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Chen R, Lukianova E, van der Loeff IS, Spegarova JS, Willet JDP, James KD, Ryder EJ, Griffin H, IJspeert H, Gajbhiye A, Lamoliatte F, Marin-Rubio JL, Woodbine L, Lemos H, Swan DJ, Pintar V, Sayes K, Ruiz-Morales ER, Eastham S, Dixon D, Prete M, Prigmore E, Jeggo P, Boyes J, Mellor A, Huang L, van der Burg M, Engelhardt KR, Stray-Pedersen A, Erichsen HC, Gennery AR, Trost M, Adams DJ, Anderson G, Lorenc A, Trynka G, Hambleton S. NUDCD3 deficiency disrupts V(D)J recombination to cause SCID and Omenn syndrome. Sci Immunol 2024; 9:eade5705. [PMID: 38787962 DOI: 10.1126/sciimmunol.ade5705] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2022] [Accepted: 04/24/2024] [Indexed: 05/26/2024]
Abstract
Inborn errors of T cell development present a pediatric emergency in which timely curative therapy is informed by molecular diagnosis. In 11 affected patients across four consanguineous kindreds, we detected homozygosity for a single deleterious missense variant in the gene NudC domain-containing 3 (NUDCD3). Two infants had severe combined immunodeficiency with the complete absence of T and B cells (T -B- SCID), whereas nine showed classical features of Omenn syndrome (OS). Restricted antigen receptor gene usage by residual T lymphocytes suggested impaired V(D)J recombination. Patient cells showed reduced expression of NUDCD3 protein and diminished ability to support RAG-mediated recombination in vitro, which was associated with pathologic sequestration of RAG1 in the nucleoli. Although impaired V(D)J recombination in a mouse model bearing the homologous variant led to milder immunologic abnormalities, NUDCD3 is absolutely required for healthy T and B cell development in humans.
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Affiliation(s)
- Rui Chen
- Translational and Clinical Research Institute, Newcastle University, NE2 4HH Newcastle upon Tyne, UK
| | - Elena Lukianova
- Wellcome Sanger Institute, Wellcome Genome Campus, CB10 1SA Hinxton, UK
| | - Ina Schim van der Loeff
- Translational and Clinical Research Institute, Newcastle University, NE2 4HH Newcastle upon Tyne, UK
- Great North Children's Hospital, Newcastle upon Tyne Hospitals NHS Foundation Trust, NE1 4LP Newcastle upon Tyne, UK
| | | | - Joseph D P Willet
- Translational and Clinical Research Institute, Newcastle University, NE2 4HH Newcastle upon Tyne, UK
| | - Kieran D James
- Institute of Immunology and Immunotherapy, University of Birmingham. B15 2TT Birmingham, UK
| | - Edward J Ryder
- Wellcome Sanger Institute, Wellcome Genome Campus, CB10 1SA Hinxton, UK
| | - Helen Griffin
- Translational and Clinical Research Institute, Newcastle University, NE2 4HH Newcastle upon Tyne, UK
| | - Hanna IJspeert
- Department of Immunology, Erasmus University Medical Center, Rotterdam 3000 CA, Netherlands
| | - Akshada Gajbhiye
- Biosciences Institute, Newcastle University, NE2 4HH Newcastle upon Tyne, UK
| | - Frederic Lamoliatte
- Biosciences Institute, Newcastle University, NE2 4HH Newcastle upon Tyne, UK
| | - Jose L Marin-Rubio
- Biosciences Institute, Newcastle University, NE2 4HH Newcastle upon Tyne, UK
| | - Lisa Woodbine
- Genome Damage and Stability Centre, University of Sussex, BN1 9RQ Brighton, UK
| | - Henrique Lemos
- Translational and Clinical Research Institute, Newcastle University, NE2 4HH Newcastle upon Tyne, UK
| | - David J Swan
- Translational and Clinical Research Institute, Newcastle University, NE2 4HH Newcastle upon Tyne, UK
| | - Valeria Pintar
- Translational and Clinical Research Institute, Newcastle University, NE2 4HH Newcastle upon Tyne, UK
| | - Kamal Sayes
- Translational and Clinical Research Institute, Newcastle University, NE2 4HH Newcastle upon Tyne, UK
| | | | - Simon Eastham
- Wellcome Sanger Institute, Wellcome Genome Campus, CB10 1SA Hinxton, UK
| | - David Dixon
- Biosciences Institute, Newcastle University, NE2 4HH Newcastle upon Tyne, UK
| | - Martin Prete
- Wellcome Sanger Institute, Wellcome Genome Campus, CB10 1SA Hinxton, UK
| | - Elena Prigmore
- Wellcome Sanger Institute, Wellcome Genome Campus, CB10 1SA Hinxton, UK
| | - Penny Jeggo
- Genome Damage and Stability Centre, University of Sussex, BN1 9RQ Brighton, UK
| | - Joan Boyes
- Faculty of Biological Sciences, University of Leeds, LS2 9JT Leeds, UK
| | - Andrew Mellor
- Translational and Clinical Research Institute, Newcastle University, NE2 4HH Newcastle upon Tyne, UK
| | - Lei Huang
- Translational and Clinical Research Institute, Newcastle University, NE2 4HH Newcastle upon Tyne, UK
| | - Mirjam van der Burg
- Department of Immunology, Erasmus University Medical Center, Rotterdam 3000 CA, Netherlands
| | - Karin R Engelhardt
- Translational and Clinical Research Institute, Newcastle University, NE2 4HH Newcastle upon Tyne, UK
| | - Asbjørg Stray-Pedersen
- Norwegian National Unit for Newborn Screening, Division of Pediatric and Adolescent Medicine, Oslo University Hospital, Oslo 0424, Norway
| | - Hans Christian Erichsen
- Division of Pediatric and Adolescent Medicine, Oslo University Hospital and Institute of Clinical Medicine, University of Oslo, Oslo 0424, Norway
| | - Andrew R Gennery
- Translational and Clinical Research Institute, Newcastle University, NE2 4HH Newcastle upon Tyne, UK
- Great North Children's Hospital, Newcastle upon Tyne Hospitals NHS Foundation Trust, NE1 4LP Newcastle upon Tyne, UK
| | - Matthias Trost
- Biosciences Institute, Newcastle University, NE2 4HH Newcastle upon Tyne, UK
| | - David J Adams
- Wellcome Sanger Institute, Wellcome Genome Campus, CB10 1SA Hinxton, UK
| | - Graham Anderson
- Institute of Immunology and Immunotherapy, University of Birmingham. B15 2TT Birmingham, UK
| | - Anna Lorenc
- Wellcome Sanger Institute, Wellcome Genome Campus, CB10 1SA Hinxton, UK
| | - Gosia Trynka
- Wellcome Sanger Institute, Wellcome Genome Campus, CB10 1SA Hinxton, UK
- Open Targets, Wellcome Genome Campus, CB10 1SA Hinxton, UK
| | - Sophie Hambleton
- Translational and Clinical Research Institute, Newcastle University, NE2 4HH Newcastle upon Tyne, UK
- Great North Children's Hospital, Newcastle upon Tyne Hospitals NHS Foundation Trust, NE1 4LP Newcastle upon Tyne, UK
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2
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van Schouwenburg PA, van der Burg M, IJspeert H. NGS-Based B-Cell Receptor Repertoire AnalysisRepertoire analyses in the Context of Inborn Errors of Immunity. METHODS IN MOLECULAR BIOLOGY (CLIFTON, N.J.) 2022; 2453:169-190. [PMID: 35622327 DOI: 10.1007/978-1-0716-2115-8_11] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
Inborn errors of immunity (IEI) are genetic defects that can affect both the innate and the adaptive immune system. Patients with IEI usually present with recurrent infections, but many also suffer from immune dysregulation, autoimmunity, and malignancies.Inborn errors of the immune system can cause defects in the development and selection of the B-cell receptor (BCR ) repertoire. Patients with IEI can have a defect in one of the key processes of immune repertoire formation like V(D)J recombination, somatic hypermutation (SHM), class switch recombination (CSR), or (pre-)BCR signalling and proliferation. However, also other genetic defects can lead to quantitative and qualitative differences in the immune repertoire.In this chapter, we will give an overview of protocols that can be used to study the immune repertoire in patients with IEI, provide considerations to take into account before setting up experiments, and discuss analysis of the immune repertoire data using Antigen Receptor Galaxy (ARGalaxy).
