/j.bcp.2020.114195] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2020] [Revised: 08/03/2020] [Accepted: 08/10/2020] [Indexed: 12/17/2022]
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31
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Wengner AM, Scholz A, Haendler B. Targeting DNA Damage Response in Prostate and Breast Cancer. Int J Mol Sci 2020; 21:E8273. [PMID: 33158305 PMCID: PMC7663807 DOI: 10.3390/ijms21218273] [Citation(s) in RCA: 52] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2020] [Revised: 10/29/2020] [Accepted: 10/30/2020] [Indexed: 02/06/2023] Open
Abstract
Steroid hormone signaling induces vast gene expression programs which necessitate the local formation of transcription factories at regulatory regions and large-scale alterations of the genome architecture to allow communication among distantly related cis-acting regions. This involves major stress at the genomic DNA level. Transcriptionally active regions are generally instable and prone to breakage due to the torsional stress and local depletion of nucleosomes that make DNA more accessible to damaging agents. A dedicated DNA damage response (DDR) is therefore essential to maintain genome integrity at these exposed regions. The DDR is a complex network involving DNA damage sensor proteins, such as the poly(ADP-ribose) polymerase 1 (PARP-1), the DNA-dependent protein kinase catalytic subunit (DNA-PKcs), the ataxia-telangiectasia-mutated (ATM) kinase and the ATM and Rad3-related (ATR) kinase, as central regulators. The tight interplay between the DDR and steroid hormone receptors has been unraveled recently. Several DNA repair factors interact with the androgen and estrogen receptors and support their transcriptional functions. Conversely, both receptors directly control the expression of agents involved in the DDR. Impaired DDR is also exploited by tumors to acquire advantageous mutations. Cancer cells often harbor germline or somatic alterations in DDR genes, and their association with disease outcome and treatment response led to intensive efforts towards identifying selective inhibitors targeting the major players in this process. The PARP-1 inhibitors are now approved for ovarian, breast, and prostate cancer with specific genomic alterations. Additional DDR-targeting agents are being evaluated in clinical studies either as single agents or in combination with treatments eliciting DNA damage (e.g., radiation therapy, including targeted radiotherapy, and chemotherapy) or addressing targets involved in maintenance of genome integrity. Recent preclinical and clinical findings made in addressing DNA repair dysfunction in hormone-dependent and -independent prostate and breast tumors are presented. Importantly, the combination of anti-hormonal therapy with DDR inhibition or with radiation has the potential to enhance efficacy but still needs further investigation.
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Affiliation(s)
| | | | - Bernard Haendler
- Preclinical Research, Research & Development, Pharmaceuticals, Bayer AG, Müllerstr. 178, 13353 Berlin, Germany; (A.M.W.); (A.S.)
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32
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Tobalina L, Armenia J, Irving E, O'Connor MJ, Forment JV. A meta-analysis of reversion mutations in BRCA genes identifies signatures of DNA end-joining repair mechanisms driving therapy resistance. Ann Oncol 2020; 32:103-112. [PMID: 33091561 DOI: 10.1016/j.annonc.2020.10.470] [Citation(s) in RCA: 84] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2020] [Revised: 09/27/2020] [Accepted: 10/04/2020] [Indexed: 01/31/2023] Open
Abstract
BACKGROUND Germline mutations in the BRCA1 or BRCA2 (BRCA) genes predispose to hereditary breast and ovarian cancer and, mostly in the case of BRCA2, are also prevalent in cases of pancreatic and prostate malignancies. Tumours from these patients tend to lose both copies of the wild-type BRCA gene, which makes them exquisitely sensitive to platinum drugs and poly(ADP-ribose) polymerase inhibitors (PARPi), treatments of choice in these disease settings. Reversion secondary mutations with the capacity of restoring BRCA protein expression have been documented in the literature as bona fide mechanisms of resistance to these treatments. PATIENTS AND METHODS We analysed published sequencing data of BRCA genes (from tumour or circulating tumour DNA) in 327 patients with tumours harbouring mutations in BRCA1 or BRCA2 (234 patients with ovarian cancer, 27 with breast cancer, 13 with pancreatic cancer, 11 with prostate cancer and 42 with a cancer of unknown origin) that progressed on platinum or PARPi treatment. RESULTS We describe 269 cases of reversion mutations in 86 patients in this cohort (26.0%). Detailed analyses of the reversion events highlight that most amino acid sequences encoded by exon 11 in BRCA1 and BRCA2 are dispensable to generate resistance to platinum or PARPi, whereas other regions are more refractory to sizeable amino acid losses. They also underline the key role of mutagenic end-joining DNA repair pathways in generating reversions, especially in those affecting BRCA2, as indicated by the significant accumulation of DNA sequence microhomologies surrounding deletions leading to reversion events. CONCLUSIONS Our analyses suggest that pharmacological inhibition of DNA end-joining repair pathways could improve durability of drug treatments by preventing the acquisition of reversion mutations in BRCA genes. They also highlight potential new therapeutic opportunities when reversions result in expression of hypomorphic versions of BRCA proteins, especially with agents targeting the response to DNA replication stress.
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Affiliation(s)
- L Tobalina
- Bioinformatics and Data Science, Oncology R&D, AstraZeneca, Cambridge, UK
| | - J Armenia
- Bioinformatics and Data Science, Oncology R&D, AstraZeneca, Cambridge, UK
| | - E Irving
- DDR Biology, Bioscience, Oncology R&D, AstraZeneca, Cambridge, UK
| | - M J O'Connor
- DDR Biology, Bioscience, Oncology R&D, AstraZeneca, Cambridge, UK
| | - J V Forment
- DDR Biology, Bioscience, Oncology R&D, AstraZeneca, Cambridge, UK.
