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Takada S, Weitering TJ, van Os NJH, Du L, Pico-Knijnenburg I, Kuipers TB, Mei H, Salzer E, Willemsen MAAP, Weemaes CMR, Pan-Hammarstrom Q, van der Burg M. Causative mechanisms and clinical impact of immunoglobulin deficiencies in ataxia telangiectasia. J Allergy Clin Immunol 2024; 153:1392-1405. [PMID: 38280573 DOI: 10.1016/j.jaci.2023.12.029] [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: 08/10/2023] [Revised: 12/07/2023] [Accepted: 12/19/2023] [Indexed: 01/29/2024]
Abstract
BACKGROUND Ataxia telangiectasia (AT) is characterized by cerebellar ataxia, telangiectasia, immunodeficiency, and increased cancer susceptibility and is caused by mutations in the ataxia telangiectasia mutated (ATM) gene. The immunodeficiency comprises predominantly immunoglobulin deficiency, mainly IgA and IgG2, with a variable severity. So far, the exact mechanisms underlying the immunoglobulin deficiency, especially the variable severity, remain unelucidated. OBJECTIVE We characterized the clinical impact of immunoglobulin deficiencies in AT and elucidated their mechanisms in AT. METHODS We analyzed long-term immunoglobulin levels, immunophenotyping, and survival time in our cohort (n = 87, median age 16 years; maximum 64 years). Somatic hypermutation and class-switch junctions in B cells were analyzed by next-generation sequencing. Furthermore, an in vitro class-switching induction assay was performed, followed by RNA sequencing, to assess the effect of ATM inhibition. RESULTS Only the hyper-IgM AT phenotype significantly worsened survival time, while IgA or IgG2 deficiencies did not. The immunoglobulin levels showed predominantly decreased IgG2 and IgA. Moreover, flow cytometric analysis demonstrated reduced naive B and T lymphocytes and a deficiency of class-switched IgG2 and IgA memory B cells. Somatic hypermutation frequencies were lowered in IgA- and IgG2-deficient patients, indicating hampered germinal center reaction. In addition, the microhomology of switch junctions was elongated, suggesting alternative end joining during class-switch DNA repair. The in vitro class switching and proliferation were negatively affected by ATM inhibition. RNA sequencing analysis showed that ATM inhibitor influenced expression of germinal center reaction genes. CONCLUSION Immunoglobulin deficiency in AT is caused by disturbed development of class-switched memory B cells. ATM deficiency affects both germinal center reaction and choice of DNA-repair pathway in class switching.
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Affiliation(s)
- Sanami Takada
- Department of Pediatrics, Laboratory for Pediatric Immunology, Willem-Alexander Children's Hospital, Leiden University Medical Center, Leiden, The Netherlands
| | - Thomas J Weitering
- Department of Pediatrics, Laboratory for Pediatric Immunology, Willem-Alexander Children's Hospital, Leiden University Medical Center, Leiden, The Netherlands
| | - Nienke J H van Os
- Department of Pediatric Neurology, Amalia Children's Hospital, Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, Nijmegen, The Netherlands; Department of Neurology, Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Likun Du
- Department of Biosciences and Nutrition, Karolinska Institute, Stockholm, Sweden
| | - Ingrid Pico-Knijnenburg
- Department of Pediatrics, Laboratory for Pediatric Immunology, Willem-Alexander Children's Hospital, Leiden University Medical Center, Leiden, The Netherlands
| | - Thomas B Kuipers
- Sequencing Analysis Support Core Department of Biomedical Data Sciences, Leiden University Medical Center, Leiden, The Netherlands
| | - Hailiang Mei
- Sequencing Analysis Support Core Department of Biomedical Data Sciences, Leiden University Medical Center, Leiden, The Netherlands
| | - Elisabeth Salzer
- Department of Pediatrics, Laboratory for Pediatric Immunology, Willem-Alexander Children's Hospital, Leiden University Medical Center, Leiden, The Netherlands
| | - Michèl A A P Willemsen
- Department of Pediatric Neurology, Amalia Children's Hospital, Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Corry M R Weemaes
- Department of Pediatrics, Amalia Children's Hospital, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Qiang Pan-Hammarstrom
- Department of Neurology, Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Mirjam van der Burg
- Department of Pediatrics, Laboratory for Pediatric Immunology, Willem-Alexander Children's Hospital, Leiden University Medical Center, Leiden, The Netherlands.
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Wang Y, Abolhassani H, Hammarström L, Pan-Hammarström Q. SARS-CoV-2 infection in patients with inborn errors of immunity due to DNA repair defects. Acta Biochim Biophys Sin (Shanghai) 2022; 54:836-846. [PMID: 35713311 PMCID: PMC9827799 DOI: 10.3724/abbs.2022071] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Clinical information on severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection in patients with inborn errors of immunity (IEI) during the current Coronavirus disease 2019 (COVID-19) pandemic is still limited. Proper DNA repair machinery is required for the development of the adaptive immune system, which provides specific and long-term protection against SARS-CoV-2. This review highlights the impact of SARS-CoV-2 infections on IEI patients with DNA repair disorders and summarizes susceptibility risk factors, pathogenic mechanisms, clinical manifestations and management strategies of COVID-19 in this special patient population.
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3
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Gullickson P, Xu YW, Niedernhofer LJ, Thompson EL, Yousefzadeh MJ. The Role of DNA Repair in Immunological Diversity: From Molecular Mechanisms to Clinical Ramifications. Front Immunol 2022; 13:834889. [PMID: 35432317 PMCID: PMC9010869 DOI: 10.3389/fimmu.2022.834889] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2021] [Accepted: 03/02/2022] [Indexed: 12/18/2022] Open
Abstract
An effective humoral immune response necessitates the generation of diverse and high-affinity antibodies to neutralize pathogens and their products. To generate this assorted immune repertoire, DNA damage is introduced at specific regions of the genome. Purposeful genotoxic insults are needed for the successful completion of multiple immunological diversity processes: V(D)J recombination, class-switch recombination, and somatic hypermutation. These three processes, in concert, yield a broad but highly specific immune response. This review highlights the importance of DNA repair mechanisms involved in each of these processes and the catastrophic diseases that arise from DNA repair deficiencies impacting immune system function. These DNA repair disorders underline not only the importance of maintaining genomic integrity for preventing disease but also for robust adaptive immunity.
