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Roth-Walter F, Adcock IM, Benito-Villalvilla C, Bianchini R, Bjermer L, Caramori G, Cari L, Chung KF, Diamant Z, Eguiluz-Gracia I, Knol EF, Jesenak M, Levi-Schaffer F, Nocentini G, O'Mahony L, Palomares O, Redegeld F, Sokolowska M, Van Esch BCAM, Stellato C. Metabolic pathways in immune senescence and inflammaging: Novel therapeutic strategy for chronic inflammatory lung diseases. An EAACI position paper from the Task Force for Immunopharmacology. Allergy 2024; 79:1089-1122. [PMID: 38108546 DOI: 10.1111/all.15977] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2023] [Revised: 11/24/2023] [Accepted: 11/27/2023] [Indexed: 12/19/2023]
Abstract
The accumulation of senescent cells drives inflammaging and increases morbidity of chronic inflammatory lung diseases. Immune responses are built upon dynamic changes in cell metabolism that supply energy and substrates for cell proliferation, differentiation, and activation. Metabolic changes imposed by environmental stress and inflammation on immune cells and tissue microenvironment are thus chiefly involved in the pathophysiology of allergic and other immune-driven diseases. Altered cell metabolism is also a hallmark of cell senescence, a condition characterized by loss of proliferative activity in cells that remain metabolically active. Accelerated senescence can be triggered by acute or chronic stress and inflammatory responses. In contrast, replicative senescence occurs as part of the physiological aging process and has protective roles in cancer surveillance and wound healing. Importantly, cell senescence can also change or hamper response to diverse therapeutic treatments. Understanding the metabolic pathways of senescence in immune and structural cells is therefore critical to detect, prevent, or revert detrimental aspects of senescence-related immunopathology, by developing specific diagnostics and targeted therapies. In this paper, we review the main changes and metabolic alterations occurring in senescent immune cells (macrophages, B cells, T cells). Subsequently, we present the metabolic footprints described in translational studies in patients with chronic asthma and chronic obstructive pulmonary disease (COPD), and review the ongoing preclinical studies and clinical trials of therapeutic approaches aiming at targeting metabolic pathways to antagonize pathological senescence. Because this is a recently emerging field in allergy and clinical immunology, a better understanding of the metabolic profile of the complex landscape of cell senescence is needed. The progress achieved so far is already providing opportunities for new therapies, as well as for strategies aimed at disease prevention and supporting healthy aging.
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Affiliation(s)
- F Roth-Walter
- Comparative Medicine, The Interuniversity Messerli Research Institute of the University of Veterinary Medicine Vienna, Medical University Vienna and University Vienna, Vienna, Austria
- Institute of Pathophysiology and Allergy Research, Center of Pathophysiology, Infectiology and Immunology, Medical University of Vienna, Vienna, Austria
| | - I M Adcock
- Molecular Cell Biology Group, National Heart & Lung Institute, Imperial College London, London, UK
| | - C Benito-Villalvilla
- Department of Biochemistry and Molecular Biology, School of Chemistry, Complutense University of Madrid, Madrid, Spain
| | - R Bianchini
- Comparative Medicine, The Interuniversity Messerli Research Institute of the University of Veterinary Medicine Vienna, Medical University Vienna and University Vienna, Vienna, Austria
| | - L Bjermer
- Department of Respiratory Medicine and Allergology, Lung and Allergy research, Allergy, Asthma and COPD Competence Center, Lund University, Lund, Sweden
| | - G Caramori
- Department of Medicine and Surgery, University of Parma, Pneumologia, Italy
| | - L Cari
- Department of Medicine, Section of Pharmacology, University of Perugia, Perugia, Italy
| | - K F Chung
- Experimental Studies Medicine at National Heart & Lung Institute, Imperial College London & Royal Brompton & Harefield Hospital, London, UK
| | - Z Diamant
- Department of Respiratory Medicine and Allergology, Institute for Clinical Science, Skane University Hospital, Lund, Sweden
- Department of Respiratory Medicine, First Faculty of Medicine, Charles University and Thomayer Hospital, Prague, Czech Republic
- Department of Clinical Pharmacy & Pharmacology, University Groningen, University Medical Center Groningen and QPS-NL, Groningen, The Netherlands
| | - I Eguiluz-Gracia
- Allergy Unit, Hospital Regional Universitario de Málaga-Instituto de Investigación Biomédica de Málaga (IBIMA)-ARADyAL, Málaga, Spain
| | - E F Knol
- Departments of Center of Translational Immunology and Dermatology/Allergology, University Medical Center Utrecht, Utrecht, The Netherlands
| | - M Jesenak
- Department of Paediatrics, Department of Pulmonology and Phthisiology, Comenius University in Bratislava, Jessenius Faculty of Medicine in Martin, University Teaching Hospital, Martin, Slovakia
| | - F Levi-Schaffer
- Institute for Drug Research, Pharmacology Unit, Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - G Nocentini
- Department of Medicine, Section of Pharmacology, University of Perugia, Perugia, Italy
| | - L O'Mahony
- APC Microbiome Ireland, University College Cork, Cork, Ireland
- Department of Medicine, University College Cork, Cork, Ireland
- School of Microbiology, University College Cork, Cork, Ireland
| | - O Palomares
- Department of Biochemistry and Molecular Biology, School of Chemistry, Complutense University of Madrid, Madrid, Spain
| | - F Redegeld
- Division of Pharmacology, Utrecht Institute for Pharmaceutical Sciences, Faculty of Science, Utrecht University, Utrecht, The Netherlands
| | - M Sokolowska
- Swiss Institute of Allergy and Asthma Research (SIAF), University of Zürich, Davos, Switzerland
- Christine Kühne - Center for Allergy Research and Education (CK-CARE), Davos, Switzerland
| | - B C A M Van Esch
- Division of Pharmacology, Utrecht Institute for Pharmaceutical Sciences, Faculty of Science, Utrecht University, Utrecht, The Netherlands
| | - C Stellato
- Department of Medicine, Surgery and Dentistry "Scuola Medica Salernitana", University of Salerno, Salerno, Italy
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Morabito G, Ryabova A, Valenzano DR. Immune aging in annual killifish. Immun Ageing 2024; 21:18. [PMID: 38459521 PMCID: PMC10921792 DOI: 10.1186/s12979-024-00418-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2023] [Accepted: 02/12/2024] [Indexed: 03/10/2024]
Abstract
Turquoise killifish (Nothobranchius furzeri) evolved a naturally short lifespan of about six months and exhibit aging hallmarks that affect multiple organs. These hallmarks include protein aggregation, telomere shortening, cellular senescence, and systemic inflammation. Turquoise killifish possess the full spectrum of vertebrate-specific innate and adaptive immune system. However, during their recent evolutionary history, they lost subsets of mucosal-specific antibody isoforms that are present in other teleosts. As they age, the immune system of turquoise killifish undergoes dramatic cellular and systemic changes. These changes involve increased inflammation, reduced antibody diversity, an increased prevalence of pathogenic microbes in the intestine, and extensive DNA damage in immune progenitor cell clusters. Collectively, the wide array of age-related changes occurring in turquoise killifish suggest that, despite an evolutionary separation spanning hundreds of millions of years, teleosts and mammals share common features of immune system aging. Hence, the spontaneous aging observed in the killifish immune system offers an excellent opportunity for discovering fundamental and conserved aspects associated with immune system aging across vertebrates. Additionally, the species' naturally short lifespan of only a few months, along with its experimental accessibility, offers a robust platform for testing interventions to improve age-related dysfunctions in the whole organism and potentially inform the development of immune-based therapies for human aging-related diseases.
