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Du L, Oksenych V, Wan H, Ye X, Dong J, Ye AY, Abolhassani H, Vlachiotis S, Zhang X, de la Rosa K, Hammarström L, van der Burg M, Alt FW, Pan-Hammarström Q. Orientation Regulation of Class-switch Recombination in Human B Cells. JOURNAL OF IMMUNOLOGY (BALTIMORE, MD. : 1950) 2024; 213:1093-1104. [PMID: 39248600 PMCID: PMC11457721 DOI: 10.4049/jimmunol.2300842] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/07/2023] [Accepted: 08/16/2024] [Indexed: 09/10/2024]
Abstract
We developed a linear amplification-mediated high-throughput genome-wide translocation sequencing method to profile Ig class-switch recombination (CSR) in human B cells in an unbiased and quantitative manner. This enables us to characterize CSR junctions resulting from either deletional recombination or inversion for each Ig class/subclass. Our data showed that more than 90% of CSR junctions detected in peripheral blood in healthy control subjects were due to deletional recombination. We further identified two major CSR junction signatures/patterns in human B cells. Signature 1 consists of recombination junctions resulting from both IgG and IgA switching, with a dominance of Sµ-Sγ junctions (72%) and deletional recombination (87%). Signature 2 is contributed mainly by Sµ-Sα junctions (96%), and these junctions were almost all due to deletional recombination (99%) and were characterized by longer microhomologies. CSR junctions identified in healthy individuals can be assigned to both signatures but with a dominance of signature 1, whereas almost all CSR junctions found in patients with defects in DNA-PKcs or Artemis, two classical nonhomologous end joining (c-NHEJ) factors, align with signature 2. Thus, signature 1 may represent c-NHEJ activity during CSR, whereas signature 2 is associated with microhomology-mediated alternative end joining in the absence of the studied c-NHEJ factors. Our findings suggest that in human B cells, the efficiency of the c-NHEJ machinery and the features of switch regions are crucial for the regulation of CSR orientation. Finally, our high-throughput method can also be applied to study the mechanism of rare types of recombination, such as switching to IgD and locus suicide switching.
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Affiliation(s)
- Likun Du
- Division of Immunology, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
| | - Valentyn Oksenych
- Division of Immunology, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
- Broegelmann Research Laboratory, Department of Clinical Science, University of Bergen, Bergen, Norway
| | - Hui Wan
- Division of Immunology, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
| | - Xiaofei Ye
- Division of Immunology, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
| | - Junchao Dong
- Department of Immunology, Zhongshan School of Medicine, Sun Yat-Sen University, Guangzhou, China
| | - Adam Yongxin Ye
- Department of Genetics, Harvard Medical School, Boston, MA
- Program in Cellular and Molecular Medicine, Boston Children’s Hospital, Boston, MA
- Howard Hughes Medical Institute, Boston, MA
| | - Hassan Abolhassani
- Division of Immunology, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
| | - Stelios Vlachiotis
- Division of Immunology, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
| | - Xuefei Zhang
- Department of Genetics, Harvard Medical School, Boston, MA
- Program in Cellular and Molecular Medicine, Boston Children’s Hospital, Boston, MA
- Howard Hughes Medical Institute, Boston, MA
| | - Kathrin de la Rosa
- Department of Cancer and Immunology, Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin, Germany
| | - Lennart Hammarström
- Division of Immunology, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
| | - Mirjam van der Burg
- Department of Pediatrics, Laboratory for Pediatric Immunology, Leiden University Medical Center, Leiden, the Netherlands
| | - Frederick W. Alt
- Department of Genetics, Harvard Medical School, Boston, MA
- Program in Cellular and Molecular Medicine, Boston Children’s Hospital, Boston, MA
- Howard Hughes Medical Institute, Boston, MA
| | - Qiang Pan-Hammarström
- Division of Immunology, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
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2
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Takada S, Weitering TJ, van Os NJH, Du L, Pico-Knijnenburg I, Kuipers TB, Mei H, Salzer E, Willemsen MAAP, Weemaes CMR, Pan-Hammarstrom Q, van der Burg M. Causative mechanisms and clinical impact of immunoglobulin deficiencies in ataxia telangiectasia. J Allergy Clin Immunol 2024; 153:1392-1405. [PMID: 38280573 DOI: 10.1016/j.jaci.2023.12.029] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2023] [Revised: 12/07/2023] [Accepted: 12/19/2023] [Indexed: 01/29/2024]
Abstract
BACKGROUND Ataxia telangiectasia (AT) is characterized by cerebellar ataxia, telangiectasia, immunodeficiency, and increased cancer susceptibility and is caused by mutations in the ataxia telangiectasia mutated (ATM) gene. The immunodeficiency comprises predominantly immunoglobulin deficiency, mainly IgA and IgG2, with a variable severity. So far, the exact mechanisms underlying the immunoglobulin deficiency, especially the variable severity, remain unelucidated. OBJECTIVE We characterized the clinical impact of immunoglobulin deficiencies in AT and elucidated their mechanisms in AT. METHODS We analyzed long-term immunoglobulin levels, immunophenotyping, and survival time in our cohort (n = 87, median age 16 years; maximum 64 years). Somatic hypermutation and class-switch junctions in B cells were analyzed by next-generation sequencing. Furthermore, an in vitro class-switching induction assay was performed, followed by RNA sequencing, to assess the effect of ATM inhibition. RESULTS Only the hyper-IgM AT phenotype significantly worsened survival time, while IgA or IgG2 deficiencies did not. The immunoglobulin levels showed predominantly decreased IgG2 and IgA. Moreover, flow cytometric analysis demonstrated reduced naive B and T lymphocytes and a deficiency of class-switched IgG2 and IgA memory B cells. Somatic hypermutation frequencies were lowered in IgA- and IgG2-deficient patients, indicating hampered germinal center reaction. In addition, the microhomology of switch junctions was elongated, suggesting alternative end joining during class-switch DNA repair. The in vitro class switching and proliferation were negatively affected by ATM inhibition. RNA sequencing analysis showed that ATM inhibitor influenced expression of germinal center reaction genes. CONCLUSION Immunoglobulin deficiency in AT is caused by disturbed development of class-switched memory B cells. ATM deficiency affects both germinal center reaction and choice of DNA-repair pathway in class switching.
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Affiliation(s)
- Sanami Takada
- Department of Pediatrics, Laboratory for Pediatric Immunology, Willem-Alexander Children's Hospital, Leiden University Medical Center, Leiden, The Netherlands
| | - Thomas J Weitering
- Department of Pediatrics, Laboratory for Pediatric Immunology, Willem-Alexander Children's Hospital, Leiden University Medical Center, Leiden, The Netherlands
| | - Nienke J H van Os
- Department of Pediatric Neurology, Amalia Children's Hospital, Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, Nijmegen, The Netherlands; Department of Neurology, Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Likun Du
- Department of Biosciences and Nutrition, Karolinska Institute, Stockholm, Sweden
| | - Ingrid Pico-Knijnenburg
- Department of Pediatrics, Laboratory for Pediatric Immunology, Willem-Alexander Children's Hospital, Leiden University Medical Center, Leiden, The Netherlands
| | - Thomas B Kuipers
- Sequencing Analysis Support Core Department of Biomedical Data Sciences, Leiden University Medical Center, Leiden, The Netherlands
| | - Hailiang Mei
- Sequencing Analysis Support Core Department of Biomedical Data Sciences, Leiden University Medical Center, Leiden, The Netherlands
| | - Elisabeth Salzer
- Department of Pediatrics, Laboratory for Pediatric Immunology, Willem-Alexander Children's Hospital, Leiden University Medical Center, Leiden, The Netherlands
| | - Michèl A A P Willemsen
- Department of Pediatric Neurology, Amalia Children's Hospital, Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Corry M R Weemaes
- Department of Pediatrics, Amalia Children's Hospital, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Qiang Pan-Hammarstrom
- Department of Neurology, Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Mirjam van der Burg
- Department of Pediatrics, Laboratory for Pediatric Immunology, Willem-Alexander Children's Hospital, Leiden University Medical Center, Leiden, The Netherlands.
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3
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Poyer F, Jimenez Heredia R, Novak W, Zeitlhofer P, Nebral K, Dworzak MN, Haas OA, Boztug K, Kager L. Case Report: Refractory Cytopenia With a Switch From a Transient Monosomy 7 to a Disease-Ameliorating del(20q) in a NHEJ1-Deficient Long-term Survivor. Front Immunol 2022; 13:869047. [PMID: 35812385 PMCID: PMC9263211 DOI: 10.3389/fimmu.2022.869047] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2022] [Accepted: 05/20/2022] [Indexed: 11/30/2022] Open
Abstract
We report the case of a male Pakistani patient with a pathogenic homozygous loss of function variant in the non-homologous end-joining factor 1 (NHEJ1) gene. The growth retarded and microcephalic boy with clinodactyly of both hands and hyperpigmentation of the skin suffered from recurrent respiratory infections. He was five and a half years old when he came to our attention with refractory cytopenia and monosomy 7. Hematopoietic stem cell transplantation was considered but not feasible because there was no suitable donor available. Monosomy 7 was not detected anymore in subsequent bone marrow biopsies that were repeated in yearly intervals. Instead, seven and a half years later, a novel clone with a del(20q) appeared and steadily increased thereafter. In parallel, the patient’s blood count, which had remained stable for over 20 years without necessitating any specific therapeutic interventions, improved gradually and the erythropoiesis-associated dysplasia resolved.
