1
|
Hofstad M, Woods A, Parra K, Sychev ZE, Mazzagatti A, Yu L, Gilbreath C, Ly P, Drake JM, Kittler R. Dual inhibition of ATR and DNA-PKcs radiosensitizes ATM-mutant prostate cancer. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.07.10.602941. [PMID: 39026771 PMCID: PMC11257504 DOI: 10.1101/2024.07.10.602941] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/20/2024]
Abstract
In advanced castration resistant prostate cancer (CRPC), mutations in the DNA damage response (DDR) gene ataxia telangiectasia mutated ( ATM ) are common. While poly(ADP-ribose) polymerase inhibitors are approved in this context, their clinical efficacy remains limited. Thus, there is a compelling need to identify alternative therapeutic avenues for ATM mutant prostate cancer patients. Here, we generated matched ATM-proficient and ATM-deficient CRPC lines to elucidate the impact of ATM loss on DDR in response to DNA damage via irradiation. Through unbiased phosphoproteomic screening, we unveiled that ATM-deficient CRPC lines maintain dependence on downstream ATM targets through activation of ATR and DNA-PKcs kinases. Dual inhibition of ATR and DNA-PKcs effectively inhibited downstream γH2AX foci formation in response to irradiation and radiosensitized ATM-deficient lines to a greater extent than either ATM-proficient controls or single drug treatment. Further, dual inhibition abrogated residual downstream ATM pathway signaling and impaired replication fork dynamics. To circumvent potential toxicity, we leveraged the RUVBL1/2 ATPase inhibitor Compound B, which leads to the degradation of both ATR and DNA-PKcs kinases. Compound B effectively radiosensitized ATM-deficient CRPC in vitro and in vivo , and impacted replication fork dynamics. Overall, dual targeting of both ATR and DNA-PKcs is necessary to block DDR in ATM-deficient CRPC, and Compound B could be utilized as a novel therapy in combination with irradiation in these patients.
Collapse
|
2
|
Wu J, Song L, Lu M, Gao Q, Xu S, Zhou P, Ma T. The multifaceted functions of DNA-PKcs: implications for the therapy of human diseases. MedComm (Beijing) 2024; 5:e613. [PMID: 38898995 PMCID: PMC11185949 DOI: 10.1002/mco2.613] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2023] [Revised: 05/07/2024] [Accepted: 05/09/2024] [Indexed: 06/21/2024] Open
Abstract
The DNA-dependent protein kinase (DNA-PK), catalytic subunit, also known as DNA-PKcs, is complexed with the heterodimer Ku70/Ku80 to form DNA-PK holoenzyme, which is well recognized as initiator in the nonhomologous end joining (NHEJ) repair after double strand break (DSB). During NHEJ, DNA-PKcs is essential for both DNA end processing and end joining. Besides its classical function in DSB repair, DNA-PKcs also shows multifaceted functions in various biological activities such as class switch recombination (CSR) and variable (V) diversity (D) joining (J) recombination in B/T lymphocytes development, innate immunity through cGAS-STING pathway, transcription, alternative splicing, and so on, which are dependent on its function in NHEJ or not. Moreover, DNA-PKcs deficiency has been proven to be related with human diseases such as neurological pathogenesis, cancer, immunological disorder, and so on through different mechanisms. Therefore, it is imperative to summarize the latest findings about DNA-PKcs and diseases for better targeting DNA-PKcs, which have shown efficacy in cancer treatment in preclinical models. Here, we discuss the multifaceted roles of DNA-PKcs in human diseases, meanwhile, we discuss the progresses of DNA-PKcs inhibitors and their potential in clinical trials. The most updated review about DNA-PKcs will hopefully provide insights and ideas to understand DNA-PKcs associated diseases.
Collapse
Affiliation(s)
- Jinghong Wu
- Cancer Research CenterBeijing Chest HospitalCapital Medical University/Beijing Tuberculosis and Thoracic Tumor Research InstituteBeijingChina
| | - Liwei Song
- Department of Thoracic SurgeryBeijing Chest HospitalCapital Medical University, Beijing Tuberculosis and Thoracic Tumor Research InstituteBeijingChina
| | - Mingjun Lu
- Cancer Research CenterBeijing Chest HospitalCapital Medical University/Beijing Tuberculosis and Thoracic Tumor Research InstituteBeijingChina
| | - Qing Gao
- Cancer Research CenterBeijing Chest HospitalCapital Medical University/Beijing Tuberculosis and Thoracic Tumor Research InstituteBeijingChina
| | - Shaofa Xu
- Department of Thoracic SurgeryBeijing Chest HospitalCapital Medical University, Beijing Tuberculosis and Thoracic Tumor Research InstituteBeijingChina
| | - Ping‐Kun Zhou
- Beijing Key Laboratory for RadiobiologyBeijing Institute of Radiation MedicineBeijingChina
| | - Teng Ma
- Cancer Research CenterBeijing Chest HospitalCapital Medical University/Beijing Tuberculosis and Thoracic Tumor Research InstituteBeijingChina
| |
Collapse
|
3
|
Wang J, Sadeghi CA, Frock RL. DNA-PKcs suppresses illegitimate chromosome rearrangements. Nucleic Acids Res 2024; 52:5048-5066. [PMID: 38412274 PMCID: PMC11109964 DOI: 10.1093/nar/gkae140] [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: 07/11/2023] [Revised: 02/09/2024] [Accepted: 02/14/2024] [Indexed: 02/29/2024] Open
Abstract
Two DNA repair pathways, non-homologous end joining (NHEJ) and alternative end joining (A-EJ), are involved in V(D)J recombination and chromosome translocation. Previous studies reported distinct repair mechanisms for chromosome translocation, with NHEJ involved in humans and A-EJ in mice predominantly. NHEJ depends on DNA-PKcs, a critical partner in synapsis formation and downstream component activation. While DNA-PKcs inhibition promotes chromosome translocations harboring microhomologies in mice, its synonymous effect in humans is not known. We find partial DNA-PKcs inhibition in human cells leads to increased translocations and the continued involvement of a dampened NHEJ. In contrast, complete DNA-PKcs inhibition substantially increased microhomology-mediated end joining (MMEJ), thus bridging the two different translocation mechanisms between human and mice. Similar to a previous study on Ku70 deletion, DNA-PKcs deletion in G1/G0-phase mouse progenitor B cell lines, significantly impairs V(D)J recombination and generated higher rates of translocations as a consequence of dysregulated coding and signal end joining. Genetic DNA-PKcs inhibition suppresses NHEJ entirely, with repair phenotypically resembling Ku70-deficient A-EJ. In contrast, we find DNA-PKcs necessary in generating the near-exclusive MMEJ associated with Lig4 deficiency. Our study underscores DNA-PKcs in suppressing illegitimate chromosome rearrangement while also contributing to MMEJ in both species.
Collapse
Affiliation(s)
- Jinglong Wang
- Division of Radiation and Cancer Biology, Department of Radiation Oncology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Cheyenne A Sadeghi
- Division of Radiation and Cancer Biology, Department of Radiation Oncology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Richard L Frock
- Division of Radiation and Cancer Biology, Department of Radiation Oncology, Stanford University School of Medicine, Stanford, CA 94305, USA
| |
Collapse
|
4
|
Samuels M, Falkenius J, Bar-Ad V, Dunst J, van Triest B, Yachnin J, Rodriguez-Gutierrez A, Kuipers M, You X, Sarholz B, Locatelli G, Becker A, Troost EGC. A Phase 1 Study of the DNA-PK Inhibitor Peposertib in Combination With Radiation Therapy With or Without Cisplatin in Patients With Advanced Head and Neck Tumors. Int J Radiat Oncol Biol Phys 2024; 118:743-756. [PMID: 37751793 DOI: 10.1016/j.ijrobp.2023.09.024] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2023] [Revised: 09/05/2023] [Accepted: 09/14/2023] [Indexed: 09/28/2023]
Abstract
PURPOSE DNA-dependent protein kinase (DNA-PK) plays a key role in the repair of DNA double strand breaks via nonhomologous end joining. Inhibition of DNA-PK can enhance the effect of DNA double strand break inducing anticancer therapies. Peposertib (formerly "M3814") is an orally administered, potent, and selective small molecule DNA-PK inhibitor that has demonstrated radiosensitizing and antitumor activity in xenograft models and was well-tolerated in monotherapy. This phase 1 trial (National Clinical Trial 02516813) investigated the maximum tolerated dose, recommended phase 2 dose (RP2D), safety, and tolerability of peposertib in combination with palliative radiation therapy (RT) in patients with thoracic or head and neck tumors (arm A) and of peposertib in combination with cisplatin and curative-intent RT in patients with squamous cell carcinoma of the head and neck (arm B). METHODS AND MATERIALS Patients received peposertib once daily in ascending dose cohorts as a tablet or capsule in combination with palliative RT (arm A) or in combination with intensity modulated curative-intent RT and cisplatin (arm B). RESULTS The most frequently observed treatment-emergent adverse events were radiation skin injury, fatigue, and nausea in arm A (n = 34) and stomatitis, nausea, radiation skin injury, and dysgeusia in arm B (n = 11). Based on evaluations of dose-limiting toxicities, tolerability, and pharmacokinetic data, RP2D for arm A was declared as 200 mg peposertib tablet once daily in combination with RT. In arm B (n = 11), 50 mg peposertib was declared tolerable in combination with curative-intent RT and cisplatin. However, enrollment was discontinued because of insufficient exposure at that dose, and the RP2D was not formally declared. CONCLUSIONS Peposertib in combination with palliative RT was well-tolerated up to doses of 200 mg once daily as tablet with each RT fraction. When combined with RT and cisplatin, a tolerable peposertib dose yielded insufficient exposure.
Collapse
Affiliation(s)
| | - Johan Falkenius
- Theme Cancer, Karolinska University Hospital, Stockholm, Sweden
| | - Voichita Bar-Ad
- Department of Radiation Oncology, Thomas Jefferson University, Philadelphia, Pennsylvania
| | - Juergen Dunst
- Department of Radiotherapy, University Hospital Schleswig-Holstein, Lübeck, Germany
| | - Baukelien van Triest
- Department of Radiation Oncology, Netherlands Cancer Institute, Amsterdam, Netherlands
| | - Jeffrey Yachnin
- Theme Cancer, Karolinska University Hospital, Stockholm, Sweden
| | | | - Mirjam Kuipers
- The health care business of Merck KGaA, Darmstadt, Germany
| | | | | | | | - Andreas Becker
- The health care business of Merck KGaA, Darmstadt, Germany
| | - Esther G C Troost
- Department of Radiotherapy and Radiation Oncology, Faculty of Medicine and University Hospital Carl Gustav Carus, Technische Universität Dresden, Dresden, Germany; OncoRay - National Center for Radiation Research in Oncology, Faculty of Medicine and University Hospital Carl Gustav Carus, Technische Universität Dresden, Helmholtz-Zentrum Dresden-Rossendorf, Dresden, Germany; Institute of Radiooncology - OncoRay, Helmholtz-Zentrum Dresden-Rossendorf, Dresden, Germany; National Center for Tumor Diseases, Partner Site Dresden, Germany; German Cancer Research Center, Heidelberg, Germany; Faculty of Medicine and University Hospital Carl Gustav Carus, Technische Universität Dresden, Helmholtz-Zentrum Dresden-Rossendorf, Dresden, Germany.
| |
Collapse
|
5
|
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.
Collapse
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
| |
Collapse
|
6
|
Rose JC, Wong ITL, Daniel B, Jones MG, Yost KE, Hung KL, Curtis EJ, Mischel PS, Chang HY. Disparate pathways for extrachromosomal DNA biogenesis and genomic DNA repair. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.10.22.563489. [PMID: 37961138 PMCID: PMC10634728 DOI: 10.1101/2023.10.22.563489] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/15/2023]
Abstract
Oncogene amplification on extrachromosomal DNA (ecDNA) is a pervasive driver event in cancer, yet our understanding of how ecDNA forms is limited. Here, we couple a CRISPR-based method for induction of ecDNA with extensive characterization of newly formed ecDNA to examine ecDNA biogenesis. We find that DNA circularization is efficient, irrespective of 3D genome context, with formation of a 1 Mb and 1.8 Mb ecDNA both reaching 15%. We show non-homologous end joining and microhomology mediated end joining both contribute to ecDNA formation, while inhibition of DNA-PKcs and ATM have opposing impacts on ecDNA formation. EcDNA and the corresponding chromosomal excision scar form at significantly different rates and respond differently to DNA-PKcs and ATM inhibition. Taken together, our results support a model of ecDNA formation in which double strand break ends dissociate from their legitimate ligation partners prior to joining of illegitimate ends to form the ecDNA and excision scar.
Collapse
Affiliation(s)
- John C Rose
- Center for Personal Dynamic Regulomes, Stanford University, Stanford, CA, USA
| | - Ivy Tsz-Lo Wong
- Sarafan ChEM-H, Stanford University, Stanford, CA, USA
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
| | - Bence Daniel
- Center for Personal Dynamic Regulomes, Stanford University, Stanford, CA, USA
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
| | - Matthew G Jones
- Center for Personal Dynamic Regulomes, Stanford University, Stanford, CA, USA
| | - Kathryn E Yost
- Center for Personal Dynamic Regulomes, Stanford University, Stanford, CA, USA
| | - King L Hung
- Center for Personal Dynamic Regulomes, Stanford University, Stanford, CA, USA
| | - Ellis J Curtis
- Sarafan ChEM-H, Stanford University, Stanford, CA, USA
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
| | - Paul S Mischel
- Sarafan ChEM-H, Stanford University, Stanford, CA, USA
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
| | - Howard Y Chang
- Center for Personal Dynamic Regulomes, Stanford University, Stanford, CA, USA
- Howard Hughes Medical Institute, Stanford, CA, USA
| |
Collapse
|
7
|
Bugoye FC, Torrorey-Sawe R, Biegon R, Dharsee N, Mafumiko FMS, Patel K, Mining SK. Mutational spectrum of DNA damage and mismatch repair genes in prostate cancer. Front Genet 2023; 14:1231536. [PMID: 37732318 PMCID: PMC10507418 DOI: 10.3389/fgene.2023.1231536] [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: 05/30/2023] [Accepted: 08/16/2023] [Indexed: 09/22/2023] Open
Abstract
Over the past few years, a number of studies have revealed that a significant number of men with prostate cancer had genetic defects in the DNA damage repair gene response and mismatch repair genes. Certain of these modifications, notably gene alterations known as homologous recombination (HRR) genes; PALB2, CHEK2 BRCA1, BRCA2, ATM, and genes for DNA mismatch repair (MMR); MLH1, MSH2, MSH6, and PMS2 are connected to a higher risk of prostate cancer and more severe types of the disease. The DNA damage repair (DDR) is essential for constructing and diversifying the antigen receptor genes required for T and B cell development. But this DDR imbalance results in stress on DNA replication and transcription, accumulation of mutations, and even cell death, which compromises tissue homeostasis. Due to these impacts of DDR anomalies, tumor immunity may be impacted, which may encourage the growth of tumors, the release of inflammatory cytokines, and aberrant immune reactions. In a similar vein, people who have altered MMR gene may benefit greatly from immunotherapy. Therefore, for these treatments, mutational genetic testing is indicated. Mismatch repair gene (MMR) defects are also more prevalent than previously thought, especially in patients with metastatic disease, high Gleason scores, and diverse histologies. This review summarizes the current information on the mutation spectrum and clinical significance of DDR mechanisms, such as HRR and MMR abnormalities in prostate cancer, and explains how patient management is evolving as a result of this understanding.
