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Goff NJ, Mikhova M, Schmidt JC, Meek K. DNA-PK: A synopsis beyond synapsis. DNA Repair (Amst) 2024; 141:103716. [PMID: 38996771 PMCID: PMC11369974 DOI: 10.1016/j.dnarep.2024.103716] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2024] [Revised: 06/26/2024] [Accepted: 06/27/2024] [Indexed: 07/14/2024]
Abstract
Given its central role in life, DNA is remarkably easy to damage. Double strand breaks (DSBs) are the most toxic form of DNA damage, and DSBs pose the greatest danger to genomic integrity. In higher vertebrates, the non-homologous end joining pathway (NHEJ) is the predominate pathway that repairs DSBs. NHEJ has three steps: 1) DNA end recognition by the DNA dependent protein kinase [DNA-PK], 2) DNA end-processing by numerous NHEJ accessory factors, and 3) DNA end ligation by the DNA ligase IV complex (LX4). Although this would appear to be a relatively simple mechanism, it has become increasingly apparent that it is not. Recently, much insight has been derived regarding the mechanism of non-homologous end joining through a proliferation of cryo-EM studies, structure-function mutational experiments informed by these new structural data, and novel single-molecule imaging approaches. An emerging consensus in the field is that NHEJ progresses from initial DSB end recognition by DNA-PK to synapsis of the two DNA ends in a long-range synaptic complex where ends are held too far apart (115 Å) for ligation, and then progress to a short-range synaptic complex where ends are positioned close enough for ligation. What was surprising from these structural studies was the observation of two distinct types of DNA-PK dimers that represent NHEJ long-range complexes. In this review, we summarize current knowledge about the function of the distinct NHEJ synaptic complexes and align this new information with emerging cellular single-molecule microscopy studies as well as with previous studies of DNA-PK's function in repair.
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Affiliation(s)
- Noah J Goff
- College of Veterinary Medicine, Department of Microbiology Genetics & Immunology, Department of Pathobiology & Diagnostic Investigation, Michigan State University, East Lansing, MI 48824, USA
| | - Mariia Mikhova
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI, USA; Institute for Quantitative Health Sciences and Engineering, Michigan State University, East Lansing, MI, USA
| | - Jens C Schmidt
- Institute for Quantitative Health Sciences and Engineering, Michigan State University, East Lansing, MI, USA; Department of Obstetrics, Gynecology, and Reproductive Biology, Michigan State University, East Lansing, MI, USA
| | - Katheryn Meek
- College of Veterinary Medicine, Department of Microbiology Genetics & Immunology, Department of Pathobiology & Diagnostic Investigation, Michigan State University, East Lansing, MI 48824, USA
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2
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Tong J, Song J, Zhang W, Zhai J, Guan Q, Wang H, Liu G, Zheng C. When DNA-damage responses meet innate and adaptive immunity. Cell Mol Life Sci 2024; 81:185. [PMID: 38630271 PMCID: PMC11023972 DOI: 10.1007/s00018-024-05214-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2023] [Revised: 03/17/2024] [Accepted: 03/18/2024] [Indexed: 04/19/2024]
Abstract
When cells proliferate, stress on DNA replication or exposure to endogenous or external insults frequently results in DNA damage. DNA-Damage Response (DDR) networks are complex signaling pathways used by multicellular organisms to prevent DNA damage. Depending on the type of broken DNA, the various pathways, Base-Excision Repair (BER), Nucleotide Excision Repair (NER), Mismatch Repair (MMR), Homologous Recombination (HR), Non-Homologous End-Joining (NHEJ), Interstrand Crosslink (ICL) repair, and other direct repair pathways, can be activated separately or in combination to repair DNA damage. To preserve homeostasis, innate and adaptive immune responses are effective defenses against endogenous mutation or invasion by external pathogens. It is interesting to note that new research keeps showing how closely DDR components and the immune system are related. DDR and immunological response are linked by immune effectors such as the cyclic GMP-AMP synthase (cGAS)-Stimulator of Interferon Genes (STING) pathway. These effectors act as sensors of DNA damage-caused immune response. Furthermore, DDR components themselves function in immune responses to trigger the generation of inflammatory cytokines in a cascade or even trigger programmed cell death. Defective DDR components are known to disrupt genomic stability and compromise immunological responses, aggravating immune imbalance and leading to serious diseases such as cancer and autoimmune disorders. This study examines the most recent developments in the interaction between DDR elements and immunological responses. The DDR network's immune modulators' dual roles may offer new perspectives on treating infectious disorders linked to DNA damage, including cancer, and on the development of target immunotherapy.
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Affiliation(s)
- Jie Tong
- College of Life Science, Hebei University, Baoding, 071002, China
- Institute of Life Science and Green Development, Hebei University, Baoding, 071002, China
| | - Jiangwei Song
- Beijing Key Laboratory for Prevention and Control of Infectious Diseases in Livestock and Poultry, Institute of Animal Husbandry and Veterinary Medicine, Beijing Academy of Agriculture and Forestry Sciences, Beijing, 100089, China
| | - Wuchao Zhang
- College of Veterinary Medicine, Hebei Agricultural University, Baoding, 071000, China
| | - Jingbo Zhai
- Key Laboratory of Zoonose Prevention and Control at Universities of Inner Mongolia Autonomous Region, Medical College, Inner Mongolia Minzu University, Tongliao, 028000, China
| | - Qingli Guan
- The Affiliated Hospital of Chinese PLA 80th Group Army, Weifang, 261000, China
| | - Huiqing Wang
- Department of Pediatrics, West China Second University Hospital, Sichuan University, Chengdu, 610041, China.
| | - Gentao Liu
- Department of Oncology, Tenth People's Hospital Affiliated to Tongji University & Cancer Center, Tongji University School of Medicine, Shanghai, 20000, China.
| | - Chunfu Zheng
- Department of Microbiology, Immunology and Infectious Diseases, University of Calgary, Calgary, AB, Canada.
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3
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Pinton A, Courtois L, Doublet C, Cabannes-Hamy A, Andrieu G, Smith C, Balducci E, Cieslak A, Touzart A, Simonin M, Lhéritier V, Huguet F, Balsat M, Dombret H, Rousselot P, Spicuglia S, Macintyre E, Boissel N, Asnafi V. PHF6-altered T-ALL Harbor Epigenetic Repressive Switch at Bivalent Promoters and Respond to 5-Azacitidine and Venetoclax. Clin Cancer Res 2024; 30:94-105. [PMID: 37889114 DOI: 10.1158/1078-0432.ccr-23-2159] [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: 07/18/2023] [Revised: 09/27/2023] [Accepted: 10/25/2023] [Indexed: 10/28/2023]
Abstract
PURPOSE To assess the impact of PHF6 alterations on clinical outcome and therapeutical actionability in T-cell acute lymphoblastic leukemia (T-ALL). EXPERIMENTAL DESIGN We described PHF6 alterations in an adult cohort of T-ALL from the French trial Group for Research on Adult Acute Lymphoblastic Leukemia (GRAALL)-2003/2005 and retrospectively analyzed clinical outcomes between PHF6-altered (PHF6ALT) and wild-type patients. We also used EPIC and chromatin immunoprecipitation sequencing data of patient samples to analyze the epigenetic landscape of PHF6ALT T-ALLs. We consecutively evaluated 5-azacitidine efficacy, alone or combined with venetoclax, in PHF6ALT T-ALL. RESULTS We show that PHF6 alterations account for 47% of cases in our cohort and demonstrate that PHF6ALT T-ALL presented significantly better clinical outcomes. Integrative analysis of DNA methylation and histone marks shows that PHF6ALT are characterized by DNA hypermethylation and H3K27me3 loss at promoters physiologically bivalent in thymocytes. Using patient-derived xenografts, we show that PHF6ALT T-ALL respond to the 5-azacytidine alone. Finally, synergism with the BCL2-inhibitor venetoclax was demonstrated in refractory/relapsing (R/R) PHF6ALT T-ALL using fresh samples. Importantly, we report three cases of R/R PHF6ALT patients who were successfully treated with this combination. CONCLUSIONS Overall, our study supports the use of PHF6 alterations as a biomarker of sensitivity to 5-azacytidine and venetoclax combination in R/R T-ALL.
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Affiliation(s)
- Antoine Pinton
- Institut Necker Enfants-Malades, INSERM U1151, Hôpital Necker Enfants-Malades, Laboratoire d'Onco-Hématologie, Assistance Publique - Hôpitaux de Paris, and Université Paris-Cité, Paris, France
| | - Lucien Courtois
- Institut Necker Enfants-Malades, INSERM U1151, Hôpital Necker Enfants-Malades, Laboratoire d'Onco-Hématologie, Assistance Publique - Hôpitaux de Paris, and Université Paris-Cité, Paris, France
| | | | | | - Guillaume Andrieu
- Institut Necker Enfants-Malades, INSERM U1151, Hôpital Necker Enfants-Malades, Laboratoire d'Onco-Hématologie, Assistance Publique - Hôpitaux de Paris, and Université Paris-Cité, Paris, France
| | - Charlotte Smith
- Institut Necker Enfants-Malades, INSERM U1151, Hôpital Necker Enfants-Malades, Laboratoire d'Onco-Hématologie, Assistance Publique - Hôpitaux de Paris, and Université Paris-Cité, Paris, France
| | - Estelle Balducci
- Institut Necker Enfants-Malades, INSERM U1151, Hôpital Necker Enfants-Malades, Laboratoire d'Onco-Hématologie, Assistance Publique - Hôpitaux de Paris, and Université Paris-Cité, Paris, France
| | - Agata Cieslak
- Institut Necker Enfants-Malades, INSERM U1151, Hôpital Necker Enfants-Malades, Laboratoire d'Onco-Hématologie, Assistance Publique - Hôpitaux de Paris, and Université Paris-Cité, Paris, France
| | - Aurore Touzart
- Institut Necker Enfants-Malades, INSERM U1151, Hôpital Necker Enfants-Malades, Laboratoire d'Onco-Hématologie, Assistance Publique - Hôpitaux de Paris, and Université Paris-Cité, Paris, France
| | - Mathieu Simonin
- Institut Necker Enfants-Malades, INSERM U1151, Hôpital Necker Enfants-Malades, Laboratoire d'Onco-Hématologie, Assistance Publique - Hôpitaux de Paris, and Université Paris-Cité, Paris, France
| | - Véronique Lhéritier
- Coordination du Groupe Group for Research in Adult Acute Lymphoblastic Leukemia, Hospices Civils de Lyon, Hôpital Lyon Sud, Lyon, France
| | - Françoise Huguet
- Service d'Hématologie, CHU de Toulouse, IUCT-Oncopole, Toulouse, France
| | - Marie Balsat
- Service d'Hématologie Clinique, Hôpital Lyon Sud, Lyon, France
| | - Hervé Dombret
- Service d'Hématologie Adolescents et Jeunes Adultes, Hôpital Saint-Louis, Assistance Publique-Hôpitaux de Paris, Paris, France
- Institut de Recherche Saint-Louis, UPR-3518, Université Paris Cité, Paris, France
| | - Philippe Rousselot
- Centre Hospitalier de Versailles, Versailles, France
- Université Versailles Saint Quentin en Yvelines Paris Saclay, INSERM U1184, Paris, France
| | - Salvatore Spicuglia
- Aix-Marseille University, Inserm, TAGC, UMR1090, Marseille, France
- Equipe Labélisée Ligue Contre le Cancer, Marseille, France
| | - Elizabeth Macintyre
- Institut Necker Enfants-Malades, INSERM U1151, Hôpital Necker Enfants-Malades, Laboratoire d'Onco-Hématologie, Assistance Publique - Hôpitaux de Paris, and Université Paris-Cité, Paris, France
| | - Nicolas Boissel
- Service d'Hématologie Adolescents et Jeunes Adultes, Hôpital Saint-Louis, Assistance Publique-Hôpitaux de Paris, Paris, France
- Institut de Recherche Saint-Louis, UPR-3518, Université Paris Cité, Paris, France
| | - Vahid Asnafi
- Institut Necker Enfants-Malades, INSERM U1151, Hôpital Necker Enfants-Malades, Laboratoire d'Onco-Hématologie, Assistance Publique - Hôpitaux de Paris, and Université Paris-Cité, Paris, France
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4
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Kabrani E, Saha T, Di Virgilio M. DNA repair and antibody diversification: the 53BP1 paradigm. Trends Immunol 2023; 44:782-791. [PMID: 37640588 DOI: 10.1016/j.it.2023.08.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2023] [Revised: 08/01/2023] [Accepted: 08/03/2023] [Indexed: 08/31/2023]
Abstract
The DNA double-strand break (DSB) repair factor 53BP1 has long been implicated in V(D)J and class switch recombination (CSR) of mammalian lymphocyte receptors. However, the dissection of the underlying molecular activities is hampered by a paucity of studies [V(D)J] and plurality of phenotypes (CSR) associated with 53BP1 deficiency. Here, we revisit the currently accepted roles of 53BP1 in antibody diversification in view of the recent identification of its downstream effectors in DSB protection and latest advances in genome architecture. We propose that, in addition to end protection, 53BP1-mediated end-tethering stabilization is essential for CSR. Furthermore, we support a pre-DSB role during V(D)J recombination. Our perspective underscores the importance of evaluating repair of DSBs in relation to their dynamic architectural contexts.
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Affiliation(s)
- Eleni Kabrani
- Laboratory of Genome Diversification and Integrity, Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Berlin 13125, Germany.
| | - Tannishtha Saha
- Laboratory of Genome Diversification and Integrity, Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Berlin 13125, Germany; Freie Universität Berlin, Berlin 14195, 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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5
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Upfold NLE, Petakh P, Kamyshnyi A, Oksenych V. Tyrosine Kinase Inhibitors Target B Lymphocytes. Biomolecules 2023; 13:biom13030438. [PMID: 36979373 PMCID: PMC10046234 DOI: 10.3390/biom13030438] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2022] [Revised: 02/18/2023] [Accepted: 02/22/2023] [Indexed: 03/02/2023] Open
Abstract
Autoimmune disorders and some types of blood cancer originate when B lymphocytes malfunction. In particular, when B cells produce antibodies recognizing the body’s proteins, it leads to various autoimmune disorders. Additionally, when B cells of various developmental stages transform into cancer cells, it results in blood cancers, including multiple myeloma, lymphoma, and leukemia. Thus, new methods of targeting B cells are required for various patient groups. Here, we used protein kinase inhibitors alectinib, brigatinib, ceritinib, crizotinib, entrectinib, and lorlatinib previously approved as drugs treating anaplastic lymphoma kinase (ALK)-positive lung cancer cells. We hypothesized that the same inhibitors will efficiently target leukocyte tyrosine kinase (LTK)-positive, actively protein-secreting mature B lymphocytes, including plasma cells. We isolated CD19-positive human B cells from the blood of healthy donors and used two alternative methods to stimulate cell maturation toward plasma cells. Using cell proliferation and flow cytometry assays, we found that ceritinib and entrectinib eliminate plasma cells from B cell populations. Alectinib, brigatinib, and crizotinib also inhibited B cell proliferation, while lorlatinib had no or limited effect on B cells. More generally, we concluded that several drugs previously developed to treat ALK-positive malignant cells can be also used to treat LTK-positive B cells.