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Crosstalk between Long Non Coding RNAs, microRNAs and DNA Damage Repair in Prostate Cancer: New Therapeutic Opportunities? Cancers (Basel) 2022; 14:cancers14030755. [PMID: 35159022 PMCID: PMC8834032 DOI: 10.3390/cancers14030755] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2021] [Revised: 01/20/2022] [Accepted: 01/21/2022] [Indexed: 02/04/2023] Open
Abstract
Simple Summary Non-coding RNAs are a type of genetic material that doesn’t make protein, but performs diverse regulatory functions. In prostate cancer, most treatments target proteins, and resistance to such therapies is common, leading to disease progression. Targeting non-coding RNAs may provide alterative treatment options and potentially overcome drug resistance. Major types of non-coding RNAs include tiny ‘microRNAs’ and much longer ‘long non-coding RNAs’. Scientific studies have shown that these form a major part of the human genome, and play key roles in altering gene activity and determining the fate of cells. Importantly, in cancer, their activity is altered. Recent evidence suggests that microRNAs and long non-coding RNAs play important roles in controlling response to DNA damage. In this review, we explore how different types of non-coding RNA interact to control cell DNA damage responses, and how this knowledge may be used to design better prostate cancer treatments and tests. Abstract It is increasingly appreciated that transcripts derived from non-coding parts of the human genome, such as long non-coding RNAs (lncRNAs) and microRNAs (miRNAs), are key regulators of biological processes both in normal physiology and disease. Their dysregulation during tumourigenesis has attracted significant interest in their exploitation as novel cancer therapeutics. Prostate cancer (PCa), as one of the most diagnosed malignancies and a leading cause of cancer-related death in men, continues to pose a major public health problem. In particular, survival of men with metastatic disease is very poor. Defects in DNA damage response (DDR) pathways culminate in genomic instability in PCa, which is associated with aggressive disease and poor patient outcome. Treatment options for metastatic PCa remain limited. Thus, researchers are increasingly targeting ncRNAs and DDR pathways to develop new biomarkers and therapeutics for PCa. Increasing evidence points to a widespread and biologically-relevant regulatory network of interactions between lncRNAs and miRNAs, with implications for major biological and pathological processes. This review summarises the current state of knowledge surrounding the roles of the lncRNA:miRNA interactions in PCa DDR, and their emerging potential as predictive and diagnostic biomarkers. We also discuss their therapeutic promise for the clinical management of PCa.
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Pálinkás HL, Pongor L, Balajti M, Nagy Á, Nagy K, Békési A, Bianchini G, Vértessy BG, Győrffy B. Primary Founder Mutations in the PRKDC Gene Increase Tumor Mutation Load in Colorectal Cancer. Int J Mol Sci 2022; 23:ijms23020633. [PMID: 35054819 PMCID: PMC8775830 DOI: 10.3390/ijms23020633] [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] [Subscribe] [Scholar Register] [Received: 10/19/2021] [Revised: 12/21/2021] [Accepted: 12/28/2021] [Indexed: 11/16/2022] Open
Abstract
The clonal composition of a malignant tumor strongly depends on cellular dynamics influenced by the asynchronized loss of DNA repair mechanisms. Here, our aim was to identify founder mutations leading to subsequent boosts in mutation load. The overall mutation burden in 591 colorectal cancer tumors was analyzed, including the mutation status of DNA-repair genes. The number of mutations was first determined across all patients and the proportion of genes having mutation in each percentile was ranked. Early mutations in DNA repair genes preceding a mutational expansion were designated as founder mutations. Survival analysis for gene expression was performed using microarray data with available relapse-free survival. Of the 180 genes involved in DNA repair, the top five founder mutations were in PRKDC (n = 31), ATM (n = 26), POLE (n = 18), SRCAP (n = 18), and BRCA2 (n = 15). PRKDC expression was 6.4-fold higher in tumors compared to normal samples, and higher expression led to longer relapse-free survival in 1211 patients (HR = 0.72, p = 4.4 × 10-3). In an experimental setting, the mutational load resulting from UV radiation combined with inhibition of PRKDC was analyzed. Upon treatments, the mutational load exposed a significant two-fold increase. Our results suggest PRKDC as a new key gene driving tumor heterogeneity.
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Affiliation(s)
- Hajnalka Laura Pálinkás
- Genome Metabolism Research Group, Institute of Enzymology, Research Centre for Natural Sciences, Magyar Tudósok Körútja 2, H-1117 Budapest, Hungary; (H.L.P.); (K.N.); (A.B.)
- Department of Applied Biotechnology and Food Sciences, BME Budapest University of Technology and Economics, Szt Gellért tér 4, H-1111 Budapest, Hungary
| | - Lőrinc Pongor
- TTK Lendület Cancer Biomarker Research Group, Institute of Enzymology, Research Centre for Natural Sciences, Magyar Tudósok Körútja 2, H-1117 Budapest, Hungary; (L.P.); (M.B.); (Á.N.)
- Department of Bioinformatics and 2nd Department of Pediatrics, Semmelweis University, Tűzoltó u. 7-9, H-1094 Budapest, Hungary
| | - Máté Balajti
- TTK Lendület Cancer Biomarker Research Group, Institute of Enzymology, Research Centre for Natural Sciences, Magyar Tudósok Körútja 2, H-1117 Budapest, Hungary; (L.P.); (M.B.); (Á.N.)
| | - Ádám Nagy
- TTK Lendület Cancer Biomarker Research Group, Institute of Enzymology, Research Centre for Natural Sciences, Magyar Tudósok Körútja 2, H-1117 Budapest, Hungary; (L.P.); (M.B.); (Á.N.)
