1
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Rodriguez OL, Sharp AJ, Watson CT. Limitations of lymphoblastoid cell lines for establishing genetic reference datasets in the immunoglobulin loci. PLoS One 2021; 16:e0261374. [PMID: 34898642 PMCID: PMC8668129 DOI: 10.1371/journal.pone.0261374] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2021] [Accepted: 11/30/2021] [Indexed: 11/18/2022] Open
Abstract
Lymphoblastoid cell lines (LCLs) have been critical to establishing genetic resources for biomedical science. They have been used extensively to study human genetic diversity, genome function, and inform the development of tools and methodologies for augmenting disease genetics research. While the validity of variant callsets from LCLs has been demonstrated for most of the genome, previous work has shown that DNA extracted from LCLs is modified by V(D)J recombination within the immunoglobulin (IG) loci, regions that harbor antibody genes critical to immune system function. However, the impacts of V(D)J on short read sequencing data generated from LCLs has not been extensively investigated. In this study, we used LCL-derived short read sequencing data from the 1000 Genomes Project (n = 2,504) to identify signatures of V(D)J recombination. Our analyses revealed sample-level impacts of V(D)J recombination that varied depending on the degree of inferred monoclonality. We showed that V(D)J associated somatic deletions impacted genotyping accuracy, leading to adulterated population-level estimates of allele frequency and linkage disequilibrium. These findings illuminate limitations of using LCLs and short read data for building genetic resources in the IG loci, with implications for interpreting previous disease association studies in these regions.
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Affiliation(s)
- Oscar L. Rodriguez
- Department of Biochemistry and Molecular Genetics, University of Louisville School of Medicine, Louisville, KY, United States of America
| | - Andrew J. Sharp
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, United States of America
| | - Corey T. Watson
- Department of Biochemistry and Molecular Genetics, University of Louisville School of Medicine, Louisville, KY, United States of America
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2
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Magadan S, Mondot S, Palti Y, Gao G, Lefranc MP, Boudinot P. Genomic analysis of a second rainbow trout line (Arlee) leads to an extended description of the IGH VDJ gene repertoire. Dev Comp Immunol 2021; 118:103998. [PMID: 33450314 DOI: 10.1016/j.dci.2021.103998] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/01/2020] [Revised: 01/07/2021] [Accepted: 01/07/2021] [Indexed: 06/12/2023]
Abstract
High-throughput sequencing technologies brought a renewed interest for immune repertoires. Fish Ab and B cell repertoires are no exception, and their comprehensive analysis can both provide new insights into poorly understood immune mechanisms, and identify markers of protection after vaccination. However, the lack of genomic description and standardized nomenclature of IG genes hampers accurate annotation of Ig mRNA deep sequencing data. Complete genome sequences of Atlantic salmon and rainbow trout (Swanson line) recently allowed us to establish a comprehensive and coherent annotation of Salmonid IGH genes following IMGT standards. Here we analyzed the IGHV, D, and J genes from the newly released genome of a second rainbow trout line (Arlee). We confirmed the validity of salmonid IGHV subgroups, and extended the description of the rainbow trout IGH gene repertoire with novel sequences, while keeping nomenclature continuity. This work provides an important resource for annotation of high-throughput Ab repertoire sequencing data.
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Affiliation(s)
- Susana Magadan
- Centro de Investigaciones Biomédicas, Universidade de Vigo, Campus Universitario Lagoas Marcosende, 36310, Vigo, Spain.
| | - Stanislas Mondot
- Université Paris-Saclay, INRAE, AgroParisTech, Micalis Institute, 78350, Jouy-en-Josas, France
| | - Yniv Palti
- USDA-ARS National Center for Cool and Cold Water Aquaculture, 11861 Leetown Road, Kearneysville, WV, 25430, USA
| | - Guangtu Gao
- USDA-ARS National Center for Cool and Cold Water Aquaculture, 11861 Leetown Road, Kearneysville, WV, 25430, USA
| | - Marie Paule Lefranc
- IMGT®, The International ImMunoGeneTics Information System®, Laboratoire d'ImmunoGénétique Moléculaire (LIGM), Institut de Génétique Humaine (IGH), UMR9002 CNRS, Université de Montpellier, Montpellier, France
| | - Pierre Boudinot
- Université Paris-Saclay, INRAE, UVSQ, VIM, 78350, Jouy-en-Josas, France.
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3
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Koning MT, Vletter EM, Rademaker R, Vergroesen RD, Trollmann IJ, Parren P, van Bergen CA, Scherer HU, Kiełbasa SM, Toes RE, Veelken H. Templated insertions at VD and DJ junctions create unique B-cell receptors in the healthy B-cell repertoire. Eur J Immunol 2020; 50:2099-2101. [PMID: 32762049 PMCID: PMC7754338 DOI: 10.1002/eji.202048828] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2020] [Accepted: 08/03/2020] [Indexed: 11/07/2022]
Abstract
RAG complexes recognise (cryptic) RSS sites both in and outside immunoglobulin sites. Excision circles may be reinserted into V(D)J rearrangements as long templated insertions to diversify the adaptive immune repertoire. We show that such VDJ with templated insertions are incidentally found in the repertoire of healthy donors.
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Affiliation(s)
- Marvyn T. Koning
- Department of HematologyLeiden University Medical CenterLeidenThe Netherlands
| | - Esther M. Vletter
- Department of HematologyLeiden University Medical CenterLeidenThe Netherlands
- Department of RheumatologyLeiden University Medical CenterLeidenThe Netherlands
| | | | | | | | | | | | - Hans U. Scherer
- Department of RheumatologyLeiden University Medical CenterLeidenThe Netherlands
| | - Szymon M. Kiełbasa
- Department of Medical Statistics and BioinformaticsLeiden University Medical CenterLeidenThe Netherlands
| | - René E.M. Toes
- Department of RheumatologyLeiden University Medical CenterLeidenThe Netherlands
| | - Hendrik Veelken
- Department of HematologyLeiden University Medical CenterLeidenThe Netherlands
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4
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Abstract
Despite the extreme diversity of T-cell repertoires, many identical T-cell receptor (TCR) sequences are found in a large number of individual mice and humans. These widely shared sequences, often referred to as "public," have been suggested to be over-represented due to their potential immune functionality or their ease of generation by V(D)J recombination. Here, we show that even for large cohorts, the observed degree of sharing of TCR sequences between individuals is well predicted by a model accounting for the known quantitative statistical biases in the generation process, together with a simple model of thymic selection. Whether a sequence is shared by many individuals is predicted to depend on the number of queried individuals and the sampling depth, as well as on the sequence itself, in agreement with the data. We introduce the degree of publicness conditional on the queried cohort size and the size of the sampled repertoires. Based on these observations, we propose a public/private sequence classifier, "PUBLIC" (Public Universal Binary Likelihood Inference Classifier), based on the generation probability, which performs very well even for small cohort sizes.