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Affiliation(s)
- Nikki Lyn Esnardo Upfold
- Department of Clinical and Molecular Medicine (IKOM), Norwegian University of Science and Technology (NTNU), 7028 Trondheim, Norway
| | - Pavlo Petakh
- Department of Biochemistry and Pharmacology, Uzhhorod National University, 88000 Uzhhorod, Ukraine
- Department of Microbiology, Virology, and Immunology, I. Horbachevsky Ternopil National Medical University, 46001 Ternopil, Ukraine
| | - Aleksandr Kamyshnyi
- Department of Microbiology, Virology, and Immunology, I. Horbachevsky Ternopil National Medical University, 46001 Ternopil, Ukraine
| | - Valentyn Oksenych
- Department of Clinical and Molecular Medicine (IKOM), Norwegian University of Science and Technology (NTNU), 7028 Trondheim, Norway
- Institute of Clinical Medicine (Klinmed), University of Oslo, 0318 Oslo, Norway
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6
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Oksenych V. DNA Repair and Immune Response: Editorial. Biomolecules 2022; 13:biom13010084. [PMID: 36671469 PMCID: PMC9855733 DOI: 10.3390/biom13010084] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2022] [Accepted: 12/29/2022] [Indexed: 01/03/2023] Open
Abstract
Developing B and T lymphocytes requires programmed DNA double-strand breaks followed by the activation of the DNA damage response (DDR) pathway and DNA repair [...].
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Affiliation(s)
- Valentyn Oksenych
- Institute of Clinical Medicine, University of Oslo, 0318 Oslo, Norway
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7
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Vincendeau E, Wei W, Zhang X, Planchais C, Yu W, Lenden-Hasse H, Cokelaer T, Pipoli da Fonseca J, Mouquet H, Adams DJ, Alt FW, Jackson SP, Balmus G, Lescale C, Deriano L. SHLD1 is dispensable for 53BP1-dependent V(D)J recombination but critical for productive class switch recombination. Nat Commun 2022; 13:3707. [PMID: 35764636 PMCID: PMC9240092 DOI: 10.1038/s41467-022-31287-3] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2021] [Accepted: 06/13/2022] [Indexed: 11/21/2022] Open
Abstract
SHLD1 is part of the Shieldin (SHLD) complex, which acts downstream of 53BP1 to counteract DNA double-strand break (DSB) end resection and promote DNA repair via non-homologous end-joining (NHEJ). While 53BP1 is essential for immunoglobulin heavy chain class switch recombination (CSR), long-range V(D)J recombination and repair of RAG-induced DSBs in XLF-deficient cells, the function of SHLD during these processes remains elusive. Here we report that SHLD1 is dispensable for lymphocyte development and RAG-mediated V(D)J recombination, even in the absence of XLF. By contrast, SHLD1 is essential for restricting resection at AID-induced DSB ends in both NHEJ-proficient and NHEJ-deficient B cells, providing an end-protection mechanism that permits productive CSR by NHEJ and alternative end-joining. Finally, we show that this SHLD1 function is required for orientation-specific joining of AID-initiated DSBs. Our data thus suggest that 53BP1 promotes V(D)J recombination and CSR through two distinct mechanisms: SHLD-independent synapsis of V(D)J segments and switch regions within chromatin, and SHLD-dependent protection of AID-DSB ends against resection.
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Affiliation(s)
- Estelle Vincendeau
- Institut Pasteur, Université Paris Cité, INSERM U1223, Équipe Labellisée Ligue Contre Le Cancer, Genome Integrity, Immunity and Cancer Unit, 75015, Paris, France
| | - Wenming Wei
- Institut Pasteur, Université Paris Cité, INSERM U1223, Équipe Labellisée Ligue Contre Le Cancer, Genome Integrity, Immunity and Cancer Unit, 75015, Paris, France
| | - Xuefei Zhang
- Howard Hughes Medical Institute, Program in Cellular and Molecular Medicine at Boston Children's Hospital, Department of Genetics, Harvard Medical School, Boston, MA, 02115, USA
- Biomedical Pioneering Innovation Center (BIOPIC) and Beijing Advanced Innovation Center for Genomics (ICG), Peking University, Beijing, 100871, China
| | - Cyril Planchais
- Institut Pasteur, Université de Paris, INSERM U1222, Laboratory of Humoral Immunology, 75015, Paris, France
| | - Wei Yu
- Institut Pasteur, Université Paris Cité, INSERM U1223, Équipe Labellisée Ligue Contre Le Cancer, Genome Integrity, Immunity and Cancer Unit, 75015, Paris, France
| | - Hélène Lenden-Hasse
- Institut Pasteur, Université Paris Cité, INSERM U1223, Équipe Labellisée Ligue Contre Le Cancer, Genome Integrity, Immunity and Cancer Unit, 75015, Paris, France
| | - Thomas Cokelaer
- Institut Pasteur, Plate-forme Technologique Biomics, Centre de Ressources et Recherches Technologiques, 75015, Paris, France
- Institut Pasteur, Hub de Bioinformatique et Biostatistique, Département de Biologie Computationnelle, 75015, Paris, France
| | - Juliana Pipoli da Fonseca
- Institut Pasteur, Plate-forme Technologique Biomics, Centre de Ressources et Recherches Technologiques, 75015, Paris, France
| | - Hugo Mouquet
- Institut Pasteur, Université de Paris, INSERM U1222, Laboratory of Humoral Immunology, 75015, Paris, France
| | - David J Adams
- Wellcome Trust Sanger Institute, Cambridge, CB10 1SA, UK
| | - Frederick W Alt
- Howard Hughes Medical Institute, Program in Cellular and Molecular Medicine at Boston Children's Hospital, Department of Genetics, Harvard Medical School, Boston, MA, 02115, USA
| | - Stephen P Jackson
- Wellcome Trust/Cancer Research UK Gurdon Institute, Department of Biochemistry, University of Cambridge, Cambridge, CB2 1QN, UK
| | - Gabriel Balmus
- UK Dementia Research Institute at University of Cambridge, Department of Clinical Neurosciences, University of Cambridge, Cambridge, CB2 0AH, UK
| | - Chloé Lescale
- Institut Pasteur, Université Paris Cité, INSERM U1223, Équipe Labellisée Ligue Contre Le Cancer, Genome Integrity, Immunity and Cancer Unit, 75015, Paris, France.
| | - Ludovic Deriano
- Institut Pasteur, Université Paris Cité, INSERM U1223, Équipe Labellisée Ligue Contre Le Cancer, Genome Integrity, Immunity and Cancer Unit, 75015, Paris, France.
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8
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Bai W, Zhao B, Gu M, Dong J. Alternative end-joining in BCR gene rearrangements and translocations. Acta Biochim Biophys Sin (Shanghai) 2022; 54:782-795. [PMID: 35593472 PMCID: PMC9828324 DOI: 10.3724/abbs.2022051] [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] [Indexed: 12/18/2022] Open
Abstract
Programmed DNA double-strand breaks (DSBs) occur during antigen receptor gene recombination, namely V(D)J recombination in developing B lymphocytes and class switch recombination (CSR) in mature B cells. Repair of these DSBs by classical end-joining (c-NHEJ) enables the generation of diverse BCR repertoires for efficient humoral immunity. Deletion of or mutation in c-NHEJ genes in mice and humans confer various degrees of primary immune deficiency and predisposition to lymphoid malignancies that often harbor oncogenic chromosomal translocations. In the absence of c-NHEJ, alternative end-joining (A-EJ) catalyzes robust CSR and to a much lesser extent, V(D)J recombination, but the mechanisms of A-EJ are only poorly defined. In this review, we introduce recent advances in the understanding of A-EJ in the context of V(D)J recombination and CSR with emphases on DSB end processing, DNA polymerases and ligases, and discuss the implications of A-EJ to lymphoid development and chromosomal translocations.
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Affiliation(s)
- Wanyu Bai
- Department of ImmunologyZhongshan School of MedicineSun Yat-sen UniversityGuangzhou510080China,Key Laboratory of Tropical Disease Control (Sun Yat-sen University)Ministry of EducationGuangzhou510080China
| | - Bo Zhao
- Department of ImmunologyZhongshan School of MedicineSun Yat-sen UniversityGuangzhou510080China,Key Laboratory of Tropical Disease Control (Sun Yat-sen University)Ministry of EducationGuangzhou510080China
| | - Mingyu Gu
- Department of ImmunologyZhongshan School of MedicineSun Yat-sen UniversityGuangzhou510080China,Key Laboratory of Tropical Disease Control (Sun Yat-sen University)Ministry of EducationGuangzhou510080China
| | - Junchao Dong
- Department of ImmunologyZhongshan School of MedicineSun Yat-sen UniversityGuangzhou510080China,Key Laboratory of Tropical Disease Control (Sun Yat-sen University)Ministry of EducationGuangzhou510080China,Correspondence address. Tel: +86-20-87330571; E-mail:
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9
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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.
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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
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10
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Cancer mutation profiles predict ICIs efficacy in patients with non-small cell lung cancer. Expert Rev Mol Med 2022; 24:e16. [PMID: 35373730 DOI: 10.1017/erm.2022.9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Although immune checkpoint inhibitors (ICIs) have produced remarkable responses in non-small cell lung cancer (NSCLC) patients, receivers still have a relatively low response rate. Initial response assessment by conventional imaging and evaluation criteria is often unable to identify whether patients can achieve durable clinical benefit from ICIs. Overall, there are sparse effective biomarkers identified to screen NSCLC patients responding to this therapy. A lot of studies have reported that patients with specific gene mutations may benefit from or resist to immunotherapy. However, the single gene mutation may be not effective enough to predict the benefit from immunotherapy for patients. With the advancement in sequencing technology, further studies indicate that many mutations often co-occur and suggest a drastic transformation of tumour microenvironment phenotype. Moreover, co-mutation events have been reported to synergise to activate or suppress signalling pathways of anti-tumour immune response, which also indicates a potential target for combining intervention. Thus, the different mutation profile (especially co-mutation) of patients may be an important concern for predicting or promoting the efficacy of ICIs. However, there is a lack of comprehensive knowledge of this field until now. Therefore, in this study, we reviewed and elaborated the value of cancer mutation profile in predicting the efficacy of immunotherapy and analysed the underlying mechanisms, to provide an alternative way for screening dominant groups, and thereby, optimising individualised therapy for NSCLC patients.
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11
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Libri A, Marton T, Deriano L. The (Lack of) DNA Double-Strand Break Repair Pathway Choice During V(D)J Recombination. Front Genet 2022; 12:823943. [PMID: 35082840 PMCID: PMC8785701 DOI: 10.3389/fgene.2021.823943] [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: 11/28/2021] [Accepted: 12/13/2021] [Indexed: 01/08/2023] Open
Abstract
DNA double-strand breaks (DSBs) are highly toxic lesions that can be mended via several DNA repair pathways. Multiple factors can influence the choice and the restrictiveness of repair towards a given pathway in order to warrant the maintenance of genome integrity. During V(D)J recombination, RAG-induced DSBs are (almost) exclusively repaired by the non-homologous end-joining (NHEJ) pathway for the benefit of antigen receptor gene diversity. Here, we review the various parameters that constrain repair of RAG-generated DSBs to NHEJ, including the peculiarity of DNA DSB ends generated by the RAG nuclease, the establishment and maintenance of a post-cleavage synaptic complex, and the protection of DNA ends against resection and (micro)homology-directed repair. In this physiological context, we highlight that certain DSBs have limited DNA repair pathway choice options.
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Affiliation(s)
- Alice Libri
- Genome Integrity, Immunity and Cancer Unit, Institut Pasteur, Université de Paris, INSERM U1223, Equipe Labellisée Ligue Contre Le Cancer, Paris, France
| | - Timea Marton
- Genome Integrity, Immunity and Cancer Unit, Institut Pasteur, Université de Paris, INSERM U1223, Equipe Labellisée Ligue Contre Le Cancer, Paris, France
| | - Ludovic Deriano
- Genome Integrity, Immunity and Cancer Unit, Institut Pasteur, Université de Paris, INSERM U1223, Equipe Labellisée Ligue Contre Le Cancer, Paris, France
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12
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Acetyltransferases GCN5 and PCAF Are Required for B Lymphocyte Maturation in Mice. Biomolecules 2021; 12:biom12010061. [PMID: 35053209 PMCID: PMC8773862 DOI: 10.3390/biom12010061] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2021] [Revised: 12/28/2021] [Accepted: 12/30/2021] [Indexed: 01/28/2023] Open
Abstract
B lymphocyte development has two DNA recombination processes: V(D)J recombination of the immunoglobulin (Igh) gene variable region, and class switching of the Igh constant regions from IgM to IgG, IgA, or IgE. V(D)J recombination is required for the successful maturation of B cells from pro-B to pre-B to immature-B and then to mature B cells in the bone marrow. CSR occurs outside of the bone marrow when mature B cells migrate to peripheral lymphoid organs, such as spleen and lymph nodes. Both V(D)J recombination and CSR depend on an open chromatin state that makes DNA accessible to specific enzymes, recombination activating gene (RAG), and activation-induced cytidine deaminase (AID). Acetyltransferases GCN5 and PCAF possess redundant functions acetylating histone H3 lysine 9 (H3K9). Here, we generated a mouse model that lacked both GCN5 and PCAF in B cells. Double-deficient mice possessed low levels of mature B cells in the bone marrow and peripheral organs, an accumulation of pro-B cells in bone marrow, and reduced CSR levels. We concluded that both GCN5 and PCAF are required for B-cell development in vivo.
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13
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Lozinski M, Bowden NA, Graves MC, Fay M, Tooney PA. DNA damage repair in glioblastoma: current perspectives on its role in tumour progression, treatment resistance and PIKKing potential therapeutic targets. Cell Oncol (Dordr) 2021; 44:961-981. [PMID: 34057732 DOI: 10.1007/s13402-021-00613-0] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2020] [Accepted: 05/17/2021] [Indexed: 12/31/2022] Open
Abstract
BACKGROUND The aggressive, invasive and treatment resistant nature of glioblastoma makes it one of the most lethal cancers in humans. Total surgical resection is difficult, and a combination of radiation and chemotherapy is used to treat the remaining invasive cells beyond the tumour border by inducing DNA damage and activating cell death pathways in glioblastoma cells. Unfortunately, recurrence is common and a major hurdle in treatment, often met with a more aggressive and treatment resistant tumour. A mechanism of resistance is the response of DNA repair pathways upon treatment-induced DNA damage, which enact cell-cycle arrest and repair of DNA damage that would otherwise cause cell death in tumour cells. CONCLUSIONS In this review, we discuss the significance of DNA repair mechanisms in tumour formation, aggression and treatment resistance. We identify an underlying trend in the literature, wherein alterations in DNA repair pathways facilitate glioma progression, while established high-grade gliomas benefit from constitutively active DNA repair pathways in the repair of treatment-induced DNA damage. We also consider the clinical feasibility of inhibiting DNA repair in glioblastoma and current strategies of using DNA repair inhibitors as agents in combination with chemotherapy, radiation or immunotherapy. Finally, the importance of blood-brain barrier penetrance when designing novel small-molecule inhibitors is discussed.
