1
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Cheong TC, Jang A, Wang Q, Leonardi GC, Ricciuti B, Alessi JV, Di Federico A, Awad MM, Lehtinen MK, Harris MH, Chiarle R. Mechanistic patterns and clinical implications of oncogenic tyrosine kinase fusions in human cancers. Nat Commun 2024; 15:5110. [PMID: 38877018 PMCID: PMC11178778 DOI: 10.1038/s41467-024-49499-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2024] [Accepted: 06/04/2024] [Indexed: 06/16/2024] Open
Abstract
Tyrosine kinase (TK) fusions are frequently found in cancers, either as initiating events or as a mechanism of resistance to targeted therapy. Partner genes and exons in most TK fusions are followed typical recurrent patterns, but the underlying mechanisms and clinical implications of these patterns are poorly understood. By developing Functionally Active Chromosomal Translocation Sequencing (FACTS), we discover that typical TK fusions involving ALK, ROS1, RET and NTRK1 are selected from pools of chromosomal rearrangements by two major determinants: active transcription of the fusion partner genes and protein stability. In contrast, atypical TK fusions that are rarely seen in patients showed reduced protein stability, decreased downstream oncogenic signaling, and were less responsive to inhibition. Consistently, patients with atypical TK fusions were associated with a reduced response to TKI therapies. Our findings highlight the principles of oncogenic TK fusion formation and selection in cancers, with clinical implications for guiding targeted therapy.
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Affiliation(s)
- Taek-Chin Cheong
- Department of Pathology, Boston Children's Hospital and Harvard Medical School, Boston, MA, 02115, USA.
| | - Ahram Jang
- Department of Pathology, Boston Children's Hospital and Harvard Medical School, Boston, MA, 02115, USA
- Division of Endocrinology, Diabetes, and Metabolism, Department of Medicine, Beth Israel Deaconess Medical Center, Boston, MA, 02115, USA
| | - Qi Wang
- Department of Pathology, Boston Children's Hospital and Harvard Medical School, Boston, MA, 02115, USA
| | - Giulia C Leonardi
- Department of Pathology, Boston Children's Hospital and Harvard Medical School, Boston, MA, 02115, USA
- Department of Biomedical and Biotechnological Sciences, University of Catania, 95123, Catania, Italy
| | - Biagio Ricciuti
- Lowe Center for Thoracic Oncology, Dana-Farber Cancer Institute, Boston, MA, 02115, USA
| | - Joao V Alessi
- Lowe Center for Thoracic Oncology, Dana-Farber Cancer Institute, Boston, MA, 02115, USA
| | | | - Mark M Awad
- Lowe Center for Thoracic Oncology, Dana-Farber Cancer Institute, Boston, MA, 02115, USA
| | - Maria K Lehtinen
- Department of Pathology, Boston Children's Hospital and Harvard Medical School, Boston, MA, 02115, USA
| | - Marian H Harris
- Department of Pathology, Boston Children's Hospital and Harvard Medical School, Boston, MA, 02115, USA
| | - Roberto Chiarle
- Department of Pathology, Boston Children's Hospital and Harvard Medical School, Boston, MA, 02115, USA.
- Department of Molecular Biotechnology and Health Sciences, University of Torino, Torino, 10126, Italy.
- Division of Hematopathology, IEO European Institute of Oncology IRCCS, 20141, Milan, Italy.
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2
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Chiarle R, Cheong TC, Jang A, Wang Q, Leonardi G, Ricciuti B, Alessi J, Federico AD, Awad M, Lehtinen M, Harris M. Mechanistic patterns and clinical implications of oncogenic tyrosine kinase fusions in human cancers. RESEARCH SQUARE 2024:rs.3.rs-3782958. [PMID: 38313284 PMCID: PMC10836111 DOI: 10.21203/rs.3.rs-3782958/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/06/2024]
Abstract
Tyrosine kinase (TK) fusions are frequently found in cancers, either as initiating events or as a mechanism of resistance to targeted therapy. Partner genes and exons in most TK fusions are typical and recurrent, but the underlying mechanisms and clinical implications of these patterns are poorly understood. Here, we investigated structures of > 8,000 kinase fusions and explore their generative mechanisms by applying newly developed experimental framework integrating high-throughput genome-wide gene fusion sequencing and clonal selection called Functionally Active Chromosomal Translocation Sequencing (FACTS). We discovered that typical oncogenic TK fusions recurrently seen in patients are selected from large pools of chromosomal rearrangements spontaneously occurring in cells based on two major determinants: active transcription of the fusion partner genes and protein stability. In contrast, atypical TK fusions that are rarely seen in patients showed reduced protein stability, decreased downstream oncogenic signaling, and were less responsive to inhibition. Consistently, patients with atypical TK fusions were associated with a reduced response to TKI therapies, as well as a shorter progression-free survival (PFS) and overall survival (OS) compared to patients with typical TK fusions. These findings highlight the principles of oncogenic TK fusion formation and their selection in cancers, with clinical implications for guiding targeted therapy.
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Affiliation(s)
| | | | - Ahram Jang
- Boston Children's Hospital and Harvard Medical School
| | - Qi Wang
- Boston Children's Hospital and Harvard Medical School
| | | | | | | | | | | | | | - Marian Harris
- Boston Children's Hospital and Harvard Medical School
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3
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Abstract
Transcription and replication both require large macromolecular complexes to act on a DNA template, yet these machineries cannot simultaneously act on the same DNA sequence. Conflicts between the replication and transcription machineries (transcription-replication conflicts, or TRCs) are widespread in both prokaryotes and eukaryotes and have the capacity to both cause DNA damage and compromise complete, faithful replication of the genome. This review will highlight recent studies investigating the genomic locations of TRCs and the mechanisms by which they may be prevented, mitigated, or resolved. We address work from both model organisms and mammalian systems but predominantly focus on multicellular eukaryotes owing to the additional complexities inherent in the coordination of replication and transcription in the context of cell type-specific gene expression and higher-order chromatin organization.
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Affiliation(s)
- Liana Goehring
- Department of Biochemistry & Molecular Pharmacology, New York University School of Medicine, New York, NY, USA;
| | - Tony T Huang
- Department of Biochemistry & Molecular Pharmacology, New York University School of Medicine, New York, NY, USA;
| | - Duncan J Smith
- Center for Genomics and Systems Biology, Department of Biology, New York University, New York, NY, USA;
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4
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Hao Q, Zhan C, Lian C, Luo S, Cao W, Wang B, Xie X, Ye X, Gui T, Voena C, Pighi C, Wang Y, Tian Y, Wang X, Dai P, Cai Y, Liu X, Ouyang S, Sun S, Hu Q, Liu J, Ye Y, Zhao J, Lu A, Wang JY, Huang C, Su B, Meng FL, Chiarle R, Pan-Hammarström Q, Yeap LS. DNA repair mechanisms that promote insertion-deletion events during immunoglobulin gene diversification. Sci Immunol 2023; 8:eade1167. [PMID: 36961908 PMCID: PMC10351598 DOI: 10.1126/sciimmunol.ade1167] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2022] [Accepted: 03/01/2023] [Indexed: 03/26/2023]
Abstract
Insertions and deletions (indels) are low-frequency deleterious genomic DNA alterations. Despite their rarity, indels are common, and insertions leading to long complementarity-determining region 3 (CDR3) are vital for antigen-binding functions in broadly neutralizing and polyreactive antibodies targeting viruses. Because of challenges in detecting indels, the mechanism that generates indels during immunoglobulin diversification processes remains poorly understood. We carried out ultra-deep profiling of indels and systematically dissected the underlying mechanisms using passenger-immunoglobulin mouse models. We found that activation-induced cytidine deaminase-dependent ±1-base pair (bp) indels are the most prevalent indel events, biasing deleterious outcomes, whereas longer in-frame indels, especially insertions that can extend the CDR3 length, are rare outcomes. The ±1-bp indels are channeled by base excision repair, but longer indels require additional DNA-processing factors. Ectopic expression of a DNA exonuclease or perturbation of the balance of DNA polymerases can increase the frequency of longer indels, thus paving the way for models that can generate antibodies with long CDR3. Our study reveals the mechanisms that generate beneficial and deleterious indels during the process of antibody somatic hypermutation and has implications in understanding the detrimental genomic alterations in various conditions, including tumorigenesis.
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Affiliation(s)
- Qian Hao
- Center for Immune-Related Diseases at Shanghai Institute of Immunology, Department of Endocrinology and Metabolic Diseases, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
- Shanghai Institute of Immunology, Department of Immunology and Microbiology, State Key Laboratory of Oncogenes and Related Genes, Shanghai Jiao Tong University School of Medicine; 280 South Chongqing Road, Shanghai, 200025, China
| | - Chuanzong Zhan
- Center for Immune-Related Diseases at Shanghai Institute of Immunology, Department of Endocrinology and Metabolic Diseases, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
- Shanghai Institute of Immunology, Department of Immunology and Microbiology, State Key Laboratory of Oncogenes and Related Genes, Shanghai Jiao Tong University School of Medicine; 280 South Chongqing Road, Shanghai, 200025, China
| | - Chaoyang Lian
- Shanghai Institute of Immunology, Department of Immunology and Microbiology, State Key Laboratory of Oncogenes and Related Genes, Shanghai Jiao Tong University School of Medicine; 280 South Chongqing Road, Shanghai, 200025, China
| | - Simin Luo
- Shanghai Institute of Immunology, Department of Immunology and Microbiology, State Key Laboratory of Oncogenes and Related Genes, Shanghai Jiao Tong University School of Medicine; 280 South Chongqing Road, Shanghai, 200025, China
| | - Wenyi Cao
- Shanghai Institute of Immunology, Department of Immunology and Microbiology, State Key Laboratory of Oncogenes and Related Genes, Shanghai Jiao Tong University School of Medicine; 280 South Chongqing Road, Shanghai, 200025, China
| | - Binbin Wang
- Shanghai Institute of Immunology, Department of Immunology and Microbiology, State Key Laboratory of Oncogenes and Related Genes, Shanghai Jiao Tong University School of Medicine; 280 South Chongqing Road, Shanghai, 200025, China
| | - Xia Xie
- 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; 320 Yueyang Road, Shanghai 200031, China
| | - Xiaofei Ye
- Department of Biosciences and Nutrition, Karolinska Institutet; SE141-83, Huddinge, Stockholm, Sweden
- Present address: Kindstar Global Precision Medicine Institute, Wuhan, China and Kindstar Biotech, Wuhan, China
| | - Tuantuan Gui
- Shanghai Institute of Immunology, Department of Immunology and Microbiology, State Key Laboratory of Oncogenes and Related Genes, Shanghai Jiao Tong University School of Medicine; 280 South Chongqing Road, Shanghai, 200025, China
| | - Claudia Voena
- Department of Molecular Biotechnology and Health Sciences, University of Torino; 10126 Torino, Italy
| | - Chiara Pighi
- Department of Molecular Biotechnology and Health Sciences, University of Torino; 10126 Torino, Italy
- Department of Pathology, Boston Children’s Hospital, and Harvard Medical School; Boston, MA 02115, USA
| | - Yanyan Wang
- 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; 320 Yueyang Road, Shanghai 200031, China
| | - Ying Tian
- Shanghai Institute of Immunology, Department of Immunology and Microbiology, State Key Laboratory of Oncogenes and Related Genes, Shanghai Jiao Tong University School of Medicine; 280 South Chongqing Road, Shanghai, 200025, China
| | - Xin Wang
- Shanghai Institute of Immunology, Department of Immunology and Microbiology, State Key Laboratory of Oncogenes and Related Genes, Shanghai Jiao Tong University School of Medicine; 280 South Chongqing Road, Shanghai, 200025, China
| | - Pengfei Dai
- 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; 320 Yueyang Road, Shanghai 200031, China
| | - Yanni Cai
- 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; 320 Yueyang Road, Shanghai 200031, China
| | - Xiaojing Liu
- 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; 320 Yueyang Road, Shanghai 200031, China
| | - Shengqun Ouyang
- Center for Immune-Related Diseases at Shanghai Institute of Immunology, Department of Endocrinology and Metabolic Diseases, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
- Shanghai Institute of Immunology, Department of Immunology and Microbiology, State Key Laboratory of Oncogenes and Related Genes, Shanghai Jiao Tong University School of Medicine; 280 South Chongqing Road, Shanghai, 200025, China
| | - Shiqi Sun
- Shanghai Institute of Immunology, Department of Immunology and Microbiology, State Key Laboratory of Oncogenes and Related Genes, Shanghai Jiao Tong University School of Medicine; 280 South Chongqing Road, Shanghai, 200025, China
| | - Qianwen Hu
- Shanghai Institute of Immunology, Department of Immunology and Microbiology, State Key Laboratory of Oncogenes and Related Genes, Shanghai Jiao Tong University School of Medicine; 280 South Chongqing Road, Shanghai, 200025, China
| | - Jun Liu
- Department of Immunology, School of Basic Medical Sciences, Fudan University, Shanghai 200032, China
| | - Youqiong Ye
- Shanghai Institute of Immunology, Department of Immunology and Microbiology, State Key Laboratory of Oncogenes and Related Genes, Shanghai Jiao Tong University School of Medicine; 280 South Chongqing Road, Shanghai, 200025, China
| | - Jingkun Zhao
- Department of General Surgery, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
| | - Aiguo Lu
- Department of General Surgery, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
| | - Ji-Yang Wang
- Department of Immunology, School of Basic Medical Sciences, Fudan University, Shanghai 200032, China
- Department of Microbiology and Immunology, College of Basic Medical Sciences, Zhengzhou University, Zhengzhou, China
| | - Chuanxin Huang
- Shanghai Institute of Immunology, Department of Immunology and Microbiology, State Key Laboratory of Oncogenes and Related Genes, Shanghai Jiao Tong University School of Medicine; 280 South Chongqing Road, Shanghai, 200025, China
| | - Bing Su
- Shanghai Institute of Immunology, Department of Immunology and Microbiology, State Key Laboratory of Oncogenes and Related Genes, Shanghai Jiao Tong University School of Medicine; 280 South Chongqing Road, Shanghai, 200025, China
- Center for Immune-Related Diseases at Shanghai Institute of Immunology, Departments of Endocrinology and Gastroenterology, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
- Shanghai Jiao Tong University School of Medicine-Yale Institute for Immune Metabolism, Shanghai Jiao Tong University School of Medicine, Shanghai 200025
| | - 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; 320 Yueyang Road, Shanghai 200031, China
| | - Roberto Chiarle
- Department of Molecular Biotechnology and Health Sciences, University of Torino; 10126 Torino, Italy
- Department of Pathology, Boston Children’s Hospital, and Harvard Medical School; Boston, MA 02115, USA
| | - Qiang Pan-Hammarström
- Department of Biosciences and Nutrition, Karolinska Institutet; SE141-83, Huddinge, Stockholm, Sweden
| | - Leng-Siew Yeap
- Center for Immune-Related Diseases at Shanghai Institute of Immunology, Department of Endocrinology and Metabolic Diseases, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
- Shanghai Institute of Immunology, Department of Immunology and Microbiology, State Key Laboratory of Oncogenes and Related Genes, Shanghai Jiao Tong University School of Medicine; 280 South Chongqing Road, Shanghai, 200025, China
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5
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Zagelbaum J, Schooley A, Zhao J, Schrank BR, Callen E, Zha S, Gottesman ME, Nussenzweig A, Rabadan R, Dekker J, Gautier J. Multiscale reorganization of the genome following DNA damage facilitates chromosome translocations via nuclear actin polymerization. Nat Struct Mol Biol 2023; 30:99-106. [PMID: 36564591 PMCID: PMC10104780 DOI: 10.1038/s41594-022-00893-6] [Citation(s) in RCA: 20] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2022] [Accepted: 11/04/2022] [Indexed: 12/24/2022]
Abstract
Nuclear actin-based movements have been shown to orchestrate clustering of DNA double-strand breaks (DSBs) into homology-directed repair domains. Here we describe multiscale three-dimensional genome reorganization following DNA damage and analyze the contribution of the nuclear WASP-ARP2/3-actin pathway toward chromatin topology alterations and pathologic repair. Hi-C analysis reveals genome-wide, DNA damage-induced chromatin compartment flips facilitated by ARP2/3 that enrich for open, A compartments. Damage promotes interactions between DSBs, which in turn facilitate aberrant, actin-dependent intra- and inter-chromosomal rearrangements. Our work establishes that clustering of resected DSBs into repair domains by nuclear actin assembly is coordinated with multiscale alterations in genome architecture that enable homology-directed repair while also increasing nonhomologous end-joining-dependent translocation frequency.