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Affiliation(s)
| | - Alina Ryabova
- Leibniz Institute on Aging, Fritz Lipmann Institute, Jena, Germany
| | - Dario Riccardo Valenzano
- Leibniz Institute on Aging, Fritz Lipmann Institute, Jena, Germany.
- Friedrich Schiller University, Jena, Germany.
- Cluster of Excellence Balance of the Microverse, Friedrich Schiller University, Jena, Germany.
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3
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Feng F, Yuen R, Wang Y, Hua A, Kepler TB, Wetzler LM. Characterizing adjuvants' effects at murine immunoglobulin repertoire level. iScience 2024; 27:108749. [PMID: 38269092 PMCID: PMC10805652 DOI: 10.1016/j.isci.2023.108749] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2023] [Revised: 09/29/2023] [Accepted: 12/12/2023] [Indexed: 01/26/2024] Open
Abstract
Generating large-scale, high-fidelity sequencing data is challenging and, furthermore, not much has been done to characterize adjuvants' effects at the repertoire level. Thus, we introduced an IgSeq pipeline that standardized library prep protocols and data analysis functions for accurate repertoire profiling. We then studied systemically effects of CpG and Alum on the Ig heavy chain repertoire using the ovalbumin (OVA) murine model. Ig repertoires of different tissues (spleen and bone marrow) and isotypes (IgG and IgM) were examined and compared in IGHV mutation, gene usage, CDR3 length, clonal diversity, and clonal selection. We found Ig repertoires of different compartments exhibited distinguishable profiles at the non-immunized steady state, and distinctions became more pronounced upon adjuvanted immunizations. Notably, Alum and CpG effects exhibited different tissue- and isotype-preferences. The former led to increased diversity of abundant clones in bone marrow, and the latter promoted the selection of IgG clones in both tissues.
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Affiliation(s)
- Feng Feng
- Department of Microbiology, Boston University, Boston, MA 02118, USA
| | - Rachel Yuen
- Department of Microbiology, Boston University, Boston, MA 02118, USA
| | - Yumei Wang
- Department of Microbiology, Boston University, Boston, MA 02118, USA
| | - Axin Hua
- Department of Microbiology, Boston University, Boston, MA 02118, USA
| | - Thomas B. Kepler
- Department of Microbiology, Boston University, Boston, MA 02118, USA
- Department of Mathematics and Statistics, Boston University, Boston, MA 02118, USA
| | - Lee M. Wetzler
- Department of Microbiology, Boston University, Boston, MA 02118, USA
- Department of Medicine, Boston University School of Medicine, Boston University, Boston, MA 02118, USA
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Rodriguez OL, Safonova Y, Silver CA, Shields K, Gibson WS, Kos JT, Tieri D, Ke H, Jackson KJL, Boyd SD, Smith ML, Marasco WA, Watson CT. Genetic variation in the immunoglobulin heavy chain locus shapes the human antibody repertoire. Nat Commun 2023; 14:4419. [PMID: 37479682 PMCID: PMC10362067 DOI: 10.1038/s41467-023-40070-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2022] [Accepted: 07/11/2023] [Indexed: 07/23/2023] Open
Abstract
Variation in the antibody response has been linked to differential outcomes in disease, and suboptimal vaccine and therapeutic responsiveness, the determinants of which have not been fully elucidated. Countering models that presume antibodies are generated largely by stochastic processes, we demonstrate that polymorphisms within the immunoglobulin heavy chain locus (IGH) impact the naive and antigen-experienced antibody repertoire, indicating that genetics predisposes individuals to mount qualitatively and quantitatively different antibody responses. We pair recently developed long-read genomic sequencing methods with antibody repertoire profiling to comprehensively resolve IGH genetic variation, including novel structural variants, single nucleotide variants, and genes and alleles. We show that IGH germline variants determine the presence and frequency of antibody genes in the expressed repertoire, including those enriched in functional elements linked to V(D)J recombination, and overlapping disease-associated variants. These results illuminate the power of leveraging IGH genetics to better understand the regulation, function, and dynamics of the antibody response in disease.
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Affiliation(s)
- Oscar L Rodriguez
- Department of Biochemistry and Molecular Genetics, University of Louisville School of Medicine, Louisville, KY, USA
| | - Yana Safonova
- Department of Computer Science, Johns Hopkins University, Baltimore, MD, USA
| | - Catherine A Silver
- Department of Biochemistry and Molecular Genetics, University of Louisville School of Medicine, Louisville, KY, USA
| | - Kaitlyn Shields
- Department of Biochemistry and Molecular Genetics, University of Louisville School of Medicine, Louisville, KY, USA
| | - William S Gibson
- Department of Biochemistry and Molecular Genetics, University of Louisville School of Medicine, Louisville, KY, USA
| | - Justin T Kos
- Department of Biochemistry and Molecular Genetics, University of Louisville School of Medicine, Louisville, KY, USA
| | - David Tieri
- Department of Biochemistry and Molecular Genetics, University of Louisville School of Medicine, Louisville, KY, USA
| | - Hanzhong Ke
- Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
- Department of Medicine, Harvard Medical School, Boston, MA, USA
| | | | - Scott D Boyd
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
| | - Melissa L Smith
- Department of Biochemistry and Molecular Genetics, University of Louisville School of Medicine, Louisville, KY, USA.
| | - Wayne A Marasco
- Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA.