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33
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Jeffries AM, Marriott I. Cytosolic DNA Sensors and CNS Responses to Viral Pathogens. Front Cell Infect Microbiol 2020; 10:576263. [PMID: 33042875 PMCID: PMC7525022 DOI: 10.3389/fcimb.2020.576263] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2020] [Accepted: 08/12/2020] [Indexed: 12/17/2022] Open
Abstract
Viral central nervous system (CNS) infections can lead to life threatening encephalitis and long-term neurological deficits in survivors. Resident CNS cell types, such as astrocytes and microglia, are known to produce key inflammatory and antiviral mediators following infection with neurotropic DNA viruses. However, the mechanisms by which glia mediate such responses remain poorly understood. Recently, a class of intracellular pattern recognition receptors (PRRs), collectively known as DNA sensors, have been identified in both leukocytic and non-leukocytic cell types. The ability of such DNA sensors to initiate immune mediator production and contribute to infection resolution in the periphery is increasingly recognized, but our understanding of their role in the CNS remains limited at best. In this review, we describe the evidence for the expression and functionality of DNA sensors in resident brain cells, with a focus on their role in neurotropic virus infections. The available data indicate that glia and neurons can constitutively express, and/or can be induced to express, various disparate DNA sensing molecules previously described in peripheral cell types. Furthermore, multiple lines of investigation suggest that these sensors are functional in resident CNS cells and are required for innate immune responses to viral infections. However, it is less clear whether DNA sensormediated glial responses are beneficial or detrimental, and the answer to this question appears to dependent on the context of the infection with regard to the identity of the pathogen, host cell type, and host species. Defining such parameters will be essential if we are to successfully target these molecules to limit damaging inflammation while allowing beneficial host responses to improve patient outcomes.
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Affiliation(s)
- Austin M Jeffries
- Department of Biological Sciences, The University of North Carolina at Charlotte, Charlotte, NC, United States
| | - Ian Marriott
- Department of Biological Sciences, The University of North Carolina at Charlotte, Charlotte, NC, United States
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34
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Karim MF, Liu S, Laciak AR, Volk L, Koszelak-Rosenblum M, Lieber MR, Wu M, Curtis R, Huang NN, Carr G, Zhu G. Structural analysis of the catalytic domain of Artemis endonuclease/SNM1C reveals distinct structural features. J Biol Chem 2020; 295:12368-12377. [PMID: 32576658 PMCID: PMC7458816 DOI: 10.1074/jbc.ra120.014136] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2020] [Revised: 06/22/2020] [Indexed: 12/31/2022] Open
Abstract
The endonuclease Artemis is responsible for opening DNA hairpins during V(D)J recombination and for processing a subset of pathological DNA double-strand breaks. Artemis is an attractive target for the development of therapeutics to manage various B cell and T cell tumors, because failure to open DNA hairpins and accumulation of chromosomal breaks may reduce the proliferation and viability of pre-T and pre-B cell derivatives. However, structure-based drug discovery of specific Artemis inhibitors has been hampered by a lack of crystal structures. Here, we report the structure of the catalytic domain of recombinant human Artemis. The catalytic domain displayed a polypeptide fold similar overall to those of other members in the DNA cross-link repair gene SNM1 family and in mRNA 3'-end-processing endonuclease CPSF-73, containing metallo-β-lactamase and β-CASP domains and a cluster of conserved histidine and aspartate residues capable of binding two metal atoms in the catalytic site. As in SNM1A, only one zinc ion was located in the Artemis active site. However, Artemis displayed several unique features. Unlike in other members of this enzyme class, a second zinc ion was present in the β-CASP domain that leads to structural reorientation of the putative DNA-binding surface and extends the substrate-binding pocket to a new pocket, pocket III. Moreover, the substrate-binding surface exhibited a dominant and extensive positive charge distribution compared with that in the structures of SNM1A and SNM1B, presumably because of the structurally distinct DNA substrate of Artemis. The structural features identified here may provide opportunities for designing selective Artemis inhibitors.
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Affiliation(s)
- Md Fazlul Karim
- Discovery Biology, Albany Molecular Research Inc., Buffalo, New York, USA
| | - Shanshan Liu
- Discovery Biology, Albany Molecular Research Inc., Buffalo, New York, USA
| | - Adrian R Laciak
- Discovery Biology, Albany Molecular Research Inc., Buffalo, New York, USA
| | - Leah Volk
- Discovery Biology, Albany Molecular Research Inc., Buffalo, New York, USA
| | | | - Michael R Lieber
- USC Norris Comprehensive Cancer Center, Departments of Pathology, Biochemistry & Molecular Biology, and Molecular Microbiology & Immunology, and the Molecular and Computational Biology Section of the Department of Biological Sciences, University of Southern California Keck School of Medicine, Los Angeles, California, USA
| | - Mousheng Wu
- Chemistry Department, Drug Discovery Division, Southern Research, Birmingham, Alabama, USA
| | - Rory Curtis
- Discovery Biology, Albany Molecular Research Inc., Buffalo, New York, USA
| | - Nian N Huang
- Discovery Biology, Albany Molecular Research Inc., Buffalo, New York, USA
| | - Grant Carr
- Discovery Biology, Albany Molecular Research Inc., Buffalo, New York, USA
| | - Guangyu Zhu
- Discovery Biology, Albany Molecular Research Inc., Buffalo, New York, USA
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35
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Zhang J, Si J, Gan L, Zhou R, Guo M, Zhang H. Harnessing the targeting potential of differential radiobiological effects of photon versus particle radiation for cancer treatment. J Cell Physiol 2020; 236:1695-1711. [PMID: 32691425 DOI: 10.1002/jcp.29960] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2020] [Accepted: 07/09/2020] [Indexed: 01/04/2023]
Abstract
Radiotherapy is one of the major modalities for malignancy treatment. High linear energy transfer (LET) charged-particle beams, like proton and carbon ions, exhibit favourable depth-dose distributions and radiobiological enhancement over conventional low-LET photon irradiation, thereby marking a new era in high precision medicine. Tumour cells have developed multicomponent signal transduction networks known as DNA damage responses (DDRs), which initiate cell-cycle checkpoints and induce double-strand break (DSB) repairs in the nucleus by nonhomologous end joining or homologous recombination pathways, to manage ionising radiation (IR)-induced DNA lesions. DNA damage induction and DSB repair pathways are reportedly dependent on the quality of radiation delivered. In this review, we summarise various types of DNA lesion and DSB repair mechanisms, upon irradiation with low and high-LET radiation, respectively. We also analyse factors influencing DNA repair efficiency. Inhibition of DNA damage repair pathways and dysfunctional cell-cycle checkpoint sensitises tumour cells to IR. Radio-sensitising agents, including DNA-PK inhibitors, Rad51 inhibitors, PARP inhibitors, ATM/ATR inhibitors, chk1 inhibitors, wee1 kinase inhibitors, Hsp90 inhibitors, and PI3K/AKT/mTOR inhibitors have been found to enhance cell killing by IR through interference with DDRs, cell-cycle arrest, or other cellular processes. The cotreatment of these inhibitors with IR may represent a promising therapeutic strategy for cancer.