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Affiliation(s)
- Pauline A van Schouwenburg
- Department of Pediatrics, Laboratory for Pediatric Immunology, Willem-Alexander Children's Hospital, Leiden University Medical Center, Leiden, 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
| | - Hanna IJspeert
- Department of Immunology, Laboratory Medical Immunology, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands.
- Academic Center for Rare Immunological Diseases (RIDC), Erasmus University Medical Center, Rotterdam, The Netherlands.
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3
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Niewolik D, Schwarz K. Physical ARTEMIS:DNA-PKcs interaction is necessary for V(D)J recombination. Nucleic Acids Res 2022; 50:2096-2110. [PMID: 35150269 PMCID: PMC8887466 DOI: 10.1093/nar/gkac071] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2021] [Revised: 01/12/2022] [Accepted: 01/25/2022] [Indexed: 02/06/2023] Open
Abstract
The nuclease ARTEMIS and the DNA-dependent protein kinase catalytic subunit (DNA-PKcs) are involved in the repair of physiological and pathogenic DNA double strand breaks. Both proteins are indispensable for the hairpin-opening activity in V(D)J recombination and therefore essential for the adaptive immune response. ARTEMIS and DNA-PKcs interact, however experimental evidence for in vivo significance is missing. We demonstrate that mutations abolishing this protein-protein interaction affect nuclease function. In DNA-PKcs, mutation L3062R impairs the physical interaction with ARTEMIS and was previously identified as pathogenic variant, resulting in radiosensitive severe combined immunodeficiency. In ARTEMIS, specific mutations in two conserved regions affect interaction with DNA-PKcs. In combination they impair V(D)J recombination activity, independent of ARTEMIS autoinhibitory self-interaction between the ARTEMIS C-terminus and the N-terminal nuclease domain. We describe small fragments from both proteins, capable of interaction with the corresponding full-length partner proteins: In DNA-PKcs 42 amino acids out of FAT region 2 (PKcs3041-3082) can mediate interaction with ARTEMIS. In the nuclease we have defined 26 amino acids (ARM378-403) as minimal DNA-PKcs interacting fragment. The exact mapping of the ARTEMIS:DNA-PKcs interaction may pave the way for the design of specific inhibitors targeting the repair of DNA double strand breaks.
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Affiliation(s)
- Doris Niewolik
- Institute for Transfusion Medicine, University of Ulm, Ulm 89081, Germany
| | - Klaus Schwarz
- Institute for Transfusion Medicine, University of Ulm, Ulm 89081, Germany.,Institute for Clinical Transfusion Medicine and Immunogenetics Ulm, German Red Cross Blood Service Baden-Wuerttemberg-Hessen, Ulm 89081, Germany
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4
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Wu HY, Zheng Y, Laciak AR, Huang NN, Koszelak-Rosenblum M, Flint AJ, Carr G, Zhu G. Structure and Function of SNM1 Family Nucleases. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2022; 1414:1-26. [PMID: 35708844 DOI: 10.1007/5584_2022_724] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/09/2022]
Abstract
Three human nucleases, SNM1A, SNM1B/Apollo, and SNM1C/Artemis, belong to the SNM1 gene family. These nucleases are involved in various cellular functions, including homologous recombination, nonhomologous end-joining, cell cycle regulation, and telomere maintenance. These three proteins share a similar catalytic domain, which is characterized as a fused metallo-β-lactamase and a CPSF-Artemis-SNM1-PSO2 domain. SNM1A and SNM1B/Apollo are exonucleases, whereas SNM1C/Artemis is an endonuclease. This review contains a summary of recent research on SNM1's cellular and biochemical functions, as well as structural biology studies. In addition, protein structure prediction by the artificial intelligence program AlphaFold provides a different view of the proteins' non-catalytic domain features, which may be used in combination with current results from X-ray crystallography and cryo-EM to understand their mechanism more clearly.
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5
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Xiao F, Lu Y, Wu B, Liu B, Li G, Zhang P, Zhou Q, Sun J, Wang H, Zhou W. High-Frequency Exon Deletion of DNA Cross-Link Repair 1C Accounting for Severe Combined Immunodeficiency May Be Missed by Whole-Exome Sequencing. Front Genet 2021; 12:677748. [PMID: 34421990 PMCID: PMC8372405 DOI: 10.3389/fgene.2021.677748] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2021] [Accepted: 06/28/2021] [Indexed: 11/18/2022] Open
Abstract
Next-generation sequencing (NGS) has been used to detect severe combined immunodeficiency (SCID) in patients, and some patients with DNA cross-link repair 1C (DCLRE1C) variants have been identified. Moreover, some compound variants, such as copy number variants (CNV) and single nucleotide variants (SNV), have been reported. The purpose of this study was to expand the genetic data related to patients with SCID carrying the compound DCLRE1C variant. Whole-exome sequencing (WES) was performed for genetic analysis, and variants were verified by performing Sanger sequencing or quantitative PCR. Moreover, we searched PubMed and summarized the data of the reported variants. Four SCID patients with DCLRE1C variants were identified in this study. WES revealed a homozygous deletion in the DCLRE1C gene from exons 1–5 in patient 1, exons 1–3 deletion and a novel rare variant (c.92T>C, p.L31P) in patient 2, exons 1–3 deletion and a novel rare variant (c.328C>G, p.L110V) in patient 3, and exons 1–4 deletion and a novel frameshift variant (c.449dup, p.His151Alafs*20) in patient 4. Based on literature review, exons 1–3 was recognized as a hotspot region for deletion variation. Moreover, we found that compound variations (CNV + SNV) accounted for approximately 7% variations in all variants. When patients are screened for T-cell receptor excision circles (TRECs), NGS can be used to expand genetic testing. Deletion of the DCLRE1C gene should not be ignored when a variant has been found in patients with SCID.