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Affiliation(s)
- Fiona Poyer
- St. Anna Children’s Hospital, Department of Pediatrics and Adolescent Medicine, Medical University of Vienna, Vienna, Austria
| | - Raúl Jimenez Heredia
- St. Anna Children’s Cancer Research Institute (CCRI), Vienna, Austria
- Ludwig Boltzmann Institute for Rare and Undiagnosed Diseases, Vienna, Austria
- Center for Molecular Medicine Center for Molecular Medicine (CeMM) Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - Wolfgang Novak
- St. Anna Children’s Hospital, Department of Pediatrics and Adolescent Medicine, Medical University of Vienna, Vienna, Austria
| | - Petra Zeitlhofer
- St. Anna Children’s Cancer Research Institute (CCRI), Vienna, Austria
- Labdia, Labordiagnostik, Vienna, Austria
| | - Karin Nebral
- St. Anna Children’s Cancer Research Institute (CCRI), Vienna, Austria
- Labdia, Labordiagnostik, Vienna, Austria
| | - Michael N. Dworzak
- St. Anna Children’s Hospital, Department of Pediatrics and Adolescent Medicine, Medical University of Vienna, Vienna, Austria
- St. Anna Children’s Cancer Research Institute (CCRI), Vienna, Austria
| | - Oskar A. Haas
- St. Anna Children’s Hospital, Department of Pediatrics and Adolescent Medicine, Medical University of Vienna, Vienna, Austria
- St. Anna Children’s Cancer Research Institute (CCRI), Vienna, Austria
- Labdia, Labordiagnostik, Vienna, Austria
- *Correspondence: Oskar A. Haas, ; Kaan Boztug, ; Leo Kager,
| | - Kaan Boztug
- St. Anna Children’s Hospital, Department of Pediatrics and Adolescent Medicine, Medical University of Vienna, Vienna, Austria
- St. Anna Children’s Cancer Research Institute (CCRI), Vienna, Austria
- Ludwig Boltzmann Institute for Rare and Undiagnosed Diseases, Vienna, Austria
- Center for Molecular Medicine Center for Molecular Medicine (CeMM) Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
- *Correspondence: Oskar A. Haas, ; Kaan Boztug, ; Leo Kager,
| | - Leo Kager
- St. Anna Children’s Hospital, Department of Pediatrics and Adolescent Medicine, Medical University of Vienna, Vienna, Austria
- St. Anna Children’s Cancer Research Institute (CCRI), Vienna, Austria
- *Correspondence: Oskar A. Haas, ; Kaan Boztug, ; Leo Kager,
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Jamee M, Khakbazan Fard N, Fallah S, Golchehre Z, Fallahi M, Shamsian BS, Sharafian S, Chavoshzadeh Z. Cernunnos defect in an Iranian patient with T - B + NK + severe combined immunodeficiency: A case report and review of the literature. Mol Genet Genomic Med 2022; 10:e1990. [PMID: 35656589 PMCID: PMC9356558 DOI: 10.1002/mgg3.1990] [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: 03/14/2022] [Revised: 05/09/2022] [Accepted: 05/12/2022] [Indexed: 12/02/2022] Open
Abstract
Background Defective Cernunnos gene in nonhomologous end‐joining (NHEJ) pathway of the DNA repair is responsible for radiosensitive severe combined immunodeficiency (SCID). Herein, presented a new patient with Cernunnos deficiency and summarized the clinical, immunological, and molecular features of reported patients in the literature. Case The patient was a 6‐month‐old female born to consanguineous parents. She presented with long‐lasting fever, diarrhea, poor feeding, and restlessness. She had suffered from recurrent fever of unknown origin and multiple episodes of oral candidiasis. In the physical examination, microcephaly, failure to thrive, oral candidiasis, pustular rash on fingers, and perianal ulcers, but no dysmorphic feature were observed. The immunologic workup revealed lymphopenia, neutropenia, normocytic anemia, low T‐ but normal B‐ and natural killer (NK)‐ cells, low immunoglobulin (Ig)G, and normal IgA, IgM, and IgE. The T‐cell receptor excision circle (TREC) was low and the lymphocyte transformation test (LTT) was abnormal to mitogens and antigens. She was diagnosed with T− B+ NK+ SCID and improved by intravenous immunoglobulin along with antimicrobials. A homozygous splice site variant, c.390 + 1G > T, at the intron 3 of the NHEJ1, was identified and the diagnosis of Cernunnos deficiency was established. However, while a candidate for hematopoietic stem cell transplantation, she developed sepsis and died at 11 months of age. Conclusions Cernunnos deficiency should be considered as a differential diagnosis in patients with microcephaly, growth retardation, recurrent infections, T‐cell defects, and hypogammaglobulinemia. The normal B‐cell level in the index patient is an unexpected finding in Cernunnos deficiency which requires further evaluation.
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Affiliation(s)
- Mahnaz Jamee
- Pediatric Nephrology Research Center, Research Institute for Children's Health, Shahid Beheshti University of Medical Sciences, Tehran, Iran.,Immunology and Allergy Department, Mofid Children's Hospital, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Nasrin Khakbazan Fard
- Immunology and Allergy Department, Mofid Children's Hospital, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Shahrzad Fallah
- Immunology and Allergy Department, Mofid Children's Hospital, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Zahra Golchehre
- Department of Medical Genetics, School of Medicine, Tehran University of Medical Sciences, Tehran, Iran
| | - Mazdak Fallahi
- Immunology and Allergy Department, Mofid Children's Hospital, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Bibi Shahin Shamsian
- Pediatric Congenital Hematologic Disorders Research Center, Research Institute for Children's Health, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Samin Sharafian
- Immunology and Allergy Department, Mofid Children's Hospital, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Zahra Chavoshzadeh
- Immunology and Allergy Department, Mofid Children's Hospital, Shahid Beheshti University of Medical Sciences, Tehran, Iran
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5
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Fournier B, Mahlaoui N, Moshous D, de Villartay JP. Inborn errors of immunity caused by defects in the DNA damage response pathways: Importance of minimizing treatment-related genotoxicity. Pediatr Allergy Immunol 2022; 33:e13820. [PMID: 35754136 PMCID: PMC9327728 DOI: 10.1111/pai.13820] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/04/2022] [Revised: 05/25/2022] [Accepted: 05/30/2022] [Indexed: 12/11/2022]
Abstract
Several primary immunodeficiencies are caused by defects in the general DNA repair machinery as exemplified by the T-B- radiosensitive SCID condition owing to impaired resolution of programmed DNA double-strand breaks introduced by RAG1/2 during V(D)J recombination. The genome instability generally associated with these conditions results in an increased propensity to develop malignancies requiring genotoxic-based anti-cancer treatments. Moreover, the extent of immune deficiency often calls for hematopoietic stem cell transplantation as a definitive treatment, also requiring genotoxic-based conditioning regimen prior to transplantation. In both cases, the underlying general DNA repair defect may result in catastrophic iatrogenic consequences. It is, therefore, of paramount importance to assess the functionality of the DNA repair apparatus prior to any genotoxic treatment when the exact molecular cause of the disease is unknown. For this purpose, two simple assays can be used on patients derived peripheral blood lymphocytes: (1) the PROMIDISα biomarker, based on the next-generation sequencing analysis of the TCRα repertoire, will highlight specific signatures of DNA repair deficiencies; (2) direct analysis of the sensitivity of peripheral lymphocytes to ionizing radiation will formally identify patients at risk to develop toxicity toward genotoxic-based treatments.
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Affiliation(s)
- Benjamin Fournier
- Pediatric Hematology-Immunology and Rheumatology Department, APHP-Centre Université de Paris (CUP), Necker Hospital, Paris, France
| | - Nizar Mahlaoui
- Pediatric Hematology-Immunology and Rheumatology Department, APHP-Centre Université de Paris (CUP), Necker Hospital, Paris, France.,French National Reference Center for Primary Immune Deficiencies (CEREDIH), Necker Enfants Malades University Hospital, Assistance Publique-Hôpitaux de Paris (AP-HP), Paris, France
| | - Despina Moshous
- Pediatric Hematology-Immunology and Rheumatology Department, APHP-Centre Université de Paris (CUP), Necker Hospital, Paris, France.,Laboratory "Genome Dynamics in the Immune System" INSERM UMR 1163, Imagine Institute, Université de Paris Cité, Paris, France
| | - Jean-Pierre de Villartay
- Laboratory "Genome Dynamics in the Immune System" INSERM UMR 1163, Imagine Institute, Université de Paris Cité, Paris, France.,Equipe Labellisée Ligue Nationale Contre le Cancer, Paris, France
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6
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Frizinsky S, Rechavi E, Barel O, Lee YN, Simon AJ, Lev A, Stauber T, Adam E, Somech R. Novel NHEJ1 pathogenic variant linked to severe combined immunodeficiency, microcephaly, and abnormal T and B cell receptor repertoires. Front Pediatr 2022; 10:883173. [PMID: 35967585 PMCID: PMC9363661 DOI: 10.3389/fped.2022.883173] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/24/2022] [Accepted: 06/22/2022] [Indexed: 11/13/2022] Open
Abstract
BACKGROUND During the process of generating diverse T and B cell receptor (TCR and BCR, respectively) repertoires, double-strand DNA breaks are produced. Subsequently, these breaks are corrected by a complex system led by the non-homologous end-joining (NHEJ). Pathogenic variants in genes involved in this process, such as the NHEJ1 gene, cause severe combined immunodeficiency syndrome (SCID) along with neurodevelopmental disease and sensitivity to ionizing radiation. OBJECTIVE To provide new clinical and immunological insights on NHEJ1 deficiency arising from a newly diagnosed patient with severe immunodeficiency. MATERIALS AND METHODS A male infant, born to consanguineous parents, suspected of having primary immunodeficiency underwent immunological and genetic workup. This included a thorough assessment of T cell phenotyping and lymphocyte activation by mitogen stimulation tests, whole-exome sequencing (WES), TCR repertoire Vβ repertoire via flow cytometry analysis, and TCR and BCR repertoire analysis via next-generation sequencing (NGS). RESULTS Clinical findings included microcephaly, recurrent pneumonia, and failure to thrive. An immune workup revealed lymphopenia, reduced T cell function, and hypogammaglobulinemia. Skewed TCR Vβ repertoire, TCR gamma (TRG) repertoire, and BCR repertoire were determined in the patient. Genetic analysis identified a novel homozygous missense pathogenic variant in XLF/Cernunnos: c.A580Ins.T; p.M194fs. The patient underwent a successful hematopoietic stem cell transplantation (HSCT). CONCLUSION A novel NHEJ1 pathogenic variant is reported in a patient who presented with SCID phenotype that displayed clonally expanded T and B cells. An adjusted HSCT was safe to ensure full T cell immune reconstitution.