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Affiliation(s)
- Jinhua Zhang
- Department of Medical Physics, Institute of Modern Physics, Chinese Academy of Sciences, Lanzhou, China
- Key Laboratory of Heavy Ion Radiation Biology and Medicine of Chinese Academy of Sciences, Lanzhou, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Jing Si
- Department of Medical Physics, Institute of Modern Physics, Chinese Academy of Sciences, Lanzhou, China
- Key Laboratory of Heavy Ion Radiation Biology and Medicine of Chinese Academy of Sciences, Lanzhou, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Lu Gan
- Department of Medical Physics, Institute of Modern Physics, Chinese Academy of Sciences, Lanzhou, China
- Key Laboratory of Heavy Ion Radiation Biology and Medicine of Chinese Academy of Sciences, Lanzhou, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Rong Zhou
- Research Center for Ecological Impacts and Environmental Health Effects of Toxic and Hazardous Chemicals, Nanjing Institute of Environmental Sciences, Ministry of Ecology and Environment of the People's Republic of China, Nanjing, China
| | - Menghuan Guo
- School of Pharmacy, Lanzhou University, Lanzhou, China
| | - Hong Zhang
- Department of Medical Physics, Institute of Modern Physics, Chinese Academy of Sciences, Lanzhou, China
- Key Laboratory of Heavy Ion Radiation Biology and Medicine of Chinese Academy of Sciences, Lanzhou, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
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36
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Anne Esguerra Z, Watanabe G, Okitsu CY, Hsieh CL, Lieber MR. DNA-PKcs chemical inhibition versus genetic mutation: Impact on the junctional repair steps of V(D)J recombination. Mol Immunol 2020; 120:93-100. [PMID: 32113132 DOI: 10.1016/j.molimm.2020.01.018] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2019] [Revised: 01/14/2020] [Accepted: 01/24/2020] [Indexed: 12/20/2022]
Abstract
Spontaneous DNA-PKcs deficiencies in animals result in a severe combined immunodeficiency (SCID) phenotype because DNA-PKcs is required to activate Artemis for V(D)J recombination coding end hairpin opening. The impact on signal joint formation in these spontaneous mutant mammals is variable. Genetically engineered DNA-PKcs null mice and cells from them show a >1,000-fold reduction in coding joint formation and minimal reduction in signal joint formation during V(D)J recombination. Does chemical inhibition of DNA-PKcs mimic this phenotype? M3814 (also known as Nedisertib) is a potent DNA-PKcs inhibitor. We find here that M3814 causes a quantitative reduction in coding joint formation relative to signal joint formation. The sequences of signal and coding junctions were within normal limits, though rare coding joints showed novel features. The signal junctions generally did not show evidence of resection into the signal ends that is often seen in cells that have genetic defects in DNA-PKcs. Comparison of the chemical inhibition findings here with the known results for spontaneous and engineered DNA-PKcs mutant mammals is informative for considering pharmacologic small molecule inhibition of DNA-PKcs in various types of neoplasia.
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Affiliation(s)
- Z Anne Esguerra
- USC Norris Comprehensive Cancer Ctr, Departments of Pathology, of Biochemistry & Molecular Biology, of Molecular Microbiology & Immunology, University of Southern California Keck School of Medicine, and the Molecular and Computational Biology Section of the Department of Biological Sciences, 1441 Eastlake Ave., Rm. 5428, Los Angeles, CA, 90089-9176, United States
| | - Go Watanabe
- USC Norris Comprehensive Cancer Ctr, Departments of Pathology, of Biochemistry & Molecular Biology, of Molecular Microbiology & Immunology, University of Southern California Keck School of Medicine, and the Molecular and Computational Biology Section of the Department of Biological Sciences, 1441 Eastlake Ave., Rm. 5428, Los Angeles, CA, 90089-9176, United States
| | - Cindy Y Okitsu
- Department of Urology, USC Norris Comprehensive Cancer Ctr, Los Angeles, CA, 90089 United States
| | - Chih-Lin Hsieh
- Department of Urology, USC Norris Comprehensive Cancer Ctr, Los Angeles, CA, 90089 United States
| | - Michael R Lieber
- USC Norris Comprehensive Cancer Ctr, Departments of Pathology, of Biochemistry & Molecular Biology, of Molecular Microbiology & Immunology, University of Southern California Keck School of Medicine, and the Molecular and Computational Biology Section of the Department of Biological Sciences, 1441 Eastlake Ave., Rm. 5428, Los Angeles, CA, 90089-9176, United States.
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Abstract
DNA-dependent protein kinase (DNA-PK) is involved in many cellular pathways. It has a key role in the cellular response to DNA damage, in the repair of DNA double-strand break (DNA-DSBs) and as a consequence an important role in maintaining genomic integrity. In addition, DNA-PK has been shown to modulate transcription, to be involved in the development of the immune system and to protect telomeres. These pleotropic involvements and the fact that its expression is de-regulated in cancer have made DNA-PK an intriguing therapeutic target in cancer therapy, especially when combined with agents causing DNA-DSBs such as topoisomerase II inhibitors and ionizing radiation. Different small molecule inhibitors of DNA-PK have been recently synthesized and some are now being tested in clinical trials. This review discusses what is known about DNA-PK, its role in tumor biology, DNA repair and cancer therapy and critically discusses its inhibition as a potential therapeutic approach.
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Affiliation(s)
- Giovanna Damia
- Laboratory of Molecular Pharmacology, Department of Oncology, Istituto di Ricerche Farmacologiche Mario Negri IRCCS, Via Mario Negri 2, 20156 Milan, Italy.