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Affiliation(s)
- Feifan Xiao
- Center for Molecular Medicine, Children's Hospital of Fudan University, National Children's Medical Center, Shanghai, China
| | - Yulan Lu
- Center for Molecular Medicine, Children's Hospital of Fudan University, National Children's Medical Center, Shanghai, China
| | - Bingbing Wu
- Center for Molecular Medicine, Children's Hospital of Fudan University, National Children's Medical Center, Shanghai, China
| | - Bo Liu
- Center for Molecular Medicine, Children's Hospital of Fudan University, National Children's Medical Center, Shanghai, China
| | - Gang Li
- Center for Molecular Medicine, Children's Hospital of Fudan University, National Children's Medical Center, Shanghai, China
| | - Ping Zhang
- Center for Molecular Medicine, Children's Hospital of Fudan University, National Children's Medical Center, Shanghai, China
| | - Qinhua Zhou
- Department of Immunology, Children's Hospital of Fudan University, National Children's Medical Center, Shanghai, China
| | - Jinqiao Sun
- Department of Immunology, Children's Hospital of Fudan University, National Children's Medical Center, Shanghai, China
| | - Huijun Wang
- Center for Molecular Medicine, Children's Hospital of Fudan University, National Children's Medical Center, Shanghai, China
| | - Wenhao Zhou
- Center for Molecular Medicine, Children's Hospital of Fudan University, National Children's Medical Center, Shanghai, China.,Key Laboratory of Neonatal Diseases, Ministry of Health, Department of Neonates, Children's Hospital of Fudan University, National Children's Medical Center, Shanghai, China
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6
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Mou W, Gao L, He J, Yin J, Xu B, Gui J. Compound heterozygous DCLRE1C mutations lead to clinically typical Severe Combined Immunodeficiency presenting with Graft Versus Host Disease. Immunogenetics 2021; 73:425-434. [PMID: 34406419 DOI: 10.1007/s00251-021-01219-4] [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: 03/20/2021] [Accepted: 05/11/2021] [Indexed: 11/28/2022]
Abstract
Artemis (DCLRE1C) is involved in opening recombination-activating gene (RAG1/RAG2)-generated hairpins during V(D)J recombination, an essential process for the differentiation and maturation of T and B cells. Here, we reported a case of 5-month-old boy with recurrent respiratory infections, disseminated Bacille Calmette-Guérin (BCG) infection, generalized erythroderma, hepatosplenomegaly, lymphadenopathy, eosinophillia and failure to thrive, symptoms often observed in Omenn syndrome. Genetic analysis revealed compound heterozygous mutations of the DCLRE1C gene, including deletions of exons 1 and 2, and a c. 352G>T (p. G118X) nonsense mutation in exon 5. Flow cytometry analysis of the patient PBMCs indicated a TlowB-NK+ immunophenotype. Short tandem repeat (STR) analysis confirmed transplacental maternal lymphocytes engraftment in circulating blood of the patient. Collectively, we reported a patient showing atypical immunophenotypic and typical clinical presentations of Severe Combined Immunodeficiency (SCID) with Graft Versus Host Disease (GVHD) in the context of compound heterozygous mutations of the DCLRE1C gene. This study adds to the ever-growing knowledge on the broad immunological and clinical spectrum associated with DCLRE1C mutations.
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Affiliation(s)
- Wenjun Mou
- Laboratory of Tumor Immunology, Beijing Pediatric Research Institute, Beijing Children's Hospital, Capital Medical University, National Center for Children's Health, Beijing, 100045, China
| | - Liwei Gao
- Department of Respiratory Medicine, Beijing Children's Hospital, Capital Medical University, National Center for Children's Health, Beijing, 100045, China.,China National Clinical Research Center for Respiratory Diseases, Beijing, 100045, China
| | - Jianxin He
- Department of Respiratory Medicine, Beijing Children's Hospital, Capital Medical University, National Center for Children's Health, Beijing, 100045, China.,China National Clinical Research Center for Respiratory Diseases, Beijing, 100045, China
| | - Ju Yin
- Department of Respiratory Medicine, Beijing Children's Hospital, Capital Medical University, National Center for Children's Health, Beijing, 100045, China.,China National Clinical Research Center for Respiratory Diseases, Beijing, 100045, China
| | - Baoping Xu
- Department of Respiratory Medicine, Beijing Children's Hospital, Capital Medical University, National Center for Children's Health, Beijing, 100045, China. .,China National Clinical Research Center for Respiratory Diseases, Beijing, 100045, China.
| | - Jingang Gui
- Laboratory of Tumor Immunology, Beijing Pediatric Research Institute, Beijing Children's Hospital, Capital Medical University, National Center for Children's Health, Beijing, 100045, China.
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7
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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: 20] [Impact Index Per Article: 6.7] [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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8
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IJspeert H, van Schouwenburg PA, van Zessen D, Pico-Knijnenburg I, Stubbs AP, van der Burg M. Antigen Receptor Galaxy: A User-Friendly, Web-Based Tool for Analysis and Visualization of T and B Cell Receptor Repertoire Data. THE JOURNAL OF IMMUNOLOGY 2017; 198:4156-4165. [PMID: 28416602 DOI: 10.4049/jimmunol.1601921] [Citation(s) in RCA: 39] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/14/2016] [Accepted: 03/13/2017] [Indexed: 11/19/2022]
Abstract
Antigen Receptor Galaxy (ARGalaxy) is a Web-based tool for analyses and visualization of TCR and BCR sequencing data of 13 species. ARGalaxy consists of four parts: the demultiplex tool, the international ImMunoGeneTics information system (IMGT) concatenate tool, the immune repertoire pipeline, and the somatic hypermutation (SHM) and class switch recombination (CSR) pipeline. Together they allow the analysis of all different aspects of the immune repertoire. All pipelines can be run independently or combined, depending on the available data and the question of interest. The demultiplex tool allows data trimming and demultiplexing, whereas with the concatenate tool multiple IMGT/HighV-QUEST output files can be merged into a single file. The immune repertoire pipeline is an extended version of our previously published ImmunoGlobulin Galaxy (IGGalaxy) virtual machine that was developed to visualize V(D)J gene usage. It allows analysis of both BCR and TCR rearrangements, visualizes CDR3 characteristics (length and amino acid usage) and junction characteristics, and calculates the diversity of the immune repertoire. Finally, ARGalaxy includes the newly developed SHM and CSR pipeline to analyze SHM and/or CSR in BCR rearrangements. It analyzes the frequency and patterns of SHM, Ag selection (including BASELINe), clonality (Change-O), and CSR. The functionality of the ARGalaxy tool is illustrated in several clinical examples of patients with primary immunodeficiencies. In conclusion, ARGalaxy is a novel tool for the analysis of the complete immune repertoire, which is applicable to many patient groups with disturbances in the immune repertoire such as autoimmune diseases, allergy, and leukemia, but it can also be used to address basic research questions in repertoire formation and selection.
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Affiliation(s)
- Hanna IJspeert
- Department of Immunology, Erasmus University Medical Center, 3015 CN Rotterdam, the Netherlands; and
| | | | - David van Zessen
- Department of Immunology, Erasmus University Medical Center, 3015 CN Rotterdam, the Netherlands; and.,Department of Bioinformatics, Erasmus University Medical Center, 3015 CE Rotterdam, the Netherlands
| | - Ingrid Pico-Knijnenburg
- Department of Immunology, Erasmus University Medical Center, 3015 CN Rotterdam, the Netherlands; and
| | - Andrew P Stubbs
- Department of Bioinformatics, Erasmus University Medical Center, 3015 CE Rotterdam, the Netherlands
| | - Mirjam van der Burg
- Department of Immunology, Erasmus University Medical Center, 3015 CN Rotterdam, the Netherlands; and
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9
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XLF deficiency results in reduced N-nucleotide addition during V(D)J recombination. Blood 2016; 128:650-9. [PMID: 27281794 DOI: 10.1182/blood-2016-02-701029] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/29/2016] [Accepted: 05/31/2016] [Indexed: 12/12/2022] Open
Abstract
Repair of DNA double-strand breaks (DSBs) by the nonhomologous end-joining pathway (NHEJ) is important not only for repair of spontaneous breaks but also for breaks induced in developing lymphocytes during V(D)J (variable [V], diversity [D], and joining [J] genes) recombination of their antigen receptor loci to create a diverse repertoire. Mutations in the NHEJ factor XLF result in extreme sensitivity for ionizing radiation, microcephaly, and growth retardation comparable to mutations in LIG4 and XRCC4, which together form the NHEJ ligation complex. However, the effect on the immune system is variable (mild to severe immunodeficiency) and less prominent than that seen in deficiencies of NHEJ factors ARTEMIS and DNA-dependent protein kinase catalytic subunit, with defects in the hairpin opening step, which is crucial and unique for V(D)J recombination. Therefore, we aimed to study the role of XLF during V(D)J recombination. We obtained clinical data from 9 XLF-deficient patients and performed immune phenotyping and antigen receptor repertoire analysis of immunoglobulin (Ig) and T-cell receptor (TR) rearrangements, using next-generation sequencing in 6 patients. The results were compared with XRCC4 and LIG4 deficiency. Both Ig and TR rearrangements showed a significant decrease in the number of nontemplated (N) nucleotides inserted by terminal deoxynucleotidyl transferase, which resulted in a decrease of 2 to 3 amino acids in the CDR3. Such a reduction in the number of N-nucleotides has a great effect on the junctional diversity, and thereby on the total diversity of the Ig and TR repertoire. This shows that XLF has an important role during V(D)J recombination in creating diversity of the repertoire by stimulating N-nucleotide insertion.