Collapse
Affiliation(s)
- Fidelis Charles Bugoye
- Government Chemist Laboratory Authority, Directorate of Forensic Science and DNA Services, Dar es Salaam, Tanzania
- Department of Pathology, Moi Teaching and Referral Hospital, Moi University, Eldoret, Kenya
| | - Rispah Torrorey-Sawe
- Department of Pathology, Moi Teaching and Referral Hospital, Moi University, Eldoret, Kenya
| | - Richard Biegon
- Department of Pathology, Moi Teaching and Referral Hospital, Moi University, Eldoret, Kenya
| | | | - Fidelice M. S. Mafumiko
- Government Chemist Laboratory Authority, Directorate of Forensic Science and DNA Services, Dar es Salaam, Tanzania
| | - Kirtika Patel
- Department of Pathology, Moi Teaching and Referral Hospital, Moi University, Eldoret, Kenya
| | - Simeon K. Mining
- Department of Pathology, Moi Teaching and Referral Hospital, Moi University, Eldoret, Kenya
| |
Collapse
|
8
|
Lal S, Bhola NE, Sun BC, Chen Y, Huang T, Morton V, Chen KX, Xia S, Zhang H, Parikh NS, Ye Q, Veiby OP, Bellovin DI, Ji Y. Discovery and Characterization of ZL-2201, a Potent, Highly Selective, and Orally Bioavailable Small-molecule DNA-PK Inhibitor. CANCER RESEARCH COMMUNICATIONS 2023; 3:1731-1742. [PMID: 37663435 PMCID: PMC10473160 DOI: 10.1158/2767-9764.crc-23-0304] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/17/2023] [Revised: 08/03/2023] [Accepted: 08/04/2023] [Indexed: 09/05/2023]
Abstract
DNA-dependent protein kinase (DNA-PK), a driver of the non-homologous end-joining (NHEJ) DNA damage response pathway, plays an instrumental role in repairing double-strand breaks (DSB) induced by DNA-damaging poisons. We evaluate ZL-2201, an orally bioavailable, highly potent, and selective pharmacologic inhibitor of DNA-PK activity, for the treatment of human cancerous malignancies. ZL-2201 demonstrated greater selectivity for DNA-PK and effectively inhibited DNA-PK autophosphorylation in a concentration- and time-dependent manner. Initial data suggested a potential correlation between ataxia-telangiectasia mutated (ATM) deficiency and ZL-2201 sensitivity. More so, ZL-2201 showed strong synergy with topoisomerase II inhibitors independent of ATM status in vitro. In vivo oral administration of ZL-2201 demonstrated dose-dependent antitumor activity in the NCI-H1703 xenograft model and significantly enhanced the activity of approved DNA-damaging agents in A549 and FaDu models. From a phosphoproteomic mass spectrometry screen, we identified and validated that ZL-2201 and PRKDC siRNA decreased Ser108 phosphorylation of MCM2, a key DNA replication factor. Collectively, we have characterized a potent and selective DNA-PK inhibitor with promising monotherapy and combinatory therapeutic potential with approved DNA-damaging agents. More importantly, we identified phospho-MCM2 (Ser108) as a potential proximal biomarker of DNA-PK inhibition that warrants further preclinical and clinical evaluation. Significance ZL-2201, a potent and selective DNA-PK inhibitor, can target tumor models in combination with DNA DSB-inducing agents such as radiation or doxorubicin, with potential to improve recurrent therapies in the clinic.
Collapse
Affiliation(s)
- Shruti Lal
- Biologics Discovery, Zai Lab (US) LLC, Menlo Park, California
| | - Neil E. Bhola
- Biologics Discovery, Zai Lab (US) LLC, Menlo Park, California
| | - Bee-Chun Sun
- Biologics Discovery, Zai Lab (US) LLC, Menlo Park, California
| | - Yuping Chen
- Biologics Discovery, Zai Lab (US) LLC, Menlo Park, California
| | - Tom Huang
- Biologics Discovery, Zai Lab (US) LLC, Menlo Park, California
| | - Vivian Morton
- Biologics Discovery, Zai Lab (US) LLC, Menlo Park, California
| | | | | | | | - Nehal S. Parikh
- Biologics Discovery, Zai Lab (US) LLC, Menlo Park, California
| | - Qiuping Ye
- Biologics Discovery, Zai Lab (US) LLC, Menlo Park, California
| | - O. Petter Veiby
- Biologics Discovery, Zai Lab (US) LLC, Menlo Park, California
| | | | - Yuhua Ji
- Biologics Discovery, Zai Lab (US) LLC, Menlo Park, California
| |
Collapse
|
9
|
Markowska M, Budzinska MA, Coenen-Stass A, Kang S, Kizling E, Kolmus K, Koras K, Staub E, Szczurek E. Synthetic lethality prediction in DNA damage repair, chromatin remodeling and the cell cycle using multi-omics data from cell lines and patients. Sci Rep 2023; 13:7049. [PMID: 37120674 PMCID: PMC10148866 DOI: 10.1038/s41598-023-34161-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2022] [Accepted: 04/25/2023] [Indexed: 05/01/2023] Open
Abstract
Discovering synthetic lethal (SL) gene partners of cancer genes is an important step in developing cancer therapies. However, identification of SL interactions is challenging, due to a large number of possible gene pairs, inherent noise and confounding factors in the observed signal. To discover robust SL interactions, we devised SLIDE-VIP, a novel framework combining eight statistical tests, including a new patient data-based test iSurvLRT. SLIDE-VIP leverages multi-omics data from four different sources: gene inactivation cell line screens, cancer patient data, drug screens and gene pathways. We applied SLIDE-VIP to discover SL interactions between genes involved in DNA damage repair, chromatin remodeling and cell cycle, and their potentially druggable partners. The top 883 ranking SL candidates had strong evidence in cell line and patient data, 250-fold reducing the initial space of 200K pairs. Drug screen and pathway tests provided additional corroboration and insights into these interactions. We rediscovered well-known SL pairs such as RB1 and E2F3 or PRKDC and ATM, and in addition, proposed strong novel SL candidates such as PTEN and PIK3CB. In summary, SLIDE-VIP opens the door to the discovery of SL interactions with clinical potential. All analysis and visualizations are available via the online SLIDE-VIP WebApp.
Collapse
Affiliation(s)
- Magda Markowska
- Faculty of Mathematics, Informatics and Mechanics, University of Warsaw, Stefana Banacha 2, 02-097, Warsaw, Poland
- Postgraduate School of Molecular Medicine, Medical University of Warsaw, Zwirki i Wigury 61, 02-091, Warsaw, Poland
| | - Magdalena A Budzinska
- Faculty of Mathematics, Informatics and Mechanics, University of Warsaw, Stefana Banacha 2, 02-097, Warsaw, Poland
- Ardigen S.A., Podole 76, 30-394, Cracow, Poland
| | - Anna Coenen-Stass
- Translational Medicine, Oncology Bioinformatics, Merck Healthcare KGaA, Frankfurt Strasse 250, 64293, Darmstadt, Germany
| | - Senbai Kang
- Faculty of Mathematics, Informatics and Mechanics, University of Warsaw, Stefana Banacha 2, 02-097, Warsaw, Poland
| | - Ewa Kizling
- Faculty of Mathematics, Informatics and Mechanics, University of Warsaw, Stefana Banacha 2, 02-097, Warsaw, Poland
| | | | - Krzysztof Koras
- Faculty of Mathematics, Informatics and Mechanics, University of Warsaw, Stefana Banacha 2, 02-097, Warsaw, Poland
| | - Eike Staub
- Translational Medicine, Oncology Bioinformatics, Merck Healthcare KGaA, Frankfurt Strasse 250, 64293, Darmstadt, Germany
| | - Ewa Szczurek
- Faculty of Mathematics, Informatics and Mechanics, University of Warsaw, Stefana Banacha 2, 02-097, Warsaw, Poland.
| |
Collapse
|
10
|
Tirilomi A, Elakad O, Yao S, Li Y, Hinterthaner M, Danner BC, Ströbel P, Tirilomis T, Bohnenberger H, von Hammerstein-Equord A. Expression and prognostic impact of DNA-PK in human lung cancer. Medicine (Baltimore) 2023; 102:e33143. [PMID: 36862864 PMCID: PMC9981429 DOI: 10.1097/md.0000000000033143] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 03/04/2023] Open
Abstract
Among all cancer patient's lung cancer is the leading cause of death. Prognostic biomarkers continue to be investigated for the detection and stratification of lung cancer for clinical use. The DNA-dependent protein kinase is involved in mechanisms of DNA damage repair. Deregulation and overexpression of DNA-dependent protein kinase is associated with poor prognosis in various tumor entities. In this study, we investigated the expression of DNA-dependent protein kinase in relation to clinicopathological features and overall survival in patients with lung cancer. By immunohistochemistry, expression of DNA-dependent protein kinase was analyzed in 205 cases of lung cancer; 95 cases of adenocarcinoma, 83 cases of squamous cell lung carcinoma and 27 cases of small cell lung cancer and correlated with clinicopathological characteristics as well as patient's overall survival. In patients with adenocarcinoma, a significant correlation between strong expression of DNA-dependent protein kinase and worse overall survival was found. No significant association was observed in patients with squamous cell lung carcinoma and small cell lung cancer. Strong detection of DNA-dependent protein kinase expression was most evident in small cell lung cancer (81.48 %), followed by squamous cell lung carcinoma (62.65 %) and adenocarcinoma (61.05 %). In our study, expression of DNA-dependent protein kinase was associated with poor overall survival in patients with adenocarcinoma. DNA-dependent protein kinase could serve as a new prognostic biomarker.
Collapse
Affiliation(s)
- Anna Tirilomi
- Department of Cardio-Thoracic and Vascular Surgery, University Medical Center, Göttingen, Germany
| | - Omar Elakad
- Institute of Pathology, University Medical Center, Göttingen, Germany
| | - Sha Yao
- Institute of Pathology, University Medical Center, Göttingen, Germany
| | - Yuchan Li
- Institute of Pathology, University Medical Center, Göttingen, Germany
| | - Marc Hinterthaner
- Department of Cardio-Thoracic and Vascular Surgery, University Medical Center, Göttingen, Germany
| | - Bernhard C. Danner
- Department of Cardio-Thoracic and Vascular Surgery, University Medical Center, Göttingen, Germany
| | - Philipp Ströbel
- Institute of Pathology, University Medical Center, Göttingen, Germany
| | - Theodor Tirilomis
- Department of Cardio-Thoracic and Vascular Surgery, University Medical Center, Göttingen, Germany
| | | | - Alexander von Hammerstein-Equord
- Department of Cardio-Thoracic and Vascular Surgery, University Medical Center, Göttingen, Germany
- * Correspondence: Alexander von Hammerstein-Equord, Department of Cardio-Thoracic and Vascular Surgery, University Medical Center, Robert-Koch-Str. 40, Göttingen 37075, Germany (e-mail: )
| |
Collapse
|
11
|
Sible E, Attaway M, Fiorica G, Michel G, Chaudhuri J, Vuong BQ. Ataxia Telangiectasia Mutated and MSH2 Control Blunt DNA End Joining in Ig Class Switch Recombination. JOURNAL OF IMMUNOLOGY (BALTIMORE, MD. : 1950) 2023; 210:369-376. [PMID: 36603026 PMCID: PMC9915862 DOI: 10.4049/jimmunol.2200590] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/15/2022] [Accepted: 12/09/2022] [Indexed: 01/06/2023]
Abstract
Class-switch recombination (CSR) produces secondary Ig isotypes and requires activation-induced cytidine deaminase (AID)-dependent DNA deamination of intronic switch regions within the IgH (Igh) gene locus. Noncanonical repair of deaminated DNA by mismatch repair (MMR) or base excision repair (BER) creates DNA breaks that permit recombination between distal switch regions. Ataxia telangiectasia mutated (ATM)-dependent phosphorylation of AID at serine 38 (pS38-AID) promotes its interaction with apurinic/apyrimidinic endonuclease 1 (APE1), a BER protein, suggesting that ATM regulates CSR through BER. However, pS38-AID may also function in MMR during CSR, although the mechanism remains unknown. To examine whether ATM modulates BER- and/or MMR-dependent CSR, Atm-/- mice were bred to mice deficient for the MMR gene mutS homolog 2 (Msh2). Surprisingly, the predicted Mendelian frequencies of Atm-/-Msh2-/- adult mice were not obtained. To generate ATM and MSH2-deficient B cells, Atm was conditionally deleted on an Msh2-/- background using a floxed ATM allele (Atmf) and B cell-specific Cre recombinase expression (CD23-cre) to produce a deleted ATM allele (AtmD). As compared with AtmD/D and Msh2-/- mice and B cells, AtmD/DMsh2-/- mice and B cells display a reduced CSR phenotype. Interestingly, Sμ-Sγ1 junctions from AtmD/DMsh2-/- B cells that were induced to switch to IgG1 in vitro showed a significant loss of blunt end joins and an increase in insertions as compared with wild-type, AtmD/D, or Msh2-/- B cells. These data indicate that the absence of both ATM and MSH2 blocks nonhomologous end joining, leading to inefficient CSR. We propose a model whereby ATM and MSH2 function cooperatively to regulate end joining during CSR through pS38-AID.
Collapse
Affiliation(s)
- Emily Sible
- Biology PhD Program, The Graduate Center, The City University of New York, New York, NY
- Department of Biology, City College of New York, The City University of New York, New York, NY; and
| | - Mary Attaway
- Department of Biology, City College of New York, The City University of New York, New York, NY; and
| | - Giuseppe Fiorica
- Department of Biology, City College of New York, The City University of New York, New York, NY; and
| | - Genesis Michel
- Department of Biology, City College of New York, The City University of New York, New York, NY; and
| | | | - Bao Q. Vuong
- Biology PhD Program, The Graduate Center, The City University of New York, New York, NY
- Department of Biology, City College of New York, The City University of New York, New York, NY; and
| |
Collapse
|
12
|
Groelly FJ, Fawkes M, Dagg RA, Blackford AN, Tarsounas M. Targeting DNA damage response pathways in cancer. Nat Rev Cancer 2023; 23:78-94. [PMID: 36471053 DOI: 10.1038/s41568-022-00535-5] [Citation(s) in RCA: 190] [Impact Index Per Article: 190.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 11/01/2022] [Indexed: 12/12/2022]
Abstract
Cells have evolved a complex network of biochemical pathways, collectively known as the DNA damage response (DDR), to prevent detrimental mutations from being passed on to their progeny. The DDR coordinates DNA repair with cell-cycle checkpoint activation and other global cellular responses. Genes encoding DDR factors are frequently mutated in cancer, causing genomic instability, an intrinsic feature of many tumours that underlies their ability to grow, metastasize and respond to treatments that inflict DNA damage (such as radiotherapy). One instance where we have greater insight into how genetic DDR abrogation impacts on therapy responses is in tumours with mutated BRCA1 or BRCA2. Due to compromised homologous recombination DNA repair, these tumours rely on alternative repair mechanisms and are susceptible to chemical inhibitors of poly(ADP-ribose) polymerase (PARP), which specifically kill homologous recombination-deficient cancer cells, and have become a paradigm for targeted cancer therapy. It is now clear that many other synthetic-lethal relationships exist between DDR genes. Crucially, some of these interactions could be exploited in the clinic to target tumours that become resistant to PARP inhibition. In this Review, we discuss state-of-the-art strategies for DDR inactivation using small-molecule inhibitors and highlight those compounds currently being evaluated in the clinic.
Collapse
Affiliation(s)
- Florian J Groelly
- Genome Stability and Tumourigenesis Group, Oxford Institute for Radiation Oncology, Department of Oncology, University of Oxford, Oxford, UK
| | - Matthew Fawkes
- Department of Oncology, MRC Weatherall Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital, Oxford, UK
| | - Rebecca A Dagg
- Genome Stability and Tumourigenesis Group, Oxford Institute for Radiation Oncology, Department of Oncology, University of Oxford, Oxford, UK
| | - Andrew N Blackford
- Department of Oncology, MRC Weatherall Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital, Oxford, UK.
| | - Madalena Tarsounas
- Genome Stability and Tumourigenesis Group, Oxford Institute for Radiation Oncology, Department of Oncology, University of Oxford, Oxford, UK.
| |
Collapse
|
13
|
Uhlemeyer C, Müller N, Rieck M, Kuboth J, Schlegel C, Grieß K, Dorweiler TF, Heiduschka S, Eckel J, Roden M, Lammert E, Stoffel M, Belgardt BF. Selective ablation of P53 in pancreatic beta cells fails to ameliorate glucose metabolism in genetic, dietary and pharmacological models of diabetes mellitus. Mol Metab 2022; 67:101650. [PMID: 36470401 PMCID: PMC9791454 DOI: 10.1016/j.molmet.2022.101650] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/13/2022] [Revised: 11/25/2022] [Accepted: 11/29/2022] [Indexed: 12/12/2022] Open
Abstract
OBJECTIVE Beta cell dysfunction and death are critical steps in the development of both type 1 and type 2 diabetes (T1D and T2D), but the underlying mechanisms are incompletely understood. Activation of the essential tumor suppressor and transcription factor P53 (also known as TP53 and Trp53 in mice) was linked to beta cell death in vitro and has been reported in several diabetes mouse models and beta cells of humans with T2D. In this article, we set out to determine the beta cell specific role of P53 in beta cell dysfunction, cell death and development of diabetes in vivo. METHODS We generated beta cell specific P53 knockout (P53BKO) mice and used complementary genetic, dietary and pharmacological models of glucose intolerance, beta cell dysfunction and diabetes development to evaluate the functional role of P53 selectively in beta cells. We further analyzed the effect of P53 ablation on beta cell survival in isolated pancreatic islets exposed to diabetogenic stress inducers ex vivo by flow cytometry. RESULTS Beta cell specific ablation of P53/Trp53 failed to ameliorate glucose tolerance, insulin secretion or to increase beta cell numbers in genetic, dietary and pharmacological models of diabetes. Additionally, loss of P53 in beta cells did not protect against streptozotocin (STZ) induced hyperglycemia and beta cell death, although STZ-induced activation of classical pro-apoptotic P53 target genes was significantly reduced in P53BKO mice. In contrast, Olaparib mediated PARP1 inhibition protected against acute ex vivo STZ-induced beta cell death and islet destruction. CONCLUSIONS Our study reveals that ablation of P53 specifically in beta cells is unexpectedly unable to attenuate beta cell failure and death in vivo and ex vivo. While during development and progression of diabetes, P53 and P53-regulated pathways are activated, our study suggests that P53 signaling is not essential for loss of beta cells or beta cell dysfunction. P53 in other cell types and organs may predominantly regulate systemic glucose homeostasis.