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Affiliation(s)
- Mathew Lozinski
- School of Biomedical Sciences and Pharmacy, Faculty of Health and Medicine, University of Newcastle, Newcastle, NSW, Australia
- Centre for Drug Repurposing and Medicines Research, University of Newcastle, Newcastle, NSW, Australia
- Hunter Medical Research Institute, Newcastle, NSW, Australia
| | - Nikola A Bowden
- Centre for Drug Repurposing and Medicines Research, University of Newcastle, Newcastle, NSW, Australia
- Hunter Medical Research Institute, Newcastle, NSW, Australia
- School of Medicine and Public Health, Faculty of Health and Medicine, University of Newcastle, Newcastle, NSW, Australia
| | - Moira C Graves
- Centre for Drug Repurposing and Medicines Research, University of Newcastle, Newcastle, NSW, Australia
- Hunter Medical Research Institute, Newcastle, NSW, Australia
- School of Medicine and Public Health, Faculty of Health and Medicine, University of Newcastle, Newcastle, NSW, Australia
| | - Michael Fay
- Centre for Drug Repurposing and Medicines Research, University of Newcastle, Newcastle, NSW, Australia
- Hunter Medical Research Institute, Newcastle, NSW, Australia
- Genesis Cancer Care, Gateshead, New South Wales, Australia
| | - Paul A Tooney
- School of Biomedical Sciences and Pharmacy, Faculty of Health and Medicine, University of Newcastle, Newcastle, NSW, Australia.
- Centre for Drug Repurposing and Medicines Research, University of Newcastle, Newcastle, NSW, Australia.
- Hunter Medical Research Institute, Newcastle, NSW, Australia.
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14
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Oksenych V, Kainov DE. DNA Damage Response. Biomolecules 2021; 11:biom11010123. [PMID: 33477863 PMCID: PMC7832852 DOI: 10.3390/biom11010123] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2020] [Accepted: 01/14/2021] [Indexed: 11/16/2022] Open
Abstract
DNA in our cells is constantly modified by internal and external factors [...].
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Affiliation(s)
- Valentyn Oksenych
- Department for Cancer Research and Molecular Medicine (IKOM), Norwegian University of Science and Technology, 7491 Trondheim, 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, 0316 Oslo, Norway
- Institute of Clinical Medicine, University of Oslo, 0318 Oslo, Norway
- Correspondence: (V.O.); (D.E.K.)
| | - Denis E. Kainov
- Department for Cancer Research and Molecular Medicine (IKOM), Norwegian University of Science and Technology, 7491 Trondheim, Norway
- Institute of Technology, University of Tartu, 50090 Tartu, Estonia
- Correspondence: (V.O.); (D.E.K.)
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15
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Gago-Fuentes R, Oksenych V. Non-Homologous End Joining Factors XLF, PAXX and DNA-PKcs Maintain the Neural Stem and Progenitor Cell Population. Biomolecules 2020; 11:biom11010020. [PMID: 33379193 PMCID: PMC7823790 DOI: 10.3390/biom11010020] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2020] [Revised: 12/19/2020] [Accepted: 12/23/2020] [Indexed: 12/26/2022] Open
Abstract
Non-homologous end-joining (NHEJ) is a major DNA repair pathway in mammalian cells that recognizes, processes and fixes DNA damage throughout the cell cycle and is specifically important for homeostasis of post-mitotic neurons and developing lymphocytes. Neuronal apoptosis increases in the mice lacking NHEJ factors Ku70 and Ku80. Inactivation of other NHEJ genes, either Xrcc4 or Lig4, leads to massive neuronal apoptosis in the central nervous system (CNS) that correlates with embryonic lethality in mice. Inactivation of either Paxx, Mri or Dna-pkcs NHEJ gene results in normal CNS development due to compensatory effects of Xlf. Combined inactivation of Xlf/Paxx, Xlf/Mri and Xlf/Dna-pkcs, however, results in late embryonic lethality and high levels of apoptosis in CNS. To determine the impact of NHEJ factors on the early stages of neurodevelopment, we isolated neural stem and progenitor cells from mouse embryos and investigated proliferation, self-renewal and differentiation capacity of these cells lacking either Xlf, Paxx, Dna-pkcs, Xlf/Paxx or Xlf/Dna-pkcs. We found that XRCC4-like factor (XLF), DNA-dependent protein kinase catalytic subunit (DNA-PKcs) and paralogue of XRCC4 and XLF (PAXX) maintain the neural stem and progenitor cell populations and neurodevelopment in mammals, which is particularly evident in the double knockout models.
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Affiliation(s)
- Raquel Gago-Fuentes
- Department for Cancer Research and Molecular Medicine (IKOM), Norwegian University of Science and Technology, 7491 Trondheim, Norway;
- Department of Circulation and Medical Imaging, Norwegian University of Science and Technology, 7491 Trondheim, Norway
| | - Valentyn Oksenych
- Department for Cancer Research and Molecular Medicine (IKOM), Norwegian University of Science and Technology, 7491 Trondheim, Norway;
- KG Jebsen Centre for B Cell Malignancies, Institute of Clinical Medicine, University of Oslo, 0316 Oslo, Norway
- Institute of Clinical Medicine, University of Oslo, 0318 Oslo, Norway
- Correspondence:
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16
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Castañeda-Zegarra S, Zhang Q, Alirezaylavasani A, Fernandez-Berrocal M, Yao R, Oksenych V. Leaky severe combined immunodeficiency in mice lacking non-homologous end joining factors XLF and MRI. Aging (Albany NY) 2020; 12:23578-23597. [PMID: 33289702 PMCID: PMC7762521 DOI: 10.18632/aging.202346] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2020] [Accepted: 09/21/2020] [Indexed: 11/25/2022]
Abstract
Non-homologous end-joining (NHEJ) is a DNA repair pathway required to detect, process, and ligate DNA double-stranded breaks (DSBs) throughout the cell cycle. The NHEJ pathway is necessary for V(D)J recombination in developing B and T lymphocytes. During NHEJ, Ku70 and Ku80 form a heterodimer that recognizes DSBs and promotes recruitment and function of downstream factors PAXX, MRI, DNA-PKcs, Artemis, XLF, XRCC4, and LIG4. Mutations in several known NHEJ genes result in severe combined immunodeficiency (SCID). Inactivation of Mri, Paxx or Xlf in mice results in normal or mild phenotype, while combined inactivation of Xlf/Mri, Xlf/Paxx, or Xlf/Dna-pkcs leads to late embryonic lethality. Here, we describe three new mouse models. We demonstrate that deletion of Trp53 rescues embryonic lethality in mice with combined deficiencies of Xlf and Mri. Furthermore, Xlf-/-Mri-/-Trp53+/- and Xlf-/-Paxx-/-Trp53+/- mice possess reduced body weight, severely reduced mature lymphocyte counts, and accumulation of progenitor B cells. We also report that combined inactivation of Mri/Paxx results in live-born mice with modest phenotype, and combined inactivation of Mri/Dna-pkcs results in embryonic lethality. Therefore, we conclude that XLF is functionally redundant with MRI and PAXX during lymphocyte development in vivo. Moreover, Mri genetically interacts with Dna-pkcs and Paxx.
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Affiliation(s)
- Sergio Castañeda-Zegarra
- Department of Clinical and Molecular Medicine (IKOM), Norwegian University of Science and Technology, Trondheim, Norway.,Science for Life Laboratory, Department of Oncology-Pathology, Karolinska Institutet, Stockholm, Sweden
| | - Qindong Zhang
- Department of Clinical and Molecular Medicine (IKOM), Norwegian University of Science and Technology, Trondheim, Norway.,Department of Cancer Immunology, Institute for Cancer Research, The Norwegian Radium Hospital, Oslo University Hospital, Oslo, Norway
| | - Amin Alirezaylavasani
- Department of Clinical and Molecular Medicine (IKOM), Norwegian University of Science and Technology, Trondheim, Norway
| | - Marion Fernandez-Berrocal
- Department of Clinical and Molecular Medicine (IKOM), Norwegian University of Science and Technology, Trondheim, Norway
| | - Rouan Yao
- 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.,Department of Biosciences and Nutrition (BioNut), Karolinska Institutet, Huddinge, Sweden.,Institute of Clinical Medicine, UiT The Arctic University of Norway, Tromsø, Norway
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17
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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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18
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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.
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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
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19
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Liu X, Liu T, Shang Y, Dai P, Zhang W, Lee BJ, Huang M, Yang D, Wu Q, Liu LD, Zheng X, Zhou BO, Dong J, Yeap LS, Hu J, Xiao T, Zha S, Casellas R, Liu XS, Meng FL. ERCC6L2 promotes DNA orientation-specific recombination in mammalian cells. Cell Res 2020; 30:732-744. [PMID: 32355287 PMCID: PMC7608219 DOI: 10.1038/s41422-020-0328-3] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2020] [Accepted: 04/16/2020] [Indexed: 01/05/2023] Open
Abstract
Programmed DNA recombination in mammalian cells occurs predominantly in a directional manner. While random DNA breaks are typically repaired both by deletion and by inversion at approximately equal proportions, V(D)J and class switch recombination (CSR) of immunoglobulin heavy chain gene overwhelmingly delete intervening sequences to yield productive rearrangement. What factors channel chromatin breaks to deletional CSR in lymphocytes is unknown. Integrating CRISPR knockout and chemical perturbation screening we here identify the Snf2-family helicase-like ERCC6L2 as one such factor. We show that ERCC6L2 promotes double-strand break end-joining and facilitates optimal CSR in mice. At the cellular levels, ERCC6L2 rapidly engages in DNA repair through its C-terminal domains. Mechanistically, ERCC6L2 interacts with other end-joining factors and plays a functionally redundant role with the XLF end-joining factor in V(D)J recombination. Strikingly, ERCC6L2 controls orientation-specific joining of broken ends during CSR, which relies on its helicase activity. Thus, ERCC6L2 facilitates programmed recombination through directional repair of distant breaks.
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Affiliation(s)
- Xiaojing Liu
- State Key Laboratory of Molecular Biology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, Shanghai, 200031, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Tingting Liu
- State Key Laboratory of Molecular Biology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, Shanghai, 200031, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Yafang Shang
- State Key Laboratory of Molecular Biology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, Shanghai, 200031, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Pengfei Dai
- State Key Laboratory of Molecular Biology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, Shanghai, 200031, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Wubing Zhang
- Clinical Translational Research Center, Shanghai Pulmonary Hospital, School of Life Sciences and Technology, Tongji University, Shanghai, 200092, China
| | - Brian J Lee
- Institute for Cancer Genetics, Vagelos College of Physicians and Surgeons, Columbia University, New York, NY, 10032, USA
| | - Min Huang
- State Key Laboratory of Molecular Biology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, Shanghai, 200031, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Dingpeng Yang
- State Key Laboratory of Molecular Biology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, Shanghai, 200031, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Qiu Wu
- Clinical Translational Research Center, Shanghai Pulmonary Hospital, School of Life Sciences and Technology, Tongji University, Shanghai, 200092, China
| | - Liu Daisy Liu
- State Key Laboratory of Molecular Biology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, Shanghai, 200031, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Xiaoqi Zheng
- Department of Mathematics, Shanghai Normal University, Shanghai, 200234, China
| | - Bo O Zhou
- State Key Laboratory of Molecular Biology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, Shanghai, 200031, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Junchao Dong
- Department of Immunology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, 510080, China
| | - Leng-Siew Yeap
- Shanghai Institute of Immunology, Department of Immunology and Microbiology, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
| | - Jiazhi Hu
- The MOE Key Laboratory of Cell Proliferation and Differentiation, Genome Editing Research Center, School of Life Sciences, Peking-Tsinghua Center for Life Sciences, Peking University, 100871, Beijing, China
| | - Tengfei Xiao
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, 02115, USA
| | - Shan Zha
- Institute for Cancer Genetics, Vagelos College of Physicians and Surgeons, Columbia University, New York, NY, 10032, USA
| | - Rafael Casellas
- Lymphocyte Nuclear Biology, NIAMS, Center of Cancer Research, NCI, NIH, Bethesda, MD, 20892, USA
| | - X Shirley Liu
- Department of Data Sciences, Dana-Farber Cancer Institute and Harvard T.H.Chan School of Public Health, Boston, MA, 02215, USA
| | - Fei-Long Meng
- State Key Laboratory of Molecular Biology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, Shanghai, 200031, China. .,University of Chinese Academy of Sciences, Beijing, 100049, China.
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20
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Chu SH, Chabon JR, Matovina CN, Minehart JC, Chen BR, Zhang J, Kumar V, Xiong Y, Callen E, Hung PJ, Feng Z, Koche RP, Liu XS, Chaudhuri J, Nussenzweig A, Sleckman BP, Armstrong SA. Loss of H3K36 Methyltransferase SETD2 Impairs V(D)J Recombination during Lymphoid Development. iScience 2020; 23:100941. [PMID: 32169821 PMCID: PMC7066224 DOI: 10.1016/j.isci.2020.100941] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2019] [Revised: 01/25/2020] [Accepted: 02/21/2020] [Indexed: 12/17/2022] Open
Abstract
Repair of DNA double-stranded breaks (DSBs) during lymphocyte development is essential for V(D)J recombination and forms the basis of immunoglobulin variable region diversity. Understanding of this process in lymphogenesis has historically been centered on the study of RAG1/2 recombinases and a set of classical non-homologous end-joining factors. Much less has been reported regarding the role of chromatin modifications on this process. Here, we show a role for the non-redundant histone H3 lysine methyltransferase, Setd2, and its modification of lysine-36 trimethylation (H3K36me3), in the processing and joining of DNA ends during V(D)J recombination. Loss leads to mis-repair of Rag-induced DNA DSBs, especially when combined with loss of Atm kinase activity. Furthermore, loss reduces immune repertoire and a severe block in lymphogenesis as well as causes post-mitotic neuronal apoptosis. Together, these studies are suggestive of an important role of Setd2/H3K36me3 in these two mammalian developmental processes that are influenced by double-stranded break repair.
