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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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Björkman A, Du L, Felgentreff K, Rosner C, Pankaj Kamdar R, Kokaraki G, Matsumoto Y, Davies EG, van der Burg M, Notarangelo LD, Hammarström L, Pan-Hammarström Q. DNA-PKcs Is Involved in Ig Class Switch Recombination in Human B Cells. THE JOURNAL OF IMMUNOLOGY 2015; 195:5608-15. [DOI: 10.4049/jimmunol.1501633] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/21/2015] [Accepted: 10/06/2015] [Indexed: 01/03/2023]
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Volk T, Pannicke U, Reisli I, Bulashevska A, Ritter J, Björkman A, Schäffer AA, Fliegauf M, Sayar EH, Salzer U, Fisch P, Pfeifer D, Di Virgilio M, Cao H, Yang F, Zimmermann K, Keles S, Caliskaner Z, Güner SÜ, Schindler D, Hammarström L, Rizzi M, Hummel M, Pan-Hammarström Q, Schwarz K, Grimbacher B. DCLRE1C (ARTEMIS) mutations causing phenotypes ranging from atypical severe combined immunodeficiency to mere antibody deficiency. Hum Mol Genet 2015; 24:7361-72. [PMID: 26476407 DOI: 10.1093/hmg/ddv437] [Citation(s) in RCA: 59] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2015] [Accepted: 10/12/2015] [Indexed: 11/14/2022] Open
Abstract
Null mutations in genes involved in V(D)J recombination cause a block in B- and T-cell development, clinically presenting as severe combined immunodeficiency (SCID). Hypomorphic mutations in the non-homologous end-joining gene DCLRE1C (encoding ARTEMIS) have been described to cause atypical SCID, Omenn syndrome, Hyper IgM syndrome and inflammatory bowel disease-all with severely impaired T-cell immunity. By whole-exome sequencing, we investigated the molecular defect in a consanguineous family with three children clinically diagnosed with antibody deficiency. We identified perfectly segregating homozygous variants in DCLRE1C in three index patients with recurrent respiratory tract infections, very low B-cell numbers and serum IgA levels. In patients, decreased colony survival after irradiation, impaired proliferative response and reduced counts of naïve T cells were observed in addition to a restricted T-cell receptor repertoire, increased palindromic nucleotides in the complementarity determining regions 3 and long stretches of microhomology at switch junctions. Defective V(D)J recombination was complemented by wild-type ARTEMIS protein in vitro. Subsequently, homozygous or compound heterozygous DCLRE1C mutations were identified in nine patients from the same geographic region. We demonstrate that DCLRE1C mutations can cause a phenotype presenting as only antibody deficiency. This novel association broadens the clinical spectrum associated with ARTEMIS mutations. Clinicians should consider the possibility that an immunodeficiency with a clinically mild initial presentation could be a combined immunodeficiency, so as to provide appropriate care for affected patients.
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Affiliation(s)
- Timo Volk
- Center for Chronic Immunodeficiency (CCI), University Medical Center Freiburg and University of Freiburg, Freiburg, Germany
| | - Ulrich Pannicke
- Institute for Transfusion Medicine, University Ulm, Ulm, Germany
| | | | - Alla Bulashevska
- Center for Chronic Immunodeficiency (CCI), University Medical Center Freiburg and University of Freiburg, Freiburg, Germany
| | - Julia Ritter
- Institute of Pathology, Campus Benjamin Franklin, Charité - University Medicine Berlin, Berlin, Germany
| | - Andrea Björkman
- Division of Clinical Immunology and Transfusion Medicine, Department of Laboratory Medicine, Karolinska University Hospital Huddinge, Stockholm, Sweden
| | - Alejandro A Schäffer
- Department of Health and Human Services, National Center for Biotechnology Information, National Institutes of Health, Bethesda, MD, USA
| | - Manfred Fliegauf
- Center for Chronic Immunodeficiency (CCI), University Medical Center Freiburg and University of Freiburg, Freiburg, Germany
| | | | - Ulrich Salzer
- Center for Chronic Immunodeficiency (CCI), University Medical Center Freiburg and University of Freiburg, Freiburg, Germany
| | - Paul Fisch