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Affiliation(s)
- Yuval Elhanati
- Joseph Henry LaboratoriesPrinceton UniversityPrincetonNJUSA
| | - Zachary Sethna
- Joseph Henry LaboratoriesPrinceton UniversityPrincetonNJUSA
| | | | - Thierry Mora
- Laboratoire de physique statistiqueCNRSSorbonne UniversitéUniversité Paris‐Diderot, and École Normale Supérieure (PSL University)ParisFrance
| | - Aleksandra M. Walczak
- Laboratoire de physique théoriqueCNRSSorbonne Université, and École Normale Supérieure (PSL University)ParisFrance
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5
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Abstract
Probabilistic modeling is fundamental to the statistical analysis of complex data. In addition to forming a coherent description of the data-generating process, probabilistic models enable parameter inference about given datasets. This procedure is well developed in the Bayesian perspective, in which one infers probability distributions describing to what extent various possible parameters agree with the data. In this paper, we motivate and review probabilistic modeling for adaptive immune receptor repertoire data then describe progress and prospects for future work, from germline haplotyping to adaptive immune system deployment across tissues. The relevant quantities in immune sequence analysis include not only continuous parameters such as gene use frequency but also discrete objects such as B-cell clusters and lineages. Throughout this review, we unravel the many opportunities for probabilistic modeling in adaptive immune receptor analysis, including settings for which the Bayesian approach holds substantial promise (especially if one is optimistic about new computational methods). From our perspective, the greatest prospects for progress in probabilistic modeling for repertoires concern ancestral sequence estimation for B-cell receptor lineages, including uncertainty from germline genotype, rearrangement, and lineage development.
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Affiliation(s)
- Branden Olson
- Computational Biology Program Fred Hutchinson Cancer Research Center, 1100 Fairview Ave. N., Mail stop: M1-B514 Seattle, WA 98109-1024 phone: +1 206 667 7318
| | - Frederick A. Matsen
- Computational Biology Program Fred Hutchinson Cancer Research Center, 1100 Fairview Ave. N., Mail stop: M1-B514 Seattle, WA 98109-1024 phone: +1 206 667 7318
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6
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Bahjat M, Guikema JEJ. The Complex Interplay between DNA Injury and Repair in Enzymatically Induced Mutagenesis and DNA Damage in B Lymphocytes. Int J Mol Sci 2017; 18:ijms18091876. [PMID: 28867784 PMCID: PMC5618525 DOI: 10.3390/ijms18091876] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2017] [Revised: 08/24/2017] [Accepted: 08/29/2017] [Indexed: 11/25/2022] Open
Abstract
Lymphocytes are endowed with unique and specialized enzymatic mutagenic properties that allow them to diversify their antigen receptors, which are crucial sensors for pathogens and mediators of adaptive immunity. During lymphocyte development, the antigen receptors expressed by B and T lymphocytes are assembled in an antigen-independent fashion by ordered variable gene segment recombinations (V(D)J recombination), which is a highly ordered and regulated process that requires the recombination activating gene products 1 & 2 (RAG1, RAG2). Upon activation by antigen, B lymphocytes undergo additional diversifications of their immunoglobulin B-cell receptors. Enzymatically induced somatic hypermutation (SHM) and immunoglobulin class switch recombination (CSR) improves the affinity for antigen and shape the effector function of the humoral immune response, respectively. The activation-induced cytidine deaminase (AID) enzyme is crucial for both SHM and CSR. These processes have evolved to both utilize as well as evade different DNA repair and DNA damage response pathways. The delicate balance between enzymatic mutagenesis and DNA repair is crucial for effective immune responses and the maintenance of genomic integrity. Not surprisingly, disturbances in this balance are at the basis of lymphoid malignancies by provoking the formation of oncogenic mutations and chromosomal aberrations. In this review, we discuss recent mechanistic insight into the regulation of RAG1/2 and AID expression and activity in lymphocytes and the complex interplay between these mutagenic enzymes and DNA repair and DNA damage response pathways, focusing on the base excision repair and mismatch repair pathways. We discuss how disturbances of this interplay induce genomic instability and contribute to oncogenesis.
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Affiliation(s)
- Mahnoush Bahjat
- Department of Pathology, Academic Medical Center, University of Amsterdam; Lymphoma and Myeloma Center Amsterdam (LYMMCARE), Amsterdam 1105 AZ, The Netherlands.
| | - Jeroen E J Guikema
- Department of Pathology, Academic Medical Center, University of Amsterdam; Lymphoma and Myeloma Center Amsterdam (LYMMCARE), Amsterdam 1105 AZ, The Netherlands.
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7
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Chen N, Trible BR, Rowland RRR. Amplification and selection of PRRSV-activated VDJ repertoires in pigs secreting distinct neutralizing antiboidies. Vet Immunol Immunopathol 2017; 189:53-57. [PMID: 28669387 DOI: 10.1016/j.vetimm.2017.06.005] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2016] [Revised: 04/25/2017] [Accepted: 06/19/2017] [Indexed: 12/19/2022]
Abstract
Neutralizing antibodies (nAbs) play an important role in protective immunity against porcine reproductive and respiratory syndrome virus (PRRSV) infection. However, the characterization of PRRSV nAb repertoires is rarely investigated. In this study, we developed a swine VDJ amplification method and selection criteria for the characterization of PRRSV-activated VDJ repertoires. According to clonal expansion theory, two separated aliquots of lymph nodes from pigs producing different PRRSV nAbs were utilized to determine the activated B-cell repertoires. Swine VDJ repertoires from a mock-infected pig and PRRSV-infected pigs secreting no detectable nAbs, only homologous nAbs, and broad nAbs were amplified by a single pair of primers that could detect all seven major VDJ genes. The amplicons were cloned and sequenced to generate 385 VDJ sequences. Sequence alignment showed that the diversification of VDJ genes was mainly due to the variation in complementarity determining regions (CDRs), especially CDR3. Based on selection criteria, shared and abundant sequences were identified in two separated aliquots from PRRSV-infected pigs but not from the mock-infected pig, suggesting they were secreted from PRRSV-activated B cells. Thus, the amplification and selection method provide a potential alternative for the characterization of swine VDJ repertoires. However, additional experiments are required to determine whether the shared and abundant VDJ lineages identified in this study are PRRSV-specific or distinct neutralizing-antibodies-associated.