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10
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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: 56] [Impact Index Per Article: 6.2] [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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11
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Wiekmeijer AS, Pike-Overzet K, IJspeert H, Brugman MH, Wolvers-Tettero ILM, Lankester AC, Bredius RGM, van Dongen JJM, Fibbe WE, Langerak AW, van der Burg M, Staal FJT. Identification of checkpoints in human T-cell development using severe combined immunodeficiency stem cells. J Allergy Clin Immunol 2015; 137:517-526.e3. [PMID: 26441229 DOI: 10.1016/j.jaci.2015.08.022] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2015] [Revised: 08/12/2015] [Accepted: 08/14/2015] [Indexed: 01/10/2023]
Abstract
BACKGROUND Severe combined immunodeficiency (SCID) represents congenital disorders characterized by a deficiency of T cells caused by arrested development in the thymus. Yet the nature of these developmental blocks has remained elusive because of the difficulty of taking thymic biopsy specimens from affected children. OBJECTIVE We sought to identify the stages of arrest in human T-cell development caused by various major types of SCID. METHODS We performed transplantation of SCID CD34(+) bone marrow stem/progenitor cells into an optimized NSG xenograft mouse model, followed by detailed phenotypic and molecular characterization using flow cytometry, immunoglobulin and T-cell receptor spectratyping, and deep sequencing of immunoglobulin heavy chain (IGH) and T-cell receptor δ (TRD) loci. RESULTS Arrests in T-cell development caused by mutations in IL-7 receptor α (IL7RA) and IL-2 receptor γ (IL2RG) were observed at the most immature thymocytes much earlier than expected based on gene expression profiling of human thymocyte subsets and studies with corresponding mouse mutants. T-cell receptor rearrangements were functionally required at the CD4(-)CD8(-)CD7(+)CD5(+) stage given the developmental block and extent of rearrangements in mice transplanted with Artemis-SCID cells. The xenograft model used is not informative for adenosine deaminase-SCID, whereas hypomorphic mutations lead to less severe arrests in development. CONCLUSION Transplanting CD34(+) stem cells from patients with SCID into a xenograft mouse model provides previously unattainable insight into human T-cell development and functionally identifies the arrest in thymic development caused by several SCID mutations.
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Affiliation(s)
- Anna-Sophia Wiekmeijer
- Department of Immunohematology and Blood Transfusion, Leiden University Medical Center, Leiden, The Netherlands
| | - Karin Pike-Overzet
- Department of Immunohematology and Blood Transfusion, Leiden University Medical Center, Leiden, The Netherlands
| | - Hanna IJspeert
- Department of Immunology, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - Martijn H Brugman
- Department of Immunohematology and Blood Transfusion, Leiden University Medical Center, Leiden, The Netherlands
| | | | - Arjan C Lankester
- Department of Pediatrics, Leiden University Medical Center, Leiden, The Netherlands
| | - Robbert G M Bredius
- Department of Pediatrics, Leiden University Medical Center, Leiden, The Netherlands
| | - Jacques J M van Dongen
- Department of Immunology, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - Willem E Fibbe
- Department of Immunohematology and Blood Transfusion, Leiden University Medical Center, Leiden, The Netherlands
| | - Anton W Langerak
- Department of Immunology, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - Mirjam van der Burg
- Department of Immunology, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - Frank J T Staal
- Department of Immunohematology and Blood Transfusion, Leiden University Medical Center, Leiden, The Netherlands.
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12
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Functional analysis of naturally occurring DCLRE1C mutations and correlation with the clinical phenotype of ARTEMIS deficiency. J Allergy Clin Immunol 2015; 136:140-150.e7. [PMID: 25917813 DOI: 10.1016/j.jaci.2015.03.005] [Citation(s) in RCA: 48] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2015] [Revised: 03/04/2015] [Accepted: 03/13/2015] [Indexed: 02/07/2023]
Abstract
BACKGROUND The endonuclease ARTEMIS, which is encoded by the DCLRE1C gene, is a component of the nonhomologous end-joining pathway and participates in hairpin opening during the V(D)J recombination process and repair of a subset of DNA double-strand breaks. Patients with ARTEMIS deficiency usually present with severe combined immunodeficiency (SCID) and cellular radiosensitivity, but hypomorphic mutations can cause milder phenotypes (leaky SCID). OBJECTIVE We sought to correlate the functional effect of human DCLRE1C mutations on phenotypic presentation in patients with ARTEMIS deficiency. METHODS We studied the recombination and DNA repair activity of 41 human DCLRE1C mutations in Dclre1c(-/-) v-abl kinase-transformed pro-B cells retrovirally engineered with a construct that allows quantification of recombination activity by means of flow cytometry. For assessment of DNA repair efficacy, resolution of γH2AX accumulation was studied after ionizing radiation. RESULTS Low or absent activity was detected for mutations causing a typical SCID phenotype. Most of the patients with leaky SCID were compound heterozygous for 1 loss-of-function and 1 hypomorphic allele, with significant residual levels of recombination and DNA repair activity. Deletions disrupting the C-terminus result in truncated but partially functional proteins and are often associated with leaky SCID. Overexpression of hypomorphic mutants might improve the functional defect. CONCLUSIONS Correlation between the nature and location of DCLRE1C mutations, functional activity, and the clinical phenotype has been observed. Hypomorphic variants that have been reported in the general population can be disease causing if combined in trans with a loss-of-function allele. Therapeutic strategies aimed at inducing overexpression of hypomorphic alleles might be beneficial.
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13
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IJspeert H, Wentink M, van Zessen D, Driessen GJ, Dalm VASH, van Hagen MP, Pico-Knijnenburg I, Simons EJ, van Dongen JJM, Stubbs AP, van der Burg M. Strategies for B-cell receptor repertoire analysis in primary immunodeficiencies: from severe combined immunodeficiency to common variable immunodeficiency. Front Immunol 2015; 6:157. [PMID: 25904919 PMCID: PMC4389565 DOI: 10.3389/fimmu.2015.00157] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2015] [Accepted: 03/23/2015] [Indexed: 01/08/2023] Open
Abstract
The antigen receptor repertoires of B- and T-cells form the basis of the adaptive immune response. The repertoires should be sufficiently diverse to recognize all possible pathogens. However, careful selection is needed to prevent responses to self or harmless antigens. Limited antigen receptor repertoire diversity leads to immunodeficiency, whereas unselected or misdirected repertoires can result in autoimmunity. The antigen receptor repertoire harbors information about abnormalities in many immunological disorders. Recent developments in next generation sequencing allow the analysis of the antigen receptor repertoire in much greater detail than ever before. Analyzing the antigen receptor repertoire in patients with mutations in genes responsible for the generation of the antigen receptor repertoire will give new insights into repertoire formation and selection. In this perspective, we describe strategies and considerations for analysis of the naive and antigen-selected B-cell repertoires in primary immunodeficiency patients with a focus on severe combined immunodeficiency and common variable immunodeficiency.