- Center for Pathology, Medical Center, University of Freiburg, Freiburg, Germany
| | - Dietmar Pfeifer
- Department of Hematology, Oncology and Stem Cell Transplantation, University Medical Center, Freiburg, Germany
| | | | - Hongzhi Cao
- Science and Technology Department, BGI-Shenzhen, Shenzhen, China
| | - Fang Yang
- Science and Technology Department, BGI-Shenzhen, Shenzhen, China
| | - Karin Zimmermann
- Institute of Pathology, Campus Benjamin Franklin, Charité - University Medicine Berlin, Berlin, Germany
| | - Sevgi Keles
- Department of Pediatric Immunology and Allergy
| | - Zafer Caliskaner
- Department of Immunology and Allergy, Meram Medical Faculty, Necmettin Erbakan University, Konya, Turkey
| | | | - Detlev Schindler
- Institute of Human Genetics, University of Würzburg, Würzburg, Germany
| | - Lennart Hammarström
- Institute of Pathology, Campus Benjamin Franklin, Charité - University Medicine Berlin, Berlin, Germany
| | - Marta Rizzi
- Center for Chronic Immunodeficiency (CCI), University Medical Center Freiburg and University of Freiburg, Freiburg, Germany
| | - Michael Hummel
- Institute of Pathology, Campus Benjamin Franklin, Charité - University Medicine Berlin, Berlin, Germany
| | - Qiang Pan-Hammarström
- Division of Clinical Immunology and Transfusion Medicine, Department of Laboratory Medicine, Karolinska University Hospital Huddinge, Stockholm, Sweden
| | - Klaus Schwarz
- Institute for Transfusion Medicine, University Ulm, Ulm, Germany, Institute for Clinical Transfusion Medicine and Immunogenetics Ulm, German Red Cross Blood Service Baden-Württemberg, Hessen, Germany and
| | - Bodo Grimbacher
- Center for Chronic Immunodeficiency (CCI), University Medical Center Freiburg and University of Freiburg, Freiburg, Germany, Institute of Immunity and Transplantation, University College London, Royal Free Campus, London, UK
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Guo C, Nakazawa Y, Woodbine L, Björkman A, Shimada M, Fawcett H, Jia N, Ohyama K, Li TS, Nagayama Y, Mitsutake N, Pan-Hammarström Q, Gennery AR, Lehmann AR, Jeggo PA, Ogi T. XRCC4 deficiency in human subjects causes a marked neurological phenotype but no overt immunodeficiency. J Allergy Clin Immunol 2015; 136:1007-17. [PMID: 26255102 DOI: 10.1016/j.jaci.2015.06.007] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2015] [Revised: 05/27/2015] [Accepted: 06/08/2015] [Indexed: 01/18/2023]
Abstract
BACKGROUND Nonhomologous end-joining (NHEJ) is the major DNA double-strand break (DSB) repair mechanism in human cells. The final rejoining step requires DNA ligase IV (LIG4) together with the partner proteins X-ray repair cross-complementing protein 4 (XRCC4) and XRCC4-like factor. Patients with mutations in genes encoding LIG4, XRCC4-like factor, or the other NHEJ proteins DNA-dependent protein kinase catalytic subunit and Artemis are DSB repair defective and immunodeficient because of the requirement for NHEJ during V(D)J recombination. OBJECTIVE We found a patient displaying microcephaly and progressive ataxia but a normal immune response. We sought to determine pathogenic mutations and to describe the molecular pathogenesis of the patient. METHODS We performed next-generation exome sequencing. We evaluated the DSB repair activities and V(D)J recombination capacity of the patient's cells, as well as performing a standard blood immunologic characterization. RESULTS We identified causal mutations in the XRCC4 gene. The patient's cells are radiosensitive and display the most severe DSB repair defect we have encountered using patient-derived cell lines. In marked contrast, a V(D)J recombination plasmid assay revealed that the patient's cells did not display the junction abnormalities that are characteristic of other NHEJ-defective cell lines. The mutant protein can interact efficiently with LIG4 and functions normally in in vitro assays and when transiently expressed in vivo. However, the mutation makes the protein unstable, and it undergoes proteasome-mediated degradation. CONCLUSION Our findings reveal a novel separation of impact phenotype: there is a pronounced DSB repair defect and marked clinical neurological manifestation but no clinical immunodeficiency.