- Department of Medicine, Harvard Medical School, Boston, MA, USA.
| | - Corey T Watson
- Department of Biochemistry and Molecular Genetics, University of Louisville School of Medicine, Louisville, KY, USA.
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5
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Betjes MGH, De Weerd A. Lowering maintenance immune suppression in elderly kidney transplant recipients; connecting the immunological and clinical dots. Front Med (Lausanne) 2023; 10:1215167. [PMID: 37502354 PMCID: PMC10368955 DOI: 10.3389/fmed.2023.1215167] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2023] [Accepted: 06/09/2023] [Indexed: 07/29/2023] Open
Abstract
The management of long-term immune suppressive medication in kidney transplant recipients is a poorly explored field in the area of transplant medicine. In particular, older recipients are at an increased risk for side effects and have an exponentially increased risk of infection-related death. In contrast, an aged immune system decreases the risk of acute T-cell-mediated rejection in older recipients. Recent advances in alloimmunity research have shown a rapid and substantial decline in polyfunctional, high-risk CD4+ T cells post-transplantation. This lowers the direct alloreactivity responsible for T-cell-mediated rejection, also known as donor-specific hyporesponsiveness. Chronic antibody-mediated rejection (c-aABMR) is the most frequent cause of kidney graft loss in the long term. However, in older adults, c-aABMR as a cause of graft loss is outnumbered by death with a functioning graft. In addition, DSA development and a diagnosis of c-aABMR plateau ~10 years after transplantation, resulting in a very low risk for rejection thereafter. The intensity of immune suppression regimes could likely be reduced accordingly, but trials in this area are scarce. Tacrolimus monotherapy for 1 year after transplantation seems feasible in older kidney transplant recipients with standard immunological risk, showing the expected benefits of fewer infections and better vaccination responses.
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Monzó C, Gkioni L, Beyer A, Valenzano DR, Grönke S, Partridge L. Dietary restriction mitigates the age-associated decline in mouse B cell receptor repertoire diversity. Cell Rep 2023; 42:112722. [PMID: 37384530 PMCID: PMC10391628 DOI: 10.1016/j.celrep.2023.112722] [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: 01/16/2023] [Revised: 05/07/2023] [Accepted: 06/13/2023] [Indexed: 07/01/2023] Open
Abstract
Aging impairs the capacity to respond to novel antigens, reducing immune protection against pathogens and vaccine efficacy. Dietary restriction (DR) extends life- and health span in diverse animals. However, little is known about the capacity of DR to combat the decline in immune function. Here, we study the changes in B cell receptor (BCR) repertoire during aging in DR and control mice. By sequencing the variable region of the BCR heavy chain in the spleen, we show that DR preserves diversity and attenuates the increase in clonal expansions throughout aging. Remarkably, mice starting DR in mid-life have repertoire diversity and clonal expansion rates indistinguishable from chronic DR mice. In contrast, in the intestine, these traits are unaffected by either age or DR. Reduced within-individual B cell repertoire diversity and increased clonal expansions are correlated with higher morbidity, suggesting a potential contribution of B cell repertoire dynamics to health during aging.
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Affiliation(s)
- Carolina Monzó
- Department Biological Mechanisms of Ageing, Max Planck Institute for Biology of Ageing, 50931 Cologne, North Rhine Westphalia, Germany; Cologne Excellence Cluster on Cellular Stress Responses in Age-Associated Diseases (CECAD), Faculty of Medicine and Faculty of Mathematics and Natural Sciences, University of Cologne, 50931 Cologne, Germany
| | - Lisonia Gkioni
- Department Biological Mechanisms of Ageing, Max Planck Institute for Biology of Ageing, 50931 Cologne, North Rhine Westphalia, Germany
| | - Andreas Beyer
- Cologne Excellence Cluster on Cellular Stress Responses in Age-Associated Diseases (CECAD), Faculty of Medicine and Faculty of Mathematics and Natural Sciences, University of Cologne, 50931 Cologne, Germany
| | - Dario Riccardo Valenzano
- Microbiome-Host Interactions in Ageing Group, Max Planck Institute for Biology of Ageing, 50931 Cologne, North Rhine Westphalia, Germany; Evolutionary Biology/Microbiome-Host Interactions in Aging Group: Fritz Lipmann Institute - Leibniz Institute on Aging, 07745 Jena, Thuringia, Germany.
| | - Sebastian Grönke
- Department Biological Mechanisms of Ageing, Max Planck Institute for Biology of Ageing, 50931 Cologne, North Rhine Westphalia, Germany.
| | - Linda Partridge
- Department Biological Mechanisms of Ageing, Max Planck Institute for Biology of Ageing, 50931 Cologne, North Rhine Westphalia, Germany; Genetics, Evolution & Environment Group, Institute of Healthy Ageing, University College London, London WC1E 6BT, UK.
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7
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Paschold L, Gottschick C, Langer S, Klee B, Diexer S, Aksentijevich I, Schultheiß C, Purschke O, Riese P, Trittel S, Haase R, Dressler F, Eberl W, Hübner J, Strowig T, Guzman CA, Mikolajczyk R, Binder M. T cell repertoire breadth is associated with the number of acute respiratory infections in the LoewenKIDS birth cohort. Sci Rep 2023; 13:9516. [PMID: 37308563 DOI: 10.1038/s41598-023-36144-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2023] [Accepted: 05/30/2023] [Indexed: 06/14/2023] Open
Abstract
We set out to gain insight into peripheral blood B and T cell repertoires from 120 infants of the LoewenKIDS birth cohort to investigate potential determinants of early life respiratory infections. Low antigen-dependent somatic hypermutation of B cell repertoires, as well as low T and B cell repertoire clonality, high diversity, and high richness especially in public T cell clonotypes reflected the immunological naivety at 12 months of age when high thymic and bone marrow output are associated with relatively few prior antigen encounters. Infants with inadequately low T cell repertoire diversity or high clonality showed higher numbers of acute respiratory infections over the first 4 years of life. No correlation of T or B cell repertoire metrics with other parameters such as sex, birth mode, older siblings, pets, the onset of daycare, or duration of breast feeding was noted. Together, this study supports that-regardless of T cell functionality-the breadth of the T cell repertoire is associated with the number of acute respiratory infections in the first 4 years of life. Moreover, this study provides a valuable resource of millions of T and B cell receptor sequences from infants with available metadata for researchers in the field.