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Affiliation(s)
- Nanhua Chen
- College of Veterinary Medicine, Yangzhou University, Jiangsu 225009, PR China; Department of Diagnostic Medicine and Pathobiology, College of Veterinary Medicine, Kansas State University, Manhattan, KS 66506, United States.
| | - Benjamin R Trible
- Department of Diagnostic Medicine and Pathobiology, College of Veterinary Medicine, Kansas State University, Manhattan, KS 66506, United States
| | - Raymond R R Rowland
- Department of Diagnostic Medicine and Pathobiology, College of Veterinary Medicine, Kansas State University, Manhattan, KS 66506, United States
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8
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Dubois ARSX, Buerckert JP, Sinner R, Faison WJ, Molitor AM, Muller CP. High-resolution analysis of the B cell repertoire before and after polyethylene glycol fusion reveals preferential fusion of rare antigen-specific B cells. Hum Antibodies 2016; 24:1-15. [PMID: 27472868 DOI: 10.3233/hab-150288] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
OBJECTIVE The hybridoma technology is one of the most important advances in clinical immunology. Little is known about the differences between the antibodies produced during the in vivo immune response and those recovered in hybridoma libraries. Here, we investigate a potential fusion bias inherent to the hybridoma production process. METHODS Transgenic rats carrying human Ig heavy and light chain loci were immunized with measles virus (MV) to generate human mAbs. Usin g high-throughput sequencing of IgH mRNA, we compared the IgH repertoire of lymph nodes and the derived hybridoma library using the sequences of the MV-specific hybridoma clones as a reference set with known specificity. RESULTS We observed that large clonotypes from the lymph nodes were not represented in the hybridoma library, but low-frequency B cell populations became highly enriched and most hybridoma clones were derived from these. Our data also showed that identical CDR3s evolved from diverse VDJ recombinations, indicating convergence of different B cells subpopulations towards expression of antibodies with similar paratopes. CONCLUSION The efficient generation of mAbs results from a fusion process highly selective for rare antigen-specific B cells rather than in vivo expanded populations. Antibodies of particular interest may therefore be missed during classical hybridoma production.
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9
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Manoharan A, Du Roure C, Rolink AG, Matthias P. De novo DNA Methyltransferases Dnmt3a and Dnmt3b regulate the onset of Igκ light chain rearrangement during early B-cell development. Eur J Immunol 2015; 45:2343-55. [PMID: 26059604 DOI: 10.1002/eji.201445035] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2014] [Revised: 04/24/2015] [Accepted: 05/19/2015] [Indexed: 02/01/2023]
Abstract
Immunoglobulin genes V(D)J rearrangement during early lymphopoiesis is a critical process involving sequential recombination of the heavy and light chain loci. A number of transcription factors act together with temporally activated recombinases and chromatin accessibility changes to regulate this complex process. Here, we deleted the de novo DNA methyltransferases Dnmt3a and Dnmt3b in early B cells of conditionally targeted mice, and monitored the process of V(D)J recombination. Dnmt3a and Dnmt3b deletion resulted in precocious recombination of the immunoglobulin κ light chain without impairing the differentiation of mature B cells or overall B-cell development. Ex vivo culture of IL-7 restricted early B-cell progenitors lacking Dnmt3a and Dnmt3b showed precocious Vκ-Jκ rearrangements that are limited to the proximal Vκ genes. Furthermore, B-cell progenitors deficient in Dnmt3a and Dnmt3b showed elevated levels of germline transcripts at the proximal Vκ genes, alterations in methylation patterns at Igκ enhancer sites and increased expression of the transcription factor E2A. Our data suggest that Dnmt3a and Dnmt3b are critical to regulate the onset of Igκ light chain rearrangement during early B-cell development.
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Affiliation(s)
- Anand Manoharan
- Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland
| | - Camille Du Roure
- Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland
| | | | - Patrick Matthias
- Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland
- Faculty of Sciences, University of Basel, Basel, Switzerland
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10
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Mathieu AL, Verronese E, Rice GI, Fouyssac F, Bertrand Y, Picard C, Chansel M, Walter JE, Notarangelo LD, Butte MJ, Nadeau KC, Csomos K, Chen DJ, Chen K, Delgado A, Rigal C, Bardin C, Schuetz C, Moshous D, Reumaux H, Plenat F, Phan A, Zabot MT, Balme B, Viel S, Bienvenu J, Cochat P, van der Burg M, Caux C, Kemp EH, Rouvet I, Malcus C, Méritet JF, Lim A, Crow YJ, Fabien N, Ménétrier-Caux C, De Villartay JP, Walzer T, Belot A. PRKDC mutations associated with immunodeficiency, granuloma, and autoimmune regulator-dependent autoimmunity. J Allergy Clin Immunol 2015; 135:1578-88.e5. [PMID: 25842288 PMCID: PMC4487867 DOI: 10.1016/j.jaci.2015.01.040] [Citation(s) in RCA: 67] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2014] [Revised: 12/28/2014] [Accepted: 01/06/2015] [Indexed: 02/05/2023]
Abstract
BACKGROUND PRKDC encodes for DNA-dependent protein kinase catalytic subunit (DNA-PKcs), a kinase that forms part of a complex (DNA-dependent protein kinase [DNA-PK]) crucial for DNA double-strand break repair and V(D)J recombination. In mice DNA-PK also interacts with the transcription factor autoimmune regulator (AIRE) to promote central T-cell tolerance. OBJECTIVE We sought to understand the causes of an inflammatory disease with granuloma and autoimmunity associated with decreasing T- and B-cell counts over time that had been diagnosed in 2 unrelated patients. METHODS Genetic, molecular, and functional analyses were performed to characterize an inflammatory disease evocative of a combined immunodeficiency. RESULTS We identified PRKDC mutations in both patients. These patients exhibited a defect in DNA double-strand break repair and V(D)J recombination. Whole-blood mRNA analysis revealed a strong interferon signature. On activation, memory T cells displayed a skewed cytokine response typical of TH2 and TH1 but not TH17. Moreover, mutated DNA-PKcs did not promote AIRE-dependent transcription of peripheral tissue antigens in vitro. The latter defect correlated in vivo with production of anti-calcium-sensing receptor autoantibodies, which are typically found in AIRE-deficient patients. In addition, 9 months after bone marrow transplantation, patient 1 had Hashimoto thyroiditis, suggesting that organ-specific autoimmunity might be linked to nonhematopoietic cells, such as AIRE-expressing thymic epithelial cells. CONCLUSION Deficiency of DNA-PKcs, a key AIRE partner, can present as an inflammatory disease with organ-specific autoimmunity, suggesting a role for DNA-PKcs in regulating autoimmune responses and maintaining AIRE-dependent tolerance in human subjects.