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Affiliation(s)
- Jennifer Zagelbaum
- Institute for Cancer Genetics, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA
- Integrated Program in Cellular, Molecular, and Biomedical Studies, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA
| | - Allana Schooley
- Department of Systems Biology, University of Massachusetts Medical School, Worcester, MA, USA
| | - Junfei Zhao
- Department of Systems Biology, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA
| | - Benjamin R Schrank
- Institute for Cancer Genetics, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA
- The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Elsa Callen
- Laboratory of Genome Integrity, National Institutes of Health, Bethesda, MD, USA
| | - Shan Zha
- Institute for Cancer Genetics, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA
- Department of Pathology and Cell Biology and Department of Pediatrics, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA
- Herbert Irving Comprehensive Cancer Center, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA
| | - Max E Gottesman
- Department of Biochemistry and Biophysics, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA
| | - André Nussenzweig
- Laboratory of Genome Integrity, National Institutes of Health, Bethesda, MD, USA
| | - Raul Rabadan
- Department of Systems Biology, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA
- Herbert Irving Comprehensive Cancer Center, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA
| | - Job Dekker
- Department of Systems Biology, University of Massachusetts Medical School, Worcester, MA, USA
- Howard Hughes Medical Institute, Chevy Chase, MD, USA
| | - Jean Gautier
- Institute for Cancer Genetics, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA.
- Herbert Irving Comprehensive Cancer Center, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA.
- Department of Genetics and Development, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA.
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6
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Peycheva M, Neumann T, Malzl D, Nazarova M, Schoeberl UE, Pavri R. DNA replication timing directly regulates the frequency of oncogenic chromosomal translocations. Science 2022; 377:eabj5502. [DOI: 10.1126/science.abj5502] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
Abstract
Chromosomal translocations result from the joining of DNA double-strand breaks (DSBs) and frequently cause cancer. However, the steps linking DSB formation to DSB ligation remain undeciphered. We report that DNA replication timing (RT) directly regulates lymphomagenic
Myc
translocations during antibody maturation in B cells downstream of DSBs and independently of DSB frequency. Depletion of minichromosome maintenance complexes alters replication origin activity, decreases translocations, and deregulates global RT. Ablating a single origin at
Myc
causes an early-to-late RT switch, loss of translocations, and reduced proximity with the immunoglobulin heavy chain (
Igh
) gene, its major translocation partner. These phenotypes were reversed by restoring early RT. Disruption of early RT also reduced tumorigenic translocations in human leukemic cells. Thus, RT constitutes a general mechanism in translocation biogenesis linking DSB formation to DSB ligation.
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Affiliation(s)
- Mihaela Peycheva
- Research Institute of Molecular Pathology (IMP), Vienna Biocenter, 1030 Vienna, Austria
| | - Tobias Neumann
- Research Institute of Molecular Pathology (IMP), Vienna Biocenter, 1030 Vienna, Austria
- Vienna BioCenter PhD Program, Doctoral School of the University of Vienna and Medical University of Vienna, Vienna Biocenter, 1030 Vienna, Austria
| | - Daniel Malzl
- Research Institute of Molecular Pathology (IMP), Vienna Biocenter, 1030 Vienna, Austria
| | - Mariia Nazarova
- Research Institute of Molecular Pathology (IMP), Vienna Biocenter, 1030 Vienna, Austria
| | - Ursula E. Schoeberl
- Research Institute of Molecular Pathology (IMP), Vienna Biocenter, 1030 Vienna, Austria
| | - Rushad Pavri
- Research Institute of Molecular Pathology (IMP), Vienna Biocenter, 1030 Vienna, Austria
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7
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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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8
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So A, Dardillac E, Muhammad A, Chailleux C, Sesma-Sanz L, Ragu S, Le Cam E, Canitrot Y, Masson J, Dupaigne P, Lopez BS, Guirouilh-Barbat J. OUP accepted manuscript. Nucleic Acids Res 2022; 50:2651-2666. [PMID: 35137208 PMCID: PMC8934640 DOI: 10.1093/nar/gkac073] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2021] [Revised: 01/18/2022] [Accepted: 01/25/2022] [Indexed: 11/23/2022] Open
Abstract
Selection of the appropriate DNA double-strand break (DSB) repair pathway is decisive for genetic stability. It is proposed to act according to two steps: 1-canonical nonhomologous end-joining (C-NHEJ) versus resection that generates single-stranded DNA (ssDNA) stretches; 2-on ssDNA, gene conversion (GC) versus nonconservative single-strand annealing (SSA) or alternative end-joining (A-EJ). Here, we addressed the mechanisms by which RAD51 regulates this second step, preventing nonconservative repair in human cells. Silencing RAD51 or BRCA2 stimulated both SSA and A-EJ, but not C-NHEJ, validating the two-step model. Three different RAD51 dominant-negative forms (DN-RAD51s) repressed GC and stimulated SSA/A-EJ. However, a fourth DN-RAD51 repressed SSA/A-EJ, although it efficiently represses GC. In living cells, the three DN-RAD51s that stimulate SSA/A-EJ failed to load efficiently onto damaged chromatin and inhibited the binding of endogenous RAD51, while the fourth DN-RAD51, which inhibits SSA/A-EJ, efficiently loads on damaged chromatin. Therefore, the binding of RAD51 to DNA, rather than its ability to promote GC, is required for SSA/A-EJ inhibition by RAD51. We showed that RAD51 did not limit resection of endonuclease-induced DSBs, but prevented spontaneous and RAD52-induced annealing of complementary ssDNA in vitro. Therefore, RAD51 controls the selection of the DSB repair pathway, protecting genome integrity from nonconservative DSB repair through ssDNA occupancy, independently of the promotion of CG.
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Affiliation(s)
- Ayeong So
- Université de Paris, INSERM U1016, UMR 8104 CNRS, Institut Cochin, Equipe Labellisée Ligue Contre le Cancer, France
- CNRS UMR 8200, Gustave-Roussy, Université Paris-Saclay, 114 rue Edouard Vaillant, 94805 Villejuif, France
| | - Elodie Dardillac
- Université de Paris, INSERM U1016, UMR 8104 CNRS, Institut Cochin, Equipe Labellisée Ligue Contre le Cancer, France
- CNRS UMR 8200, Gustave-Roussy, Université Paris-Saclay, 114 rue Edouard Vaillant, 94805 Villejuif, France
| | - Ali Muhammad
- Genome Maintenance and Molecular Microscopy UMR 9019 CNRS, Université Paris-Saclay, Gustave Roussy, F-94805, Villejuif Cedex, France
| | | | - Laura Sesma-Sanz
- Genome Stability Laboratory, CHU de Québec Research Center (Oncology Division), Quebec City, QC, Canada
- Department of Molecular Biology, Medical Biochemistry and Pathology, Laval University Cancer Research Center, Quebec City, QC, Canada
| | - Sandrine Ragu
- Université de Paris, INSERM U1016, UMR 8104 CNRS, Institut Cochin, Equipe Labellisée Ligue Contre le Cancer, France
- CNRS UMR 8200, Gustave-Roussy, Université Paris-Saclay, 114 rue Edouard Vaillant, 94805 Villejuif, France
| | - Eric Le Cam
- Genome Maintenance and Molecular Microscopy UMR 9019 CNRS, Université Paris-Saclay, Gustave Roussy, F-94805, Villejuif Cedex, France
| | - Yvan Canitrot
- CBI, CNRS UMR5088, LBCMCP, Toulouse University, Toulouse, France
| | - Jean Yves Masson
- Genome Stability Laboratory, CHU de Québec Research Center (Oncology Division), Quebec City, QC, Canada
- Department of Molecular Biology, Medical Biochemistry and Pathology, Laval University Cancer Research Center, Quebec City, QC, Canada
| | - Pauline Dupaigne
- Genome Maintenance and Molecular Microscopy UMR 9019 CNRS, Université Paris-Saclay, Gustave Roussy, F-94805, Villejuif Cedex, France
| | - Bernard S Lopez
- To whom correspondence should be addressed. Tel: +33 1 53 73 27 40;
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9
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Liu D, Lieber MR. The mechanisms of human lymphoid chromosomal translocations and their medical relevance. Crit Rev Biochem Mol Biol 2021; 57:227-243. [PMID: 34875186 DOI: 10.1080/10409238.2021.2004576] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Abstract
The most common human lymphoid chromosomal translocations involve concurrent failures of the recombination activating gene (RAG) complex and Activation-Induced Deaminase (AID). These are two enzymes that are normally expressed for purposes of the two site-specific DNA recombination processes: V(D)J recombination and class switch recombination (CSR). First, though it is rare, a low level of expression of AID can introduce long-lived T:G mismatch lesions at 20-600 bp fragile zones. Second, the V(D)J recombination process can occasionally fail to rejoin coding ends, and this failure may permit an opportunity for Artemis:DNA-dependent kinase catalytic subunit (DNA-PKcs) to convert the T:G mismatch sites at the fragile zones into double-strand breaks. The 20-600 bp fragile zones must be, at least transiently, in a single-stranded DNA (ssDNA) state for the first step to occur, because AID only acts on ssDNA. Here we discuss the key DNA sequence features that lead to AID action at a fragile zone, which are (a) the proximity and density of strings of cytosine nucleotides (C-strings) that cause a B/A-intermediate DNA conformation; (b) overlapping AID hotspots that contain a methyl CpG (WRCG), which AID converts to a long-lived T:G mismatch; and (c) transcription, which, though not essential, favors increased ssDNA in the fragile zone. We also summarize chromosomal features of the focal fragile zones in lymphoid malignancies and discuss the clinical relevance of understanding the translocation mechanisms. Many of the key principles covered here are also relevant to chromosomal translocations in non-lymphoid somatic cells as well.
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Affiliation(s)
- Di Liu
- Department of Pathology & Laboratory Medicine, Department of Biochemistry & Molecular Biology, Department of Molecular Microbiology and Immunology, and Section of Computational Biology in the Department of Biological Sciences, USC Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Michael R Lieber
- Department of Pathology & Laboratory Medicine, Department of Biochemistry & Molecular Biology, Department of Molecular Microbiology and Immunology, and Section of Computational Biology in the Department of Biological Sciences, USC Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
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10
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Frequent mutations of FBXO11 highlight BCL6 as a therapeutic target in Burkitt lymphoma. Blood Adv 2021; 5:5239-5257. [PMID: 34625792 DOI: 10.1182/bloodadvances.2021005682] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2021] [Accepted: 09/07/2021] [Indexed: 11/20/2022] Open
Abstract
The expression of BCL6 in B cell lymphoma can be deregulated by chromosomal translocations, somatic mutations in the promoter regulatory regions or reduced proteasome-mediated degradation. FBXO11 was recently identified as a ubiquitin ligase involved in the degradation of BCL6 and is frequently inactivated in lymphoma or other tumors. Here, we show that FBXO11 mutations are found in 23% of Burkitt lymphoma (BL) patients. FBXO11 mutations impaired BCL6 degradation and the deletion of FBXO11 protein completely stabilized BCL6 levels in human BL cell lines. Conditional deletion of either one or two copies of the FBXO11 gene in mice cooperated with oncogenic MYC and accelerated B cell lymphoma onset, providing experimental evidence that FBXO11 is a haplo-insufficient oncosuppressor in B cell lymphoma. In WT and FBXO11-deficient BL mouse and human cell lines, targeting BCL6 via specific degrader or inhibitors partially impaired lymphoma growth in vitro and in vivo. Inhibition of MYC by the Omomyc mini-protein blocked cell proliferation and increased apoptosis, effects further increased by combined BCL6 targeting. Thus, by validating the functional role of FBXO11 mutations in BL we further highlight the key role of BCL6 in BL biology and provide evidence that innovative therapeutic approaches such as BCL6 degraders and direct MYC inhibition could be exploited as a targeted therapy for BL.
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11
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Böttcher K, Braunschmidt K, Hirth G, Schärich K, Klassert TE, Stock M, Sorgatz J, Fischer-Burkart S, Ullrich S, Frankenberger S, Kritsch D, Kosan C, Küppers R, Strobl LJ, Slevogt H, Zimber-Strobl U, Jungnickel B. Context-dependent regulation of immunoglobulin mutagenesis by p53. Mol Immunol 2021; 138:128-136. [PMID: 34392111 DOI: 10.1016/j.molimm.2021.08.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2021] [Revised: 07/22/2021] [Accepted: 08/04/2021] [Indexed: 10/20/2022]
Abstract
p53 plays a major role in genome maintenance. In addition to multiple p53 functions in the control of DNA repair, a regulation of DNA damage bypass via translesion synthesis has been implied in vitro. Somatic hypermutation of immunoglobulin genes for affinity maturation of antibody responses is based on aberrant translesion polymerase action and must be subject to stringent control to prevent genetic alterations and lymphomagenesis. When studying the role of p53 in somatic hypermutation in vivo, we found altered translesion polymerase-mediated A:T mutagenesis in mice lacking p53 in all organs, but notably not in mice with B cell-specific p53 inactivation, implying that p53 functions in non-B cells may alter mutagenesis in B cells. During class switch recombination, when p53 prevents formation of chromosomal translocations, we in addition detected a B cell-intrinsic role for p53 in altering G:C and A:T mutagenesis. Thus, p53 regulates translesion polymerase activity and shows differential activity during somatic hypermutation versus class switch recombination in vivo. Finally, p53 inhibition leads to increased somatic hypermutation in human B lymphoma cells. We conclude that loss of p53 function may promote genetic instability via multiple routes during antibody diversification in vivo.