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Affiliation(s)
- Chaowan Guo
- Department of Genetics, Research Institute of Environmental Medicine (RIeM), Nagoya University, Furo-cho, Chikusa-ku, Nagoya, Japan; Nagasaki University Research Centre for Genomic Instability and Carcinogenesis (NRGIC), Nagasaki, Japan; Department of Molecular Medicine, Atomic Bomb Disease Institute, Nagasaki University, Nagasaki, Japan
| | - Yuka Nakazawa
- Department of Genetics, Research Institute of Environmental Medicine (RIeM), Nagoya University, Furo-cho, Chikusa-ku, Nagoya, Japan; Nagasaki University Research Centre for Genomic Instability and Carcinogenesis (NRGIC), Nagasaki, Japan; Department of Molecular Medicine, Atomic Bomb Disease Institute, Nagasaki University, Nagasaki, Japan
| | - Lisa Woodbine
- Genome Damage and Stability Centre, University of Sussex, Falmer, Brighton, United Kingdom
| | - Andrea Björkman
- Department of Laboratory Medicine, Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden
| | - Mayuko Shimada
- Nagasaki University Research Centre for Genomic Instability and Carcinogenesis (NRGIC), Nagasaki, Japan; Department of Molecular Medicine, Atomic Bomb Disease Institute, Nagasaki University, Nagasaki, Japan
| | - Heather Fawcett
- Genome Damage and Stability Centre, University of Sussex, Falmer, Brighton, United Kingdom
| | - Nan Jia
- Department of Genetics, Research Institute of Environmental Medicine (RIeM), Nagoya University, Furo-cho, Chikusa-ku, Nagoya, Japan; Nagasaki University Research Centre for Genomic Instability and Carcinogenesis (NRGIC), Nagasaki, Japan; Department of Molecular Medicine, Atomic Bomb Disease Institute, Nagasaki University, Nagasaki, Japan
| | - Kaname Ohyama
- Nagasaki University Research Centre for Genomic Instability and Carcinogenesis (NRGIC), Nagasaki, Japan; Course of Pharmaceutical Sciences, Graduate School of Biomedical Sciences, Nagasaki University, Nagasaki, Japan
| | - Tao-Sheng Li
- Department of Stem Cell Biology, Atomic Bomb Disease Institute, Nagasaki University, Nagasaki, Japan
| | - Yuji Nagayama
- Department of Molecular Medicine, Atomic Bomb Disease Institute, Nagasaki University, Nagasaki, Japan
| | - Norisato Mitsutake
- Nagasaki University Research Centre for Genomic Instability and Carcinogenesis (NRGIC), Nagasaki, Japan; Department of Radiation Medical Sciences, Atomic Bomb Disease Institute, Nagasaki University, Nagasaki, Japan
| | - Qiang Pan-Hammarström
- Department of Laboratory Medicine, Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden
| | - Andrew R Gennery
- Institute of Cellular Medicine, Newcastle University, Newcastle upon Tyne Hospitals NHS Foundation Trust, Newcastle upon Tyne, United Kingdom
| | - Alan R Lehmann
- Genome Damage and Stability Centre, University of Sussex, Falmer, Brighton, United Kingdom
| | - Penny A Jeggo
- Genome Damage and Stability Centre, University of Sussex, Falmer, Brighton, United Kingdom.
| | - Tomoo Ogi
- Department of Genetics, Research Institute of Environmental Medicine (RIeM), Nagoya University, Furo-cho, Chikusa-ku, Nagoya, Japan; Nagasaki University Research Centre for Genomic Instability and Carcinogenesis (NRGIC), Nagasaki, Japan; Department of Molecular Medicine, Atomic Bomb Disease Institute, Nagasaki University, Nagasaki, Japan; Microbial Genetics Laboratory, Genetic Strains Research Center, National Institute of Genetics, Mishima, Japan.