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Affiliation(s)
- Anne-Laure Mathieu
- CIRI, International Center for Infectiology Research, Université de Lyon, Lyon, France; Inserm U1111, Lyon, France; Ecole Normale Supérieure de Lyon, Lyon, France; CNRS, UMR5308, Lyon, France
| | - Estelle Verronese
- Université de Lyon, INSERM U1052, Centre de Recherche en Cancérologie de Lyon, Plateforme d'Innovation en Immuno-monitoring et Immunothérapie, Centre Léon Bérard, and in the framework of the LABEX DevWeCan (ANR-10-LABX-0061) of University de Lyon, within the program "Investissements d'Avenir" (ANR-11-IDEX-0007) operated by the French National Research Agency (ANR), Lyon, France
| | - Gillian I Rice
- Manchester Centre for Genomic Medicine, Institute of Human Development, Faculty of Medical and Human Sciences, Manchester Academic Health Centre, Manchester, United Kingdom
| | - Fanny Fouyssac
- Pediatric Haematology and Oncology Department, Children Hospital-CHU NANCY Vandoeuvre les Nancy, Nancy, France
| | - Yves Bertrand
- Institut d'Hématologie et d'Oncologie Pédiatrique (Hospices Civils de Lyon), Université Claude Bernard Lyon I, Lyon, France
| | - Capucine Picard
- Study Center for Primary Immunodeficiencies, Assistance Publique-Hôpitaux de Paris, Necker Hospital, Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM U1163, Sorbonne Paris Cité, Paris Descartes University, Imagine Institute, Paris Descartes University, Paris, France
| | - Marie Chansel
- INSERM UMR 1163, Laboratoire Dynamique du Génome et Système Immunitaire Université Paris Descartes-Sorbonne Paris Cité, Imagine Institute, Paris, France
| | - Jolan E Walter
- Pediatric Allergy & Immunology and the Center for Immunology and Inflammatory Diseases, Massachusetts General Hospital, Harvard Medical School, Boston, Mass
| | - Luigi D Notarangelo
- Division of Immunology, Boston Children's Hospital and Harvard Medical School, Boston, Mass
| | - Manish J Butte
- Department of Pediatrics, Division of Immunology, Allergy and Rheumatology, Stanford University, Stanford, Calif
| | - Kari Christine Nadeau
- Department of Pediatrics, Division of Immunology, Allergy and Rheumatology, Stanford University, Stanford, Calif
| | - Krisztian Csomos
- Pediatric Allergy & Immunology and the Center for Immunology and Inflammatory Diseases, Massachusetts General Hospital, Harvard Medical School, Boston, Mass
| | - David J Chen
- Division of Molecular Radiation Biology Department of Radiation Oncology, University of Texas Southwestern Medical Center, Dallas, Tex
| | - Karin Chen
- Department of Pediatrics, Division of Allergy, Immunology & Rheumatology, University of Utah School of Medicine, Salt Lake City, Utah
| | - Ana Delgado
- Université de Lyon, INSERM U1052, Centre de Recherche en Cancérologie de Lyon, Plateforme d'Innovation en Immuno-monitoring et Immunothérapie, Centre Léon Bérard, and in the framework of the LABEX DevWeCan (ANR-10-LABX-0061) of University de Lyon, within the program "Investissements d'Avenir" (ANR-11-IDEX-0007) operated by the French National Research Agency (ANR), Lyon, France
| | - Chantal Rigal
- Université de Lyon, INSERM U1052, Centre de Recherche en Cancérologie de Lyon, Plateforme d'Innovation en Immuno-monitoring et Immunothérapie, Centre Léon Bérard, and in the framework of the LABEX DevWeCan (ANR-10-LABX-0061) of University de Lyon, within the program "Investissements d'Avenir" (ANR-11-IDEX-0007) operated by the French National Research Agency (ANR), Lyon, France
| | - Christine Bardin
- Université de Lyon, INSERM U1052, Centre de Recherche en Cancérologie de Lyon, Plateforme d'Innovation en Immuno-monitoring et Immunothérapie, Centre Léon Bérard, and in the framework of the LABEX DevWeCan (ANR-10-LABX-0061) of University de Lyon, within the program "Investissements d'Avenir" (ANR-11-IDEX-0007) operated by the French National Research Agency (ANR), Lyon, France
| | - Catharina Schuetz
- Department of Pediatrics and Adolescent Medicine, University Medical Center Ulm, Ulm, Germany
| | - Despina Moshous
- INSERM UMR 1163, Laboratoire Dynamique du Génome et Système Immunitaire Université Paris Descartes-Sorbonne Paris Cité, Imagine Institute, Paris, France
| | - Héloïse Reumaux
- Pediatric Rheumatology and Emergency Unit, Jeanne de Flandre Hospital, Lille, France
| | - François Plenat
- Pathology Department, Hémato-Oncologie Pédiatrique, CHU Nancy, Nancy, France
| | - Alice Phan
- Pediatric Rheumatology, Nephrology and Dermatology Department and EPICIME Hospices Civils de Lyon and Université Claude-Bernard Lyon 1, Lyon, France
| | | | - Brigitte Balme
- Pathology Department, Centre Hospitalier Lyon Sud, Hospices Civils de Lyon, Lyon, France
| | - Sébastien Viel
- CIRI, International Center for Infectiology Research, Université de Lyon, Lyon, France; Inserm U1111, Lyon, France; Ecole Normale Supérieure de Lyon, Lyon, France; CNRS, UMR5308, Lyon, France; Immunobiology Department, Hospices Civils de Lyon, Centre Hospitalier Lyon Sud, Lyon, France
| | - Jacques Bienvenu
- CIRI, International Center for Infectiology Research, Université de Lyon, Lyon, France; Inserm U1111, Lyon, France; Ecole Normale Supérieure de Lyon, Lyon, France; CNRS, UMR5308, Lyon, France; Immunobiology Department, Hospices Civils de Lyon, Centre Hospitalier Lyon Sud, Lyon, France
| | - Pierre Cochat
- Pediatric Rheumatology, Nephrology and Dermatology Department and EPICIME Hospices Civils de Lyon and Université Claude-Bernard Lyon 1, Lyon, France
| | - Mirjam van der Burg
- Department of Immunology, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - Christophe Caux
- Université de Lyon, INSERM U1052, Centre de Recherche en Cancérologie de Lyon, Plateforme d'Innovation en Immuno-monitoring et Immunothérapie, Centre Léon Bérard, and in the framework of the LABEX DevWeCan (ANR-10-LABX-0061) of University de Lyon, within the program "Investissements d'Avenir" (ANR-11-IDEX-0007) operated by the French National Research Agency (ANR), Lyon, France
| | - E Helen Kemp
- Department of Human Metabolism, University of Sheffield, Sheffield, United Kingdom
| | - Isabelle Rouvet
- Biotechnology Department, Hospices Civils de Lyon, Lyon, France
| | - Christophe Malcus
- Cell Immunology Department, Hôpital Edouard Herriot, Hospices Civils de Lyon, Lyon, France
| | | | - Annick Lim
- Immunoscope Group, Immunology Department, Institut Pasteur, Paris, France
| | - Yanick J Crow
- Manchester Centre for Genomic Medicine, Institute of Human Development, Faculty of Medical and Human Sciences, Manchester Academic Health Centre, Manchester, United Kingdom
| | - Nicole Fabien
- Immunobiology Department, Hospices Civils de Lyon, Centre Hospitalier Lyon Sud, Lyon, France
| | - Christine Ménétrier-Caux
- Université de Lyon, INSERM U1052, Centre de Recherche en Cancérologie de Lyon, Plateforme d'Innovation en Immuno-monitoring et Immunothérapie, Centre Léon Bérard, and in the framework of the LABEX DevWeCan (ANR-10-LABX-0061) of University de Lyon, within the program "Investissements d'Avenir" (ANR-11-IDEX-0007) operated by the French National Research Agency (ANR), Lyon, France
| | - Jean-Pierre De Villartay
- INSERM UMR 1163, Laboratoire Dynamique du Génome et Système Immunitaire Université Paris Descartes-Sorbonne Paris Cité, Imagine Institute, Paris, France
| | - Thierry Walzer
- CIRI, International Center for Infectiology Research, Université de Lyon, Lyon, France; Inserm U1111, Lyon, France; Ecole Normale Supérieure de Lyon, Lyon, France; CNRS, UMR5308, Lyon, France
| | - Alexandre Belot
- CIRI, International Center for Infectiology Research, Université de Lyon, Lyon, France; Inserm U1111, Lyon, France; Ecole Normale Supérieure de Lyon, Lyon, France; CNRS, UMR5308, Lyon, France; Pediatric Rheumatology, Nephrology and Dermatology Department and EPICIME Hospices Civils de Lyon and Université Claude-Bernard Lyon 1, Lyon, France.