- Department of Bioinformatics and 2nd Department of Pediatrics, Semmelweis University, Tűzoltó u. 7-9, H-1094 Budapest, Hungary
| | - Kinga Nagy
- Genome Metabolism Research Group, Institute of Enzymology, Research Centre for Natural Sciences, Magyar Tudósok Körútja 2, H-1117 Budapest, Hungary; (H.L.P.); (K.N.); (A.B.)
- Department of Applied Biotechnology and Food Sciences, BME Budapest University of Technology and Economics, Szt Gellért tér 4, H-1111 Budapest, Hungary
| | - Angéla Békési
- Genome Metabolism Research Group, Institute of Enzymology, Research Centre for Natural Sciences, Magyar Tudósok Körútja 2, H-1117 Budapest, Hungary; (H.L.P.); (K.N.); (A.B.)
- Department of Applied Biotechnology and Food Sciences, BME Budapest University of Technology and Economics, Szt Gellért tér 4, H-1111 Budapest, Hungary
| | - Giampaolo Bianchini
- Department of Medical Oncology, San Raffaele Scientific Institute, via Olgettina 60, 20132 Milan, Italy;
| | - Beáta G. Vértessy
- Genome Metabolism Research Group, Institute of Enzymology, Research Centre for Natural Sciences, Magyar Tudósok Körútja 2, H-1117 Budapest, Hungary; (H.L.P.); (K.N.); (A.B.)
- Department of Applied Biotechnology and Food Sciences, BME Budapest University of Technology and Economics, Szt Gellért tér 4, H-1111 Budapest, Hungary
- Correspondence: (B.G.V.); (B.G.)
| | - Balázs Győrffy
- TTK Lendület Cancer Biomarker Research Group, Institute of Enzymology, Research Centre for Natural Sciences, Magyar Tudósok Körútja 2, H-1117 Budapest, Hungary; (L.P.); (M.B.); (Á.N.)
- Department of Bioinformatics and 2nd Department of Pediatrics, Semmelweis University, Tűzoltó u. 7-9, H-1094 Budapest, Hungary
- Correspondence: (B.G.V.); (B.G.)
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Tessier TM, Dodge MJ, MacNeil KM, Evans AM, Prusinkiewicz MA, Mymryk JS. Almost famous: Human adenoviruses (and what they have taught us about cancer). Tumour Virus Res 2021; 12:200225. [PMID: 34500123 PMCID: PMC8449131 DOI: 10.1016/j.tvr.2021.200225] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2021] [Revised: 08/25/2021] [Accepted: 09/03/2021] [Indexed: 12/11/2022] Open
Abstract
Papillomaviruses, polyomaviruses and adenoviruses are collectively categorized as the small DNA tumour viruses. Notably, human adenoviruses were the first human viruses demonstrated to be able to cause cancer, albeit in non-human animal models. Despite their long history, no human adenovirus is a known causative agent of human cancers, unlike a subset of their more famous cousins, including human papillomaviruses and human Merkel cell polyomavirus. Nevertheless, seminal research using human adenoviruses has been highly informative in understanding the basics of cell cycle control, gene expression, apoptosis and cell differentiation. This review highlights the contributions of human adenovirus research in advancing our knowledge of the molecular basis of cancer.
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Affiliation(s)
- Tanner M Tessier
- Department of Microbiology and Immunology, The University of Western Ontario, London, ON, Canada
| | - Mackenzie J Dodge
- Department of Microbiology and Immunology, The University of Western Ontario, London, ON, Canada
| | - Katelyn M MacNeil
- Department of Microbiology and Immunology, The University of Western Ontario, London, ON, Canada
| | - Andris M Evans
- Department of Microbiology and Immunology, The University of Western Ontario, London, ON, Canada
| | - Martin A Prusinkiewicz
- Department of Microbiology and Immunology, The University of Western Ontario, London, ON, Canada
| | - Joe S Mymryk
- Department of Microbiology and Immunology, The University of Western Ontario, London, ON, Canada; Department of Otolaryngology, Head & Neck Surgery, The University of Western Ontario, London, ON, Canada; Department of Oncology, The University of Western Ontario, London, ON, Canada; London Regional Cancer Program, Lawson Health Research Institute, London, ON, Canada.
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7
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Nakamura K, Karmokar A, Farrington PM, James NH, Ramos-Montoya A, Bickerton SJ, Hughes GD, Illidge TM, Cadogan EB, Davies BR, Dovedi SJ, Valge-Archer V. Inhibition of DNA-PK with AZD7648 Sensitizes Tumor Cells to Radiotherapy and Induces Type I IFN-Dependent Durable Tumor Control. Clin Cancer Res 2021; 27:4353-4366. [PMID: 34011558 PMCID: PMC9401489 DOI: 10.1158/1078-0432.ccr-20-3701] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2020] [Revised: 03/12/2021] [Accepted: 05/14/2021] [Indexed: 01/07/2023]
Abstract
PURPOSE Combining radiotherapy (RT) with DNA damage response inhibitors may lead to increased tumor cell death through radiosensitization. DNA-dependent protein kinase (DNA-PK) plays an important role in DNA double-strand break repair via the nonhomologous end joining (NHEJ) pathway. We hypothesized that in addition to a radiosensitizing effect from the combination of RT with AZD7648, a potent and specific inhibitor of DNA-PK, combination therapy may also lead to modulation of an anticancer immune response. EXPERIMENTAL DESIGN AZD7648 and RT efficacy, as monotherapy and in combination, was investigated in fully immunocompetent mice in MC38, CT26, and B16-F10 models. Immunologic consequences were analyzed by gene expression and flow-cytometric analysis. RESULTS AZD7648, when delivered in combination with RT, induced complete tumor regressions in a significant proportion of mice. The antitumor efficacy was dependent on the presence of CD8+ T cells but independent of NK cells. Analysis of the tumor microenvironment revealed a reduction in T-cell PD-1 expression, increased NK-cell granzyme B expression, and elevated type I IFN signaling in mice treated with the combination when compared with RT treatment alone. Blocking of the type I IFN receptor in vivo also demonstrated a critical role for type I IFN in tumor growth control following combined therapy. Finally, this combination was able to generate tumor antigen-specific immunologic memory capable of suppressing tumor growth following rechallenge. CONCLUSIONS Blocking the NHEJ DNA repair pathway with AZD7648 in combination with RT leads to durable immune-mediated tumor control.