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38
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Goldberg FW, Finlay MRV, Ting AKT, Beattie D, Lamont GM, Fallan C, Wrigley GL, Schimpl M, Howard MR, Williamson B, Vazquez-Chantada M, Barratt DG, Davies BR, Cadogan EB, Ramos-Montoya A, Dean E. The Discovery of 7-Methyl-2-[(7-methyl[1,2,4]triazolo[1,5- a]pyridin-6-yl)amino]-9-(tetrahydro-2 H-pyran-4-yl)-7,9-dihydro-8 H-purin-8-one (AZD7648), a Potent and Selective DNA-Dependent Protein Kinase (DNA-PK) Inhibitor. J Med Chem 2020; 63:3461-3471. [PMID: 31851518 DOI: 10.1021/acs.jmedchem.9b01684] [Citation(s) in RCA: 42] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
DNA-PK is a key component within the DNA damage response, as it is responsible for recognizing and repairing double-strand DNA breaks (DSBs) via non-homologous end joining. Historically it has been challenging to identify inhibitors of the DNA-PK catalytic subunit (DNA-PKcs) with good selectivity versus the structurally related PI3 (lipid) and PI3K-related protein kinases. We screened our corporate collection for DNA-PKcs inhibitors with good PI3 kinase selectivity, identifying compound 1. Optimization focused on further improving selectivity while improving physical and pharmacokinetic properties, notably co-optimization of permeability and metabolic stability, to identify compound 16 (AZD7648). Compound 16 had no significant off-target activity in the protein kinome and only weak activity versus PI3Kα/γ lipid kinases. Monotherapy activity in murine xenograft models was observed, and regressions were observed when combined with inducers of DSBs (doxorubicin or irradiation) or PARP inhibition (olaparib). These data support progression into clinical studies (NCT03907969).
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | | | - Derek G Barratt
- Discovery Sciences, R&D, AstraZeneca, Cambridge CB4 0FZ, U.K
| | | | | | | | - Emma Dean
- Oncology R&D, AstraZeneca, Cambridge CB4 0FZ, U.K
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39
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Wu ZX, Peng Z, Yang Y, Wang JQ, Teng QX, Lei ZN, Fu YG, Patel K, Liu L, Lin L, Zou C, Chen ZS. M3814, a DNA-PK Inhibitor, Modulates ABCG2-Mediated Multidrug Resistance in Lung Cancer Cells. Front Oncol 2020; 10:674. [PMID: 32477940 PMCID: PMC7235170 DOI: 10.3389/fonc.2020.00674] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2020] [Accepted: 04/09/2020] [Indexed: 12/13/2022] Open
Abstract
M3814, also known as nedisertib, is a potent and selective DNA-dependent protein kinase (DNA-PK) inhibitor under phase 2 clinical trials. ABCG2 is a member of the ATP-binding cassette (ABC) transporter family that is closely related to multidrug resistance (MDR) in cancer treatment. In this study, we demonstrated that M3814 can modulate the function of ABCG2 and overcome ABCG2-mediated MDR. Mechanistic studies showed that M3814 can attenuate the efflux activity of ABCG2 transporter, leading to increased ABCG2 substrate drugs accumulation. Furthermore, M3814 can stimulate the ABCG2 ATPase activity in a concentration-dependent manner without affecting the ABCG2 protein expression or cell surface localization of ABCG2. Moreover, the molecular docking analysis indicated a high affinity between M3814 and ABCG2 transporter at the drug-binding cavity. Taken together, our work reveals M3814 as an ABCG2 modulator and provides a potential combination of co-administering M3814 with ABCG2 substrate-drugs to overcome MDR.
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Affiliation(s)
- Zhuo-Xun Wu
- Department of Pharmaceutical Sciences, College of Pharmacy and Health Sciences, St. John's University, Queens, NY, United States
| | - Zheng Peng
- The Second Clinical Medical College of Jinan University, The First Affiliated Hospital of Southern University of Science and Technology, Shenzhen People's Hospital, Shenzhen, China
| | - Yuqi Yang
- Department of Pharmaceutical Sciences, College of Pharmacy and Health Sciences, St. John's University, Queens, NY, United States
| | - Jing-Quan Wang
- Department of Pharmaceutical Sciences, College of Pharmacy and Health Sciences, St. John's University, Queens, NY, United States
| | - Qiu-Xu Teng
- Department of Pharmaceutical Sciences, College of Pharmacy and Health Sciences, St. John's University, Queens, NY, United States
| | - Zi-Ning Lei
- Department of Pharmaceutical Sciences, College of Pharmacy and Health Sciences, St. John's University, Queens, NY, United States
| | - Yi-Ge Fu
- Department of Pharmaceutical Sciences, College of Pharmacy and Health Sciences, St. John's University, Queens, NY, United States
| | - Ketankumar Patel
- Department of Pharmaceutical Sciences, College of Pharmacy and Health Sciences, St. John's University, Queens, NY, United States
| | - Lili Liu
- Guangdong Provincial Key Laboratory of Occupational Disease Prevention and Treatment, Guangdong Province Hospital for Occupational Disease Prevention and Treatment, Guangzhou, China
| | - Lizhu Lin
- Cancer Center, The First Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Chang Zou
- The Second Clinical Medical College of Jinan University, The First Affiliated Hospital of Southern University of Science and Technology, Shenzhen People's Hospital, Shenzhen, China
- *Correspondence: Chang Zou
| | - Zhe-Sheng Chen
- Department of Pharmaceutical Sciences, College of Pharmacy and Health Sciences, St. John's University, Queens, NY, United States
- Zhe-Sheng Chen
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40
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Wise HC, Iyer GV, Moore K, Temkin SM, Gordon S, Aghajanian C, Grisham RN. Activity of M3814, an Oral DNA-PK Inhibitor, In Combination with Topoisomerase II Inhibitors in Ovarian Cancer Models. Sci Rep 2019; 9:18882. [PMID: 31827119 PMCID: PMC6906487 DOI: 10.1038/s41598-019-54796-6] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2019] [Accepted: 11/19/2019] [Indexed: 12/20/2022] Open
Abstract
DNA-dependent protein kinase (DNA-PK) has been shown to play a crucial role in repair of DNA double-strand breaks, facilitating nonhomologous end-joining. DNA-PK inhibitors have the potential to block DNA repair and therefore enhance DNA-damaging agents. M3814 is a DNA-PK inhibitor that has shown preclinical activity in combination with DNA-damaging agents, including radiotherapy and topoisomerase II inhibitors. Here we evaluated the activity of M3814 in combination with multiple topoisomerase II inhibitors, doxorubicin, etoposide, and pegylated liposomal doxorubicin (PLD) in vivo, utilizing ovarian cancer xenografts. Using cell lines representative of P53 wild-type ovarian cancer (A2780), and P53 mutant ovarian cancer (SKOV3), cells were implanted in the flank of athymic nude female mice. Mice were treated with vehicle, M3814 alone, topoisomerase II inhibitor alone, and M3814 in combination with topoisomerase II inhibitor, and change in tumor volume over time was documented. The addition of M3814 was well tolerated. We demonstrated that M3814 shows limited efficacy as a single agent in ovarian cancer models. The combination of M3814 with PLD showed enhanced activity over PLD as a single agent. Further study of this combination is warranted.