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Affiliation(s)
- Katrin Böttcher
- Department of Cell Biology, Institute of Biochemistry and Biophysics, Faculty of Biological Sciences, Friedrich Schiller University Jena, Jena, Germany.
| | - Kerstin Braunschmidt
- Department of Cell Biology, Institute of Biochemistry and Biophysics, Faculty of Biological Sciences, Friedrich Schiller University Jena, Jena, Germany; Institute of Clinical Molecular Biology, Helmholtz Center Munich, German Research Center for Environmental Health, Munich, Germany.
| | - Gianna Hirth
- Department of Cell Biology, Institute of Biochemistry and Biophysics, Faculty of Biological Sciences, Friedrich Schiller University Jena, Jena, Germany.
| | - Karsten Schärich
- Department of Cell Biology, Institute of Biochemistry and Biophysics, Faculty of Biological Sciences, Friedrich Schiller University Jena, Jena, Germany.
| | - Tilman E Klassert
- Host Septomics, ZIK Septomics, Jena University Hospital, Jena, Germany.
| | - Magdalena Stock
- Host Septomics, ZIK Septomics, Jena University Hospital, Jena, Germany.
| | - Janine Sorgatz
- Department of Cell Biology, Institute of Biochemistry and Biophysics, Faculty of Biological Sciences, Friedrich Schiller University Jena, Jena, Germany.
| | - Sabine Fischer-Burkart
- Institute of Clinical Molecular Biology, Helmholtz Center Munich, German Research Center for Environmental Health, Munich, Germany.
| | - Steffen Ullrich
- Department of Cell Biology, Institute of Biochemistry and Biophysics, Faculty of Biological Sciences, Friedrich Schiller University Jena, Jena, Germany.
| | - Samantha Frankenberger
- Institute of Clinical Molecular Biology, Helmholtz Center Munich, German Research Center for Environmental Health, Munich, Germany
| | - Daniel Kritsch
- Department of Cell Biology, Institute of Biochemistry and Biophysics, Faculty of Biological Sciences, Friedrich Schiller University Jena, Jena, Germany; Institute of Biochemistry and Biophysics, Faculty of Biological Sciences, Friedrich Schiller University Jena, Jena, Germany.
| | - Christian Kosan
- Institute of Biochemistry and Biophysics, Faculty of Biological Sciences, Friedrich Schiller University Jena, Jena, Germany.
| | - Ralf Küppers
- Institute of Cell Biology (Cancer Research), University of Duisburg-Essen, Medical School, Essen, Germany.
| | - Lothar J Strobl
- Department of Gene Vectors, Helmholtz Center Munich, German Research Center for Environmental Health, Munich, Germany.
| | - Hortense Slevogt
- Host Septomics, ZIK Septomics, Jena University Hospital, Jena, Germany.
| | - Ursula Zimber-Strobl
- Department of Gene Vectors, Helmholtz Center Munich, German Research Center for Environmental Health, Munich, Germany.
| | - Berit Jungnickel
- Department of Cell Biology, Institute of Biochemistry and Biophysics, Faculty of Biological Sciences, Friedrich Schiller University Jena, Jena, Germany; Institute of Clinical Molecular Biology, Helmholtz Center Munich, German Research Center for Environmental Health, Munich, Germany.
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12
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Zhu Y, Dai H, Wang Y, Liang Y, Feng W, Yuan Y. Targeting FEN1 Suppresses the Proliferation of Chronic Myeloid Leukemia Cells Through Regulating Alternative End-Joining Pathways. DNA Cell Biol 2021; 40:1101-1111. [PMID: 34156283 DOI: 10.1089/dna.2021.0239] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023] Open
Abstract
Chronic myeloid leukemia (CML) is characterized by the formation of the BCR-ABL fusion gene. The BCR-ABL protein leads to an increased level of reactive oxygen species, which is a major cause of endogenous DNA double-strand breaks (DSBs). CML cells are prone to rely on a highly mutagenic alternative end-joining (Alt-EJ) pathway to cope with enhanced DSBs, which aggravates chromosomal instability. Hence, targeting dysregulated DNA repair proteins provides new insights into cancer treatment. In this study, we discovered the abnormal upregulation of Flap endonuclease 1 (FEN1) in CML, as well as FEN1's participation in the error-prone Alt-EJ repair pathway and its interplay with DNA Ligase1 and proliferating cell nuclear antigen in DSB repair. Knockdown of FEN1 by shRNA not only inhibited the proliferation and induced apoptosis but also enhanced the efficacy of imatinib (IM) in drug-resistant CML cell K562/G01. Moreover, excessive DSB accumulation was detected after FEN1 inhibition. In summary, our results demonstrated that FEN1 is a promising therapeutic target in CML treatment. This work extends the understanding of regulating abnormal DSB repair for cancer treatment.
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Affiliation(s)
- Yalin Zhu
- Department of Laboratory Medicine, Key Laboratory of Laboratory Medical Diagnostics Designated by the Ministry of Education, Chongqing Medical University, Chongqing, China
| | - Hongdan Dai
- Department of Laboratory Medicine, Key Laboratory of Laboratory Medical Diagnostics Designated by the Ministry of Education, Chongqing Medical University, Chongqing, China
| | - Yonghong Wang
- Department of Laboratory Medicine, Key Laboratory of Laboratory Medical Diagnostics Designated by the Ministry of Education, Chongqing Medical University, Chongqing, China
| | - Yang Liang
- Department of Laboratory Medicine, Key Laboratory of Laboratory Medical Diagnostics Designated by the Ministry of Education, Chongqing Medical University, Chongqing, China
| | - Wenli Feng
- Department of Laboratory Medicine, Key Laboratory of Laboratory Medical Diagnostics Designated by the Ministry of Education, Chongqing Medical University, Chongqing, China
| | - Ying Yuan
- Department of Respiratory and Critical Care Medicine, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China
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13
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Niazi Y, Thomsen H, Smolkova B, Vodickova L, Vodenkova S, Kroupa M, Vymetalkova V, Kazimirova A, Barancokova M, Volkovova K, Staruchova M, Hoffmann P, Nöthen MM, Dusinska M, Musak L, Vodicka P, Försti A, Hemminki K. DNA repair gene polymorphisms and chromosomal aberrations in healthy, nonsmoking population. DNA Repair (Amst) 2021; 101:103079. [PMID: 33676360 DOI: 10.1016/j.dnarep.2021.103079] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2020] [Revised: 02/21/2021] [Accepted: 02/24/2021] [Indexed: 02/05/2023]
Abstract
Nonspecific structural chromosomal aberrations (CAs) can be found at around 1% of circulating lymphocytes from healthy individuals but the frequency may be higher after exposure to carcinogenic chemicals or radiation. The frequency of CAs has been measured in occupational monitoring and an increased frequency of CAs has also been associated with cancer risk. Alterations in DNA damage repair and telomere maintenance are thought to contribute to the formation of CAs, which include chromosome type of aberrations and chromatid type of aberrations. In the present study, we used the result of our published genome-wide association studies to extract data on 153 DNA repair genes from 866 nonsmoking persons who had no known occupational exposure to genotoxic substances. Considering an arbitrary cut-off level of P< 5 × 10-3, single nucleotide polymorphisms (SNPs) tagging 22 DNA repair genes were significantly associated with CAs and they remained significant at P < 0.05 when adjustment for multiple comparisons was done by the Binomial Sequential Goodness of Fit test. Nucleotide excision repair pathway genes showed most associations with 6 genes. Among the associated genes were several in which mutations manifest CA phenotype, including Fanconi anemia, WRN, BLM and genes that are important in maintaining genome stability, as well as PARP2 and mismatch repair genes. RPA2 and RPA3 may participate in telomere maintenance through the synthesis of the C strand of telomeres. Errors in NHEJ1 function may lead to translocations. The present results show associations with some genes with known CA phenotype and suggest other pathways with mechanistic rationale for the formation of CAs in healthy nonsmoking population.
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Affiliation(s)
- Yasmeen Niazi
- Department of Molecular Genetic Epidemiology, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 580, 69120 Heidelberg, Germany; Hopp Children's Cancer Center (KiTZ), 69120, Heidelberg, Germany; Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ), German Cancer Consortium (DKTK), 69120, Heidelberg, Germany.
| | - Hauke Thomsen
- Department of Molecular Genetic Epidemiology, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 580, 69120 Heidelberg, Germany; GeneWerk GmbH, Im Neuenheimer Feld 582, 6910 Heidelberg, Germany
| | - Bozena Smolkova
- Department of Molecular Oncology, Cancer Research Institute, Biomedical Research Center, Slovak Academy of Sciences, Dubravska cesta 9, 84505 Bratislava, Slovakia
| | - Ludmila Vodickova
- Department of Molecular Biology of Cancer, Institute of Experimental Medicine, of the Czech Academy of Sciences, Videnska 1083, 142 00 Prague, Czech Republic; Institute of Biology and Medical Genetics, First Faculty of Medicine, Charles University, Albertov 4, 128 00 Prague, Czech Republic; Faculty of Medicine and Biomedical Center in Pilsen, Charles University in Prague, 30605 Pilsen, Czech Republic
| | - Soňa Vodenkova
- Department of Molecular Biology of Cancer, Institute of Experimental Medicine, of the Czech Academy of Sciences, Videnska 1083, 142 00 Prague, Czech Republic
| | - Michal Kroupa
- Department of Molecular Biology of Cancer, Institute of Experimental Medicine, of the Czech Academy of Sciences, Videnska 1083, 142 00 Prague, Czech Republic; Faculty of Medicine and Biomedical Center in Pilsen, Charles University in Prague, 30605 Pilsen, Czech Republic
| | - Veronika Vymetalkova
- Department of Molecular Biology of Cancer, Institute of Experimental Medicine, of the Czech Academy of Sciences, Videnska 1083, 142 00 Prague, Czech Republic; Institute of Biology and Medical Genetics, First Faculty of Medicine, Charles University, Albertov 4, 128 00 Prague, Czech Republic; Faculty of Medicine and Biomedical Center in Pilsen, Charles University in Prague, 30605 Pilsen, Czech Republic
| | - Alena Kazimirova
- Department of Biology, Faculty of Medicine, Slovak Medical University, Limbova 12, 833 03 Bratislava, Slovakia
| | - Magdalena Barancokova
- Department of Biology, Faculty of Medicine, Slovak Medical University, Limbova 12, 833 03 Bratislava, Slovakia
| | - Katarina Volkovova
- Department of Biology, Faculty of Medicine, Slovak Medical University, Limbova 12, 833 03 Bratislava, Slovakia
| | - Marta Staruchova
- Department of Biology, Faculty of Medicine, Slovak Medical University, Limbova 12, 833 03 Bratislava, Slovakia
| | - Per Hoffmann
- Institute of Human Genetics, University of Bonn School of Medicine & University Hospital Bonn, Bonn, Germany; Division of Medical Genetics, Department of Biomedicine, University of Basel, 4003 Basel, Switzerland
| | - Markus M Nöthen
- Institute of Human Genetics, University of Bonn School of Medicine & University Hospital Bonn, Bonn, Germany
| | - Maria Dusinska
- Health Effects Laboratory, Department of Environmental Chemistry, NILU-Norwegian Institute for Air Research, Instituttveien 18, 2007 Kjeller, Norway
| | - Ludovit Musak
- Biomedical Center Martin, Comenius University in Bratislava, Jessenius Faculty of Medicine, Malá Hora 4D, 03601 Martin, Slovakia
| | - Pavel Vodicka
- Department of Molecular Biology of Cancer, Institute of Experimental Medicine, of the Czech Academy of Sciences, Videnska 1083, 142 00 Prague, Czech Republic; Institute of Biology and Medical Genetics, First Faculty of Medicine, Charles University, Albertov 4, 128 00 Prague, Czech Republic; Faculty of Medicine and Biomedical Center in Pilsen, Charles University in Prague, 30605 Pilsen, Czech Republic
| | - Asta Försti
- Department of Molecular Genetic Epidemiology, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 580, 69120 Heidelberg, Germany; Hopp Children's Cancer Center (KiTZ), 69120, Heidelberg, Germany; Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ), German Cancer Consortium (DKTK), 69120, Heidelberg, Germany
| | - Kari Hemminki
- Department of Molecular Genetic Epidemiology, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 580, 69120 Heidelberg, Germany; Faculty of Medicine and Biomedical Center in Pilsen, Charles University in Prague, 30605 Pilsen, Czech Republic; Division of Cancer Epidemiology, German Cancer Research Centre (DKFZ), 69120 Heidelberg, Germany
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14
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How Chaotic Is Genome Chaos? Cancers (Basel) 2021; 13:cancers13061358. [PMID: 33802828 PMCID: PMC8002653 DOI: 10.3390/cancers13061358] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2021] [Revised: 03/08/2021] [Accepted: 03/09/2021] [Indexed: 12/11/2022] Open
Abstract
Simple Summary Cancer genomes can undergo major restructurings involving many chromosomal locations at key stages in tumor development. This restructuring process has been designated “genome chaos” by some authors. In order to examine how chaotic cancer genome restructuring may be, the cell and molecular processes for DNA restructuring are reviewed. Examination of the action of these processes in various cancers reveals a degree of specificity that indicates genome restructuring may be sufficiently reproducible to enable possible therapies that interrupt tumor progression to more lethal forms. Abstract Cancer genomes evolve in a punctuated manner during tumor evolution. Abrupt genome restructuring at key steps in this evolution has been called “genome chaos.” To answer whether widespread genome change is truly chaotic, this review (i) summarizes the limited number of cell and molecular systems that execute genome restructuring, (ii) describes the characteristic signatures of DNA changes that result from activity of those systems, and (iii) examines two cases where genome restructuring is determined to a significant degree by cell type or viral infection. The conclusion is that many restructured cancer genomes display sufficiently unchaotic signatures to identify the cellular systems responsible for major oncogenic transitions, thereby identifying possible targets for therapies to inhibit tumor progression to greater aggressiveness.
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15
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Malfatti MC, Antoniali G, Codrich M, Burra S, Mangiapane G, Dalla E, Tell G. New perspectives in cancer biology from a study of canonical and non-canonical functions of base excision repair proteins with a focus on early steps. Mutagenesis 2021; 35:129-149. [PMID: 31858150 DOI: 10.1093/mutage/gez051] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2019] [Accepted: 12/05/2019] [Indexed: 12/15/2022] Open
Abstract
Alterations of DNA repair enzymes and consequential triggering of aberrant DNA damage response (DDR) pathways are thought to play a pivotal role in genomic instabilities associated with cancer development, and are further thought to be important predictive biomarkers for therapy using the synthetic lethality paradigm. However, novel unpredicted perspectives are emerging from the identification of several non-canonical roles of DNA repair enzymes, particularly in gene expression regulation, by different molecular mechanisms, such as (i) non-coding RNA regulation of tumour suppressors, (ii) epigenetic and transcriptional regulation of genes involved in genotoxic responses and (iii) paracrine effects of secreted DNA repair enzymes triggering the cell senescence phenotype. The base excision repair (BER) pathway, canonically involved in the repair of non-distorting DNA lesions generated by oxidative stress, ionising radiation, alkylation damage and spontaneous or enzymatic deamination of nucleotide bases, represents a paradigm for the multifaceted roles of complex DDR in human cells. This review will focus on what is known about the canonical and non-canonical functions of BER enzymes related to cancer development, highlighting novel opportunities to understand the biology of cancer and representing future perspectives for designing new anticancer strategies. We will specifically focus on APE1 as an example of a pleiotropic and multifunctional BER protein.