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Affiliation(s)
- Kyoko Nakamura
- Bioscience, Early Oncology, Oncology R&D, AstraZeneca, Alderley Park, Macclesfield, United Kingdom
| | - Ankur Karmokar
- Bioscience, Early Oncology, Oncology R&D, AstraZeneca, Alderley Park, Macclesfield, United Kingdom
| | - Paul M Farrington
- Bioscience, Early Oncology, Oncology R&D, AstraZeneca, Alderley Park, Macclesfield, United Kingdom
| | - Neil H James
- Bioscience, Early Oncology, Oncology R&D, AstraZeneca, Alderley Park, Macclesfield, United Kingdom
| | | | - Susan J Bickerton
- Bioscience, Early Oncology, Oncology R&D, AstraZeneca, Alderley Park, Macclesfield, United Kingdom
| | - Gareth D Hughes
- Bioscience, Early Oncology, Oncology R&D, AstraZeneca, Cambridge, United Kingdom
| | - Timothy M Illidge
- Targeted Therapy Group, Division of Cancer Sciences, University of Manchester, Christie Hospital, Manchester NIHR Biomedical Research Centre, Manchester, United Kingdom
| | - Elaine B Cadogan
- Bioscience, Early Oncology, Oncology R&D, AstraZeneca, Cambridge, United Kingdom
| | - Barry R Davies
- Bioscience, Early Oncology, Oncology R&D, AstraZeneca, Cambridge, United Kingdom
| | - Simon J Dovedi
- Bioscience, Early Oncology, Oncology R&D, AstraZeneca, Cambridge, United Kingdom.
| | - Viia Valge-Archer
- Bioscience, Early Oncology, Oncology R&D, AstraZeneca, Cambridge, United Kingdom
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Molinaro C, Martoriati A, Cailliau K. Proteins from the DNA Damage Response: Regulation, Dysfunction, and Anticancer Strategies. Cancers (Basel) 2021; 13:3819. [PMID: 34359720 PMCID: PMC8345162 DOI: 10.3390/cancers13153819] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2021] [Revised: 07/22/2021] [Accepted: 07/26/2021] [Indexed: 12/21/2022] Open
Abstract
Cells respond to genotoxic stress through a series of complex protein pathways called DNA damage response (DDR). These monitoring mechanisms ensure the maintenance and the transfer of a correct genome to daughter cells through a selection of DNA repair, cell cycle regulation, and programmed cell death processes. Canonical or non-canonical DDRs are highly organized and controlled to play crucial roles in genome stability and diversity. When altered or mutated, the proteins in these complex networks lead to many diseases that share common features, and to tumor formation. In recent years, technological advances have made it possible to benefit from the principles and mechanisms of DDR to target and eliminate cancer cells. These new types of treatments are adapted to the different types of tumor sensitivity and could benefit from a combination of therapies to ensure maximal efficiency.
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Affiliation(s)
| | | | - Katia Cailliau
- Univ. Lille, CNRS, UMR 8576-UGSF-Unité de Glycobiologie Structurale et Fonctionnelle, F-59000 Lille, France; (C.M.); (A.M.)
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9
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Long Q, Liu Z, Gullerova M. Sweet Melody or Jazz? Transcription Around DNA Double-Strand Breaks. Front Mol Biosci 2021; 8:655786. [PMID: 33959637 PMCID: PMC8096065 DOI: 10.3389/fmolb.2021.655786] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2021] [Accepted: 03/22/2021] [Indexed: 12/23/2022] Open
Abstract
Genomic integrity is continuously threatened by thousands of endogenous and exogenous damaging factors. To preserve genome stability, cells developed comprehensive DNA damage response (DDR) pathways that mediate the recognition of damaged DNA lesions, the activation of signaling cascades, and the execution of DNA repair. Transcription has been understood to pose a threat to genome stability in the presence of DNA breaks. Interestingly, accumulating evidence in recent years shows that the transient transcriptional activation at DNA double-strand break (DSB) sites is required for efficient repair, while the rest of the genome exhibits temporary transcription silencing. This genomic shut down is a result of multiple signaling cascades involved in the maintenance of DNA/RNA homeostasis, chromatin stability, and genome fidelity. The regulation of transcription of protein-coding genes and non-coding RNAs has been extensively studied; however, the exact regulatory mechanisms of transcription at DSBs remain enigmatic. These complex processes involve many players such as transcription-associated protein complexes, including kinases, transcription factors, chromatin remodeling complexes, and helicases. The damage-derived transcripts themselves also play an essential role in DDR regulation. In this review, we summarize the current findings on the regulation of transcription at DSBs and discussed the roles of various accessory proteins in these processes and consequently in DDR.