Collapse
Affiliation(s)
- Celina Uhlemeyer
- Institute for Vascular and Islet Cell Biology, German Diabetes Center, Leibniz Center for Diabetes Research at Heinrich-Heine University, Düsseldorf, Germany; German Center for Diabetes Research (DZD e.V.), Neuherberg, Germany.
| | - Nadine Müller
- Institute for Vascular and Islet Cell Biology, German Diabetes Center, Leibniz Center for Diabetes Research at Heinrich-Heine University, Düsseldorf, Germany,German Center for Diabetes Research (DZD e.V.), Neuherberg, Germany
| | - Michael Rieck
- Institute for Vascular and Islet Cell Biology, German Diabetes Center, Leibniz Center for Diabetes Research at Heinrich-Heine University, Düsseldorf, Germany,German Center for Diabetes Research (DZD e.V.), Neuherberg, Germany
| | - Jennifer Kuboth
- Institute for Vascular and Islet Cell Biology, German Diabetes Center, Leibniz Center for Diabetes Research at Heinrich-Heine University, Düsseldorf, Germany,German Center for Diabetes Research (DZD e.V.), Neuherberg, Germany
| | - Caroline Schlegel
- Institute for Vascular and Islet Cell Biology, German Diabetes Center, Leibniz Center for Diabetes Research at Heinrich-Heine University, Düsseldorf, Germany,German Center for Diabetes Research (DZD e.V.), Neuherberg, Germany
| | - Kerstin Grieß
- Institute for Vascular and Islet Cell Biology, German Diabetes Center, Leibniz Center for Diabetes Research at Heinrich-Heine University, Düsseldorf, Germany,German Center for Diabetes Research (DZD e.V.), Neuherberg, Germany
| | - Tim Florian Dorweiler
- Institute for Vascular and Islet Cell Biology, German Diabetes Center, Leibniz Center for Diabetes Research at Heinrich-Heine University, Düsseldorf, Germany,German Center for Diabetes Research (DZD e.V.), Neuherberg, Germany
| | - Sonja Heiduschka
- Institute for Vascular and Islet Cell Biology, German Diabetes Center, Leibniz Center for Diabetes Research at Heinrich-Heine University, Düsseldorf, Germany,German Center for Diabetes Research (DZD e.V.), Neuherberg, Germany
| | - Jürgen Eckel
- German Center for Diabetes Research (DZD e.V.), Neuherberg, Germany,Institute for Clinical Diabetology, German Diabetes Center, Leibniz Center for Diabetes, Düsseldorf, Germany
| | - Michael Roden
- German Center for Diabetes Research (DZD e.V.), Neuherberg, Germany,Institute for Clinical Diabetology, German Diabetes Center, Leibniz Center for Diabetes, Düsseldorf, Germany,Department of Endocrinology and Diabetology, Medical Faculty and University Hospital Düsseldorf, Heinrich Heine University, Düsseldorf, Germany
| | - Eckhard Lammert
- Institute for Vascular and Islet Cell Biology, German Diabetes Center, Leibniz Center for Diabetes Research at Heinrich-Heine University, Düsseldorf, Germany,German Center for Diabetes Research (DZD e.V.), Neuherberg, Germany,Institute of Metabolic Physiology, Heinrich Heine University, Düsseldorf, Germany
| | - Markus Stoffel
- Institute of Molecular Health Sciences (IMHS), ETH Zürich, Zürich, Switzerland; Competence Center Personalized Medicine, ETH Zürich, Zürich, Switzerland; Medical Faculty, University of Zürich, Zürich, Switzerland
| | - Bengt-Frederik Belgardt
- Institute for Vascular and Islet Cell Biology, German Diabetes Center, Leibniz Center for Diabetes Research at Heinrich-Heine University, Düsseldorf, Germany; German Center for Diabetes Research (DZD e.V.), Neuherberg, Germany.
| |
Collapse
|
14
|
Manolakou T, Nikolopoulos D, Gkikas D, Filia A, Samiotaki M, Stamatakis G, Fanouriakis A, Politis P, Banos A, Alissafi T, Verginis P, Boumpas DT. ATR-mediated DNA damage responses underlie aberrant B cell activity in systemic lupus erythematosus. SCIENCE ADVANCES 2022; 8:eabo5840. [PMID: 36306362 PMCID: PMC9616496 DOI: 10.1126/sciadv.abo5840] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
B cells orchestrate autoimmune responses in patients with systemic lupus erythematosus (SLE), but broad-based B cell-directed therapies show only modest efficacy while blunting humoral immune responses to vaccines and inducing immunosuppression. Development of more effective therapies targeting pathogenic clones is a currently unmet need. Here, we demonstrate enhanced activation of the ATR/Chk1 pathway of the DNA damage response (DDR) in B cells of patients with active SLE disease. Treatment of B cells with type I IFN, a key driver of immunity in SLE, induced expression of ATR via binding of interferon regulatory factor 1 to its gene promoter. Pharmacologic targeting of ATR in B cells, via a specific inhibitor (VE-822), attenuated their immunogenic profile, including proinflammatory cytokine secretion, plasmablast formation, and antibody production. Together, these findings identify the ATR-mediated DDR axis as the orchestrator of the type I IFN-mediated B cell responses in SLE and as a potential novel therapeutic target.
Collapse
Affiliation(s)
- Theodora Manolakou
- Center for Clinical, Experimental Surgery and Translational Research, Biomedical Research Foundation of the Academy of Athens, 115 27 Athens, Greece
- School of Medicine, National and Kapodistrian University of Athens, 115 27 Athens, Greece
- Corresponding author. (T.M.); (P.V.); (D.T.B.)
| | - Dionysis Nikolopoulos
- Center for Clinical, Experimental Surgery and Translational Research, Biomedical Research Foundation of the Academy of Athens, 115 27 Athens, Greece
- School of Medicine, National and Kapodistrian University of Athens, 115 27 Athens, Greece
| | - Dimitrios Gkikas
- Center for Basic Research, Biomedical Research Foundation of the Academy of Athens, 115 27, Athens, Greece
| | - Anastasia Filia
- Center for Clinical, Experimental Surgery and Translational Research, Biomedical Research Foundation of the Academy of Athens, 115 27 Athens, Greece
| | - Martina Samiotaki
- Institute for Bioinnovation, Biomedical Sciences Research Center Alexander Fleming, Vari, Attica, Greece
- Centre of New Biotechnologies and Precision Medicine (CNBPM) School of Medicine, National and Kapodistrian University of Athens, Athens 115 27, Greece
| | - George Stamatakis
- Institute for Bioinnovation, Biomedical Sciences Research Center Alexander Fleming, Vari, Attica, Greece
- Centre of New Biotechnologies and Precision Medicine (CNBPM) School of Medicine, National and Kapodistrian University of Athens, Athens 115 27, Greece
| | | | - Panagiotis Politis
- Center for Basic Research, Biomedical Research Foundation of the Academy of Athens, 115 27, Athens, Greece
- School of Medicine, European University Cyprus, 1516, Nicosia, Cyprus
| | - Aggelos Banos
- Center for Clinical, Experimental Surgery and Translational Research, Biomedical Research Foundation of the Academy of Athens, 115 27 Athens, Greece
| | - Themis Alissafi
- Center for Basic Research, Biomedical Research Foundation of the Academy of Athens, 115 27, Athens, Greece
- Laboratory of Biology, National and Kapodistrian University of Athens Medical School, 124 62 Athens, Greece
| | - Panayotis Verginis
- Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology, 700 13 Heraklion, Greece
- Laboratory of Immune Regulation and Tolerance, Division of Basic Sciences, University of Crete Medical School, 700 13 Heraklion, Greece
- Corresponding author. (T.M.); (P.V.); (D.T.B.)
| | - Dimitrios T. Boumpas
- Center for Clinical, Experimental Surgery and Translational Research, Biomedical Research Foundation of the Academy of Athens, 115 27 Athens, Greece
- Joint Rheumatology Program, 4th Department of Internal Medicine, Attikon University Hospital, National and Kapodistrian University of Athens Medical School, 124 62 Athens, Greece
- Corresponding author. (T.M.); (P.V.); (D.T.B.)
| |
Collapse
|
15
|
Patricio DDO, Dias GBM, Granella LW, Trigg B, Teague HC, Bittencourt D, Báfica A, Zanotto-Filho A, Ferguson B, Mansur DS. DNA-PKcs restricts Zika virus spreading and is required for effective antiviral response. Front Immunol 2022; 13:1042463. [PMID: 36311766 PMCID: PMC9606669 DOI: 10.3389/fimmu.2022.1042463] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2022] [Accepted: 09/27/2022] [Indexed: 04/23/2024] Open
Abstract
Zika virus (ZIKV) is a single-strand RNA mosquito-borne flavivirus with significant public health impact. ZIKV infection induces double-strand DNA breaks (DSBs) in human neural progenitor cells that may contribute to severe neuronal manifestations in newborns. The DNA-PK complex plays a critical role in repairing DSBs and in the innate immune response to infection. It is unknown, however, whether DNA-PK regulates ZIKV infection. Here we investigated the role of DNA-PKcs, the catalytic subunit of DNA-PK, during ZIKV infection. We demonstrate that DNA-PKcs restricts the spread of ZIKV infection in human epithelial cells. Increased ZIKV replication and spread in DNA-PKcs deficient cells is related to a notable decrease in transcription of type I and III interferons as well as IFIT1, IFIT2, and IL6. This was shown to be independent of IRF1, IRF3, or p65, canonical transcription factors necessary for activation of both type I and III interferon promoters. The mechanism of DNA-PKcs to restrict ZIKV infection is independent of DSB. Thus, these data suggest a non-canonical role for DNA-PK during Zika virus infection, acting downstream of IFNs transcription factors for an efficient antiviral immune response.
Collapse
Affiliation(s)
- Daniel de Oliveira Patricio
- Laboratório de Imunobiologia, Departamento de Microbiologia, Imunologia e Parasitologia, Universidade Federal de Santa Catarina, Florianópolis, Brazil
| | - Greicy Brisa Malaquias Dias
- Laboratório de Imunobiologia, Departamento de Microbiologia, Imunologia e Parasitologia, Universidade Federal de Santa Catarina, Florianópolis, Brazil
| | - Lucilene Wildner Granella
- Laboratório de Imunobiologia, Departamento de Microbiologia, Imunologia e Parasitologia, Universidade Federal de Santa Catarina, Florianópolis, Brazil
| | - Ben Trigg
- Department of Pathology, University of Cambridge, Cambridge, United Kingdom
| | | | - Dina Bittencourt
- Laboratório de Imunobiologia, Departamento de Microbiologia, Imunologia e Parasitologia, Universidade Federal de Santa Catarina, Florianópolis, Brazil
| | - André Báfica
- Laboratório de Imunobiologia, Departamento de Microbiologia, Imunologia e Parasitologia, Universidade Federal de Santa Catarina, Florianópolis, Brazil
| | - Alfeu Zanotto-Filho
- Laboratório de Farmacologia e Bioquímica do Câncer, Departamento de Farmacologia, Universidade Federal de Santa Catarina, Florianópolis, Brazil
| | - Brian Ferguson
- Department of Pathology, University of Cambridge, Cambridge, United Kingdom
| | - Daniel Santos Mansur
- Laboratório de Imunobiologia, Departamento de Microbiologia, Imunologia e Parasitologia, Universidade Federal de Santa Catarina, Florianópolis, Brazil
| |
Collapse
|
16
|
Hou W, Li Y, Zhang J, Xia Y, Wang X, Chen H, Lou H. Cohesin in DNA damage response and double-strand break repair. Crit Rev Biochem Mol Biol 2022; 57:333-350. [PMID: 35112600 DOI: 10.1080/10409238.2022.2027336] [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: 08/05/2021] [Revised: 01/03/2022] [Accepted: 01/06/2022] [Indexed: 11/03/2022]
Abstract
Cohesin, a four-subunit ring comprising SMC1, SMC3, RAD21 and SA1/2, tethers sister chromatids by DNA replication-coupled cohesion (RC-cohesion) to guarantee correct chromosome segregation during cell proliferation. Postreplicative cohesion, also called damage-induced cohesion (DI-cohesion), is an emerging critical player in DNA damage response (DDR). In this review, we sum up recent progress on how cohesin regulates the DNA damage checkpoint activation and repair pathway choice, emphasizing postreplicative cohesin loading and DI-cohesion establishment in yeasts and mammals. DI-cohesion and RC-cohesion show distinct features in many aspects. DI-cohesion near or far from the break sites might undergo different regulations and execute different tasks in DDR and DSB repair. Furthermore, some open questions in this field and the significance of this new scenario to our understanding of genome stability maintenance and cohesinopathies are discussed.
Collapse
Affiliation(s)
- Wenya Hou
- Shenzhen University General Hospital, Guangdong Key Laboratory for Genome Stability & Disease Prevention, Shenzhen University School of Medicine, Shenzhen, Guangdong, China
| | - Yan Li
- Shenzhen University General Hospital, Guangdong Key Laboratory for Genome Stability & Disease Prevention, Shenzhen University School of Medicine, Shenzhen, Guangdong, China
| | - Jiaxin Zhang
- Shenzhen University General Hospital, Guangdong Key Laboratory for Genome Stability & Disease Prevention, Shenzhen University School of Medicine, Shenzhen, Guangdong, China
| | - Yisui Xia
- Shenzhen University General Hospital, Guangdong Key Laboratory for Genome Stability & Disease Prevention, Shenzhen University School of Medicine, Shenzhen, Guangdong, China
| | - Xueting Wang
- Shenzhen University General Hospital, Guangdong Key Laboratory for Genome Stability & Disease Prevention, Shenzhen University School of Medicine, Shenzhen, Guangdong, China
- Union Shenzhen Hospital, Department of Dermatology, Huazhong University of Science and Technology (Nanshan Hospital), Shenzhen, Guangdong, China
| | - Hongxiang Chen
- Union Shenzhen Hospital, Department of Dermatology, Huazhong University of Science and Technology (Nanshan Hospital), Shenzhen, Guangdong, China
| | - Huiqiang Lou
- Shenzhen University General Hospital, Guangdong Key Laboratory for Genome Stability & Disease Prevention, Shenzhen University School of Medicine, Shenzhen, Guangdong, China
| |
Collapse
|
17
|
Shah P, McGuigan CW, Cheng S, Vanpouille-Box C, Demaria S, Weiss RS, Lammerding J. ATM Modulates Nuclear Mechanics by Regulating Lamin A Levels. Front Cell Dev Biol 2022; 10:875132. [PMID: 35721517 PMCID: PMC9198445 DOI: 10.3389/fcell.2022.875132] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2022] [Accepted: 05/13/2022] [Indexed: 12/18/2022] Open
Abstract
Ataxia-telangiectasia mutated (ATM) is one of the three main apical kinases at the crux of DNA damage response and repair in mammalian cells. ATM activates a cascade of downstream effector proteins to regulate DNA repair and cell cycle checkpoints in response to DNA double-strand breaks. While ATM is predominantly known for its role in DNA damage response and repair, new roles of ATM have recently begun to emerge, such as in regulating oxidative stress or metabolic pathways. Here, we report the surprising discovery that ATM inhibition and deletion lead to reduced expression of the nuclear envelope protein lamin A. Lamins are nuclear intermediate filaments that modulate nuclear shape, structure, and stiffness. Accordingly, inhibition or deletion of ATM resulted in increased nuclear deformability and enhanced cell migration through confined spaces, which requires substantial nuclear deformation. These findings point to a novel connection between ATM and lamin A and may have broad implications for cells with ATM mutations—as found in patients suffering from Ataxia Telangiectasia and many human cancers—which could lead to enhanced cell migration and increased metastatic potential.