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Affiliation(s)
- S Haihua Chu
- Department of Pediatric Oncology, Dana Farber Cancer Institute, and Division of Hematology/Oncology, Boston Children's Hospital, 450 Brookline Avenue, Boston, MA 02215-5450, USA
| | - Jonathan R Chabon
- Department of Pediatric Oncology, Dana Farber Cancer Institute, and Division of Hematology/Oncology, Boston Children's Hospital, 450 Brookline Avenue, Boston, MA 02215-5450, USA
| | - Chloe N Matovina
- Department of Pediatric Oncology, Dana Farber Cancer Institute, and Division of Hematology/Oncology, Boston Children's Hospital, 450 Brookline Avenue, Boston, MA 02215-5450, USA
| | | | - Bo-Ruei Chen
- Department of Pathology and Laboratory Medicine, Weill Cornell Medical College, New York, NY, USA
| | - Jian Zhang
- Center for Computational Biology, Beijing Institute of Basic Medical Sciences, Beijing, China; Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute and Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Vipul Kumar
- Howard Hughes Medical Institute, Department of Pediatrics, Department of Genetics, Harvard Medical School, Boston, MA, USA; Harvard-MIT MD-PhD Program, Harvard Medical School, Boston, MA, USA
| | - Yijun Xiong
- Department of Pediatric Oncology, Dana Farber Cancer Institute, and Division of Hematology/Oncology, Boston Children's Hospital, 450 Brookline Avenue, Boston, MA 02215-5450, USA
| | - Elsa Callen
- Laboratory of Genome Integrity, National Cancer Institute National Institutes of Health, Bethesda, MD, USA
| | - Putzer J Hung
- Department of Pathology and Laboratory Medicine, Weill Cornell Medical College, New York, NY, USA; Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO, USA
| | - Zhaohui Feng
- Department of Pediatric Oncology, Dana Farber Cancer Institute, and Division of Hematology/Oncology, Boston Children's Hospital, 450 Brookline Avenue, Boston, MA 02215-5450, USA
| | - Richard P Koche
- Cancer Biology and Genetics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - X Shirley Liu
- Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute and Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Jayanta Chaudhuri
- Immunology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA; Immunology and Microbial Pathogenesis Program, Weill Cornell Graduate School of Medical Sciences, New York, NY, USA
| | - Andre Nussenzweig
- Laboratory of Genome Integrity, National Cancer Institute National Institutes of Health, Bethesda, MD, USA
| | - Barry P Sleckman
- Department of Pathology and Laboratory Medicine, Weill Cornell Medical College, New York, NY, USA
| | - Scott A Armstrong
- Department of Pediatric Oncology, Dana Farber Cancer Institute, and Division of Hematology/Oncology, Boston Children's Hospital, 450 Brookline Avenue, Boston, MA 02215-5450, USA.
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Musilli S, Abramowski V, Roch B, de Villartay JP. An in vivo study of the impact of deficiency in the DNA repair proteins PAXX and XLF on development and maturation of the hemolymphoid system. J Biol Chem 2020; 295:2398-2406. [PMID: 31915249 DOI: 10.1074/jbc.ac119.010924] [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: 09/03/2019] [Revised: 01/03/2020] [Indexed: 12/22/2022] Open
Abstract
Repair of DNA double-strand breaks by the nonhomologous end joining pathway is central for proper development of the adaptive immune system. This repair pathway involves eight factors, including XRCC4-like factor (XLF)/Cernunnos and the paralog of XRCC4 and XLF, PAXX nonhomologous end joining factor (PAXX). Xlf-/- and Paxx-/- mice are viable and exhibit only a mild immunophenotype. However, mice lacking both PAXX and XLF are embryonic lethal because postmitotic neurons undergo massive apoptosis in embryos. To decipher the roles of PAXX and XLF in both variable, diversity, and joining recombination and immunoglobulin class switch recombination, here, using Cre/lox-specific deletion to prevent double-KO embryonic lethality, we developed two mouse models of a conditional Xlf KO in a Paxx-/- background. Cre expressed under control of the iVav or CD21 promoter enabled Xlf deletion in early hematopoietic progenitors and splenic mature B cells, respectively. We demonstrate the XLF and PAXX interplay during variable, diversity, and joining recombination in vivo but not during class switch recombination, for which PAXX appeared to be fully dispensable. Xlf/Paxx double KO in hematopoietic progenitors resulted in a shorter lifespan associated with onset of thymic lymphomas, revealing a genome caretaking function of XLF/PAXX.
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Affiliation(s)
- Stefania Musilli
- Laboratory of Genome Dynamics in the Immune System, Imagine Institute, INSERM UMR 1163, Université de Paris, 75015 Paris, France
| | - Vincent Abramowski
- Laboratory of Genome Dynamics in the Immune System, Imagine Institute, INSERM UMR 1163, Université de Paris, 75015 Paris, France
| | - Benoit Roch
- Laboratory of Genome Dynamics in the Immune System, Imagine Institute, INSERM UMR 1163, Université de Paris, 75015 Paris, France
| | - Jean-Pierre de Villartay
- Laboratory of Genome Dynamics in the Immune System, Imagine Institute, INSERM UMR 1163, Université de Paris, 75015 Paris, France.
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22
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Beck C, Castañeda-Zegarra S, Huse C, Xing M, Oksenych V. Mediator of DNA Damage Checkpoint Protein 1 Facilitates V(D)J Recombination in Cells Lacking DNA Repair Factor XLF. Biomolecules 2019; 10:biom10010060. [PMID: 31905950 PMCID: PMC7023129 DOI: 10.3390/biom10010060] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2019] [Revised: 12/23/2019] [Accepted: 12/24/2019] [Indexed: 11/16/2022] Open
Abstract
DNA double-strand breaks (DSBs) trigger the Ataxia telangiectasia mutated (ATM)-dependent DNA damage response (DDR), which consists of histone H2AX, MDC1, RNF168, 53BP1, PTIP, RIF1, Rev7, and Shieldin. Early stages of B and T lymphocyte development are dependent on recombination activating gene (RAG)-induced DSBs that form the basis for further V(D)J recombination. Non-homologous end joining (NHEJ) pathway factors recognize, process, and ligate DSBs. Based on numerous loss-of-function studies, DDR factors were thought to be dispensable for the V(D)J recombination. In particular, mice lacking Mediator of DNA Damage Checkpoint Protein 1 (MDC1) possessed nearly wild-type levels of mature B and T lymphocytes in the spleen, thymus, and bone marrow. NHEJ factor XRCC4-like factor (XLF)/Cernunnos is functionally redundant with ATM, histone H2AX, and p53-binding protein 1 (53BP1) during the lymphocyte development in mice. Here, we genetically inactivated MDC1, XLF, or both MDC1 and XLF in murine vAbl pro-B cell lines and, using chromosomally integrated substrates, demonstrated that MDC1 stimulates the V(D)J recombination in cells lacking XLF. Moreover, combined inactivation of MDC1 and XLF in mice resulted in synthetic lethality. Together, these findings suggest that MDC1 and XLF are functionally redundant during the mouse development, in general, and the V(D)J recombination, in particular.
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Affiliation(s)
- Carole Beck
- Department of Clinical and Molecular Medicine (IKOM), Norwegian University of Science and Technology (NTNU), 7491 Trondheim, Norway
- St. Olavs Hospital, Trondheim University Hospital, Clinic of Medicine, Postboks 3250 Sluppen, 7006 Trondheim, Norway
| | - Sergio Castañeda-Zegarra
- Department of Clinical and Molecular Medicine (IKOM), Norwegian University of Science and Technology (NTNU), 7491 Trondheim, Norway
- St. Olavs Hospital, Trondheim University Hospital, Clinic of Medicine, Postboks 3250 Sluppen, 7006 Trondheim, Norway
| | - Camilla Huse
- Department of Clinical and Molecular Medicine (IKOM), Norwegian University of Science and Technology (NTNU), 7491 Trondheim, Norway
- St. Olavs Hospital, Trondheim University Hospital, Clinic of Medicine, Postboks 3250 Sluppen, 7006 Trondheim, Norway
| | - Mengtan Xing
- Department of Clinical and Molecular Medicine (IKOM), Norwegian University of Science and Technology (NTNU), 7491 Trondheim, Norway
- St. Olavs Hospital, Trondheim University Hospital, Clinic of Medicine, Postboks 3250 Sluppen, 7006 Trondheim, Norway
| | - Valentyn Oksenych
- Department of Clinical and Molecular Medicine (IKOM), Norwegian University of Science and Technology (NTNU), 7491 Trondheim, Norway
- St. Olavs Hospital, Trondheim University Hospital, Clinic of Medicine, Postboks 3250 Sluppen, 7006 Trondheim, Norway
- Department of Biosciences and Nutrition (BioNuT), Karolinska Institutet, 14183 Huddinge, Sweden
- Correspondence:
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Generation of a Mouse Model Lacking the Non-Homologous End-Joining Factor Mri/Cyren. Biomolecules 2019; 9:biom9120798. [PMID: 31795137 PMCID: PMC6995585 DOI: 10.3390/biom9120798] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2019] [Revised: 11/23/2019] [Accepted: 11/26/2019] [Indexed: 11/17/2022] Open
Abstract
Classical non-homologous end joining (NHEJ) is a molecular pathway that detects, processes, and ligates DNA double-strand breaks (DSBs) throughout the cell cycle. Mutations in several NHEJ genes result in neurological abnormalities and immunodeficiency both in humans and mice. The NHEJ pathway is required for V(D)J recombination in developing B and T lymphocytes, and for class switch recombination in mature B cells. The Ku heterodimer formed by Ku70 and Ku80 recognizes DSBs and facilitates the recruitment of accessory factors (e.g., DNA-PKcs, Artemis, Paxx and Mri/Cyren) and downstream core factor subunits X-ray repair cross-complementing group 4 (XRCC4), XRCC4-like factor (XLF), and DNA ligase 4 (Lig4). Accessory factors might be dispensable for the process, depending on the genetic background and DNA lesion type. To determine the physiological role of Mri in DNA repair and development, we introduced a frame-shift mutation in the Mri gene in mice. We then analyzed the development of Mri-deficient mice as well as wild type and immunodeficient controls. Mice lacking Mri possessed reduced levels of class switch recombination in B lymphocytes and slow proliferation of neuronal progenitors when compared to wild type littermates. Human cell lines lacking Mri were as sensitive to DSBs as the wild type controls. Overall, we concluded that Mri/Cyren is largely dispensable for DNA repair and mouse development.
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Chen Y, Chen G, Li J, Huang YY, Li Y, Lin J, Chen LZ, Lu JP, Wang YQ, Wang CX, Pan LK, Xia XF, Yi X, Chen CB, Zheng XW, Guo ZQ, Pan JJ. Association of Tumor Protein p53 and Ataxia-Telangiectasia Mutated Comutation With Response to Immune Checkpoint Inhibitors and Mortality in Patients With Non-Small Cell Lung Cancer. JAMA Netw Open 2019; 2:e1911895. [PMID: 31539077 PMCID: PMC6755545 DOI: 10.1001/jamanetworkopen.2019.11895] [Citation(s) in RCA: 47] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
IMPORTANCE Immune checkpoint inhibitors (ICIs) can elicit durable antitumor responses in patients with non-small cell lung cancer (NSCLC), but only 20% to 25% of patients respond to treatment. As important genes in the DNA damage response pathway, comutation in the tumor protein p53 (TP53) and ataxia-telangiectasia mutated (ATM) genes may be associated with genomic instability and hypermutation. However, the prevalence of TP53 and ATM comutation and its association with response to ICIs are not fully understood. OBJECTIVE To examine the prevalence of the TP53 and ATM comutation, the potential mechanism, and its association with response to ICIs among patients with NSCLC. DESIGN, SETTING, AND PARTICIPANTS This multiple-cohort study included patients with NSCLC from the Geneplus Institute, the Cancer Genome Atlas (TCGA), and the Memorial Sloan Kettering Cancer Center (MSKCC) databases and from the POPLAR and OAK randomized controlled trials. Samples in the Geneplus cohort were collected and analyzed from April 30, 2015, through February 28, 2019. Data from TCGA, the MSKCC, and the POPLAR and OAK cohorts were obtained on January 1, 2019, and analyzed from January 1 to April 10, 2019. Next-generation sequencing assays were performed on tumor samples by the Geneplus Institute. Genomic, transcriptomic, and clinical data were obtained from TCGA and MSKCC databases. EXPOSURES Comprehensive genetic profiling was performed to determine the prevalence of TP53 and ATM comutation and its association with prognosis and response to ICIs. MAIN OUTCOMES AND MEASURES The main outcomes were TP53 and ATM comutation frequency, overall survival (OS), progression-free survival, gene set enrichment analysis, and immune profile in NSCLC. RESULTS Patients with NSCLC analyzed in this study included 2020 patients in the Geneplus cohort (mean [SD] age, 59.5 [10.5] years; 1168 [57.8%] men), 1031 patients in TCGA cohort (mean [SD] age, 66.2 [9.5] years; 579 [56.2%] men), 1527 patients in the MSKCC cohort (662 [43.4%] men), 350 patients in the MSKCC cohort who were treated with ICIs (mean [SD] age, 61.4 [13.8] years; 170 [48.6%] men), and 853 patients in the POPLAR and OAK cohort (mean [SD] age, 63.0 [9.1] years; 527 [61.8%] men). Sites of TP53 and ATM comutation were found scattered throughout the genes, and no significant difference was observed in the frequency of TP53 and ATM comutation within the histologic subtypes and driver genes. In 5 independent cohorts of patients with NSCLC, TP53 and ATM comutation was associated with a significantly higher tumor mutation burden compared with the sole mutation and with no mutation (TCGA, MSKCC, Geneplus, and POPLAR and OAK cohort). Among patients treated with ICIs in the MSKCC cohort, TP53 and ATM comutation was associated with better OS than a single mutation and no mutation among patients with any cancer (median OS: TP53 and ATM comutation, not reached; TP53 mutation alone, 14.0 months; ATM mutation alone, 40.0 months; no mutation, 22.0 months; P = .001; NSCLC median OS: TP53 and ATM comutation, not reached; TP53 mutation alone, 11.0 months; ATM mutation alone, 16.0 months; no mutation, 14.0 months; P = .24). Similar results were found in the POPLAR and OAK cohort in which the disease control benefit rate, progression-free survival, and OS were all greater in patients with the TP53 and ATM comutation compared with the other 3 groups (median progression-free survival: TP53 and ATM comutation, 10.4 months; TP53 mutation, 1.6 months; ATM mutation, 3.5 months; no mutation, 2.8 months; P = .01; median OS: TP53 and ATM comutation, 22.1 months; TP53 mutation, 8.3 months; ATM mutation, 15.8 months; no mutation, 15.3 months; P = .002). CONCLUSIONS AND RELEVANCE This study's findings suggest that the TP53 and ATM comutation occurs in a subgroup of patients with NSCLC and is associated with an increased tumor mutation burden and response to ICIs. This suggests that TP53 and ATM comutation may have implications as a biomarker for guiding ICI treatment.