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Affiliation(s)
- Lisa Paschold
- Department of Internal Medicine IV, Oncology/Hematology, Martin-Luther-University Halle-Wittenberg, Ernst-Grube-Str. 40, 06120, Halle (Saale), Germany
| | - Cornelia Gottschick
- Interdisciplinary Center for Health Sciences, Institute for Medical Epidemiology, Biometrics and Informatics (IMEBI), Medical School of the Martin-Luther University Halle-Wittenberg, Magdeburger Strasse 8, 06112, Halle (Saale), Germany
| | - Susan Langer
- Interdisciplinary Center for Health Sciences, Institute for Medical Epidemiology, Biometrics and Informatics (IMEBI), Medical School of the Martin-Luther University Halle-Wittenberg, Magdeburger Strasse 8, 06112, Halle (Saale), Germany
| | - Bianca Klee
- Interdisciplinary Center for Health Sciences, Institute for Medical Epidemiology, Biometrics and Informatics (IMEBI), Medical School of the Martin-Luther University Halle-Wittenberg, Magdeburger Strasse 8, 06112, Halle (Saale), Germany
| | - Sophie Diexer
- Interdisciplinary Center for Health Sciences, Institute for Medical Epidemiology, Biometrics and Informatics (IMEBI), Medical School of the Martin-Luther University Halle-Wittenberg, Magdeburger Strasse 8, 06112, Halle (Saale), Germany
| | - Ivona Aksentijevich
- Inflammatory Disease Section, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | - Christoph Schultheiß
- Department of Internal Medicine IV, Oncology/Hematology, Martin-Luther-University Halle-Wittenberg, Ernst-Grube-Str. 40, 06120, Halle (Saale), Germany
| | - Oliver Purschke
- Interdisciplinary Center for Health Sciences, Institute for Medical Epidemiology, Biometrics and Informatics (IMEBI), Medical School of the Martin-Luther University Halle-Wittenberg, Magdeburger Strasse 8, 06112, Halle (Saale), Germany
| | - Peggy Riese
- Department Vaccinology and Applied Microbiology, Helmholtz Centre for Infection Research, 38124, Braunschweig, Germany
| | - Stephanie Trittel
- Department Vaccinology and Applied Microbiology, Helmholtz Centre for Infection Research, 38124, Braunschweig, Germany
| | - Roland Haase
- Department of Neonatology and Pediatric Intensive Care, Hospital St. Elisabeth und St. Barbara, 06110, Halle (Saale), Germany
| | - Frank Dressler
- Department of Pediatric Pulmonology, Allergology and Neonatology, Hannover Medical School, 30625, Hannover, Germany
| | - Wolfgang Eberl
- Department of Paediatrics, Hospital Braunschweig, 38118, Braunschweig, Germany
| | - Johannes Hübner
- Department of Paediatrics, Dr. von Hauner Children's Hospital, Ludwig- Maximilians-University Munich, 80337, Munich, Germany
| | - Till Strowig
- Department Microbial Immune Regulation, Helmholtz Centre for Infection Research, 38124, Braunschweig, Germany
| | - Carlos A Guzman
- Department Vaccinology and Applied Microbiology, Helmholtz Centre for Infection Research, 38124, Braunschweig, Germany
| | - Rafael Mikolajczyk
- Interdisciplinary Center for Health Sciences, Institute for Medical Epidemiology, Biometrics and Informatics (IMEBI), Medical School of the Martin-Luther University Halle-Wittenberg, Magdeburger Strasse 8, 06112, Halle (Saale), Germany
| | - Mascha Binder
- Department of Internal Medicine IV, Oncology/Hematology, Martin-Luther-University Halle-Wittenberg, Ernst-Grube-Str. 40, 06120, Halle (Saale), Germany.
- Division of Medical Oncology, University Hospital Basel, Petersgraben 4, 40314031, Basel, Switzerland.
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8
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Olson BJ, Schattgen SA, Thomas PG, Bradley P, Matsen IV FA. Comparing T cell receptor repertoires using optimal transport. PLoS Comput Biol 2022; 18:e1010681. [PMID: 36476997 PMCID: PMC9728925 DOI: 10.1371/journal.pcbi.1010681] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2022] [Accepted: 10/24/2022] [Indexed: 12/12/2022] Open
Abstract
The complexity of entire T cell receptor (TCR) repertoires makes their comparison a difficult but important task. Current methods of TCR repertoire comparison can incur a high loss of distributional information by considering overly simplistic sequence- or repertoire-level characteristics. Optimal transport methods form a suitable approach for such comparison given some distance or metric between values in the sample space, with appealing theoretical and computational properties. In this paper we introduce a nonparametric approach to comparing empirical TCR repertoires that applies the Sinkhorn distance, a fast, contemporary optimal transport method, and a recently-created distance between TCRs called TCRdist. We show that our methods identify meaningful differences between samples from distinct TCR distributions for several case studies, and compete with more complicated methods despite minimal modeling assumptions and a simpler pipeline.