Collapse
Affiliation(s)
- Pragya Shah
- Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, NY, United States
| | - Connor W. McGuigan
- Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, NY, United States
| | - Svea Cheng
- Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, NY, United States
| | - Claire Vanpouille-Box
- Department of Radiation Oncology, Weill Cornell Medicine, New York City, NY, United States
| | - Sandra Demaria
- Department of Radiation Oncology, Weill Cornell Medicine, New York City, NY, United States
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York City, NY, United States
| | - Robert S. Weiss
- Department of Biomedical Sciences, Cornell University, Ithaca, NY, United States
| | - Jan Lammerding
- Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, NY, United States
- Nancy E. and Peter C. Meinig School of Biomedical Engineering, Cornell University, Ithaca, NY, United States
- *Correspondence: Jan Lammerding,
| |
Collapse
|
18
|
Xue Z, Zheng S, Linghu D, Liu B, Yang Y, Chen MK, Huang H, Song J, Li H, Wang J, Hung MC, Zhong D, Sun L. PD-L1 deficiency sensitizes tumor cells to DNA-PK inhibition and enhances cGAS-STING activation. Am J Cancer Res 2022; 12:2363-2375. [PMID: 35693073 PMCID: PMC9185610] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2022] [Accepted: 05/02/2022] [Indexed: 06/15/2023] Open
Abstract
Immunotherapies that block PD-L1/PD-1 immune checkpoint proteins represent a landmark breakthrough in cancer treatment. Although the role of PD-L1 in suppressing T cell activity has been extensively studied, its cancer cell-intrinsic functions are not well understood. Herein, we demonstrated that PD-L1 is important for the repair of DNA damage in cancer cells. Mechanically, depletion of PD-L1 led to the downregulation of the critical molecules involved in the homologous recombination (HR) repair pathway, such as ATM and BRCA1, but did not obviously affect the non-homologous end joining (NHEJ) pathway. Notably, PD-L1 silence sensitized cancer cells to chemotherapy agents and the inhibitor of DNA-PK, which is an important kinase for NHEJ. Furthermore, PD-L1 depletion potentiated DNA damage-induced cGAS-STING pathway and induction of IFNβ. The regulation of DNA repair and cGAS-STING pathway by PD-L1 represents its connection with innate immunity that can be exploited to enhance the efficacy of existing immunotherapy. Our findings thus expand the focus of PD-L1 from tumor antigen-specific CD8+ T cells to innate immunity, and support targeting tumor-intrinsic PD-L1 combined with DNA-PK inhibition for tumor eradication, through promoting synthetic lethality and innate immune response.
Collapse
Affiliation(s)
- Zhen Xue
- Tianjin Key Laboratory of Lung Cancer Metastasis and Tumor Microenvironment, Lung Cancer Institute, Tianjin Medical University General HospitalTianjin 300052, P. R. China
- Department of Medical Oncology, Tianjin Medical University General HospitalTianjin 300052, P. R. China
| | - Shuang Zheng
- Tianjin Key Laboratory of Lung Cancer Metastasis and Tumor Microenvironment, Lung Cancer Institute, Tianjin Medical University General HospitalTianjin 300052, P. R. China
- Department of Medical Oncology, Tianjin Medical University General HospitalTianjin 300052, P. R. China
| | - Dongli Linghu
- Tianjin Key Laboratory of Lung Cancer Metastasis and Tumor Microenvironment, Lung Cancer Institute, Tianjin Medical University General HospitalTianjin 300052, P. R. China
| | - Boning Liu
- Tianjin Key Laboratory of Lung Cancer Metastasis and Tumor Microenvironment, Lung Cancer Institute, Tianjin Medical University General HospitalTianjin 300052, P. R. China
| | - Yi Yang
- Institute of Pathology and Southwest Cancer Center, Southwest Hospital, Third Military Medical UniversityChongqing 400038, P. R. China
| | - Mei-Kuang Chen
- Department of Molecular and Cellular Oncology, The University of Texas M. D. Anderson Cancer CenterHouston, Texas 77030, USA
| | - Hua Huang
- Tianjin Key Laboratory of Lung Cancer Metastasis and Tumor Microenvironment, Lung Cancer Institute, Tianjin Medical University General HospitalTianjin 300052, P. R. China
| | - Jiaming Song
- Tianjin Key Laboratory of Lung Cancer Metastasis and Tumor Microenvironment, Lung Cancer Institute, Tianjin Medical University General HospitalTianjin 300052, P. R. China
| | - Hongyue Li
- Tianjin General Surgery Institute, Tianjin Medical University General HospitalTianjin 300052, P. R. China
| | - Jing Wang
- Tianjin Key Laboratory of Lung Cancer Metastasis and Tumor Microenvironment, Lung Cancer Institute, Tianjin Medical University General HospitalTianjin 300052, P. R. China
| | - Mien-Chie Hung
- Department of Molecular and Cellular Oncology, The University of Texas M. D. Anderson Cancer CenterHouston, Texas 77030, USA
- Graduate Institute of Biomedical Sciences and Center for Molecular Medicine, China Medical UniversityTaichung, Taiwan
| | - Diansheng Zhong
- Tianjin Key Laboratory of Lung Cancer Metastasis and Tumor Microenvironment, Lung Cancer Institute, Tianjin Medical University General HospitalTianjin 300052, P. R. China
- Department of Medical Oncology, Tianjin Medical University General HospitalTianjin 300052, P. R. China
| | - Linlin Sun
- Tianjin Key Laboratory of Lung Cancer Metastasis and Tumor Microenvironment, Lung Cancer Institute, Tianjin Medical University General HospitalTianjin 300052, P. R. China
| |
Collapse
|
19
|
Tang J, Li Z, Wu Q, Irfan M, Li W, Liu X. Role of Paralogue of XRCC4 and XLF in DNA Damage Repair and Cancer Development. Front Immunol 2022; 13:852453. [PMID: 35309348 PMCID: PMC8926060 DOI: 10.3389/fimmu.2022.852453] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2022] [Accepted: 02/07/2022] [Indexed: 01/01/2023] Open
Abstract
Non-homologous end joining (cNHEJ) is a major pathway to repair double-strand breaks (DSBs) in DNA. Several core cNHEJ are involved in the progress of the repair such as KU70 and 80, DNA-dependent protein kinase catalytic subunit (DNA-PKcs), Artemis, X-ray repair cross-complementing protein 4 (XRCC4), DNA ligase IV, and XRCC4-like factor (XLF). Recent studies have added a number of new proteins during cNHEJ. One of the newly identified proteins is Paralogue of XRCC4 and XLF (PAXX), which acts as a scaffold that is required to stabilize the KU70/80 heterodimer at DSBs sites and promotes the assembly and/or stability of the cNHEJ machinery. PAXX plays an essential role in lymphocyte development in XLF-deficient background, while XLF/PAXX double-deficient mouse embryo died before birth. Emerging evidence also shows a connection between the expression levels of PAXX and cancer development in human patients, indicating a prognosis role of the protein. This review will summarize and discuss the function of PAXX in DSBs repair and its potential role in cancer development.
Collapse
Affiliation(s)
- Jialin Tang
- Guangdong Key Laboratory of Genome Instability and Human Disease Prevention, Department of Biochemistry and Molecular Biology, Shenzhen University School of Medicine, Shenzhen, China
| | - Zhongxia Li
- Guangdong Key Laboratory of Genome Instability and Human Disease Prevention, Department of Biochemistry and Molecular Biology, Shenzhen University School of Medicine, Shenzhen, China
| | - Qiong Wu
- Guangdong Key Laboratory of Genome Instability and Human Disease Prevention, Department of Biochemistry and Molecular Biology, Shenzhen University School of Medicine, Shenzhen, China
| | - Muhammad Irfan
- Guangdong Key Laboratory of Genome Instability and Human Disease Prevention, Department of Biochemistry and Molecular Biology, Shenzhen University School of Medicine, Shenzhen, China
| | - Weili Li
- Guangdong Key Laboratory of Genome Instability and Human Disease Prevention, Department of Biochemistry and Molecular Biology, Shenzhen University School of Medicine, Shenzhen, China
| | - Xiangyu Liu
- Guangdong Key Laboratory of Genome Instability and Human Disease Prevention, Department of Biochemistry and Molecular Biology, Shenzhen University School of Medicine, Shenzhen, China.,Department of Hematology, The Second People's Hospital of Shenzhen, Shenzhen, China
| |
Collapse
|
20
|
Bourseguin J, Cheng W, Talbot E, Hardy L, Lai J, Jeffries A, Lodato MA, Lee EA, Khoronenkova S. Persistent DNA damage associated with ATM kinase deficiency promotes microglial dysfunction. Nucleic Acids Res 2022; 50:2700-2718. [PMID: 35212385 PMCID: PMC8934660 DOI: 10.1093/nar/gkac104] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2021] [Revised: 02/01/2022] [Accepted: 02/03/2022] [Indexed: 01/21/2023] Open
Abstract
The autosomal recessive genome instability disorder Ataxia-telangiectasia, caused by mutations in ATM kinase, is characterized by the progressive loss of cerebellar neurons. We find that DNA damage associated with ATM loss results in dysfunctional behaviour of human microglia, immune cells of the central nervous system. Microglial dysfunction is mediated by the pro-inflammatory RELB/p52 non-canonical NF-κB transcriptional pathway and leads to excessive phagocytic clearance of neuronal material. Activation of the RELB/p52 pathway in ATM-deficient microglia is driven by persistent DNA damage and is dependent on the NIK kinase. Activation of non-canonical NF-κB signalling is also observed in cerebellar microglia of individuals with Ataxia-telangiectasia. These results provide insights into the underlying mechanisms of aberrant microglial behaviour in ATM deficiency, potentially contributing to neurodegeneration in Ataxia-telangiectasia.
Collapse
Affiliation(s)
- Julie Bourseguin
- Department of Biochemistry, University of Cambridge, 80 Tennis Court road, CambridgeCB2 1GA, UK
| | - Wen Cheng
- Department of Biochemistry, University of Cambridge, 80 Tennis Court road, CambridgeCB2 1GA, UK
| | - Emily Talbot
- Department of Biochemistry, University of Cambridge, 80 Tennis Court road, CambridgeCB2 1GA, UK
| | - Liana Hardy
- Department of Biochemistry, University of Cambridge, 80 Tennis Court road, CambridgeCB2 1GA, UK
| | - Jenny Lai
- Division of Genetics and Genomics, Boston Children's Hospital; Department of Pediatrics, Harvard Medical School, Boston, MA 02215, USA
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Program in Neuroscience, Harvard University, Boston, MA 02115, USA
| | - Ailsa M Jeffries
- Department of Molecular, Cell, and Cancer Biology, University of Massachusetts Medical School, Worcester, MA 01605, USA
| | - Michael A Lodato
- Department of Molecular, Cell, and Cancer Biology, University of Massachusetts Medical School, Worcester, MA 01605, USA
| | - Eunjung Alice Lee
- Division of Genetics and Genomics, Boston Children's Hospital; Department of Pediatrics, Harvard Medical School, Boston, MA 02215, USA
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Svetlana V Khoronenkova
- Department of Biochemistry, University of Cambridge, 80 Tennis Court road, CambridgeCB2 1GA, UK
| |
Collapse
|
21
|
García MEG, Kirsch DG, Reitman ZJ. Targeting the ATM Kinase to Enhance the Efficacy of Radiotherapy and Outcomes for Cancer Patients. Semin Radiat Oncol 2022; 32:3-14. [PMID: 34861994 PMCID: PMC8647772 DOI: 10.1016/j.semradonc.2021.09.008] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Targeting the DNA damage response represents a promising approach to improve the efficacy of radiation therapy. One appealing target for this approach is the serine/threonine kinase ataxia telangiectasia mutated (ATM), which is activated by DNA double strand breaks to orchestrate the cellular response to ionizing radiation. Small-molecule inhibitors targeting ATM have entered clinical trials testing their safety in combination with radiation therapy or in combination with other DNA damaging agents. Here, we review biochemical, genetic, and cellular functional studies of ATM, phenotypes associated with germline and somatic cancer mutations in ATM in humans, and experiments in genetically engineered mouse models that support a rationale for investigating ATM inhibitors as radiosensitizers for cancer therapy. These data identify important synthetic lethal relationships, which suggest that ATM inhibitors may be particularly effective in tumors with defects in other nodes of the DNA damage response. The potential for ATM inhibition to improve immunotherapy responses in preclinical models represents another emerging area of research. We summarize ongoing clinical trials of ATM inhibitors with radiotherapy. We also discuss critical ongoing areas of investigation that include discovery of biomarkers that predict for radiosensitization by ATM inhibitors and identification of effective combinations of ATM inhibitors, radiation therapy, other DNA damage response-directed therapies, and/or immunotherapies.
Collapse
Affiliation(s)
| | - David G Kirsch
- Department of Radiation Oncology, Duke University School of Medicine, Durham NC; Department of Pharmacology & Cancer Biology, Duke University School of Medicine, Durham NC
| | - Zachary J Reitman
- Department of Radiation Oncology, Duke University School of Medicine, Durham NC; The Preston Robert Tisch Brain Tumor Center at Duke University Medical Center, Durham NC.
| |
Collapse
|
22
|
Sun X, Bai J, Xu J, Xi X, Gu M, Zhu C, Xue H, Chen C, Dong J. Multiple DSB Resection Activities Redundantly Promote Alternative End Joining-Mediated Class Switch Recombination. Front Cell Dev Biol 2021; 9:767624. [PMID: 34926456 PMCID: PMC8671047 DOI: 10.3389/fcell.2021.767624] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2021] [Accepted: 10/25/2021] [Indexed: 01/13/2023] Open
Abstract
Alternative end joining (A-EJ) catalyzes substantial level of antibody class switch recombination (CSR) in B cells deficient for classical non-homologous end joining, featuring increased switch (S) region DSB resection and junctional microhomology (MH). While resection has been suggested to initiate A-EJ in model DSB repair systems using engineered endonucleases, the contribution of resection factors to A-EJ-mediated CSR remains unclear. In this study, we systematically dissected the requirement for individual DSB resection factors in A-EJ-mediated class switching with a cell-based assay system and high-throughput sequencing. We show that while CtIP and Mre11 both are mildly required for CSR in WT cells, they play more critical roles in mediating A-EJ CSR, which depend on the exonuclease activity of Mre11. While DNA2 and the helicase/HRDC domain of BLM are required for A-EJ by mediating long S region DSB resection, in contrast, Exo1's resection-related function does not play any obvious roles for class switching in either c-NHEJ or A-EJ cells, or mediated in an AID-independent manner by joining of Cas9 breaks. Furthermore, ATM and its kinase activity functions at least in part independent of CtIP/Mre11 to mediate A-EJ switching in Lig4-deficient cells. In stark contrast to Lig4 deficiency, 53BP1-deficient cells do not depend on ATM/Mre11/CtIP for residual joining. We discuss the roles for each resection factor in A-EJ-mediated CSR and suggest that the extent of requirements for resection is context dependent.
Collapse
Affiliation(s)
- Xikui Sun
- Department of Immunology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China.,Key Laboratory of Tropical Disease Control (Sun Yat-sen University), Ministry of Education, Guangzhou, China
| | - Jingning Bai
- Department of Immunology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China.,Key Laboratory of Tropical Disease Control (Sun Yat-sen University), Ministry of Education, Guangzhou, China
| | - Jiejie Xu
- Department of Immunology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China.,Key Laboratory of Tropical Disease Control (Sun Yat-sen University), Ministry of Education, Guangzhou, China
| | - Xiaoli Xi
- Department of Gastroenterology, the Third Affiliated Hospital of Sun Yat-sen University, Guangzhou, China
| | - Mingyu Gu
- Department of Immunology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China.,Key Laboratory of Tropical Disease Control (Sun Yat-sen University), Ministry of Education, Guangzhou, China
| | - Chengming Zhu
- Research Center of the Seventh Affiliated Hospital, Sun Yat-sen University, Shenzhen, China
| | - Hongman Xue
- Department of Pediatrics, the Seventh Affiliated Hospital of Sun Yat-Sen University, Shenzhen, China
| | - Chun Chen
- Department of Pediatrics, the Seventh Affiliated Hospital of Sun Yat-Sen University, Shenzhen, China
| | - Junchao Dong
- Department of Immunology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China.,Key Laboratory of Tropical Disease Control (Sun Yat-sen University), Ministry of Education, Guangzhou, China.,Department of Pediatrics, the Seventh Affiliated Hospital of Sun Yat-Sen University, Shenzhen, China
| |
Collapse
|
23
|
Djuzenova CS, Fischer T, Katzer A, Sisario D, Korsa T, Steussloff G, Sukhorukov VL, Flentje M. Opposite effects of the triple target (DNA-PK/PI3K/mTOR) inhibitor PI-103 on the radiation sensitivity of glioblastoma cell lines proficient and deficient in DNA-PKcs. BMC Cancer 2021; 21:1201. [PMID: 34763650 PMCID: PMC8582108 DOI: 10.1186/s12885-021-08930-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2020] [Accepted: 10/28/2021] [Indexed: 12/26/2022] Open
Abstract
BACKGROUND Radiotherapy is routinely used to combat glioblastoma (GBM). However, the treatment efficacy is often limited by the radioresistance of GBM cells. METHODS Two GBM lines MO59K and MO59J, differing in intrinsic radiosensitivity and mutational status of DNA-PK and ATM, were analyzed regarding their response to DNA-PK/PI3K/mTOR inhibition by PI-103 in combination with radiation. To this end we assessed colony-forming ability, induction and repair of DNA damage by γH2AX and 53BP1, expression of marker proteins, including those belonging to NHEJ and HR repair pathways, degree of apoptosis, autophagy, and cell cycle alterations. RESULTS We found that PI-103 radiosensitized MO59K cells but, surprisingly, it induced radiation resistance in MO59J cells. Treatment of MO59K cells with PI-103 lead to protraction of the DNA damage repair as compared to drug-free irradiated cells. In PI-103-treated and irradiated MO59J cells the foci numbers of both proteins was higher than in the drug-free samples, but a large portion of DNA damage was quickly repaired. Another cell line-specific difference includes diminished expression of p53 in MO59J cells, which was further reduced by PI-103. Additionally, PI-103-treated MO59K cells exhibited an increased expression of the apoptosis marker cleaved PARP and increased subG1 fraction. Moreover, irradiation induced a strong G2 arrest in MO59J cells (~ 80% vs. ~ 50% in MO59K), which was, however, partially reduced in the presence of PI-103. In contrast, treatment with PI-103 increased the G2 fraction in irradiated MO59K cells. CONCLUSIONS The triple-target inhibitor PI-103 exerted radiosensitization on MO59K cells, but, unexpectedly, caused radioresistance in the MO59J line, lacking DNA-PK. The difference is most likely due to low expression of the DNA-PK substrate p53 in MO59J cells, which was further reduced by PI-103. This led to less apoptosis as compared to drug-free MO59J cells and enhanced survival via partially abolished cell-cycle arrest. The findings suggest that the lack of DNA-PK-dependent NHEJ in MO59J line might be compensated by DNA-PK independent DSB repair via a yet unknown mechanism.