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11
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Silva-Sanchez A, Liu CR, Vale AM, Khass M, Kapoor P, Elgavish A, Ivanov II, Ippolito GC, Schelonka RL, Schoeb TR, Burrows PD, Schroeder HW. Violation of an evolutionarily conserved immunoglobulin diversity gene sequence preference promotes production of dsDNA-specific IgG antibodies. PLoS One 2015; 10:e0118171. [PMID: 25706374 PMCID: PMC4338297 DOI: 10.1371/journal.pone.0118171] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2014] [Accepted: 01/08/2015] [Indexed: 11/24/2022] Open
Abstract
Variability in the developing antibody repertoire is focused on the third complementarity determining region of the H chain (CDR-H3), which lies at the center of the antigen binding site where it often plays a decisive role in antigen binding. The power of VDJ recombination and N nucleotide addition has led to the common conception that the sequence of CDR-H3 is unrestricted in its variability and random in its composition. Under this view, the immune response is solely controlled by somatic positive and negative clonal selection mechanisms that act on individual B cells to promote production of protective antibodies and prevent the production of self-reactive antibodies. This concept of a repertoire of random antigen binding sites is inconsistent with the observation that diversity (DH) gene segment sequence content by reading frame (RF) is evolutionarily conserved, creating biases in the prevalence and distribution of individual amino acids in CDR-H3. For example, arginine, which is often found in the CDR-H3 of dsDNA binding autoantibodies, is under-represented in the commonly used DH RFs rearranged by deletion, but is a frequent component of rarely used inverted RF1 (iRF1), which is rearranged by inversion. To determine the effect of altering this germline bias in DH gene segment sequence on autoantibody production, we generated mice that by genetic manipulation are forced to utilize an iRF1 sequence encoding two arginines. Over a one year period we collected serial serum samples from these unimmunized, specific pathogen-free mice and found that more than one-fifth of them contained elevated levels of dsDNA-binding IgG, but not IgM; whereas mice with a wild type DH sequence did not. Thus, germline bias against the use of arginine enriched DH sequence helps to reduce the likelihood of producing self-reactive antibodies.
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Affiliation(s)
- Aaron Silva-Sanchez
- Department of Medicine, Division of Clinical Immunology and Rheumatology, University of Alabama at Birmingham, Birmingham, Alabama, United States of America
| | - Cun Ren Liu
- Department of Medicine, Division of Clinical Immunology and Rheumatology, University of Alabama at Birmingham, Birmingham, Alabama, United States of America
| | - Andre M. Vale
- Department of Medicine, Division of Clinical Immunology and Rheumatology, University of Alabama at Birmingham, Birmingham, Alabama, United States of America
- Program in Immunobiology, Carlos Chagas Filho Institute of Biophysics, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil
| | - Mohamed Khass
- Department of Medicine, Division of Clinical Immunology and Rheumatology, University of Alabama at Birmingham, Birmingham, Alabama, United States of America
- Genetic Engineering Division, National Research Center of Egypt, Ad Doqi, Egypt
| | - Pratibha Kapoor
- Department of Medicine, Division of Clinical Immunology and Rheumatology, University of Alabama at Birmingham, Birmingham, Alabama, United States of America
| | - Ada Elgavish
- Department of Medicine, Division of Clinical Immunology and Rheumatology, University of Alabama at Birmingham, Birmingham, Alabama, United States of America
| | - Ivaylo I. Ivanov
- Department of Microbiology, University of Alabama at Birmingham, Birmingham, Alabama, United States of America
| | - Gregory C. Ippolito
- Department of Microbiology, University of Alabama at Birmingham, Birmingham, Alabama, United States of America
| | - Robert L. Schelonka
- Department of Pediatrics, University of Alabama at Birmingham, Birmingham, Alabama, United States of America
| | - Trenton R. Schoeb
- Department of Genetics, University of Alabama at Birmingham, Birmingham, Alabama, United States of America
| | - Peter D. Burrows
- Department of Microbiology, University of Alabama at Birmingham, Birmingham, Alabama, United States of America
- Department of Genetics, University of Alabama at Birmingham, Birmingham, Alabama, United States of America
| | - Harry W. Schroeder
- Department of Medicine, Division of Clinical Immunology and Rheumatology, University of Alabama at Birmingham, Birmingham, Alabama, United States of America
- Department of Microbiology, University of Alabama at Birmingham, Birmingham, Alabama, United States of America
- Department of Genetics, University of Alabama at Birmingham, Birmingham, Alabama, United States of America
- * E-mail:
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12
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Alves-Pereira CF, de Freitas R, Lopes T, Gardner R, Marta F, Vieira P, Barreto VM. Independent recruitment of Igh alleles in V(D)J recombination. Nat Commun 2014; 5:5623. [PMID: 25517887 PMCID: PMC4351640 DOI: 10.1038/ncomms6623] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2014] [Accepted: 10/20/2014] [Indexed: 01/05/2023] Open
Abstract
How the vast majority of B cells express only one of the two alleles at their immunoglobulin loci remains a biological puzzle. Here, in mice reconstituted with a single haematopoietic stem cell, we demonstrate that each of the two immunoglobulin heavy chain (Igh) alleles has a similar probability to be the first to undergo V(H) to DJ(H) rearrangement. We also observe this similar probability in clones from multipotent and common lymphoid precursors. The extreme biases in the expression of the alleles that we find in more differentiated subsets are mostly due to constraints imposed by early rearrangements. Our data demonstrate that each of the two Igh alleles in a B cell behaves independently of the other, up to the moment when a successful rearrangement in one allele triggers a feedback mechanism that prevents further recombination.