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Affiliation(s)
- Yu Chen
- Fujian Provincial Key Laboratory of Translational Cancer Medicine, Fuzhou, China
- Cancer Bio-immunotherapy Center, Fujian Medical University Cancer Hospital and Fujian Cancer Hospital, Fuzhou, China
- Department of Medical Oncology, Fujian Medical University Cancer Hospital and Fujian Cancer Hospital, Fuzhou, China
| | - Gang Chen
- Fujian Provincial Key Laboratory of Translational Cancer Medicine, Fuzhou, China
- Department of Pathology, Fujian Medical University Cancer Hospital and Fujian Cancer Hospital, Fuzhou, China
| | - Jin Li
- Geneplus-Beijing Institute, Beijing, China
| | | | - Yi Li
- Fujian Medical University Cancer Hospital, Fuzhou, China
| | - Jing Lin
- Fujian Provincial Key Laboratory of Translational Cancer Medicine, Fuzhou, China
- Cancer Bio-immunotherapy Center, Fujian Medical University Cancer Hospital and Fujian Cancer Hospital, Fuzhou, China
- Department of Medical Oncology, Fujian Medical University Cancer Hospital and Fujian Cancer Hospital, Fuzhou, China
| | - Li-Zhu Chen
- Cancer Bio-immunotherapy Center, Fujian Medical University Cancer Hospital and Fujian Cancer Hospital, Fuzhou, China
- Department of Medical Oncology, Fujian Medical University Cancer Hospital and Fujian Cancer Hospital, Fuzhou, China
| | - Jian-Ping Lu
- Department of Pathology, Fujian Medical University Cancer Hospital and Fujian Cancer Hospital, Fuzhou, China
| | - Yu-Qi Wang
- Geneplus-Beijing Institute, Beijing, China
| | | | - Leong Kin Pan
- China Certification and Inspection Group, Kuok Kim Medical Center III, Macao, China
- Hui Xian Medical Center, Macao, China
| | | | - Xin Yi
- Geneplus-Beijing Institute, Beijing, China
| | - Chuan-Ben Chen
- Fujian Provincial Key Laboratory of Translational Cancer Medicine, Fuzhou, China
- Cancer Bio-immunotherapy Center, Fujian Medical University Cancer Hospital and Fujian Cancer Hospital, Fuzhou, China
- Department of Radiation Oncology, Fujian Medical University Cancer Hospital and Fujian Cancer Hospital, Fuzhou, China
| | - Xiong-Wei Zheng
- Fujian Provincial Key Laboratory of Translational Cancer Medicine, Fuzhou, China
- Department of Pathology, Fujian Medical University Cancer Hospital and Fujian Cancer Hospital, Fuzhou, China
| | - Zeng-Qing Guo
- Fujian Provincial Key Laboratory of Translational Cancer Medicine, Fuzhou, China
- Cancer Bio-immunotherapy Center, Fujian Medical University Cancer Hospital and Fujian Cancer Hospital, Fuzhou, China
- Department of Medical Oncology, Fujian Medical University Cancer Hospital and Fujian Cancer Hospital, Fuzhou, China
| | - Jian-Ji Pan
- Fujian Provincial Key Laboratory of Translational Cancer Medicine, Fuzhou, China
- Cancer Bio-immunotherapy Center, Fujian Medical University Cancer Hospital and Fujian Cancer Hospital, Fuzhou, China
- Department of Radiation Oncology, Fujian Medical University Cancer Hospital and Fujian Cancer Hospital, Fuzhou, China
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25
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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.
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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
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26
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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.
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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.
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Yeap LS, Meng FL. Cis- and trans-factors affecting AID targeting and mutagenic outcomes in antibody diversification. Adv Immunol 2019; 141:51-103. [PMID: 30904133 DOI: 10.1016/bs.ai.2019.01.002] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Antigen receptor diversification is a hallmark of adaptive immunity which allows specificity of the receptor to particular antigen. B cell receptor (BCR) or its secreted form, antibody, is diversified through antigen-independent and antigen-dependent mechanisms. During B cell development in bone marrow, BCR is diversified via V(D)J recombination mediated by RAG endonuclease. Upon stimulation by antigen, B cell undergo somatic hypermutation (SHM) to allow affinity maturation and class switch recombination (CSR) to change the effector function of the antibody. Both SHM and CSR are initiated by activation-induced cytidine deaminase (AID). Repair of AID-initiated lesions through different DNA repair pathways results in diverse mutagenic outcomes. Here, we focus on discussing cis- and trans-factors that target AID to its substrates and factors that affect different outcomes of AID-initiated lesions. The knowledge of mechanisms that govern AID targeting and outcomes could be harnessed to elicit rare functional antibodies and develop ex vivo antibody diversification approaches with diversifying base editors.
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Affiliation(s)
- Leng-Siew Yeap
- Shanghai Institute of Immunology, Department of Immunology and Microbiology, Shanghai Jiao Tong University School of Medicine, Shanghai, China.
| | - Fei-Long Meng
- State Key Laboratory of Molecular Biology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai, China.
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28
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Castañeda-Zegarra S, Xing M, Gago-Fuentes R, Sæterstad S, Oksenych V. Synthetic lethality between DNA repair factors Xlf and Paxx is rescued by inactivation of Trp53. DNA Repair (Amst) 2018; 73:164-169. [PMID: 30579708 DOI: 10.1016/j.dnarep.2018.12.002] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2018] [Revised: 12/04/2018] [Accepted: 12/14/2018] [Indexed: 02/03/2023]
Abstract
Non-homologous end joining (NHEJ) is a DNA repair pathway that senses, processes and ligates DNA double-strand breaks (DSBs) throughout the cell cycle. During NHEJ, core Ku70 and Ku80 subunits bind DSBs as a heterodimer and promote further recruitment of accessory factors (e.g., PAXX, Mri, DNA-PKcs, Artemis) and downstream core subunits XRCC4 and DNA ligase 4 (Lig4). Inactivation of Ku70 or Ku80 genes in mice results in immunodeficiency and high levels of genomic instability; deletion of individual Dna-pkcs, Xlf, Paxx or Mri genes results in viable mice with no or modest DNA repair defects. However, combined inactivation of either Xlf and Dna-pkcs, or Xlf and Paxx, or Xlf and Mri, leads to synthetic lethality in mice, which correlates with increased levels of apoptosis in the central nervous system. Here, we demonstrated that inactivation of pro-apoptotic factor Trp53 rescues embryonic lethality of Xlf-/-Paxx-/- and Xlf-/-Dna-pkcs-/- double knockout mice. Moreover, combined inactivation of Paxx and Dna-pkcs results in live-born fertile Paxx-/-Dna-pkcs-/- mice indistinguishable from Dna-pkcs-/- knockout controls.
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Affiliation(s)
- Sergio Castañeda-Zegarra
- Department of Clinical and Molecular Medicine, Norwegian University of Science and Technology, Laboratory Center, Erling Skjalgssons gate 1, 7491, Trondheim, Norway; St. Olavs Hospital, Trondheim University Hospital, Clinic of Medicine, Postboks 3250 Sluppen, 7006, Trondheim, Norway; Department of Biomedicine, University of Bergen, Bergen, Norway
| | - Mengtan Xing
- Department of Clinical and Molecular Medicine, Norwegian University of Science and Technology, Laboratory Center, Erling Skjalgssons gate 1, 7491, Trondheim, Norway; St. Olavs Hospital, Trondheim University Hospital, Clinic of Medicine, Postboks 3250 Sluppen, 7006, Trondheim, Norway
| | - Raquel Gago-Fuentes
- Department of Clinical and Molecular Medicine, Norwegian University of Science and Technology, Laboratory Center, Erling Skjalgssons gate 1, 7491, Trondheim, Norway; St. Olavs Hospital, Trondheim University Hospital, Clinic of Medicine, Postboks 3250 Sluppen, 7006, Trondheim, Norway
| | - Siri Sæterstad
- Department of Clinical and Molecular Medicine, Norwegian University of Science and Technology, Laboratory Center, Erling Skjalgssons gate 1, 7491, Trondheim, Norway; St. Olavs Hospital, Trondheim University Hospital, Clinic of Medicine, Postboks 3250 Sluppen, 7006, Trondheim, Norway
| | - Valentyn Oksenych
- Department of Clinical and Molecular Medicine, Norwegian University of Science and Technology, Laboratory Center, Erling Skjalgssons gate 1, 7491, Trondheim, Norway; St. Olavs Hospital, Trondheim University Hospital, Clinic of Medicine, Postboks 3250 Sluppen, 7006, Trondheim, Norway; Department of Biosciences and Nutrition, Karolinska Institutet, Huddinge, Sweden.
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29
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Barros FS, Marussi VHR, Amaral LLF, da Rocha AJ, Campos CMS, Freitas LF, Huisman TAGM, Soares BP. The Rare Neurocutaneous Disorders: Update on Clinical, Molecular, and Neuroimaging Features. Top Magn Reson Imaging 2018; 27:433-462. [PMID: 30516694 DOI: 10.1097/rmr.0000000000000185] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Phakomatoses, also known as neurocutaneous disorders, comprise a vast number of entities that predominantly affect structures originated from the ectoderm such as the central nervous system and the skin, but also the mesoderm, particularly the vascular system. Extensive literature exists about the most common phakomatoses, namely neurofibromatosis, tuberous sclerosis, von Hippel-Lindau and Sturge-Weber syndrome. However, recent developments in the understanding of the molecular underpinnings of less common phakomatoses have sparked interest in these disorders. In this article, we review the clinical features, current pathogenesis, and modern neuroimaging findings of melanophakomatoses, vascular phakomatoses, and other rare neurocutaneous syndromes that may also include tissue overgrowth or neoplastic predisposition.
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Affiliation(s)
- Felipe S Barros
- Division of Neuroradiology, BP Medicina Diagnóstica, Hospital da Beneficência Portuguesa de São Paulo
| | - Victor Hugo R Marussi
- Division of Neuroradiology, BP Medicina Diagnóstica, Hospital da Beneficência Portuguesa de São Paulo
| | - Lázaro L F Amaral
- Division of Neuroradiology, BP Medicina Diagnóstica, Hospital da Beneficência Portuguesa de São Paulo
| | - Antônio José da Rocha
- Division of Neuroradiology, Department of Radiology, Santa Casa de São Paulo School of Medical Sciences, São Paulo, Brazil
| | - Christiane M S Campos
- Division of Neuroradiology, BP Medicina Diagnóstica, Hospital da Beneficência Portuguesa de São Paulo
| | - Leonardo F Freitas
- Division of Neuroradiology, BP Medicina Diagnóstica, Hospital da Beneficência Portuguesa de São Paulo
| | - Thierry A G M Huisman
- Division of Pediatric Radiology and Pediatric Neuroradiology, Russell H. Morgan Department of Radiology and Radiological Science, Johns Hopkins University School of Medicine, Baltimore, MD
| | - Bruno P Soares
- Division of Pediatric Radiology and Pediatric Neuroradiology, Russell H. Morgan Department of Radiology and Radiological Science, Johns Hopkins University School of Medicine, Baltimore, MD
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Dewan A, Xing M, Lundbæk MB, Gago‐Fuentes R, Beck C, Aas PA, Liabakk N, Sæterstad S, Chau KTP, Kavli BM, Oksenych V. Robust DNA repair in PAXX-deficient mammalian cells. FEBS Open Bio 2018; 8:442-448. [PMID: 29511621 PMCID: PMC5832976 DOI: 10.1002/2211-5463.12380] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2017] [Revised: 12/19/2017] [Accepted: 01/04/2018] [Indexed: 12/02/2022] Open
Abstract
To ensure genome stability, mammalian cells employ several DNA repair pathways. Nonhomologous DNA end joining (NHEJ) is the DNA repair process that fixes double-strand breaks throughout the cell cycle. NHEJ is involved in the development of B and T lymphocytes through its function in V(D)J recombination and class switch recombination (CSR). NHEJ consists of several core and accessory factors, including Ku70, Ku80, XRCC4, DNA ligase 4, DNA-PKcs, Artemis, and XLF. Paralog of XRCC4 and XLF (PAXX) is the recently described accessory NHEJ factor that structurally resembles XRCC4 and XLF and interacts with Ku70/Ku80. To determine the physiological role of PAXX in mammalian cells, we purchased and characterized a set of custom-generated and commercially available NHEJ-deficient human haploid HAP1 cells, PAXXΔ, XRCC4Δ , and XLFΔ . In our studies, HAP1 PAXXΔ cells demonstrated modest sensitivity to DNA damage, which was comparable to wild-type controls. By contrast, XRCC4Δ and XLFΔ HAP1 cells possessed significant DNA repair defects measured as sensitivity to double-strand break inducing agents and chromosomal breaks. To investigate the role of PAXX in CSR, we generated and characterized Paxx-/- and Aid-/- murine lymphoid CH12F3 cells. CSR to IgA was nearly at wild-type levels in the Paxx-/- cells and completely ablated in the absence of activation-induced cytidine deaminase (AID). In addition, Paxx-/- CH12F3 cells were hypersensitive to zeocin when compared to wild-type controls. We concluded that Paxx-deficient mammalian cells maintain robust NHEJ and CSR.
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Affiliation(s)
- Alisa Dewan
- Department of Clinical and Molecular Medicine (IKOM)Norwegian University of Science and TechnologyTrondheimNorway
- Present address:
Centre for Immune Regulation and Department of ImmunologyUniversity of Oslo and Oslo University Hospital‐RikshospitaletOsloNorway
- Present address:
KG Jebsen Coeliac Disease Research CentreUniversity of OsloOsloNorway
| | - Mengtan Xing
- Department of Clinical and Molecular Medicine (IKOM)Norwegian University of Science and TechnologyTrondheimNorway
| | - Marie Benner Lundbæk
- Department of Clinical and Molecular Medicine (IKOM)Norwegian University of Science and TechnologyTrondheimNorway
| | - Raquel Gago‐Fuentes
- Department of Clinical and Molecular Medicine (IKOM)Norwegian University of Science and TechnologyTrondheimNorway
| | - Carole Beck
- Department of Clinical and Molecular Medicine (IKOM)Norwegian University of Science and TechnologyTrondheimNorway
| | - Per Arne Aas
- Department of Clinical and Molecular Medicine (IKOM)Norwegian University of Science and TechnologyTrondheimNorway
| | - Nina‐Beate Liabakk
- Department of Clinical and Molecular Medicine (IKOM)Norwegian University of Science and TechnologyTrondheimNorway
| | - Siri Sæterstad
- Department of Clinical and Molecular Medicine (IKOM)Norwegian University of Science and TechnologyTrondheimNorway
| | - Khac Thanh Phong Chau
- Department of Clinical and Molecular Medicine (IKOM)Norwegian University of Science and TechnologyTrondheimNorway
| | - Bodil Merete Kavli
- Department of Clinical and Molecular Medicine (IKOM)Norwegian University of Science and TechnologyTrondheimNorway
| | - Valentyn Oksenych
- Department of Clinical and Molecular Medicine (IKOM)Norwegian University of Science and TechnologyTrondheimNorway
- St. Olavs HospitalTrondheim University Hospital, Clinic of MedicineNorway
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31
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Gago‐Fuentes R, Xing M, Sæterstad S, Sarno A, Dewan A, Beck C, Bradamante S, Bjørås M, Oksenych V. Normal development of mice lacking PAXX, the paralogue of XRCC4 and XLF. FEBS Open Bio 2018; 8:426-434. [PMID: 29511619 PMCID: PMC5832975 DOI: 10.1002/2211-5463.12381] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2017] [Revised: 12/18/2017] [Accepted: 01/04/2018] [Indexed: 02/05/2023] Open
Abstract
DNA repair consists of several cellular pathways which recognize and repair damaged DNA. The classical nonhomologous DNA end-joining (NHEJ) pathway repairs double-strand breaks in DNA. It is required for maturation of both B and T lymphocytes by supporting V(D)J recombination as well as B-cell differentiation during class switch recombination (CSR). Inactivation of NHEJ factors Ku70, Ku80, XRCC4, DNA ligase 4, DNA-PKcs, and Artemis impairs V(D)J recombination and blocks lymphocyte development. Paralogue of XRCC4 and XLF (PAXX) is an accessory NHEJ factor that has a significant impact on the repair of DNA lesions induced by ionizing radiation in human, murine, and chicken cells. However, the role of PAXX during development is poorly understood. To determine the physiological role of PAXX, we deleted part of the Paxx promoter and the first two exons in mice. Further, we compared Paxx-knockout mice with wild-type (WT) and NHEJ-deficient controls including Ku80- and Dna-pkcs-null and severe combined immunodeficiency mice. Surprisingly, Paxx-deficient mice were not distinguishable from the WT littermates; they were the same weight and size, fertility status, had normal spleen, thymus, and bone marrow. Paxx-deficient mice had the same number of chromosomal and chromatid breaks as WT mice. Moreover, Paxx-deficient primary B lymphocytes had the same level of CSR as lymphocytes isolated from WT mice. We concluded that PAXX is dispensable for normal mouse development.