Collapse
Affiliation(s)
- Cholpon S Djuzenova
- Department of Radiation Oncology, University Hospital of Würzburg, Josef-Schneider-Strasse 11, 97080, Würzburg, Germany.
| | - Thomas Fischer
- Department of Radiation Oncology, University Hospital of Würzburg, Josef-Schneider-Strasse 11, 97080, Würzburg, Germany
| | - Astrid Katzer
- Department of Radiation Oncology, University Hospital of Würzburg, Josef-Schneider-Strasse 11, 97080, Würzburg, Germany
| | - Dmitri Sisario
- Department of Biotechnology and Biophysics, University of Würzburg, Würzburg, Germany
| | - Tessa Korsa
- Department of Biotechnology and Biophysics, University of Würzburg, Würzburg, Germany
| | - Gudrun Steussloff
- Department of Radiation Oncology, University Hospital of Würzburg, Josef-Schneider-Strasse 11, 97080, Würzburg, Germany
| | - Vladimir L Sukhorukov
- Department of Biotechnology and Biophysics, University of Würzburg, Würzburg, Germany
| | - Michael Flentje
- Department of Radiation Oncology, University Hospital of Würzburg, Josef-Schneider-Strasse 11, 97080, Würzburg, Germany
| |
Collapse
|
24
|
Feng W, Simpson DA, Cho JE, Carvajal-Garcia J, Smith CM, Headley KM, Hathaway N, Ramsden DA, Gupta GP. Marker-free quantification of repair pathway utilization at Cas9-induced double-strand breaks. Nucleic Acids Res 2021; 49:5095-5105. [PMID: 33963863 PMCID: PMC8136827 DOI: 10.1093/nar/gkab299] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2020] [Revised: 03/24/2021] [Accepted: 05/05/2021] [Indexed: 12/14/2022] Open
Abstract
Genome integrity and genome engineering require efficient repair of DNA double-strand breaks (DSBs) by non-homologous end joining (NHEJ), homologous recombination (HR), or alternative end-joining pathways. Here we describe two complementary methods for marker-free quantification of DSB repair pathway utilization at Cas9-targeted chromosomal DSBs in mammalian cells. The first assay features the analysis of amplicon next-generation sequencing data using ScarMapper, an iterative break-associated alignment algorithm to classify individual repair products based on deletion size, microhomology usage, and insertions. The second assay uses repair pathway-specific droplet digital PCR assays ('PathSig-dPCR') for absolute quantification of signature DSB repair outcomes. We show that ScarMapper and PathSig-dPCR enable comprehensive assessment of repair pathway utilization in different cell models, after a variety of experimental perturbations. We use these assays to measure the differential impact of DNA end resection on NHEJ, HR and polymerase theta-mediated end joining (TMEJ) repair. These approaches are adaptable to any cellular model system and genomic locus where Cas9-mediated targeting is feasible. Thus, ScarMapper and PathSig-dPCR allow for systematic fate mapping of a targeted DSB with facile and accurate quantification of DSB repair pathway choice at endogenous chromosomal loci.
Collapse
Affiliation(s)
- Wanjuan Feng
- Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, NC 27599, USA
| | - Dennis A Simpson
- Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, NC 27599, USA
| | - Jang-Eun Cho
- Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, NC 27599, USA
| | - Juan Carvajal-Garcia
- Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, NC 27599, USA.,Curriculum in Genetics and Molecular Biology, University of North Carolina, Chapel Hill, NC 27599, USA.,Biological and Biomedical Sciences Program, University of North Carolina, Chapel Hill, NC 27599, USA
| | - Chelsea M Smith
- Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, NC 27599, USA.,Biological and Biomedical Sciences Program, University of North Carolina, Chapel Hill, NC 27599, USA
| | - Kathryn M Headley
- School of Pharmacy, University of North Carolina, Chapel Hill, NC 27599, USA
| | - Nate Hathaway
- School of Pharmacy, University of North Carolina, Chapel Hill, NC 27599, USA
| | - Dale A Ramsden
- Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, NC 27599, USA.,Department of Biochemistry and Biophysics, University of North Carolina, Chapel Hill, NC 27599, USA
| | - Gaorav P Gupta
- Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, NC 27599, USA.,Department of Biochemistry and Biophysics, University of North Carolina, Chapel Hill, NC 27599, USA.,Department of Radiation Oncology, University of North Carolina, Chapel Hill, NC 27599, USA
| |
Collapse
|
25
|
Effect of Reducing Ataxia-Telangiectasia Mutated (ATM) in Experimental Autosomal Dominant Polycystic Kidney Disease. Cells 2021; 10:cells10030532. [PMID: 33802342 PMCID: PMC8000896 DOI: 10.3390/cells10030532] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2021] [Revised: 02/15/2021] [Accepted: 02/25/2021] [Indexed: 12/20/2022] Open
Abstract
The DNA damage response (DDR) pathway is upregulated in autosomal dominant polycystic kidney disease (ADPKD) but its functional role is not known. The ataxia-telangiectasia mutated (ATM) and AT and Rad3-related (ATR) protein kinases are key proximal transducers of the DDR. This study hypothesized that reducing either ATM or ATR attenuates kidney cyst formation and growth in experimental ADPKD. In vitro, pharmacological ATM inhibition by AZD0156 reduced three-dimensional cyst growth in MDCK and human ADPKD cells by up to 4.4- and 4.1-fold, respectively. In contrast, the ATR inhibitor, VE-821, reduced in vitro MDCK cyst growth but caused dysplastic changes. In vivo, treatment with AZD0156 by oral gavage for 10 days reduced renal cell proliferation and increased p53 expression in Pkd1RC/RC mice (a murine genetic ortholog of ADPKD). However, the progression of cystic kidney disease in Pkd1RC/RC mice was not altered by genetic ablation of ATM from birth, in either heterozygous (Pkd1RC/RC/Atm+/−) or homozygous (Pkd1RC/RC/Atm−/−) mutant mice at 3 months. In conclusion, despite short-term effects on reducing renal cell proliferation, chronic progression was not altered by reducing ATM in vivo, suggesting that this DDR kinase is dispensable for kidney cyst formation in ADPKD.
Collapse
|
26
|
Luong TMH, Matsuda K, Niino D, Kurohama H, Ito M, Nakashima M. Significance of abnormal 53BP1 expression as a novel molecular pathologic parameter of follicular-shaped B-cell lymphoid lesions in human digestive tract. Sci Rep 2021; 11:3074. [PMID: 33542453 PMCID: PMC7862599 DOI: 10.1038/s41598-021-82867-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2020] [Accepted: 01/19/2021] [Indexed: 11/24/2022] Open
Abstract
The digestive tract is a common site of extranodal malignant lymphomas (MLs) and benign lymphoid lesions (BLs). TP53-binding protein 1 (53BP1) expression has been widely investigated in class switch recombination but rarely in human lymphoid tissues with respect to tumorigenesis. We previously reported that immunofluorescence (IF) analysis of 53BP1 nuclear foci (NF), reflecting DNA double strand breaks, is useful for estimating genomic instability in different tumor types. In this study, we evaluated the potential of IF-based analysis of 53BP1 expression in differentiating MLs from BLs. We examined 231 biopsied tissue samples of primary MLs and BLs in the digestive tract. The 53BP1 immunoreactivity pattern was determined by multicolor IF. Compared to BLs, MLs showed a high frequency of abnormal 53BP1 expression (p < 0.0001). Statistically, abnormal 53BP1 expression is an effective test for distinguishing follicular lymphomas from BLs (specificity 98.6%, sensitivity 86.8%) and for distinguishing small B-cell lymphomas from BLs (specificity 98.3%, sensitivity 77.6%). Furthermore, a high frequency of abnormal 53BP1 expression was associated with “high-risk” MALT lymphomas, which exhibited t(11;18)(q21;21) (p = 0.0145). Collectively, these results suggest that IF-based analysis of 53BP1 expression in biopsy samples is a promising technique for diagnosing MLs in the digestive system.
Collapse
Affiliation(s)
- Thi My Hanh Luong
- Department of Tumor and Diagnostic Pathology, Atomic Bomb Disease Institute, Nagasaki University Graduate School of Biomedical Sciences, 1-12-4 Sakamoto, Nagasaki, 852-8523, Japan
| | - Katsuya Matsuda
- Department of Tumor and Diagnostic Pathology, Atomic Bomb Disease Institute, Nagasaki University Graduate School of Biomedical Sciences, 1-12-4 Sakamoto, Nagasaki, 852-8523, Japan
| | - Daisuke Niino
- Department of Pathology, Local Incorporated Administrative Agency Sasebo City General Hospital, Sasebo, Japan
| | - Hirokazu Kurohama
- Department of Tumor and Diagnostic Pathology, Atomic Bomb Disease Institute, Nagasaki University Graduate School of Biomedical Sciences, 1-12-4 Sakamoto, Nagasaki, 852-8523, Japan
| | - Masahiro Ito
- Department of Pathology, National Hospital Organization Nagasaki Medical Center, Omura, Japan
| | - Masahiro Nakashima
- Department of Tumor and Diagnostic Pathology, Atomic Bomb Disease Institute, Nagasaki University Graduate School of Biomedical Sciences, 1-12-4 Sakamoto, Nagasaki, 852-8523, Japan.
| |
Collapse
|
27
|
Eki R, She J, Parlak M, Benamar M, Du KP, Kumar P, Abbas T. A robust CRISPR-Cas9-based fluorescent reporter assay for the detection and quantification of DNA double-strand break repair. Nucleic Acids Res 2020; 48:e126. [PMID: 33068408 PMCID: PMC7708081 DOI: 10.1093/nar/gkaa897] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2020] [Revised: 09/25/2020] [Accepted: 09/30/2020] [Indexed: 12/30/2022] Open
Abstract
DNA double-strand breaks (DSBs) are highly cytotoxic lesions that can lead to chromosome rearrangements, genomic instability and cell death. Consequently, cells have evolved multiple mechanisms to efficiently repair DSBs to preserve genomic integrity. We have developed a DSB repair assay system, designated CDDR (CRISPR-Cas9-based Dual-fluorescent DSB Repair), that enables the detection and quantification of DSB repair outcomes in mammalian cells with high precision. CDDR is based on the introduction and subsequent resolution of one or two DSB(s) in an intrachromosomal fluorescent reporter following the expression of Cas9 and sgRNAs targeting the reporter. CDDR can discriminate between high-fidelity (HF) and error-prone non-homologous end-joining (NHEJ), as well as between proximal and distal NHEJ repair. Furthermore, CDDR can detect homology-directed repair (HDR) with high sensitivity. Using CDDR, we found HF-NHEJ to be strictly dependent on DNA Ligase IV, XRCC4 and XLF, members of the canonical branch of NHEJ pathway (c-NHEJ). Loss of these genes also stimulated HDR, and promoted error-prone distal end-joining. Deletion of the DNA repair kinase ATM, on the other hand, stimulated HF-NHEJ and suppressed HDR. These findings demonstrate the utility of CDDR in characterizing the effect of repair factors and in elucidating the balance between competing DSB repair pathways.
Collapse
Affiliation(s)
- Rebeka Eki
- Department of Radiation Oncology, University of Virginia, Charlottesville, VA 22908, USA.,Department of Biochemistry and Molecular Genetics, University of Virginia, Charlottesville, VA 22908, USA.,Center for Cell Signaling, University of Virginia, Charlottesville, VA 22908, USA
| | - Jane She
- Department of Radiation Oncology, University of Virginia, Charlottesville, VA 22908, USA
| | - Mahmut Parlak
- Department of Radiation Oncology, University of Virginia, Charlottesville, VA 22908, USA
| | - Mouadh Benamar
- Department of Radiation Oncology, University of Virginia, Charlottesville, VA 22908, USA.,Department of Biochemistry and Molecular Genetics, University of Virginia, Charlottesville, VA 22908, USA.,Center for Cell Signaling, University of Virginia, Charlottesville, VA 22908, USA
| | - Kang-Ping Du
- Department of Radiation Oncology, University of Virginia, Charlottesville, VA 22908, USA
| | - Pankaj Kumar
- Department of Biochemistry and Molecular Genetics, University of Virginia, Charlottesville, VA 22908, USA
| | - Tarek Abbas
- Department of Radiation Oncology, University of Virginia, Charlottesville, VA 22908, USA.,Department of Biochemistry and Molecular Genetics, University of Virginia, Charlottesville, VA 22908, USA.,Center for Cell Signaling, University of Virginia, Charlottesville, VA 22908, USA.,Cancer Center, University of Virginia, Charlottesville, VA 22908, USA
| |
Collapse
|
28
|
Castañeda-Zegarra S, Fernandez-Berrocal M, Tkachov M, Yao R, Upfold NLE, Oksenych V. Genetic interaction between the non-homologous end-joining factors during B and T lymphocyte development: In vivo mouse models. Scand J Immunol 2020; 92:e12936. [PMID: 32654175 DOI: 10.1111/sji.12936] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2020] [Revised: 06/07/2020] [Accepted: 07/06/2020] [Indexed: 12/16/2022]
Abstract
Non-homologous end joining (NHEJ) is the main DNA repair mechanism for the repair of double-strand breaks (DSBs) throughout the course of the cell cycle. DSBs are generated in developing B and T lymphocytes during V(D)J recombination to increase the repertoire of B and T cell receptors. DSBs are also generated during the class switch recombination (CSR) process in mature B lymphocytes, providing distinct effector functions of antibody heavy chain constant regions. Thus, NHEJ is important for both V(D)J recombination and CSR. NHEJ comprises core Ku70 and Ku80 subunits that form the Ku heterodimer, which binds DSBs and promotes the recruitment of accessory factors (e.g., DNA-PKcs, Artemis, PAXX, MRI) and downstream core factors (XLF, Lig4 and XRCC4). In recent decades, new NHEJ proteins have been reported, increasing complexity of this molecular pathway. Numerous in vivo mouse models have been generated and characterized to identify the interplay of NHEJ factors and their role in development of adaptive immune system. This review summarizes the currently available mouse models lacking one or several NHEJ factors, with a particular focus on early B cell development. We also underline genetic interactions and redundancy in the NHEJ pathway in mice.