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Affiliation(s)
- Clara F. Alves-Pereira
- Epigenetics and Soma Laboratory, Instituto Gulbenkian de Ciência, Rua da Quinta Grande, n° 6, 2780-156 Oeiras, Portugal
| | - Raquel de Freitas
- Epigenetics and Soma Laboratory, Instituto Gulbenkian de Ciência, Rua da Quinta Grande, n° 6, 2780-156 Oeiras, Portugal
| | - Telma Lopes
- Flow Cytometry Laboratory UIC, Instituto Gulbenkian de Ciência, Rua da Quinta Grande, n° 6, 2780-156 Oeiras, Portugal
| | - Rui Gardner
- Flow Cytometry Laboratory UIC, Instituto Gulbenkian de Ciência, Rua da Quinta Grande, n° 6, 2780-156 Oeiras, Portugal
| | - Filipa Marta
- Epigenetics and Soma Laboratory, Instituto Gulbenkian de Ciência, Rua da Quinta Grande, n° 6, 2780-156 Oeiras, Portugal
| | - Paulo Vieira
- Unité Lymphopoïèse, Institut Pasteur, 25, Rue du Dr Roux, 75724 Paris, France
- INSERM U668, F-75015 Paris, France
| | - Vasco M. Barreto
- Epigenetics and Soma Laboratory, Instituto Gulbenkian de Ciência, Rua da Quinta Grande, n° 6, 2780-156 Oeiras, Portugal
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Chen MY, Chen YP, Wu MS, Yu GY, Lin WJ, Tan TH, Su YW. PP4 is essential for germinal center formation and class switch recombination in mice. PLoS One 2014; 9:e107505. [PMID: 25215539 PMCID: PMC4162579 DOI: 10.1371/journal.pone.0107505] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2014] [Accepted: 08/11/2014] [Indexed: 01/12/2023] Open
Abstract
PP4 is a serine/threonine phosphatase required for immunoglobulin (Ig) VDJ recombination and pro-B/pre-B cell development in mice. To elucidate the role of PP4 in mature B cells, we ablated the catalytic subunit of murine PP4 invivo utilizing the CD23 promoter and cre-loxP recombination and generated CD23crePP4F/F mice. The development of follicular and marginal zone B cells was unaffected in these mutants, but the proliferation of mature PP4-deficient B cells stimulated by invitro treatment with either anti-IgM antibody (Ab) or LPS was partially impaired. Interestingly, the induction of CD80 and CD86 expression on these stimulated B cells was normal. Basal levels of serum Igs of all isotypes were strongly reduced in CD23crePP4F/F mice, and their B cells showed a reduced efficiency of class switch recombination (CSR) invitro upon stimulation by LPS or LPS plus IL-4. When CD23crePP4F/F mice were challenged with either the T cell-dependent antigen TNP-KLH or the T cell-independent antigen TNP-Ficoll, or by H1N1 virus infection, the mutant animals failed to form germinal centers (GCs) in the spleen and the draining mediastinal lymph nodes, and did not efficiently mount antigen-specific humoral responses. In the resting state, PP4-deficient B cells exhibited pre-existing DNA fragmentation. Upon stimulation by DNA-damaging drug etoposide invitro, mutant B cells showed increased cleavage of caspase 3. In addition, the mutant B cells displayed impaired CD40-mediated MAPK activation, abnormal IgM-mediated NF-κB activation, and reduced S phase entry upon IgM/CD40-stimulation. Taken together, our results establish a novel role for PP4 in CSR, and reveal crucial functions for PP4 in the maintenance of genomic stability, GC formation, and B cell-mediated immune responses.
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Affiliation(s)
- Ming-Yu Chen
- Immunology Research Center, National Health Research Institutes, Zhunan, Miaoli County, Taiwan
| | - Ya-Ping Chen
- Immunology Research Center, National Health Research Institutes, Zhunan, Miaoli County, Taiwan
| | - Ming-Sian Wu
- National Institute of Infectious Diseases and Vaccinology, National Health Research Institutes, Zhunan, Miaoli County, Taiwan
| | - Guanni-Yi Yu
- National Institute of Infectious Diseases and Vaccinology, National Health Research Institutes, Zhunan, Miaoli County, Taiwan
| | - Wen-Jye Lin
- Immunology Research Center, National Health Research Institutes, Zhunan, Miaoli County, Taiwan
| | - Tse-Hua Tan
- Immunology Research Center, National Health Research Institutes, Zhunan, Miaoli County, Taiwan
- Department of Pathology & Immunology, Baylor College of Medicine, Houston, Texas, United States of America
| | - Yu-Wen Su
- Immunology Research Center, National Health Research Institutes, Zhunan, Miaoli County, Taiwan
- * E-mail:
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14
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Abstract
V(D)J recombination is the process by which the diversity of antigen receptor genes is generated and is also indispensable for lymphocyte development. This recombination event occurs in a cell lineage- and stage-specific manner, and is carefully controlled by chromatin structure and ordered histone modifications. The recombinationally active V(D)J loci are associated with hypermethylation at lysine4 of histone H3 and hyperacetylation of histones H3/H4. The recombination activating gene 1 (RAG1) and RAG2 complex initiates recombination by introducing double-strand DNA breaks at recombination signal sequences (RSS) adjacent to each coding sequence. To be recognized by the RAG complex, RSS sites must be within an open chromatin context. In addition, the RAG complex specifically recognizes hypermethylated H3K4 through its plant homeodomain (PHD) finger in the RAG2 C terminus, which stimulates RAG catalytic activity via that interaction. In this review, we describe how histone methylation controls V(D)J recombination and discuss its potential role in lymphoid malignancy by mistargeting the RAG complex.