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Affiliation(s)
- Raquel Gago‐Fuentes
- Institute of Clinical and Molecular Medicine (IKOM)Laboratory CenterNorwegian University of Science and TechnologyTrondheimNorway
| | - Mengtan Xing
- Institute of Clinical and Molecular Medicine (IKOM)Laboratory CenterNorwegian University of Science and TechnologyTrondheimNorway
| | - Siri Sæterstad
- Institute of Clinical and Molecular Medicine (IKOM)Laboratory CenterNorwegian University of Science and TechnologyTrondheimNorway
| | - Antonio Sarno
- Institute of Clinical and Molecular Medicine (IKOM)Laboratory CenterNorwegian University of Science and TechnologyTrondheimNorway
- St. Olavs HospitalClinic of MedicineTrondheim University HospitalTrondheimNorway
| | - Alisa Dewan
- Institute of Clinical and Molecular Medicine (IKOM)Laboratory CenterNorwegian University of Science and TechnologyTrondheimNorway
- Present address:
Centre for Immune Regulation and Department of ImmunologyOslo University Hospital‐RikshospitaletUniversity of OsloOsloNorway
- Present address:
KG Jebsen Coeliac Disease Research CentreUniversity of OsloOsloNorway
| | - Carole Beck
- Institute of Clinical and Molecular Medicine (IKOM)Laboratory CenterNorwegian University of Science and TechnologyTrondheimNorway
| | - Stefano Bradamante
- Institute of Clinical and Molecular Medicine (IKOM)Laboratory CenterNorwegian University of Science and TechnologyTrondheimNorway
| | - Magnar Bjørås
- Institute of Clinical and Molecular Medicine (IKOM)Laboratory CenterNorwegian University of Science and TechnologyTrondheimNorway
- Department of MicrobiologyOslo University HospitalUniversity of OsloOsloNorway
| | - Valentyn Oksenych
- Institute of Clinical and Molecular Medicine (IKOM)Laboratory CenterNorwegian University of Science and TechnologyTrondheimNorway
- St. Olavs HospitalClinic of MedicineTrondheim University HospitalTrondheimNorway
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32
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Zaki-Dizaji M, Akrami SM, Abolhassani H, Rezaei N, Aghamohammadi A. Ataxia telangiectasia syndrome: moonlighting ATM. Expert Rev Clin Immunol 2017; 13:1155-1172. [PMID: 29034753 DOI: 10.1080/1744666x.2017.1392856] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
INTRODUCTION Ataxia-telangiectasia (A-T) a multisystem disorder primarily characterized by cerebellar degeneration, telangiectasia, immunodeficiency, cancer susceptibility and radiation sensitivity. Identification of the gene defective in this syndrome, ataxia-telangiectasia mutated gene (ATM), and further characterization of the disorder together with a greater insight into the function of the ATM protein have expanded our knowledge about the molecular pathogenesis of this disease. Area covered: In this review, we have attempted to summarize the different roles of ATM signaling that have provided new insights into the diverse clinical phenotypes exhibited by A-T patients. Expert commentary: ATM, in addition to DNA repair response, is involved in many cytoplasmic roles that explain diverse phenotypes of A-T patients. It seems accumulation of DNA damage, persistent DNA damage response signaling, and chronic oxidative stress are the main players in the pathogenesis of this disease.
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Affiliation(s)
- Majid Zaki-Dizaji
- a Department of Medical Genetics, School of Medicine , Tehran University of Medical Sciences , Tehran , Iran.,b Research Center for Immunodeficiencies, Children's Medical Center , Tehran University of Medical Science , Tehran , Iran
| | - Seyed Mohammad Akrami
- a Department of Medical Genetics, School of Medicine , Tehran University of Medical Sciences , Tehran , Iran
| | - Hassan Abolhassani
- b Research Center for Immunodeficiencies, Children's Medical Center , Tehran University of Medical Science , Tehran , Iran.,c Division of Clinical Immunology, Department of Laboratory Medicine , Karolinska Institute at Karolinska University Hospital Huddinge , Stockholm , Sweden.,d Primary Immunodeficiency Diseases Network (PIDNet ), Universal Scientific Education and Research Network (USERN) , Stockholm , Sweden
| | - Nima Rezaei
- b Research Center for Immunodeficiencies, Children's Medical Center , Tehran University of Medical Science , Tehran , Iran.,e Department of Immunology and Biology, School of Medicine , Tehran University of Medical Sciences , Tehran , Iran.,f Network of Immunity in Infection, Malignancy and Autoimmunity (NIIMA) , Universal Scientific Education and Research Network (USERN) , Tehran , Iran
| | - Asghar Aghamohammadi
- b Research Center for Immunodeficiencies, Children's Medical Center , Tehran University of Medical Science , Tehran , Iran
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Li J, Summerlin M, Nitiss KC, Nitiss JL, Hanakahi LA. TDP1 is required for efficient non-homologous end joining in human cells. DNA Repair (Amst) 2017; 60:40-49. [PMID: 29078113 DOI: 10.1016/j.dnarep.2017.10.003] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2017] [Revised: 10/09/2017] [Accepted: 10/10/2017] [Indexed: 11/29/2022]
Abstract
Tyrosyl-DNA phosphodiesterase 1 (TDP1) can remove a wide variety of 3' and 5' terminal DNA adducts. Genetic studies in yeast identified TDP1 as a regulator of non-homologous end joining (NHEJ) fidelity in the repair of double-strand breaks (DSBs) lacking terminal adducts. In this communication, we show that TDP1 plays an important role in joining cohesive DSBs in human cells. To investigate the role of TDP1 in NHEJ in live human cells we used CRISPR/cas9 to produce TDP1-knockout (TDP1-KO) HEK-293 cells. As expected, human TDP1-KO cells were highly sensitive to topoisomerase poisons and ionizing radiation. Using a chromosomally-integrated NHEJ reporter substrate to compare end joining between wild type and TDP1-KO cells, we found that TDP1-KO cells have a 5-fold reduced ability to repair I-SceI-generated DSBs. Extracts prepared from TDP1-KO cells had reduced NHEJ activity in vitro, as compared to extracts from wild type cells. Analysis of end-joining junctions showed that TDP1 deficiency reduced end-joining fidelity, with a significant increase in insertion events, similar to previous observations in yeast. It has been reported that phosphorylation of TDP1 serine 81 (TDP1-S81) by ATM and DNA-PK stabilizes TDP1 and recruits TDP1 to sites of DNA damage. We found that end joining in TDP1-KO cells was partially restored by the non-phosphorylatable mutant TDP1-S81A, but not by the phosphomimetic TDP1-S81E. We previously reported that TDP1 physically interacted with XLF. In this study, we found that XLF binding by TDP1 was reduced 2-fold by the S81A mutation, and 10-fold by the S81E phosphomimetic mutation. Our results demonstrate a novel role for TDP1 in NHEJ in human cells. We hypothesize that TDP1 participation in human NHEJ is mediated by interaction with XLF, and that TDP1-XLF interactions and subsequent NHEJ events are regulated by phosphorylation of TDP1-S81.
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Affiliation(s)
- Jing Li
- Department of Medicinal Chemistry and Pharmacognosy, University of Illinois, 1601 Parkview Ave. Rockford, Chicago, IL, 61107, United States
| | - Matthew Summerlin
- Department of Medicinal Chemistry and Pharmacognosy, University of Illinois, 1601 Parkview Ave. Rockford, Chicago, IL, 61107, United States
| | - Karin C Nitiss
- Biopharmaceutical Sciences, College of Pharmacy, University of Illinois, 1601 Parkview Ave. Rockford, Chicago, IL, 61107, United States
| | - John L Nitiss
- Biopharmaceutical Sciences, College of Pharmacy, University of Illinois, 1601 Parkview Ave. Rockford, Chicago, IL, 61107, United States
| | - Leslyn A Hanakahi
- Biopharmaceutical Sciences, College of Pharmacy, University of Illinois, 1601 Parkview Ave. Rockford, Chicago, IL, 61107, United States.
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Lenden Hasse H, Lescale C, Bianchi JJ, Yu W, Bedora-Faure M, Deriano L. Generation and CRISPR/Cas9 editing of transformed progenitor B cells as a pseudo-physiological system to study DNA repair gene function in V(D)J recombination. J Immunol Methods 2017; 451:71-77. [PMID: 28882611 PMCID: PMC5714433 DOI: 10.1016/j.jim.2017.08.007] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2017] [Revised: 08/22/2017] [Accepted: 08/22/2017] [Indexed: 11/18/2022]
Abstract
Antigen receptor gene assembly is accomplished in developing lymphocytes by the V(D)J recombination reaction, which can be separated into two steps: DNA cleavage by the recombination-activating gene (RAG) nuclease and joining of DNA double strand breaks (DSBs) by components of the nonhomologous end joining (NHEJ) pathway. Deficiencies for NHEJ factors can result in immunodeficiency and a propensity to accumulate genomic instability, thus highlighting the importance of identifying all players in this process and deciphering their functions. Bcl2 transgenic v-Abl kinase-transformed pro-B cells provide a pseudo-physiological cellular system to study V(D)J recombination. Treatment of v-Abl/Bcl2 pro-B cells with the Abl kinase inhibitor Imatinib leads to G1 cell cycle arrest, the rapid induction of Rag1/2 gene expression and V(D)J recombination. In this system, the Bcl2 transgene alleviates Imatinib-induced apoptosis enabling the analysis of induced V(D)J recombination. Although powerful, the use of mouse models carrying the Bcl2 transgene for the generation of v-Abl pro-B cell lines is time and money consuming. Here, we describe a method for generating v-Abl/Bcl2 pro-B cell lines from wild type mice and for performing gene knock-out using episomal CRISPR/Cas9 targeting vectors. Using this approach, we generated distinct NHEJ-deficient pro-B cell lines and quantified V(D)J recombination levels in these cells. Furthermore, this methodology can be adapted to generate pro-B cell lines deficient for any gene suspected to play a role in V(D)J recombination, and more generally DSB repair.
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Affiliation(s)
- Hélène Lenden Hasse
- Genome Integrity, Immunity and Cancer Unit, Department of Immunology, Department of Genomes and Genetics, Institut Pasteur, 75015 Paris, France
| | - Chloé Lescale
- Genome Integrity, Immunity and Cancer Unit, Department of Immunology, Department of Genomes and Genetics, Institut Pasteur, 75015 Paris, France
| | - Joy J Bianchi
- Genome Integrity, Immunity and Cancer Unit, Department of Immunology, Department of Genomes and Genetics, Institut Pasteur, 75015 Paris, France; Cellule Pasteur, University of Paris René Descartes, Sorbonne Paris Cité, Paris 75015, France
| | - Wei Yu
- Genome Integrity, Immunity and Cancer Unit, Department of Immunology, Department of Genomes and Genetics, Institut Pasteur, 75015 Paris, France
| | - Marie Bedora-Faure
- Genome Integrity, Immunity and Cancer Unit, Department of Immunology, Department of Genomes and Genetics, Institut Pasteur, 75015 Paris, France
| | - Ludovic Deriano
- Genome Integrity, Immunity and Cancer Unit, Department of Immunology, Department of Genomes and Genetics, Institut Pasteur, 75015 Paris, France.
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35
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Xing M, Bjørås M, Daniel JA, Alt FW, Oksenych V. Synthetic lethality between murine DNA repair factors XLF and DNA-PKcs is rescued by inactivation of Ku70. DNA Repair (Amst) 2017; 57:133-138. [PMID: 28759779 PMCID: PMC5584571 DOI: 10.1016/j.dnarep.2017.07.008] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2017] [Revised: 06/25/2017] [Accepted: 07/24/2017] [Indexed: 11/18/2022]
Abstract
DNA double-strand breaks (DSBs) are recognized and repaired by the Classical Non-Homologous End-Joining (C-NHEJ) and Homologous Recombination pathways. C-NHEJ includes the core Ku70 and Ku80 (or Ku86) heterodimer that binds DSBs and thus promotes recruitment of accessory downstream NHEJ factors XLF, PAXX, DNA-PKcs, Artemis and other core subunits, XRCC4 and DNA Ligase 4 (Lig4). In the absence of core C-NHEJ factors, DNA repair can be performed by Alternative End-Joining, which likely depends on DNA Ligase 1 and DNA Ligase 3. Genetic inactivation of C-NHEJ factors, such as Ku70, Ku80, XLF, PAXX and DNA-PKcs results in viable mice showing increased levels of genomic instability and sensitivity to DSBs. Knockouts of XRCC4 or Lig4, on the other hand, as well as combined inactivation of XLF and DNA-PKcs, or XLF and PAXX, result in late embryonic lethality in mice, which in most cases correlate with severe apoptosis in the central nervous system. Here, we demonstrate that inactivation of the Ku70 gene rescues the synthetic lethality between XLF and DNA-PKcs, resulting in triple knockout mice that are indistinguishable from Ku70-deficient littermates by size or levels of genomic instability. Moreover, we find that combined inactivation of Ku70 and XLF results in viable mice. Together, these findings suggest that Ku70 is epistatic with XLF and DNA-PKcs and support a model in which inactivation of Ku70 allows DNA lesions to become accessible to alternative DNA repair pathways.
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Affiliation(s)
- Mengtan Xing
- Institute for Cancer Research and Molecular Medicine, Norwegian University of Science and Technology, Laboratory Center, Erling Skjalgssons Gate 1, 7491 Trondheim, Norway
| | - Magnar Bjørås
- Institute for Cancer Research and Molecular Medicine, Norwegian University of Science and Technology, Laboratory Center, Erling Skjalgssons Gate 1, 7491 Trondheim, Norway
| | - Jeremy A Daniel
- The NNF Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3B, 2200 Copenhagen, Denmark
| | - Frederick W Alt
- Howard Hughes Medical Institute, Program in Cellular and Molecular Medicine, Boston Children's Hospital, Department of Genetics, Harvard Medical School, Boston, MA 02115, United States.
| | - Valentyn Oksenych
- Institute for Cancer Research and Molecular Medicine, Norwegian University of Science and Technology, Laboratory Center, Erling Skjalgssons Gate 1, 7491 Trondheim, Norway; The NNF Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3B, 2200 Copenhagen, Denmark; Howard Hughes Medical Institute, Program in Cellular and Molecular Medicine, Boston Children's Hospital, Department of Genetics, Harvard Medical School, Boston, MA 02115, United States; St. Olavs Hospital, Trondheim University Hospital, Clinic of Medicine, Postboks 3250 Sluppen, 7006 Trondheim, Norway.