Collapse
Affiliation(s)
- Sergio Castañeda-Zegarra
- Department of Clinical and Molecular Medicine (IKOM), Norwegian University of Science and Technology, Trondheim, Norway.,St. Olavs Hospital, Clinic of Medicine, Trondheim University Hospital, Trondheim, Norway
| | - Marion Fernandez-Berrocal
- Department of Clinical and Molecular Medicine (IKOM), Norwegian University of Science and Technology, Trondheim, Norway.,St. Olavs Hospital, Clinic of Medicine, Trondheim University Hospital, Trondheim, Norway.,Behavioural Neurobiology MS Program, Theodor-Boveri-Institute, Biocenter, University of Würzburg, Würzburg, Germany
| | - Max Tkachov
- Department of Clinical and Molecular Medicine (IKOM), Norwegian University of Science and Technology, Trondheim, Norway.,St. Olavs Hospital, Clinic of Medicine, Trondheim University Hospital, Trondheim, Norway
| | - Rouan Yao
- Department of Clinical and Molecular Medicine (IKOM), Norwegian University of Science and Technology, Trondheim, Norway.,St. Olavs Hospital, Clinic of Medicine, Trondheim University Hospital, Trondheim, Norway
| | - Nikki Lyn Esnardo Upfold
- Department of Clinical and Molecular Medicine (IKOM), Norwegian University of Science and Technology, Trondheim, Norway.,St. Olavs Hospital, Clinic of Medicine, Trondheim University Hospital, Trondheim, Norway
| | - Valentyn Oksenych
- Department of Clinical and Molecular Medicine (IKOM), Norwegian University of Science and Technology, Trondheim, Norway.,St. Olavs Hospital, Clinic of Medicine, Trondheim University Hospital, Trondheim, Norway.,Department of Biosciences and Nutrition (BioNut), Karolinska Institutet, Huddinge, Sweden.,Department of Clinical Medicine, Faculty of Health Sciences, UiT-The Arctic University of Norway, Tromsø, Norway
| |
Collapse
|
29
|
DNA-PKcs phosphorylation at the T2609 cluster alters the repair pathway choice during immunoglobulin class switch recombination. Proc Natl Acad Sci U S A 2020; 117:22953-22961. [PMID: 32868446 DOI: 10.1073/pnas.2007455117] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
The DNA-dependent protein kinase (DNA-PK), which is composed of the KU heterodimer and the large catalytic subunit (DNA-PKcs), is a classical nonhomologous end-joining (cNHEJ) factor. Naïve B cells undergo class switch recombination (CSR) to generate antibodies with different isotypes by joining two DNA double-strand breaks at different switching regions via the cNHEJ pathway. DNA-PK and the cNHEJ pathway play important roles in the DNA repair phase of CSR. To initiate cNHEJ, KU binds to DNA ends and recruits and activates DNA-PK. Activated DNA-PK phosphorylates DNA-PKcs at the S2056 and T2609 clusters. Loss of T2609 cluster phosphorylation increases radiation sensitivity but whether T2609 phosphorylation has a role in physiological DNA repair remains elusive. Using the DNA-PKcs 5A mouse model carrying alanine substitutions at the T2609 cluster, here we show that loss of T2609 phosphorylation of DNA-PKcs does not affect the CSR efficiency. Yet, the CSR junctions recovered from DNA-PKcs 5A/5A B cells reveal increased chromosomal translocations, extensive use of distal switch regions (consistent with end resection), and preferential usage of microhomology-all signs of the alternative end-joining pathway. Thus, these results uncover a role of DNA-PKcs T2609 phosphorylation in promoting cNHEJ repair pathway choice during CSR.
Collapse
|
30
|
Farhat T, Dudakovic A, Chung JH, van Wijnen AJ, St-Arnaud R. Inhibition of the catalytic subunit of DNA-dependent protein kinase (DNA-PKcs) stimulates osteoblastogenesis by potentiating bone morphogenetic protein 2 (BMP2) responses. J Cell Physiol 2020; 236:1195-1213. [PMID: 32686190 DOI: 10.1002/jcp.29927] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2020] [Revised: 06/03/2020] [Accepted: 07/01/2020] [Indexed: 12/13/2022]
Abstract
The catalytic subunit of DNA-dependent protein kinase (DNA-PKcs) is a pleiotropic enzyme involved in DNA repair, cell cycle control, and transcription regulation. A potential role for DNA-PKcs in the regulation of osteoblastogenesis remains to be established. We show that pharmacological inhibition of DNA-PKcs kinase activity or gene silencing of Prkdc (encoding DNA-PKcs) in murine osteoblastic MC3T3-E1 cells and human adipose-derived mesenchymal stromal cells markedly enhanced osteogenesis and the expression of osteoblast differentiation marker genes. Inhibition of DNA-PKcs inhibited cell cycle progression and increased osteogenesis by significantly enhancing the bone morphogenetic protein 2 response in osteoblasts and other mesenchymal cell types. Importantly, in vivo pharmacological inhibition of the kinase enhanced bone biomechanical properties. Bones from osteoblast-specific conditional Prkdc-knockout mice exhibited a similar phenotype of increased stiffness. In conclusion, DNA-PKcs negatively regulates osteoblast differentiation, and therefore DNA-PKcs inhibitors may have therapeutic potential for bone regeneration and metabolic bone diseases.
Collapse
Affiliation(s)
- Theresa Farhat
- Research Centre, Shriners Hospital for Children - Canada, Montreal, Quebec, Canada.,Department of Human Genetics, McGill University, Montreal, Quebec, Canada
| | - Amel Dudakovic
- Department of Orthopedic Surgery, Mayo Clinic, Rochester, Minnesota.,Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, Minnesota
| | - Jay H Chung
- Laboratory of Obesity & Aging Research, Genetics and Developmental Biology Center, National Heart Lung and Blood Institute (NIH), Bethesda, Maryland
| | - Andre J van Wijnen
- Department of Orthopedic Surgery, Mayo Clinic, Rochester, Minnesota.,Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, Minnesota
| | - René St-Arnaud
- Research Centre, Shriners Hospital for Children - Canada, Montreal, Quebec, Canada.,Department of Human Genetics, McGill University, Montreal, Quebec, Canada.,Department of Surgery, McGill University, Montreal, Quebec, Canada.,Department of Medicine, McGill University, Montreal, Quebec, Canada
| |
Collapse
|
31
|
Wang XS, Lee BJ, Zha S. The recent advances in non-homologous end-joining through the lens of lymphocyte development. DNA Repair (Amst) 2020; 94:102874. [PMID: 32623318 DOI: 10.1016/j.dnarep.2020.102874] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2020] [Revised: 05/16/2020] [Accepted: 05/24/2020] [Indexed: 12/17/2022]
Abstract
Lymphocyte development requires ordered assembly and subsequent modifications of the antigen receptor genes through V(D)J recombination and Immunoglobulin class switch recombination (CSR), respectively. While the programmed DNA cleavage events are initiated by lymphocyte-specific factors, the resulting DNA double-strand break (DSB) intermediates activate the ATM kinase-mediated DNA damage response (DDR) and rely on the ubiquitously expressed classical non-homologous end-joining (cNHEJ) pathway including the DNA-dependent protein kinase (DNA-PK), and, in the case of CSR, also the alternative end-joining (Alt-EJ) pathway, for repair. Correspondingly, patients and animal models with cNHEJ or DDR defects develop distinct types of immunodeficiency reflecting their specific DNA repair deficiency. The unique end-structure, sequence context, and cell cycle regulation of V(D)J recombination and CSR also provide a valuable platform to study the mechanisms of, and the interplay between, cNHEJ and DDR. Here, we compare and contrast the genetic consequences of DNA repair defects in V(D)J recombination and CSR with a focus on the newly discovered cNHEJ factors and the kinase-dependent structural roles of ATM and DNA-PK in animal models. Throughout, we try to highlight the pending questions and emerging differences that will extend our understanding of cNHEJ and DDR in the context of primary immunodeficiency and lymphoid malignancies.
Collapse
Affiliation(s)
- Xiaobin S Wang
- Institute for Cancer Genetics, Vagelos College of Physicians and Surgeons, Columbia University, New York City, NY 10032, United States; Graduate Program of Pathobiology and Molecular Medicine, Vagelos College of Physicians and Surgeons, Columbia University, New York City, NY 10032, United States
| | - Brian J Lee
- Institute for Cancer Genetics, Vagelos College of Physicians and Surgeons, Columbia University, New York City, NY 10032, United States
| | - Shan Zha
- Institute for Cancer Genetics, Vagelos College of Physicians and Surgeons, Columbia University, New York City, NY 10032, United States; Department of Pediatrics, Vagelos College of Physicians and Surgeons, Columbia University, New York City, NY 10032, United States; Department of Pathology and Cell Biology, Vagelos College of Physicians and Surgeons, Columbia University, New York City, NY 10032, United States; Department of Immunology and Microbiology, Vagelos College of Physicians and Surgeons, Columbia University, New York City, NY 10032, United States.
| |
Collapse
|
32
|
Triptolide impairs genome integrity by directly blocking the enzymatic activity of DNA-PKcs in human cells. Biomed Pharmacother 2020; 129:110427. [PMID: 32574974 DOI: 10.1016/j.biopha.2020.110427] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2020] [Revised: 06/09/2020] [Accepted: 06/13/2020] [Indexed: 01/02/2023] Open
Abstract
Triptolide is a multi-functional natural small molecular compound extracted from a traditional Chinese medicinal herb. Triptolide and its derivatives exhibit cytotoxicity through inducing DNA damage, therefore increasing sensitivity to DNA-damage based chemotherapy or radiotherapy in different types of cells. However, the regulatory mechanism of genotoxicity by triptolide, and the loss of genome integrity induced by triptolide are not fully understood. Here, we measured the effects of triptolide on genome integrity in a human fibroblast line HCA2-hTERT using the neutral comet assay. We demonstrated that treating cells with triptolide induced genomic instability in HCA2-hTERT cells. Furthermore, we observed the accumulation of γH2AX foci in triptolide treated cells than control cells at 24 h post ionizing radiation. Further mechanistic studies indicated that triptolide inhibited the enzymatic activity of DNA-PKcs, the critical nonhomologous end joining factor. In vitro kinase activity assays showed that triptolide suppressed the kinase activity of DNA-PKcs and molecular docking also predicted a potential interaction between triptolide and DNA-PKcs. As a consequence, we found that triptolide treatment enhanced the interaction between DNA-PKcs and KU80 and hampered the following recruitment of 53BP1. Altogether, our finding provides a new perspective about the toxicity of triptolide in non-cancer cells and highlights the necessity of taking genome effects of triptolide and its derivatives into consideration in the future clinical and research applications.
Collapse
|
33
|
Guo Z, Wang S, Xie Y, Han Y, Hu S, Guan H, Xie D, Bai C, Liu X, Gu Y, Zhou PK, Ma T. HUWE1-dependent DNA-PKcs neddylation modulates its autophosphorylation in DNA damage response. Cell Death Dis 2020; 11:400. [PMID: 32457294 PMCID: PMC7250858 DOI: 10.1038/s41419-020-2611-0] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2020] [Revised: 05/07/2020] [Accepted: 05/11/2020] [Indexed: 02/07/2023]
Abstract
DNA-dependent protein kinase catalytic subunit (DNA-PKcs) is the core component of DNA-PK complex in the non-homologous end-joining (NHEJ) repair of DNA double-strand breaks, and its activity is strictly controlled by DNA-PKcs phosphorylation. The ubiquitin-like protein, NEDD8 is involved in regulation of DNA damage response, but it remains mysterious whether and how NEDD8-related neddylation affects DNA-PKcs and the NHEJ process. Here, we show that DNA-PKcs is poly-neddylated at its kinase domain. The neddylation E2-conjugating enzyme UBE2M and E3 ligase HUWE1 (HECT, UBA, and WWE domain containing E3 ubiquitin protein ligase 1) are responsible for the DNA-PKcs neddylation. Moreover, inhibition of HUWE1-dependent DNA-PKcs neddylation impairs DNA-PKcs autophosphorylation at Ser2056. Finally, depletion of HUWE1-dependent DNA-PKcs neddylation reduces the efficiency of NHEJ. These studies provide insights how neddylation modulates the activity of NHEJ core complex.
Collapse
Affiliation(s)
- Zongpei Guo
- Department of Radiation Toxicology and Oncology, Beijing Key Laboratory for Radiobiology, Beijing Institute of Radiation Medicine, Beijing, 100850, P. R. China
| | - Shaozheng Wang
- Department of Radiation Toxicology and Oncology, Beijing Key Laboratory for Radiobiology, Beijing Institute of Radiation Medicine, Beijing, 100850, P. R. China
| | - Ying Xie
- Department of Radiation Toxicology and Oncology, Beijing Key Laboratory for Radiobiology, Beijing Institute of Radiation Medicine, Beijing, 100850, P. R. China
| | - Yang Han
- Department of Radiation Toxicology and Oncology, Beijing Key Laboratory for Radiobiology, Beijing Institute of Radiation Medicine, Beijing, 100850, P. R. China.,Institute for Environmental Medicine and Radiation Hygiene, School of Public Health, University of South China, Hengyang, Hunan Province, 421001, P. R. China
| | - Sai Hu
- Department of Radiation Toxicology and Oncology, Beijing Key Laboratory for Radiobiology, Beijing Institute of Radiation Medicine, Beijing, 100850, P. R. China.,Institute for Environmental Medicine and Radiation Hygiene, School of Public Health, University of South China, Hengyang, Hunan Province, 421001, P. R. China
| | - Hua Guan
- Department of Radiation Toxicology and Oncology, Beijing Key Laboratory for Radiobiology, Beijing Institute of Radiation Medicine, Beijing, 100850, P. R. China
| | - Dafei Xie
- Department of Radiation Toxicology and Oncology, Beijing Key Laboratory for Radiobiology, Beijing Institute of Radiation Medicine, Beijing, 100850, P. R. China
| | - Chenjun Bai
- Department of Radiation Toxicology and Oncology, Beijing Key Laboratory for Radiobiology, Beijing Institute of Radiation Medicine, Beijing, 100850, P. R. China
| | - Xiaodan Liu
- Department of Radiation Toxicology and Oncology, Beijing Key Laboratory for Radiobiology, Beijing Institute of Radiation Medicine, Beijing, 100850, P. R. China
| | - Yongqing Gu
- Department of Radiation Toxicology and Oncology, Beijing Key Laboratory for Radiobiology, Beijing Institute of Radiation Medicine, Beijing, 100850, P. R. China
| | - Ping-Kun Zhou
- Department of Radiation Toxicology and Oncology, Beijing Key Laboratory for Radiobiology, Beijing Institute of Radiation Medicine, Beijing, 100850, P. R. China. .,Institute for Environmental Medicine and Radiation Hygiene, School of Public Health, University of South China, Hengyang, Hunan Province, 421001, P. R. China.
| | - Teng Ma
- Department of Radiation Toxicology and Oncology, Beijing Key Laboratory for Radiobiology, Beijing Institute of Radiation Medicine, Beijing, 100850, P. R. China. .,Department of Cellular and Molecular Biology, Beijing Chest Hospital, Capital Medical University/Beijing Tuberculosis and Thoracic Tumor Research Institute, Beijing, 101149, P. R. China.
| |
Collapse
|
34
|
Eke I, Zong D, Aryankalayil MJ, Sandfort V, Bylicky MA, Rath BH, Graves EE, Nussenzweig A, Coleman CN. 53BP1/RIF1 signaling promotes cell survival after multifractionated radiotherapy. Nucleic Acids Res 2020; 48:1314-1326. [PMID: 31822909 DOI: 10.1093/nar/gkz1139] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2019] [Revised: 10/30/2019] [Accepted: 12/02/2019] [Indexed: 12/20/2022] Open
Abstract
Multifractionated irradiation is the mainstay of radiation treatment in cancer therapy. Yet, little is known about the cellular DNA repair processes that take place between radiation fractions, even though understanding the molecular mechanisms promoting cancer cell recovery and survival could improve patient outcome and identify new avenues for targeted intervention. To address this knowledge gap, we systematically characterized how cells respond differentially to multifractionated and single-dose radiotherapy, using a combination of genetics-based and functional approaches. We found that both cancer cells and normal fibroblasts exhibited enhanced survival after multifractionated irradiation compared with an equivalent single dose of irradiation, and this effect was entirely dependent on 53BP1-mediated NHEJ. Furthermore, we identified RIF1 as the critical effector of 53BP1. Inhibiting 53BP1 recruitment to damaged chromatin completely abolished the survival advantage after multifractionated irradiation and could not be reversed by suppressing excessive end resection. Analysis of the TCGA database revealed lower expression of 53BP1 pathway genes in prostate cancer, suggesting that multifractionated radiotherapy might be a favorable option for radio-oncologic treatment in this tumor type. We propose that elucidation of DNA repair mechanisms elicited by different irradiation dosing regimens could improve radiotherapy selection for the individual patient and maximize the efficacy of radiotherapy.