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Aberrant recombination and repair during immunoglobulin class switching in BRCA1-deficient human B cells. Proc Natl Acad Sci U S A 2015; 112:2157-62. [PMID: 25646469 DOI: 10.1073/pnas.1418947112] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Breast cancer type 1 susceptibility protein (BRCA1) has a multitude of functions that contribute to genome integrity and tumor suppression. Its participation in the repair of DNA double-strand breaks (DSBs) during homologous recombination (HR) is well recognized, whereas its involvement in the second major DSB repair pathway, nonhomologous end-joining (NHEJ), remains controversial. Here we have studied the role of BRCA1 in the repair of DSBs in switch (S) regions during immunoglobulin class switch recombination, a physiological, deletion/recombination process that relies on the classical NHEJ machinery. A shift to the use of microhomology-based, alternative end-joining (A-EJ) and increased frequencies of intra-S region deletions as well as insertions of inverted S sequences were observed at the recombination junctions amplified from BRCA1-deficient human B cells. Furthermore, increased use of long microhomologies was found at recombination junctions derived from E3 ubiquitin-protein ligase RNF168-deficient, Fanconi anemia group J protein (FACJ, BRIP1)-deficient, or DNA endonuclease RBBP8 (CtIP)-compromised cells, whereas an increased frequency of S-region inversions was observed in breast cancer type 2 susceptibility protein (BRCA2)-deficient cells. Thus, BRCA1, together with its interaction partners, seems to play an important role in repairing DSBs generated during class switch recombination by promoting the classical NHEJ pathway. This may not only provide a general mechanism underlying BRCA1's function in maintaining genome stability and tumor suppression but may also point to a previously unrecognized role of BRCA1 in B-cell lymphomagenesis.
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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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Du L, Peng R, Björkman A, Filipe de Miranda N, Rosner C, Kotnis A, Berglund M, Liu C, Rosenquist R, Enblad G, Sundström C, Hojjat-Farsangi M, Rabbani H, Teixeira MR, Revy P, Durandy A, Zeng Y, Gennery AR, de Villartay JP, Pan-Hammarström Q. Cernunnos influences human immunoglobulin class switch recombination and may be associated with B cell lymphomagenesis. ACTA ACUST UNITED AC 2012; 209:291-305. [PMID: 22312109 PMCID: PMC3280866 DOI: 10.1084/jem.20110325] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
B cells from Cernunnos-deficient patients contain aberrant class switch recombination junctions, and a dominant-negative Cernunnos mutation was detected in a diffuse large B cell lymphoma sample. Cernunnos is involved in the nonhomologous end-joining (NHEJ) process during DNA double-strand break (DSB) repair. Here, we studied immunoglobulin (Ig) class switch recombination (CSR), a physiological process which relies on proper repair of the DSBs, in B cells from Cernunnos-deficient patients. The pattern of in vivo generated CSR junctions is altered in these cells, with unusually long microhomologies and a lack of direct end-joining. The CSR junctions from Cernunnos-deficient patients largely resemble those from patients lacking DNA ligase IV, Artemis, or ATM, suggesting that these factors are involved in the same end-joining pathway during CSR. By screening 269 mature B cell lymphoma biopsies, we also identified a somatic missense Cernunnos mutation in a diffuse large B cell lymphoma sample. This mutation has a dominant-negative effect on joining of a subset of DNA ends in an in vitro NHEJ assay. Translocations involving both Ig heavy chain loci and clonal-like, dynamic IgA switching activities were observed in this tumor. Collectively, our results suggest a link between defects in the Cernunnos-dependent NHEJ pathway and aberrant CSR or switch translocations during the development of B cell malignancies.