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Affiliation(s)
- Matilde Clarissa Malfatti
- Laboratory of Molecular Biology and DNA repair, Department of Medicine (DAME), University of Udine, Udine, Italy
| | - Giulia Antoniali
- Laboratory of Molecular Biology and DNA repair, Department of Medicine (DAME), University of Udine, Udine, Italy
| | - Marta Codrich
- Laboratory of Molecular Biology and DNA repair, Department of Medicine (DAME), University of Udine, Udine, Italy
| | - Silvia Burra
- Laboratory of Molecular Biology and DNA repair, Department of Medicine (DAME), University of Udine, Udine, Italy
| | - Giovanna Mangiapane
- Laboratory of Molecular Biology and DNA repair, Department of Medicine (DAME), University of Udine, Udine, Italy
| | - Emiliano Dalla
- Laboratory of Molecular Biology and DNA repair, Department of Medicine (DAME), University of Udine, Udine, Italy
| | - Gianluca Tell
- Laboratory of Molecular Biology and DNA repair, Department of Medicine (DAME), University of Udine, Udine, Italy
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16
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Niazi Y, Thomsen H, Smolkova B, Vodickova L, Vodenkova S, Kroupa M, Vymetalkova V, Kazimirova A, Barancokova M, Volkovova K, Staruchova M, Hoffmann P, Nöthen MM, Dusinska M, Musak L, Vodicka P, Hemminki K, Försti A. DNA Repair Gene Polymorphisms and Chromosomal Aberrations in Exposed Populations. Front Genet 2021; 12:691947. [PMID: 34220964 PMCID: PMC8242355 DOI: 10.3389/fgene.2021.691947] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2021] [Accepted: 04/30/2021] [Indexed: 02/05/2023] Open
Abstract
DNA damage and unrepaired or insufficiently repaired DNA double-strand breaks as well as telomere shortening contribute to the formation of structural chromosomal aberrations (CAs). Non-specific CAs have been used in the monitoring of individuals exposed to potential carcinogenic chemicals and radiation. The frequency of CAs in peripheral blood lymphocytes (PBLs) has been associated with cancer risk and the association has also been found in incident cancer patients. CAs include chromosome-type aberrations (CSAs) and chromatid-type aberrations (CTAs) and their sum CAtot. In the present study, we used data from our published genome-wide association studies (GWASs) and extracted the results for 153 DNA repair genes for 607 persons who had occupational exposure to diverse harmful substances/radiation and/or personal exposure to tobacco smoking. The analyses were conducted using linear and logistic regression models to study the association of DNA repair gene polymorphisms with CAs. Considering an arbitrary cutoff level of 5 × 10-3, 14 loci passed the threshold, and included 7 repair pathways for CTA, 4 for CSA, and 3 for CAtot; 10 SNPs were eQTLs influencing the expression of the target repair gene. For the base excision repair pathway, the implicated genes PARP1 and PARP2 encode poly(ADP-ribosyl) transferases with multiple regulatory functions. PARP1 and PARP2 have an important role in maintaining genome stability through diverse mechanisms. Other candidate genes with known roles for CSAs included GTF2H (general transcription factor IIH subunits 4 and 5), Fanconi anemia pathway genes, and PMS2, a mismatch repair gene. The present results suggest pathways with mechanistic rationale for the formation of CAs and emphasize the need to further develop techniques for measuring individual sensitivity to genotoxic exposure.
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Affiliation(s)
- Yasmeen Niazi
- Department of Molecular Genetic Epidemiology, German Cancer Research Center (DKFZ), Heidelberg, Germany
- Hopp Children’s Cancer Center (KiTZ), Heidelberg, Germany
- Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ), German Cancer Consortium (DKTK), Heidelberg, Germany
- *Correspondence: Yasmeen Niazi,
| | - Hauke Thomsen
- Department of Molecular Genetic Epidemiology, German Cancer Research Center (DKFZ), Heidelberg, Germany
- GeneWerk GmbH, Heidelberg, Germany
| | - Bozena Smolkova
- Department of Molecular Oncology, Cancer Research Institute, Biomedical Research Center of the Slovak Academy of Sciences, Bratislava, Slovakia
| | - Ludmila Vodickova
- Department of Molecular Biology of Cancer, Institute of Experimental Medicine, Czech Academy of Sciences, Prague, Czechia
- First Faculty of Medicine, Institute of Biology and Medical Genetics, Charles University, Prague, Czechia
- Faculty of Medicine and Biomedical Center in Pilsen, Charles University in Prague, Prague, Czecia
| | - Sona Vodenkova
- Department of Molecular Biology of Cancer, Institute of Experimental Medicine, Czech Academy of Sciences, Prague, Czechia
| | - Michal Kroupa
- Department of Molecular Biology of Cancer, Institute of Experimental Medicine, Czech Academy of Sciences, Prague, Czechia
- Faculty of Medicine and Biomedical Center in Pilsen, Charles University in Prague, Prague, Czecia
| | - Veronika Vymetalkova
- Department of Molecular Biology of Cancer, Institute of Experimental Medicine, Czech Academy of Sciences, Prague, Czechia
- First Faculty of Medicine, Institute of Biology and Medical Genetics, Charles University, Prague, Czechia
- Faculty of Medicine and Biomedical Center in Pilsen, Charles University in Prague, Prague, Czecia
| | - Alena Kazimirova
- Department of Biology, Faculty of Medicine, Slovak Medical University, Bratislava, Slovakia
| | - Magdalena Barancokova
- Department of Biology, Faculty of Medicine, Slovak Medical University, Bratislava, Slovakia
| | - Katarina Volkovova
- Department of Biology, Faculty of Medicine, Slovak Medical University, Bratislava, Slovakia
| | - Marta Staruchova
- Department of Biology, Faculty of Medicine, Slovak Medical University, Bratislava, Slovakia
| | - Per Hoffmann
- Institute of Human Genetics, School of Medicine and University Hospital Bonn, University of Bonn, Bonn, Germany
- Division of Medical Genetics, Department of Biomedicine, University of Basel, Basel, Switzerland
| | - Markus M. Nöthen
- Institute of Human Genetics, School of Medicine and University Hospital Bonn, University of Bonn, Bonn, Germany
| | - Maria Dusinska
- Health Effects Laboratory, Department of Environmental Chemistry, NILU-Norwegian Institute for Air Research, Kjeller, Norway
| | - Ludovit Musak
- Jessenius Faculty of Medicine, Biomedical Center Martin, Comenius University in Bratislava, Bratislava, Slovakia
| | - Pavel Vodicka
- Department of Molecular Biology of Cancer, Institute of Experimental Medicine, Czech Academy of Sciences, Prague, Czechia
- First Faculty of Medicine, Institute of Biology and Medical Genetics, Charles University, Prague, Czechia
- Faculty of Medicine and Biomedical Center in Pilsen, Charles University in Prague, Prague, Czecia
| | - Kari Hemminki
- Department of Molecular Genetic Epidemiology, German Cancer Research Center (DKFZ), Heidelberg, Germany
- Faculty of Medicine and Biomedical Center in Pilsen, Charles University in Prague, Prague, Czecia
- Division of Cancer Epidemiology, German Cancer Research Centre (DKFZ), Heidelberg, Germany
- Kari Hemminki,
| | - Asta Försti
- Department of Molecular Genetic Epidemiology, German Cancer Research Center (DKFZ), Heidelberg, Germany
- Hopp Children’s Cancer Center (KiTZ), Heidelberg, Germany
- Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ), German Cancer Consortium (DKTK), Heidelberg, Germany
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17
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Sebastian R, Hosogane EK, Sun EG, Tran AD, Reinhold WC, Burkett S, Sturgill DM, Gudla PR, Pommier Y, Aladjem MI, Oberdoerffer P. Epigenetic Regulation of DNA Repair Pathway Choice by MacroH2A1 Splice Variants Ensures Genome Stability. Mol Cell 2020; 79:836-845.e7. [PMID: 32649884 PMCID: PMC7483679 DOI: 10.1016/j.molcel.2020.06.028] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2019] [Revised: 04/24/2020] [Accepted: 06/17/2020] [Indexed: 12/12/2022]
Abstract
The inactive X chromosome (Xi) is inherently susceptible to genomic aberrations. Replication stress (RS) has been proposed as an underlying cause, but the mechanisms that protect from Xi instability remain unknown. Here, we show that macroH2A1.2, an RS-protective histone variant enriched on the Xi, is required for Xi integrity and female survival. Mechanistically, macroH2A1.2 counteracts its structurally distinct and equally Xi-enriched alternative splice variant, macroH2A1.1. Comparative proteomics identified a role for macroH2A1.1 in alternative end joining (alt-EJ), which accounts for Xi anaphase defects in the absence of macroH2A1.2. Genomic instability was rescued by simultaneous depletion of macroH2A1.1 or alt-EJ factors, and mice deficient for both macroH2A1 variants harbor no overt female defects. Notably, macroH2A1 splice variant imbalance affected alt-EJ capacity also in tumor cells. Together, these findings identify macroH2A1 splicing as a modulator of genome maintenance that ensures Xi integrity and may, more broadly, predict DNA repair outcome in malignant cells.
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Affiliation(s)
- Robin Sebastian
- Laboratory of Receptor Biology and Gene Expression, National Cancer Institute, NIH, Bethesda, MD 20892, USA; Developmental Therapeutics Branch, National Cancer Institute, NIH, Bethesda, MD 20892, USA.
| | - Eri K Hosogane
- Laboratory of Receptor Biology and Gene Expression, National Cancer Institute, NIH, Bethesda, MD 20892, USA
| | - Eric G Sun
- Laboratory of Receptor Biology and Gene Expression, National Cancer Institute, NIH, Bethesda, MD 20892, USA
| | - Andy D Tran
- Laboratory of Receptor Biology and Gene Expression, National Cancer Institute, NIH, Bethesda, MD 20892, USA
| | - William C Reinhold
- Developmental Therapeutics Branch, National Cancer Institute, NIH, Bethesda, MD 20892, USA
| | - Sandra Burkett
- Molecular Cytogenetics Core Facility, National Cancer Institute, Frederick, MD 21702, USA
| | - David M Sturgill
- Laboratory of Receptor Biology and Gene Expression, National Cancer Institute, NIH, Bethesda, MD 20892, USA
| | - Prabhakar R Gudla
- Laboratory of Receptor Biology and Gene Expression, National Cancer Institute, NIH, Bethesda, MD 20892, USA
| | - Yves Pommier
- Developmental Therapeutics Branch, National Cancer Institute, NIH, Bethesda, MD 20892, USA
| | - Mirit I Aladjem
- Developmental Therapeutics Branch, National Cancer Institute, NIH, Bethesda, MD 20892, USA
| | - Philipp Oberdoerffer
- Laboratory of Receptor Biology and Gene Expression, National Cancer Institute, NIH, Bethesda, MD 20892, USA.
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18
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Trancoso I, Morimoto R, Boehm T. Co-evolution of mutagenic genome editors and vertebrate adaptive immunity. Curr Opin Immunol 2020; 65:32-41. [PMID: 32353821 PMCID: PMC7768089 DOI: 10.1016/j.coi.2020.03.001] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2020] [Revised: 02/18/2020] [Accepted: 03/02/2020] [Indexed: 12/28/2022]
Abstract
The adaptive immune systems of all vertebrates rely on self-DNA mutating enzymes to assemble their antigen receptors in lymphocytes of their two principal lineages. In jawed vertebrates, the RAG1/2 recombinase directs V(D)J recombination of B cell and T cell receptor genes, whereas the activation-induced cytidine deaminase AID engages in their secondary modification. The recombination activating genes (RAG) 1 and 2 evolved from an ancient transposon-encoded genome modifier into a self-DNA mutator serving adaptive immunity; this was possible as a result of domestication, involving several changes in RAG1 and RAG2 proteins suppressing transposition and instead facilitating-coupled cleavage and recombination. By contrast, recent evidence supports the notion that the antigen receptors of T-like and B-like cells of jawless vertebrates, designated variable lymphocyte receptors (VLRs), are somatically assembled through a process akin to gene conversion that is believed to be dependent on the activities of distant relatives of AID, the cytidine deaminases CDA1 and CDA2, respectively. It appears, therefore, that the precursors of AID and CDAs underwent a domestication process that changed their target range from foreign nucleic acids to self-DNA; this multi-step evolutionary process ensured that the threat to host genome integrity was minimized. Here, we review recent findings illuminating the evolutionary steps associated with the domestication of the two groups of genome editors, RAG1/2 and cytidine deaminases, indicating how they became the driving forces underlying the emergence of vertebrate adaptive immune systems.
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Affiliation(s)
- Inês Trancoso
- Department of Developmental Immunology, Max Planck Institute of Immunobiology and Epigenetics, 79108 Freiburg, Germany
| | - Ryo Morimoto
- Department of Developmental Immunology, Max Planck Institute of Immunobiology and Epigenetics, 79108 Freiburg, Germany
| | - Thomas Boehm
- Department of Developmental Immunology, Max Planck Institute of Immunobiology and Epigenetics, 79108 Freiburg, Germany.
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19
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Che L, Alavattam KG, Stambrook PJ, Namekawa SH, Du C. BRUCE preserves genomic stability in the male germline of mice. Cell Death Differ 2020; 27:2402-2416. [PMID: 32139899 DOI: 10.1038/s41418-020-0513-4] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2019] [Revised: 01/30/2020] [Accepted: 01/31/2020] [Indexed: 01/01/2023] Open
Abstract
BRUCE is a DNA damage response protein that promotes the activation of ATM and ATR for homologous recombination (HR) repair in somatic cells, making BRUCE a key protector of genomic stability. Preservation of genomic stability in the germline is essential for the maintenance of species. Here, we show that BRUCE is required for the preservation of genomic stability in the male germline of mice, specifically in spermatogonia and spermatocytes. Conditional knockout of Bruce in the male germline leads to profound defects in spermatogenesis, including impaired maintenance of spermatogonia and increased chromosomal anomalies during meiosis. Bruce-deficient pachytene spermatocytes frequently displayed persistent DNA breaks. Homologous synapsis was impaired, and nonhomologous associations and rearrangements were apparent in up to 10% of Bruce-deficient spermatocytes. Genomic instability was apparent in the form of chromosomal fragmentation, translocations, and synapsed quadrivalents and hexavalents. In addition, unsynapsed regions of rearranged autosomes were devoid of ATM and ATR signaling, suggesting an impairment in the ATM- and ATR-dependent DNA damage response of meiotic HR. Taken together, our study unveils crucial functions for BRUCE in the maintenance of spermatogonia and in the regulation of meiotic HR-functions that preserve the genomic stability of the male germline.