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Affiliation(s)
- Shirly Frizinsky
- Pediatric Department A and the Immunology Service, Jeffrey Modell Foundation Center, Edmond and Lily Safra Children's Hospital, Sheba Medical Center, Ramat Gan, Israel.,Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Erez Rechavi
- Pediatric Department A and the Immunology Service, Jeffrey Modell Foundation Center, Edmond and Lily Safra Children's Hospital, Sheba Medical Center, Ramat Gan, Israel.,Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Ortal Barel
- The Wohl Institute for Translational Medicine and Cancer Research Center, Sheba Medical Center, Ramat Gan, Israel
| | - Yu Nee Lee
- Pediatric Department A and the Immunology Service, Jeffrey Modell Foundation Center, Edmond and Lily Safra Children's Hospital, Sheba Medical Center, Ramat Gan, Israel.,The Wohl Institute for Translational Medicine and Cancer Research Center, Sheba Medical Center, Ramat Gan, Israel
| | - Amos J Simon
- Pediatric Department A and the Immunology Service, Jeffrey Modell Foundation Center, Edmond and Lily Safra Children's Hospital, Sheba Medical Center, Ramat Gan, Israel.,The Wohl Institute for Translational Medicine and Cancer Research Center, Sheba Medical Center, Ramat Gan, Israel
| | - Atar Lev
- Pediatric Department A and the Immunology Service, Jeffrey Modell Foundation Center, Edmond and Lily Safra Children's Hospital, Sheba Medical Center, Ramat Gan, Israel.,The Wohl Institute for Translational Medicine and Cancer Research Center, Sheba Medical Center, Ramat Gan, Israel
| | - Tali Stauber
- Pediatric Department A and the Immunology Service, Jeffrey Modell Foundation Center, Edmond and Lily Safra Children's Hospital, Sheba Medical Center, Ramat Gan, Israel.,Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel.,The Wohl Institute for Translational Medicine and Cancer Research Center, Sheba Medical Center, Ramat Gan, Israel
| | - Etai Adam
- Department of Pediatric Hematology, Oncology and Bone Marrow Transplant, Edmond and Lily Safra Children's Hospital, Sheba Medical Center, Ramat Gan, Israel
| | - Raz Somech
- Pediatric Department A and the Immunology Service, Jeffrey Modell Foundation Center, Edmond and Lily Safra Children's Hospital, Sheba Medical Center, Ramat Gan, Israel.,Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel.,The Wohl Institute for Translational Medicine and Cancer Research Center, Sheba Medical Center, Ramat Gan, Israel
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7
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Gago-Fuentes R, Oksenych V. Non-Homologous End Joining Factors XLF, PAXX and DNA-PKcs Maintain the Neural Stem and Progenitor Cell Population. Biomolecules 2020; 11:biom11010020. [PMID: 33379193 PMCID: PMC7823790 DOI: 10.3390/biom11010020] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2020] [Revised: 12/19/2020] [Accepted: 12/23/2020] [Indexed: 12/26/2022] Open
Abstract
Non-homologous end-joining (NHEJ) is a major DNA repair pathway in mammalian cells that recognizes, processes and fixes DNA damage throughout the cell cycle and is specifically important for homeostasis of post-mitotic neurons and developing lymphocytes. Neuronal apoptosis increases in the mice lacking NHEJ factors Ku70 and Ku80. Inactivation of other NHEJ genes, either Xrcc4 or Lig4, leads to massive neuronal apoptosis in the central nervous system (CNS) that correlates with embryonic lethality in mice. Inactivation of either Paxx, Mri or Dna-pkcs NHEJ gene results in normal CNS development due to compensatory effects of Xlf. Combined inactivation of Xlf/Paxx, Xlf/Mri and Xlf/Dna-pkcs, however, results in late embryonic lethality and high levels of apoptosis in CNS. To determine the impact of NHEJ factors on the early stages of neurodevelopment, we isolated neural stem and progenitor cells from mouse embryos and investigated proliferation, self-renewal and differentiation capacity of these cells lacking either Xlf, Paxx, Dna-pkcs, Xlf/Paxx or Xlf/Dna-pkcs. We found that XRCC4-like factor (XLF), DNA-dependent protein kinase catalytic subunit (DNA-PKcs) and paralogue of XRCC4 and XLF (PAXX) maintain the neural stem and progenitor cell populations and neurodevelopment in mammals, which is particularly evident in the double knockout models.
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Affiliation(s)
- Raquel Gago-Fuentes
- Department for Cancer Research and Molecular Medicine (IKOM), Norwegian University of Science and Technology, 7491 Trondheim, Norway;
- Department of Circulation and Medical Imaging, Norwegian University of Science and Technology, 7491 Trondheim, Norway
| | - Valentyn Oksenych
- Department for Cancer Research and Molecular Medicine (IKOM), Norwegian University of Science and Technology, 7491 Trondheim, Norway;
- KG Jebsen Centre for B Cell Malignancies, Institute of Clinical Medicine, University of Oslo, 0316 Oslo, Norway
- Institute of Clinical Medicine, University of Oslo, 0318 Oslo, Norway
- Correspondence:
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8
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Saha T, Sundaravinayagam D, Di Virgilio M. Charting a DNA Repair Roadmap for Immunoglobulin Class Switch Recombination. Trends Biochem Sci 2020; 46:184-199. [PMID: 33250286 DOI: 10.1016/j.tibs.2020.10.005] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2020] [Revised: 10/08/2020] [Accepted: 10/23/2020] [Indexed: 01/18/2023]
Abstract
Immunoglobulin (Ig) class switch recombination (CSR) is the process occurring in mature B cells that diversifies the effector component of antibody responses. CSR is initiated by the activity of the B cell-specific enzyme activation-induced cytidine deaminase (AID), which leads to the formation of programmed DNA double-strand breaks (DSBs) at the Ig heavy chain (Igh) locus. Mature B cells use a multilayered and complex regulatory framework to ensure that AID-induced DNA breaks are channeled into productive repair reactions leading to CSR, and to avoid aberrant repair events causing lymphomagenic chromosomal translocations. Here, we review the DNA repair pathways acting on AID-induced DSBs and their functional interplay, with a particular focus on the latest developments in their molecular composition and mechanistic regulation.
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Affiliation(s)
- Tannishtha Saha
- Laboratory of Genome Diversification and Integrity, Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Berlin 13125, Germany
| | - Devakumar Sundaravinayagam
- Laboratory of Genome Diversification and Integrity, Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Berlin 13125, Germany.
| | - Michela Di Virgilio
- Laboratory of Genome Diversification and Integrity, Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Berlin 13125, Germany; Charité-Universitätsmedizin Berlin, Berlin 10117, Germany.
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9
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Beck C, Castañeda-Zegarra S, Huse C, Xing M, Oksenych V. Mediator of DNA Damage Checkpoint Protein 1 Facilitates V(D)J Recombination in Cells Lacking DNA Repair Factor XLF. Biomolecules 2019; 10:biom10010060. [PMID: 31905950 PMCID: PMC7023129 DOI: 10.3390/biom10010060] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2019] [Revised: 12/23/2019] [Accepted: 12/24/2019] [Indexed: 11/16/2022] Open
Abstract
DNA double-strand breaks (DSBs) trigger the Ataxia telangiectasia mutated (ATM)-dependent DNA damage response (DDR), which consists of histone H2AX, MDC1, RNF168, 53BP1, PTIP, RIF1, Rev7, and Shieldin. Early stages of B and T lymphocyte development are dependent on recombination activating gene (RAG)-induced DSBs that form the basis for further V(D)J recombination. Non-homologous end joining (NHEJ) pathway factors recognize, process, and ligate DSBs. Based on numerous loss-of-function studies, DDR factors were thought to be dispensable for the V(D)J recombination. In particular, mice lacking Mediator of DNA Damage Checkpoint Protein 1 (MDC1) possessed nearly wild-type levels of mature B and T lymphocytes in the spleen, thymus, and bone marrow. NHEJ factor XRCC4-like factor (XLF)/Cernunnos is functionally redundant with ATM, histone H2AX, and p53-binding protein 1 (53BP1) during the lymphocyte development in mice. Here, we genetically inactivated MDC1, XLF, or both MDC1 and XLF in murine vAbl pro-B cell lines and, using chromosomally integrated substrates, demonstrated that MDC1 stimulates the V(D)J recombination in cells lacking XLF. Moreover, combined inactivation of MDC1 and XLF in mice resulted in synthetic lethality. Together, these findings suggest that MDC1 and XLF are functionally redundant during the mouse development, in general, and the V(D)J recombination, in particular.
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Affiliation(s)
- Carole Beck
- Department of Clinical and Molecular Medicine (IKOM), Norwegian University of Science and Technology (NTNU), 7491 Trondheim, Norway
- St. Olavs Hospital, Trondheim University Hospital, Clinic of Medicine, Postboks 3250 Sluppen, 7006 Trondheim, Norway
| | - Sergio Castañeda-Zegarra
- Department of Clinical and Molecular Medicine (IKOM), Norwegian University of Science and Technology (NTNU), 7491 Trondheim, Norway
- St. Olavs Hospital, Trondheim University Hospital, Clinic of Medicine, Postboks 3250 Sluppen, 7006 Trondheim, Norway
| | - Camilla Huse
- Department of Clinical and Molecular Medicine (IKOM), Norwegian University of Science and Technology (NTNU), 7491 Trondheim, Norway
- St. Olavs Hospital, Trondheim University Hospital, Clinic of Medicine, Postboks 3250 Sluppen, 7006 Trondheim, Norway
| | - Mengtan Xing
- Department of Clinical and Molecular Medicine (IKOM), Norwegian University of Science and Technology (NTNU), 7491 Trondheim, Norway
- St. Olavs Hospital, Trondheim University Hospital, Clinic of Medicine, Postboks 3250 Sluppen, 7006 Trondheim, Norway
| | - Valentyn Oksenych
- Department of Clinical and Molecular Medicine (IKOM), Norwegian University of Science and Technology (NTNU), 7491 Trondheim, Norway
- St. Olavs Hospital, Trondheim University Hospital, Clinic of Medicine, Postboks 3250 Sluppen, 7006 Trondheim, Norway
- Department of Biosciences and Nutrition (BioNuT), Karolinska Institutet, 14183 Huddinge, Sweden
- Correspondence:
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10
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Kumrah R, Vignesh P, Patra P, Singh A, Anjani G, Saini P, Sharma M, Kaur A, Rawat A. Genetics of severe combined immunodeficiency. Genes Dis 2019; 7:52-61. [PMID: 32181275 PMCID: PMC7063414 DOI: 10.1016/j.gendis.2019.07.004] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2019] [Revised: 07/07/2019] [Accepted: 07/09/2019] [Indexed: 01/19/2023] Open
Abstract
Severe Combined Immunodeficiency (SCID) is an inherited group of rare, life-threatening disorders due to the defect in T cell development and function. Clinical manifestations are characterised by recurrent and severe bacterial, viral, and fungal opportunistic infections that start from early infancy period. Haematopoietic stem cell transplantation (HSCT) is the treatment of choice. The pattern of inheritance of SCID may be X-linked or autosomal recessive. Though the diagnosis of SCID is usually established by flow cytometry-based tests, genetic diagnosis is often needed for genetic counselling, prognostication, and modification of pre-transplant chemotherapeutic agents. This review aims to highlight the genetic aspects of SCID.