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Affiliation(s)
| | | | - Monika Gullerova
- Sir William Dunn School of Pathology, University of Oxford, Oxford, United Kingdom
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10
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Harrison DK, Waldrip ZJ, Burdine L, Shalin SC, Burdine MS. DNA-PKcs Inhibition Extends Allogeneic Skin Graft Survival. Transplantation 2021; 105:540-549. [PMID: 32890138 PMCID: PMC7902289 DOI: 10.1097/tp.0000000000003442] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
BACKGROUND Organ transplantation is life-saving and continued investigations into immunologic mechanisms that drive organ rejection are needed to improve immunosuppression therapies and prevent graft failure. DNA-dependent protein kinase catalytic subunit, DNA dependent-protein kinase catalytic subunit (DNA-PKcs), is a critical component of both the cellular and humoral immune responses. In this study, we investigate the contribution of DNA-PKcs to allogeneic skin graft rejection to potentially highlight a novel strategy for inhibiting transplant rejection. METHODS Fully MHC mismatched murine allogeneic skin graft studies were performed by transplanting skin from BalbC mice to C57bl6 mice and treating with either vehicle or the DNA-PKcs inhibitor NU7441. Graft rejection, cytokine production, immune cell infiltration, and donor-specific antibody formation were analyzed. RESULTS DNA-PKcs inhibition significantly reduced necrosis and extended graft survival compared with controls (mean survival 14 d versus 9 d, respectively). Inhibition reduced the production of the cytokines interleukin (IL)-2, IL-4, IL-6, IL-10, TNF-α, and IFN-γ and the infiltration of CD3+ lymphocytes into grafts. Furthermore, DNA-PKcs inhibition reduced the number of CD19+ B cells and CD19+ CD138+ plasma cells coinciding with a significant reduction in donor-specific antibodies. At a molecular level, we determined that the immunosuppressive effects of DNA-PKcs inhibition were mediated, in part, via inhibition of nuclear factor kappa-light-chain-enhancer of activated B cells signaling through reduced expression of the p65 subunit. CONCLUSIONS Our data confirm that DNA-PKcs contributes to allogeneic graft rejection and highlight a novel immunologic function for DNA-PKcs in the regulation of nuclear factor kappa-light-chain-enhancer of activated B cells and concomitant cytokine production.
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Affiliation(s)
- David K. Harrison
- Division of Surgical Research, University of Arkansas for Medical Sciences, Little Rock, Arkansas, United States of America
- Arkansas Children’s Research Institute, Little Rock, Arkansas, United States of America
| | - Zachary J. Waldrip
- Division of Surgical Research, University of Arkansas for Medical Sciences, Little Rock, Arkansas, United States of America
- Arkansas Children’s Research Institute, Little Rock, Arkansas, United States of America
| | - Lyle Burdine
- Division of Surgical Research, University of Arkansas for Medical Sciences, Little Rock, Arkansas, United States of America
- Department of Surgery, University of Arkansas for Medical Sciences, Little Rock, Arkansas, United States of America
| | - Sara C. Shalin
- Department of Pathology and Dermatology, University of Arkansas for Medical Sciences, Little Rock, Arkansas, United States of America
| | - Marie Schluterman Burdine
- Division of Surgical Research, University of Arkansas for Medical Sciences, Little Rock, Arkansas, United States of America
- Arkansas Children’s Research Institute, Little Rock, Arkansas, United States of America
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11
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Saha T, Sundaravinayagam D, Di Virgilio M. Charting a DNA Repair Roadmap for Immunoglobulin Class Switch Recombination. Trends Biochem Sci 2020; 46:184-199. [PMID: 33250286 DOI: 10.1016/j.tibs.2020.10.005] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2020] [Revised: 10/08/2020] [Accepted: 10/23/2020] [Indexed: 01/18/2023]
Abstract
Immunoglobulin (Ig) class switch recombination (CSR) is the process occurring in mature B cells that diversifies the effector component of antibody responses. CSR is initiated by the activity of the B cell-specific enzyme activation-induced cytidine deaminase (AID), which leads to the formation of programmed DNA double-strand breaks (DSBs) at the Ig heavy chain (Igh) locus. Mature B cells use a multilayered and complex regulatory framework to ensure that AID-induced DNA breaks are channeled into productive repair reactions leading to CSR, and to avoid aberrant repair events causing lymphomagenic chromosomal translocations. Here, we review the DNA repair pathways acting on AID-induced DSBs and their functional interplay, with a particular focus on the latest developments in their molecular composition and mechanistic regulation.
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Affiliation(s)
- Tannishtha Saha
- Laboratory of Genome Diversification and Integrity, Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Berlin 13125, Germany
| | - Devakumar Sundaravinayagam
- Laboratory of Genome Diversification and Integrity, Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Berlin 13125, Germany.
| | - Michela Di Virgilio
- Laboratory of Genome Diversification and Integrity, Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Berlin 13125, Germany; Charité-Universitätsmedizin Berlin, Berlin 10117, Germany.
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12
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Beyond DNA Repair: DNA-PKcs in Tumor Metastasis, Metabolism and Immunity. Cancers (Basel) 2020; 12:cancers12113389. [PMID: 33207636 PMCID: PMC7698146 DOI: 10.3390/cancers12113389] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2020] [Revised: 11/10/2020] [Accepted: 11/12/2020] [Indexed: 01/07/2023] Open
Abstract
The DNA-dependent protein kinase catalytic subunit (DNA-PKcs) is a key component of the DNA-PK complex that has a well-characterized function in the non-homologous end-joining repair of DNA double-strand breaks. Since its identification, a large body of evidence has demonstrated that DNA-PKcs is frequently overexpressed in cancer, plays a critical role in tumor development and progression, and is associated with poor prognosis of cancer patients. Intriguingly, recent studies have suggested novel functions beyond the canonical role of DNA-PKcs, which has transformed the paradigm of DNA-PKcs in tumorigenesis and has reinvigorated the interest to target DNA-PKcs for cancer treatment. In this review, we update recent advances in DNA-PKcs, in particular the emerging roles in tumor metastasis, metabolic dysregulation, and immune escape. We further discuss the possible molecular basis that underpins the pleiotropism of DNA-PKcs in cancer. Finally, we outline the biomarkers that may predict the therapeutic response to DNA-PKcs inhibitor therapy. Understanding the functional repertoire of DNA-PKcs will provide mechanistic insights of DNA-PKcs in malignancy and, more importantly, may revolutionize the design and utility of DNA-PKcs-based precision cancer therapy.