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Affiliation(s)
- Lixiao Che
- Department of Cell and Cancer Biology, University of Cincinnati College of Medicine, Cincinnati, OH, 45267, USA
| | - Kris G Alavattam
- Division of Reproductive Sciences, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, 45229, USA
| | - Peter J Stambrook
- Department of Molecular Genetics, University of Cincinnati College of Medicine, Cincinnati, OH, 45267, USA
| | - Satoshi H Namekawa
- Division of Reproductive Sciences, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, 45229, USA
| | - Chunying Du
- Department of Cell and Cancer Biology, University of Cincinnati College of Medicine, Cincinnati, OH, 45267, USA.
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20
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Raboso-Gallego J, Casado-García A, Isidro-Hernández M, Vicente-Dueñas C. Epigenetic Priming in Childhood Acute Lymphoblastic Leukemia. Front Cell Dev Biol 2019; 7:137. [PMID: 31380372 PMCID: PMC6652134 DOI: 10.3389/fcell.2019.00137] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2019] [Accepted: 07/05/2019] [Indexed: 01/28/2023] Open
Abstract
Leukemogenesis is considered to be a process by which a normal cell acquires new but aberrant identity in order to disseminate a malignant clonal population. Under this setting, the phenotype of the leukemic cells is identical to the leukemia-initiating cell in which the genetic insult is taking place. Thus, with some exceptions, B-cell and T-cell childhood leukemias are supposed to arise from B- or T-committed cells. In contrast, several recent studies have revealed that genetic alterations may act in a “hit-and-run” way in the cell-of-origin by imposing the tumor cell identity giving rise to either B-cell or T-cell leukemias. This novel mechanism of cell transformation is mediated by an epigenetic priming mechanism that is established by the initial genetic lesion. This initial hit might be unnecessary for the subsequent tumor evolution and conservation, being the epigenetic priming the engine for the tumor evolution.
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Affiliation(s)
- Javier Raboso-Gallego
- Experimental Therapeutics and Translational Oncology Program, Instituto de Biología Molecular y Celular del Cáncer, CSIC/Universidad de Salamanca, Salamanca, Spain.,Institute of Biomedical Research of Salamanca (IBSAL), Salamanca, Spain
| | - Ana Casado-García
- Experimental Therapeutics and Translational Oncology Program, Instituto de Biología Molecular y Celular del Cáncer, CSIC/Universidad de Salamanca, Salamanca, Spain.,Institute of Biomedical Research of Salamanca (IBSAL), Salamanca, Spain
| | - Marta Isidro-Hernández
- Experimental Therapeutics and Translational Oncology Program, Instituto de Biología Molecular y Celular del Cáncer, CSIC/Universidad de Salamanca, Salamanca, Spain.,Institute of Biomedical Research of Salamanca (IBSAL), Salamanca, Spain
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21
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DNA Repair Deficiency in Breast Cancer: Opportunities for Immunotherapy. JOURNAL OF ONCOLOGY 2019; 2019:4325105. [PMID: 31320901 PMCID: PMC6607732 DOI: 10.1155/2019/4325105] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/22/2019] [Revised: 05/04/2019] [Accepted: 05/29/2019] [Indexed: 12/19/2022]
Abstract
Historically the development of anticancer treatments has been focused on their effect on tumor cells alone. However, newer treatments have shifted attention to targets on immune cells, resulting in dramatic responses. The effect of DNA repair deficiency on the microenvironment remains an area of key interest. Moreover, established therapies such as DNA damaging treatments such as chemotherapy and PARP inhibitors further modify the tumor microenvironment. Here we describe DNA repair pathways in breast cancer and activation of innate immune pathways in DNA repair deficiency, in particular, the STING (STimulator of INterferon Genes) pathway. Breast tumors with DNA repair deficiency are associated with upregulation of immune checkpoints including PD-L1 (Programmed Death Ligand-1) and may represent a target population for single agent or combination immunotherapy treatment.
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22
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Abstract
PURPOSE OF REVIEW Recent lymphoma genome sequencing projects have shed light on the genomic landscape of indolent and aggressive lymphomas, as well as some of the molecular mechanisms underlying recurrent mutations and translocations in these entities. Here, we review these recent genomic discoveries, focusing on acquired DNA repair defects in lymphoma. In addition, we highlight recently identified actionable molecular vulnerabilities associated with recurrent mutations in chronic lymphocytic leukemia (CLL), which serves as a model entity. RECENT FINDINGS The results of several large lymphoma genome sequencing projects have recently been reported, including CLL, T-PLL and DLBCL. We align these discoveries with proposed mechanisms of mutation acquisition in B-cell lymphomas. Moreover, novel autochthonous mouse models of CLL have recently been generated and we discuss how these models serve as preclinical tools to drive the development of novel targeted therapeutic interventions. Lastly, we highlight the results of early clinical data on novel compounds targeting defects in the DNA damage response of CLL with a particular focus on deleterious ATM mutations. SUMMARY Defects in DNA repair pathways are selected events in cancer, including lymphomas. Specifically, ATM deficiency is associated with PARP1- and DNA-PKcs inhibitor sensitivity in vitro and in vivo.
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23
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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: 20] [Impact Index Per Article: 4.0] [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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24
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Frossi B, Antoniali G, Yu K, Akhtar N, Kaplan MH, Kelley MR, Tell G, Pucillo CEM. Endonuclease and redox activities of human apurinic/apyrimidinic endonuclease 1 have distinctive and essential functions in IgA class switch recombination. J Biol Chem 2019; 294:5198-5207. [PMID: 30705092 DOI: 10.1074/jbc.ra118.006601] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2018] [Revised: 01/28/2019] [Indexed: 11/06/2022] Open
Abstract
The base excision repair (BER) pathway is an important DNA repair pathway and is essential for immune responses. In fact, it regulates both the antigen-stimulated somatic hypermutation (SHM) process and plays a central function in the process of class switch recombination (CSR). For both processes, a central role for apurinic/apyrimidinic endonuclease 1 (APE1) has been demonstrated. APE1 acts also as a master regulator of gene expression through its redox activity. APE1's redox activity stimulates the DNA-binding activity of several transcription factors, including NF-κB and a few others involved in inflammation and in immune responses. Therefore, it is possible that APE1 has a role in regulating the CSR through its function as a redox coactivator. The present study was undertaken to address this question. Using the CSR-competent mouse B-cell line CH12F3 and a combination of specific inhibitors of APE1's redox (APX3330) and repair (compound 3) activities, APE1-deficient or -reconstituted cell lines expressing redox-deficient or endonuclease-deficient proteins, and APX3330-treated mice, we determined the contributions of both endonuclease and redox functions of APE1 in CSR. We found that APE1's endonuclease activity is essential for IgA-class switch recombination. We provide evidence that the redox function of APE1 appears to play a role in regulating CSR through the interleukin-6 signaling pathway and in proper IgA expression. Our results shed light on APE1's redox function in the control of cancer growth through modulation of the IgA CSR process.
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Affiliation(s)
- Barbara Frossi
- From the Laboratory of Immunology, Department of Medicine, University of Udine, 33100 Udine, Italy
| | - Giulia Antoniali
- the Laboratory of Molecular Biology and DNA Repair, Department of Medicine, University of Udine, 33100 Udine, Italy
| | - Kefei Yu
- the Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, Michigan 48824, and
| | - Nahid Akhtar
- the Herman B. Wells Center for Pediatric Research, Department of Pediatrics, Indiana University School of Medicine, Indianapolis, Indiana 46202
| | - Mark H Kaplan
- the Herman B. Wells Center for Pediatric Research, Department of Pediatrics, Indiana University School of Medicine, Indianapolis, Indiana 46202
| | - Mark R Kelley
- the Herman B. Wells Center for Pediatric Research, Department of Pediatrics, Indiana University School of Medicine, Indianapolis, Indiana 46202
| | - Gianluca Tell
- the Laboratory of Molecular Biology and DNA Repair, Department of Medicine, University of Udine, 33100 Udine, Italy,
| | - Carlo E M Pucillo
- From the Laboratory of Immunology, Department of Medicine, University of Udine, 33100 Udine, Italy,
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25
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Niazi Y, Thomsen H, Smolkova B, Vodickova L, Vodenkova S, Kroupa M, Vymetalkova V, Kazimirova A, Barancokova M, Volkovova K, Staruchova M, Hoffmann P, Nöthen MM, Dušinská M, Musak L, Vodicka P, Hemminki K, Försti A. Genetic variation associated with chromosomal aberration frequency: A genome-wide association study. ENVIRONMENTAL AND MOLECULAR MUTAGENESIS 2019; 60:17-28. [PMID: 30368896 DOI: 10.1002/em.22236] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/14/2018] [Revised: 05/18/2018] [Accepted: 07/03/2018] [Indexed: 02/05/2023]
Abstract
Chromosomal aberrations (CAs) in human peripheral blood lymphocytes (PBL) measured with the conventional cytogenetic assay have been used for human biomonitoring of genotoxic exposure for decades. CA frequency in peripheral blood is a marker of cancer susceptibility. Previous studies have shown associations between genetic variants in metabolic pathway, DNA repair and major mitotic checkpoint genes and CAs. We conducted a genome-wide association study on 576 individuals from the Czech Republic and Slovakia followed by a replication in two different sample sets of 482 (replication 1) and 1288 (replication 2) samples. To have a broad look at the genetic susceptibility associated with CA frequency, the sample sets composed of individuals either differentially exposed to smoking, occupational/environmental hazards, or they were untreated cancer patients. Phenotypes were divided into chromosome- and chromatid-type aberrations (CSAs and CTAs, respectively) and total chromosomal aberrations (CAtot). The arbitrary cutoff point between individuals with high and low CA frequency was 2% for CAtot and 1% for CSA and CTA. The data were analyzed using age, sex, occupation/cancer and smoking history as covariates. Altogether 11 loci reached the P-value of 10-5 in the GWAS. Replication 1 supported the association of rs1383997 (8q13.3) and rs2824215 (21q21.1) in CAtot and rs983889 (5p15.1) in CTA analysis. These loci were found to be associated with genes involved in mitosis, response to environmental and chemical factors and genes involved in syndromes linked to chromosomal abnormalities. Identification of new genetic variants for the frequency of CAs offers prediction tools for cancer risk in future. Environ. Mol. Mutagen. 60:17-28, 2019. © 2018 Wiley Periodicals, Inc.
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Affiliation(s)
- Yasmeen Niazi
- Department of Molecular Genetic Epidemiology, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 580, 69120, Heidelberg, Germany
- Medizinische Fakultät, Universität Heidelberg, Im Neuenheimer Feld 672, 69120, Heidelberg
| | - Hauke Thomsen
- Department of Molecular Genetic Epidemiology, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 580, 69120, Heidelberg, Germany
| | - Bozena Smolkova
- Department of Molecular Oncology, Cancer Research Institute, Biomedical Research Center, Slovak Academy of Sciences, Dubravska cesta 9, 84505, Bratislava, Slovakia
| | - Ludmila Vodickova
- Department of Molecular Biology of Cancer, Institute of Experimental Medicine, The Czech Academy of Sciences, Videnska 1083, 142 00, Prague, Czech Republic
- Institute of Biology and Medical Genetics, First Faculty of Medicine, Charles University, Albertov 4, 128 00, Prague, Czech Republic
- Biomedical Centre, Faculty of Medicine in Pilsen, Charles University in Prague, Pilsen, Czech Republic
| | - Sona Vodenkova
- Department of Molecular Biology of Cancer, Institute of Experimental Medicine, The Czech Academy of Sciences, Videnska 1083, 142 00, Prague, Czech Republic
- Institute of Biology and Medical Genetics, First Faculty of Medicine, Charles University, Albertov 4, 128 00, Prague, Czech Republic
- Department of Medical Genetics, Third Faculty of Medicine, Charles University, Prague, Czech Republic
| | - Michal Kroupa
- Department of Molecular Biology of Cancer, Institute of Experimental Medicine, The Czech Academy of Sciences, Videnska 1083, 142 00, Prague, Czech Republic
- Biomedical Centre, Faculty of Medicine in Pilsen, Charles University in Prague, Pilsen, Czech Republic
| | - Veronika Vymetalkova
- Department of Molecular Biology of Cancer, Institute of Experimental Medicine, The Czech Academy of Sciences, Videnska 1083, 142 00, Prague, Czech Republic
- Institute of Biology and Medical Genetics, First Faculty of Medicine, Charles University, Albertov 4, 128 00, Prague, Czech Republic
| | - Alena Kazimirova
- Department of Biology, Faculty of Medicine, Slovak Medical University, Limbova 12, 833 03, Bratislava, Slovakia
| | - Magdalena Barancokova
- Department of Biology, Faculty of Medicine, Slovak Medical University, Limbova 12, 833 03, Bratislava, Slovakia
| | - Katarina Volkovova
- Department of Biology, Faculty of Medicine, Slovak Medical University, Limbova 12, 833 03, Bratislava, Slovakia
| | - Marta Staruchova
- Department of Biology, Faculty of Medicine, Slovak Medical University, Limbova 12, 833 03, Bratislava, Slovakia
| | - Per Hoffmann
- Institute of Human Genetics, University of Bonn, D-53127, Bonn, Germany
- Division of Medical Genetics, Department of Biomedicine, University of Basel, 4003, Basel, Switzerland
| | - Markus M Nöthen
- Institute of Human Genetics, University of Bonn, D-53127, Bonn, Germany
- Department of Genomics, Life & Brain Center, University of Bonn, D-53127, Bonn, Germany
| | - Maria Dušinská
- Health Effects Laboratory, Department of Environmental Chemistry, NILU-Norwegian Institute for Air Research, Instituttveien 18, 2007, Kjeller, Norway
| | - Ludovit Musak
- Clinic of Occupational Medicine and Toxicology, Jessenius Faculty of Medicine in Martin, Comenius University in Bratislava and University Hospital Martin, Kollarova 2, 03601, Martin, Slovakia
| | - Pavel Vodicka
- Department of Molecular Biology of Cancer, Institute of Experimental Medicine, The Czech Academy of Sciences, Videnska 1083, 142 00, Prague, Czech Republic
- Institute of Biology and Medical Genetics, First Faculty of Medicine, Charles University, Albertov 4, 128 00, Prague, Czech Republic
- Biomedical Centre, Faculty of Medicine in Pilsen, Charles University in Prague, Pilsen, Czech Republic
| | - Kari Hemminki
- Department of Molecular Genetic Epidemiology, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 580, 69120, Heidelberg, Germany
- Center of Primary Health Care Research, Clinical Research Center, Lund University, 20502, Malmö, Sweden
| | - Asta Försti
- Department of Molecular Genetic Epidemiology, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 580, 69120, Heidelberg, Germany
- Center of Primary Health Care Research, Clinical Research Center, Lund University, 20502, Malmö, Sweden
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26
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Naik AK, Byrd AT, Lucander ACK, Krangel MS. Hierarchical assembly and disassembly of a transcriptionally active RAG locus in CD4 +CD8 + thymocytes. J Exp Med 2018; 216:231-243. [PMID: 30545902 PMCID: PMC6314527 DOI: 10.1084/jem.20181402] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2018] [Revised: 10/29/2018] [Accepted: 11/21/2018] [Indexed: 01/17/2023] Open
Abstract
Naik et al. show that GATA3, Runx1, and E2A are essential for hierarchical assembly of a transcriptionally active RAG locus chromatin hub in CD4+CD8+ thymocytes. Signal-dependent down-regulation of RAG expression is associated with hub disassembly and depends on Ikaros. Expression of Rag1 and Rag2 is tightly regulated in developing T cells to mediate TCR gene assembly. Here we have investigated the molecular mechanisms governing the assembly and disassembly of a transcriptionally active RAG locus chromatin hub in CD4+CD8+ thymocytes. Rag1 and Rag2 gene expression in CD4+CD8+ thymocytes depends on Rag1 and Rag2 promoter activation by a distant antisilencer element (ASE). We identify GATA3 and E2A as critical regulators of the ASE, and Runx1 and E2A as critical regulators of the Rag1 promoter. We reveal hierarchical assembly of a transcriptionally active chromatin hub containing the ASE and RAG promoters, with Rag2 recruitment and expression dependent on assembly of a functional ASE–Rag1 framework. Finally, we show that signal-dependent down-regulation of RAG gene expression in CD4+CD8+ thymocytes depends on Ikaros and occurs with disassembly of the RAG locus chromatin hub. Our results provide important new insights into the molecular mechanisms that orchestrate RAG gene expression in developing T cells.