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Affiliation(s)
- Rajni Kumrah
- Allergy Immunology Unit, Department of Pediatrics, Advanced Pediatrics Centre, Postgraduate Institute of Medical Education and Research, Chandigarh, India
| | - Pandiarajan Vignesh
- Allergy Immunology Unit, Department of Pediatrics, Advanced Pediatrics Centre, Postgraduate Institute of Medical Education and Research, Chandigarh, India
| | - Pratap Patra
- Allergy Immunology Unit, Department of Pediatrics, Advanced Pediatrics Centre, Postgraduate Institute of Medical Education and Research, Chandigarh, India
| | - Ankita Singh
- Allergy Immunology Unit, Department of Pediatrics, Advanced Pediatrics Centre, Postgraduate Institute of Medical Education and Research, Chandigarh, India
| | - Gummadi Anjani
- Allergy Immunology Unit, Department of Pediatrics, Advanced Pediatrics Centre, Postgraduate Institute of Medical Education and Research, Chandigarh, India
| | - Poonam Saini
- Allergy Immunology Unit, Department of Pediatrics, Advanced Pediatrics Centre, Postgraduate Institute of Medical Education and Research, Chandigarh, India
| | - Madhubala Sharma
- Allergy Immunology Unit, Department of Pediatrics, Advanced Pediatrics Centre, Postgraduate Institute of Medical Education and Research, Chandigarh, India
| | - Anit Kaur
- Allergy Immunology Unit, Department of Pediatrics, Advanced Pediatrics Centre, Postgraduate Institute of Medical Education and Research, Chandigarh, India
| | - Amit Rawat
- Allergy Immunology Unit, Department of Pediatrics, Advanced Pediatrics Centre, Postgraduate Institute of Medical Education and Research, Chandigarh, India
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11
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Roch B, Abramowski V, Chaumeil J, de Villartay JP. Cernunnos/Xlf Deficiency Results in Suboptimal V(D)J Recombination and Impaired Lymphoid Development in Mice. Front Immunol 2019; 10:443. [PMID: 30923523 PMCID: PMC6426757 DOI: 10.3389/fimmu.2019.00443] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2018] [Accepted: 02/19/2019] [Indexed: 12/23/2022] Open
Abstract
Xlf/Cernunnos is unique among the core factors of the non-homologous end joining (NHEJ) DNA double strand breaks (DSBs) repair pathway, in the sense that it is not essential for V(D)J recombination in vivo and in vitro. Unlike other NHEJ deficient mice showing a SCID phenotype, Xlf−/− mice present a unique immune phenotype with a moderate B- and T-cell lymphopenia, a decreased cellularity in the thymus, and a characteristic TCRα repertoire bias associated with the P53-dependent apoptosis of CD4+CD8+ DP thymocytes. Here, we thoroughly analyzed Xlf−/− mice immune phenotype and showed that it is specifically related to the DP stage but independent of the MHC-driven antigen presentation and T-cell activation during positive selection. Instead, we show that V(D)J recombination is subefficient in Xlf−/− mice in vivo, exemplified by the presence of unrepaired DSBs in the thymus. This results in a moderate developmental delay of both B- and T-lymphocytes at key V(D)J recombination dependent stages. Furthermore, subefficient V(D)J recombination waves are accumulating during TCRα rearrangement, causing the typical TCRα repertoire bias with loss of distal Vα and Jα rearrangements.
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Affiliation(s)
- Benoit Roch
- Laboratory "Genome Dynamics in the Immune System", INSERM UMR1163, Paris, France.,Institut Imagine, Université Paris Descartes Sorbonne Paris Cité, Paris, France
| | - Vincent Abramowski
- Laboratory "Genome Dynamics in the Immune System", INSERM UMR1163, Paris, France.,Institut Imagine, Université Paris Descartes Sorbonne Paris Cité, Paris, France
| | - Julie Chaumeil
- Institut Cochin, INSERM U1016, CNRS UMR8104, Université Paris-Descartes, Paris, France
| | - Jean-Pierre de Villartay
- Laboratory "Genome Dynamics in the Immune System", INSERM UMR1163, Paris, France.,Institut Imagine, Université Paris Descartes Sorbonne Paris Cité, Paris, France
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12
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Recio MJ, Dominguez-Pinilla N, Perrig MS, Rodriguez Vigil-Iturrate C, Salmón-Rodriguez N, Martinez Faci C, Castro-Panete MJ, Blas-Espada J, López-Nevado M, Ruiz-Garcia R, Chaparro-García R, Allende LM, Gonzalez-Granado LI. Extreme Phenotypes With Identical Mutations: Two Patients With Same Non-sense NHEJ1 Homozygous Mutation. Front Immunol 2019; 9:2959. [PMID: 30666249 PMCID: PMC6330288 DOI: 10.3389/fimmu.2018.02959] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2018] [Accepted: 11/30/2018] [Indexed: 12/22/2022] Open
Abstract
Cernunnos/XLF deficiency is a rare primary immunodeficiency classified within the DNA repair defects. Patients present with severe growth retardation, microcephaly, lymphopenia and increased cellular sensitivity to ionizing radiation. Here, we describe two unrelated cases with the same non-sense mutation in the NHEJ1 gene showing significant differences in clinical presentation and immunological profile but a similar DNA repair defect.
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Affiliation(s)
- Maria J Recio
- Department of Immunology, Ophthalmology and ENT, School of Medicine, Complutense University, 12 de Octubre Health Research Institute (imas12), Madrid, Spain.,Hospital 12 de Octubre Health Research Institute (imas12), Madrid, Spain
| | - Nerea Dominguez-Pinilla
- Hospital 12 de Octubre Health Research Institute (imas12), Madrid, Spain.,Pediatric Hematology and Oncology Unit, University Hospital Virgen de la Salud, Toledo, Spain
| | - Melina Soledad Perrig
- Department of Immunology, Ophthalmology and ENT, School of Medicine, Complutense University, 12 de Octubre Health Research Institute (imas12), Madrid, Spain.,Hospital 12 de Octubre Health Research Institute (imas12), Madrid, Spain
| | | | - Nerea Salmón-Rodriguez
- Hospital 12 de Octubre Health Research Institute (imas12), Madrid, Spain.,Immunodeficiencies Unit, Pediatrics, University Hospital 12 octubre, Madrid, Spain.,Complutense University School of Medicine, Madrid, Spain
| | - Cristina Martinez Faci
- Pediatric Hematology and Oncology Unit, University Hospital Miguel Servet, Zaragoza, Spain
| | | | - Javier Blas-Espada
- Hospital 12 de Octubre Health Research Institute (imas12), Madrid, Spain.,Department of Immunology, University Hospital 12 Octubre, Madrid, Spain
| | - Marta López-Nevado
- Hospital 12 de Octubre Health Research Institute (imas12), Madrid, Spain.,Department of Immunology, University Hospital 12 Octubre, Madrid, Spain
| | - Raquel Ruiz-Garcia
- Hospital 12 de Octubre Health Research Institute (imas12), Madrid, Spain.,Department of Immunology, University Hospital 12 Octubre, Madrid, Spain
| | - Rebeca Chaparro-García
- Department of Immunology, Ophthalmology and ENT, School of Medicine, Complutense University, 12 de Octubre Health Research Institute (imas12), Madrid, Spain
| | - Luis M Allende
- Hospital 12 de Octubre Health Research Institute (imas12), Madrid, Spain.,Department of Immunology, University Hospital 12 Octubre, Madrid, Spain
| | - Luis Ignacio Gonzalez-Granado
- Hospital 12 de Octubre Health Research Institute (imas12), Madrid, Spain.,Immunodeficiencies Unit, Pediatrics, University Hospital 12 octubre, Madrid, Spain.,Complutense University School of Medicine, Madrid, Spain
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13
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Genomic and transcriptomic landscapes of Epstein-Barr virus in extranodal natural killer T-cell lymphoma. Leukemia 2018; 33:1451-1462. [PMID: 30546078 PMCID: PMC6756073 DOI: 10.1038/s41375-018-0324-5] [Citation(s) in RCA: 78] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2018] [Accepted: 11/22/2018] [Indexed: 12/13/2022]
Abstract
Extranodal natural killer T-cell lymphoma (nasal type; NKTCL) is an aggressive malignancy strongly associated with Epstein-Barr virus (EBV) infection. However, the role of EBV in NKTCL development is unclear, largely due to the lack of information about EBV genome and transcriptome in NKTCL. Here, using high-throughput sequencing, we obtained whole genome (n = 27) and transcriptome datasets (n = 18) of EBV derived from NKTCL tumor biopsies. We assembled 27 EBV genomes and detected an average of 1,152 single nucleotide variants and 44.8 indels (<50 bp) of EBV per sample. We also identified frequent focal EBV genome deletions and integrated EBV fragments in the host genome. Moreover, Phylogenetic analysis revealed that NKTCL-derived EBVs are closely clustered; transcriptome analysis revealed less activation of both latent and lytic genes and larger amount of T-cell epitope alterations in NKTCL, as compared with other EBV-associated cancers. Furthermore, we observed transcriptional defects of the BARTs miRNA by deletion, and the disruption of host NHEJ1 by integrated EBV fragment, implying novel pathogenic mechanisms of EBV. Taken together, we reported for the first time global mutational and transcriptional profiles of EBV in NKTCL clinical samples, revealing important somatic events of EBV and providing insights to better understanding of EBV’s contribution in tumorigenesis.