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Affiliation(s)
- Branden J. Olson
- Department of Computational Biology, Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America
- Department of Statistics, University of Washington, Seattle, Washington, United States of America
| | - Stefan A. Schattgen
- Department of Immunology, St. Jude Children’s Research Hospital, Memphis, Tennessee, United States of America
| | - Paul G. Thomas
- Department of Immunology, St. Jude Children’s Research Hospital, Memphis, Tennessee, United States of America
| | - Philip Bradley
- Department of Computational Biology, Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America
- Institute for Protein Design, Department of Biochemistry, University of Washington, Seattle, Washington, United States of America
- * E-mail: (PB); (FAM)
| | - Frederick A. Matsen IV
- Department of Computational Biology, Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America
- Department of Statistics, University of Washington, Seattle, Washington, United States of America
- Department of Genome Sciences, University of Washington, Seattle, Washington, United States of America
- Howard Hughes Medical Institute, Seattle, Washington, United States of America
- * E-mail: (PB); (FAM)
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9
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A preliminary study of tracking B-cell kinetics in patients with lung transplantation by monitoring kappa-deleting recombination excision circles. TURK GOGUS KALP DAMAR CERRAHISI DERGISI 2022; 30:611-621. [PMID: 36605322 PMCID: PMC9801467 DOI: 10.5606/tgkdc.dergisi.2022.21672] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 03/01/2021] [Accepted: 08/31/2021] [Indexed: 11/06/2022]
Abstract
Background This study aims to evaluate humoral immune system response by measuring copy numbers of kappa-deleting recombination excision circles (KREC) gene segment from B lymphocytes in patients with lung transplantation. Methods Between September 2015 and November 2016, a total of 11 patients (8 males, 3 females; mean age: 45.4±12.0 years; range, 23 to 59 years) who underwent lung transplantation with different primary indications were included. The copy numbers of KREC gene segment were quantified using real-time polymerase chain reaction method in peripheral blood samples collected pre- and post-transplantation. The samples of the patients were compared with the KREC l evels i n deoxyribonucleic acid extracted from blood samples of healthy children. Results There was no significant change in KREC levels between pre- and post-operation (p=0.594 and p=0.657), although the median values indicated that the highest increase in the KREC levels (7x105- 12x105; 85-170) was on Day 7 of transplantation. There was a positive correlation between the KREC levels (mL in blood) and lymphocytes at 24 h after transplantation (p=0.043) and between KREC copies per 106 of blood and age on Day 7. Conclusion Our preliminary results suggest that KREC l evels a s an indicator of B lymphocyte production are elevated after lung transplantation. A prognostic algorithm by tracking B cell kinetics after post-transplantation for long-term follow-up can be developed following the confirmation of these preliminary results with more patient samples.
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10
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Hong SB, Shin YW, Hong JB, Lee SK, Han B. Exploration of shared features of B cell receptor and T cell receptor repertoires reveals distinct clonotype clusters. Front Immunol 2022; 13:1006136. [PMID: 36341404 PMCID: PMC9632170 DOI: 10.3389/fimmu.2022.1006136] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2022] [Accepted: 10/04/2022] [Indexed: 11/20/2022] Open
Abstract
Although B cells and T cells are integral players of the adaptive immune system and act in co-dependent ways to orchestrate immune responses, existing methods to study the immune repertoire have largely focused on separate analyses of B cell receptor (BCR) and T cell receptor (TCR) repertoires. Based on our hypothesis that the shared history of immune exposures and the shared cellular machinery for recombination result in similarities between BCR and TCR repertoires in an individual, we examine any commonalities and interrelationships between BCR and TCR repertoires. We find that the BCR and TCR repertoires have covarying clonal architecture and diversity, and that the pattern of correlations appears to be altered in immune-mediated diseases. Furthermore, hierarchical clustering of public B and T cell clonotypes in both health and disease based on correlation of clonal proportion revealed distinct clusters of B and T cell clonotypes that exhibit increased sequence similarity, share motifs, and have distinct amino acid characteristics. Our findings point to common principles governing memory formation, recombination, and clonal expansion to antigens in B and T cells within an individual. A significant proportion of public BCR and TCR repertoire can be clustered into nonoverlapping and correlated clusters, suggesting a novel way of grouping B and T cell clonotypes.
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Affiliation(s)
- Sang Bin Hong
- Department of Medicine, Seoul National University College of Medicine, Seoul, South Korea
| | - Yong-Won Shin
- Center for Hospital Medicine, Department of Neurosurgery, Seoul National University Hospital, Seoul, South Korea
| | - Ja Bin Hong
- Department of Neurology, Charité Universitätsmedizin Berlin, Berlin, Germany
| | - Sang Kun Lee
- Department of Neurology, Seoul National University Hospital, Seoul, South Korea
| | - Buhm Han
- Department of Medicine, Seoul National University College of Medicine, Seoul, South Korea
- Department of Biomedical Sciences, Brain Korea 21 (BK21) Plus Biomedical Science Project, Seoul National University College of Medicine, Seoul, South Korea
- Interdisciplinary Program in Bioengineering, Seoul National University, Seoul, South Korea
- *Correspondence: Buhm Han,
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11
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Abdollahi N, Jeusset L, De Septenville AL, Ripoche H, Davi F, Bernardes JS. A multi-objective based clustering for inferring BCR clonal lineages from high-throughput B cell repertoire data. PLoS Comput Biol 2022; 18:e1010411. [PMID: 36037250 PMCID: PMC9462827 DOI: 10.1371/journal.pcbi.1010411] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2021] [Revised: 09/09/2022] [Accepted: 07/18/2022] [Indexed: 11/30/2022] Open
Abstract
The adaptive B cell response is driven by the expansion, somatic hypermutation, and selection of B cell clonal lineages. A high number of clonal lineages in a B cell population indicates a highly diverse repertoire, while clonal size distribution and sequence diversity reflect antigen selective pressure. Identifying clonal lineages is fundamental to many repertoire studies, including repertoire comparisons, clonal tracking, and statistical analysis. Several methods have been developed to group sequences from high-throughput B cell repertoire data. Current methods use clustering algorithms to group clonally-related sequences based on their similarities or distances. Such approaches create groups by optimizing a single objective that typically minimizes intra-clonal distances. However, optimizing several objective functions can be advantageous and boost the algorithm convergence rate. Here we propose MobiLLe, a new method based on multi-objective clustering. Our approach requires V(D)J annotations to obtain the initial groups and iteratively applies two objective functions that optimize cohesion and separation within clonal lineages simultaneously. We show that our method greatly improves clonal lineage grouping on simulated benchmarks with varied mutation rates compared to other tools. When applied to experimental repertoires generated from high-throughput sequencing, its clustering results are comparable to the most performing tools and can reproduce the results of previous publications. The method based on multi-objective clustering can accurately identify clonally-related antibody sequences and presents the lowest running time among state-of-art tools. All these features constitute an attractive option for repertoire analysis, particularly in the clinical context. MobiLLe can potentially help unravel the mechanisms involved in developing and evolving B cell malignancies. High-throughput sequencing can produce a large set of sequences and has profoundly changed our ability to study immune repertoires, particularly B cell receptor sequences. An important application is the analysis of the clonal lineage composition of B cell populations; it is the starting point of many immune repertoire studies, for instance, to differentiate between healthy individuals and those with lymphoid malignancies or other diseases. Several computational methods have been developed to identify clonal lineages from a set of B cell receptor sequences. Most of them apply clustering algorithms and optimize a single objective function that typically minimizes intra-clonal distances. However, optimizing several objective functions in parallel can benefit and increase the clustering performance and efficiency. We propose MobiLLe, the first multi-objective clonal lineage grouping method, which simultaneously optimizes two objective functions for minimizing intra-clonal diversity and maximizing inter-clonal differences. Our approach greatly improved clonal grouping on simulated benchmarks and performed comparably to the most powerful and recent methods on experimental samples. MobiLLe is computationally more efficient than existing tools and does not require any training process or hyper-parameter optimization. It can easily manage large-scale experimental repertoires, providing useful plots to help researchers detect clonally-related sequences in high-throughput B cell repertoire data.