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Affiliation(s)
- Hanna IJspeert
- Department of Immunology, Erasmus MC, University Medical Center Rotterdam , Rotterdam , Netherlands
| | - Marjolein Wentink
- Department of Immunology, Erasmus MC, University Medical Center Rotterdam , Rotterdam , Netherlands
| | - David van Zessen
- Department of Immunology, Erasmus MC, University Medical Center Rotterdam , Rotterdam , Netherlands ; Department of Bioinformatics, Erasmus MC, University Medical Center Rotterdam , Rotterdam , Netherlands
| | - Gertjan J Driessen
- Department of Pediatrics, Erasmus MC, University Medical Center Rotterdam , Rotterdam , Netherlands
| | - Virgil A S H Dalm
- Department of Immunology, Erasmus MC, University Medical Center Rotterdam , Rotterdam , Netherlands
| | - Martin P van Hagen
- Department of Immunology, Erasmus MC, University Medical Center Rotterdam , Rotterdam , Netherlands
| | - Ingrid Pico-Knijnenburg
- Department of Immunology, Erasmus MC, University Medical Center Rotterdam , Rotterdam , Netherlands
| | - Erik J Simons
- Department of Immunology, Erasmus MC, University Medical Center Rotterdam , Rotterdam , Netherlands
| | - Jacques J M van Dongen
- Department of Immunology, Erasmus MC, University Medical Center Rotterdam , Rotterdam , Netherlands
| | - Andrew P Stubbs
- Department of Bioinformatics, Erasmus MC, University Medical Center Rotterdam , Rotterdam , Netherlands
| | - Mirjam van der Burg
- Department of Immunology, Erasmus MC, University Medical Center Rotterdam , Rotterdam , Netherlands
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14
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Mutations in the NHEJ component XRCC4 cause primordial dwarfism. Am J Hum Genet 2015; 96:412-24. [PMID: 25728776 DOI: 10.1016/j.ajhg.2015.01.013] [Citation(s) in RCA: 62] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2014] [Accepted: 01/16/2015] [Indexed: 11/20/2022] Open
Abstract
Non-homologous end joining (NHEJ) is a key cellular process ensuring genome integrity. Mutations in several components of the NHEJ pathway have been identified, often associated with severe combined immunodeficiency (SCID), consistent with the requirement for NHEJ during V(D)J recombination to ensure diversity of the adaptive immune system. In contrast, we have recently found that biallelic mutations in LIG4 are a common cause of microcephalic primordial dwarfism (MPD), a phenotype characterized by prenatal-onset extreme global growth failure. Here we provide definitive molecular genetic evidence supported by biochemical, cellular, and immunological data for mutations in XRCC4, encoding the obligate binding partner of LIG4, causing MPD. We report the identification of biallelic mutations in XRCC4 in five families. Biochemical and cellular studies demonstrate that these alterations substantially decrease XRCC4 protein levels leading to reduced cellular ligase IV activity. Consequently, NHEJ-dependent repair of ionizing-radiation-induced DNA double-strand breaks is compromised in XRCC4 cells. Similarly, immunoglobulin junctional diversification is impaired in cells. However, immunoglobulin levels are normal, and individuals lack overt signs of immunodeficiency. Additionally, in contrast to individuals with LIG4 mutations, pancytopenia leading to bone marrow failure has not been observed. Hence, alterations that alter different NHEJ proteins give rise to a phenotypic spectrum, from SCID to extreme growth failure, with deficiencies in certain key components of this repair pathway predominantly exhibiting growth deficits, reflecting differential developmental requirements for NHEJ proteins to support growth and immune maturation.
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15
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Ochi T, Wu Q, Blundell TL. The spatial organization of non-homologous end joining: from bridging to end joining. DNA Repair (Amst) 2014; 17:98-109. [PMID: 24636752 PMCID: PMC4037875 DOI: 10.1016/j.dnarep.2014.02.010] [Citation(s) in RCA: 57] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2013] [Revised: 01/27/2014] [Accepted: 02/10/2014] [Indexed: 01/24/2023]
Abstract
Non-homologous end joining (NHEJ) repairs DNA double-strand breaks generated by DNA damage and also those occurring in V(D)J recombination in immunoglobulin and T cell receptor production in the immune system. In NHEJ DNA-PKcs assembles with Ku heterodimer on the DNA ends at double-strand breaks, in order to bring the broken ends together and to assemble other proteins, including DNA ligase IV (LigIV), required for DNA repair. Here we focus on structural aspects of the interactions of LigIV with XRCC4, XLF, Artemis and DNA involved in the bridging and end-joining steps of NHEJ. We begin with a discussion of the role of XLF, which interacts with Ku and forms a hetero-filament with XRCC4; this likely forms a scaffold bridging the DNA ends. We then review the well-defined interaction of XRCC4 with LigIV, and discuss the possibility of this complex interrupting the filament formation, so positioning the ligase at the correct positions close to the broken ends. We also describe the interactions of LigIV with Artemis, the nuclease that prepares the ends for ligation and also interacts with DNA-PK. Lastly we review the likely affects of Mendelian mutations on these multiprotein assemblies and their impacts on the form of inherited disease.
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Affiliation(s)
- Takashi Ochi
- Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, Cambridge CB2 1GA, UK.
| | - Qian Wu
- Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, Cambridge CB2 1GA, UK
| | - Tom L Blundell
- Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, Cambridge CB2 1GA, UK
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16
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IJspeert H, Warris A, van der Flier M, Reisli I, Keles S, Chishimba S, van Dongen JJM, van Gent DC, van der Burg M. Clinical spectrum of LIG4 deficiency is broadened with severe dysmaturity, primordial dwarfism, and neurological abnormalities. Hum Mutat 2013; 34:1611-4. [PMID: 24027040 PMCID: PMC3910166 DOI: 10.1002/humu.22436] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2013] [Accepted: 08/20/2013] [Indexed: 01/15/2023]
Abstract
DNA double-strand break repair via non-homologous end joining (NHEJ) is involved in recombination of immunoglobulin and T-cell receptor genes. Mutations in NHEJ components result in syndromes that are characterized by microcephaly and immunodeficiency. We present a patient with lymphopenia, extreme radiosensitivity, severe dysmaturity, corpus callosum agenesis, polysyndactily, dysmorphic appearance, and erythema, which are suggestive of a new type of NHEJ deficiency. We identified two heterozygous mutations in LIG4. The p.S205LfsX29 mutation results in lack of the nuclear localization signal and appears to be a null mutation. The second mutation p.K635RfsX10 lacks the C-terminal region responsible for XRCC4 binding and LIG4 stability and activity, and therefore this mutant might be a null mutation as well or have very low residual activity. This is remarkable since Lig4 knockout mice are embryonic lethal and so far in humans no complete LIG4 deficiencies have been described. This case broadens the clinical spectrum of LIG4 deficiencies.
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Affiliation(s)
- Hanna IJspeert
- Department of Immunology, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands; Department of Pediatrics, Erasmus MC, Rotterdam, The Netherlands
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17
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Barthels C, Puchałka J, Racek T, Klein C, Brocker T. Novel spontaneous deletion of artemis exons 10 and 11 in mice leads to T- and B-cell deficiency. PLoS One 2013; 8:e74838. [PMID: 24069355 PMCID: PMC3775751 DOI: 10.1371/journal.pone.0074838] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2013] [Accepted: 07/24/2013] [Indexed: 11/18/2022] Open
Abstract
Here we describe a novel, spontaneous, 4035 basepairs long deletion in the DNA cross-link repair 1C (Dclre1c)-locus in C57BL/6-mice, which leads to loss of exons 10 and 11 of the gene encoding for Artemis, a protein involved into V(D) J-recombination of antigen receptors of T and B cells. While several spontaneous mutations of Artemis have been described to cause SCID in humans, in mice, only targeted deletions by knockout technology are known to cause the same phenotype so far. The deletion we observed causes a loss of Artemis function in the C57BL/6 strain and, consequently, the absence of T and B cells, in presence of normal numbers of NK cells and cells of the myeloid lineage. Thus, for the first time we present T-B-NK+ severe combined immunodeficiency (SCID) phenotype after spontaneously occurring modification of Artemis gene in mice. Our mouse model may serve as a valuable tool to study mechanisms as well as potential therapies of SCID in humans.