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Affiliation(s)
- Likun Du
- Department of Laboratory Medicine, Karolinska Institutet, Karolinska University Hospital, Huddinge, SE-14186 Stockholm, Sweden
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Artemis splice defects cause atypical SCID and can be restored in vitro by an antisense oligonucleotide. Genes Immun 2011; 12:434-44. [PMID: 21390052 DOI: 10.1038/gene.2011.16] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Artemis deficiency is known to result in classical T-B- severe combined immunodeficiency (SCID) in case of Artemis null mutations, or Omenn's syndrome in case of hypomorphic mutations in the Artemis gene. We describe two unrelated patients with a relatively mild clinical T-B- SCID phenotype, caused by different homozygous Artemis splice-site mutations. The splice-site mutations concern either dysfunction of a 5' splice-site or an intronic point mutation creating a novel 3' splice-site, resulting in mutated Artemis protein with residual activity or low levels of wild type (WT) Artemis transcripts. During the first 10 years of life, the patients suffered from recurrent infections necessitating antibiotic prophylaxis and intravenous immunoglobulins. Both mutations resulted in increased ionizing radiation sensitivity and insufficient variable, diversity and joining (V(D)J) recombination, causing B-lymphopenia and exhaustion of the naive T-cell compartment. The patient with the novel 3' splice-site had progressive granulomatous skin lesions, which disappeared after stem cell transplantation (SCT). We showed that an alternative approach to SCT can, in principle, be used in this case; an antisense oligonucleotide (AON) covering the intronic mutation restored WT Artemis transcript levels and non-homologous end-joining pathway activity in the patient fibroblasts.
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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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Abstract
Abstract
Nonhomologous end-joining DNA repair factors, including Artemis, are all required for the repair of DNA double-strand breaks, which occur during the assembly of the variable antigen recognition domain of B-cell receptors and T-cell receptors through the V(D)J recombination. Mature B cells further shape their immunoglobulin repertoire on antigen recognition notably through the class switch recombination (CSR) process. To analyze the role of Artemis during CSR, we developed a mature B-cell–specific Artemis conditional knockout mouse to bypass the absence of B cells caused by its early deficit. Although CSR is not overwhelmingly affected in these mice, class switching to certain isotypes is clearly reduced both in vitro on B-cell activation and in vivo after keyhole limpet hemocyanin immunization. The reduced CSR in Artemis-deficient B cells is accompanied by the increase in DNA microhomology usage at CSR junctions, the imprint of an alternative DNA end-joining pathway. Likewise, significant increase in DNA microhomology usage is the signature of CSR junctions obtained from human RS-SCID patients harboring hypomorphic Artemis mutations. Altogether, this indicates that Artemis participates in the repair of a subset of DNA breaks generated during CSR.
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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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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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Pan-Hammarström Q, Lähdesmäki A, Zhao Y, Du L, Zhao Z, Wen S, Ruiz-Perez VL, Dunn-Walters DK, Goodship JA, Hammarström L. Disparate roles of ATR and ATM in immunoglobulin class switch recombination and somatic hypermutation. ACTA ACUST UNITED AC 2006; 203:99-110. [PMID: 16390936 PMCID: PMC2118080 DOI: 10.1084/jem.20050595] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Class switch recombination (CSR) and somatic hypermutation (SHM) are mechanistically related processes initiated by activation-induced cytidine deaminase. Here, we have studied the role of ataxia telangiectasia and Rad3-related protein (ATR) in CSR by analyzing the recombinational junctions, resulting from in vivo switching, in cells from patients with mutations in the ATR gene. The proportion of cells that have switched to immunoglobulin (Ig)A and IgG in the peripheral blood seems to be normal in ATR-deficient (ATRD) patients and the recombined S regions show a normal “blunt end-joining,” but impaired end joining with partially complementary (1–3 bp) DNA ends. There was also an increased usage of microhomology at the μ-α switch junctions, but only up to 9 bp, suggesting that the end-joining pathway requiring longer microhomologies (≥10 bp) may be ATR dependent. The SHM pattern in the Ig variable heavy chain genes is altered, with fewer mutations occurring at A and more mutations at T residues and thus a loss of strand bias in targeting A/T pairs within certain hotspots. These data suggest that the role of ATR is partially overlapping with that of ataxia telangiectasia–mutated protein, but that the former is also endowed with unique functional properties in the repair processes during CSR and SHM.
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Affiliation(s)
- Qiang Pan-Hammarström
- Division of Clinical Immunology, Department of Laboratory Medicine, Karolinska University Hospital, Huddinge, SE-14186 Stockholm, Sweden.