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Affiliation(s)
- Nika Abdollahi
- Sorbonne Université, CNRS, UMR 7238, Laboratoire de Biologie Computationnelle et Quantitative, Paris, France
| | - Lucile Jeusset
- Sorbonne Université, CNRS, UMR 7238, Laboratoire de Biologie Computationnelle et Quantitative, Paris, France
- Sorbonne Université, AP-HP, Hôpital Pitié-Salpêtrière, UMR_S 1138 Department of Hematology, Paris, France
| | | | - Hugues Ripoche
- Sorbonne Université, CNRS, UMR 7238, Laboratoire de Biologie Computationnelle et Quantitative, Paris, France
| | - Frédéric Davi
- Sorbonne Université, AP-HP, Hôpital Pitié-Salpêtrière, UMR_S 1138 Department of Hematology, Paris, France
| | - Juliana Silva Bernardes
- Sorbonne Université, CNRS, UMR 7238, Laboratoire de Biologie Computationnelle et Quantitative, Paris, France
- * E-mail:
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12
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Gilboa A, Hope R, Ben Simon S, Polak P, Koren O, Yaari G. Ontogeny of the B Cell Receptor Repertoire and Microbiome in Mice. JOURNAL OF IMMUNOLOGY (BALTIMORE, MD. : 1950) 2022; 208:2713-2725. [PMID: 35623663 DOI: 10.4049/jimmunol.2100955] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/05/2021] [Accepted: 03/30/2022] [Indexed: 06/15/2023]
Abstract
The immune system matures throughout childhood to achieve full functionality in protecting our bodies against threats. The immune system has a strong reciprocal symbiosis with the host bacterial population and the two systems co-develop, shaping each other. Despite their fundamental role in health physiology, the ontogeny of these systems is poorly characterized. In this study, we investigated the development of the BCR repertoire by analyzing high-throughput sequencing of their receptors in several time points of young C57BL/6J mice. In parallel, we explored the development of the gut microbiome. We discovered that the gut IgA repertoires change from birth to adolescence, including an increase in CDR3 lengths and somatic hypermutation levels. This contrasts with the spleen IgM repertoires that remain stable and distinct from the IgA repertoires in the gut. We also discovered that large clones that germinate in the gut are initially confined to a specific gut compartment, then expand to nearby compartments and later on expand also to the spleen and remain there. Finally, we explored the associations between diversity indices of the B cell repertoires and the microbiome, as well as associations between bacterial and BCR clusters. Our results shed light on the ontogeny of the adaptive immune system and the microbiome, providing a baseline for future research.
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Affiliation(s)
- Amit Gilboa
- Bioengineering, Faculty of Engineering, Bar Ilan University, Ramat Gan, Israel
- Bar Ilan Institute of Nanotechnologies and Advanced Materials, Bar Ilan University, Ramat Gan, Israel; and
| | - Ronen Hope
- Bioengineering, Faculty of Engineering, Bar Ilan University, Ramat Gan, Israel
| | - Shira Ben Simon
- Azrieli Faculty of Medicine, Bar Ilan University, Safed, Israel
| | - Pazit Polak
- Bioengineering, Faculty of Engineering, Bar Ilan University, Ramat Gan, Israel
- Bar Ilan Institute of Nanotechnologies and Advanced Materials, Bar Ilan University, Ramat Gan, Israel; and
| | - Omry Koren
- Azrieli Faculty of Medicine, Bar Ilan University, Safed, Israel
| | - Gur Yaari
- Bioengineering, Faculty of Engineering, Bar Ilan University, Ramat Gan, Israel;
- Bar Ilan Institute of Nanotechnologies and Advanced Materials, Bar Ilan University, Ramat Gan, Israel; and
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13
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Myc-Interacting Zinc Finger Protein 1 (Miz-1) Is Essential to Maintain Homeostasis and Immunocompetence of the B Cell Lineage. BIOLOGY 2022; 11:biology11040504. [PMID: 35453704 PMCID: PMC9027237 DOI: 10.3390/biology11040504] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/14/2022] [Revised: 03/18/2022] [Accepted: 03/23/2022] [Indexed: 11/16/2022]
Abstract
Aging of the immune system is described as a progressive loss of the ability to respond to immunologic stimuli and is commonly referred to as immunosenescence. B cell immunosenescence is characterized by a decreased differentiation rate in the bone marrow and accumulation of antigen-experienced and age-associated B cells in secondary lymphoid organs (SLOs). A specific deletion of the POZ-domain of the transcription factor Miz-1 in pro-B cells, which is known to be involved in bone marrow hematopoiesis, leads to premature aging of the B cell lineage. In mice, this causes a severe reduction in bone marrow-derived B cells with a drastic decrease from the pre-B cell stage on. Further, mature, naïve cells in SLOs are reduced at an early age, while post-activation-associated subpopulations increase prematurely. We propose that Miz-1 interferes at several key regulatory checkpoints, critical during B cell aging, and counteracts a premature loss of immunocompetence. This enables the use of our mouse model to gain further insights into mechanisms of B cell aging and it can significantly contribute to understand molecular causes of impaired adaptive immune responses to counteract loss of immunocompetence and restore a functional immune response in the elderly.