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Affiliation(s)
- Christian Barthels
- Institute for Immunology, Ludwig-Maximilians-Universität, München, Germany
| | - Jacek Puchałka
- Dr. von Hauner Children’s Hospital, Department of Pediatrics, Ludwig-Maximilians-Universität, München, Germany
| | - Tomas Racek
- Dr. von Hauner Children’s Hospital, Department of Pediatrics, Ludwig-Maximilians-Universität, München, Germany
| | - Christoph Klein
- Dr. von Hauner Children’s Hospital, Department of Pediatrics, Ludwig-Maximilians-Universität, München, Germany
| | - Thomas Brocker
- Institute for Immunology, Ludwig-Maximilians-Universität, München, Germany
- * E-mail:
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18
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Lee PP, Woodbine L, Gilmour KC, Bibi S, Cale CM, Amrolia PJ, Veys PA, Davies EG, Jeggo PA, Jones A. The many faces of Artemis-deficient combined immunodeficiency - Two patients with DCLRE1C mutations and a systematic literature review of genotype-phenotype correlation. Clin Immunol 2013; 149:464-74. [PMID: 24230999 DOI: 10.1016/j.clim.2013.08.006] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2013] [Revised: 08/04/2013] [Accepted: 08/07/2013] [Indexed: 12/31/2022]
Abstract
Defective V(D)J recombination and DNA double-strand break (DSB) repair severely impair the development of T-lymphocytes and B-lymphocytes. Most patients manifest a severe combined immunodeficiency during infancy. We report 2 siblings with combined immunodeficiency (CID) and immunodysregulation caused by compound heterozygous Artemis mutations, including an exon 1-3 deletion generating a null allele, and a missense change (p.T71P). Skin fibroblasts demonstrated normal DSB repair by gamma-H2AX analysis, supporting the predicted hypomorphic nature of the p.T71P allele. In addition to these two patients, 12 patients with Artemis-deficient CID were previously reported. All had significant morbidities including recurrent infections, autoimmunity, EBV-associated lymphoma, and carcinoma despite having hypomorphic mutants with residual Artemis expression, V(D)J recombination or DSB repair capacity. Nine patients underwent stem cell transplant and six survived, while four patients who did not receive transplant died. The progressive nature of immunodeficiency and genomic instability accounts for poor survival, and early HSCT should be considered.
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Affiliation(s)
- Pamela P Lee
- Department of Immunology, Great Ormond Street Hospital NHS Foundation Trust, London, UK
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19
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Driessen GJ, Ijspeert H, Weemaes CMR, Haraldsson Á, Trip M, Warris A, van der Flier M, Wulffraat N, Verhagen MMM, Taylor MA, van Zelm MC, van Dongen JJM, van Deuren M, van der Burg M. Antibody deficiency in patients with ataxia telangiectasia is caused by disturbed B- and T-cell homeostasis and reduced immune repertoire diversity. J Allergy Clin Immunol 2013; 131:1367-75.e9. [PMID: 23566627 DOI: 10.1016/j.jaci.2013.01.053] [Citation(s) in RCA: 68] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2012] [Revised: 12/27/2012] [Accepted: 01/28/2013] [Indexed: 12/13/2022]
Abstract
BACKGROUND Ataxia telangiectasia (AT) is a multisystem DNA-repair disorder caused by mutations in the ataxia telangiectasia mutated (ATM) gene. Patients with AT have reduced B- and T-cell numbers and a highly variable immunodeficiency. ATM is important for V(D)J recombination and immunoglobulin class-switch recombination (CSR); however, little is known about the mechanisms resulting in antibody deficiency severity. OBJECTIVE We sought to examine the immunologic mechanisms responsible for antibody deficiency heterogeneity in patients with AT. METHODS In this study we included patients with classical AT plus early-onset hypogammaglobulinemia (n = 3), classical AT (n = 8), and variant AT (late onset, n = 4). We studied peripheral B- and T-cell subsets, B-cell subset replication history, somatic hypermutation frequencies, CSR patterns, B-cell repertoire, and ATM kinase activity. RESULTS Patients with classical AT lacked ATM kinase activity, whereas patients with variant AT showed residual function. Most patients had disturbed naive B-cell and T-cell homeostasis, as evidenced by low cell numbers, increased proliferation, a large proportion CD21(low)CD38(low) anergic B cells, and decreased antigen receptor repertoire diversity. Impaired formation of T cell-dependent memory B cells was predominantly found in patients with AT plus hypogammaglobulinemia. These patients had extremely low naive CD4(+) T-cell counts, which were more severely reduced compared with those seen in patients with classical AT without hypogammaglobulinemia. Finally, AT deficiency resulted in defective CSR to distal constant regions that might reflect an impaired ability of B cells to undergo multiple germinal center reactions. CONCLUSION The severity of the antibody deficiency in patients with AT correlates with disturbances in B- and T-cell homeostasis resulting in reduced immune repertoire diversity, which consequently affects the chance of successful antigen-dependent cognate B-T interaction.
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Affiliation(s)
- Gertjan J Driessen
- Department of Pediatric Infectious Disease and Immunology, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands
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20
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Malu S, Malshetty V, Francis D, Cortes P. Role of non-homologous end joining in V(D)J recombination. Immunol Res 2013; 54:233-46. [PMID: 22569912 DOI: 10.1007/s12026-012-8329-z] [Citation(s) in RCA: 56] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
The pathway of V(D)J recombination was discovered almost three decades ago. Yet it continues to baffle scientists because of its inherent complexity and the multiple layers of regulation that are required to efficiently generate a diverse repertoire of T and B cells. The non-homologous end-joining (NHEJ) DNA repair pathway is an integral part of the V(D)J reaction, and its numerous players perform critical functions in generating this vast diversity, while ensuring genomic stability. In this review, we summarize the efforts of a number of laboratories including ours in providing the mechanisms of V(D)J regulation with a focus on the NHEJ pathway. This involves discovering new players, unraveling unknown roles for known components, and understanding how deregulation of these pathways contributes to generation of primary immunodeficiencies. A long-standing interest of our laboratory has been to elucidate various mechanisms that control RAG activity. Our recent work has focused on understanding the multiple protein-protein interactions and protein-DNA interactions during V(D)J recombination, which allow efficient and regulated generation of the antigen receptors. Exploring how deregulation of this process contributes to immunodeficiencies also continues to be an important area of research for our group.
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Affiliation(s)
- Shruti Malu
- Department of Medicine, Immunology Institute, Mount Sinai School of Medicine, 1425 Madison Avenue, New York, NY 10029, USA
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21
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Abstract
Proper repair of DNA double strand breaks (DSBs) is vital for the preservation of genomic integrity. There are two main pathways that repair DSBs, Homologous recombination (HR) and Non-homologous end-joining (NHEJ). HR is restricted to the S and G2 phases of the cell cycle due to the requirement for the sister chromatid as a template, while NHEJ is active throughout the cell cycle and does not rely on a template. The balance between both pathways is essential for genome stability and numerous assays have been developed to measure the efficiency of the two pathways. Several proteins are known to affect the balance between HR and NHEJ and the complexity of the break also plays a role. In this review we describe several repair assays to determine the efficiencies of both pathways. We discuss how disturbance of the balance between HR and NHEJ can lead to disease, but also how it can be exploited for cancer treatment.
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Affiliation(s)
- Inger Brandsma
- Department of Genetics, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands.
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22
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Malu S, De Ioannes P, Kozlov M, Greene M, Francis D, Hanna M, Pena J, Escalante CR, Kurosawa A, Erdjument-Bromage H, Tempst P, Adachi N, Vezzoni P, Villa A, Aggarwal AK, Cortes P. Artemis C-terminal region facilitates V(D)J recombination through its interactions with DNA Ligase IV and DNA-PKcs. ACTA ACUST UNITED AC 2012; 209:955-63. [PMID: 22529269 PMCID: PMC3348108 DOI: 10.1084/jem.20111437] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Interactions of Artemis with DNA Ligase IV and DNA-PKcs are required for efficient coding joint formation. Artemis is an endonuclease that opens coding hairpin ends during V(D)J recombination and has critical roles in postirradiation cell survival. A direct role for the C-terminal region of Artemis in V(D)J recombination has not been defined, despite the presence of immunodeficiency and lymphoma development in patients with deletions in this region. Here, we report that the Artemis C-terminal region directly interacts with the DNA-binding domain of Ligase IV, a DNA Ligase which plays essential roles in DNA repair and V(D)J recombination. The Artemis–Ligase IV interaction is specific and occurs independently of the presence of DNA and DNA–protein kinase catalytic subunit (DNA-PKcs), another protein known to interact with the Artemis C-terminal region. Point mutations in Artemis that disrupt its interaction with Ligase IV or DNA-PKcs reduce V(D)J recombination, and Artemis mutations that affect interactions with Ligase IV and DNA-PKcs show additive detrimental effects on coding joint formation. Signal joint formation remains unaffected. Our data reveal that the C-terminal region of Artemis influences V(D)J recombination through its interaction with both Ligase IV and DNA-PKcs.
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Affiliation(s)
- Shruti Malu
- Immunology Institute, Mount Sinai School of Medicine, New York, NY 10029, USA
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23
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Berkowska MA, van der Burg M, van Dongen JJM, van Zelm MC. Checkpoints of B cell differentiation: visualizing Ig-centric processes. Ann N Y Acad Sci 2012; 1246:11-25. [PMID: 22236426 DOI: 10.1111/j.1749-6632.2011.06278.x] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
The generation of antibody responses and B cell memory can only take place following multiple steps of differentiation. Key molecular processes during precursor B cell differentiation in bone marrow generate unique antibodies. These antibodies are further optimized via molecular modifications during immune responses in peripheral lymphoid organs. Multiple checkpoints ensure proper differentiation of precursor and mature B lymphocytes. Many of these checkpoints have been found disrupted in patients with a primary immunodeficiency. Based on studies in these patients and in mouse models, new insights have been generated in B cell differentiation and antibody responses. Still, in many patients with impaired antibody formation, it remains unclear how B cells are affected. In this perspective, we present 11 critical processes in B cell differentiation. We discuss how defects in these processes can result in impaired checkpoint selection and how they can be visualized in healthy subjects and patients with immunodeficiency or other immunological disease.
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Affiliation(s)
- Magdalena A Berkowska
- Department of Immunology, Erasmus MC, University Medical Center, Rotterdam, the Netherlands
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24
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Nakada S. Abnormalities in DNA double-strand break response beyond primary immunodeficiency. Int J Hematol 2011; 93:425-433. [PMID: 21479981 DOI: 10.1007/s12185-011-0836-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2011] [Revised: 03/28/2011] [Accepted: 03/28/2011] [Indexed: 10/18/2022]
Abstract
V(D)J recombination and class switch recombination are achieved by the cooperative processes of recombination activation gene- or activation-induced cytidine deaminase-dependent DNA cleaving, DNA double-strand break (DSB) response signaling, and DNA repair. Primary immunodeficiency due to dysfunctional DNA recombination can be categorized as severe combined immunodeficiency or other conditions, based on the presence or absence of T cells. We can also classify these diseases as radiosensitive or non-radiosensitive immunodeficiencies. While diseases unable to trigger DNA cleavage do not exhibit radiosensitivity, dysfunction in DSB response signaling or repair does lead to radiosensitive immunodeficiency. Recent studies have begun to clarify the mechanisms underlying the molecular pathogenesis of such DNA DSB-related primary immunodeficiency.
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Affiliation(s)
- Shinichiro Nakada
- Center of Integrated Medical Research, School of Medicine, Keio University, 35 Shinanomachi, Shinjuku-ku, Tokyo, 160-8582, Japan.
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25
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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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van der Burg M, Gennery AR. Educational paper. The expanding clinical and immunological spectrum of severe combined immunodeficiency. Eur J Pediatr 2011; 170:561-71. [PMID: 21479529 PMCID: PMC3078321 DOI: 10.1007/s00431-011-1452-3] [Citation(s) in RCA: 107] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/14/2011] [Accepted: 03/10/2011] [Indexed: 12/20/2022]
Abstract
Severe combined immunodeficiency (SCID) is one of the most severe forms of primary immunodeficiency characterized by absence of functional T lymphocytes. It is a paediatric emergency, which is life-threatening when recognized too late. The clinical presentation varies from the classical form of SCID through atypical SCID to Omenn syndrome. In addition, there is a considerable immunological variation, which can hamper the diagnosis. In this educational review, we describe the immunopathological background, clinical presentations and diagnostic process of SCID, as well as the therapeutic possibilities.
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Affiliation(s)
- Mirjam van der Burg
- Department of Immunology, Erasmus MC, University Medical Center Rotterdam, Dr. Molewaterplein 50, Rotterdam 3015 GE, The Netherlands.
| | - Andy R. Gennery
- Department of Pediatric Immunology, Great North Children’s Hospital, Royal Victoria Infirmary, Newcastle upon Tyne, UK ,Institute of Cellular Medicine, Child Health, University of Newcastle upon Tyne, Newcastle upon Tyne, UK
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Jacobs C, Huang Y, Masud T, Lu W, Westfield G, Giblin W, Sekiguchi JM. A hypomorphic Artemis human disease allele causes aberrant chromosomal rearrangements and tumorigenesis. Hum Mol Genet 2010; 20:806-19. [PMID: 21147755 DOI: 10.1093/hmg/ddq524] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
The Artemis gene encodes a DNA nuclease that plays important roles in non-homologous end-joining (NHEJ), a major double-strand break (DSB) repair pathway in mammalian cells. NHEJ factors repair general DSBs as well as programmed breaks generated during the lymphoid-specific DNA rearrangement, V(D)J recombination, which is required for lymphocyte development. Mutations that inactivate Artemis cause a human severe combined immunodeficiency syndrome associated with cellular radiosensitivity. In contrast, hypomorphic Artemis mutations result in combined immunodeficiency syndromes of varying severity, but, in addition, are hypothesized to predispose to lymphoid malignancy. To elucidate the distinct molecular defects caused by hypomorphic compared with inactivating Artemis mutations, we examined tumor predisposition in a mouse model harboring a targeted partial loss-of-function disease allele. We find that, in contrast to Artemis nullizygosity, the hypomorphic mutation leads to increased aberrant intra- and interchromosomal V(D)J joining events. We also observe that dysfunctional Artemis activity combined with p53 inactivation predominantly predisposes to thymic lymphomas harboring clonal translocations distinct from those observed in Artemis nullizygosity. Thus, the Artemis hypomorphic allele results in unique molecular defects, tumor spectrum and oncogenic chromosomal rearrangements. Our findings have significant implications for disease outcomes and treatment of patients with different Artemis mutations.
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Affiliation(s)
- Cheryl Jacobs
- Department of Human Genetics, University of Michigan Medical School, Ann Arbor, MI 48109, USA
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Pannicke U, Hönig M, Schulze I, Rohr J, Heinz GA, Braun S, Janz I, Rump EM, Seidel MG, Matthes-Martin S, Soerensen J, Greil J, Stachel DK, Belohradsky BH, Albert MH, Schulz A, Ehl S, Friedrich W, Schwarz K. The most frequentDCLRE1C(ARTEMIS) mutations are based on homologous recombination events. Hum Mutat 2010; 31:197-207. [DOI: 10.1002/humu.21168] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
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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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Beucher A, Birraux J, Tchouandong L, Barton O, Shibata A, Conrad S, Goodarzi AA, Krempler A, Jeggo PA, Löbrich M. ATM and Artemis promote homologous recombination of radiation-induced DNA double-strand breaks in G2. EMBO J 2009; 28:3413-27. [PMID: 19779458 PMCID: PMC2752027 DOI: 10.1038/emboj.2009.276] [Citation(s) in RCA: 406] [Impact Index Per Article: 27.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2009] [Accepted: 08/06/2009] [Indexed: 01/03/2023] Open
Abstract
Homologous recombination (HR) and non-homologous end joining (NHEJ) represent distinct pathways for repairing DNA double-strand breaks (DSBs). Previous work implicated Artemis and ATM in an NHEJ-dependent process, which repairs a defined subset of radiation-induced DSBs in G1-phase. Here, we show that in G2, as in G1, NHEJ represents the major DSB-repair pathway whereas HR is only essential for repair of approximately 15% of X- or gamma-ray-induced DSBs. In addition to requiring the known HR proteins, Brca2, Rad51 and Rad54, repair of radiation-induced DSBs by HR in G2 also involves Artemis and ATM suggesting that they promote NHEJ during G1 but HR during G2. The dependency for ATM for repair is relieved by depleting KAP-1, providing evidence that HR in G2 repairs heterochromatin-associated DSBs. Although not core HR proteins, ATM and Artemis are required for efficient formation of single-stranded DNA and Rad51 foci at radiation-induced DSBs in G2 with Artemis function requiring its endonuclease activity. We suggest that Artemis endonuclease removes lesions or secondary structures, which inhibit end resection and preclude the completion of HR or NHEJ.
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Affiliation(s)
- Andrea Beucher
- Darmstadt University of Technology, Radiation Biology and DNA Repair, Darmstadt, Germany
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Huang Y, Giblin W, Kubec M, Westfield G, St Charles J, Chadde L, Kraftson S, Sekiguchi J. Impact of a hypomorphic Artemis disease allele on lymphocyte development, DNA end processing, and genome stability. ACTA ACUST UNITED AC 2009; 206:893-908. [PMID: 19349461 PMCID: PMC2715118 DOI: 10.1084/jem.20082396] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
Artemis was initially discovered as the gene inactivated in human radiosensitive T(-)B(-) severe combined immunodeficiency, a syndrome characterized by the absence of B and T lymphocytes and cellular hypersensitivity to ionizing radiation. Hypomorphic Artemis alleles have also been identified in patients and are associated with combined immunodeficiencies of varying severity. We examine the molecular mechanisms underlying a syndrome of partial immunodeficiency caused by a hypomorphic Artemis allele using the mouse as a model system. This mutation, P70, leads to premature translation termination that deletes a large portion of a nonconserved C terminus. We find that homozygous Artemis-P70 mice exhibit reduced numbers of B and T lymphocytes, thereby recapitulating the patient phenotypes. The hypomorphic mutation results in impaired end processing during the lymphoid-specific DNA rearrangement known as V(D)J recombination, defective double-strand break repair, and increased chromosomal instability. Biochemical analyses reveal that the Artemis-P70 mutant protein interacts with the DNA-dependent protein kinase catalytic subunit and retains significant, albeit reduced, exo- and endonuclease activities but does not undergo phosphorylation. Together, our findings indicate that the Artemis C terminus has critical in vivo functions in ensuring efficient V(D)J rearrangements and maintaining genome integrity.
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Affiliation(s)
- Ying Huang
- Department of Internal Medicine, University of Michigan, Ann Arbor, 48109, USA
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The Ku80 carboxy terminus stimulates joining and artemis-mediated processing of DNA ends. Mol Cell Biol 2008; 29:1134-42. [PMID: 19103741 DOI: 10.1128/mcb.00971-08] [Citation(s) in RCA: 49] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
Repair of DNA double-strand breaks (DSBs) is predominantly mediated by nonhomologous end joining (NHEJ) in mammalian cells. NHEJ requires binding of the Ku70-Ku80 heterodimer (Ku70/80) to the DNA ends and subsequent recruitment of the DNA-dependent protein kinase catalytic subunit (DNA-PK(CS)) and the XRCC4/ligase IV complex. Activation of the DNA-PK(CS) serine/threonine kinase requires an interaction with Ku70/80 and is essential for NHEJ-mediated DSB repair. In contrast to previous models, we found that the carboxy terminus of Ku80 is not absolutely required for the recruitment and activation of DNA-PK(CS) at DSBs, although cells that harbored a carboxy-terminal deletion in the Ku80 gene were sensitive to ionizing radiation and showed reduced end-joining capacity. More detailed analysis of this repair defect showed that DNA-PK(CS) autophosphorylation at Thr2647 was diminished, while Ser2056 was phosphorylated to normal levels. This resulted in severely reduced levels of Artemis nuclease activity in vivo and in vitro. We therefore conclude that the Ku80 carboxy terminus is important to support DNA-PK(CS) autophosphorylation at specific sites, which facilitates DNA end processing by the Artemis endonuclease and the subsequent joining reaction.
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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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van der Burg M, Ijspeert H, Verkaik NS, Turul T, Wiegant WW, Morotomi-Yano K, Mari PO, Tezcan I, Chen DJ, Zdzienicka MZ, van Dongen JJM, van Gent DC. A DNA-PKcs mutation in a radiosensitive T-B- SCID patient inhibits Artemis activation and nonhomologous end-joining. J Clin Invest 2008; 119:91-8. [PMID: 19075392 DOI: 10.1172/jci37141] [Citation(s) in RCA: 125] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2008] [Accepted: 10/29/2008] [Indexed: 01/12/2023] Open
Abstract
Radiosensitive T-B- severe combined immunodeficiency (RS-SCID) is caused by defects in the nonhomologous end-joining (NHEJ) DNA repair pathway, which results in failure of functional V(D)J recombination. Here we have identified the first human RS-SCID patient to our knowledge with a DNA-PKcs missense mutation (L3062R). The causative mutation did not affect the kinase activity or DNA end-binding capacity of DNA-PKcs itself; rather, the presence of long P-nucleotide stretches in the immunoglobulin coding joints indicated that it caused insufficient Artemis activation, something that is dependent on Artemis interaction with autophosphorylated DNA-PKcs. Moreover, overall end-joining activity was hampered, suggesting that Artemis-independent DNA-PKcs functions were also inhibited. This study demonstrates that the presence of DNA-PKcs kinase activity is not sufficient to rule out a defect in this gene during diagnosis and treatment of RS-SCID patients. Further, the data suggest that residual DNA-PKcs activity is indispensable in humans.
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Affiliation(s)
- Mirjam van der Burg
- Department of Immunology, Erasmus Medical Center, University Medical Center Rotterdam, Rotterdam, The Netherlands
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Abstract
Rejoining of broken chromosomes is crucial for cell survival and prevention of malignant transformation. Most mammalian cells rely primarily on the non-homologous end-joining pathway of DNA double-strand break (DSB) repair to accomplish this task. This review focuses both on the core non-homologous end-joining machinery, which consists of DNA-dependent protein kinase and the ligase IV/XRCC4 complex, and on accessory factors that facilitate rejoining of a subset of the DSBs. We discuss how the ATM protein kinase and the Mre11/Rad50/Nbs1 complex might function in DSB repair and what role ionizing radiation-induced foci may play in this process.
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