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Abstract
This review discusses evolution of the process of Ig heavy chain class switching, relating it to the first appearance of somatic hypermutation (SHM) of variable region genes. First, we discuss recent findings on the mechanism of class switch recombination (CSR) in mice and humans, and then review the mechanisms of expression of Ig heavy chain isotypes from fishes to mammals. Importantly, activation-induced cytidine deaminase (AID), which is essential for CSR and somatic hypermutation, is found in fishes. Although at least some fishes are likely to undergo SHM, CSR is highly unlikely to occur in this group. We discuss the first appearance of CSR in amphibians and how it differs in birds and mammals.
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Affiliation(s)
- Janet Stavnezer
- Department of Molecular Genetics and Microbiology, Program in Immunology and Virology, University of Massachusetts Medical School, 55 Lake Ave N, Worcester, MA 01655-0122, USA.
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Pan-Hammarström Q, Jones AM, Lähdesmäki A, Zhou W, Gatti RA, Hammarström L, Gennery AR, Ehrenstein MR. Impact of DNA ligase IV on nonhomologous end joining pathways during class switch recombination in human cells. ACTA ACUST UNITED AC 2005; 201:189-94. [PMID: 15657289 PMCID: PMC2212791 DOI: 10.1084/jem.20040772] [Citation(s) in RCA: 121] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Class switch recombination (CSR) is a region-specific, transcriptionally regulated, nonhomologous recombinational process that is initiated by activation-induced cytidine deaminase (AID). The initial lesions in the switch (S) regions are subsequently processed and resolved, leading to recombination of the two targeted S regions. The mechanisms by which repair and ligation of the broken DNA ends occurs is still elusive. Recently, a small number of patients lacking DNA ligase IV, a critical component of the nonhomologous end joining (NHEJ) machinery, have been identified. We show that these patients display a considerably increased donor/acceptor homology at Sμ–Sα junctions compared with healthy controls. In contrast, Sμ–Sγ junctions show an increased frequency of insertions but no increase in junctional homology. These altered patterns of junctional resolution may be related to differences in the homology between the Sμ and the downstream isotype S regions, and could reflect different modes of switch junction resolution when NHEJ is impaired. These findings link DNA ligase IV, and thus NHEJ, to CSR.
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Affiliation(s)
- Qiang Pan-Hammarström
- Clinical Immunology, Department of Laboratory Medicine, Karolinska University Hospital Huddinge, SE-14186 Stockholm, Sweden
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Pan-Hammarström Q, Dai S, Zhao Y, van Dijk-Härd IF, Gatti RA, Børresen-Dale AL, Hammarström L. ATM is not required in somatic hypermutation of VH, but is involved in the introduction of mutations in the switch mu region. JOURNAL OF IMMUNOLOGY (BALTIMORE, MD. : 1950) 2003; 170:3707-16. [PMID: 12646636 DOI: 10.4049/jimmunol.170.7.3707] [Citation(s) in RCA: 69] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
Class switch recombination (CSR) and somatic hypermutation (SHM) are mechanistically related processes that share common key factors such as activation-induced cytidine deaminase. We have previously shown a role for ATM (mutated in ataxia-telangiectasia) in CSR. In this paper we show that the frequency, distribution, and nature of base pair substitutions in the Ig variable (V) heavy chain genes in ataxia-telangiectasia patients are largely similar to those in normal donors, suggesting a normal SHM process. Characterization of the third complementarity-determining region in B cells from ataxia-telangiectasia patients also shows a normal V(D)J recombination process. SHM-like mutations could be identified in the switch (S) mu region (up to several hundred base pairs upstream of the S mu -S(alpha) breakpoints) in normal in vivo switched human B cells. In the absence of ATM, mutations can still be found in this region, but at less than half the frequency of that in normal donors. The latter mutations are mainly due to transitions (86% compared with 58% in controls) and are biased to A or T nucleotides. An ATM-dependent mechanism, different from that generating SHM in V genes, is therefore likely to be involved in introducing SHM-like mutations in the S region. ATM may thus be one of the factors that is not shared by the CSR and SHM processes.
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Affiliation(s)
- Qiang Pan-Hammarström
- Division of Clinical Immunology, IMPI, Karolinska Institute at Huddinge Hospital, Stockholm, Sweden
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