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14
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Braddom AE, Bol S, Gonzales SJ, Reyes RA, Musinguzi K, Nankya F, Ssewanyana I, Greenhouse B, Bunnik EM. B Cell Receptor Repertoire Analysis in Malaria-Naive and Malaria-Experienced Individuals Reveals Unique Characteristics of Atypical Memory B Cells. mSphere 2021; 6:e0072621. [PMID: 34523978 PMCID: PMC8550134 DOI: 10.1128/msphere.00726-21] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2021] [Accepted: 08/31/2021] [Indexed: 11/24/2022] Open
Abstract
Malaria, caused by parasites of the Plasmodium genus, is responsible for significant morbidity and mortality globally. Chronic Plasmodium falciparum exposure affects the B cell compartment, leading to the accumulation of atypical memory B cells (atMBCs). IgM-positive (IgM+) and IgG+ atMBCs have not been compared in-depth in the context of malaria, nor is it known if atMBCs in malaria-experienced individuals are different from phenotypically similar B cells in individuals with no known history of Plasmodium exposure. To address these questions, we characterized the B cell receptor (BCR) repertoire of naive B cells (NBCs), IgM+ and IgG+ classical MBCs (cMBCs), and IgM+ and IgG+ atMBCs from 13 malaria-naive American adults and 7 malaria-experienced Ugandan adults. Our results demonstrate that P. falciparum exposure mainly drives changes in atMBCs. In comparison to malaria-naive adults, the BCR repertoire of Plasmodium-exposed adults showed increased levels of somatic hypermutation in the heavy chain V region in IgM+ and IgG+ atMBCs, shorter heavy chain complementarity-determining region 3 (HCDR3) in IgG+ atMBCs, and increased usage of IGHV3-73 in IgG+ cMBCs and both IgM+ and IgG+ atMBCs. Irrespective of Plasmodium exposure, IgM+ atMBCs closely resembled NBCs, while IgG+ atMBCs resembled IgG+ cMBCs. Physicochemical properties of the HCDR3 seemed to be intrinsic to cell type and independent of malaria experience. The resemblance between atMBCs from Plasmodium-exposed and naive adults suggests similar differentiation pathways regardless of chronic antigen exposure. Moreover, these data demonstrate that IgM+ and IgG+ atMBCs are distinct populations that should be considered separately in future analyses. IMPORTANCE Malaria, caused by Plasmodium parasites, still contributes to a high global burden of disease, mainly in children under 5 years of age. Chronic and recurrent Plasmodium infections affect the development of B cell memory against the parasite and promote the accumulation of atypical memory B cells (atMBCs), which have an unclear function in the immune response. Understanding where these cells originate from and whether they are beneficial in the immune response to Plasmodium will help inform vaccination development efforts. We found differences in B cell receptor (BCR) properties of atMBCs between malaria-naive and malaria-experienced adults that are suggestive of divergent selection processes, resulting in more somatic hypermutation and differential immunoglobulin heavy chain V (IGHV) gene usage. Despite these differences, atMBCs from malaria-naive and malaria-experienced adults also showed many similarities in BCR characteristics, such as physicochemical properties of the HCDR3 region, suggesting that atMBCs undergo similar differentiation pathways in response to different pathogens. Our study provides new insights into the effects of malaria experience on the B cell compartment and the relationships between atMBCs and other B cell populations.
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Affiliation(s)
- Ashley E. Braddom
- Department of Microbiology, Immunology and Molecular Genetics, Long School of Medicine, The University of Texas Health Science Center at San Antonio, San Antonio, Texas, USA
| | - Sebastiaan Bol
- Department of Microbiology, Immunology and Molecular Genetics, Long School of Medicine, The University of Texas Health Science Center at San Antonio, San Antonio, Texas, USA
| | - S. Jake Gonzales
- Department of Microbiology, Immunology and Molecular Genetics, Long School of Medicine, The University of Texas Health Science Center at San Antonio, San Antonio, Texas, USA
| | - Raphael A. Reyes
- Department of Microbiology, Immunology and Molecular Genetics, Long School of Medicine, The University of Texas Health Science Center at San Antonio, San Antonio, Texas, USA
| | | | | | - Isaac Ssewanyana
- Infectious Disease Research Collaboration, Kampala, Uganda
- London School of Hygiene and Tropical Medicine, London, UK
| | - Bryan Greenhouse
- Department of Medicine, University of California San Francisco, San Francisco, California, USA
| | - Evelien M. Bunnik
- Department of Microbiology, Immunology and Molecular Genetics, Long School of Medicine, The University of Texas Health Science Center at San Antonio, San Antonio, Texas, USA
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15
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Age-related changes in the TRB and IGH repertoires in healthy adult males and females. Immunol Lett 2021; 240:71-76. [PMID: 34666136 DOI: 10.1016/j.imlet.2021.10.002] [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: 07/04/2021] [Revised: 09/27/2021] [Accepted: 10/08/2021] [Indexed: 11/22/2022]
Abstract
A diverse immune repertoire is capable of recognizing the enormous universe of foreign antigens encountered over life. Aging has a profound impact on the immune repertoires. However, whether continuous age-related changes in the immune repertoires differ between sexes is unclear. In this study, the characteristics of immune repertoires stratified by sex during aging are deciphered by analyzing T-cell receptor β-chain (TRB) and immunoglobulin heavy chain (IGH) sequences in 361 healthy adults. A similar change was observed between males and females across their lifespan, whereas age-subgroup analysis revealed sex-specific signatures in TRB and IGH repertoires. In regard to TRB, in males, repertoire richness and evenness increases slightly before the age of 32 years and 45 years respectively, and decreases sharply thereafter. Intriguingly, in females, they decrease significantly until around the age 57 years old, and subsequently undergo a stable stage up to the age of 83 years. Although IGH repertoire evenness increases significantly with age in both sexes, richness decreases significantly with age in males but remains stable in females. Moreover, average length of IGH CDR3 increases with age. In conclusion, these findings provide fundamental insights into the mechanisms underlying sex differences in adaptive immunity.
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16
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Abstract
Innate and adaptive immune responses decline with age, leading to greater susceptibility to infectious diseases and reduced responses to vaccines. Diseases are more severe in old than in young individuals and have a greater impact on health outcomes such as morbidity, disability, and mortality. Aging is characterized by increased low-grade chronic inflammation, so-called inflammaging, that represents a link between changes in immune cells and a number of diseases and syndromes typical of old age. In this review we summarize current knowledge on age-associated changes in immune cells with special emphasis on B cells, which are more inflammatory and less responsive to infections and vaccines in the elderly. We highlight recent findings on factors and pathways contributing to inflammaging and how these lead to dysfunctional immune responses. We summarize recent published studies showing that adipose tissue, which increases in size with aging, contributes to inflammaging and dysregulated B cell function.