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Affiliation(s)
- Abani Kanta Naik
- Department of Immunology, Duke University Medical Center, Durham, NC
| | - Aaron T Byrd
- Department of Immunology, Duke University Medical Center, Durham, NC
| | | | - Michael S Krangel
- Department of Immunology, Duke University Medical Center, Durham, NC
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27
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Cheong TC, Blasco RB, Chiarle R. The CRISPR/Cas9 System as a Tool to Engineer Chromosomal Translocation In Vivo. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2018; 1044:39-48. [PMID: 29956290 DOI: 10.1007/978-981-13-0593-1_4] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
The CRISPR/Cas9 system has emerged as a powerful tool to edit the genome. Among many applications, the system generates the exciting possibility of engineering small and large portions of chromosomes to induce a variety of structural alterations such as deletions, inversions, insertions and inter-chromosomal translocations. Furthermore, the availability of viral vectors that express Cas9 has been critical to deliver the CRISPR/Cas9 system directly in vivo to induce chromosomal rearrangements. This review provides an overview of the state-of-the-art CRISPR/Cas9 technology to model a variety of rearrangements in vivo in animal models.
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Affiliation(s)
- Taek-Chin Cheong
- Department of Pathology, Boston Children's Hospital, Boston, MA, USA.,Harvard Medical School, Boston, MA, USA
| | - Rafael B Blasco
- Department of Pathology, Boston Children's Hospital, Boston, MA, USA.,Harvard Medical School, Boston, MA, USA
| | - Roberto Chiarle
- Department of Pathology, Boston Children's Hospital, Boston, MA, USA. .,Harvard Medical School, Boston, MA, USA.
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28
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Lin SG, Ba Z, Alt FW, Zhang Y. RAG Chromatin Scanning During V(D)J Recombination and Chromatin Loop Extrusion are Related Processes. Adv Immunol 2018; 139:93-135. [PMID: 30249335 DOI: 10.1016/bs.ai.2018.07.001] [Citation(s) in RCA: 39] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
An effective adaptive immune system depends on the ability of developing B and T cells to generate diverse immunoglobulin (Ig) and T cell receptor repertoires, respectively. Such diversity is achieved through a programmed somatic recombination process whereby germline V, D, and J segments of antigen receptor loci are assembled to form the variable region V(D)J exons of Ig and TCRs. Studies of this process, termed V(D)J recombination, have provided key insights into our understanding of a variety of general gene regulatory and DNA repair processes over the last several decades. V(D)J recombination is initiated by the RAG endonuclease which generates DNA double-stranded breaks at the borders of V, D, and J segments. In this review, we cover recent work that has elucidated RAG structure and work that revealed that RAG has a novel chromatin scanning activity, likely mediated by chromatin loop extrusion, that contributes to its ability to locate V, D, J gene segment substrates within large chromosomal loop domains bounded by CTCF-binding elements (CBEs). This latter function, coupled with the role CBE-based chromatin loop domains and subdomains within them play in focusing V(D)J recombination activity within antigen receptor loci, provide mechanistic explanations for long-standing questions regarding V(D)J segment usage diversification and in limiting potentially deleterious off-target RAG-initiated recombination events genome-wide. This review will focus mainly on studies of the mouse Ig heavy chain locus, but the principles described also apply to other Ig loci and to TCR loci in mice and humans.
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Affiliation(s)
- Sherry G Lin
- Program in Cellular and Molecular Medicine, Boston Children's Hospital, and Department of Genetics, Howard Hughes Medical Institute, Harvard Medical School, Boston, MA, United States
| | - Zhaoqing Ba
- Program in Cellular and Molecular Medicine, Boston Children's Hospital, and Department of Genetics, Howard Hughes Medical Institute, Harvard Medical School, Boston, MA, United States
| | - Frederick W Alt
- Program in Cellular and Molecular Medicine, Boston Children's Hospital, and Department of Genetics, Howard Hughes Medical Institute, Harvard Medical School, Boston, MA, United States.
| | - Yu Zhang
- Program in Cellular and Molecular Medicine, Boston Children's Hospital, and Department of Genetics, Howard Hughes Medical Institute, Harvard Medical School, Boston, MA, United States
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29
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Vodicka P, Musak L, Vodickova L, Vodenkova S, Catalano C, Kroupa M, Naccarati A, Polivkova Z, Vymetalkova V, Försti A, Hemminki K. Genetic variation of acquired structural chromosomal aberrations. MUTATION RESEARCH-GENETIC TOXICOLOGY AND ENVIRONMENTAL MUTAGENESIS 2018; 836:13-21. [PMID: 30389156 DOI: 10.1016/j.mrgentox.2018.05.014] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/22/2018] [Revised: 04/24/2018] [Accepted: 05/10/2018] [Indexed: 12/21/2022]
Abstract
Human malignancies are often hallmarked with genomic instability, which itself is also considered a causative event in malignant transformation. Genomic instability may manifest itself as genetic changes in the nucleotide sequence of DNA, or as structural or numerical changes of chromosomes. Unrepaired or insufficiently repaired DNA double-strand breaks, as well as telomere shortening, are important contributors in the formation of structural chromosomal aberrations (CAs). In the present review, we discuss potential mechanisms behind the formation of CAs and their relation to cancer. Based on our own studies, we also illustrate how inherited genetic variation may modify the frequency and types of CAs occurring in humans. Recently, we published a series of studies on variations in genes relevant to maintaining genomic integrity, such as those encoding xenobiotic-metabolising enzymes, DNA repair, the tumour suppressor TP53, the spindle assembly checkpoint, and cyclin D1 (CCND1). While individually genetic variation in these genes exerted small modulating effects, in interactions they were associated with CA frequencies in peripheral blood lymphocytes of healthy volunteers. Moreover, we observed opposite associations between the CCND1 splice site polymorphism rs9344 G870A and the frequency of CAs compared to their association with translocation t(11,14). We discuss the functional consequences of the CCND1 gene in interplay with DNA damage response and DNA repair during malignant transformation. Our review summarizes existing evidence that gene variations in relevant cellular pathways modulate the frequency of CAs, predominantly in a complex interaction. More functional/mechanistic studies elucidating these observations are required. Several questions emerge, such as the role of CAs in malignancies with respect to a particular phenotype and heterogeneity, the formation of CAs during the process of malignant transformation, and the formation of CAs in individual types of lymphocytes in relation to the immune response.
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Affiliation(s)
- Pavel Vodicka
- Department of Molecular Biology of Cancer, Institute of Experimental Medicine, Czech Academy of Sciences, Prague, 14220, Czech Republic; Institute of Biology and Medical Genetics, First Faculty of Medicine, Charles University, Prague, 12800, Czech Republic; Faculty of Medicine and Biomedical Center in Pilsen, Charles University, Pilsen, 30605, Czech Republic.
| | - Ludovit Musak
- Biomedical Center Martin, Comenius University in Bratislava, Jessenius Faculty of Medicine, Martin, 03601, Slovakia
| | - Ludmila Vodickova
- Department of Molecular Biology of Cancer, Institute of Experimental Medicine, Czech Academy of Sciences, Prague, 14220, Czech Republic; Institute of Biology and Medical Genetics, First Faculty of Medicine, Charles University, Prague, 12800, Czech Republic; Faculty of Medicine and Biomedical Center in Pilsen, Charles University, Pilsen, 30605, Czech Republic
| | - Sona Vodenkova
- Department of Molecular Biology of Cancer, Institute of Experimental Medicine, Czech Academy of Sciences, Prague, 14220, Czech Republic; Institute of Biology and Medical Genetics, First Faculty of Medicine, Charles University, Prague, 12800, Czech Republic; Department of Medical Genetics, Third Faculty of Medicine, Charles University, Prague, 10000, Czech Republic
| | - Calogerina Catalano
- Division of Molecular Genetic Epidemiology, German Cancer Research Center (DKFZ), Heidelberg, D69120, Germany
| | - Michal Kroupa
- Department of Molecular Biology of Cancer, Institute of Experimental Medicine, Czech Academy of Sciences, Prague, 14220, Czech Republic; Faculty of Medicine and Biomedical Center in Pilsen, Charles University, Pilsen, 30605, Czech Republic
| | - Alessio Naccarati
- Department of Molecular Biology of Cancer, Institute of Experimental Medicine, Czech Academy of Sciences, Prague, 14220, Czech Republic; Italian Institute for Genomic Medicine (IIGM), Torino, 10126, Italy
| | - Zdena Polivkova
- Department of Medical Genetics, Third Faculty of Medicine, Charles University, Prague, 10000, Czech Republic
| | - Veronika Vymetalkova
- Department of Molecular Biology of Cancer, Institute of Experimental Medicine, Czech Academy of Sciences, Prague, 14220, Czech Republic; Institute of Biology and Medical Genetics, First Faculty of Medicine, Charles University, Prague, 12800, Czech Republic; Faculty of Medicine and Biomedical Center in Pilsen, Charles University, Pilsen, 30605, Czech Republic
| | - Asta Försti
- Division of Molecular Genetic Epidemiology, German Cancer Research Center (DKFZ), Heidelberg, D69120, Germany; Center for Primary Health Care Research, Lund University, Malmö, 214 28, Sweden
| | - Kari Hemminki
- Division of Molecular Genetic Epidemiology, German Cancer Research Center (DKFZ), Heidelberg, D69120, Germany; Center for Primary Health Care Research, Lund University, Malmö, 214 28, Sweden
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Dahal S, Dubey S, Raghavan SC. Homologous recombination-mediated repair of DNA double-strand breaks operates in mammalian mitochondria. Cell Mol Life Sci 2018; 75:1641-1655. [PMID: 29116362 PMCID: PMC11105789 DOI: 10.1007/s00018-017-2702-y] [Citation(s) in RCA: 37] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2017] [Revised: 10/23/2017] [Accepted: 10/30/2017] [Indexed: 10/18/2022]
Abstract
Mitochondrial DNA is frequently exposed to oxidative damage, as compared to nuclear DNA. Previously, we have shown that while microhomology-mediated end joining can account for DNA deletions in mitochondria, classical nonhomologous DNA end joining, the predominant double-strand break (DSB) repair pathway in nucleus, is undetectable. In the present study, we investigated the presence of homologous recombination (HR) in mitochondria to maintain its genomic integrity. Biochemical studies revealed that HR-mediated repair of DSBs is more efficient in the mitochondria of testes as compared to that of brain, kidney and spleen. Interestingly, a significant increase in the efficiency of HR was observed when a DSB was introduced. Analyses of the clones suggest that most of the recombinants were generated through reciprocal exchange, while ~ 30% of recombinants were due to gene conversion in testicular extracts. Colocalization and immunoblotting studies showed the presence of RAD51 and MRN complex proteins in the mitochondria and immunodepletion of MRE11, RAD51 or NIBRIN suppressed the HR-mediated repair. Thus, our results reveal importance of homologous recombination in the maintenance of mitochondrial genome stability.
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Affiliation(s)
- Sumedha Dahal
- Department of Biochemistry, Indian Institute of Science, Bangalore, 560 012, India
| | - Shubham Dubey
- Department of Biochemistry, Indian Institute of Science, Bangalore, 560 012, India
| | - Sathees C Raghavan
- Department of Biochemistry, Indian Institute of Science, Bangalore, 560 012, India.
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Processing-Challenges Generated by Clusters of DNA Double-Strand Breaks Underpin Increased Effectiveness of High-LET Radiation and Chromothripsis. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2018; 1044:149-168. [DOI: 10.1007/978-981-13-0593-1_10] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
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Kroupa M, Polivkova Z, Rachakonda S, Schneiderova M, Vodenkova S, Buchler T, Jiraskova K, Urbanova M, Vodickova L, Hemminki K, Kumar R, Vodicka P. Bleomycin‐induced chromosomal damage and shortening of telomeres in peripheral blood lymphocytes of incident cancer patients. Genes Chromosomes Cancer 2017; 57:61-69. [DOI: 10.1002/gcc.22508] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2017] [Revised: 10/02/2017] [Accepted: 10/11/2017] [Indexed: 12/16/2022] Open
Affiliation(s)
- Michal Kroupa
- Faculty of Medicine and Biomedical Center in Pilsen, Charles UniversityPilsen30605 Czech Republic
- Department of Molecular Biology of CancerInstitute of Experimental Medicine, The Czech Academy of SciencesPrague14220 Czech Republic
| | - Zdenka Polivkova
- Department of Medical GeneticsThird Faculty of Medicine, Charles UniversityPrague10000 Czech Republic
| | | | - Michaela Schneiderova
- Department of SurgeryGeneral University Hospital in PraguePrague12800 Czech Republic
| | - Sona Vodenkova
- Department of Molecular Biology of CancerInstitute of Experimental Medicine, The Czech Academy of SciencesPrague14220 Czech Republic
- Department of Medical GeneticsThird Faculty of Medicine, Charles UniversityPrague10000 Czech Republic
- Institute of Biology and Medical Genetics, First Faculty of Medicine, Charles UniversityPrague12800 Czech Republic
| | - Tomas Buchler
- Department of OncologyFirst Faculty of Medicine, Charles University and Thomayer HospitalPrague, 14059 Czech Republic
| | - Katerina Jiraskova
- Department of Molecular Biology of CancerInstitute of Experimental Medicine, The Czech Academy of SciencesPrague14220 Czech Republic
- Institute of Biology and Medical Genetics, First Faculty of Medicine, Charles UniversityPrague12800 Czech Republic
| | - Marketa Urbanova
- Department of Molecular Biology of CancerInstitute of Experimental Medicine, The Czech Academy of SciencesPrague14220 Czech Republic
- Institute of Biology and Medical Genetics, First Faculty of Medicine, Charles UniversityPrague12800 Czech Republic
| | - Ludmila Vodickova
- Faculty of Medicine and Biomedical Center in Pilsen, Charles UniversityPilsen30605 Czech Republic
- Department of Molecular Biology of CancerInstitute of Experimental Medicine, The Czech Academy of SciencesPrague14220 Czech Republic
- Institute of Biology and Medical Genetics, First Faculty of Medicine, Charles UniversityPrague12800 Czech Republic
| | - Kari Hemminki
- Division of Molecular Genetic EpidemiologyGerman Cancer Research CenterHeidelberg69120 Germany
| | - Rajiv Kumar
- Division of Molecular Genetic EpidemiologyGerman Cancer Research CenterHeidelberg69120 Germany
| | - Pavel Vodicka
- Faculty of Medicine and Biomedical Center in Pilsen, Charles UniversityPilsen30605 Czech Republic
- Department of Molecular Biology of CancerInstitute of Experimental Medicine, The Czech Academy of SciencesPrague14220 Czech Republic
- Institute of Biology and Medical Genetics, First Faculty of Medicine, Charles UniversityPrague12800 Czech Republic
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Vitelli V, Galbiati A, Iannelli F, Pessina F, Sharma S, d'Adda di Fagagna F. Recent Advancements in DNA Damage-Transcription Crosstalk and High-Resolution Mapping of DNA Breaks. Annu Rev Genomics Hum Genet 2017; 18:87-113. [PMID: 28859573 DOI: 10.1146/annurev-genom-091416-035314] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Until recently, DNA damage arising from physiological DNA metabolism was considered a detrimental by-product for cells. However, an increasing amount of evidence has shown that DNA damage could have a positive role in transcription activation. In particular, DNA damage has been detected in transcriptional elements following different stimuli. These physiological DNA breaks are thought to be instrumental for the correct expression of genomic loci through different mechanisms. In this regard, although a plethora of methods are available to precisely map transcribed regions and transcription start sites, commonly used techniques for mapping DNA breaks lack sufficient resolution and sensitivity to draw a robust correlation between DNA damage generation and transcription. Recently, however, several methods have been developed to map DNA damage at single-nucleotide resolution, thus providing a new set of tools to correlate DNA damage and transcription. Here, we review how DNA damage can positively regulate transcription initiation, the current techniques for mapping DNA breaks at high resolution, and how these techniques can benefit future studies of DNA damage and transcription.