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Ragunathan K, Upfold NLE, Oksenych V. Interaction between Fibroblasts and Immune Cells Following DNA Damage Induced by Ionizing Radiation. Int J Mol Sci 2020; 21:ijms21228635. [PMID: 33207781 PMCID: PMC7696681 DOI: 10.3390/ijms21228635] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2020] [Revised: 11/10/2020] [Accepted: 11/12/2020] [Indexed: 12/18/2022] Open
Abstract
Cancer-associated fibroblasts (CAF) form the basis of tumor microenvironment and possess immunomodulatory functions by interacting with other cells surrounding tumor, including T lymphocytes, macrophages, dendritic cells and natural killer cells. Ionizing radiation is a broadly-used method in radiotherapy to target tumors. In mammalian cells, ionizing radiation induces various types of DNA damages and DNA damage response. Being unspecific, radiotherapy affects all the cells in tumor microenvironment, including the tumor itself, CAFs and immune cells. CAFs are extremely radio-resistant and do not initiate apoptosis even at high doses of radiation. However, following radiation, CAFs become senescent and produce a distinct combination of immunoregulatory molecules. Radiosensitivity of immune cells varies depending on the cell type due to inefficient DNA repair in, for example, monocytes and granulocytes. In this minireview, we are summarizing recent findings on the interaction between CAF, ionizing radiation and immune cells in the tumor microenvironment.
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Affiliation(s)
- Kalaiyarasi Ragunathan
- Department of Clinical and Molecular Medicine, Norwegian University of Science and Technology (NTNU), 7028 Trondheim, Norway; (K.R.); (N.L.E.U.)
| | - Nikki Lyn Esnardo Upfold
- Department of Clinical and Molecular Medicine, Norwegian University of Science and Technology (NTNU), 7028 Trondheim, Norway; (K.R.); (N.L.E.U.)
| | - Valentyn Oksenych
- Department of Clinical and Molecular Medicine, Norwegian University of Science and Technology (NTNU), 7028 Trondheim, Norway; (K.R.); (N.L.E.U.)
- Department of Clinical Medicine, Faculty of Health Sciences, UiT-The Arctic University of Norway, 9037 Tromsø, Norway
- Department of Biosciences and Nutrition (BioNuT), Karolinska Institutet, 14183 Huddinge, Sweden
- KG Jebsen Centre for B Cell Malignancies, Institute of Clinical Medicine, University of Oslo, N-0316 Oslo, Norway
- Institute of Clinical Medicine, University of Oslo, 0318 Oslo, Norway
- Correspondence:
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Carrassa L, Colombo I, Damia G, Bertoni F. Targeting the DNA damage response for patients with lymphoma: Preclinical and clinical evidences. Cancer Treat Rev 2020; 90:102090. [DOI: 10.1016/j.ctrv.2020.102090] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2020] [Revised: 08/09/2020] [Accepted: 08/11/2020] [Indexed: 12/11/2022]
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15
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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.
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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.
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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.
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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.
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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
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Khattar E, Maung KZY, Chew CL, Ghosh A, Mok MMH, Lee P, Zhang J, Chor WHJ, Cildir G, Wang CQ, Mohd-Ismail NK, Chin DWL, Lee SC, Yang H, Shin YJ, Nam DH, Chen L, Kumar AP, Deng LW, Ikawa M, Gunaratne J, Osato M, Tergaonkar V. Rap1 regulates hematopoietic stem cell survival and affects oncogenesis and response to chemotherapy. Nat Commun 2019; 10:5349. [PMID: 31836706 PMCID: PMC6911077 DOI: 10.1038/s41467-019-13082-9] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2018] [Accepted: 10/14/2019] [Indexed: 11/09/2022] Open
Abstract
Increased levels and non-telomeric roles have been reported for shelterin proteins, including RAP1 in cancers. Herein using Rap1 null mice, we provide the genetic evidence that mammalian Rap1 plays a major role in hematopoietic stem cell survival, oncogenesis and response to chemotherapy. Strikingly, this function of RAP1 is independent of its association with the telomere or with its known partner TRF2. We show that RAP1 interacts with many members of the DNA damage response (DDR) pathway. RAP1 depleted cells show reduced interaction between XRCC4/DNA Ligase IV and DNA-PK, and are impaired in DNA Ligase IV recruitment to damaged chromatin for efficient repair. Consistent with its role in DNA damage repair, RAP1 loss decreases double-strand break repair via NHEJ in vivo, and consequently reduces B cell class switch recombination. Finally, we discover that RAP1 levels are predictive of the success of chemotherapy in breast and colon cancer.
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Affiliation(s)
- Ekta Khattar
- Institute of Molecular and Cell Biology (IMCB), Agency for Science, Technology and Research (A-STAR), Singapore, Singapore
| | - Kyaw Ze Ya Maung
- Institute of Molecular and Cell Biology (IMCB), Agency for Science, Technology and Research (A-STAR), Singapore, Singapore
| | - Chen Li Chew
- Institute of Molecular and Cell Biology (IMCB), Agency for Science, Technology and Research (A-STAR), Singapore, Singapore
| | - Arkasubhra Ghosh
- Institute of Molecular and Cell Biology (IMCB), Agency for Science, Technology and Research (A-STAR), Singapore, Singapore
| | - Michelle Meng Huang Mok
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore
| | - Pei Lee
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Jun Zhang
- Jiangsu Key Laboratory for Molecular and Medical Biotechnology, College of Life Science, Nanjing Normal University, 210023, Nanjing, P.R. China
| | - Wei Hong Jeff Chor
- Institute of Molecular and Cell Biology (IMCB), Agency for Science, Technology and Research (A-STAR), Singapore, Singapore
| | - Gökhan Cildir
- Institute of Molecular and Cell Biology (IMCB), Agency for Science, Technology and Research (A-STAR), Singapore, Singapore
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Chelsia Qiuxia Wang
- Institute of Molecular and Cell Biology (IMCB), Agency for Science, Technology and Research (A-STAR), Singapore, Singapore
| | - Nur Khairiah Mohd-Ismail
- Institute of Molecular and Cell Biology (IMCB), Agency for Science, Technology and Research (A-STAR), Singapore, Singapore
| | - Desmond Wai Loon Chin
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore
| | - Soo Chin Lee
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore
| | - Henry Yang
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore
| | - Yong-Jae Shin
- Institute for Refractory Cancer Research, Samsung Medical Center, Seoul, Republic of Korea
| | - Do-Hyun Nam
- Institute for Refractory Cancer Research, Samsung Medical Center, Seoul, Republic of Korea
| | - Liming Chen
- Jiangsu Key Laboratory for Molecular and Medical Biotechnology, College of Life Science, Nanjing Normal University, 210023, Nanjing, P.R. China
| | - Alan Prem Kumar
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore
| | - Lih Wen Deng
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Masahito Ikawa
- Research Institute for Microbial Diseases, Osaka University, Suita, Osaka, 565-0871, Japan
- Graduate School of Medicine, Osaka University, Suita, Osaka, 565-0871, Japan
| | - Jayantha Gunaratne
- Institute of Molecular and Cell Biology (IMCB), Agency for Science, Technology and Research (A-STAR), Singapore, Singapore
| | - Motomi Osato
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore
| | - Vinay Tergaonkar
- Institute of Molecular and Cell Biology (IMCB), Agency for Science, Technology and Research (A-STAR), Singapore, Singapore.