Collapse
Affiliation(s)
- Iris Eke
- Radiation Oncology Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA.,Department of Radiation Oncology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Dali Zong
- Laboratory of Genome Integrity; National Cancer Institute; National Institutes of Health; Bethesda, MD 20892, USA
| | - Molykutty J Aryankalayil
- Radiation Oncology Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Veit Sandfort
- Department of Radiology and Imaging Sciences, Clinical Center, National Institutes of Health, Bethesda, MD 20892, USA
| | - Michelle A Bylicky
- Radiation Oncology Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Barbara H Rath
- Radiation Oncology Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Edward E Graves
- Department of Radiation Oncology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - André Nussenzweig
- Laboratory of Genome Integrity; National Cancer Institute; National Institutes of Health; Bethesda, MD 20892, USA
| | - C Norman Coleman
- Radiation Oncology Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA.,Radiation Research Program, National Cancer Institute, National Institutes of Health, Rockville, MD 20850, USA
| |
Collapse
|
35
|
Menolfi D, Zha S. ATM, ATR and DNA-PKcs kinases-the lessons from the mouse models: inhibition ≠ deletion. Cell Biosci 2020; 10:8. [PMID: 32015826 PMCID: PMC6990542 DOI: 10.1186/s13578-020-0376-x] [Citation(s) in RCA: 117] [Impact Index Per Article: 29.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2019] [Accepted: 01/14/2020] [Indexed: 01/11/2023] Open
Abstract
DNA damage, especially DNA double strand breaks (DSBs) and replication stress, activates a complex post-translational network termed DNA damage response (DDR). Our review focuses on three PI3-kinase related protein kinases-ATM, ATR and DNA-PKcs, which situate at the apex of the mammalian DDR. They are recruited to and activated at the DNA damage sites by their respective sensor protein complexes-MRE11/RAD50/NBS1 for ATM, RPA/ATRIP for ATR and KU70-KU80/86 (XRCC6/XRCC5) for DNA-PKcs. Upon activation, ATM, ATR and DNA-PKcs phosphorylate a large number of partially overlapping substrates to promote efficient and accurate DNA repair and to coordinate DNA repair with other DNA metabolic events (e.g., transcription, replication and mitosis). At the organism level, robust DDR is critical for normal development, aging, stem cell maintenance and regeneration, and physiological genomic rearrangements in lymphocytes and germ cells. In addition to endogenous damage, oncogene-induced replication stresses and genotoxic chemotherapies also activate DDR. On one hand, DDR factors suppress genomic instability to prevent malignant transformation. On the other hand, targeting DDR enhances the therapeutic effects of anti-cancer chemotherapy, which led to the development of specific kinase inhibitors for ATM, ATR and DNA-PKcs. Using mouse models expressing kinase dead ATM, ATR and DNA-PKcs, an unexpected structural function of these kinases was revealed, where the expression of catalytically inactive kinases causes more genomic instability than the loss of the proteins themselves. The spectrum of genomic instabilities and physiological consequences are unique for each kinase and depends on their activating complexes, suggesting a model in which the catalysis is coupled with DNA/chromatin release and catalytic inhibition leads to the persistence of the kinases at the DNA lesion, which in turn affects repair pathway choice and outcomes. Here we discuss the experimental evidences supporting this mode of action and their implications in the design and use of specific kinase inhibitors for ATM, ATR and DNA-PKcs for cancer therapy.
Collapse
Affiliation(s)
- Demis Menolfi
- Institute for Cancer Genetics, College of Physicians & Surgeons, Columbia University, New York, NY 10032 USA
| | - Shan Zha
- Institute for Cancer Genetics, College of Physicians & Surgeons, Columbia University, New York, NY 10032 USA
- Department of Pathology and Cell Biology, College of Physicians & Surgeons, Columbia University, New York, NY 10032 USA
- Division of Pediatric Oncology, Hematology and Stem Cell Transplantation, Department of Pediatrics, College of Physicians & Surgeons, Columbia University, New York, NY 10032 USA
| |
Collapse
|
36
|
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.
Collapse
|
37
|
Ferreira S, Dutreix M. DNA repair inhibitors to enhance radiotherapy: Progresses and limitations. Cancer Radiother 2019; 23:883-890. [PMID: 31615730 DOI: 10.1016/j.canrad.2019.08.008] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2019] [Revised: 08/29/2019] [Accepted: 08/31/2019] [Indexed: 02/08/2023]
Abstract
Radiotherapy is one of the most common form of treatment in oncology care. Indeed, radiotherapy proved to be very effective in treating a wide range of malignancies. Nevertheless, certain tumours are intrinsically radioresistant or may evolve to become radioresistant. Resistance to radiotherapy is often associated with dysregulated DNA damage response and repair. Recently, a number of strategies have been developed to improve radiotherapy efficacy by targeting the DNA damage response and repair pathways. Ongoing clinical trials showed the potential of some of these approaches in enhancing radiotherapy, but also highlighted the possible limitations. Here, we will describe (i) the main mechanisms involved in double-strand break repair; (ii) available strategies that target these DNA repair processes to improve radiotherapy and (iii) the clinical outcomes and challenges that have emerged so far.
Collapse
Affiliation(s)
- S Ferreira
- Centre universitaire, institut Curie, UMR « Etic », bâtiment 110, 91405 Orsay cedex, France; Université PSL, 91405 Orsay, France; CNRS, UMR 3347, 91405 Orsay, France; Inserm, UMR 3347, 91405 Orsay, France; Université Paris-Sud université Paris-Saclay, 91405 Orsay, France
| | - M Dutreix
- Centre universitaire, institut Curie, UMR « Etic », bâtiment 110, 91405 Orsay cedex, France; Université PSL, 91405 Orsay, France; CNRS, UMR 3347, 91405 Orsay, France; Inserm, UMR 3347, 91405 Orsay, France; Université Paris-Sud université Paris-Saclay, 91405 Orsay, France.
| |
Collapse
|
38
|
Lu H, Saha J, Beckmann PJ, Hendrickson EA, Davis AJ. DNA-PKcs promotes chromatin decondensation to facilitate initiation of the DNA damage response. Nucleic Acids Res 2019; 47:9467-9479. [PMID: 31396623 PMCID: PMC6765147 DOI: 10.1093/nar/gkz694] [Citation(s) in RCA: 57] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2019] [Revised: 07/29/2019] [Accepted: 07/31/2019] [Indexed: 11/14/2022] Open
Abstract
The DNA damage response (DDR) encompasses the cellular response to DNA double-stranded breaks (DSBs), and includes recognition of the DSB, recruitment of numerous factors to the DNA damage site, initiation of signaling cascades, chromatin remodeling, cell-cycle checkpoint activation, and repair of the DSB. Key drivers of the DDR are multiple members of the phosphatidylinositol 3-kinase-related kinase family, including ataxia telangiectasia mutated (ATM), ataxia telangiectasia and Rad3-related (ATR), and the DNA-dependent protein kinase catalytic subunit (DNA-PKcs). ATM and ATR modulate multiple portions of the DDR, but DNA-PKcs is believed to primarily function in the DSB repair pathway, non-homologous end joining. Utilizing a human cell line in which the kinase domain of DNA-PKcs is inactivated, we show here that DNA-PKcs kinase activity is required for the cellular response to DSBs immediately after their induction. Specifically, DNA-PKcs kinase activity initiates phosphorylation of the chromatin factors H2AX and KAP1 following ionizing radiation exposure and drives local chromatin decondensation near the DSB site. Furthermore, loss of DNA-PKcs kinase activity results in a marked decrease in the recruitment of numerous members of the DDR machinery to DSBs. Collectively, these results provide clear evidence that DNA-PKcs activity is pivotal for the initiation of the DDR.
Collapse
Affiliation(s)
- Huiming Lu
- Division of Molecular Radiation Biology, Department of Radiation Oncology, UT Southwestern Medical Center, Dallas, TX 75390, USA
| | - Janapriya Saha
- Division of Molecular Radiation Biology, Department of Radiation Oncology, UT Southwestern Medical Center, Dallas, TX 75390, USA
| | - Pauline J Beckmann
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota Medical School, Minneapolis, MN 55455, USA
| | - Eric A Hendrickson
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota Medical School, Minneapolis, MN 55455, USA
| | - Anthony J Davis
- Division of Molecular Radiation Biology, Department of Radiation Oncology, UT Southwestern Medical Center, Dallas, TX 75390, USA
| |
Collapse
|
39
|
Li W, Bai X, Li J, Zhao Y, Liu J, Zhao H, Liu L, Ding M, Wang Q, Shi FY, Hou M, Ji J, Gao G, Guo R, Sun Y, Liu Y, Xu D. The nucleoskeleton protein IFFO1 immobilizes broken DNA and suppresses chromosome translocation during tumorigenesis. Nat Cell Biol 2019; 21:1273-1285. [DOI: 10.1038/s41556-019-0388-0] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2019] [Accepted: 08/09/2019] [Indexed: 01/19/2023]
|
40
|
Lanz MC, Dibitetto D, Smolka MB. DNA damage kinase signaling: checkpoint and repair at 30 years. EMBO J 2019; 38:e101801. [PMID: 31393028 PMCID: PMC6745504 DOI: 10.15252/embj.2019101801] [Citation(s) in RCA: 151] [Impact Index Per Article: 30.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2019] [Revised: 07/03/2019] [Accepted: 07/24/2019] [Indexed: 12/27/2022] Open
Abstract
From bacteria to mammalian cells, damaged DNA is sensed and targeted by DNA repair pathways. In eukaryotes, kinases play a central role in coordinating the DNA damage response. DNA damage signaling kinases were identified over two decades ago and linked to the cell cycle checkpoint concept proposed by Weinert and Hartwell in 1988. Connections between the DNA damage signaling kinases and DNA repair were scant at first, and the initial perception was that the importance of these kinases for genome integrity was largely an indirect effect of their roles in checkpoints, DNA replication, and transcription. As more substrates of DNA damage signaling kinases were identified, it became clear that they directly regulate a wide range of DNA repair factors. Here, we review our current understanding of DNA damage signaling kinases, delineating the key substrates in budding yeast and humans. We trace the progress of the field in the last 30 years and discuss our current understanding of the major substrate regulatory mechanisms involved in checkpoint responses and DNA repair.
Collapse
Affiliation(s)
- Michael Charles Lanz
- Department of Molecular Biology and GeneticsWeill Institute for Cell and Molecular BiologyCornell UniversityIthacaNYUSA
| | - Diego Dibitetto
- Department of Molecular Biology and GeneticsWeill Institute for Cell and Molecular BiologyCornell UniversityIthacaNYUSA
| | - Marcus Bustamante Smolka
- Department of Molecular Biology and GeneticsWeill Institute for Cell and Molecular BiologyCornell UniversityIthacaNYUSA
| |
Collapse
|
41
|
Abstract
HIV-1 has evolved many strategies to circumvent the host’s antiviral innate immune responses and establishes disseminated infection; the molecular mechanisms of these strategies are not entirely clear. We showed previously that USP18 contributes to HIV-1 replication by abrogating p21 antiviral function. Here, we demonstrate a mechanism by which USP18 mediates p21 downregulation in myeloid cells. USP18, by its protease activity, accumulates misfolded p53, which requires ISG15 for clearance. Depletion of ISG15 causes accumulation of misfolded dominant negative p53, which supports HIV-1 replication. This work clarifies the function and consequences of p53 modification by ISG15 and implicates USP18 in HIV-1 infection and potentially in carcinogenesis. Macrophages and dendritic cells dominate early immune responses to lentiviruses. HIV-1 sensing by pathogen recognition receptors induces signaling cascades that culminate in type I alpha/beta interferon (IFN-α/β) induction. IFN-α/β signals back via the IFN-α/β receptors, inducing a plethora of IFN-stimulated gene (ISGs), including ISG15, p53, and p21Cip1. p21 inhibits HIV-1 replication by inactivating the deoxynucleoside triphosphate (dNTP) biosynthesis pathway and activating the restriction factor SAMHD1. p21 is induced by functional p53. ISG15-specific isopeptidase USP18 negatively regulates IFN signaling. We showed previously that USP18 contributes to HIV-1 replication by abrogating p21 antiviral function. Here, we demonstrate a mechanism by which USP18 mediates p21 downregulation in myeloid cells. USP18, by its protease activity, accumulates misfolded p53, which requires ISG15 for its degradation. Depletion of ISG15 causes accumulation of misfolded dominant negative p53, which enhances HIV-1 replication. This work clarifies the function and consequences of p53 modification by ISG15 and implicates USP18 in HIV-1 infection and potentially in carcinogenesis.
Collapse
|
42
|
Fang Z, Pan Z. Essential Role of Ubiquitin-Fold Modifier 1 Conjugation in DNA Damage Response. DNA Cell Biol 2019; 38:1030-1039. [PMID: 31368785 DOI: 10.1089/dna.2019.4861] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
Both endogenous and exogenous factors can cause DNA damage that compromises genomic integrity and cell viability. A proper DNA damage response (DDR) plays a role in maintaining genome stability and preventing tumorigenesis. DNA double-strand breaks (DSBs) are the most toxic DNA lesion, whose response is dominated by the ataxia-telangiectasia mutated (ATM) protein kinase. After being activated by the sensor Mre11-Rad50-Nbs1 (MRN) complex or acetyltransferase Tip60, ATM rapidly phosphorylates downstream targets to launch DDR signaling when DNA is damaged. However, the exact mechanism of DDR is complex and ambiguous. Ufmylation, one type of ubiquitin-like modification, proceeds mainly through a three-step enzymatic reaction to help ubiquitin-fold modifier 1 (Ufm1), attach to substrates with ubiquitin-like modifier-activating enzyme 5 (Uba5), Ufm1-conjugating enzyme 1 (Ufc1) and Ufm1-specific ligase 1 (Ufl1). Although ubiquitination is essential to the DSBs response, the potential function of ufmylation in DDR is largely unknown. Herein, we review the relationship between ufmylation and DDR to elucidate the function and mechanism of ufmylation in DDR, which would reveal the pathogenesis of some diseases and provide new guidance to create a therapeutic method.
Collapse
Affiliation(s)
- Zhi Fang
- Jiangxi Medical College, Nanchang University, Nanchang, China
| | - Zezheng Pan
- Faculty of Basic Medical Science, Jiangxi Medical College, Nanchang University, Nanchang, China
| |
Collapse
|
43
|
Xing M, Oksenych V. Genetic interaction between DNA repair factors PAXX, XLF, XRCC4 and DNA-PKcs in human cells. FEBS Open Bio 2019; 9:1315-1326. [PMID: 31141305 PMCID: PMC6609761 DOI: 10.1002/2211-5463.12681] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2019] [Revised: 05/03/2019] [Accepted: 05/28/2019] [Indexed: 01/26/2023] Open
Abstract
DNA double-strand breaks (DSBs) are highly cytotoxic lesions, and unrepaired or misrepaired DSBs can lead to various human diseases, including immunodeficiency, neurological abnormalities, growth retardation, and cancer. Nonhomologous end joining (NHEJ) is the major DSB repair pathway in mammals. Ku70 and Ku80 are DSB sensors that facilitate the recruitment of downstream factors, including protein kinase DNA-dependent protein kinase, catalytic subunit (DNA-PKcs), structural components [X-ray repair cross-complementing protein 4 (XRCC4), XRCC4-like factor (XLF), and paralogue of XRCC4 and XLF (PAXX)], and DNA ligase IV (LIG4), which complete DNA repair. DSBs also trigger the activation of the DNA damage response pathway, in which protein kinase ataxia-telangiectasia mutated (ATM) phosphorylates multiple substrates, including histone H2AX. Traditionally, research on NHEJ factors was performed using in vivo mouse models and murine cells. However, the current knowledge of the genetic interactions between NHEJ factors in human cells is incomplete. Here, we obtained genetically modified human HAP1 cell lines, which lacked one or two NHEJ factors, including LIG4, XRCC4, XLF, PAXX, DNA-PKcs, DNA-PKcs/XRCC4, and DNA-PKcs/PAXX. We examined the genomic instability of HAP1 cells, as well as their sensitivity to DSB-inducing agents. In addition, we determined the genetic interaction between XRCC4 paralogues (XRCC4, XLF, and PAXX) and DNA-PKcs. We found that in human cells, XLF, but not PAXX or XRCC4, genetically interacts with DNA-PKcs. Moreover, ATM possesses overlapping functions with DNA-PKcs, XLF, and XRCC4, but not with PAXX in response to DSBs. Finally, NHEJ-deficient HAP1 cells show increased chromosomal and chromatid breaks, when compared to the WT parental control. Overall, we found that HAP1 is a suitable model to study the genetic interactions in human cells.
Collapse
Affiliation(s)
- Mengtan Xing
- Department of Clinical and Molecular Medicine (IKOM), Norwegian University of Science and Technology, Trondheim, Norway
| | - Valentyn Oksenych
- Department of Clinical and Molecular Medicine (IKOM), Norwegian University of Science and Technology, Trondheim, Norway
| |
Collapse
|
44
|
Mladenov E, Fan X, Dueva R, Soni A, Iliakis G. Radiation-dose-dependent functional synergisms between ATM, ATR and DNA-PKcs in checkpoint control and resection in G 2-phase. Sci Rep 2019; 9:8255. [PMID: 31164689 PMCID: PMC6547644 DOI: 10.1038/s41598-019-44771-6] [Citation(s) in RCA: 42] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2019] [Accepted: 04/23/2019] [Indexed: 12/31/2022] Open
Abstract
Using data generated with cells exposed to ionizing-radiation (IR) in G2-phase of the cell cycle, we describe dose-dependent interactions between ATM, ATR and DNA-PKcs revealing unknown mechanistic underpinnings for two key facets of the DNA damage response: DSB end-resection and G2-checkpoint activation. At low IR-doses that induce low DSB-numbers in the genome, ATM and ATR regulate epistatically the G2-checkpoint, with ATR at the output-node, interfacing with the cell-cycle predominantly through Chk1. Strikingly, at low IR-doses, ATM and ATR epistatically regulate also resection, and inhibition of either activity fully suppresses resection. At high IR-doses that induce high DSB-numbers in the genome, the tight ATM/ATR coupling relaxes and independent outputs to G2-checkpoint and resection occur. Consequently, both kinases must be inhibited to fully suppress checkpoint activation and resection. DNA-PKcs integrates to the ATM/ATR module by regulating resection at all IR-doses, with defects in DNA-PKcs causing hyper-resection and G2-checkpoint hyper-activation. Notably, hyper-resection is absent from other c-NHEJ mutants. Thus, DNA-PKcs specifically regulates resection and adjusts the activation of the ATM/ATR module. We propose that selected DSBs are shepherd by DNA-PKcs from c-NHEJ to resection-dependent pathways for processing under the regulatory supervision of the ATM/ATR module.