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Affiliation(s)
- Valerio Vitelli
- FIRC Institute of Molecular Oncology (IFOM), Milan 20139, Italy;
| | | | - Fabio Iannelli
- FIRC Institute of Molecular Oncology (IFOM), Milan 20139, Italy;
| | - Fabio Pessina
- FIRC Institute of Molecular Oncology (IFOM), Milan 20139, Italy;
| | - Sheetal Sharma
- FIRC Institute of Molecular Oncology (IFOM), Milan 20139, Italy;
| | - Fabrizio d'Adda di Fagagna
- FIRC Institute of Molecular Oncology (IFOM), Milan 20139, Italy; .,Istituto di Genetica Molecolare, Consiglio Nazionale delle Ricerche (CNR), Pavia 27100, Italy
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Biochemical Regulatory Features of Activation-Induced Cytidine Deaminase Remain Conserved from Lampreys to Humans. Mol Cell Biol 2017; 37:MCB.00077-17. [PMID: 28716949 DOI: 10.1128/mcb.00077-17] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2017] [Accepted: 07/10/2017] [Indexed: 01/17/2023] Open
Abstract
Activation-induced cytidine deaminase (AID) is a genome-mutating enzyme that initiates class switch recombination and somatic hypermutation of antibodies in jawed vertebrates. We previously described the biochemical properties of human AID and found that it is an unusual enzyme in that it exhibits binding affinities for its substrate DNA and catalytic rates several orders of magnitude higher and lower, respectively, than a typical enzyme. Recently, we solved the functional structure of AID and demonstrated that these properties are due to nonspecific DNA binding on its surface, along with a catalytic pocket that predominantly assumes a closed conformation. Here we investigated the biochemical properties of AID from a sea lamprey, nurse shark, tetraodon, and coelacanth: representative species chosen because their lineages diverged at the earliest critical junctures in evolution of adaptive immunity. We found that these earliest-diverged AID orthologs are active cytidine deaminases that exhibit unique substrate specificities and thermosensitivities. Significant amino acid sequence divergence among these AID orthologs is predicted to manifest as notable structural differences. However, despite major differences in sequence specificities, thermosensitivities, and structural features, all orthologs share the unusually high DNA binding affinities and low catalytic rates. This absolute conservation is evidence for biological significance of these unique biochemical properties.
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Srivastava S, Dahal S, Naidu SJ, Anand D, Gopalakrishnan V, Kooloth Valappil R, Raghavan SC. DNA double-strand break repair in Penaeus monodon is predominantly dependent on homologous recombination. DNA Res 2017; 24:117-128. [PMID: 28431013 PMCID: PMC5397610 DOI: 10.1093/dnares/dsw059] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2016] [Accepted: 12/08/2016] [Indexed: 11/13/2022] Open
Abstract
DNA double-strand breaks (DSBs) are mostly repaired by nonhomologous end joining (NHEJ) and homologous recombination (HR) in higher eukaryotes. In contrast, HR-mediated DSB repair is the major double-strand break repair pathway in lower order organisms such as bacteria and yeast. Penaeus monodon, commonly known as black tiger shrimp, is one of the economically important crustaceans facing large-scale mortality due to exposure to infectious diseases. The animals can also get exposed to chemical mutagens under the culture conditions as well as in wild. Although DSB repair mechanisms have been described in mammals and some invertebrates, its mechanism is unknown in the shrimp species. In the present study, we show that HR-mediated DSB repair is the predominant mode of repair in P. monodon. Robust repair was observed at a temperature of 30 °C, when 2 µg of cell-free extract derived from hepatopancreas was used for the study. Although HR occurred through both reciprocal recombination and gene conversion, the latter was predominant when the bacterial colonies containing recombinants were evaluated. Unlike mammals, NHEJ-mediated DSB repair was undetectable in P. monodon. However, we could detect evidence for an alternative mode of NHEJ that uses microhomology, termed as microhomology-mediated end joining (MMEJ). Interestingly, unlike HR, MMEJ was predominant at lower temperatures. Therefore, the results suggest that, while HR is major DSB repair pathway in shrimp, MMEJ also plays a role in ensuring the continuity and stability of the genome.
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Affiliation(s)
- Shikha Srivastava
- Department of Biochemistry, Indian Institute of Science, Bangalore 560 012, India
| | - Sumedha Dahal
- Department of Biochemistry, Indian Institute of Science, Bangalore 560 012, India
| | - Sharanya J Naidu
- Department of Biochemistry, Indian Institute of Science, Bangalore 560 012, India
| | - Deepika Anand
- ICAR-Central Institute of Fisheries Education, Mumbai 400 061, India
| | - Vidya Gopalakrishnan
- Department of Biochemistry, Indian Institute of Science, Bangalore 560 012, India
| | | | - Sathees C Raghavan
- Department of Biochemistry, Indian Institute of Science, Bangalore 560 012, India
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Non-homologous DNA end joining and alternative pathways to double-strand break repair. Nat Rev Mol Cell Biol 2017; 18:495-506. [PMID: 28512351 DOI: 10.1038/nrm.2017.48] [Citation(s) in RCA: 975] [Impact Index Per Article: 139.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
DNA double-strand breaks (DSBs) are the most dangerous type of DNA damage because they can result in the loss of large chromosomal regions. In all mammalian cells, DSBs that occur throughout the cell cycle are repaired predominantly by the non-homologous DNA end joining (NHEJ) pathway. Defects in NHEJ result in sensitivity to ionizing radiation and the ablation of lymphocytes. The NHEJ pathway utilizes proteins that recognize, resect, polymerize and ligate the DNA ends in a flexible manner. This flexibility permits NHEJ to function on a wide range of DNA-end configurations, with the resulting repaired DNA junctions often containing mutations. In this Review, we discuss the most recent findings regarding the relative involvement of the different NHEJ proteins in the repair of various DNA-end configurations. We also discuss the shunting of DNA-end repair to the auxiliary pathways of alternative end joining (a-EJ) or single-strand annealing (SSA) and the relevance of these different pathways to human disease.
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So A, Le Guen T, Lopez BS, Guirouilh-Barbat J. Genomic rearrangements induced by unscheduled DNA double strand breaks in somatic mammalian cells. FEBS J 2017; 284:2324-2344. [PMID: 28244221 DOI: 10.1111/febs.14053] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2016] [Revised: 02/02/2017] [Accepted: 02/24/2017] [Indexed: 12/13/2022]
Abstract
DNA double-strand breaks (DSBs) are highly toxic lesions that can lead to profound genome rearrangements and/or cell death. They routinely occur in genomes due to endogenous or exogenous stresses. Efficient repair systems, canonical non-homologous end-joining and homologous recombination exist in the cell and not only ensure the maintenance of genome integrity but also, via specific programmed DNA double-strand breaks, permit its diversity and plasticity. However, these repair systems need to be tightly controlled because they can also generate genomic rearrangements. Thus, when DSB repair is not properly regulated, genome integrity is no longer guaranteed. In this review, we will focus on non-programmed genome rearrangements generated by DSB repair, in somatic cells. We first discuss genome rearrangements induced by homologous recombination and end-joining. We then discuss recently described rearrangement mechanisms, driven by microhomologies, that do not involve the joining of DNA ends but rather initiate DNA synthesis (microhomology-mediated break-induced replication, fork stalling and template switching and microhomology-mediated template switching). Finally, we discuss chromothripsis, which is the shattering of a localized region of the genome followed by erratic rejoining.
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Affiliation(s)
- Ayeong So
- CNRS UMR 8200, Institut de Cancérologie Gustave-Roussy, Université Paris-Saclay, Equipe Labellisée Ligue Contre le Cancer, Villejuif, France
| | - Tangui Le Guen
- CNRS UMR 8200, Institut de Cancérologie Gustave-Roussy, Université Paris-Saclay, Equipe Labellisée Ligue Contre le Cancer, Villejuif, France
| | - Bernard S Lopez
- CNRS UMR 8200, Institut de Cancérologie Gustave-Roussy, Université Paris-Saclay, Equipe Labellisée Ligue Contre le Cancer, Villejuif, France
| | - Josée Guirouilh-Barbat
- CNRS UMR 8200, Institut de Cancérologie Gustave-Roussy, Université Paris-Saclay, Equipe Labellisée Ligue Contre le Cancer, Villejuif, France
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Evaluation of Structural Factors Potentially Implicated in Acute Lymphoblastic Leukemia: A report of the MIGICCL. Arch Med Res 2017; 47:515-520. [PMID: 28262192 DOI: 10.1016/j.arcmed.2016.11.012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2016] [Accepted: 11/23/2016] [Indexed: 11/27/2022]
Abstract
BACKGROUND AND AIMS Acute lymphoblastic leukemia (ALL) is the most common cancer in the pediatric population; ∼80% of the cases show some translocation. Translocations that result in ALL are due to chromosome breaks. However, the exact mechanisms that cause these breaks have not been well studied. A detailed search of the breakpoints associated with ALL reported in the NCBI database shows that some are concentrated in limited regions of the chromosome, whereas others are scattered throughout. Therefore, the objective of this study was to identify the structural factors involved in chromosomal breaks in ALL. METHODS We performed several bioinformatic studies on the sequences where chromosomal breakpoints have been reported in search of rearrangements: areas of high similarity, thermodynamic stability, composition and conformation of the DNA. RESULTS Certain factors may influence chromosome breaks and are capable of predicting the propensity towards these types of events. CONCLUSIONS These findings may be useful in the design of molecular techniques able to detect these changes in ALL.
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Abstract
Mycosis Fungoides (MF) and Sézary Syndrome (SS) are clonal proliferations of mature T-cells manifesting as lymphoproliferative disorders in which the neoplastic cells show a strong propensity for skin-homing. While the predominant site of presentation in MF is the skin, the peripheral blood carries a significant tumor burden in Sézary Syndrome such that it resembles a "leukemic" disease. While the genetic basis of these diseases has been studied using different approaches in the previous years, recent genome-wide studies employing massively parallel sequencing techniques now offer new insights into the molecular pathogenesis of these diseases. In this chapter, we discuss the recent findings elucidating the genomic landscape of MF and SS. The pathways targeted by mutational alterations are discussed and a model for understanding the pathogenesis of these diseases is proposed. It is anticipated that prognostic stratification and therapeutic targeting based on mutational signatures will be achieved in the near future based on the improved understanding of the molecular pathogenesis of these diseases.
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Affiliation(s)
- Kojo S J Elenitoba-Johnson
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, 609 Stellar Chance Laboratories, 422 Curie Boulevard, Philadelphia, PA 19104, USA.
| | - Ryan Wilcox
- Department of Internal Medicine, University of Michigan Medical School, Ann Arbor, MI 48105, USA
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Abstract
The AID/APOBEC family enzymes convert cytosines in single-stranded DNA to uracils, causing base substitutions and strand breaks. They are induced by cytokines produced during the body's inflammatory response to infections, and they help combat infections through diverse mechanisms. AID is essential for the maturation of antibodies and causes mutations and deletions in antibody genes through somatic hypermutation (SHM) and class-switch recombination (CSR) processes. One member of the APOBEC family, APOBEC1, edits mRNA for a protein involved in lipid transport. Members of the APOBEC3 subfamily in humans (APOBEC3A, APOBEC3B, APOBEC3C, APOBEC3D, APOBEC3F, APOBEC3G, and APOBEC3H) inhibit infections of viruses such as HIV-1, HBV, and HCV, and retrotransposition of endogenous retroelements through mutagenic and nonmutagenic mechanisms. There is emerging consensus that these enzymes can cause mutations in the cellular genome at replication forks or within transcription bubbles depending on the physiological state of the cell and the phase of the cell cycle during which they are expressed. We describe here the state of knowledge about the structures of these enzymes, regulation of their expression, and both the advantageous and deleterious consequences of their expression, including carcinogenesis. We highlight similarities among them and present a holistic view of their regulation and function.
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Affiliation(s)
- Sachini U Siriwardena
- Department of Chemistry, Wayne State University , Detroit, Michigan 48202, United States
| | - Kang Chen
- Department of Obstetrics and Gynecology, Wayne State University , Detroit, Michigan 48201, United States
- Mucosal Immunology Studies Team, National Institute of Allergy and Infectious Diseases, National Institutes of Health , Bethesda, Maryland 20892, United States
- Department of Immunology and Microbiology, Wayne State University School of Medicine , Detroit, Michigan 48201, United States
| | - Ashok S Bhagwat
- Department of Chemistry, Wayne State University , Detroit, Michigan 48202, United States
- Department of Immunology and Microbiology, Wayne State University School of Medicine , Detroit, Michigan 48201, United States
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Abstract
Analysis of chromosomal translocation sequence locations in human lymphomas has provided valuable clues about the mechanism of the translocations and when they occur. Biochemical analyses on the mechanisms of DNA breakage and rejoining permit formulation of detailed models of the human chromosomal translocation process in lymphoid neoplasms. Most human lymphomas are derived from B cells in which a DNA break at an oncogene is initiated by activation-induced deaminase (AID). The partner locus in many cases is located at one of the antigen receptor loci, and this break is generated by the recombination activating gene (RAG) complex or by AID. After breakage, the joining process typically occurs by non-homologous DNA end-joining (NHEJ). Some of the insights into this mechanism also apply to translocations that occur in non-lymphoid neoplasms.