- Department of Pathology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore.
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19
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Current insights into the mechanism of mammalian immunoglobulin class switch recombination. Crit Rev Biochem Mol Biol 2019; 54:333-351. [PMID: 31509023 DOI: 10.1080/10409238.2019.1659227] [Citation(s) in RCA: 65] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Immunoglobulin (Ig) class switch recombination (CSR) is the gene rearrangement process by which B lymphocytes change the Ig heavy chain constant region to permit a switch of Ig isotype from IgM to IgG, IgA, or IgE. At the DNA level, CSR occurs via generation and joining of DNA double strand breaks (DSBs) at intronic switch regions located just upstream of each of the heavy chain constant regions. Activation-induced deaminase (AID), a B cell specific enzyme, catalyzes cytosine deaminations (converting cytosines to uracils) as the initial DNA lesions that eventually lead to DSBs and CSR. Progress on AID structure integrates very well with knowledge about Ig class switch region nucleic acid structures that are supported by functional studies. It is an ideal time to review what is known about the mechanism of Ig CSR and its relation to somatic hypermutation. There have been many comprehensive reviews on various aspects of the CSR reaction and regulation of AID expression and activity. This review is focused on the relation between AID and switch region nucleic acid structures, with a particular emphasis on R-loops.
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20
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Mohiuddin IS, Kang MH. DNA-PK as an Emerging Therapeutic Target in Cancer. Front Oncol 2019; 9:635. [PMID: 31380275 PMCID: PMC6650781 DOI: 10.3389/fonc.2019.00635] [Citation(s) in RCA: 117] [Impact Index Per Article: 23.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2019] [Accepted: 06/27/2019] [Indexed: 12/21/2022] Open
Abstract
The DNA-dependent protein kinase (DNA-PK) plays an instrumental role in the overall survival and proliferation of cells. As a member of the phosphatidylinositol 3-kinase-related kinase (PIKK) family, DNA-PK is best known as a mediator of the cellular response to DNA damage. In this context, DNA-PK has emerged as an intriguing therapeutic target in the treatment of a variety of cancers, especially when used in conjunction with genotoxic chemotherapy or ionizing radiation. Beyond the DNA damage response, DNA-PK activity is necessary for multiple cellular functions, including the regulation of transcription, progression of the cell cycle, and in the maintenance of telomeres. Here, we review what is currently known about DNA-PK regarding its structure and established roles in DNA repair. We also discuss its lesser-known functions, the pharmacotherapies inhibiting its function in DNA repair, and its potential as a therapeutic target in a broader context.
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Affiliation(s)
- Ismail S Mohiuddin
- Cancer Center, Department of Pediatrics, Pharmacology and Neuroscience, School of Medicine, Texas Tech University Health Sciences Center, Lubbock, TX, United States
| | - Min H Kang
- Cancer Center, Department of Pediatrics, Pharmacology and Neuroscience, School of Medicine, Texas Tech University Health Sciences Center, Lubbock, TX, United States
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21
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Xue R, Peng Y, Han B, Li X, Chen Y, Pei H. Metastasis suppressor NME1 promotes non-homologous end joining of DNA double-strand breaks. DNA Repair (Amst) 2019; 77:27-35. [DOI: 10.1016/j.dnarep.2019.03.003] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2018] [Revised: 03/03/2019] [Accepted: 03/03/2019] [Indexed: 10/27/2022]
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Unoki M, Funabiki H, Velasco G, Francastel C, Sasaki H. CDCA7 and HELLS mutations undermine nonhomologous end joining in centromeric instability syndrome. J Clin Invest 2018; 129:78-92. [PMID: 30307408 DOI: 10.1172/jci99751] [Citation(s) in RCA: 51] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2018] [Accepted: 10/04/2018] [Indexed: 02/06/2023] Open
Abstract
Mutations in CDCA7 and HELLS that respectively encode a CXXC-type zinc finger protein and an SNF2 family chromatin remodeler cause immunodeficiency, centromeric instability, and facial anomalies (ICF) syndrome types 3 and 4. Here, we demonstrate that the classical nonhomologous end joining (C-NHEJ) proteins Ku80 and Ku70, as well as HELLS, coimmunoprecipitated with CDCA7. The coimmunoprecipitation of the repair proteins was sensitive to nuclease treatment and an ICF3 mutation in CDCA7 that impairs its chromatin binding. The functional importance of these interactions was strongly suggested by the compromised C-NHEJ activity and significant delay in Ku80 accumulation at DNA damage sites in CDCA7- and HELLS-deficient HEK293 cells. Consistent with the repair defect, these cells displayed increased apoptosis, abnormal chromosome segregation, aneuploidy, centrosome amplification, and significant accumulation of γH2AX signals. Although less prominent, cells with mutations in the other ICF genes DNMT3B and ZBTB24 (responsible for ICF types 1 and 2, respectively) showed similar defects. Importantly, lymphoblastoid cells from ICF patients shared the same changes detected in the mutant HEK293 cells to varying degrees. Although the C-NHEJ defect alone did not cause CG hypomethylation, CDCA7 and HELLS are involved in maintaining CG methylation at centromeric and pericentromeric repeats. The defect in C-NHEJ may account for some common features of ICF cells, including centromeric instability, abnormal chromosome segregation, and apoptosis.