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Affiliation(s)
- Daniela Frasca
- Department of Microbiology and Immunology, University of Miami Miller School of Medicine, Miami, Florida 33136, USA; .,Sylvester Comprehensive Cancer Center, University of Miami Miller School of Medicine, Miami, Florida 33136, USA.,Miami Integrative Metabolomics Research Center, University of Miami Miller School of Medicine, Miami, Florida 33136, USA
| | - Alain Diaz
- Department of Microbiology and Immunology, University of Miami Miller School of Medicine, Miami, Florida 33136, USA;
| | - Maria Romero
- Department of Microbiology and Immunology, University of Miami Miller School of Medicine, Miami, Florida 33136, USA;
| | - Denisse Garcia
- Department of Microbiology and Immunology, University of Miami Miller School of Medicine, Miami, Florida 33136, USA;
| | - Bonnie B Blomberg
- Department of Microbiology and Immunology, University of Miami Miller School of Medicine, Miami, Florida 33136, USA; .,Sylvester Comprehensive Cancer Center, University of Miami Miller School of Medicine, Miami, Florida 33136, USA
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17
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Ciocca M, Zaffina S, Fernandez Salinas A, Bocci C, Palomba P, Conti MG, Terreri S, Frisullo G, Giorda E, Scarsella M, Brugaletta R, Vinci MR, Magnavita N, Carsetti R, Piano Mortari E. Evolution of Human Memory B Cells From Childhood to Old Age. Front Immunol 2021; 12:690534. [PMID: 34367150 PMCID: PMC8343175 DOI: 10.3389/fimmu.2021.690534] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2021] [Accepted: 07/09/2021] [Indexed: 01/08/2023] Open
Abstract
High quality medical assistance and preventive strategies, including pursuing a healthy lifestyle, result in a progressively growing percentage of older people. The population and workforce is aging in all countries of the world. It is widely recognized that older individuals show an increased susceptibility to infections and a reduced response to vaccination suggesting that the aged immune system is less able to react and consequently protect the organism. The SARS-CoV-2 pandemic is dramatically showing us that the organism reacts to novel pathogens in an age-dependent manner. The decline of the immune system observed in aging remains unclear. We aimed to understand the role of B cells. We analyzed peripheral blood from children (4-18 years); young people (23-60 years) and elderly people (65-91 years) by flow cytometry. We also measured antibody secretion by ELISA following a T-independent stimulation. Here we show that the elderly have a significant reduction of CD27dull memory B cells, a population that bridges innate and adaptive immune functions. In older people, memory B cells are mostly high specialized antigen-selected CD27bright. Moreover, after in vitro stimulation with CpG, B cells from older individuals produced significantly fewer IgM and IgA antibodies compared to younger individuals. Aging is a complex process characterized by a functional decline in multiple physiological systems. The immune system of older people is well equipped to react to often encountered antigens but has a low ability to respond to new pathogens.
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Affiliation(s)
- Michela Ciocca
- Diagnostic Immunology Research Unit, Multimodal Medicine Research Area, Bambino Gesù Children’s Hospital, IRCCS, Rome, Italy
| | - Salvatore Zaffina
- Occupational Medicine/Health Technology Assessment and Safety Research Unit, Clinical-Technological Innovations Research Area, Bambino Gesù Children’s Hospital, IRCCS, Rome, Italy
- Health Directorate, Occupational Medicine, Bambino Gesù Children’s Hospital, IRCCS, Rome, Italy
| | - Ane Fernandez Salinas
- Diagnostic Immunology Research Unit, Multimodal Medicine Research Area, Bambino Gesù Children’s Hospital, IRCCS, Rome, Italy
- Department of Molecular Medicine, Sapienza University of Rome, Rome, Italy
| | - Chiara Bocci
- Diagnostic Immunology Research Unit, Multimodal Medicine Research Area, Bambino Gesù Children’s Hospital, IRCCS, Rome, Italy
| | - Patrizia Palomba
- Diagnostic Immunology Clinical Unit, Department of Diagnostic and Laboratory Medicine, Bambino Gesù Children’s Hospital, IRCCS, Rome, Italy
| | - Maria Giulia Conti
- Department of Molecular Medicine, Sapienza University of Rome, Rome, Italy
- Department of Maternal and Child Health, Policlinico Umberto I, Sapienza University of Rome, Rome, Italy
| | - Sara Terreri
- Diagnostic Immunology Research Unit, Multimodal Medicine Research Area, Bambino Gesù Children’s Hospital, IRCCS, Rome, Italy
| | - Giuseppe Frisullo
- Diagnostic Immunology Research Unit, Multimodal Medicine Research Area, Bambino Gesù Children’s Hospital, IRCCS, Rome, Italy
| | - Ezio Giorda
- Core Facilities, Bambino Gesù Children’s Hospital, IRCCS, Rome, Italy
| | - Marco Scarsella
- Core Facilities, Bambino Gesù Children’s Hospital, IRCCS, Rome, Italy
| | - Rita Brugaletta
- Occupational Medicine/Health Technology Assessment and Safety Research Unit, Clinical-Technological Innovations Research Area, Bambino Gesù Children’s Hospital, IRCCS, Rome, Italy
- Health Directorate, Occupational Medicine, Bambino Gesù Children’s Hospital, IRCCS, Rome, Italy
| | - Maria Rosaria Vinci
- Occupational Medicine/Health Technology Assessment and Safety Research Unit, Clinical-Technological Innovations Research Area, Bambino Gesù Children’s Hospital, IRCCS, Rome, Italy
- Health Directorate, Occupational Medicine, Bambino Gesù Children’s Hospital, IRCCS, Rome, Italy
| | - Nicola Magnavita
- Post-Graduate School of Occupational Health, Section of Occupational Medicine and Labor Law, Università Cattolica del Sacro Cuore, Rome, Italy
- Department of Woman, Child & Public Health, Fondazione Policlinico Universitario A. Gemelli IRCCS, Rome, Italy
| | - Rita Carsetti
- Diagnostic Immunology Research Unit, Multimodal Medicine Research Area, Bambino Gesù Children’s Hospital, IRCCS, Rome, Italy
- Diagnostic Immunology Clinical Unit, Department of Diagnostic and Laboratory Medicine, Bambino Gesù Children’s Hospital, IRCCS, Rome, Italy
| | - Eva Piano Mortari
- Diagnostic Immunology Research Unit, Multimodal Medicine Research Area, Bambino Gesù Children’s Hospital, IRCCS, Rome, Italy
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18
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Baizan-Edge A, Stubbs BA, Stubbington MJT, Bolland DJ, