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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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Bello A, Hirth G, Voigt S, Tepper S, Jungnickel B. Mechanism and regulation of secondary immunoglobulin diversification. Cell Cycle 2023; 22:2070-2087. [PMID: 37909747 PMCID: PMC10761156 DOI: 10.1080/15384101.2023.2275397] [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: 05/04/2023] [Accepted: 10/20/2023] [Indexed: 11/03/2023] Open
Abstract
Secondary immunoglobulin diversification by somatic hypermutation and class switch recombination in B cells is instrumental for an adequate adaptive humoral immune response. These genetic events may, however, also introduce aberrations into other cellular genes and thereby cause B cell malignancies. While the basic mechanism of somatic hypermutation and class switch recombination is now well understood, their regulation and in particular the mechanism of their specific targeting to immunoglobulin genes is still rather mysterious. In this review, we summarize the current knowledge on the mechanism and regulation of secondary immunoglobulin diversification and discuss known mechanisms of physiological targeting to immunoglobulin genes and mistargeting to other cellular genes. We summarize open questions in the field and provide an outlook on future research.
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Affiliation(s)
- Amanda Bello
- Institute of Biochemistry and Biophysics, Faculty of Biological Sciences, Friedrich Schiller University, Jena, Germany
| | - Gianna Hirth
- Institute of Biochemistry and Biophysics, Faculty of Biological Sciences, Friedrich Schiller University, Jena, Germany
| | - Stefanie Voigt
- Institute of Biochemistry and Biophysics, Faculty of Biological Sciences, Friedrich Schiller University, Jena, Germany
| | - Sandra Tepper
- Institute of Biochemistry and Biophysics, Faculty of Biological Sciences, Friedrich Schiller University, Jena, Germany
| | - Berit Jungnickel
- Institute of Biochemistry and Biophysics, Faculty of Biological Sciences, Friedrich Schiller University, Jena, Germany
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4
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Menolfi D, Lee BJ, Zhang H, Jiang W, Bowen NE, Wang Y, Zhao J, Holmes A, Gershik S, Rabadan R, Kim B, Zha S. ATR kinase supports normal proliferation in the early S phase by preventing replication resource exhaustion. Nat Commun 2023; 14:3618. [PMID: 37336885 DOI: 10.1038/s41467-023-39332-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2022] [Accepted: 06/08/2023] [Indexed: 06/21/2023] Open
Abstract
The ATR kinase, which coordinates cellular responses to DNA replication stress, is also essential for the proliferation of normal unstressed cells. Although its role in the replication stress response is well defined, the mechanisms by which ATR supports normal cell proliferation remain elusive. Here, we show that ATR is dispensable for the viability of G0-arrested naïve B cells. However, upon cytokine-induced proliferation, Atr-deficient B cells initiate DNA replication efficiently, but by mid-S phase they display dNTP depletion, fork stalling, and replication failure. Nonetheless, productive DNA replication and dNTP levels can be restored in Atr-deficient cells by suppressing origin firing, such as partial inhibition of CDC7 and CDK1 kinase activities. Together, these findings indicate that ATR supports the proliferation of normal unstressed cells by tempering the pace of origin firing during the early S phase to avoid exhaustion of dNTPs and importantly also other replication factors.
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Affiliation(s)
- Demis Menolfi
- Institute for Cancer Genetics, Vagelos College for Physicians and Surgeons, Columbia University, New York City, NY, 10032, USA
| | - Brian J Lee
- Institute for Cancer Genetics, Vagelos College for Physicians and Surgeons, Columbia University, New York City, NY, 10032, USA
| | - Hanwen Zhang
- Institute for Cancer Genetics, Vagelos College for Physicians and Surgeons, Columbia University, New York City, NY, 10032, USA
| | - Wenxia Jiang
- Institute for Cancer Genetics, Vagelos College for Physicians and Surgeons, Columbia University, New York City, NY, 10032, USA
| | - Nicole E Bowen
- Department of Pediatrics, Emory University School of Medicine, Atlanta, GA, 30322, USA
| | - Yunyue Wang
- Institute for Cancer Genetics, Vagelos College for Physicians and Surgeons, Columbia University, New York City, NY, 10032, USA
| | - Junfei Zhao
- Program for Mathematical Genomics, Department of Systems Biology, Vagelos College for Physicians and Surgeons, Columbia University, New York City, NY, 10032, USA
| | - Antony Holmes
- Institute for Cancer Genetics, Vagelos College for Physicians and Surgeons, Columbia University, New York City, NY, 10032, USA
| | - Steven Gershik
- Institute for Cancer Genetics, Vagelos College for Physicians and Surgeons, Columbia University, New York City, NY, 10032, USA
| | - Raul Rabadan
- Program for Mathematical Genomics, Department of Systems Biology, Vagelos College for Physicians and Surgeons, Columbia University, New York City, NY, 10032, USA
| | - Baek Kim
- Department of Pediatrics, Emory University School of Medicine, Atlanta, GA, 30322, USA
| | - Shan Zha
- Institute for Cancer Genetics, Vagelos College for Physicians and Surgeons, Columbia University, New York City, NY, 10032, USA.
- Department of Pathology and Cell Biology, Herbert Irvine Comprehensive Cancer Center, Vagelos College for Physicians and Surgeons, Columbia University, New York City, NY, 10032, USA.
- Division of Pediatric Hematology, Oncology and Stem Cell Transplantation, Department of Pediatrics, Vagelos College for Physicians and Surgeons, Columbia University, New York City, NY, 10032, USA.
- Department of Immunology and Microbiology, Vagelos College for Physicians and Surgeons, Columbia University, New York City, NY, 10032, USA.
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5
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Menolfi D, Lee BJ, Zhang H, Jiang W, Bowen NE, Wang Y, Zhao J, Holmes A, Gershik S, Rabadan R, Kim B, Zha S. ATR kinase supports normal proliferation in the early S phase by preventing replication resource exhaustion. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.05.26.542515. [PMID: 37292881 PMCID: PMC10246007 DOI: 10.1101/2023.05.26.542515] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
The ATR kinase, which coordinates cellular responses to DNA replication stress, is also essential for the proliferation of normal unstressed cells. Although its role in the replication stress response is well defined, the mechanisms by which ATR supports normal cell proliferation remain elusive. Here, we show that ATR is dispensable for the viability of G0-arrested naïve B cells. However, upon cytokine-induced proliferation, Atr-deficient B cells initiate DNA replication efficiently in early S phase, but by mid-S phase they display dNTP depletion, fork stalling, and replication failure. Nonetheless, productive DNA replication can be restored in Atr-deficient cells by pathways that suppress origin firing, such as downregulation of CDC7 and CDK1 kinase activities. Together, these findings indicate that ATR supports the proliferation of normal unstressed cells by tempering the pace of origin firing during the early S phase to avoid exhaustion of dNTPs and other replication factors.
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6
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Petrackova A, Savara J, Turcsanyi P, Gajdos P, Papajik T, Kriegova E. Rare germline ATM variants of uncertain significance in chronic lymphocytic leukaemia and other cancers. Br J Haematol 2022; 199:371-381. [PMID: 36029002 DOI: 10.1111/bjh.18419] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2022] [Revised: 08/05/2022] [Accepted: 08/09/2022] [Indexed: 12/26/2022]
Abstract
Germline pathogenic ATM (ataxia-telangiectasia mutated) variants are associated with the risk of multiple cancers; however, genetic testing reveals a large number of ATM variants of uncertain significance (VUS). Here, we studied germline ATM variants occurring in a real-world cohort of 336 patients with chronic lymphocytic leukaemia (CLL) and public cancer whole-exome/genome-sequencing datasets (445 CLL, 75 mantle cell lymphoma, 216 metastatic breast cancer, 140 lung cancer patients). We found that two-thirds of rare germline ATM variants are pathogenic (18%-50%) or VUS-predicted pathogenic (50%-82%), depending on cancer type and reaching a prevalence of up to 8%, and one-third are VUS-predicted benign. Patients with both pathogenic and VUS-predicted pathogenic variants, all heterozygous, mostly missense, are more predisposed to biallelic ATM inactivation by acquiring deletion (del)11q than patients without these variants, similar to patients with somatic ATM variants. A functional assay of ATM activity in primary CLL cells proved that VUS-predicted pathogenic ATM variants partially reduce ATM activity and concurrent del(11q) leads to complete loss of ATM activity. The rare germline variants were associated with reduced progression-free survival in CLL on novel agents, comparable to somatic ATM or TP53 disruptions. Our results highlight the need to determine the pathogenicity of VUS in clinically relevant genes such as ATM.