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36
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Blackford AN, Jackson SP. ATM, ATR, and DNA-PK: The Trinity at the Heart of the DNA Damage Response. Mol Cell 2017; 66:801-817. [PMID: 28622525 DOI: 10.1016/j.molcel.2017.05.015] [Citation(s) in RCA: 1196] [Impact Index Per Article: 170.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2017] [Revised: 04/28/2017] [Accepted: 05/16/2017] [Indexed: 01/09/2023]
Abstract
In vertebrate cells, the DNA damage response is controlled by three related kinases: ATM, ATR, and DNA-PK. It has been 20 years since the cloning of ATR, the last of the three to be identified. During this time, our understanding of how these kinases regulate DNA repair and associated events has grown profoundly, although major questions remain unanswered. Here, we provide a historical perspective of their discovery and discuss their established functions in sensing and responding to genotoxic stress. We also highlight what is known regarding their structural similarities and common mechanisms of regulation, as well as emerging non-canonical roles and how our knowledge of ATM, ATR, and DNA-PK is being translated to benefit human health.
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Affiliation(s)
- Andrew N Blackford
- Weatherall Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital, Oxford OX3 9DS, UK; Cancer Research UK and Medical Research Council Oxford Institute for Radiation Oncology, Department of Oncology, University of Oxford, Oxford OX3 7DQ, UK; Wellcome Trust and Cancer Research UK Gurdon Institute, University of Cambridge, Tennis Court Road, Cambridge CB2 1QN, UK.
| | - Stephen P Jackson
- Wellcome Trust and Cancer Research UK Gurdon Institute, University of Cambridge, Tennis Court Road, Cambridge CB2 1QN, UK; Department of Biochemistry, University of Cambridge, Tennis Court Road, Cambridge CB2 1GA, UK.
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37
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Lescale C, Lenden Hasse H, Deriano L. Paralogie et redondance : maintenir l’intégrité du génome au cours de la recombinaison V(D)J. Med Sci (Paris) 2017; 33:474-477. [DOI: 10.1051/medsci/20173305005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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38
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Lescale C, Deriano L. The RAG recombinase: Beyond breaking. Mech Ageing Dev 2016; 165:3-9. [PMID: 27863852 DOI: 10.1016/j.mad.2016.11.003] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2016] [Revised: 11/04/2016] [Accepted: 11/11/2016] [Indexed: 11/17/2022]
Abstract
DNA double-strand breaks (DSBs) are commonly seen as lesions that threaten genome integrity and contribute to cancer and aging processes. However, in the context of antigen receptor gene assembly, known as V(D)J recombination, DSBs are obligatory intermediates that allow the establishment of genetic diversity and adaptive immunity. V(D)J recombination is initiated when the lymphoid-restricted recombination-activating genes RAG1 and RAG2 are expressed and form a site-specific endonuclease (the RAG nuclease or RAG recombinase). Here, we discuss the ability of the RAG nuclease to minimize the risks of genome disruption by coupling the breakage and repair steps of the V(D)J reaction. This implies that the RAG genes, derived from an ancient transposon, have undergone strong selective pressure to prohibit transposition in favor of promoting controlled DNA end joining in cis by the ubiquitous DNA damage response and DNA repair machineries. We also discuss the idea that, in addition to being essential for the rearrangement of antigen receptor genes, RAG-mediated DSBs could impact cellular processes and outcomes by affecting genetic and epigenetic programs.
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Affiliation(s)
- Chloé Lescale
- Department of Immunology and Department of Genomes and Genetics, Institut Pasteur, 75015 Paris, France
| | - Ludovic Deriano
- Department of Immunology and Department of Genomes and Genetics, Institut Pasteur, 75015 Paris, France.
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39
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Hung PJ, Chen BR, George R, Liberman C, Morales AJ, Colon-Ortiz P, Tyler JK, Sleckman BP, Bredemeyer AL. Deficiency of XLF and PAXX prevents DNA double-strand break repair by non-homologous end joining in lymphocytes. Cell Cycle 2016; 16:286-295. [PMID: 27830975 DOI: 10.1080/15384101.2016.1253640] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022] Open
Abstract
Non-homologous end joining (NHEJ) is a major DNA double-strand break (DSB) repair pathway that functions in all phases of the cell cycle. NHEJ repairs genotoxic and physiological DSBs, such as those generated by ionizing radiation and during V(D)J recombination at antigen receptor loci, respectively. DNA end joining by NHEJ relies on the core factors Ku70, Ku80, XRCC4, and DNA Ligase IV. Additional proteins also play important roles in NHEJ. The XRCC4-like factor (XLF) participates in NHEJ through its interaction with XRCC4, and XLF deficiency in humans leads to immunodeficiency and increased sensitivity to ionizing radiation. However, XLF is dispensable for NHEJ-mediated DSB repair during V(D)J recombination in murine lymphocytes, where it may have redundant functions with other DSB repair factors. Paralog of XRCC4 and XLF (PAXX) is a recently identified NHEJ factor that has structural similarity to XRCC4 and XLF. Here we show that PAXX is also dispensable for NHEJ during V(D)J recombination and during the repair of genotoxic DSBs in lymphocytes. However, a combined deficiency of PAXX and XLF blocks NHEJ with a severity comparable to that observed in DNA Ligase IV-deficient cells. Similar to XLF, PAXX interacts with Ku through its C-terminal region, and mutations that disrupt Ku binding prevent PAXX from promoting NHEJ in XLF-deficient lymphocytes. Our findings suggest that the PAXX and XLF proteins may have redundant functions during NHEJ.
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Affiliation(s)
- Putzer J Hung
- a Department of Pathology and Laboratory Medicine , Weill Cornell Medical College , New York , NY , USA.,b Department of Pathology and Immunology , Washington University School of Medicine , St. Louis , MO , USA
| | - Bo-Ruei Chen
- a Department of Pathology and Laboratory Medicine , Weill Cornell Medical College , New York , NY , USA.,b Department of Pathology and Immunology , Washington University School of Medicine , St. Louis , MO , USA
| | - Rosmy George
- b Department of Pathology and Immunology , Washington University School of Medicine , St. Louis , MO , USA
| | - Caleb Liberman
- b Department of Pathology and Immunology , Washington University School of Medicine , St. Louis , MO , USA
| | - Abigail J Morales
- a Department of Pathology and Laboratory Medicine , Weill Cornell Medical College , New York , NY , USA.,b Department of Pathology and Immunology , Washington University School of Medicine , St. Louis , MO , USA
| | - Pedro Colon-Ortiz
- a Department of Pathology and Laboratory Medicine , Weill Cornell Medical College , New York , NY , USA
| | - Jessica K Tyler
- a Department of Pathology and Laboratory Medicine , Weill Cornell Medical College , New York , NY , USA
| | - Barry P Sleckman
- a Department of Pathology and Laboratory Medicine , Weill Cornell Medical College , New York , NY , USA.,b Department of Pathology and Immunology , Washington University School of Medicine , St. Louis , MO , USA
| | - Andrea L Bredemeyer
- b Department of Pathology and Immunology , Washington University School of Medicine , St. Louis , MO , USA
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40
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Lescale C, Lenden Hasse H, Blackford AN, Balmus G, Bianchi JJ, Yu W, Bacoccina L, Jarade A, Clouin C, Sivapalan R, Reina-San-Martin B, Jackson SP, Deriano L. Specific Roles of XRCC4 Paralogs PAXX and XLF during V(D)J Recombination. Cell Rep 2016; 16:2967-2979. [PMID: 27601299 PMCID: PMC5033762 DOI: 10.1016/j.celrep.2016.08.069] [Citation(s) in RCA: 51] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2016] [Revised: 08/02/2016] [Accepted: 08/23/2016] [Indexed: 11/04/2022] Open
Abstract
Paralog of XRCC4 and XLF (PAXX) is a member of the XRCC4 superfamily and plays a role in nonhomologous end-joining (NHEJ), a DNA repair pathway critical for lymphocyte antigen receptor gene assembly. Here, we find that the functions of PAXX and XLF in V(D)J recombination are masked by redundant joining activities. Thus, combined PAXX and XLF deficiency leads to an inability to join RAG-cleaved DNA ends. Additionally, we demonstrate that PAXX function in V(D)J recombination depends on its interaction with Ku. Importantly, we show that, unlike XLF, the role of PAXX during the repair of DNA breaks does not overlap with ATM and the RAG complex. Our findings illuminate the role of PAXX in V(D)J recombination and support a model in which PAXX and XLF function during NHEJ repair of DNA breaks, whereas XLF, the RAG complex, and the ATM-dependent DNA damage response promote end joining by stabilizing DNA ends.
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Affiliation(s)
- Chloé Lescale
- Departments of Immunology and Genomes and Genetics, Institut Pasteur, 75015 Paris, France
| | - Hélène Lenden Hasse
- Departments of Immunology and Genomes and Genetics, Institut Pasteur, 75015 Paris, France
| | - Andrew N Blackford
- Weatherall Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital, Oxford OX3 9DS, UK; CRUK/MRC Oxford Institute for Radiation Oncology, Department of Oncology, University of Oxford, Oxford OX3 7DQ, UK; The Wellcome Trust and Cancer Research UK Gurdon Institute, University of Cambridge, Cambridge CB2 1QN, UK
| | - Gabriel Balmus
- The Wellcome Trust and Cancer Research UK Gurdon Institute, University of Cambridge, Cambridge CB2 1QN, UK; Maintenance of Genome Stability, Genome Campus, Wellcome Trust Sanger Institute, Cambridge CB10 1SA, UK
| | - Joy J Bianchi
- Departments of Immunology and Genomes and Genetics, Institut Pasteur, 75015 Paris, France; Cellule Pasteur, University of Paris René Descartes, Sorbonne Paris Cité, Paris 75015, France
| | - Wei Yu
- Departments of Immunology and Genomes and Genetics, Institut Pasteur, 75015 Paris, France
| | - Léa Bacoccina
- Departments of Immunology and Genomes and Genetics, Institut Pasteur, 75015 Paris, France
| | - Angélique Jarade
- Departments of Immunology and Genomes and Genetics, Institut Pasteur, 75015 Paris, France
| | - Christophe Clouin
- Departments of Immunology and Genomes and Genetics, Institut Pasteur, 75015 Paris, France
| | - Rohan Sivapalan
- The Wellcome Trust and Cancer Research UK Gurdon Institute, University of Cambridge, Cambridge CB2 1QN, UK
| | - Bernardo Reina-San-Martin
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, INSERM-U964, CNRS-UMR7104, University of Strasbourg, 67400 Illkirch, France
| | - Stephen P Jackson
- The Wellcome Trust and Cancer Research UK Gurdon Institute, University of Cambridge, Cambridge CB2 1QN, UK; Maintenance of Genome Stability, Genome Campus, Wellcome Trust Sanger Institute, Cambridge CB10 1SA, UK
| | - Ludovic Deriano
- Departments of Immunology and Genomes and Genetics, Institut Pasteur, 75015 Paris, France.
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PAXX and XLF DNA repair factors are functionally redundant in joining DNA breaks in a G1-arrested progenitor B-cell line. Proc Natl Acad Sci U S A 2016; 113:10619-24. [PMID: 27601633 DOI: 10.1073/pnas.1611882113] [Citation(s) in RCA: 78] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
Classical nonhomologous end joining (C-NHEJ) is a major mammalian DNA double-strand break (DSB) repair pathway. Core C-NHEJ factors, such as XRCC4, are required for joining DSB intermediates of the G1 phase-specific V(D)J recombination reaction in progenitor lymphocytes. Core factors also contribute to joining DSBs in cycling mature B-lineage cells, including DSBs generated during antibody class switch recombination (CSR) and DSBs generated by ionizing radiation. The XRCC4-like-factor (XLF) C-NHEJ protein is dispensable for V(D)J recombination in normal cells, but because of functional redundancy, it is absolutely required for this process in cells deficient for the ataxia telangiectasia-mutated (ATM) DSB response factor. The recently identified paralogue of XRCC4 and XLF (PAXX) factor has homology to these two proteins and variably contributes to ionizing radiation-induced DSB repair in human and chicken cells. We now report that PAXX is dispensable for joining V(D)J recombination DSBs in G1-arrested mouse pro-B-cell lines, dispensable for joining CSR-associated DSBs in a cycling mouse B-cell line, and dispensable for normal ionizing radiation resistance in both G1-arrested and cycling pro-B lines. However, we find that combined deficiency for PAXX and XLF in G1-arrested pro-B lines abrogates DSB joining during V(D)J recombination and sensitizes the cells to ionizing radiation exposure. Thus, PAXX provides core C-NHEJ factor-associated functions in the absence of XLF and vice versa in G1-arrested pro-B-cell lines. Finally, we also find that PAXX deficiency has no impact on V(D)J recombination DSB joining in ATM-deficient pro-B lines. We discuss implications of these findings with respect to potential PAXX and XLF functions in C-NHEJ.
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Related Mechanisms of Antibody Somatic Hypermutation and Class Switch Recombination. Microbiol Spectr 2016; 3:MDNA3-0037-2014. [PMID: 26104555 DOI: 10.1128/microbiolspec.mdna3-0037-2014] [Citation(s) in RCA: 64] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023] Open
Abstract
The primary antibody repertoire is generated by mechanisms involving the assembly of the exons that encode the antigen-binding variable regions of immunoglobulin heavy (IgH) and light (IgL) chains during the early development of B lymphocytes. After antigen-dependent activation, mature B lymphocytes can further alter their IgH and IgL variable region exons by the process of somatic hypermutation (SHM), which allows the selection of B cells in which SHMs resulted in the production of antibodies with increased antigen affinity. In addition, during antigen-dependent activation, B cells can also change the constant region of their IgH chain through a DNA double-strand-break (DSB) dependent process referred to as IgH class switch recombination (CSR), which generates B cell progeny that produce antibodies with different IgH constant region effector functions that are best suited for a elimination of a particular pathogen or in a particular setting. Both the mutations that underlie SHM and the DSBs that underlie CSR are initiated in target genes by activation-induced cytidine deaminase (AID). This review describes in depth the processes of SHM and CSR with a focus on mechanisms that direct AID cytidine deamination in activated B cells and mechanisms that promote the differential outcomes of such cytidine deamination.
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43
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Neal JA, Xu Y, Abe M, Hendrickson E, Meek K. Restoration of ATM Expression in DNA-PKcs-Deficient Cells Inhibits Signal End Joining. THE JOURNAL OF IMMUNOLOGY 2016; 196:3032-42. [PMID: 26921311 DOI: 10.4049/jimmunol.1501654] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/24/2015] [Accepted: 01/26/2016] [Indexed: 11/19/2022]
Abstract
Unlike most DNA-dependent protein kinase, catalytic subunit (DNA-PKcs)-deficient mouse cell strains, we show in the present study that targeted deletion of DNA-PKcs in two different human cell lines abrogates VDJ signal end joining in episomal assays. Although the mechanism is not well defined, DNA-PKcs deficiency results in spontaneous reduction of ATM expression in many cultured cell lines (including those examined in this study) and in DNA-PKcs-deficient mice. We considered that varying loss of ATM expression might explain differences in signal end joining in different cell strains and animal models, and we investigated the impact of ATM and/or DNA-PKcs loss on VDJ recombination in cultured human and rodent cell strains. To our surprise, in DNA-PKcs-deficient mouse cell strains that are proficient in signal end joining, restoration of ATM expression markedly inhibits signal end joining. In contrast, in DNA-PKcs-deficient cells that are deficient in signal end joining, complete loss of ATM enhances signal (but not coding) joint formation. We propose that ATM facilitates restriction of signal ends to the classical nonhomologous end-joining pathway.
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Affiliation(s)
- Jessica A Neal
- Department of Microbiology and Molecular Genetics, College of Veterinary Medicine, Michigan State University, East Lansing, MI 48824; Department of Pathobiology and Diagnostic Investigation, College of Veterinary Medicine, Michigan State University, East Lansing, MI 48824
| | - Yao Xu
- Department of Microbiology and Molecular Genetics, College of Veterinary Medicine, Michigan State University, East Lansing, MI 48824; Department of Pathobiology and Diagnostic Investigation, College of Veterinary Medicine, Michigan State University, East Lansing, MI 48824
| | - Masumi Abe
- National Institute of Radiological Sciences, Chiba 263-8555, Japan; and
| | - Eric Hendrickson
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota Medical School, Minneapolis, MN 55455
| | - Katheryn Meek
- Department of Microbiology and Molecular Genetics, College of Veterinary Medicine, Michigan State University, East Lansing, MI 48824; Department of Pathobiology and Diagnostic Investigation, College of Veterinary Medicine, Michigan State University, East Lansing, MI 48824;
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44
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Schwer B, Wei PC, Chang AN, Kao J, Du Z, Meyers RM, Alt FW. Transcription-associated processes cause DNA double-strand breaks and translocations in neural stem/progenitor cells. Proc Natl Acad Sci U S A 2016; 113:2258-63. [PMID: 26873106 PMCID: PMC4776469 DOI: 10.1073/pnas.1525564113] [Citation(s) in RCA: 78] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
High-throughput, genome-wide translocation sequencing (HTGTS) studies of activated B cells have revealed that DNA double-strand breaks (DSBs) capable of translocating to defined bait DSBs are enriched around the transcription start sites (TSSs) of active genes. We used the HTGTS approach to investigate whether a similar phenomenon occurs in primary neural stem/progenitor cells (NSPCs). We report that breakpoint junctions indeed are enriched around TSSs that were determined to be active by global run-on sequencing analyses of NSPCs. Comparative analyses of transcription profiles in NSPCs and B cells revealed that the great majority of TSS-proximal junctions occurred in genes commonly expressed in both cell types, possibly because this common set has higher transcription levels on average than genes transcribed in only one or the other cell type. In the latter context, among all actively transcribed genes containing translocation junctions in NSPCs, those with junctions located within 2 kb of the TSS show a significantly higher transcription rate on average than genes with junctions in the gene body located at distances greater than 2 kb from the TSS. Finally, analysis of repair junction signatures of TSS-associated translocations in wild-type versus classical nonhomologous end-joining (C-NHEJ)-deficient NSPCs reveals that both C-NHEJ and alternative end-joining pathways can generate translocations by joining TSS-proximal DSBs to DSBs on other chromosomes. Our studies show that the generation of transcription-associated DSBs is conserved across divergent cell types.
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Affiliation(s)
- Bjoern Schwer
- Howard Hughes Medical Institute, Program in Cellular and Molecular Medicine, Boston Children's Hospital, Boston, MA 02115; Department of Genetics, Harvard Medical School, Boston, MA 02115; Department of Pediatrics, Harvard Medical School, Boston, MA 02115
| | - Pei-Chi Wei
- Howard Hughes Medical Institute, Program in Cellular and Molecular Medicine, Boston Children's Hospital, Boston, MA 02115; Department of Genetics, Harvard Medical School, Boston, MA 02115; Department of Pediatrics, Harvard Medical School, Boston, MA 02115
| | - Amelia N Chang
- Howard Hughes Medical Institute, Program in Cellular and Molecular Medicine, Boston Children's Hospital, Boston, MA 02115; Department of Genetics, Harvard Medical School, Boston, MA 02115; Department of Pediatrics, Harvard Medical School, Boston, MA 02115
| | - Jennifer Kao
- Howard Hughes Medical Institute, Program in Cellular and Molecular Medicine, Boston Children's Hospital, Boston, MA 02115; Department of Genetics, Harvard Medical School, Boston, MA 02115; Department of Pediatrics, Harvard Medical School, Boston, MA 02115
| | - Zhou Du
- Howard Hughes Medical Institute, Program in Cellular and Molecular Medicine, Boston Children's Hospital, Boston, MA 02115; Department of Genetics, Harvard Medical School, Boston, MA 02115; Department of Pediatrics, Harvard Medical School, Boston, MA 02115
| | - Robin M Meyers
- Howard Hughes Medical Institute, Program in Cellular and Molecular Medicine, Boston Children's Hospital, Boston, MA 02115; Department of Genetics, Harvard Medical School, Boston, MA 02115; Department of Pediatrics, Harvard Medical School, Boston, MA 02115
| | - Frederick W Alt
- Howard Hughes Medical Institute, Program in Cellular and Molecular Medicine, Boston Children's Hospital, Boston, MA 02115; Department of Genetics, Harvard Medical School, Boston, MA 02115; Department of Pediatrics, Harvard Medical School, Boston, MA 02115
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45
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Lescale C, Abramowski V, Bedora-Faure M, Murigneux V, Vera G, Roth DB, Revy P, de Villartay JP, Deriano L. RAG2 and XLF/Cernunnos interplay reveals a novel role for the RAG complex in DNA repair. Nat Commun 2016; 7:10529. [PMID: 26833222 PMCID: PMC4740868 DOI: 10.1038/ncomms10529] [Citation(s) in RCA: 55] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2015] [Accepted: 12/22/2015] [Indexed: 12/22/2022] Open
Abstract
XRCC4-like factor (XLF) functions in classical non-homologous end-joining (cNHEJ) but is dispensable for the repair of DNA double-strand breaks (DSBs) generated during V(D)J recombination. A long-standing hypothesis proposes that, in addition to its canonical nuclease activity, the RAG1/2 proteins participate in the DNA repair phase of V(D)J recombination. Here we show that in the context of RAG2 lacking the C-terminus domain (Rag2c/c mice), XLF deficiency leads to a profound lymphopenia associated with a severe defect in V(D)J recombination and, in the absence of p53, increased genomic instability at V(D)J sites. In addition, Rag2c/cXLF−/−p53−/− mice develop aggressive pro-B cell lymphomas bearing complex chromosomal translocations and gene amplifications involving Igh and c-myc/pvt1 loci. Our results reveal an unanticipated functional interplay between the RAG complex and XLF in repairing RAG-induced DSBs and maintaining genome integrity during antigen receptor gene assembly. Antigen receptor diversity relies on careful DNA cleavage and repair. Here the authors identify a functional interplay between RAG2 and XLF during V(D)J recombination, revealing an important role for the RAG complex in repairing induced DNA double-strand breaks and maintaining genome integrity.
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Affiliation(s)
- Chloé Lescale
- Departments of Immunology and Genomes and Genetics, Institut Pasteur, CNRS-URA 1961, Paris 75015, France
| | - Vincent Abramowski
- Laboratory of Genome Dynamics in the Immune System, INSERM UMR1163, Université Paris Descartes Sorbonne Paris Cité, Institut Imagine, Paris 75015, France
| | - Marie Bedora-Faure
- Departments of Immunology and Genomes and Genetics, Institut Pasteur, CNRS-URA 1961, Paris 75015, France
| | - Valentine Murigneux
- Departments of Immunology and Genomes and Genetics, Institut Pasteur, CNRS-URA 1961, Paris 75015, France
| | - Gabriella Vera
- Laboratory of Genome Dynamics in the Immune System, INSERM UMR1163, Université Paris Descartes Sorbonne Paris Cité, Institut Imagine, Paris 75015, France
| | - David B Roth
- Department of Pathology and Laboratory Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
| | - Patrick Revy
- Laboratory of Genome Dynamics in the Immune System, INSERM UMR1163, Université Paris Descartes Sorbonne Paris Cité, Institut Imagine, Paris 75015, France
| | - Jean-Pierre de Villartay
- Laboratory of Genome Dynamics in the Immune System, INSERM UMR1163, Université Paris Descartes Sorbonne Paris Cité, Institut Imagine, Paris 75015, France
| | - Ludovic Deriano
- Departments of Immunology and Genomes and Genetics, Institut Pasteur, CNRS-URA 1961, Paris 75015, France
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46
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Beagan K, McVey M. Linking DNA polymerase theta structure and function in health and disease. Cell Mol Life Sci 2016; 73:603-15. [PMID: 26514729 PMCID: PMC4715478 DOI: 10.1007/s00018-015-2078-9] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2015] [Revised: 10/10/2015] [Accepted: 10/19/2015] [Indexed: 10/22/2022]
Abstract
DNA polymerase theta (Pol θ) is an error-prone A-family polymerase that is highly conserved among multicellular eukaryotes and plays multiple roles in DNA repair and the regulation of genome integrity. Studies conducted in several model organisms have shown that Pol θ can be utilized during DNA interstrand crosslink repair and during alternative end-joining repair of double-strand breaks. Recent genetic and biochemical studies have begun to elucidate the unique structural features of Pol θ that promote alternative end-joining repair. Importantly, Pol θ-dependent end joining appears to be important for overall genome stability, as it affects chromosome translocation formation in murine and human cell lines. Pol θ has also been suggested to act as a modifier of replication timing in human cells, though the mechanism of action remains unknown. Pol θ is highly upregulated in a number of human cancer types, which could indicate that mutagenic Pol θ-dependent end joining is used during cancer cell proliferation. Here, we review the various roles of Pol θ across species and discuss how these roles may be relevant to cancer therapy.
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Affiliation(s)
- Kelly Beagan
- Department of Biology, Tufts University, 200 Boston Avenue, Suite 4700, Medford, MA, 02155, USA
| | - Mitch McVey
- Department of Biology, Tufts University, 200 Boston Avenue, Suite 4700, Medford, MA, 02155, USA.
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47
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Mistrik M, Bartek J. What a 'Ku'incidence!: parallel discoveries of a new DNA repair factor. Cell Death Differ 2015; 22:888-9. [PMID: 25941165 PMCID: PMC4423193 DOI: 10.1038/cdd.2015.32] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Affiliation(s)
- M Mistrik
- Institute of Molecular and Translational Medicine, Faculty of Medicine and Dentistry, Palacky University, Olomouc, Czech Republic
| | - J Bartek
- Institute of Molecular and Translational Medicine, Faculty of Medicine and Dentistry, Palacky University, Olomouc, Czech Republic
- Danish Cancer Society Research Center, Copenhagen, Denmark
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48
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Xing M, Yang M, Huo W, Feng F, Wei L, Jiang W, Ning S, Yan Z, Li W, Wang Q, Hou M, Dong C, Guo R, Gao G, Ji J, Zha S, Lan L, Liang H, Xu D. Interactome analysis identifies a new paralogue of XRCC4 in non-homologous end joining DNA repair pathway. Nat Commun 2015; 6:6233. [PMID: 25670504 PMCID: PMC4339890 DOI: 10.1038/ncomms7233] [Citation(s) in RCA: 131] [Impact Index Per Article: 14.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2014] [Accepted: 01/06/2015] [Indexed: 01/15/2023] Open
Abstract
Non-homologous end joining (NHEJ) is a major pathway to repair DNA double-strand breaks (DSBs), which can display different types of broken ends. However, it is unclear how NHEJ factors organize to repair diverse types of DNA breaks. Here, through systematic analysis of the human NHEJ factor interactome, we identify PAXX as a direct interactor of Ku. The crystal structure of PAXX is similar to those of XRCC4 and XLF. Importantly, PAXX-deficient cells are sensitive to DSB-causing agents. Moreover, epistasis analysis demonstrates that PAXX functions together with XLF in response to ionizing radiation-induced complex DSBs, whereas they function redundantly in response to Topo2 inhibitor-induced simple DSBs. Consistently, PAXX and XLF coordinately promote the ligation of complex but not simple DNA ends in vitro. Altogether, our data identify PAXX as a new NHEJ factor and provide insight regarding the organization of NHEJ factors responding to diverse types of DSB ends.
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Affiliation(s)
- Mengtan Xing
- State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, 5 Yiheyuan Road, Beijing 100871, China
| | - Mingrui Yang
- 1] State Key Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China [2] State Key Laboratory of Virology, School of Basic Medicine, Wuhan University, Wuhan 430071, China
| | - Wei Huo
- State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, 5 Yiheyuan Road, Beijing 100871, China
| | - Feng Feng
- State Key Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
| | - Leizhen Wei
- Department of Microbiology and Molecular Genetics, University of Pittsburgh Cancer Institute, University of Pittsburgh School of Medicine, 5117 Centre Avenue, Pittsburgh, Pennsylvania 15213, USA
| | - Wenxia Jiang
- Institute for Cancer Genetics, Columbia University Medical Center, New York City, New York 10032, USA
| | - Shaokai Ning
- State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, 5 Yiheyuan Road, Beijing 100871, China
| | - Zhenxin Yan
- State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, 5 Yiheyuan Road, Beijing 100871, China
| | - Wen Li
- State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, 5 Yiheyuan Road, Beijing 100871, China
| | - Qingsong Wang
- State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, 5 Yiheyuan Road, Beijing 100871, China
| | - Mei Hou
- State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, 5 Yiheyuan Road, Beijing 100871, China
| | - Chunxia Dong
- State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, 5 Yiheyuan Road, Beijing 100871, China
| | - Rong Guo
- State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, 5 Yiheyuan Road, Beijing 100871, China
| | - Ge Gao
- State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, 5 Yiheyuan Road, Beijing 100871, China
| | - Jianguo Ji
- State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, 5 Yiheyuan Road, Beijing 100871, China
| | - Shan Zha
- Institute for Cancer Genetics, Columbia University Medical Center, New York City, New York 10032, USA
| | - Li Lan
- Department of Microbiology and Molecular Genetics, University of Pittsburgh Cancer Institute, University of Pittsburgh School of Medicine, 5117 Centre Avenue, Pittsburgh, Pennsylvania 15213, USA
| | - Huanhuan Liang
- State Key Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
| | - Dongyi Xu
- State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, 5 Yiheyuan Road, Beijing 100871, China
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