Collapse
Affiliation(s)
- Emil Mladenov
- Institute of Medical Radiation Biology, University of Duisburg-Essen Medical School, 45122, Essen, Germany
| | - Xiaoxiang Fan
- Institute of Medical Radiation Biology, University of Duisburg-Essen Medical School, 45122, Essen, Germany
| | - Rositsa Dueva
- Institute of Medical Radiation Biology, University of Duisburg-Essen Medical School, 45122, Essen, Germany
| | - Aashish Soni
- Institute of Medical Radiation Biology, University of Duisburg-Essen Medical School, 45122, Essen, Germany
| | - George Iliakis
- Institute of Medical Radiation Biology, University of Duisburg-Essen Medical School, 45122, Essen, Germany.
| |
Collapse
|
45
|
ATM, DNA-PKcs and ATR: shaping development through the regulation of the DNA damage responses. ACTA ACUST UNITED AC 2019. [DOI: 10.1007/s42764-019-00003-9] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
|
46
|
Jiang W, Estes VM, Wang XS, Shao Z, Lee BJ, Lin X, Crowe JL, Zha S. Phosphorylation at S2053 in Murine (S2056 in Human) DNA-PKcs Is Dispensable for Lymphocyte Development and Class Switch Recombination. THE JOURNAL OF IMMUNOLOGY 2019; 203:178-187. [PMID: 31101667 DOI: 10.4049/jimmunol.1801657] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/21/2018] [Accepted: 04/22/2019] [Indexed: 11/19/2022]
Abstract
The classical nonhomologous end-joining (cNHEJ) pathway is a major DNA double-strand break repair pathway in mammalian cells and is required for lymphocyte development and maturation. The DNA-dependent protein kinase (DNA-PK) is a cNHEJ factor that encompasses the Ku70-Ku80 (KU) heterodimer and the large DNA-PK catalytic subunit (DNA-PKcs). In mouse models, loss of DNA-PKcs (DNA-PKcs-/- ) abrogates end processing (e.g., hairpin opening), but not end-ligation, whereas expression of the kinase-dead DNA-PKcs protein (DNA-PKcsKD/KD ) abrogates end-ligation, suggesting a kinase-dependent structural function of DNA-PKcs during cNHEJ. Lymphocyte development is abolished in DNA-PKcs-/- and DNA-PKcsKD/KD mice because of the requirement for both hairpin opening and end-ligation during V(D)J recombination. DNA-PKcs itself is the best-characterized substrate of DNA-PK. The S2056 cluster is the best-characterized autophosphorylation site in human DNA-PKcs. In this study, we show that radiation can induce phosphorylation of murine DNA-PKcs at the corresponding S2053. We also generated knockin mouse models with alanine- (DNA-PKcsPQR) or phospho-mimetic aspartate (DNA-PKcsSD) substitutions at the S2053 cluster. Despite moderate radiation sensitivity in the DNA-PKcsPQR/PQR fibroblasts and lymphocytes, both DNA-PKcsPQR/PQR and DNA-PKcsSD/SD mice retained normal kinase activity and underwent efficient V(D)J recombination and class switch recombination, indicating that phosphorylation at the S2053 cluster of murine DNA-PKcs (corresponding to S2056 of human DNA-PKcs), although important for radiation resistance, is dispensable for the end-ligation and hairpin-opening function of DNA-PK essential for lymphocyte development.
Collapse
Affiliation(s)
- Wenxia Jiang
- Institute for Cancer Genetics, Vagelos College of Physicians and Surgeons, Columbia University, New York, NY 10032
| | - Verna M Estes
- Institute for Cancer Genetics, Vagelos College of Physicians and Surgeons, Columbia University, New York, NY 10032
| | - Xiaobin S Wang
- Institute for Cancer Genetics, Vagelos College of Physicians and Surgeons, Columbia University, New York, NY 10032.,Graduate Program of Pathobiology and Molecular Medicine, Vagelos College of Physicians and Surgeons, Columbia University, New York, NY 10032
| | - Zhengping Shao
- Institute for Cancer Genetics, Vagelos College of Physicians and Surgeons, Columbia University, New York, NY 10032
| | - Brian J Lee
- Institute for Cancer Genetics, Vagelos College of Physicians and Surgeons, Columbia University, New York, NY 10032
| | - Xiaohui Lin
- Institute for Cancer Genetics, Vagelos College of Physicians and Surgeons, Columbia University, New York, NY 10032
| | - Jennifer L Crowe
- Institute for Cancer Genetics, Vagelos College of Physicians and Surgeons, Columbia University, New York, NY 10032.,Graduate Program of Pathobiology and Molecular Medicine, Vagelos College of Physicians and Surgeons, Columbia University, New York, NY 10032
| | - Shan Zha
- Institute for Cancer Genetics, Vagelos College of Physicians and Surgeons, Columbia University, New York, NY 10032; .,Division of Pediatric Oncology, Hematology and Stem Cell Transplantation, Department of Pediatrics, Vagelos College of Physicians and Surgeons, Columbia University, New York, NY 10032; and.,Department of Pathology and Cell Biology, Vagelos College of Physicians and Surgeons, Columbia University, New York, NY 10032
| |
Collapse
|
47
|
Minten EV, Yu DS. DNA Repair: Translation to the Clinic. Clin Oncol (R Coll Radiol) 2019; 31:303-310. [PMID: 30876709 DOI: 10.1016/j.clon.2019.02.007] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2019] [Revised: 02/18/2019] [Accepted: 02/20/2019] [Indexed: 12/18/2022]
Abstract
It has been well established that an accumulation of mutations in DNA, whether caused by external sources (e.g. ultraviolet light, radioactivity) or internal sources (e.g. metabolic by-products, such as reactive oxygen species), has the potential to cause a cell to undergo carcinogenesis and increase the risk for the development of cancer. Therefore, it is critically important for a cell to have the capacity to properly respond to and repair DNA damage as it occurs. The DNA damage response (DDR) describes a collection of DNA repair pathways that aid in the protection of genomic integrity by detecting myriad types of DNA damage and initiating the correct DNA repair pathway. In many instances, a deficiency in the DDR, whether inherited or spontaneously assumed, can increase the risk of carcinogenesis and ultimately tumorigenesis through the accumulation of mutations that fail to be properly repaired. Interestingly, although disruption of the DDR can lead to the initial genomic instability that can ultimately cause carcinogenesis, the DDR has also proven to be an invaluable target for anticancer drugs and therapies. Making matters more complicated, the DDR is also involved in the resistance to first-line cancer therapy. In this review, we will consider therapies already in use in the clinic and ongoing research into other avenues of treatment that target DNA repair pathways in cancer.
Collapse
Affiliation(s)
- E V Minten
- Department of Radiation Oncology, Emory University School of Medicine, Atlanta, GA, USA
| | - D S Yu
- Department of Radiation Oncology, Emory University School of Medicine, Atlanta, GA, USA.
| |
Collapse
|
48
|
Tal E, Alfo M, Zha S, Barzilai A, De Zeeuw CI, Ziv Y, Shiloh Y. Inactive Atm abrogates DSB repair in mouse cerebellum more than does Atm loss, without causing a neurological phenotype. DNA Repair (Amst) 2018; 72:10-17. [PMID: 30348496 DOI: 10.1016/j.dnarep.2018.10.001] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2018] [Revised: 09/22/2018] [Accepted: 10/04/2018] [Indexed: 12/11/2022]
Abstract
The genome instability syndrome, ataxia-telangiectasia (A-T) is caused by null mutations in the ATM gene, that lead to complete loss or inactivation of the gene's product, the ATM protein kinase. ATM is the primary mobilizer of the cellular response to DNA double-strand breaks (DSBs) - a broad signaling network in which many components are ATM targets. The major clinical feature of A-T is cerebellar atrophy, characterized by relentless loss of Purkinje and granule cells. In Atm-knockout (Atm-KO) mice, complete loss of Atm leads to a very mild neurological phenotype, suggesting that Atm loss is not sufficient to markedly abrogate cerebellar structure and function in this organism. Expression of inactive ("kinase-dead") Atm (AtmKD) in mice leads to embryonic lethality, raising the question of whether conditional expression of AtmKD in the murine nervous system would lead to a more pronounced neurological phenotype than Atm loss. We generated two mouse strains in which AtmKD was conditionally expressed as the sole Atm species: one in the CNS and one specifically in Purkinje cells. Focusing our analysis on Purkinje cells, the dynamics of DSB readouts indicated that DSB repair was delayed longer in the presence of AtmKD compared to Atm loss. However, both strains exhibited normal life span and displayed no gross cerebellar histological abnormalities or significant neurological phenotype. We conclude that the presence of AtmKD is indeed more harmful to DSB repair than Atm loss, but the murine central nervous system can reasonably tolerate the extent of this DSB repair impairment. Greater pressure needs to be exerted on genome stability to obtain a mouse model that recapitulates the severe A-T neurological phenotype.
Collapse
Affiliation(s)
- Efrat Tal
- The David and Inez Myers Laboratory for Cancer Research, Department of Human Molecular Genetics and Biochemistry, Sackler School of Medicine, New York, United States
| | - Marina Alfo
- The David and Inez Myers Laboratory for Cancer Research, Department of Human Molecular Genetics and Biochemistry, Sackler School of Medicine, New York, United States
| | - Shan Zha
- Institute for Cancer Genetics, Department of Pathology and Cell Biology, College of Physicians and Surgeons, Columbia University, New York, NY, United States
| | - Ari Barzilai
- Department of Neurobiology, George S. Wise Faculty of Life Sciences, and Sagol School of Neuroscience, Tel Aviv University, Tel Aviv, Israel
| | - Chris I De Zeeuw
- Department of Neuroscience, Erasmus Medical Center, Rotterdam, and the Royal Netherlands Academy of Art & Science, Amsterdam, Netherlands
| | - Yael Ziv
- The David and Inez Myers Laboratory for Cancer Research, Department of Human Molecular Genetics and Biochemistry, Sackler School of Medicine, New York, United States
| | - Yosef Shiloh
- The David and Inez Myers Laboratory for Cancer Research, Department of Human Molecular Genetics and Biochemistry, Sackler School of Medicine, New York, United States.
| |
Collapse
|
49
|
Bayley R, Blakemore D, Cancian L, Dumon S, Volpe G, Ward C, Almaghrabi R, Gujar J, Reeve N, Raghavan M, Higgs MR, Stewart GS, Petermann E, García P. MYBL2 Supports DNA Double Strand Break Repair in Hematopoietic Stem Cells. Cancer Res 2018; 78:5767-5779. [PMID: 30082276 DOI: 10.1158/0008-5472.can-18-0273] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2018] [Revised: 06/22/2018] [Accepted: 07/31/2018] [Indexed: 11/16/2022]
Abstract
Myelodysplastic syndromes (MDS) are a heterogeneous group of diseases characterized by blood cytopenias that occur as a result of somatic mutations in hematopoietic stem cells (HSC). MDS leads to ineffective hematopoiesis, and as many as 30% of patients progress to acute myeloid leukemia (AML). The mechanisms by which mutations accumulate in HSC during aging remain poorly understood. Here we identify a novel role for MYBL2 in DNA double-strand break (DSB) repair in HSC. In patients with MDS, low MYBL2 levels associated with and preceded transcriptional deregulation of DNA repair genes. Stem/progenitor cells from these patients display dysfunctional DSB repair kinetics after exposure to ionizing radiation (IR). Haploinsufficiency of Mybl2 in mice also led to a defect in the repair of DSBs induced by IR in HSC and was characterized by unsustained phosphorylation of the ATM substrate KAP1 and telomere fragility. Our study identifies MYBL2 as a crucial regulator of DSB repair and identifies MYBL2 expression levels as a potential biomarker to predict cellular response to genotoxic treatments in MDS and to identify patients with defects in DNA repair. Such patients with worse prognosis may require a different therapeutic regimen to prevent progression to AML.Significance: These findings suggest MYBL2 levels may be used as a biological biomarker to determine the DNA repair capacity of hematopoietic stem cells from patients with MDS and as a clinical biomarker to inform decisions regarding patient selection for treatments that target DNA repair.Graphical Abstract: http://cancerres.aacrjournals.org/content/canres/78/20/5767/F1.large.jpg Cancer Res; 78(20); 5767-79. ©2018 AACR.
Collapse
Affiliation(s)
- Rachel Bayley
- Institute of Cancer and Genomic Sciences, College of Medical and Dental Sciences, University of Birmingham, Birmingham, United Kingdom
| | - Daniel Blakemore
- Institute of Cancer and Genomic Sciences, College of Medical and Dental Sciences, University of Birmingham, Birmingham, United Kingdom
| | - Laila Cancian
- Institute of Cancer and Genomic Sciences, College of Medical and Dental Sciences, University of Birmingham, Birmingham, United Kingdom
| | - Stephanie Dumon
- Institute of Cancer and Genomic Sciences, College of Medical and Dental Sciences, University of Birmingham, Birmingham, United Kingdom
| | - Giacomo Volpe
- Institute of Cancer and Genomic Sciences, College of Medical and Dental Sciences, University of Birmingham, Birmingham, United Kingdom
| | - Carl Ward
- Institute of Cancer and Genomic Sciences, College of Medical and Dental Sciences, University of Birmingham, Birmingham, United Kingdom
| | - Ruba Almaghrabi
- Institute of Cancer and Genomic Sciences, College of Medical and Dental Sciences, University of Birmingham, Birmingham, United Kingdom
| | - Jidnyasa Gujar
- Institute of Cancer and Genomic Sciences, College of Medical and Dental Sciences, University of Birmingham, Birmingham, United Kingdom
| | - Natasha Reeve
- Institute of Cancer and Genomic Sciences, College of Medical and Dental Sciences, University of Birmingham, Birmingham, United Kingdom
| | - Manoj Raghavan
- Institute of Cancer and Genomic Sciences, College of Medical and Dental Sciences, University of Birmingham, Birmingham, United Kingdom.,Centre for Clinical Haematology, University Hospitals Birmingham NHS Foundation Trust, Queen Elizabeth Hospital, Queen Elizabeth Medical Centre, Birmingham, United Kingdom
| | - Martin R Higgs
- Institute of Cancer and Genomic Sciences, College of Medical and Dental Sciences, University of Birmingham, Birmingham, United Kingdom
| | - Grant S Stewart
- Institute of Cancer and Genomic Sciences, College of Medical and Dental Sciences, University of Birmingham, Birmingham, United Kingdom
| | - Eva Petermann
- Institute of Cancer and Genomic Sciences, College of Medical and Dental Sciences, University of Birmingham, Birmingham, United Kingdom
| | - Paloma García
- Institute of Cancer and Genomic Sciences, College of Medical and Dental Sciences, University of Birmingham, Birmingham, United Kingdom.
| |
Collapse
|
50
|
Kinase-dependent structural role of DNA-PKcs during immunoglobulin class switch recombination. Proc Natl Acad Sci U S A 2018; 115:8615-8620. [PMID: 30072430 DOI: 10.1073/pnas.1808490115] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
The catalytic subunit of DNA-dependent protein kinase (DNA-PKcs) is a classical nonhomologous end-joining (cNHEJ) factor. Loss of DNA-PKcs diminished mature B cell class switch recombination (CSR) to other isotypes, but not IgG1. Here, we show that expression of the kinase-dead DNA-PKcs (DNA-PKcsKD/KD ) severely compromises CSR to IgG1. High-throughput sequencing analyses of CSR junctions reveal frequent accumulation of nonproductive interchromosomal translocations, inversions, and extensive end resection in DNA-PKcsKD/KD , but not DNA-PKcs-/- , B cells. Meanwhile, the residual joints from DNA-PKcsKD/KD cells and the efficient Sµ-Sγ1 junctions from DNA-PKcs-/- B cells both display similar preferences for small (2-6 nt) microhomologies (MH). In DNA-PKcs-/- cells, Sµ-Sγ1 joints are more resistant to inversions and extensive resection than Sµ-Sε and Sµ-Sµ joints, providing a mechanism for the isotype-specific CSR defects. Together, our findings identify a kinase-dependent role of DNA-PKcs in suppressing MH-mediated end joining and a structural role of DNA-PKcs protein in the orientation of CSR.
Collapse
|