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Affiliation(s)
- Noriko Shimazaki
- Section of Molecular and Computational Biology, Departments of Pathology, Biochemistry and Molecular Biology, Molecular Microbiology and Immunology, USC Norris Comprehensive Cancer Ctr., Rm. 5428, 1441 Eastlake Ave., MC 9176, Los Angeles, CA, 90089-9176, USA,
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15
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Matthews AJ, Zheng S, DiMenna LJ, Chaudhuri J. Regulation of immunoglobulin class-switch recombination: choreography of noncoding transcription, targeted DNA deamination, and long-range DNA repair. Adv Immunol 2014; 122:1-57. [PMID: 24507154 PMCID: PMC4150736 DOI: 10.1016/b978-0-12-800267-4.00001-8] [Citation(s) in RCA: 102] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Upon encountering antigens, mature IgM-positive B lymphocytes undergo class-switch recombination (CSR) wherein exons encoding the default Cμ constant coding gene segment of the immunoglobulin (Ig) heavy-chain (Igh) locus are excised and replaced with a new constant gene segment (referred to as "Ch genes", e.g., Cγ, Cɛ, or Cα). The B cell thereby changes from expressing IgM to one producing IgG, IgE, or IgA, with each antibody isotype having a different effector function during an immune reaction. CSR is a DNA deletional-recombination reaction that proceeds through the generation of DNA double-strand breaks (DSBs) in repetitive switch (S) sequences preceding each Ch gene and is completed by end-joining between donor Sμ and acceptor S regions. CSR is a multistep reaction requiring transcription through S regions, the DNA cytidine deaminase AID, and the participation of several general DNA repair pathways including base excision repair, mismatch repair, and classical nonhomologous end-joining. In this review, we discuss our current understanding of how transcription through S regions generates substrates for AID-mediated deamination and how AID participates not only in the initiation of CSR but also in the conversion of deaminated residues into DSBs. Additionally, we review the multiple processes that regulate AID expression and facilitate its recruitment specifically to the Ig loci, and how deregulation of AID specificity leads to oncogenic translocations. Finally, we summarize recent data on the potential role of AID in the maintenance of the pluripotent stem cell state during epigenetic reprogramming.
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Affiliation(s)
- Allysia J Matthews
- Immunology Program, Memorial Sloan-Kettering Cancer Center, New York, New York, USA; Immunology and Microbial Pathogenesis Program, Weill Cornell Graduate School of Medical Sciences, New York, New York, USA
| | - Simin Zheng
- Immunology Program, Memorial Sloan-Kettering Cancer Center, New York, New York, USA; Immunology and Microbial Pathogenesis Program, Weill Cornell Graduate School of Medical Sciences, New York, New York, USA
| | - Lauren J DiMenna
- Immunology Program, Memorial Sloan-Kettering Cancer Center, New York, New York, USA; Immunology and Microbial Pathogenesis Program, Weill Cornell Graduate School of Medical Sciences, New York, New York, USA
| | - Jayanta Chaudhuri
- Immunology Program, Memorial Sloan-Kettering Cancer Center, New York, New York, USA; Immunology and Microbial Pathogenesis Program, Weill Cornell Graduate School of Medical Sciences, New York, New York, USA.
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16
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Rubelt F, Sievert V, Knaust F, Diener C, Lim TS, Skriner K, Klipp E, Reinhardt R, Lehrach H, Konthur Z. Onset of immune senescence defined by unbiased pyrosequencing of human immunoglobulin mRNA repertoires. PLoS One 2012; 7:e49774. [PMID: 23226220 PMCID: PMC3511497 DOI: 10.1371/journal.pone.0049774] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2012] [Accepted: 10/12/2012] [Indexed: 12/15/2022] Open
Abstract
The immune system protects us from foreign substances or pathogens by generating specific antibodies. The variety of immunoglobulin (Ig) paratopes for antigen recognition is a result of the V(D)J rearrangement mechanism, while a fast and efficient immune response is mediated by specific immunoglobulin isotypes obtained through class switch recombination (CSR). To get a better understanding on how antibody-based immune protection works and how it changes with age, the interdependency between these two parameters need to be addressed. Here, we have performed an in depth analysis of antibody repertoires of 14 healthy donors representing different gender and age groups. For this task, we developed a unique pyrosequencing approach, which is able to monitor the expression levels of all immunoglobulin V(D)J recombinations of all isotypes including subtypes in an unbiased and quantitative manner. Our results show that donors have individual immunoglobulin repertoires and cannot be clustered according to V(D)J recombination patterns, neither by age nor gender. However, after incorporating isotype-specific analysis and considering CSR information into hierarchical clustering the situation changes. For the first time the donors cluster according to age and separate into young adults and elderly donors (>50). As a direct consequence, this clustering defines the onset of immune senescence at the age of fifty and beyond. The observed age-dependent reduction of CSR ability proposes a feasible explanation why reduced efficacy of vaccination is seen in the elderly and implies that novel vaccine strategies for the elderly should include the "Golden Agers".
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Affiliation(s)
- Florian Rubelt
- Max Planck Institute for Molecular Genetics, Berlin, Germany
- Faculty of Biology, Chemistry, and Pharmacy, Freie Universität Berlin, Berlin, Germany
| | - Volker Sievert
- Max Planck Institute for Molecular Genetics, Berlin, Germany
| | - Florian Knaust
- Max Planck Institute for Molecular Genetics, Berlin, Germany
| | - Christian Diener
- Max Planck Institute for Molecular Genetics, Berlin, Germany
- Theoretische Biophysik, Humboldt-Universität zu Berlin, Berlin, Germany
| | - Theam Soon Lim
- Max Planck Institute for Molecular Genetics, Berlin, Germany
- Institute for Research in Molecular Medicine, Universiti Sains Malaysia, Penang, Malaysia
| | - Karl Skriner
- Department of Rheumatology and Clinical Immunology, Charité – Universitätsmedizin Berlin, Berlin, Germany
| | - Edda Klipp
- Theoretische Biophysik, Humboldt-Universität zu Berlin, Berlin, Germany
| | - Richard Reinhardt
- Max Planck Institute for Molecular Genetics, Berlin, Germany
- Max Planck Genome Centre Cologne, Max Planck Institute for Plant Breeding Research, Cologne, Germany
| | - Hans Lehrach
- Max Planck Institute for Molecular Genetics, Berlin, Germany
| | - Zoltán Konthur
- Max Planck Institute for Molecular Genetics, Berlin, Germany
- * E-mail:
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17
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Sebastián E, Alcoceba M, Balanzategui A, Marín L, Montes-Moreno S, Flores T, González D, Sarasquete ME, Chillón MC, Puig N, Corral R, Pardal E, Martín A, González-Barca E, Caballero MD, San Miguel JF, García-Sanz R, González M. Molecular characterization of immunoglobulin gene rearrangements in diffuse large B-cell lymphoma: antigen-driven origin and IGHV4-34 as a particular subgroup of the non-GCB subtype. Am J Pathol 2012; 181:1879-88. [PMID: 22982190 DOI: 10.1016/j.ajpath.2012.07.028] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/13/2012] [Revised: 07/19/2012] [Accepted: 07/30/2012] [Indexed: 01/05/2023]
Abstract
The pathogenesis of diffuse large B-cell lymphoma (DLBCL) remains partially unknown. The analysis of the B-cell receptor of the malignant cells could contribute to a better understanding of the DLBCL biology. We studied the molecular features of the immunoglobulin heavy chain (IGH) rearrangements in 165 patients diagnosed with DLBCL not otherwise specified. Clonal IGH rearrangements were amplified according to the BIOMED-2 protocol and PCR products were sequenced directly. We also analyzed the criteria for stereotyped patterns in all complete IGHV-IGHD-IGHJ (V-D-J) sequences. Complete V-D-J rearrangements were identified in 130 of 165 patients. Most cases (89%) were highly mutated, but 12 sequences were truly unmutated or minimally mutated. Three genes, IGHV4-34, IGHV3-23, and IGHV4-39, accounted for one third of the whole cohort, including an overrepresentation of IGHV4-34 (15.5% overall). Interestingly, all IGHV4-34 rearrangements and all unmutated sequences belonged to the nongerminal center B-cell-like (non-GCB) subtype. Overall, we found three cases following the current criteria for stereotyped heavy chain VH CDR3 sequences, two of them belonging to subsets previously described in CLL. IGHV gene repertoire is remarkably biased, implying an antigen-driven origin in DLBCL. The particular features in the sequence of the immunoglobulins suggest the existence of particular subgroups within the non-GCB subtype.