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Affiliation(s)
- Hannah C Wise
- Louis V. Gerstner, Jr. Graduate School of Biomedical Sciences, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Gopakumar V Iyer
- Gynecologic Medical Oncology Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA.,Weill Cornell Medical College, New York, NY, USA
| | - Kathleen Moore
- Stephenson Cancer Center, University of Oklahoma, Oklahoma City, OK, USA
| | - Sarah M Temkin
- Hematology/Oncology, Virginia Commonwealth University, Richmond, VA, USA
| | - Sarah Gordon
- Hematology/Oncology, Virginia Commonwealth University, Richmond, VA, USA
| | - Carol Aghajanian
- Gynecologic Medical Oncology Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA.,Weill Cornell Medical College, New York, NY, USA
| | - Rachel N Grisham
- Gynecologic Medical Oncology Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA. .,Weill Cornell Medical College, New York, NY, USA.
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41
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Trenner A, Sartori AA. Harnessing DNA Double-Strand Break Repair for Cancer Treatment. Front Oncol 2019; 9:1388. [PMID: 31921645 PMCID: PMC6921965 DOI: 10.3389/fonc.2019.01388] [Citation(s) in RCA: 129] [Impact Index Per Article: 25.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2019] [Accepted: 11/25/2019] [Indexed: 12/20/2022] Open
Abstract
DNA double-strand breaks (DSBs) are highly deleterious, with a single unrepaired DSB being sufficient to trigger cell death. Compared to healthy cells, cancer cells have a higher DSB burden due to oncogene-induced replication stress and acquired defects in DNA damage response (DDR) mechanisms. Consequently, hyperproliferating cancer cells rely on efficient DSB repair for their survival. Moreover, augmented DSB repair capacity is a major cause of radio- and chemoresistance and, ultimately, cancer recurrence. Although inherited DDR defects can predispose individuals to develop certain cancers, the very same vulnerability may be therapeutically exploited to preferentially kill tumor cells. A paradigm for DNA repair targeted therapy has emerged in cancers that exhibit mutations in BRCA1 or BRCA2 tumor suppressor genes, conferring a strong defect in homologous recombination, a major and error-free DSB repair pathway. Clinical validation of such approaches, commonly described as synthetic lethality (SL), has been provided by the regulatory approval of poly(ADP-ribose) polymerase 1 inhibitors (PARPi) as monotherapy for BRCA1/2-mutated breast and ovarian tumors. In this review, we will describe the different DSB repair mechanisms and discuss how their specific features could be exploited for cancer therapy. A major emphasis is put on advances in combinatorial treatment modalities and SL approaches arising from DSB repair pathway interdependencies.
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Affiliation(s)
- Anika Trenner
- Institute of Molecular Cancer Research, University of Zurich, Zurich, Switzerland
| | - Alessandro A Sartori
- Institute of Molecular Cancer Research, University of Zurich, Zurich, Switzerland
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42
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Riesenberg S, Chintalapati M, Macak D, Kanis P, Maricic T, Pääbo S. Simultaneous precise editing of multiple genes in human cells. Nucleic Acids Res 2019; 47:e116. [PMID: 31392986 PMCID: PMC6821318 DOI: 10.1093/nar/gkz669] [Citation(s) in RCA: 64] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2019] [Revised: 06/26/2019] [Accepted: 07/24/2019] [Indexed: 01/01/2023] Open
Abstract
When double-strand breaks are introduced in a genome by CRISPR they are repaired either by non-homologous end joining (NHEJ), which often results in insertions or deletions (indels), or by homology-directed repair (HDR), which allows precise nucleotide substitutions to be introduced if a donor oligonucleotide is provided. Because NHEJ is more efficient than HDR, the frequency with which precise genome editing can be achieved is so low that simultaneous editing of more than one gene has hitherto not been possible. Here, we introduced a mutation in the human PRKDC gene that eliminates the kinase activity of the DNA-dependent protein kinase catalytic subunit (DNA-PKcs). This results in an increase in HDR irrespective of cell type and CRISPR enzyme used, sometimes allowing 87% of chromosomes in a population of cells to be precisely edited. It also allows for precise editing of up to four genes simultaneously (8 chromosomes) in the same cell. Transient inhibition of DNA-PKcs by the kinase inhibitor M3814 is similarly able to enhance precise genome editing.
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Affiliation(s)
- Stephan Riesenberg
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology
| | - Manjusha Chintalapati
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology
| | - Dominik Macak
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology
| | - Philipp Kanis
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology
| | - Tomislav Maricic
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology
| | - Svante Pääbo
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology
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43
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Dziegielewski J, Bońkowska MA, Poniecka EA, Heo J, Du K, Crittenden RB, Bender TP, Brautigan DL, Larner JM. Deletion of the SAPS1 subunit of protein phosphatase 6 in mice increases radiosensitivity and impairs the cellular DNA damage response. DNA Repair (Amst) 2019; 85:102737. [PMID: 31751917 DOI: 10.1016/j.dnarep.2019.102737] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2019] [Revised: 09/17/2019] [Accepted: 10/15/2019] [Indexed: 12/24/2022]
Abstract
Cellular responses to DNA damage include activation of DNA-dependent protein kinase (DNA-PK) through, among others, the serine/threonine protein phosphatase 6 (PP6). We previously showed that recognition of DNA-PKcs is mediated by the SAPS1 PP6 regulatory subunit. Here, we report and characterize a SAPS1 null mouse and investigate the effects of deletion on DNA damage signaling and repair. Strikingly, neither SAPS1-null animals nor cells derived from them show gross defects, unless subjected to DNA damage by radiation or chemical agents. The overall survival of SAPS1-null animals following whole body irradiation is significantly shortened as compared to wild-type mice, and the clonogenic survival of null cells subjected to ionizing radiation is reduced. The dephosphorylation of DNA damage/repair markers, such as γH2AX, p53 and Kap1, is diminished in SAPS1-null cells as compared to wild-type controls. Our results demonstrate that loss of SAPS1 confers sensitivity to DNA damage and confirms previously reported cellular phenotypes of SAPS1 knock-down in human glioma cells. The results support a role for PP6 regulatory subunit SAPS1 in DNA damage responses, and offer a novel target for sensitization to enhance current tumor therapies, with a potential for limited deleterious side effects.
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Affiliation(s)
- Jaroslaw Dziegielewski
- Center for Cell Signaling, University of Virginia School of Medicine, Charlottesville, VA 22908, USA; Department of Radiation Oncology, University of Virginia School of Medicine, Charlottesville, VA 22908, USA
| | - Magdalena A Bońkowska
- Center for Cell Signaling, University of Virginia School of Medicine, Charlottesville, VA 22908, USA; Department of Microbiology, Immunology and Cancer Biology, University of Virginia School of Medicine, Charlottesville, VA 22908, USA
| | - Ewa A Poniecka
- Center for Cell Signaling, University of Virginia School of Medicine, Charlottesville, VA 22908, USA; Department of Microbiology, Immunology and Cancer Biology, University of Virginia School of Medicine, Charlottesville, VA 22908, USA
| | - Jinho Heo
- Center for Cell Signaling, University of Virginia School of Medicine, Charlottesville, VA 22908, USA; Department of Microbiology, Immunology and Cancer Biology, University of Virginia School of Medicine, Charlottesville, VA 22908, USA
| | - Kangping Du
- Center for Cell Signaling, University of Virginia School of Medicine, Charlottesville, VA 22908, USA; Department of Radiation Oncology, University of Virginia School of Medicine, Charlottesville, VA 22908, USA
| | - Rowena B Crittenden
- Department of Microbiology, Immunology and Cancer Biology, University of Virginia School of Medicine, Charlottesville, VA 22908, USA; Beirne B. Carter Center for Immunology Research, University of Virginia School of Medicine, Charlottesville, VA 22908, USA
| | - Timothy P Bender
- Department of Microbiology, Immunology and Cancer Biology, University of Virginia School of Medicine, Charlottesville, VA 22908, USA; Beirne B. Carter Center for Immunology Research, University of Virginia School of Medicine, Charlottesville, VA 22908, USA
| | - David L Brautigan
- Center for Cell Signaling, University of Virginia School of Medicine, Charlottesville, VA 22908, USA; Department of Microbiology, Immunology and Cancer Biology, University of Virginia School of Medicine, Charlottesville, VA 22908, USA
| | - James M Larner
- Center for Cell Signaling, University of Virginia School of Medicine, Charlottesville, VA 22908, USA; Department of Radiation Oncology, University of Virginia School of Medicine, Charlottesville, VA 22908, USA.
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44
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AZD7648 is a potent and selective DNA-PK inhibitor that enhances radiation, chemotherapy and olaparib activity. Nat Commun 2019; 10:5065. [PMID: 31699977 PMCID: PMC6838110 DOI: 10.1038/s41467-019-12836-9] [Citation(s) in RCA: 178] [Impact Index Per Article: 35.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2019] [Accepted: 10/04/2019] [Indexed: 02/05/2023] Open
Abstract
DNA-dependent protein kinase (DNA-PK) is a critical player in the DNA damage response (DDR) and instrumental in the non-homologous end-joining pathway (NHEJ) used to detect and repair DNA double-strand breaks (DSBs). We demonstrate that the potent and highly selective DNA-PK inhibitor, AZD7648, is an efficient sensitizer of radiation- and doxorubicin-induced DNA damage, with combinations in xenograft and patient-derived xenograft (PDX) models inducing sustained regressions. Using ATM-deficient cells, we demonstrate that AZD7648, in combination with the PARP inhibitor olaparib, increases genomic instability, resulting in cell growth inhibition and apoptosis. AZD7648 enhanced olaparib efficacy across a range of doses and schedules in xenograft and PDX models, enabling sustained tumour regression and providing a clear rationale for its clinical investigation. Through its differentiated mechanism of action as an NHEJ inhibitor, AZD7648 complements the current armamentarium of DDR-targeted agents and has potential in combination with these agents to achieve deeper responses to current therapies. DNA-dependent protein kinase (DNA-PK) plays a major role in the DNA damage response upon double-strand break formation. Here, the authors show that the DNA-PK inhibitor AZD7648, enhances the activity of radiotherapy, chemotherapy and the PARP inhibitor olaparib in multiple mouse tumour models.
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45
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Ivy SP, Kunos CA, Arnaldez FI, Kohn EC. Defining and targeting wild-type BRCA high-grade serous ovarian cancer: DNA repair and cell cycle checkpoints. Expert Opin Investig Drugs 2019; 28:771-785. [PMID: 31449760 DOI: 10.1080/13543784.2019.1657403] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Introduction: Molecular analyzes including molecular descriptor/phenotype interactions have led to better characterization of epithelial ovarian cancer patients, including a definition of a BRCA wild-type (BRCAwt) phenotype. Understanding how and when to use agents targeted against dependent BRCAwt pathways or other molecular events at disease progression is an important translational and therapeutic direction in ovarian cancer research. Areas covered: In this overview, we provide definitions and descriptions of a BRCAwt genotype and phenotype. We discuss novel investigational drugs that hold promise for the treatment of BRCAwt ovarian cancer, including inhibitors of poly(ADP-ribose) polymerase, ribonucleotide reductase, DNA protein kinase-catalytic subunit, ataxia-telangiectasia-mutated kinase (ATM), ataxia-telangiectasia mutated and Rad3-related kinase (ATR), CHK 1/2, cyclin kinases, glutaminase-1, WEE1 kinase, as well as tumor microenvironment and angiogenesis inhibitors. This article explores the known and the emerging areas of clinical research on patients with BRCAwt ovarian cancer. Expert opinion: Discovery of molecular changes tied to annotated disease information, along with an expanding array of pathway targets and targeted therapeutic agents, creates optimism and opportunity for women with ovarian cancer. Using precision oncology approaches, clinical researchers are, and will be, poised to select more effective treatments for ovarian cancer patients.
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Affiliation(s)
- S Percy Ivy
- Cancer Therapy Evaluation Program, National Cancer Institute (NCI) , Bethesda , MD , USA
| | - Charles A Kunos
- Cancer Therapy Evaluation Program, National Cancer Institute (NCI) , Bethesda , MD , USA
| | - Fernanda I Arnaldez
- Cancer Therapy Evaluation Program, National Cancer Institute (NCI) , Bethesda , MD , USA
| | - Elise C Kohn
- Cancer Therapy Evaluation Program, National Cancer Institute (NCI) , Bethesda , MD , USA
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Mohiuddin IS, Kang MH. DNA-PK as an Emerging Therapeutic Target in Cancer. Front Oncol 2019; 9:635. [PMID: 31380275 PMCID: PMC6650781 DOI: 10.3389/fonc.2019.00635] [Citation(s) in RCA: 122] [Impact Index Per Article: 24.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2019] [Accepted: 06/27/2019] [Indexed: 12/21/2022] Open
Abstract
The DNA-dependent protein kinase (DNA-PK) plays an instrumental role in the overall survival and proliferation of cells. As a member of the phosphatidylinositol 3-kinase-related kinase (PIKK) family, DNA-PK is best known as a mediator of the cellular response to DNA damage. In this context, DNA-PK has emerged as an intriguing therapeutic target in the treatment of a variety of cancers, especially when used in conjunction with genotoxic chemotherapy or ionizing radiation. Beyond the DNA damage response, DNA-PK activity is necessary for multiple cellular functions, including the regulation of transcription, progression of the cell cycle, and in the maintenance of telomeres. Here, we review what is currently known about DNA-PK regarding its structure and established roles in DNA repair. We also discuss its lesser-known functions, the pharmacotherapies inhibiting its function in DNA repair, and its potential as a therapeutic target in a broader context.
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Affiliation(s)
- Ismail S Mohiuddin
- Cancer Center, Department of Pediatrics, Pharmacology and Neuroscience, School of Medicine, Texas Tech University Health Sciences Center, Lubbock, TX, United States
| | - Min H Kang
- Cancer Center, Department of Pediatrics, Pharmacology and Neuroscience, School of Medicine, Texas Tech University Health Sciences Center, Lubbock, TX, United States
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Koike M, Yutoku Y, Koike A. Feline XLF accumulates at DNA damage sites in a Ku-dependent manner. FEBS Open Bio 2019; 9:1052-1062. [PMID: 31115163 PMCID: PMC6551493 DOI: 10.1002/2211-5463.12589] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2018] [Revised: 12/14/2018] [Accepted: 01/02/2019] [Indexed: 11/05/2022] Open
Abstract
Resistance to radiotherapy and chemotherapy is a common problem in the treatment of cancer in humans and companion animals, including cats. There is thus an urgent need to develop new treatments. Molecularly targeted therapies hold the promise of high specificity and significant cancer‐killing effects. Accumulating evidence shows that DNA double‐strand break (DSB) repair proteins, which function in Ku‐dependent non‐homologous DNA‐end joining (NHEJ), are potential target molecules for next‐generation cancer therapies. Although cancer radioresistance in cats has been previously described, there are no reports on feline Ku‐dependent NHEJ. Here, we cloned and sequenced feline XLFcDNA and characterized X‐ray repair cross‐complementing protein 4‐like factor (XLF), which is one of the core NHEJ proteins. We demonstrated that feline XLF localizes to the nuclei of feline cells and that feline XLF immediately accumulates at laser‐induced DSB sites in a Ku‐dependent manner. Amino acid sequence alignment analysis showed that feline XLF has only 80.9% identity with human XLF protein, while the predicted nuclear localization signal and putative 14‐3‐3‐binding motif are perfectly conserved among human, cat, dog, chimpanzee, and mouse. These findings are consistent with the hypothesis that regulation of subcellular localization is important for the function of XLF. Furthermore, these findings may be useful in clarifying the mechanisms underlying feline Ku‐dependent DSB repair and feline cell radioresistance, and possibly facilitate the development of new molecularly targeted therapies that target common proteins in human and feline cancers.
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Affiliation(s)
- Manabu Koike
- National Institute of Radiological Sciences, National Institutes for Quantum and Radiological Science and Technology, Chiba, Japan
| | - Yasutomo Yutoku
- National Institute of Radiological Sciences, National Institutes for Quantum and Radiological Science and Technology, Chiba, Japan
| | - Aki Koike
- National Institute of Radiological Sciences, National Institutes for Quantum and Radiological Science and Technology, Chiba, Japan
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Zhou Z, Lu H, Zhu S, Gomaa A, Chen Z, Yan J, Washington K, El-Rifai W, Dang C, Peng D. Activation of EGFR-DNA-PKcs pathway by IGFBP2 protects esophageal adenocarcinoma cells from acidic bile salts-induced DNA damage. JOURNAL OF EXPERIMENTAL & CLINICAL CANCER RESEARCH : CR 2019; 38:13. [PMID: 30626422 PMCID: PMC6327430 DOI: 10.1186/s13046-018-1021-y] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/12/2018] [Accepted: 12/26/2018] [Indexed: 12/26/2022]
Abstract
Background The incidence of esophageal adenocarcinoma (EAC) is rising rapidly in the US and Western countries. The development of Barrett’s esophagus (BE) and its progression to EAC have been linked to chronic gastroesophageal reflux disease (GERD). Exposure of BE and EAC cells to acidic bile salts (ABS) in GERD conditions induces high levels of oxidative stress and DNA damage. In this study, we investigated the role of insulin-like growth factor binding protein 2 (IGFBP2) in regulating ABS-induced DNA double-strand breaks. Methods Real-time RT-PCR, western blot, immunohistochemistry, immunofluorescence, co-immunoprecipitation, flow cytometry, and cycloheximide (CHX) chase assays were used in this study. To mimic GERD conditions, a cocktail of acidic bile salts (pH 4) was used in 2D and 3D organotypic culture models. Overexpression and knockdown of IGFBP2 in EAC cells were established to examine the functional and mechanistic roles of IGFBP2 in ABS-induced DNA damage. Results Our results demonstrated high levels of IGFBP2 mRNA and protein in EAC cell lines as compared to precancerous Barrett’s cell lines, and IGFBP2 is frequently overexpressed in EACs (31/57). Treatment of EAC cells with ABS, to mimic GERD conditions, induced high levels of IGFBP2 expression. Knocking down endogenous IGFBP2 in FLO1 cells (with constitutive high levels of IGFBP2) led to a significant increase in DNA double-strand breaks and apoptosis, following transient exposure to ABS. On the other hand, overexpression of exogenous IGFBP2 in OE33 cells (with low endogenous levels of IGFBP2) had a protective effect against ABS-induced double-strand breaks and apoptosis. We found that IGFBP2 is required for ABS-induced nuclear accumulation and phosphorylation of EGFR and DNA-PKcs, which are necessary for DNA damage repair activity. Using co-immunoprecipitation assay, we detected co-localization of IGFBP2 with EGFR and DNA-PKcs, following acidic bile salts treatment. We further demonstrated, using cycloheximide chase assay, that IGFBP2 promotes EGFR protein stability in response to ABS exposure. Conclusions IGFBP2 protects EAC cells against ABS-induced DNA damage and apoptosis through stabilization and activation of EGFR - DNA-PKcs signaling axis. Electronic supplementary material The online version of this article (10.1186/s13046-018-1021-y) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Zhangjian Zhou
- Department of Surgical Oncology, the First Affiliated Hospital of Xi'an Jiaotong University, 277 Yanta W. Road, Xi'an, 710061, Shaanxi, China.,Department of Surgery, University of Miami Miller School of Medicine, Miami, FL, 33136-1015, USA
| | - Heng Lu
- Department of Surgery, University of Miami Miller School of Medicine, Miami, FL, 33136-1015, USA
| | - Shoumin Zhu
- Department of Surgery, University of Miami Miller School of Medicine, Miami, FL, 33136-1015, USA
| | - Ahmed Gomaa
- Department of Surgery, University of Miami Miller School of Medicine, Miami, FL, 33136-1015, USA
| | - Zheng Chen
- Department of Surgery, University of Miami Miller School of Medicine, Miami, FL, 33136-1015, USA
| | - Jin Yan
- Department of Surgery, University of Miami Miller School of Medicine, Miami, FL, 33136-1015, USA.,Department of Gastroenterology, the First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Kay Washington
- Department of Pathology, Microbiology and Immunology, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Wael El-Rifai
- Department of Surgery, University of Miami Miller School of Medicine, Miami, FL, 33136-1015, USA.,Sylvester Comprehensive Cancer Center, University of Miami Miller School of Medicine, Miami, FL, 33136-1015, USA.,Department of Veterans Affairs, Miami Healthcare System, Miami, FL, USA
| | - Chengxue Dang
- Department of Surgical Oncology, the First Affiliated Hospital of Xi'an Jiaotong University, 277 Yanta W. Road, Xi'an, 710061, Shaanxi, China.
| | - Dunfa Peng
- Department of Surgery, University of Miami Miller School of Medicine, Miami, FL, 33136-1015, USA. .,Sylvester Comprehensive Cancer Center, University of Miami Miller School of Medicine, Miami, FL, 33136-1015, USA.
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Minchom A, Aversa C, Lopez J. Dancing with the DNA damage response: next-generation anti-cancer therapeutic strategies. Ther Adv Med Oncol 2018; 10:1758835918786658. [PMID: 30023007 PMCID: PMC6047242 DOI: 10.1177/1758835918786658] [Citation(s) in RCA: 86] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2018] [Accepted: 06/08/2018] [Indexed: 01/01/2023] Open
Abstract
Maintenance of genomic stability is a critical determinant of cell survival and relies on the coordinated action of the DNA damage response (DDR), which orchestrates a network of cellular processes, including DNA replication, DNA repair and cell-cycle progression. In cancer, the critical balance between the loss of genomic stability in malignant cells and the DDR provides exciting therapeutic opportunities. Drugs targeting DDR pathways taking advantage of clinical synthetic lethality have already shown therapeutic benefit - for example, the PARP inhibitor olaparib has shown benefit in BRCA-mutant ovarian and breast cancer. Olaparib has also shown benefit in metastatic prostate cancer in DDR-defective patients, expanding the potential biomarker of response beyond BRCA. Other agents and combinations aiming to block the DDR while pushing damaged DNA through the cell cycle, including PARP, ATR, ATM, CHK and DNA-PK inhibitors, are in development. Emerging work is also uncovering how the DDR interacts intimately with the host immune response, including by activating the innate immune response, further suggesting that clinical applications together with immunotherapy may be beneficial. Here, we review recent considerations related to the DDR from a clinical standpoint, providing a framework to address future directions and clinical opportunities.
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Affiliation(s)
- Anna Minchom
- Drug Development Unit at Royal Marsden Hospital/ Institute of Cancer Research, Sutton, UK
| | - Caterina Aversa
- Drug Development Unit at Royal Marsden Hospital/ Institute of Cancer Research, Sutton, UK
| | - Juanita Lopez
- Drug Development Unit at Royal Marsden Hospital/Institute of Cancer Research, Downs Rd, Sutton, SM2 5PT, UK
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