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14
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de la Morena MT. Clinical Phenotypes of Hyper-IgM Syndromes. THE JOURNAL OF ALLERGY AND CLINICAL IMMUNOLOGY-IN PRACTICE 2017; 4:1023-1036. [PMID: 27836054 DOI: 10.1016/j.jaip.2016.09.013] [Citation(s) in RCA: 68] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/15/2016] [Revised: 09/21/2016] [Accepted: 09/23/2016] [Indexed: 02/05/2023]
Abstract
The primary immunodeficiency (PID) diseases comprise a heterogeneous group of inherited disorders of immune function. Technical advancements in whole-genome, whole-exome, and RNA-sequencing have seen the explosion of genetic discoveries in the field of PIDs. The present review aims to focus on a group of immunodeficiency disorders associated with elevated levels of IgM (hyper IgM; HIGM) and provides a clinical differential diagnosis. Most patients present for evaluation of immunodeficiency due to recurrent infections, and laboratory studies show either a clear isolated elevation of serum immunoglobulin M (IgM) with low or absent IgG, IgA, and IgE. Alternatively, IgM levels may be normal or moderately elevated while other serum immunoglobulins are reported below the norms for age but not absent. Mechanistically, these disorders are recognized as defects in immunoglobulin (Ig) class switch recombination (CSR). Importantly, to safeguard genetic stability, CSR utilizes elements of the DNA repair machinery including multi-protein complexes involved in mismatch repair (MMR). Therefore, it is not uncommon for defects in the DNA repair machinery, to present with laboratory findings of HIGM. This review will discuss clinical phenotypes associated with congenital defects associated with HIGM. Clinical manifestations, relevant immunologic testing, inheritance pattern, molecular diagnosis, presumed pathogenesis, and OMIM number, when annotated are compiled. Accepted therapeutic options, when available, are reviewed for each condition discussed.
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Affiliation(s)
- M Teresa de la Morena
- Division of Allergy and Immunology, Department of Pediatrics and Internal Medicine, University of Texas, Southwestern Medical Center, Dallas, Texas.
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15
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Yazdani R, Abolhassani H, Tafaroji J, Azizi G, Hamidieh AA, Chou J, Geha RS, Aghamohammadi A. Cernunnos deficiency associated with BCG adenitis and autoimmunity: First case from the national Iranian registry and review of the literature. Clin Immunol 2017; 183:201-206. [DOI: 10.1016/j.clim.2017.07.007] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2017] [Revised: 07/15/2017] [Accepted: 07/15/2017] [Indexed: 10/19/2022]
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16
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Carrillo J, Calvete O, Pintado-Berninches L, Manguan-García C, Sevilla Navarro J, Arias-Salgado EG, Sastre L, Guenechea G, López Granados E, de Villartay JP, Revy P, Benitez J, Perona R. Mutations in XLF/NHEJ1/Cernunnos gene results in downregulation of telomerase genes expression and telomere shortening. Hum Mol Genet 2017; 26:1900-1914. [DOI: 10.1093/hmg/ddx098] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2017] [Accepted: 03/08/2017] [Indexed: 01/08/2023] Open
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17
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XLF deficiency results in reduced N-nucleotide addition during V(D)J recombination. Blood 2016; 128:650-9. [PMID: 27281794 DOI: 10.1182/blood-2016-02-701029] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/29/2016] [Accepted: 05/31/2016] [Indexed: 12/12/2022] Open
Abstract
Repair of DNA double-strand breaks (DSBs) by the nonhomologous end-joining pathway (NHEJ) is important not only for repair of spontaneous breaks but also for breaks induced in developing lymphocytes during V(D)J (variable [V], diversity [D], and joining [J] genes) recombination of their antigen receptor loci to create a diverse repertoire. Mutations in the NHEJ factor XLF result in extreme sensitivity for ionizing radiation, microcephaly, and growth retardation comparable to mutations in LIG4 and XRCC4, which together form the NHEJ ligation complex. However, the effect on the immune system is variable (mild to severe immunodeficiency) and less prominent than that seen in deficiencies of NHEJ factors ARTEMIS and DNA-dependent protein kinase catalytic subunit, with defects in the hairpin opening step, which is crucial and unique for V(D)J recombination. Therefore, we aimed to study the role of XLF during V(D)J recombination. We obtained clinical data from 9 XLF-deficient patients and performed immune phenotyping and antigen receptor repertoire analysis of immunoglobulin (Ig) and T-cell receptor (TR) rearrangements, using next-generation sequencing in 6 patients. The results were compared with XRCC4 and LIG4 deficiency. Both Ig and TR rearrangements showed a significant decrease in the number of nontemplated (N) nucleotides inserted by terminal deoxynucleotidyl transferase, which resulted in a decrease of 2 to 3 amino acids in the CDR3. Such a reduction in the number of N-nucleotides has a great effect on the junctional diversity, and thereby on the total diversity of the Ig and TR repertoire. This shows that XLF has an important role during V(D)J recombination in creating diversity of the repertoire by stimulating N-nucleotide insertion.
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18
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Chen Z, Elos MT, Viboolsittiseri SS, Gowan K, Leach SM, Rice M, Eder MD, Jones K, Wang JH. Combined deletion of Xrcc4 and Trp53 in mouse germinal center B cells leads to novel B cell lymphomas with clonal heterogeneity. J Hematol Oncol 2016; 9:2. [PMID: 26740101 PMCID: PMC4704435 DOI: 10.1186/s13045-015-0230-5] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2015] [Accepted: 12/28/2015] [Indexed: 01/19/2023] Open
Abstract
Background Activated B lymphocytes harbor programmed DNA double-strand breaks (DSBs) initiated by activation-induced deaminase (AID) and repaired by non-homologous end-joining (NHEJ). While it has been proposed that these DSBs during secondary antibody gene diversification are the primary source of chromosomal translocations in germinal center (GC)-derived B cell lymphomas, this point has not been directly addressed due to the lack of proper mouse models. Methods In the current study, we establish a unique mouse model by specifically deleting a NHEJ gene, Xrcc4, and a cell cycle checkpoint gene, Trp53, in GC B cells, which results in the spontaneous development of B cell lymphomas that possess features of GC B cells. Results We show that these NHEJ deficient lymphomas harbor translocations frequently targeting immunoglobulin (Ig) loci. Furthermore, we found that Ig translocations were associated with distinct mechanisms, probably caused by AID- or RAG-induced DSBs. Intriguingly, the AID-associated Ig loci translocations target either c-myc or Pvt-1 locus whereas the partners of RAG-associated Ig translocations scattered randomly in the genome. Lastly, these NHEJ deficient lymphomas harbor complicated genomes including segmental translocations and exhibit a high level of ongoing DNA damage and clonal heterogeneity. Conclusions We propose that combined NHEJ and p53 defects may serve as an underlying mechanism for a high level of genomic complexity and clonal heterogeneity in cancers. Electronic supplementary material The online version of this article (doi:10.1186/s13045-015-0230-5) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Zhangguo Chen
- Department of Immunology and Microbiology, University of Colorado, Anschutz Medical Campus, 12800 E. 19th Ave, Mail Stop 8333, Aurora, CO, 80045, USA.,Department of Biomedical Research, National Jewish Health, Denver, CO, 80206, USA
| | - Mihret T Elos
- Department of Immunology and Microbiology, University of Colorado, Anschutz Medical Campus, 12800 E. 19th Ave, Mail Stop 8333, Aurora, CO, 80045, USA
| | - Sawanee S Viboolsittiseri
- Department of Immunology and Microbiology, University of Colorado, Anschutz Medical Campus, 12800 E. 19th Ave, Mail Stop 8333, Aurora, CO, 80045, USA
| | - Katherine Gowan
- Department of Biochemistry and Molecular Genetics, University of Colorado, Anschutz Medical Campus, Aurora, CO, 80045, USA
| | - Sonia M Leach
- Department of Biomedical Research, National Jewish Health, Denver, CO, 80206, USA.,Integrated Center for Genes, Environment and Health, National Jewish Health, Denver, CO, 80206, USA
| | - Michael Rice
- Department of Immunology and Microbiology, University of Colorado, Anschutz Medical Campus, 12800 E. 19th Ave, Mail Stop 8333, Aurora, CO, 80045, USA
| | - Maxwell D Eder
- Department of Immunology and Microbiology, University of Colorado, Anschutz Medical Campus, 12800 E. 19th Ave, Mail Stop 8333, Aurora, CO, 80045, USA
| | - Kenneth Jones
- Department of Biochemistry and Molecular Genetics, University of Colorado, Anschutz Medical Campus, Aurora, CO, 80045, USA
| | - Jing H Wang
- Department of Immunology and Microbiology, University of Colorado, Anschutz Medical Campus, 12800 E. 19th Ave, Mail Stop 8333, Aurora, CO, 80045, USA. .,Department of Biomedical Research, National Jewish Health, Denver, CO, 80206, USA.
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Björkman A, Du L, Felgentreff K, Rosner C, Pankaj Kamdar R, Kokaraki G, Matsumoto Y, Davies EG, van der Burg M, Notarangelo LD, Hammarström L, Pan-Hammarström Q. DNA-PKcs Is Involved in Ig Class Switch Recombination in Human B Cells. THE JOURNAL OF IMMUNOLOGY 2015; 195:5608-15. [DOI: 10.4049/jimmunol.1501633] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/21/2015] [Accepted: 10/06/2015] [Indexed: 01/03/2023]
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20
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Bonilla FA, Khan DA, Ballas ZK, Chinen J, Frank MM, Hsu JT, Keller M, Kobrynski LJ, Komarow HD, Mazer B, Nelson RP, Orange JS, Routes JM, Shearer WT, Sorensen RU, Verbsky JW, Bernstein DI, Blessing-Moore J, Lang D, Nicklas RA, Oppenheimer J, Portnoy JM, Randolph CR, Schuller D, Spector SL, Tilles S, Wallace D. Practice parameter for the diagnosis and management of primary immunodeficiency. J Allergy Clin Immunol 2015; 136:1186-205.e1-78. [PMID: 26371839 DOI: 10.1016/j.jaci.2015.04.049] [Citation(s) in RCA: 421] [Impact Index Per Article: 46.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2014] [Revised: 04/18/2015] [Accepted: 04/23/2015] [Indexed: 02/07/2023]
Abstract
The American Academy of Allergy, Asthma & Immunology (AAAAI) and the American College of Allergy, Asthma & Immunology (ACAAI) have jointly accepted responsibility for establishing the "Practice parameter for the diagnosis and management of primary immunodeficiency." This is a complete and comprehensive document at the current time. The medical environment is a changing environment, and not all recommendations will be appropriate for all patients. Because this document incorporated the efforts of many participants, no single individual, including those who served on the Joint Task Force, is authorized to provide an official AAAAI or ACAAI interpretation of these practice parameters. Any request for information about or an interpretation of these practice parameters by the AAAAI or ACAAI should be directed to the Executive Offices of the AAAAI, the ACAAI, and the Joint Council of Allergy, Asthma & Immunology. These parameters are not designed for use by pharmaceutical companies in drug promotion.
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21
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Guo C, Nakazawa Y, Woodbine L, Björkman A, Shimada M, Fawcett H, Jia N, Ohyama K, Li TS, Nagayama Y, Mitsutake N, Pan-Hammarström Q, Gennery AR, Lehmann AR, Jeggo PA, Ogi T. XRCC4 deficiency in human subjects causes a marked neurological phenotype but no overt immunodeficiency. J Allergy Clin Immunol 2015; 136:1007-17. [PMID: 26255102 DOI: 10.1016/j.jaci.2015.06.007] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2015] [Revised: 05/27/2015] [Accepted: 06/08/2015] [Indexed: 01/18/2023]
Abstract
BACKGROUND Nonhomologous end-joining (NHEJ) is the major DNA double-strand break (DSB) repair mechanism in human cells. The final rejoining step requires DNA ligase IV (LIG4) together with the partner proteins X-ray repair cross-complementing protein 4 (XRCC4) and XRCC4-like factor. Patients with mutations in genes encoding LIG4, XRCC4-like factor, or the other NHEJ proteins DNA-dependent protein kinase catalytic subunit and Artemis are DSB repair defective and immunodeficient because of the requirement for NHEJ during V(D)J recombination. OBJECTIVE We found a patient displaying microcephaly and progressive ataxia but a normal immune response. We sought to determine pathogenic mutations and to describe the molecular pathogenesis of the patient. METHODS We performed next-generation exome sequencing. We evaluated the DSB repair activities and V(D)J recombination capacity of the patient's cells, as well as performing a standard blood immunologic characterization. RESULTS We identified causal mutations in the XRCC4 gene. The patient's cells are radiosensitive and display the most severe DSB repair defect we have encountered using patient-derived cell lines. In marked contrast, a V(D)J recombination plasmid assay revealed that the patient's cells did not display the junction abnormalities that are characteristic of other NHEJ-defective cell lines. The mutant protein can interact efficiently with LIG4 and functions normally in in vitro assays and when transiently expressed in vivo. However, the mutation makes the protein unstable, and it undergoes proteasome-mediated degradation. CONCLUSION Our findings reveal a novel separation of impact phenotype: there is a pronounced DSB repair defect and marked clinical neurological manifestation but no clinical immunodeficiency.
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Affiliation(s)
- Chaowan Guo
- Department of Genetics, Research Institute of Environmental Medicine (RIeM), Nagoya University, Furo-cho, Chikusa-ku, Nagoya, Japan; Nagasaki University Research Centre for Genomic Instability and Carcinogenesis (NRGIC), Nagasaki, Japan; Department of Molecular Medicine, Atomic Bomb Disease Institute, Nagasaki University, Nagasaki, Japan
| | - Yuka Nakazawa
- Department of Genetics, Research Institute of Environmental Medicine (RIeM), Nagoya University, Furo-cho, Chikusa-ku, Nagoya, Japan; Nagasaki University Research Centre for Genomic Instability and Carcinogenesis (NRGIC), Nagasaki, Japan; Department of Molecular Medicine, Atomic Bomb Disease Institute, Nagasaki University, Nagasaki, Japan
| | - Lisa Woodbine
- Genome Damage and Stability Centre, University of Sussex, Falmer, Brighton, United Kingdom
| | - Andrea Björkman
- Department of Laboratory Medicine, Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden
| | - Mayuko Shimada
- Nagasaki University Research Centre for Genomic Instability and Carcinogenesis (NRGIC), Nagasaki, Japan; Department of Molecular Medicine, Atomic Bomb Disease Institute, Nagasaki University, Nagasaki, Japan
| | - Heather Fawcett
- Genome Damage and Stability Centre, University of Sussex, Falmer, Brighton, United Kingdom
| | - Nan Jia
- Department of Genetics, Research Institute of Environmental Medicine (RIeM), Nagoya University, Furo-cho, Chikusa-ku, Nagoya, Japan; Nagasaki University Research Centre for Genomic Instability and Carcinogenesis (NRGIC), Nagasaki, Japan; Department of Molecular Medicine, Atomic Bomb Disease Institute, Nagasaki University, Nagasaki, Japan
| | - Kaname Ohyama
- Nagasaki University Research Centre for Genomic Instability and Carcinogenesis (NRGIC), Nagasaki, Japan; Course of Pharmaceutical Sciences, Graduate School of Biomedical Sciences, Nagasaki University, Nagasaki, Japan
| | - Tao-Sheng Li
- Department of Stem Cell Biology, Atomic Bomb Disease Institute, Nagasaki University, Nagasaki, Japan
| | - Yuji Nagayama
- Department of Molecular Medicine, Atomic Bomb Disease Institute, Nagasaki University, Nagasaki, Japan
| | - Norisato Mitsutake
- Nagasaki University Research Centre for Genomic Instability and Carcinogenesis (NRGIC), Nagasaki, Japan; Department of Radiation Medical Sciences, Atomic Bomb Disease Institute, Nagasaki University, Nagasaki, Japan
| | - Qiang Pan-Hammarström
- Department of Laboratory Medicine, Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden
| | - Andrew R Gennery
- Institute of Cellular Medicine, Newcastle University, Newcastle upon Tyne Hospitals NHS Foundation Trust, Newcastle upon Tyne, United Kingdom
| | - Alan R Lehmann
- Genome Damage and Stability Centre, University of Sussex, Falmer, Brighton, United Kingdom
| | - Penny A Jeggo
- Genome Damage and Stability Centre, University of Sussex, Falmer, Brighton, United Kingdom.
| | - Tomoo Ogi
- Department of Genetics, Research Institute of Environmental Medicine (RIeM), Nagoya University, Furo-cho, Chikusa-ku, Nagoya, Japan; Nagasaki University Research Centre for Genomic Instability and Carcinogenesis (NRGIC), Nagasaki, Japan; Department of Molecular Medicine, Atomic Bomb Disease Institute, Nagasaki University, Nagasaki, Japan; Microbial Genetics Laboratory, Genetic Strains Research Center, National Institute of Genetics, Mishima, Japan.
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22
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Sungalee S, Mamessier E, Morgado E, Grégoire E, Brohawn PZ, Morehouse CA, Jouve N, Monvoisin C, Menard C, Debroas G, Faroudi M, Mechin V, Navarro JM, Drevet C, Eberle FC, Chasson L, Baudimont F, Mancini SJ, Tellier J, Picquenot JM, Kelly R, Vineis P, Ruminy P, Chetaille B, Jaffe ES, Schiff C, Hardwigsen J, Tice DA, Higgs BW, Tarte K, Nadel B, Roulland S. Germinal center reentries of BCL2-overexpressing B cells drive follicular lymphoma progression. J Clin Invest 2014; 124:5337-51. [PMID: 25384217 DOI: 10.1172/jci72415] [Citation(s) in RCA: 85] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2013] [Accepted: 10/03/2014] [Indexed: 11/17/2022] Open
Abstract
It has recently been demonstrated that memory B cells can reenter and reengage germinal center (GC) reactions, opening the possibility that multi-hit lymphomagenesis gradually occurs throughout life during successive immunological challenges. Here, we investigated this scenario in follicular lymphoma (FL), an indolent GC-derived malignancy. We developed a mouse model that recapitulates the FL hallmark t(14;18) translocation, which results in constitutive activation of antiapoptotic protein B cell lymphoma 2 (BCL2) in a subset of B cells, and applied a combination of molecular and immunofluorescence approaches to track normal and t(14;18)(+) memory B cells in human and BCL2-overexpressing B cells in murine lymphoid tissues. BCL2-overexpressing B cells required multiple GC transits before acquiring FL-associated developmental arrest and presenting as GC B cells with constitutive activation-induced cytidine deaminase (AID) mutator activity. Moreover, multiple reentries into the GC were necessary for the progression to advanced precursor stages of FL. Together, our results demonstrate that protracted subversion of immune dynamics contributes to early dissemination and progression of t(14;18)(+) precursors and shapes the systemic presentation of FL patients.
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23
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Hematopoietic stem cell dysfunction underlies the progressive lymphocytopenia in XLF/Cernunnos deficiency. Blood 2014; 124:1622-5. [PMID: 25075129 DOI: 10.1182/blood-2014-05-574863] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
XRCC4-like factor (XLF/Cernunnos) is a component of the nonhomologous end-joining (NHEJ) pathway of double-strand DNA break repair. XLF-deficient patients develop a severe progressive lymphocytopenia. Although NHEJ is required for V(D)J recombination and lymphocyte development, XLF-deficient mice have normal V(D)J recombination, highlighting the need for an alternative mechanism for the lymphocytopenia. Here, we report that XLF-deficient mice recapitulate the age-dependent lymphocytopenia of patients. We show that XLF deficiency leads to premature aging of hematopoietic stem cells (HSCs), measured by decreased functional capacity in transplantation assays, preferential myeloid reconstitution, and reduced self-renewal at a young age. We propose that premature aging of HSCs, together with previously reported defects in class-switch recombination and memory immune response, underlies the progressive and severe lymphocytopenia in XLF-deficient patients in the absence of measurable V(D)J recombination defects.
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24
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Kumar V, Alt FW, Oksenych V. Reprint of "Functional overlaps between XLF and the ATM-dependent DNA double strand break response". DNA Repair (Amst) 2014; 17:52-63. [PMID: 24767946 DOI: 10.1016/j.dnarep.2014.04.004] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2013] [Revised: 01/14/2014] [Accepted: 01/24/2014] [Indexed: 02/08/2023]
Abstract
Developing B and T lymphocytes generate programmed DNA double strand breaks (DSBs) during the V(D)J recombination process that assembles exons that encode the antigen-binding variable regions of antibodies. In addition, mature B lymphocytes generate programmed DSBs during the immunoglobulin heavy chain (IgH) class switch recombination (CSR) process that allows expression of different antibody heavy chain constant regions that provide different effector functions. During both V(D)J recombination and CSR, DSB intermediates are sensed by the ATM-dependent DSB response (DSBR) pathway, which also contributes to their joining via classical non-homologous end-joining (C-NHEJ). The precise nature of the interplay between the DSBR and C-NHEJ pathways in the context of DSB repair via C-NHEJ remains under investigation. Recent studies have shown that the XLF C-NHEJ factor has functional redundancy with several members of the ATM-dependent DSBR pathway in C-NHEJ, highlighting unappreciated major roles for both XLF as well as the DSBR in V(D)J recombination, CSR and C-NHEJ in general. In this review, we discuss current knowledge of the mechanisms that contribute to the repair of DSBs generated during B lymphocyte development and activation with a focus on potential functionally redundant roles of XLF and ATM-dependent DSBR factors.
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Affiliation(s)
- Vipul Kumar
- Howard Hughes Medical Institute, Program in Cellular and Molecular Medicine, Boston Children's Hospital, Department of Genetics, Harvard Medical School, Boston, MA 02115, United States
| | - Frederick W Alt
- Howard Hughes Medical Institute, Program in Cellular and Molecular Medicine, Boston Children's Hospital, Department of Genetics, Harvard Medical School, Boston, MA 02115, United States.
| | - Valentyn Oksenych
- Howard Hughes Medical Institute, Program in Cellular and Molecular Medicine, Boston Children's Hospital, Department of Genetics, Harvard Medical School, Boston, MA 02115, United States.
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25
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Frit P, Barboule N, Yuan Y, Gomez D, Calsou P. Alternative end-joining pathway(s): bricolage at DNA breaks. DNA Repair (Amst) 2014; 17:81-97. [PMID: 24613763 DOI: 10.1016/j.dnarep.2014.02.007] [Citation(s) in RCA: 106] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2013] [Revised: 02/01/2014] [Accepted: 02/10/2014] [Indexed: 10/25/2022]
Abstract
To cope with DNA double strand break (DSB) genotoxicity, cells have evolved two main repair pathways: homologous recombination which uses homologous DNA sequences as repair templates, and non-homologous Ku-dependent end-joining involving direct sealing of DSB ends by DNA ligase IV (Lig4). During the last two decades a third player most commonly named alternative end-joining (A-EJ) has emerged, which is defined as any Ku- or Lig4-independent end-joining process. A-EJ increasingly appears as a highly error-prone bricolage on DSBs and despite expanding exploration, it still escapes full characterization. In the present review, we discuss the mechanism and regulation of A-EJ as well as its biological relevance under physiological and pathological situations, with a particular emphasis on chromosomal instability and cancer. Whether or not it is a genuine DSB repair pathway, A-EJ is emerging as an important cellular process and understanding A-EJ will certainly be a major challenge for the coming years.
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Affiliation(s)
- Philippe Frit
- CNRS, IPBS (Institut de Pharmacologie et de Biologie Structurale), BP 64182, 205 route de Narbonne, 31077 Toulouse, Cedex4, France; Université de Toulouse, UPS, IPBS, F-31077 Toulouse, France; Equipe labellisée Ligue Nationale Contre le Cancer, France
| | - Nadia Barboule
- CNRS, IPBS (Institut de Pharmacologie et de Biologie Structurale), BP 64182, 205 route de Narbonne, 31077 Toulouse, Cedex4, France; Université de Toulouse, UPS, IPBS, F-31077 Toulouse, France; Equipe labellisée Ligue Nationale Contre le Cancer, France
| | - Ying Yuan
- CNRS, IPBS (Institut de Pharmacologie et de Biologie Structurale), BP 64182, 205 route de Narbonne, 31077 Toulouse, Cedex4, France; Université de Toulouse, UPS, IPBS, F-31077 Toulouse, France; Equipe labellisée Ligue Nationale Contre le Cancer, France
| | - Dennis Gomez
- CNRS, IPBS (Institut de Pharmacologie et de Biologie Structurale), BP 64182, 205 route de Narbonne, 31077 Toulouse, Cedex4, France; Université de Toulouse, UPS, IPBS, F-31077 Toulouse, France; Equipe labellisée Ligue Nationale Contre le Cancer, France
| | - Patrick Calsou
- CNRS, IPBS (Institut de Pharmacologie et de Biologie Structurale), BP 64182, 205 route de Narbonne, 31077 Toulouse, Cedex4, France; Université de Toulouse, UPS, IPBS, F-31077 Toulouse, France; Equipe labellisée Ligue Nationale Contre le Cancer, France.
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26
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Kumar V, Alt FW, Oksenych V. Functional overlaps between XLF and the ATM-dependent DNA double strand break response. DNA Repair (Amst) 2014; 16:11-22. [PMID: 24674624 DOI: 10.1016/j.dnarep.2014.01.010] [Citation(s) in RCA: 46] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2013] [Revised: 01/14/2014] [Accepted: 01/24/2014] [Indexed: 11/27/2022]
Abstract
Developing B and T lymphocytes generate programmed DNA double strand breaks (DSBs) during the V(D)J recombination process that assembles exons that encode the antigen-binding variable regions of antibodies. In addition, mature B lymphocytes generate programmed DSBs during the immunoglobulin heavy chain (IgH) class switch recombination (CSR) process that allows expression of different antibody heavy chain constant regions that provide different effector functions. During both V(D)J recombination and CSR, DSB intermediates are sensed by the ATM-dependent DSB response (DSBR) pathway, which also contributes to their joining via classical non-homologous end-joining (C-NHEJ). The precise nature of the interplay between the DSBR and C-NHEJ pathways in the context of DSB repair via C-NHEJ remains under investigation. Recent studies have shown that the XLF C-NHEJ factor has functional redundancy with several members of the ATM-dependent DSBR pathway in C-NHEJ, highlighting unappreciated major roles for both XLF as well as the DSBR in V(D)J recombination, CSR and C-NHEJ in general. In this review, we discuss current knowledge of the mechanisms that contribute to the repair of DSBs generated during B lymphocyte development and activation with a focus on potential functionally redundant roles of XLF and ATM-dependent DSBR factors.
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Affiliation(s)
- Vipul Kumar
- Howard Hughes Medical Institute, Program in Cellular and Molecular Medicine, Boston Children's Hospital, Department of Genetics, Harvard Medical School, Boston, MA 02115, United States
| | - Frederick W Alt
- Howard Hughes Medical Institute, Program in Cellular and Molecular Medicine, Boston Children's Hospital, Department of Genetics, Harvard Medical School, Boston, MA 02115, United States.
| | - Valentyn Oksenych
- Howard Hughes Medical Institute, Program in Cellular and Molecular Medicine, Boston Children's Hospital, Department of Genetics, Harvard Medical School, Boston, MA 02115, United States.
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27
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Enervald E, Du L, Visnes T, Björkman A, Lindgren E, Wincent J, Borck G, Colleaux L, Cormier-Daire V, van Gent DC, Pie J, Puisac B, de Miranda NFCC, Kracker S, Hammarström L, de Villartay JP, Durandy A, Schoumans J, Ström L, Pan-Hammarström Q. A regulatory role for the cohesin loader NIPBL in nonhomologous end joining during immunoglobulin class switch recombination. J Exp Med 2013; 210:2503-13. [PMID: 24145515 PMCID: PMC3832922 DOI: 10.1084/jem.20130168] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2013] [Accepted: 09/30/2013] [Indexed: 11/30/2022] Open
Abstract
DNA double strand breaks (DSBs) are mainly repaired via homologous recombination (HR) or nonhomologous end joining (NHEJ). These breaks pose severe threats to genome integrity but can also be necessary intermediates of normal cellular processes such as immunoglobulin class switch recombination (CSR). During CSR, DSBs are produced in the G1 phase of the cell cycle and are repaired by the classical NHEJ machinery. By studying B lymphocytes derived from patients with Cornelia de Lange Syndrome, we observed a strong correlation between heterozygous loss-of-function mutations in the gene encoding the cohesin loading protein NIPBL and a shift toward the use of an alternative, microhomology-based end joining during CSR. Furthermore, the early recruitment of 53BP1 to DSBs was reduced in the NIPBL-deficient patient cells. Association of NIPBL deficiency and impaired NHEJ was also observed in a plasmid-based end-joining assay and a yeast model system. Our results suggest that NIPBL plays an important and evolutionarily conserved role in NHEJ, in addition to its canonical function in sister chromatid cohesion and its recently suggested function in HR.