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Affiliation(s)
- Motoko Unoki
- Division of Epigenomics and Development, Medical Institute of Bioregulation, Kyushu University, Fukuoka, Japan
| | - Hironori Funabiki
- Laboratory of Chromosome and Cell Biology, The Rockefeller University, New York, New York, USA
| | - Guillaume Velasco
- CNRS UMR7216, Epigenetics and Cell Fate, Université Paris Diderot, Sorbonne Paris Cité, Paris, France
| | - Claire Francastel
- CNRS UMR7216, Epigenetics and Cell Fate, Université Paris Diderot, Sorbonne Paris Cité, Paris, France
| | - Hiroyuki Sasaki
- Division of Epigenomics and Development, Medical Institute of Bioregulation, Kyushu University, Fukuoka, Japan
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23
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Esenboga S, Akal C, Karaatmaca B, Erman B, Dogan S, Orhan D, Boztug K, Ayvaz D, Tezcan İ. Two siblings with PRKDC defect who presented with cutaneous granulomas and review of the literature. Clin Immunol 2018; 197:1-5. [PMID: 30121298 DOI: 10.1016/j.clim.2018.08.002] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2018] [Revised: 08/09/2018] [Accepted: 08/09/2018] [Indexed: 12/13/2022]
Abstract
V(D)J recombination, during which recognition and repair of broken DNA chains are accomplished by non-homologous end joining pathway, is a critical process in B and T cell development.Null mutations of each enzyme or protein of this pathway result in T- B- NK+ severe combined immunodeficiency whereas hypomorphic mutations result in atypical(leaky)severe combined immunodeficiency forms. We present two siblings with PRKDC (Protein Kinase, DNA-Activated, Catalytic Polypeptide) mutation who presented with granulomatous skin lesions and recurrent lung infections. Primary immune deficiencies may initially present with skin findings. Disruption in central and peripheral B-cell tolerance and impaired intrathymic T-cell maturation,a central player in T-cell tolerance, have been identified as the mechanism of autoimmunity and granuloma seen in patients. The variation in clinical phenotypes of patients with PRKDC mutation suggests that additional factors such as modifying genes, epigenetic and environmental factors may affect the severity and clinical phenotype of the disease. Functional studies during the follow-up and evaluation before and after hematopoeitic stem cell transplantation will hopefully increase our knowledge about the autoimmune and inflammatory process of the disease spectrum.
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Affiliation(s)
- Saliha Esenboga
- Hacettepe University Faculty of Medicine, Department of Pediatrics, Division of Immunology, Ankara, Turkey.
| | - Can Akal
- Hacettepe University Faculty of Medicine, Department of Pediatrics, Ankara, Turkey
| | - Betül Karaatmaca
- Hacettepe University Faculty of Medicine, Department of Pediatrics, Division of Immunology, Ankara, Turkey
| | - Baran Erman
- Koç University, Research Center for Translational Medicine, İstanbul, Turkey
| | - Sibel Dogan
- Hacettepe University Faculty of Medicine, Department of Dermatology and Venereology, Ankara, Turkey
| | - Diclehan Orhan
- Hacettepe University Faculty of Medicine, Department of Pediatrics, Division of Pathology, Ankara, Turkey
| | - Kaan Boztug
- Medical University of Vienna, Department of Paediatrics and Adolescent Medicine, Vienna, Austria
| | - Deniz Ayvaz
- Hacettepe University Faculty of Medicine, Department of Pediatrics, Division of Immunology, Ankara, Turkey
| | - İlhan Tezcan
- Hacettepe University Faculty of Medicine, Department of Pediatrics, Division of Immunology, Ankara, Turkey
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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.
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25
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High-throughput sequencing reveals similar molecular signatures for class switch recombination junctions for the γ and α isotypes. Cell Mol Immunol 2018; 16:90-92. [PMID: 29572544 DOI: 10.1038/s41423-018-0025-z] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2018] [Revised: 02/28/2018] [Accepted: 02/28/2018] [Indexed: 01/18/2023] Open
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26
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The H2B deubiquitinase Usp22 promotes antibody class switch recombination by facilitating non-homologous end joining. Nat Commun 2018. [PMID: 29520062 PMCID: PMC5843634 DOI: 10.1038/s41467-018-03455-x] [Citation(s) in RCA: 38] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023] Open
Abstract
Class switch recombination (CSR) has a fundamental function during humoral immune response and involves the induction and subsequent repair of DNA breaks in the immunoglobulin (Ig) switch regions. Here we show the role of Usp22, the SAGA complex deubiquitinase that removes ubiquitin from H2B-K120, in the repair of programmed DNA breaks in vivo. Ablation of Usp22 in primary B cells results in defects in γH2AX and impairs the classical non-homologous end joining (c-NHEJ), affecting both V(D)J recombination and CSR. Surprisingly, Usp22 depletion causes defects in CSR to various Ig isotypes, but not IgA. We further demonstrate that IgG CSR primarily relies on c-NHEJ, whereas CSR to IgA is more reliant on the alternative end joining pathway, indicating that CSR to different isotypes involves distinct DNA repair pathways. Hence, Usp22 is the first deubiquitinase reported to regulate both V(D)J recombination and CSR in vivo by facilitating c-NHEJ.
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