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Affiliation(s)
- Anna Petrackova
- Department of Immunology, Faculty of Medicine and Dentistry, Palacký University and University Hospital Olomouc, Olomouc, Czech Republic
| | - Jakub Savara
- Department of Immunology, Faculty of Medicine and Dentistry, Palacký University and University Hospital Olomouc, Olomouc, Czech Republic.,Department of Computer Science, Faculty of Electrical Engineering and Computer Science, VSB-Technical University of Ostrava, Ostrava, Czech Republic
| | - Peter Turcsanyi
- Department of Hemato-Oncology, Faculty of Medicine and Dentistry, Palacký University and University Hospital Olomouc, Olomouc, Czech Republic
| | - Petr Gajdos
- Department of Computer Science, Faculty of Electrical Engineering and Computer Science, VSB-Technical University of Ostrava, Ostrava, Czech Republic
| | - Tomas Papajik
- Department of Hemato-Oncology, Faculty of Medicine and Dentistry, Palacký University and University Hospital Olomouc, Olomouc, Czech Republic
| | - Eva Kriegova
- Department of Immunology, Faculty of Medicine and Dentistry, Palacký University and University Hospital Olomouc, Olomouc, Czech Republic
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7
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Wang Y, Abolhassani H, Hammarström L, Pan-Hammarström Q. SARS-CoV-2 infection in patients with inborn errors of immunity due to DNA repair defects. Acta Biochim Biophys Sin (Shanghai) 2022; 54:836-846. [PMID: 35713311 PMCID: PMC9827799 DOI: 10.3724/abbs.2022071] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Clinical information on severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection in patients with inborn errors of immunity (IEI) during the current Coronavirus disease 2019 (COVID-19) pandemic is still limited. Proper DNA repair machinery is required for the development of the adaptive immune system, which provides specific and long-term protection against SARS-CoV-2. This review highlights the impact of SARS-CoV-2 infections on IEI patients with DNA repair disorders and summarizes susceptibility risk factors, pathogenic mechanisms, clinical manifestations and management strategies of COVID-19 in this special patient population.
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8
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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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9
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Sun X, Liu M, Bai J, Xu J, Zhu C, Dong J, Chen C. ATR kinase activity promotes antibody class switch recombination in B cells through cell cycle regulation without suppressing DSB resection and microhomology usage. J Leukoc Biol 2021; 110:1101-1112. [PMID: 33884660 DOI: 10.1002/jlb.2ma0321-064r] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2021] [Revised: 03/30/2021] [Accepted: 03/31/2021] [Indexed: 12/16/2022] Open
Abstract
Class switch recombination (CSR) changes the effector functions of antibodies and is carried out by classical and alternative nonhomologous end joining (c-NHEJ and A-EJ) of repetitive switch (S) region double-strand breaks (DSBs). The master DNA damage response (DDR) kinase ataxia-telangiectasia mutated (ATM) is critical for CSR in part by suppressing S region DSB resection. However, whether another related DDR kinase ATM- and Rad3-related (ATR) plays similar role in CSR remains elusive. In this study, we investigated the requirement for ATR kinase activity on CSR in both c-NHEJ competent and deficient B cell lines with high-throughput sequencing of S-S junctions. We found that ATR kinase inhibition efficiently blocked both c-NHEJ- and A-EJ-mediated CSR without affecting germline transcription and activation-induced cytosine deaminase expression. In contrast to ATM, ATR does not suppress S region DSB resection and microhomology usage. In addition, ATR kinase inhibition did not affect Cas9-generated DSB end joining by either c-NHEJ and A-EJ. ATR kinase-inhibited stimulated B cells proliferate much slower than controls and exhibited altered cell cycle profile with increased G1 and G2/M phase cells. In summary, our data revealed a role for ATR in promoting both c-NHEJ- and A-EJ-mediated CSR through regulating cell proliferation upon damage without negatively influencing DSB end-joining features.
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Affiliation(s)
- Xikui Sun
- Department of Pediatrics, The Seventh Affiliated Hospital of Sun Yat-Sen University, Zhongshan School of Medicine, Sun Yat-sen University, Shenzhen, Guangdong Province, China.,Key Laboratory of Tropical Disease Control (Sun Yat-sen University), Ministry of Education, Shenzhen, Guangdong Province, China
| | - Meiling Liu
- Department of Pediatrics, The Seventh Affiliated Hospital of Sun Yat-Sen University, Zhongshan School of Medicine, Sun Yat-sen University, Shenzhen, Guangdong Province, China.,Key Laboratory of Tropical Disease Control (Sun Yat-sen University), Ministry of Education, Shenzhen, Guangdong Province, China
| | - Jingning Bai
- Department of Pediatrics, The Seventh Affiliated Hospital of Sun Yat-Sen University, Zhongshan School of Medicine, Sun Yat-sen University, Shenzhen, Guangdong Province, China.,Key Laboratory of Tropical Disease Control (Sun Yat-sen University), Ministry of Education, Shenzhen, Guangdong Province, China
| | - Jiejie Xu
- Department of Pediatrics, The Seventh Affiliated Hospital of Sun Yat-Sen University, Zhongshan School of Medicine, Sun Yat-sen University, Shenzhen, Guangdong Province, China.,Key Laboratory of Tropical Disease Control (Sun Yat-sen University), Ministry of Education, Shenzhen, Guangdong Province, China
| | - Chengming Zhu
- Science Center, the Seventh Affiliated Hospital of Sun Yat-Sen University, Shenzhen, Guangdong Province, China
| | - Junchao Dong
- Department of Pediatrics, The Seventh Affiliated Hospital of Sun Yat-Sen University, Zhongshan School of Medicine, Sun Yat-sen University, Shenzhen, Guangdong Province, China.,Key Laboratory of Tropical Disease Control (Sun Yat-sen University), Ministry of Education, Shenzhen, Guangdong Province, China
| | - Chun Chen
- Department of Pediatrics, The Seventh Affiliated Hospital of Sun Yat-Sen University, Zhongshan School of Medicine, Sun Yat-sen University, Shenzhen, Guangdong Province, China
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10
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ATM: Translating the DNA Damage Response to Adaptive Immunity. Trends Immunol 2021; 42:350-365. [PMID: 33663955 DOI: 10.1016/j.it.2021.02.001] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2020] [Revised: 01/22/2021] [Accepted: 02/01/2021] [Indexed: 12/20/2022]
Abstract
ATM is often dubbed the master regulator of the DNA double stranded break (DSB) response. Since proper induction and repair of DNA DSBs forms the core of immunological diversity, it is surprising that patients with ataxia telangiectasia generally have a mild immunodeficiency in contrast to other DSB repair syndromes. In this review, we address this discrepancy by delving into the functions of ATM in DSB repair and cell cycle control and translate these to adaptive immunity. We conclude that ATM, despite its myriad functions, is not an absolute requirement for acquiring sufficient levels of immunological diversity to prevent severe viral and opportunistic infections. There is, however, a more clinically pronounced antibody deficiency in ataxia telangiectasia due to disturbed class switch recombination.
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11
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Milanovic M, Shao Z, Estes VM, Wang XS, Menolfi D, Lin X, Lee BJ, Xu J, Cupo OM, Wang D, Zha S. FATC Domain Deletion Compromises ATM Protein Stability, Blocks Lymphocyte Development, and Promotes Lymphomagenesis. THE JOURNAL OF IMMUNOLOGY 2021; 206:1228-1239. [PMID: 33536256 DOI: 10.4049/jimmunol.2000967] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/20/2020] [Accepted: 01/04/2021] [Indexed: 12/21/2022]
Abstract
Ataxia-telangiectasia mutated (ATM) kinase is a master regulator of the DNA damage response, and loss of ATM leads to primary immunodeficiency and greatly increased risk for lymphoid malignancies. The FATC domain is conserved in phosphatidylinositol-3-kinase-related protein kinases (PIKKs). Truncation mutation in the FATC domain (R3047X) selectively compromised reactive oxygen species-induced ATM activation in cell-free assays. In this article, we show that in mouse models, knock-in ATM-R3057X mutation (Atm RX , corresponding to R3047X in human ATM) severely compromises ATM protein stability and causes T cell developmental defects, B cell Ig class-switch recombination defects, and infertility resembling ATM-null. The residual ATM-R3057X protein retains minimal yet functional measurable DNA damage-induced checkpoint activation and significantly delays lymphomagenesis in Atm RX/RX mice compared with Atm -/- . Together, these results support a physiological role of the FATC domain in ATM protein stability and show that the presence of minimal residual ATM-R3057X protein can prevent growth retardation and delay tumorigenesis without restoring lymphocyte development and fertility.