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Affiliation(s)
- Elin Enervald
- Department of Cell and Molecular Biology, Department of Laboratory Medicine, Department of Molecular Medicine and Surgery, Karolinska Institutet, 171 77 Stockholm, Sweden
| | - Likun Du
- Department of Cell and Molecular Biology, Department of Laboratory Medicine, Department of Molecular Medicine and Surgery, Karolinska Institutet, 171 77 Stockholm, Sweden
| | - Torkild Visnes
- Department of Cell and Molecular Biology, Department of Laboratory Medicine, Department of Molecular Medicine and Surgery, Karolinska Institutet, 171 77 Stockholm, Sweden
| | - Andrea Björkman
- Department of Cell and Molecular Biology, Department of Laboratory Medicine, Department of Molecular Medicine and Surgery, Karolinska Institutet, 171 77 Stockholm, Sweden
| | - Emma Lindgren
- Department of Cell and Molecular Biology, Department of Laboratory Medicine, Department of Molecular Medicine and Surgery, Karolinska Institutet, 171 77 Stockholm, Sweden
| | - Josephine Wincent
- Department of Cell and Molecular Biology, Department of Laboratory Medicine, Department of Molecular Medicine and Surgery, Karolinska Institutet, 171 77 Stockholm, Sweden
| | - Guntram Borck
- Department of Genetics, Institut National de la Santé et de la Recherche Médicale U781, Hospital Necker, 75743 Paris, France
- Institute of Human Genetics, University of Ulm, 89081 Ulm, Germany
| | - Laurence Colleaux
- Department of Genetics, Institut National de la Santé et de la Recherche Médicale U781, Hospital Necker, 75743 Paris, France
| | - Valerie Cormier-Daire
- Department of Genetics, Institut National de la Santé et de la Recherche Médicale U781, Hospital Necker, 75743 Paris, France
| | - Dik C. van Gent
- Department of Cell Biology and Genetics, Cancer Genomics Center, Erasmus Medical Center, 3000 CA Rotterdam, The Netherlands
| | - Juan Pie
- Unit of Clinical Genetics and functional Genomics, Medical Faculty, Zaragosa University, 50009 Zaragoza, Spain
| | - Beatriz Puisac
- Unit of Clinical Genetics and functional Genomics, Medical Faculty, Zaragosa University, 50009 Zaragoza, Spain
| | - Noel FCC de Miranda
- Department of Cell and Molecular Biology, Department of Laboratory Medicine, Department of Molecular Medicine and Surgery, Karolinska Institutet, 171 77 Stockholm, Sweden
| | - Sven Kracker
- National Institutes of Health and Medical Research INSERM U768, Hopital Necker Enfants Malades and Medical Faculty, Descartes-Sorbone Paris Cité University of Paris, 75743 Paris, France
| | - Lennart Hammarström
- Department of Cell and Molecular Biology, Department of Laboratory Medicine, Department of Molecular Medicine and Surgery, Karolinska Institutet, 171 77 Stockholm, Sweden
| | - Jean-Pierre de Villartay
- Université Paris-Descartes, Faculté de Médicine René Descartes, Site Necker, Institut Fédératif de Recherche, F-71015 Paris, France
| | - Anne Durandy
- National Institutes of Health and Medical Research INSERM U768, Hopital Necker Enfants Malades and Medical Faculty, Descartes-Sorbone Paris Cité University of Paris, 75743 Paris, France
| | - Jacqueline Schoumans
- Department of Medical Genetics Cancer Cytogenetic Unit, University Hospital of Lausanne, 1011 Lausanne, Switzerland
| | - Lena Ström
- Department of Cell and Molecular Biology, Department of Laboratory Medicine, Department of Molecular Medicine and Surgery, Karolinska Institutet, 171 77 Stockholm, Sweden
| | - Qiang Pan-Hammarström
- Department of Cell and Molecular Biology, Department of Laboratory Medicine, Department of Molecular Medicine and Surgery, Karolinska Institutet, 171 77 Stockholm, Sweden
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28
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de Miranda NFCC, Peng R, Georgiou K, Wu C, Falk Sörqvist E, Berglund M, Chen L, Gao Z, Lagerstedt K, Lisboa S, Roos F, van Wezel T, Teixeira MR, Rosenquist R, Sundström C, Enblad G, Nilsson M, Zeng Y, Kipling D, Pan-Hammarström Q. DNA repair genes are selectively mutated in diffuse large B cell lymphomas. ACTA ACUST UNITED AC 2013; 210:1729-42. [PMID: 23960188 PMCID: PMC3754869 DOI: 10.1084/jem.20122842] [Citation(s) in RCA: 78] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
DNA repair mechanisms are fundamental for B cell development, which relies on the somatic diversification of the immunoglobulin genes by V(D)J recombination, somatic hypermutation, and class switch recombination. Their failure is postulated to promote genomic instability and malignant transformation in B cells. By performing targeted sequencing of 73 key DNA repair genes in 29 B cell lymphoma samples, somatic and germline mutations were identified in various DNA repair pathways, mainly in diffuse large B cell lymphomas (DLBCLs). Mutations in mismatch repair genes (EXO1, MSH2, and MSH6) were associated with microsatellite instability, increased number of somatic insertions/deletions, and altered mutation signatures in tumors. Somatic mutations in nonhomologous end-joining (NHEJ) genes (DCLRE1C/ARTEMIS, PRKDC/DNA-PKcs, XRCC5/KU80, and XRCC6/KU70) were identified in four DLBCL tumors and cytogenetic analyses revealed that translocations involving the immunoglobulin-heavy chain locus occurred exclusively in NHEJ-mutated samples. The novel mutation targets, CHEK2 and PARP1, were further screened in expanded DLBCL cohorts, and somatic as well as novel and rare germline mutations were identified in 8 and 5% of analyzed tumors, respectively. By correlating defects in a subset of DNA damage response and repair genes with genomic instability events in tumors, we propose that these genes play a role in DLBCL lymphomagenesis.
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Affiliation(s)
- Noel F C C de Miranda
- Clinical Immunology, Department of Laboratory Medicine, Karolinska Institutet at Karolinska University Hospital, Huddinge, Sweden
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29
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Abstract
Primary antibody deficiencies (PADs) are the most common inherited immunodeficiencies in humans. The use of novel approaches, such as whole-exome sequencing and mouse genetic engineering, has helped to identify new genes that are involved in the pathogenesis of PADs and has enabled the characterization of the molecular pathways that are involved in B cell development and function. Here, we review the different PADs in terms of their known or putative mechanisms, which can be B cell intrinsic, B cell extrinsic or not defined so far. We also describe the clinical manifestations (including susceptibility to infections, autoimmunity and cancer) that have been associated with the various PADs.
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Affiliation(s)
- Anne Durandy
- National Institute of Health and Medical Research, INSERM U768, Necker Children's Hospital, F-75015 Paris, France.
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30
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Functional redundancy between the XLF and DNA-PKcs DNA repair factors in V(D)J recombination and nonhomologous DNA end joining. Proc Natl Acad Sci U S A 2013; 110:2234-9. [PMID: 23345432 DOI: 10.1073/pnas.1222573110] [Citation(s) in RCA: 65] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023] Open
Abstract
Classical nonhomologous end joining (C-NHEJ) is a major mammalian DNA double-strand break (DSB) repair pathway that is required for assembly of antigen receptor variable region gene segments by V(D)J recombination. Recombination activating gene endonuclease initiates V(D)J recombination by generating DSBs between two V(D)J coding gene segments and flanking recombination signal sequences (RS), with the two coding ends and two RS ends joined by C-NHEJ to form coding joins and signal joins, respectively. During C-NHEJ, recombination activating gene factor generates two coding ends as covalently sealed hairpins and RS ends as blunt 5'-phosphorylated DSBs. Opening and processing of coding end hairpins before joining by C-NHEJ requires the DNA-dependent protein kinase catalytic subunit (DNA-PKcs). However, C-NHEJ of RS ends, which do not require processing, occurs relatively normally in the absence of DNA-PKcs. The XRCC4-like factor (XLF) is a C-NHEJ component that is not required for C-NHEJ of chromosomal signal joins or coding joins because of functional redundancy with ataxia telangiectasia mutated kinase, a protein that also has some functional overlap with DNA-PKcs in this process. Here, we show that XLF has dramatic functional redundancy with DNA-PKcs in the V(D)J SJ joining process, which is nearly abrogated in their combined absence. Moreover, we show that XLF functionally overlaps with DNA-PKcs in normal mouse development, promotion of genomic stability in mouse fibroblasts, and in IgH class switch recombination in mature B cells. Our findings suggest that DNA-PKcs has fundamental roles in C-NHEJ processes beyond end processing that have been masked by functional overlaps with XLF.
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31
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Boboila C, Alt FW, Schwer B. Classical and alternative end-joining pathways for repair of lymphocyte-specific and general DNA double-strand breaks. Adv Immunol 2013; 116:1-49. [PMID: 23063072 DOI: 10.1016/b978-0-12-394300-2.00001-6] [Citation(s) in RCA: 203] [Impact Index Per Article: 18.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
Classical nonhomologous end joining (C-NHEJ) is one of the two major known pathways for the repair of DNA double-strand breaks (DSBs) in mammalian cells. Our understanding of C-NHEJ has been derived, in significant part, through studies of programmed physiologic DNA DSBs formed during V(D)J recombination in the developing immune system. Studies of immunoglobulin heavy-chain (IgH) class-switch recombination (CSR) also have revealed that there is an "alternative" end-joining process (A-EJ) that can function, relatively robustly, in the repair of DSBs in activated mature B lymphocytes. This A-EJ process has also been implicated in the formation of oncogenic translocations found in lymphoid tumors. In this review, we discuss our current understanding of C-NHEJ and A-EJ in the context of V(D)J recombination, CSR, and the formation of chromosomal translocations.
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Affiliation(s)
- Cristian Boboila
- Howard Hughes Medical Institute, Immune Disease Institute, Program in Cellular and Molecular Medicine, Children's Hospital Boston, Boston, Massachusetts, USA
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32
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Mokrani-Benhelli H, Gaillard L, Biasutto P, Le Guen T, Touzot F, Vasquez N, Komatsu J, Conseiller E, Pïcard C, Gluckman E, Francannet C, Fischer A, Durandy A, Soulier J, de Villartay JP, Cavazzana-Calvo M, Revy P. Primary microcephaly, impaired DNA replication, and genomic instability caused by compound heterozygous ATR mutations. Hum Mutat 2012; 34:374-84. [PMID: 23111928 DOI: 10.1002/humu.22245] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2012] [Accepted: 10/22/2012] [Indexed: 11/10/2022]
Abstract
Ataxia telangiectasia-mutated (ATM) and ataxia telangiectasia and Rad3-related (ATR) kinases are two key regulators of DNA-damage responses (DDR) that are mainly activated in response to DNA double-strand breaks and single-stranded DNA damages, respectively. Seckel syndrome, a rare genetic disorder characterized by a microcephaly and a markedly reduced body size, has been associated with defective ATR-dependent DNA damage signaling. However, the only human genetic ATR defect reported so far is a hypomorphic splicing mutation identified in five related individuals with Seckel syndrome. Here, we report the first case of primary microcephaly with compound heterozygous mutations in ATR: a 540 kb genomic deletion on one allele and a missense mutation leading to splice dysregulation on the other, which ultimately lead to a sharp decrease in ATR expression. DNA combing technology revealed a profound spontaneous alteration of several DNA replication parameters in patient's cells and FISH analyses highlighted the genomic instability caused by ATR deficiency. Collectively, our results emphasize the crucial role for ATR in the control of DNA replication, and reinforce the complementary and nonredundant contributions of ATM and ATR in human cells to face DNA damages and warrant genome integrity.
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33
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Xu Z, Zan H, Pone EJ, Mai T, Casali P. Immunoglobulin class-switch DNA recombination: induction, targeting and beyond. Nat Rev Immunol 2012; 12:517-31. [PMID: 22728528 PMCID: PMC3545482 DOI: 10.1038/nri3216] [Citation(s) in RCA: 294] [Impact Index Per Article: 24.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Class-switch DNA recombination (CSR) of the immunoglobulin heavy chain (IGH) locus is central to the maturation of the antibody response and crucially requires the cytidine deaminase AID. CSR involves changes in the chromatin state and the transcriptional activation of the IGH locus at the upstream and downstream switch (S) regions that are to undergo S-S DNA recombination. In addition, CSR involves the induction of AID expression and the targeting of CSR factors to S regions by 14-3-3 adaptors, and it is facilitated by the transcription machinery and by histone modifications. In this Review, we focus on recent advances regarding the induction and targeting of CSR and outline an integrated model of the assembly of macromolecular complexes that transduce crucial epigenetic information to enzymatic effectors of the CSR machinery.
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Affiliation(s)
- Zhenming Xu
- Institute for Immunology and Department of Medicine, School of Medicine, University of California, Irvine, California 92697-4120, USA
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