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MESH Headings
- Adolescent
- Adult
- Aged
- Aged, 80 and over
- Amino Acid Sequence
- Amino Acids/genetics
- Antigens, Neoplasm/immunology
- Clone Cells
- Complementarity Determining Regions/chemistry
- Complementarity Determining Regions/genetics
- Female
- Gene Rearrangement, B-Lymphocyte, Heavy Chain/genetics
- Germinal Center/immunology
- Humans
- Immunoglobulin Heavy Chains/genetics
- Immunoglobulin Variable Region/genetics
- Immunohistochemistry
- Lymphoma, Large B-Cell, Diffuse/classification
- Lymphoma, Large B-Cell, Diffuse/diagnosis
- Lymphoma, Large B-Cell, Diffuse/genetics
- Lymphoma, Large B-Cell, Diffuse/immunology
- Male
- Middle Aged
- Molecular Sequence Data
- Mutation/genetics
- Somatic Hypermutation, Immunoglobulin/genetics
- Somatic Hypermutation, Immunoglobulin/immunology
- V(D)J Recombination/genetics
- V(D)J Recombination/immunology
- Young Adult
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Affiliation(s)
- Elena Sebastián
- Department of Hematology, University Hospital of Salamanca, Spain
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18
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Beham AW, Puellmann K, Laird R, Fuchs T, Streich R, Breysach C, Raddatz D, Oniga S, Peccerella T, Findeisen P, Kzhyshkowska J, Gratchev A, Schweyer S, Saunders B, Wessels JT, Möbius W, Keane J, Becker H, Ganser A, Neumaier M, Kaminski WE. A TNF-regulated recombinatorial macrophage immune receptor implicated in granuloma formation in tuberculosis. PLoS Pathog 2011; 7:e1002375. [PMID: 22114556 PMCID: PMC3219713 DOI: 10.1371/journal.ppat.1002375] [Citation(s) in RCA: 51] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2011] [Accepted: 09/28/2011] [Indexed: 12/23/2022] Open
Abstract
Macrophages play a central role in host defense against mycobacterial infection and anti- TNF therapy is associated with granuloma disorganization and reactivation of tuberculosis in humans. Here, we provide evidence for the presence of a T cell receptor (TCR) αβ based recombinatorial immune receptor in subpopulations of human and mouse monocytes and macrophages. In vitro, we find that the macrophage-TCRαβ induces the release of CCL2 and modulates phagocytosis. TNF blockade suppresses macrophage-TCRαβ expression. Infection of macrophages from healthy individuals with mycobacteria triggers formation of clusters that express restricted TCR Vβ repertoires. In vivo, TCRαβ bearing macrophages abundantly accumulate at the inner host-pathogen contact zone of caseous granulomas from patients with lung tuberculosis. In chimeric mouse models, deletion of the variable macrophage-TCRαβ or TNF is associated with structurally compromised granulomas of pulmonary tuberculosis even in the presence of intact T cells. These results uncover a TNF-regulated recombinatorial immune receptor in monocytes/macrophages and demonstrate its implication in granuloma formation in tuberculosis.
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Affiliation(s)
| | - Kerstin Puellmann
- Department of Hematology, Hemostasis, Oncology and Stem Cell Transplantation, Hannover Medical School (MHH), Hannover, Germany
| | - Rebecca Laird
- Department of Surgery, University of Göttingen, Göttingen, Germany
| | - Tina Fuchs
- Institute for Clinical Chemistry, University of Heidelberg Medical Faculty Mannheim, Mannheim, Germany
| | - Roswita Streich
- Department of Surgery, University of Göttingen, Göttingen, Germany
| | | | - Dirk Raddatz
- Department of Medicine, University of Göttingen, Göttingen, Germany
| | - Septimia Oniga
- Institute for Clinical Chemistry, University of Heidelberg Medical Faculty Mannheim, Mannheim, Germany
| | - Teresa Peccerella
- Institute for Clinical Chemistry, University of Heidelberg Medical Faculty Mannheim, Mannheim, Germany
| | - Peter Findeisen
- Institute for Clinical Chemistry, University of Heidelberg Medical Faculty Mannheim, Mannheim, Germany
| | - Julia Kzhyshkowska
- Department of Dermatology, University of Heidelberg Medical Faculty Mannheim, Mannheim, Germany
- Institute of General Pathology and Pathophysiology, Russian Academy of Medical Sciences, Moscow, Russia
| | - Alexei Gratchev
- Department of Dermatology, University of Heidelberg Medical Faculty Mannheim, Mannheim, Germany
- Institute of General Pathology and Pathophysiology, Russian Academy of Medical Sciences, Moscow, Russia
| | - Stefan Schweyer
- Department of Pathology, University of Göttingen, Göttingen, Germany
| | - Bernadette Saunders
- Medicine, Central Clinical School, Centenary Institute of Cancer Medicine and Cell Biology, Sydney, Australia
| | - Johannes T. Wessels
- Department of Nephrology/Rheumatology, University of Göttingen, Göttingen, Germany
| | - Wiebke Möbius
- Max-Planck-Institute of Experimental Medicine, Department of Neurogenetics, Göttingen, Germany
- Trinity College Dublin, Institute of Molecular Medicine, College Green, Dublin, Ireland
| | - Joseph Keane
- Trinity College Dublin, Institute of Molecular Medicine, College Green, Dublin, Ireland
| | - Heinz Becker
- Department of Surgery, University of Göttingen, Göttingen, Germany
| | - Arnold Ganser
- Department of Hematology, Hemostasis, Oncology and Stem Cell Transplantation, Hannover Medical School (MHH), Hannover, Germany
| | - Michael Neumaier
- Institute for Clinical Chemistry, University of Heidelberg Medical Faculty Mannheim, Mannheim, Germany
| | - Wolfgang E. Kaminski
- Institute for Clinical Chemistry, University of Heidelberg Medical Faculty Mannheim, Mannheim, Germany
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