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Affiliation(s)
- Maja Milanovic
- Institute for Cancer Genetics, Vagelos College of Physicians and Surgeons, Columbia University, New York, NY 10032
| | - Zhengping Shao
- Institute for Cancer Genetics, Vagelos College of Physicians and Surgeons, Columbia University, New York, NY 10032
| | - Verna M Estes
- Institute for Cancer Genetics, Vagelos College of Physicians and Surgeons, Columbia University, New York, NY 10032
| | - Xiaobin S Wang
- Institute for Cancer Genetics, Vagelos College of Physicians and Surgeons, Columbia University, New York, NY 10032.,Department of Pathology and Cell Biology, Vagelos College of Physicians and Surgeons, Columbia University, New York, NY 10032
| | - Demis Menolfi
- Institute for Cancer Genetics, Vagelos College of Physicians and Surgeons, Columbia University, New York, NY 10032
| | - Xiaohui Lin
- Institute for Cancer Genetics, Vagelos College of Physicians and Surgeons, Columbia University, New York, NY 10032
| | - Brian J Lee
- Institute for Cancer Genetics, Vagelos College of Physicians and Surgeons, Columbia University, New York, NY 10032
| | - Jun Xu
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA 92093
| | - Olivia M Cupo
- Institute for Cancer Genetics, Vagelos College of Physicians and Surgeons, Columbia University, New York, NY 10032
| | - Dong Wang
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA 92093
| | - Shan Zha
- Institute for Cancer Genetics, Vagelos College of Physicians and Surgeons, Columbia University, New York, NY 10032; .,Department of Pathology and Cell Biology, Vagelos College of Physicians and Surgeons, Columbia University, New York, NY 10032.,Division of Pediatric Oncology, Hematology and Stem Cell Transplantation, Department of Pediatrics, Vagelos College of Physicians and Surgeons, Columbia University, New York, NY 10032; and.,Department of Immunology and Microbiology, Vagelos College of Physicians and Surgeons, Columbia University, New York, NY 10032
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12
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Wang XS, Lee BJ, Zha S. The recent advances in non-homologous end-joining through the lens of lymphocyte development. DNA Repair (Amst) 2020; 94:102874. [PMID: 32623318 DOI: 10.1016/j.dnarep.2020.102874] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2020] [Revised: 05/16/2020] [Accepted: 05/24/2020] [Indexed: 12/17/2022]
Abstract
Lymphocyte development requires ordered assembly and subsequent modifications of the antigen receptor genes through V(D)J recombination and Immunoglobulin class switch recombination (CSR), respectively. While the programmed DNA cleavage events are initiated by lymphocyte-specific factors, the resulting DNA double-strand break (DSB) intermediates activate the ATM kinase-mediated DNA damage response (DDR) and rely on the ubiquitously expressed classical non-homologous end-joining (cNHEJ) pathway including the DNA-dependent protein kinase (DNA-PK), and, in the case of CSR, also the alternative end-joining (Alt-EJ) pathway, for repair. Correspondingly, patients and animal models with cNHEJ or DDR defects develop distinct types of immunodeficiency reflecting their specific DNA repair deficiency. The unique end-structure, sequence context, and cell cycle regulation of V(D)J recombination and CSR also provide a valuable platform to study the mechanisms of, and the interplay between, cNHEJ and DDR. Here, we compare and contrast the genetic consequences of DNA repair defects in V(D)J recombination and CSR with a focus on the newly discovered cNHEJ factors and the kinase-dependent structural roles of ATM and DNA-PK in animal models. Throughout, we try to highlight the pending questions and emerging differences that will extend our understanding of cNHEJ and DDR in the context of primary immunodeficiency and lymphoid malignancies.
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Affiliation(s)
- Xiaobin S Wang
- Institute for Cancer Genetics, Vagelos College of Physicians and Surgeons, Columbia University, New York City, NY 10032, United States; Graduate Program of Pathobiology and Molecular Medicine, Vagelos College of Physicians and Surgeons, Columbia University, New York City, NY 10032, United States
| | - Brian J Lee
- Institute for Cancer Genetics, Vagelos College of Physicians and Surgeons, Columbia University, New York City, NY 10032, United States
| | - Shan Zha
- Institute for Cancer Genetics, Vagelos College of Physicians and Surgeons, Columbia University, New York City, NY 10032, United States; Department of Pediatrics, Vagelos College of Physicians and Surgeons, Columbia University, New York City, NY 10032, United States; Department of Pathology and Cell Biology, Vagelos College of Physicians and Surgeons, Columbia University, New York City, NY 10032, United States; Department of Immunology and Microbiology, Vagelos College of Physicians and Surgeons, Columbia University, New York City, NY 10032, United States.
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13
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The Role for the DSB Response Pathway in Regulating Chromosome Translocations. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2018; 1044:65-87. [PMID: 29956292 DOI: 10.1007/978-981-13-0593-1_6] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
In response to DNA double strand breaks (DSB), mammalian cells activate the DNA Damage Response (DDR), a network of factors that coordinate their detection, signaling and repair. Central to this network is the ATM kinase and its substrates at chromatin surrounding DSBs H2AX, MDC1 and 53BP1. In humans, germline inactivation of ATM causes Ataxia Telangiectasia (A-T), an autosomal recessive syndrome of increased proneness to hematological malignancies driven by clonal chromosomal translocations. Studies of cancers arising in A-T patients and in genetically engineered mouse models (GEMM) deficient for ATM and its substrates have revealed complex, multilayered roles for ATM in translocation suppression and identified functional redundancies between ATM and its substrates in this context. "Programmed" DSBs at antigen receptor loci in developing lymphocytes employ ubiquitous DDR factors for signaling and repair and have been particularly useful for mechanistic studies because they are region-specific and can be monitored in vitro and in vivo. In this context, murine thymocytes deficient for ATM recapitulate the molecular events that lead to transformation in T cells from A-T patients and provide a widely used model to study the mechanisms that suppress RAG recombinase-dependent translocations. Similarly, analyses of the fate of Activation induced Cytidine Deaminase (AID)-dependent DSBs during mature B cell Class Switch Recombination (CSR) have defined the genetic requirements for end-joining and translocation suppression in this setting. Moreover, a unique role for 53BP1 in the promotion of synapsis of distant DSBs has emerged from these studies.
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14
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Gaudot L, Thomas-Claudepierre AS, Robert I, Schiavo E, Heyer V, Reina-San-Martin B. Med1 deficiency alters the somatic hypermutation spectrum in murine B cells. Eur J Immunol 2018; 48:720-723. [PMID: 29293266 DOI: 10.1002/eji.201747258] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2017] [Revised: 12/06/2017] [Accepted: 12/19/2017] [Indexed: 11/07/2022]
Abstract
The Mediator complex is known to orchestrate transcription. Here we show that B cell conditional deficient mice for the Med1 subunit display robust somatic hypermutation. Nevertheless, the mutation frequency at A residues is decreased and the expected A/T ratio is abolished, implicating Mediator in the second phase of somatic hypermutation.
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Affiliation(s)
- Léa Gaudot
- Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), Illkirch, France.,Institut National de la Santé et de la Recherche Médicale (INSERM), U 1258, Illkirch, France.,Centre National de la Recherche Scientifique (CNRS), UMR7104, Illkirch, France.,Université de Strasbourg, Illkirch, France
| | - Anne-Sophie Thomas-Claudepierre
- Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), Illkirch, France.,Institut National de la Santé et de la Recherche Médicale (INSERM), U 1258, Illkirch, France.,Centre National de la Recherche Scientifique (CNRS), UMR7104, Illkirch, France.,Université de Strasbourg, Illkirch, France
| | - Isabelle Robert
- Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), Illkirch, France.,Institut National de la Santé et de la Recherche Médicale (INSERM), U 1258, Illkirch, France.,Centre National de la Recherche Scientifique (CNRS), UMR7104, Illkirch, France.,Université de Strasbourg, Illkirch, France
| | - Ebe Schiavo
- Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), Illkirch, France.,Institut National de la Santé et de la Recherche Médicale (INSERM), U 1258, Illkirch, France.,Centre National de la Recherche Scientifique (CNRS), UMR7104, Illkirch, France.,Université de Strasbourg, Illkirch, France
| | - Vincent Heyer
- Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), Illkirch, France.,Institut National de la Santé et de la Recherche Médicale (INSERM), U 1258, Illkirch, France.,Centre National de la Recherche Scientifique (CNRS), UMR7104, Illkirch, France.,Université de Strasbourg, Illkirch, France
| | - Bernardo Reina-San-Martin
- Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), Illkirch, France.,Institut National de la Santé et de la Recherche Médicale (INSERM), U 1258, Illkirch, France.,Centre National de la Recherche Scientifique (CNRS), UMR7104, Illkirch, France.,Université de Strasbourg, Illkirch, France
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15
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Abstract
Bloom's syndrome (BS) is an autosomal recessive disease, caused by mutations in the BLM gene. This gene codes for BLM protein, which is a helicase involved in DNA repair. DNA repair is especially important for the development and maturation of the T and B cells. Since BLM is involved in DNA repair, we aimed to study if BLM deficiency affects T and B cell development and especially somatic hypermutation (SHM) and class switch recombination (CSR) processes. Clinical data of six BS patients was collected, and immunoglobulin serum levels were measured at different time points. In addition, we performed immune phenotyping of the B and T cells and analyzed the SHM and CSR in detail by analyzing IGHA and IGHG transcripts using next-generation sequencing. The serum immunoglobulin levels were relatively low, and patients had an increased number of infections. The absolute number of T, B, and NK cells were low but still in the normal range. Remarkably, all BS patients studied had a high percentage (20-80%) of CD4+ and CD8+ effector memory T cells. The process of SHM seems normal; however, the Ig subclass distribution was not normal, since the BS patients had more IGHG1 and IGHG3 transcripts. In conclusion, BS patients have low number of lymphocytes, but the immunodeficiency seems relatively mild since they have no severe or opportunistic infections. Most changes in the B cell development were seen in the CSR process; however, further studies are necessary to elucidate the exact role of BLM in CSR.