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Affiliation(s)
- Michael R Lieber
- USC Norris Comprehensive Cancer Center, Room 5428, University of Southern California Keck School of Medicine, 1441 Eastlake Avenue, MC9176, Los Angeles, California 90089-9176, USA
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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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Cheong TC, Compagno M, Chiarle R. Editing of mouse and human immunoglobulin genes by CRISPR-Cas9 system. Nat Commun 2016; 7:10934. [PMID: 26956543 PMCID: PMC4786874 DOI: 10.1038/ncomms10934] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2015] [Accepted: 02/03/2016] [Indexed: 01/12/2023] Open
Abstract
Applications of the CRISPR-Cas9 system to edit the genome have widely expanded to include DNA gene knock-out, deletions, chromosomal rearrangements, RNA editing and genome-wide screenings. Here we show the application of CRISPR-Cas9 technology to edit the mouse and human immunoglobulin (Ig) genes. By delivering Cas9 and guide-RNA (gRNA) with retro- or lenti-virus to IgM(+) mouse B cells and hybridomas, we induce class-switch recombination (CSR) of the IgH chain to the desired subclass. Similarly, we induce CSR in all human B cell lines tested with high efficiency to targeted IgH subclass. Finally, we engineer mouse hybridomas to secrete Fab' fragments instead of the whole Ig. Our results indicate that Ig genes in mouse and human cells can be edited to obtain any desired IgH switching helpful to study the biology of normal and lymphoma B cells. We also propose applications that could transform the technology of antibody production.
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Affiliation(s)
- Taek-Chin Cheong
- Department of Pathology, Children's Hospital Boston and Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Mara Compagno
- Department of Pathology, Children's Hospital Boston and Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Roberto Chiarle
- Department of Pathology, Children's Hospital Boston and Harvard Medical School, Boston, Massachusetts 02115, USA
- Department of Molecular Biotechnology and Health Sciences, University of Torino, Torino 10126, Italy
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Prochazkova J, Loizou JI. Programmed DNA breaks in lymphoid cells: repair mechanisms and consequences in human disease. Immunology 2016; 147:11-20. [PMID: 26455503 PMCID: PMC4988471 DOI: 10.1111/imm.12547] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2015] [Revised: 10/05/2015] [Accepted: 10/06/2015] [Indexed: 01/08/2023] Open
Abstract
In recent years, several novel congenital human disorders have been described with defects in lymphoid B-cell and T-cell functions that arise due to mutations in known and/or novel components of DNA repair and damage response pathways. Examples include impaired DNA double-strand break repair, as well as compromised DNA damage-induced signal transduction, including phosphorylation and ubiquitination. These disorders reinforce the importance of genome stability pathways in the development of lymphoid cells in humans. Furthermore, these conditions inform our knowledge of the biology of the mechanisms of genome stability and in some cases may provide potential routes to help exploit these pathways therapeutically. Here we review the mechanisms that repair programmed DNA lesions that occur during B-cell and T-cell development, as well as human diseases that arise through defects in these pathways.
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Affiliation(s)
- Jana Prochazkova
- CeMM Research Centre for Molecular Medicine of the Austrian Academy of SciencesViennaAustria
| | - Joanna I. Loizou
- CeMM Research Centre for Molecular Medicine of the Austrian Academy of SciencesViennaAustria
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Tadi SK, Sebastian R, Dahal S, Babu RK, Choudhary B, Raghavan SC. Microhomology-mediated end joining is the principal mediator of double-strand break repair during mitochondrial DNA lesions. Mol Biol Cell 2015; 27:223-35. [PMID: 26609070 PMCID: PMC4713127 DOI: 10.1091/mbc.e15-05-0260] [Citation(s) in RCA: 85] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2015] [Accepted: 11/18/2015] [Indexed: 12/13/2022] Open
Abstract
Repair of double-strand breaks in mammalian mitochondria depends on microhomology-mediated end joining (MMEJ). Classical NHEJ is not detectable in mitochondria. DNA ligase III, but not ligase IV or ligase I, is involved in mitochondrial MMEJ. The protein machinery involved in miitochondrial MMEJ includes CtIP, FEN1, ligase III, MRE11, and PARP1. Mitochondrial DNA (mtDNA) deletions are associated with various mitochondrial disorders. The deletions identified in humans are flanked by short, directly repeated mitochondrial DNA sequences; however, the mechanism of such DNA rearrangements has yet to be elucidated. In contrast to nuclear DNA (nDNA), mtDNA is more exposed to oxidative damage, which may result in double-strand breaks (DSBs). Although DSB repair in nDNA is well studied, repair mechanisms in mitochondria are not characterized. In the present study, we investigate the mechanisms of DSB repair in mitochondria using in vitro and ex vivo assays. Whereas classical NHEJ (C-NHEJ) is undetectable, microhomology-mediated alternative NHEJ efficiently repairs DSBs in mitochondria. Of interest, robust microhomology-mediated end joining (MMEJ) was observed with DNA substrates bearing 5-, 8-, 10-, 13-, 16-, 19-, and 22-nt microhomology. Furthermore, MMEJ efficiency was enhanced with an increase in the length of homology. Western blotting, immunoprecipitation, and protein inhibition assays suggest the involvement of CtIP, FEN1, MRE11, and PARP1 in mitochondrial MMEJ. Knockdown studies, in conjunction with other experiments, demonstrated that DNA ligase III, but not ligase IV or ligase I, is primarily responsible for the final sealing of DSBs during mitochondrial MMEJ. These observations highlight the central role of MMEJ in maintenance of mammalian mitochondrial genome integrity and is likely relevant for deletions observed in many human mitochondrial disorders.
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Affiliation(s)
- Satish Kumar Tadi
- Department of Biochemistry, Indian Institute of Science, Bangalore 560 012, India
| | - Robin Sebastian
- Department of Biochemistry, Indian Institute of Science, Bangalore 560 012, India
| | - Sumedha Dahal
- Department of Biochemistry, Indian Institute of Science, Bangalore 560 012, India
| | - Ravi K Babu
- Department of Biochemistry, Indian Institute of Science, Bangalore 560 012, India
| | - Bibha Choudhary
- Institute of Bioinformatics and Applied Biotechnology, Bangalore 560 100, India
| | - Sathees C Raghavan
- Department of Biochemistry, Indian Institute of Science, Bangalore 560 012, India
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Leibowitz ML, Zhang CZ, Pellman D. Chromothripsis: A New Mechanism for Rapid Karyotype Evolution. Annu Rev Genet 2015; 49:183-211. [DOI: 10.1146/annurev-genet-120213-092228] [Citation(s) in RCA: 123] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Mitchell L. Leibowitz
- Department of Pediatric Oncology,
- Department of Cell Biology, Harvard Medical School, Boston, Massachusetts 02115;
| | - Cheng-Zhong Zhang
- Department of Pediatric Oncology,
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts 02215;
- Department of Cell Biology, Harvard Medical School, Boston, Massachusetts 02115;
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142;
| | - David Pellman
- Department of Pediatric Oncology,
- Department of Cell Biology, Harvard Medical School, Boston, Massachusetts 02115;
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142;
- Howard Hughes Medical Institute, Boston, Massachusetts 02115
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47
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Teng G, Maman Y, Resch W, Kim M, Yamane A, Qian J, Kieffer-Kwon KR, Mandal M, Ji Y, Meffre E, Clark MR, Cowell LG, Casellas R, Schatz DG. RAG Represents a Widespread Threat to the Lymphocyte Genome. Cell 2015; 162:751-65. [PMID: 26234156 PMCID: PMC4537821 DOI: 10.1016/j.cell.2015.07.009] [Citation(s) in RCA: 87] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2014] [Revised: 04/14/2015] [Accepted: 06/02/2015] [Indexed: 11/26/2022]
Abstract
The RAG1 endonuclease, together with its cofactor RAG2, is essential for V(D)J recombination but is a potent threat to genome stability. The sources of RAG1 mis-targeting and the mechanisms that have evolved to suppress it are poorly understood. Here, we report that RAG1 associates with chromatin at thousands of active promoters and enhancers in the genome of developing lymphocytes. The mouse and human genomes appear to have responded by reducing the abundance of "cryptic" recombination signals near RAG1 binding sites. This depletion operates specifically on the RSS heptamer, whereas nonamers are enriched at RAG1 binding sites. Reversing this RAG-driven depletion of cleavage sites by insertion of strong recombination signals creates an ectopic hub of RAG-mediated V(D)J recombination and chromosomal translocations. Our findings delineate rules governing RAG binding in the genome, identify areas at risk of RAG-mediated damage, and highlight the evolutionary struggle to accommodate programmed DNA damage in developing lymphocytes.
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Affiliation(s)
- Grace Teng
- Department of Immunobiology, Yale University School of Medicine, 300 Cedar Street, Box 208011, New Haven, CT 06520-8011, USA
| | - Yaakov Maman
- Department of Immunobiology, Yale University School of Medicine, 300 Cedar Street, Box 208011, New Haven, CT 06520-8011, USA
| | - Wolfgang Resch
- Genomics and Immunity, NIAMS, Center of Cancer Research, NCI, National Institutes of Health, Bethesda, MD 20892, USA
| | - Min Kim
- Division of Biomedical Informatics, Department of Clinical Sciences, University of Texas Southwestern Medical Center, 5323 Harry Hines Boulevard, Box 9066, Dallas, TX 75390-9066, USA
| | - Arito Yamane
- Genomics and Immunity, NIAMS, Center of Cancer Research, NCI, National Institutes of Health, Bethesda, MD 20892, USA
| | - Jason Qian
- Genomics and Immunity, NIAMS, Center of Cancer Research, NCI, National Institutes of Health, Bethesda, MD 20892, USA
| | - Kyong-Rim Kieffer-Kwon
- Genomics and Immunity, NIAMS, Center of Cancer Research, NCI, National Institutes of Health, Bethesda, MD 20892, USA
| | - Malay Mandal
- Department of Medicine, Section of Rheumatology and Gwen Knapp Center for Lupus and Immunology Research, University of Chicago, Chicago, IL 60637, USA
| | - Yanhong Ji
- Department of Immunology and Microbiology, College of Medicine, Xi'an Jiao Tong University, 76 Yan Ta West Road, Box 37, Xian, Shaanxi 710061, PRC
| | - Eric Meffre
- Department of Immunobiology, Yale University School of Medicine, 300 Cedar Street, Box 208011, New Haven, CT 06520-8011, USA
| | - Marcus R Clark
- Department of Medicine, Section of Rheumatology and Gwen Knapp Center for Lupus and Immunology Research, University of Chicago, Chicago, IL 60637, USA
| | - Lindsay G Cowell
- Division of Biomedical Informatics, Department of Clinical Sciences, University of Texas Southwestern Medical Center, 5323 Harry Hines Boulevard, Box 9066, Dallas, TX 75390-9066, USA
| | - Rafael Casellas
- Genomics and Immunity, NIAMS, Center of Cancer Research, NCI, National Institutes of Health, Bethesda, MD 20892, USA.
| | - David G Schatz
- Department of Immunobiology, Yale University School of Medicine, 300 Cedar Street, Box 208011, New Haven, CT 06520-8011, USA; Howard Hughes Medical Institute, 295 Congress Avenue, New Haven, CT 06511, USA.
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Abstract
The modular, noncontiguous architecture of the antigen receptor genes necessitates their assembly through V(D)J recombination. This program of DNA breakage and rejoining occurs during early lymphocyte development, and depends on the RAG1 and RAG2 proteins, whose collaborative endonuclease activity targets specific DNA motifs enriched in the antigen receptor loci. This essential gene shuffling reaction requires lymphocytes to traverse several developmental stages wherein DNA breakage is tolerated, while minimizing the expense to overall genome integrity. Thus, RAG activity is subject to stringent temporal and spatial regulation. The RAG proteins themselves also contribute autoregulatory properties that coordinate their DNA cleavage activity with target chromatin structure, cell cycle status, and DNA repair pathways. Even so, lapses in regulatory restriction of RAG activity are apparent in the aberrant V(D)J recombination events that underlie many lymphomas. In this review, we discuss the current understanding of the RAG endonuclease, its widespread binding in the lymphocyte genome, its noncleavage activities that restrain its enzymatic potential, and the growing evidence of its evolution from an ancient transposase.
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Karo JM, Sun JC. Novel molecular mechanism for generating NK-cell fitness and memory. Eur J Immunol 2015; 45:1906-15. [PMID: 26018782 DOI: 10.1002/eji.201445339] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2015] [Revised: 04/21/2015] [Accepted: 05/27/2015] [Indexed: 12/28/2022]
Abstract
The mammalian immune system has been traditionally subdivided into two compartments known as the innate and the adaptive. T cells and B cells, which rearrange their antigen-receptor genes using the RAG recombinase, comprise the adaptive arm of immunity. Meanwhile, every other white blood cell has been grouped together under the broad umbrella of innate immunity, including NK cells. NK cells are considered innate lymphocytes because of their rapid responses to stressed cells and their ability to develop without receptor gene rearrangement (i.e. in RAG-deficient mice). However, new findings implicate a critical function for RAG proteins during NK-cell ontogeny, and suggest a novel mechanism by which controlled DNA breaks during NK-cell development dictate the fitness, function, and longevity of these cells. This review highlights recent work describing how DNA break events can impact cellular differentiation and fitness in a variety of cell types and settings.
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Affiliation(s)
- Jenny M Karo
- Immunology Program and Gerstner Sloan Kettering Graduate School of Biomedical Sciences, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Joseph C Sun
- Immunology Program and Gerstner Sloan Kettering Graduate School of Biomedical Sciences, Memorial Sloan Kettering Cancer Center, New York, NY, USA
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Sollier J, Cimprich KA. Breaking bad: R-loops and genome integrity. Trends Cell Biol 2015; 25:514-22. [PMID: 26045257 DOI: 10.1016/j.tcb.2015.05.003] [Citation(s) in RCA: 244] [Impact Index Per Article: 27.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2015] [Revised: 05/05/2015] [Accepted: 05/06/2015] [Indexed: 11/18/2022]
Abstract
R-loops, nucleic acid structures consisting of an RNA-DNA hybrid and displaced single-stranded (ss) DNA, are ubiquitous in organisms from bacteria to mammals. First described in bacteria where they initiate DNA replication, it now appears that R-loops regulate diverse cellular processes such as gene expression, immunoglobulin (Ig) class switching, and DNA repair. Changes in R-loop regulation induce DNA damage and genome instability, and recently it was shown that R-loops are associated with neurodegenerative disorders. We discuss recent developments in the field; in particular, the regulation and effects of R-loops in cells, their effect on genomic and epigenomic stability, and their potential contribution to the origin of diseases including cancer and neurodegenerative disorders.
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Affiliation(s)
- Julie Sollier
- Department of Chemical and Systems Biology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Karlene A Cimprich
- Department of Chemical and Systems Biology, Stanford University School of Medicine, Stanford, CA 94305, USA.
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