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16
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Boyer F, Boutouil H, Dalloul I, Dalloul Z, Cook-Moreau J, Aldigier JC, Carrion C, Herve B, Scaon E, Cogné M, Péron S. CSReport: A New Computational Tool Designed for Automatic Analysis of Class Switch Recombination Junctions Sequenced by High-Throughput Sequencing. THE JOURNAL OF IMMUNOLOGY 2017; 198:4148-4155. [PMID: 28416601 DOI: 10.4049/jimmunol.1601924] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/10/2016] [Accepted: 02/19/2017] [Indexed: 11/19/2022]
Abstract
B cells ensure humoral immune responses due to the production of Ag-specific memory B cells and Ab-secreting plasma cells. In secondary lymphoid organs, Ag-driven B cell activation induces terminal maturation and Ig isotype class switch (class switch recombination [CSR]). CSR creates a virtually unique IgH locus in every B cell clone by intrachromosomal recombination between two switch (S) regions upstream of each C region gene. Amount and structural features of CSR junctions reveal valuable information about the CSR mechanism, and analysis of CSR junctions is useful in basic and clinical research studies of B cell functions. To provide an automated tool able to analyze large data sets of CSR junction sequences produced by high-throughput sequencing (HTS), we designed CSReport, a software program dedicated to support analysis of CSR recombination junctions sequenced with a HTS-based protocol (Ion Torrent technology). CSReport was assessed using simulated data sets of CSR junctions and then used for analysis of Sμ-Sα and Sμ-Sγ1 junctions from CH12F3 cells and primary murine B cells, respectively. CSReport identifies junction segment breakpoints on reference sequences and junction structure (blunt-ended junctions or junctions with insertions or microhomology). Besides the ability to analyze unprecedentedly large libraries of junction sequences, CSReport will provide a unified framework for CSR junction studies. Our results show that CSReport is an accurate tool for analysis of sequences from our HTS-based protocol for CSR junctions, thereby facilitating and accelerating their study.
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Affiliation(s)
- François Boyer
- Université de Limoges, Contrôle de la Réponse Immune B et Lymphoproliférations, UMR 7276, F-87000 Limoges, France.,CNRS, Contrôle de la Réponse Immune B et Lymphoproliférations, UMR 7276, F-87000 Limoges, France
| | - Hend Boutouil
- Université de Limoges, Contrôle de la Réponse Immune B et Lymphoproliférations, UMR 7276, F-87000 Limoges, France.,CNRS, Contrôle de la Réponse Immune B et Lymphoproliférations, UMR 7276, F-87000 Limoges, France
| | - Iman Dalloul
- Université de Limoges, Contrôle de la Réponse Immune B et Lymphoproliférations, UMR 7276, F-87000 Limoges, France.,CNRS, Contrôle de la Réponse Immune B et Lymphoproliférations, UMR 7276, F-87000 Limoges, France
| | - Zeinab Dalloul
- Université de Limoges, Contrôle de la Réponse Immune B et Lymphoproliférations, UMR 7276, F-87000 Limoges, France.,CNRS, Contrôle de la Réponse Immune B et Lymphoproliférations, UMR 7276, F-87000 Limoges, France
| | - Jeanne Cook-Moreau
- Université de Limoges, Contrôle de la Réponse Immune B et Lymphoproliférations, UMR 7276, F-87000 Limoges, France.,CNRS, Contrôle de la Réponse Immune B et Lymphoproliférations, UMR 7276, F-87000 Limoges, France
| | - Jean-Claude Aldigier
- Université de Limoges, Contrôle de la Réponse Immune B et Lymphoproliférations, UMR 7276, F-87000 Limoges, France.,CNRS, Contrôle de la Réponse Immune B et Lymphoproliférations, UMR 7276, F-87000 Limoges, France
| | - Claire Carrion
- Université de Limoges, Contrôle de la Réponse Immune B et Lymphoproliférations, UMR 7276, F-87000 Limoges, France.,CNRS, Contrôle de la Réponse Immune B et Lymphoproliférations, UMR 7276, F-87000 Limoges, France
| | - Bastien Herve
- Université de Limoges,plateforme Biologie Intégrative Santé Chimie Environnement, F-87000 Limoges, France; and
| | - Erwan Scaon
- Université de Limoges,plateforme Biologie Intégrative Santé Chimie Environnement, F-87000 Limoges, France; and
| | - Michel Cogné
- Université de Limoges, Contrôle de la Réponse Immune B et Lymphoproliférations, UMR 7276, F-87000 Limoges, France.,CNRS, Contrôle de la Réponse Immune B et Lymphoproliférations, UMR 7276, F-87000 Limoges, France.,Institut Universitaire de France, F-75000 Paris, France
| | - Sophie Péron
- Université de Limoges, Contrôle de la Réponse Immune B et Lymphoproliférations, UMR 7276, F-87000 Limoges, France; .,CNRS, Contrôle de la Réponse Immune B et Lymphoproliférations, UMR 7276, F-87000 Limoges, France
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17
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Almejún MB, Campos BC, Patiño V, Galicchio M, Zelazko M, Oleastro M, Oppezzo P, Danielian S. Noninfectious complications in patients with pediatric-onset common variable immunodeficiency correlated with defects in somatic hypermutation but not in class-switch recombination. J Allergy Clin Immunol 2016; 139:913-922. [PMID: 27713077 DOI: 10.1016/j.jaci.2016.08.030] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2015] [Revised: 08/03/2016] [Accepted: 08/10/2016] [Indexed: 11/17/2022]
Abstract
BACKGROUND Common variable immunodeficiency (CVID) is a heterogeneous syndrome characterized by impaired immunoglobulin production and usually presents with a normal quantity of peripheral B cells. Most attempts aiming to classify these patients have mainly been focused on T- or B-cell phenotypes and their ability to produce protective antibodies, but it is still a major challenge to find a suitable classification that includes the clinical and immunologic heterogeneity of these patients. OBJECTIVE In this study we evaluated the late stages of B-cell differentiation in a heterogeneous population of patients with pediatric-onset CVID to clinically correlate and assess their ability to perform somatic hypermutation (SHM), class-switch recombination (CSR), or both. METHODS We performed a previously reported assay, the restriction enzyme hotspot mutation assay (IgκREHMA), to evaluate in vivo SHM status. We amplified switch regions from genomic DNA to investigate the quality of the double-strand break repairs in the class-switch recombination process in vivo. We also tested the ability to generate immunoglobulin germline and circle transcripts and to upregulate the activation-induced cytidine deaminase gene through in vitro T-dependent and T-independent stimuli. RESULTS Our results showed that patients could be classified into 2 groups according to their degree of SHM alteration. This stratification showed a significant association between patients of group A, severe alteration, and the presence of noninfectious complications. Additionally, 60% of patients presented with increased microhomology use at switched regions. In vitro activation revealed that patients with CVID behaved heterogeneously in terms of responsiveness to T-dependent stimuli. CONCLUSIONS The correlation between noninfectious complications and SHM could be an important tool for physicians to further characterize patients with CVID. This categorization would help to improve elucidation of the complex mechanisms involved in B-cell differentiation pathways.
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Affiliation(s)
- María Belén Almejún
- Servicio de Immunología y Reumatología, Hospital Nacional de Pediatría Prof. Dr Juan P. Garrahan, Buenos Aires, Argentina.
| | - Bárbara Carolina Campos
- Coordinación de Laboratorio, Hospital Nacional de Pediatría Prof. Dr Juan P. Garrahan, Buenos Aires, Argentina
| | - Virginia Patiño
- Unidad de Proteínas Recombinantes, Instituto Pasteur, Montevideo, Uruguay
| | - Miguel Galicchio
- Hospital de Niños Víctor J. Vilela, Rosario, Santa Fé, Argentina
| | - Marta Zelazko
- Servicio de Immunología y Reumatología, Hospital Nacional de Pediatría Prof. Dr Juan P. Garrahan, Buenos Aires, Argentina
| | - Matías Oleastro
- Servicio de Immunología y Reumatología, Hospital Nacional de Pediatría Prof. Dr Juan P. Garrahan, Buenos Aires, Argentina
| | - Pablo Oppezzo
- Unidad de Proteínas Recombinantes, Instituto Pasteur, Montevideo, Uruguay
| | - Silvia Danielian
- Servicio de Immunología y Reumatología, Hospital Nacional de Pediatría Prof. Dr Juan P. Garrahan, Buenos Aires, Argentina
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18
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Yamamoto K, Lee BJ, Li C, Dubois RL, Hobeika E, Bhagat G, Zha S. Early B-cell-specific inactivation of ATM synergizes with ectopic CyclinD1 expression to promote pre-germinal center B-cell lymphomas in mice. Leukemia 2015; 29:1414-24. [PMID: 25676421 PMCID: PMC5282516 DOI: 10.1038/leu.2015.41] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2014] [Revised: 01/22/2015] [Accepted: 02/06/2015] [Indexed: 01/12/2023]
Abstract
Ataxia telangiectasia-mutated (ATM) kinase is a master regulator of the DNA damage response. ATM is frequently inactivated in human B-cell non-Hodgkin lymphomas, including ~50% of mantle cell lymphomas (MCLs) characterized by ectopic expression of CyclinD1. Here we report that early and robust deletion of ATM in precursor/progenitor B cells causes cell autonomous, clonal mature B-cell lymphomas of both pre- and post-germinal center (GC) origins. Unexpectedly, naive B-cell-specific deletion of ATM is not sufficient to induce lymphomas in mice, highlighting the important tumor suppressor function of ATM in immature B cells. Although EμCyclinD1 is not sufficient to induce lymphomas, EμCyclinD1 accelerates the kinetics and increases the incidence of clonal lymphomas in ATM-deficient B-cells and skews the lymphomas toward pre-GC-derived small lymphocytic neoplasms, sharing morphological features of human MCL. This is in part due to CyclinD1-driven expansion of ATM-deficient naive B cells with genomic instability, which promotes the deletions of additional tumor suppressor genes (i.e. Trp53, Mll2, Rb1 and Cdkn2a). Together these findings define a synergistic function of ATM and CyclinD1 in pre-GC B-cell proliferation and lymphomagenesis and provide a prototypic animal model to study the pathogenesis of human MCL.
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Affiliation(s)
- Kenta Yamamoto
- Institute for Cancer Genetics, College for Physicians and Surgeons, Columbia University, New York, NY 10032
- Graduate Program for Pathobiology and Molecular Medicine, College for Physicians and Surgeons, Columbia University, New York, NY 10032
| | - Brian J. Lee
- Institute for Cancer Genetics, College for Physicians and Surgeons, Columbia University, New York, NY 10032
| | - Chen Li
- Institute for Cancer Genetics, College for Physicians and Surgeons, Columbia University, New York, NY 10032
| | - Richard L. Dubois
- Institute for Cancer Genetics, College for Physicians and Surgeons, Columbia University, New York, NY 10032
| | - Elias Hobeika
- Centre for Biological Signaling Studies BIOSS, Albert-Ludwigs-Universität Freiburg, Department of Molecular Immunology, Faculty of Biology, Albert-Ludwigs-Universität Freiburg and Max Planck Institute for Immunobiology, Stübeweg 51, 79108 Freiburg, Germany
| | - Govind Bhagat
- Department of Pathology and Cell Biology, College for Physicians and Surgeons, Columbia University, New York, NY 10032
| | - Shan Zha
- Institute for Cancer Genetics, College for Physicians and Surgeons, Columbia University, New York, NY 10032
- Department of Pathology and Cell Biology, College for Physicians and Surgeons, Columbia University, New York, NY 10032
- Department of Pediatrics, College for Physicians and Surgeons, Columbia University, New York, NY 10032
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19
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Khair L, Guikema JE, Linehan EK, Ucher AJ, Leus NG, Ogilvie C, Lou Z, Schrader CE, Stavnezer J. ATM increases activation-induced cytidine deaminase activity at downstream S regions during class-switch recombination. JOURNAL OF IMMUNOLOGY (BALTIMORE, MD. : 1950) 2014; 192:4887-96. [PMID: 24729610 PMCID: PMC4049217 DOI: 10.4049/jimmunol.1303481] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
Activation-induced cytidine deaminase (AID) initiates Ab class-switch recombination (CSR) in activated B cells resulting in exchanging the IgH C region and improved Ab effector function. During CSR, AID instigates DNA double-strand break (DSB) formation in switch (S) regions located upstream of C region genes. DSBs are necessary for CSR, but improper regulation of DSBs can lead to chromosomal translocations that can result in B cell lymphoma. The protein kinase ataxia telangiectasia mutated (ATM) is an important proximal regulator of the DNA damage response (DDR), and translocations involving S regions are increased in its absence. ATM phosphorylates H2AX, which recruits other DNA damage response (DDR) proteins, including mediator of DNA damage checkpoint 1 (Mdc1) and p53 binding protein 1 (53BP1), to sites of DNA damage. As these DDR proteins all function to promote repair and recombination of DSBs during CSR, we examined whether mouse splenic B cells deficient in these proteins would show alterations in S region DSBs when undergoing CSR. We find that in atm(-/-) cells Sμ DSBs are increased, whereas DSBs in downstream Sγ regions are decreased. We also find that mutations in the unrearranged Sγ3 segment are reduced in atm(-/-) cells. Our data suggest that ATM increases AID targeting and activity at downstream acceptor S regions during CSR and that in atm(-/-) cells Sμ DSBs accumulate as they lack a recombination partner.
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Affiliation(s)
- Lyne Khair
- Department of Microbiology and Physiological Systems, University of Massachusetts Medical School, Worcester, MA 01605
| | - Jeroen E.J. Guikema
- Department of Microbiology and Physiological Systems, University of Massachusetts Medical School, Worcester, MA 01605
| | - Erin K. Linehan
- Department of Microbiology and Physiological Systems, University of Massachusetts Medical School, Worcester, MA 01605
| | - Anna J. Ucher
- Department of Microbiology and Physiological Systems, University of Massachusetts Medical School, Worcester, MA 01605
| | - Niek G.J. Leus
- Department of Microbiology and Physiological Systems, University of Massachusetts Medical School, Worcester, MA 01605
| | - Colin Ogilvie
- Department of Microbiology and Physiological Systems, University of Massachusetts Medical School, Worcester, MA 01605
| | - Zhenkun Lou
- Division of Oncology Research, Mayo Clinic, Rochester, MN
| | - Carol E. Schrader
- Department of Microbiology and Physiological Systems, University of Massachusetts Medical School, Worcester, MA 01605
| | - Janet Stavnezer
- Department of Microbiology and Physiological Systems, University of Massachusetts Medical School, Worcester, MA 01605
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20
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Lin M, Du L, Brandtzaeg P, Pan-Hammarström Q. IgA subclass switch recombination in human mucosal and systemic immune compartments. Mucosal Immunol 2014; 7:511-20. [PMID: 24064668 DOI: 10.1038/mi.2013.68] [Citation(s) in RCA: 60] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2013] [Revised: 07/24/2013] [Accepted: 08/14/2013] [Indexed: 02/04/2023]
Abstract
Human immunoglobulin A (IgA) comprises two IgA subclasses, IgA1 and IgA2, whose distribution has been shown by immunohistochemistry to be different in various body compartments. In comparison with systemic immune compartments, we investigated the IgA switch profiles at the molecular level in salivary and lacrimal glands, nasal mucosa, and proximal and distal gut mucosa. Direct switching from IgM to IgA1 or IgA2 predominated in all immune compartments analyzed. Similar composition of the Sμ-Sα1 and Sμ-Sα2 junctions was observed, including microhomology usage, which suggested that there is no major difference in the actual recombination mechanism utilized during IgA subclass switching. The proportion of IgA1/IgA2 switch recombination events largely paralleled the previously published immunohistochemical representation of IgA1(+) and IgA2(+) plasma cells, implying that the local subclass distribution generally reflects precommitted memory/effector B cells that have undergone IgA subclass switching before extravasation at the effector site. The extremely low or undetectable levels of activation-induced cytidine deaminase (AID) and Iα-Cμ circle transcripts in intestinal lamina propria samples as compared with Peyer's patches suggest that the cellular IgA subclass distribution outside of organized gut-associated lymphoid tissue is only to a minor extent, if at all, influenced by in situ switching.
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Affiliation(s)
- M Lin
- 1] Clinical Immunology, Department of Laboratory Medicine, Karolinska Institutet at Karolinska University Hospital Huddinge, Stockholm, Sweden [2] State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-Sen University, Guangzhou, People's Republic of China
| | - L Du
- Clinical Immunology, Department of Laboratory Medicine, Karolinska Institutet at Karolinska University Hospital Huddinge, Stockholm, Sweden
| | - P Brandtzaeg
- Laboratory for Immunohistochemistry and Immunopathology (LIIPAT), Centre for Immune Regulation (CIR), University of Oslo, and Department of Pathology, Oslo University Hospital, Rikshopitalet, Norway
| | - Q Pan-Hammarström
- Clinical Immunology, Department of Laboratory Medicine, Karolinska Institutet at Karolinska University Hospital Huddinge, Stockholm, Sweden
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21
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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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Thomas-Claudepierre AS, Schiavo E, Heyer V, Fournier M, Page A, Robert I, Reina-San-Martin B. The cohesin complex regulates immunoglobulin class switch recombination. J Exp Med 2013; 210:2495-502. [PMID: 24145512 PMCID: PMC3832931 DOI: 10.1084/jem.20130166] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2013] [Accepted: 08/29/2013] [Indexed: 11/04/2022] Open
Abstract
Immunoglobulin (Ig) class switch recombination (CSR) is initiated by the transcription-coupled recruitment of activation-induced cytidine deaminase (AID) to switch regions and by the subsequent generation of double-stranded DNA breaks (DSBs). These DNA breaks are ultimately resolved through the nonhomologous end joining (NHEJ) pathway. We show that during CSR, AID associates with subunits of cohesin, a complex previously implicated in sister chromatid cohesion, DNA repair, and the formation of DNA loops between enhancers and promoters. Furthermore, we implicate the cohesin complex in the mechanism of CSR by showing that cohesin is dynamically recruited to the Sμ-Cμ region of the IgH locus during CSR and that knockdown of cohesin or its regulatory subunits results in impaired CSR and increased usage of microhomology-based end joining.
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Affiliation(s)
- Anne-Sophie Thomas-Claudepierre
- Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), Institut National de la Santé et de la Recherche Médicale (INSERM) U964/Centre National de la Recherche Scientifique (CNRS) UMR 7104/Université de Strasbourg, 67404 Illkirch, France
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Stankovic T, Skowronska A. The role of ATM mutations and 11q deletions in disease progression in chronic lymphocytic leukemia. Leuk Lymphoma 2013; 55:1227-39. [PMID: 23906020 DOI: 10.3109/10428194.2013.829919] [Citation(s) in RCA: 52] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Abstract ATM gene alteration is a frequent event in pathogenesis of chronic lymphocytic leukemia (CLL) and occurs as monoallelic loss in the form of 11q23 deletion, with and without mutation in the remaining ATM allele. ATM is a principal DNA damage response gene and biallelic ATM alterations lead to ATM functional loss and chemoresistance. The introduction of new therapies, such as intensive chemoimmunotherapy and inhibition of B-cell receptor (BCR) signaling, has changed clinical responses for the majority of CLL tumors including those with 11q deletion, but it remains to be determined whether these strategies can prevent clonal evolution of tumors with biallelic ATM alterations. In this review we discuss ATM function and the consequences of its loss during CLL pathogenesis, differences in clinical behavior of tumors with monoallelic and biallelic ATM alterations, and we outline possible approaches for targeting the ATM null CLL phenotype.
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Affiliation(s)
- Tatjana Stankovic
- School of Cancer Sciences, University of Birmingham , Birmingham , UK
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24
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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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25
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Duvvuri B, Wu GE. Gene Conversion-Like Events in the Diversification of Human Rearranged IGHV3-23*01 Gene Sequences. Front Immunol 2012; 3:158. [PMID: 22715339 PMCID: PMC3375636 DOI: 10.3389/fimmu.2012.00158] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2012] [Accepted: 05/25/2012] [Indexed: 11/13/2022] Open
Abstract
Gene conversion (GCV), a mechanism mediated by activation-induced cytidine deaminase (AID) is well established as a mechanism of immunoglobulin diversification in a few species. However, definitive evidence of GCV-like events in human immunoglobulin genes is scarce. The lack of evidence of GCV in human rearranged immunoglobulin gene sequences is puzzling given the presence of highly similar germline donors and the presence of all the enzymatic machinery required for GCV. In this study, we undertook a computational analysis of rearranged IGHV3-23(*)01 gene sequences from common variable immunodeficiency (CVID) patients, AID-deficient patients, and healthy individuals to survey "GCV-like" activities. We analyzed rearranged IGHV3-23(*)01 gene sequences obtained from total PBMC RNA and single-cell polymerase chain reaction of individual B cell lysates. Our search identified strong evidence of GCV-like activity. We observed that GCV-like tracts are flanked by AID hotspot motifs. Structural modeling of IGHV3-23(*)01 gene sequence revealed that hypermutable bases flanking GCV-like tracts are in the single stranded DNA (ssDNA) of stable stem-loop structures (SLSs). ssDNA is inherently fragile and also an optimal target for AID. We speculate that GCV could have been initiated by the targeting of hypermutable bases in ssDNA state in stable SLSs, plausibly by AID. We have observed that the frequency of GCV-like events is significantly higher in rearranged IGHV3-23-(*)01 sequences from healthy individuals compared to that of CVID patients. We did not observe GCV-like events in rearranged IGHV3-23-(*)01 sequences from AID-deficient patients. GCV, unlike somatic hypermutation (SHM), can result in multiple base substitutions that can alter many amino acids. The extensive changes in antibody affinity by GCV-like events would be instrumental in protecting humans against pathogens that diversify their genome by antigenic shift.
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Affiliation(s)
- Bhargavi Duvvuri
- School of Kinesiology and Health Science, Faculty of Health, York UniversityToronto, ON, Canada
| | - Gillian E. Wu
- School of Kinesiology and Health Science, Faculty of Health, York UniversityToronto, ON, Canada
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26
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Skowronska A, Austen B, Powell JE, Weston V, Oscier DG, Dyer MJS, Matutes E, Pratt G, Fegan C, Moss P, Taylor MA, Stankovic T. ATM germline heterozygosity does not play a role in chronic lymphocytic leukemia initiation but influences rapid disease progression through loss of the remaining ATM allele. Haematologica 2012; 97:142-6. [PMID: 21933854 PMCID: PMC3248944 DOI: 10.3324/haematol.2011.048827] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2011] [Revised: 08/23/2011] [Accepted: 09/08/2011] [Indexed: 11/09/2022] Open
Abstract
Ataxia telangiectasia patients, with constitutional bi-allelic ATM mutations, have a marked risk of lymphoid tumors and ATM mutation carriers have a smaller risk of cancer. Sporadic ATM mutations occur in 10-20% of chronic lymphocytic leukemia and are often associated with chromosome 11q deletions which cause loss of an ATM allele. The role of constitutional ATM mutations in the pathogenesis of chronic lymphocytic leukemia is unknown. Here we investigated the frequency of constitutional ATM mutations in either of two chronic lymphocytic leukemia cohorts, those with and without a chromosome 11q deletion. We found that in comparison to controls, constitutional pathogenic ATM mutations were increased in patients with chromosome 11q deletions (6 of 140 vs. 0 of 281, P = 0.001) but not in those without 11q deletions (2 of 178 vs. 0 of 281, P = 0.15). These results suggest that ATM germline heterozygosity does not play a role in chronic lymphocytic leukemia initiation but rather influences rapid disease progression through ATM loss.
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Affiliation(s)
- Anna Skowronska
- School of Cancer Sciences, University of Birmingham, University of Birmingham, Birmingham B15 2TT, UK.
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27
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Kracker S, Durandy A. Insights into the B cell specific process of immunoglobulin class switch recombination. Immunol Lett 2011; 138:97-103. [DOI: 10.1016/j.imlet.2011.02.004] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2011] [Revised: 01/31/2011] [Accepted: 02/03/2011] [Indexed: 10/18/2022]
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28
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DNAM-1 ligand expression on Ag-stimulated T lymphocytes is mediated by ROS-dependent activation of DNA-damage response: relevance for NK–T cell interaction. Blood 2011; 117:4778-86. [DOI: 10.1182/blood-2010-08-300954] [Citation(s) in RCA: 103] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Abstract
An important role for natural killer (NK) cells in the regulation of T-cell responses is emerging, although the receptor pairs regulating the NK–T-cell interaction have still not been identified. We found that superantigen-stimulated T cells express Nectin-2 (CD112) and poliovirus receptor (PVR; CD155), the ligands of the activating NK receptor DNAX accessory molecule-1 (DNAM-1; CD226). Interestingly, only PVR was present at the T cell surface, particularly on cells in the S and G2/M phases of the cell cycle. The up-regulation of PVR expression involves DNA-damage response (DDR)–dependent pathways, because we found that pharmacologic inhibition of ATM and ATR kinases reduced PVR expression and that PVR was almost exclusively induced on cells expressing the DDR marker γH2AX. Oxidative stress contributed to DDR activation, and our results showed impaired PVR levels in the presence of the reactive oxygen species (ROS) scavenger N-acetyl-cysteine (NAC), being monocytes the main ROS source needed for optimal PVR expression on activated T cells. Interestingly, in accordance with ligand expression, NK cells lysed allogeneic proliferating more efficiently than nonproliferating T lymphocytes, with a mechanism requiring the cooperation between DNAM-1 and NKG2D. These results could contribute to unraveling the role of NK cells in the down-regulation of T-cell responses in physiologic and pathologic processes such as autoimmunity or GVHD.
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29
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Duvvuri B, Duvvuri VRSK, Grigull J, Martin A, Pan-Hammarström Q, Wu GE, Larijani M. Altered spectrum of somatic hypermutation in common variable immunodeficiency disease characteristic of defective repair of mutations. Immunogenetics 2010; 63:1-11. [PMID: 20938659 DOI: 10.1007/s00251-010-0483-7] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2010] [Accepted: 09/25/2010] [Indexed: 01/08/2023]
Abstract
Pathogenic common variable immunodeficiency diseases (CVID) are genetic, usually inherited diseases for which a limited number of genetic defects have been implicated. As CVID presents with a wide range of clinical characteristics, there are likely diverse and for the most part unidentified genetic causes. In some individuals, defects in somatic hypermutation (SHM) have been suggested as the underlying cause of CVID. To address the mechanisms of SHM defects in CVID, we conducted a comprehensive mutational analysis of immunoglobulin heavy chain sequences from CVID patients. We identified several remarkably specific alterations in the spectra of SHM in comparison to healthy individuals. We provide evidence that some CVID cases are associated with defective repair of AID-induced mutations by the DNA mismatch repair (MMR) machinery. Our findings together with reports of increased chromosomal radiosensitivity and associated lymphoproliferative disorders amongst CVID patients, suggest that altered DNA damage repair may be a cause of CVID.
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Affiliation(s)
- Bhargavi Duvvuri
- The School of Kinesiology and Health Science, Faculty of Health, York University, Toronto, Ontario, Canada, M3J 1P3.
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30
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Guikema JEJ, Schrader CE, Brodsky MH, Linehan EK, Richards A, El Falaky N, Li DH, Sluss HK, Szomolanyi-Tsuda E, Stavnezer J. p53 represses class switch recombination to IgG2a through its antioxidant function. THE JOURNAL OF IMMUNOLOGY 2010; 184:6177-87. [PMID: 20483782 DOI: 10.4049/jimmunol.0904085] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
Ig class switch recombination (CSR) occurs in activated mature B cells, and causes an exchange of the IgM isotype for IgG, IgE, or IgA isotypes, which increases the effectiveness of the humoral immune response. DNA ds breaks in recombining switch (S) regions, where CSR occurs, are required for recombination. Activation-induced cytidine deaminase initiates DNA ds break formation by deamination of cytosines in S regions. This reaction requires reactive oxygen species (ROS) intermediates, such as hydroxyl radicals. In this study we show that the ROS scavenger N-acetylcysteine inhibits CSR. We also demonstrate that IFN-gamma treatment, which is used to induce IgG2a switching, increases intracellular ROS levels, and activates p53 in switching B cells, and show that p53 inhibits IgG2a class switching through its antioxidant-regulating function. Finally, we show that p53 inhibits DNA breaks and mutations in S regions in B cells undergoing CSR, suggesting that p53 inhibits the activity of activation-induced cytidine deaminase.
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Affiliation(s)
- Jeroen E J Guikema
- Department of Molecular Genetics and Microbiology, University of Massachusetts Medical School, Worcester, MA 01655, USA
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31
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Stavnezer J, Björkman A, Du L, Cagigi A, Pan-Hammarström Q. Mapping of Switch Recombination Junctions, a Tool for Studying DNA Repair Pathways during Immunoglobulin Class Switching. Adv Immunol 2010; 108:45-109. [DOI: 10.1016/b978-0-12-380995-7.00003-3] [Citation(s) in RCA: 60] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
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32
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Phenotypic variations between affected siblings with ataxia-telangiectasia: ataxia-telangiectasia in Japan. Int J Hematol 2009; 90:455-462. [PMID: 19705055 DOI: 10.1007/s12185-009-0408-0] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2009] [Revised: 07/31/2009] [Accepted: 08/03/2009] [Indexed: 01/05/2023]
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Kotnis A, Du L, Liu C, Popov SW, Pan-Hammarström Q. Non-homologous end joining in class switch recombination: the beginning of the end. Philos Trans R Soc Lond B Biol Sci 2009; 364:653-65. [PMID: 19008195 PMCID: PMC2660918 DOI: 10.1098/rstb.2008.0196] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
Abstract
Immunoglobulin class switch recombination (CSR) is initiated by a B-cell-specific factor, activation-induced deaminase, probably through deamination of deoxycytidine residues within the switch (S) regions. The initial lesions in the S regions are subsequently processed, resulting in the production of DNA double-strand breaks (DSBs). These breaks will then be recognized, edited and repaired, finally leading to the recombination of the two S regions. Two major repair pathways have been implicated in CSR, the predominant non-homologous end joining (NHEJ) and the alternative end-joining (A-EJ) pathways. The former requires not only components of the ‘classical’ NHEJ machinery, i.e. Ku70/Ku80, DNA-dependent protein kinase catalytic subunit, DNA ligase IV and XRCC4, but also a number of DNA-damage sensors or adaptors, such as ataxia–telangiectasia mutated, γH2AX, 53BP1, MDC1, the Mre11–Rad50–NBS1 complex and the ataxia telangiectasia and Rad3-related protein (ATR). The latter pathway is not well characterized yet and probably requires microhomologies. In this review, we will focus on the current knowledge of the predominant NHEJ pathway in CSR and will also give a perspective on the A-EJ pathway.
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Affiliation(s)
- Ashwin Kotnis
- Division of Clinical Immunology, Department of Laboratory Medicine, Karolinska Institutet at Karolinska University Hospital Huddinge, 14186 Stockholm, Sweden
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Du L, van der Burg M, Popov SW, Kotnis A, van Dongen JJM, Gennery AR, Pan-Hammarström Q. Involvement of Artemis in nonhomologous end-joining during immunoglobulin class switch recombination. ACTA ACUST UNITED AC 2008; 205:3031-40. [PMID: 19075292 PMCID: PMC2605234 DOI: 10.1084/jem.20081915] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
DNA double-strand breaks (DSBs) introduced in the switch (S) regions are intermediates during immunoglobulin class switch recombination (CSR). These breaks are subsequently recognized, processed, and joined, leading to recombination of the two S regions. Nonhomologous end-joining (NHEJ) is believed to be the principle mechanism involved in DSB repair during CSR. One important component in NHEJ, Artemis, has however been considered to be dispensable for efficient CSR. In this study, we have characterized the S recombinational junctions from Artemis-deficient human B cells. Sμ–Sα junctions could be amplified from all patients tested and were characterized by a complete lack of “direct” end-joining and a remarkable shift in the use of an alternative, microhomology-based end-joining pathway. Sμ–Sγ junctions could only be amplified from one patient who carries “hypomorphic” mutations. Although these Sμ–Sγ junctions appear to be normal, a significant increase of an unusual type of sequential switching from immunoglobulin (Ig)M, through one IgG subclass, to a different IgG subclass was observed, and the Sγ–Sγ junctions showed long microhomologies. Thus, when the function of Artemis is impaired, varying modes of CSR junction resolution may be used for different S regions. Our findings strongly link Artemis to the predominant NHEJ pathway during CSR.
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Affiliation(s)
- Likun Du
- Clinical Immunology, Department of Laboratory Medicine, Karolinska Institutet at Karolinska University Hospital Huddinge, Stockholm, Sweden
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35
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DNA damage and repair during lymphoid development: antigen receptor diversity, genomic integrity and lymphomagenesis. Immunol Res 2008; 41:103-22. [PMID: 18214391 DOI: 10.1007/s12026-008-8015-3] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Lymphocyte maturation requires generation of a large diversity of antigen receptors, which involves somatic rearrangements at the antigen receptor genes in a process termed V(D)J recombination. Upon encountering specific antigens, B-lymphocytes undergo rearrangements in the constant region of the immunoglobulin genes to optimize immune responses in a process called class switch recombination. Activated B-cells also undergo somatic hypermutation in the variable regions of the immunoglobulin genes to enhance their antigenic affinity. These somatic events are initiated by the infliction of DNA lesions within the antigen receptor genes that are strictly confined to a specific developmental window and cell-cycle stage. DNA lesions are then repaired by one of the general DNA repair mechanisms, such as non-homologous end-joining. Mutations in key factors of these pathways lead to the interruption of these processes and immunodeficiency, making it possible to study the mechanisms of cellular response to DNA lesions and their repair. This review briefly summarizes some of the recently developed animal models with focus on current advances in the understanding of the mechanism of DNA end-joining activities, and its role in the maintenance of genomic stability and the prevention of tumorigenesis.
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36
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Du L, Dunn-Walters DK, Chrzanowska KH, Stankovic T, Kotnis A, Li X, Lu J, Eggertsen G, Brittain C, Popov SW, Gennery AR, Taylor AMR, Pan-Hammarström Q. A regulatory role for NBS1 in strand-specific mutagenesis during somatic hypermutation. PLoS One 2008; 3:e2482. [PMID: 18575580 PMCID: PMC2423615 DOI: 10.1371/journal.pone.0002482] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2008] [Accepted: 05/14/2008] [Indexed: 11/18/2022] Open
Abstract
Activation-induced cytidine deaminase (AID) is believed to initiate somatic hypermutation (SHM) by deamination of deoxycytidines to deoxyuridines within the immunoglobulin variable regions genes. The deaminated bases can subsequently be replicated over, processed by base excision repair or mismatch repair, leading to introduction of different types of point mutations (G/C transitions, G/C transversions and A/T mutations). It is evident that the base excision repair pathway is largely dependent on uracil-DNA glycosylase (UNG) through its uracil excision activity. It is not known, however, which endonuclease acts in the step immediately downstream of UNG, i.e. that cleaves at the abasic sites generated by the latter. Two candidates have been proposed, an apurinic/apyrimidinic endonuclease (APE) and the Mre11-Rad50-NBS1 complex. The latter is intriguing as this might explain how the mutagenic pathway is primed during SHM. We have investigated the latter possibility by studying the in vivo SHM pattern in B cells from ataxia-telangiectasia-like disorder (Mre11 deficient) and Nijmegen breakage syndrome (NBS1 deficient) patients. Our results show that, although the pattern of mutations in the variable heavy chain (V(H)) genes was altered in NBS1 deficient patients, with a significantly increased number of G (but not C) transversions occurring in the SHM and/or AID targeting hotspots, the general pattern of mutations in the V(H) genes in Mre11 deficient patients was only slightly altered, with an increased frequency of A to C transversions. The Mre11-Rad50-NBS1 complex is thus unlikely to be the major nuclease involved in cleavage of the abasic sites during SHM, whereas NBS1 might have a specific role in regulating the strand-biased repair during phase Ib mutagenesis.
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Affiliation(s)
- Likun Du
- Division of Clinical Immunology, Department of Laboratory Medicine, Karolinska Institutet at Karolinska University Hospital Huddinge, Stockholm, Sweden
| | - Deborah K. Dunn-Walters
- Department of Immunobiology, King's College London School of Medicine, Guy's Hospital, London, United Kingdom
| | | | - Tanja Stankovic
- The University of Birmingham CRC Institute for Cancer Studies, the Medical School Edghaston, Birmingham, United Kingdom
| | - Ashwin Kotnis
- Division of Clinical Immunology, Department of Laboratory Medicine, Karolinska Institutet at Karolinska University Hospital Huddinge, Stockholm, Sweden
| | - Xin Li
- Division of Clinical Immunology, Department of Laboratory Medicine, Karolinska Institutet at Karolinska University Hospital Huddinge, Stockholm, Sweden
| | - Jiayi Lu
- Division of Clinical Immunology, Department of Laboratory Medicine, Karolinska Institutet at Karolinska University Hospital Huddinge, Stockholm, Sweden
| | - Gösta Eggertsen
- Division of Clinical Chemistry, Department of Laboratory Medicine, Karolinska Institutet at Karolinska University Hospital Huddinge, Stockholm, Sweden
| | - Claire Brittain
- The University of Birmingham CRC Institute for Cancer Studies, the Medical School Edghaston, Birmingham, United Kingdom
| | - Sergey W. Popov
- Division of Clinical Immunology, Department of Laboratory Medicine, Karolinska Institutet at Karolinska University Hospital Huddinge, Stockholm, Sweden
| | - Andrew R. Gennery
- Department of Pediatric Immunology, Newcastle General Hospital, Newcastle, United Kingdom
| | - A. Malcolm R. Taylor
- The University of Birmingham CRC Institute for Cancer Studies, the Medical School Edghaston, Birmingham, United Kingdom
| | - Qiang Pan-Hammarström
- Division of Clinical Immunology, Department of Laboratory Medicine, Karolinska Institutet at Karolinska University Hospital Huddinge, Stockholm, Sweden
- * E-mail:
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Primary immunodeficiency diseases: an update from the International Union of Immunological Societies Primary Immunodeficiency Diseases Classification Committee. J Allergy Clin Immunol 2007; 120:776-94. [PMID: 17952897 DOI: 10.1016/j.jaci.2007.08.053] [Citation(s) in RCA: 295] [Impact Index Per Article: 17.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Primary immunodeficiency diseases (PIDs) are a genetically heterogeneous group of disorders that affect distinct components of the innate and adaptive immune system, such as neutrophils, macrophages, dendritic cells, complement proteins, natural killer cells, and T and B lymphocytes. The study of these diseases has provided essential insights into the functioning of the immune system. More than 120 distinct genes have been identified, whose abnormalities account for more than 150 different forms of PID. The complexity of the genetic,immunologic, and clinical features of PID has prompted the need for their classification, with the ultimate goal of facilitating diagnosis and treatment. To serve this goal, an international committee of experts has met every 2 years since 1970. In its last meeting in Jackson Hole, Wyo, after 3 days of intense scientific presentations and discussions, the committee has updated the classification of PID, as reported in this article.
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Notarangelo LD, Plebani A, Mazzolari E, Soresina A, Bondioni MP. Genetic causes of bronchiectasis: primary immune deficiencies and the lung. Respiration 2007; 74:264-75. [PMID: 17534129 DOI: 10.1159/000101784] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
Primary immune deficiencies (PID) comprise a heterogeneous group of genetically determined disorders that affect development and/or function of innate or adaptive immunity. Consequently, patients with PID suffer from recurrent and/or severe infections that frequently involve the lung. While the nature of the immune defect often dictates the type of pathogens that may cause lung infection, there is substantial overlap of radiological findings, so that appropriate laboratory tests are mandatory to define the nature of the immune defect and to prompt appropriate treatment. At the same time, the recent identification of a large number of PID-causing genes now allows early, even presymptomatic diagnosis, thus representing an essential tool for prevention of lung damage. This review article describes the most common forms of PID, their cellular and molecular bases, and the associated lung abnormalities, and reports on available treatment.
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Affiliation(s)
- Luigi D Notarangelo
- Division of Immunology, Children's Hospital, Harvard Medical School, Boston, MA 02115, USA.
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Jankovic M, Nussenzweig A, Nussenzweig MC. Antigen receptor diversification and chromosome translocations. Nat Immunol 2007; 8:801-8. [PMID: 17641661 DOI: 10.1038/ni1498] [Citation(s) in RCA: 48] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Double-stranded DNA breaks (DSBs) can result in chromosomal abnormalities, including deletions, translocations and aneuploidy, which can promote neoplastic transformation. DSBs arise accidentally during DNA replication and can be induced by environmental factors such as ultraviolet light or ionizing radiation, and they are generated during antigen receptor-diversification reactions in lymphocytes. Cellular pathways that maintain genomic integrity use sophisticated mechanisms that recognize and repair all DSBs regardless of their origin. Such pathways, along with DNA-damage checkpoints, ensure that either the damage is properly repaired or cells with damaged DNA are eliminated. Here we review how impaired DNA-repair or DNA-damage checkpoints can lead to genetic instability and predispose lymphocytes undergoing diversification of antigen receptor genes to malignant transformation.
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Affiliation(s)
- Mila Jankovic
- Laboratory of Molecular Immunology, The Rockefeller University, New York, New York 10021-6399, USA
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Pan-Hammarström Q, Zhao Y, Hammarström L. Class switch recombination: a comparison between mouse and human. Adv Immunol 2007; 93:1-61. [PMID: 17383538 DOI: 10.1016/s0065-2776(06)93001-6] [Citation(s) in RCA: 71] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Humans and mice separated more than 60 million years ago. Since then, evolution has led to a multitude of changes in their genomic sequences. The divergence of genes has resulted in differences both in the innate and adaptive immune systems. In this chapter, we focus on species difference with regard to immunoglobulin class switch recombination (CSR). We have compared the immunoglobulin constant region gene loci from human and mouse, with an emphasis on the switch regions, germ line transcription promoters, and 3' enhancers. We have also compared pathways/factors that are involved in CSR. Although there are remarkable similarities in the cellular machinery involved in CSR, there are also a number of unique features in each species.
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Affiliation(s)
- Qiang Pan-Hammarström
- Department of Laboratory Medicine, Division of Clinical Immunology, Karolinska University Hospital Huddinge, SE-14186 Stockholm, Sweden
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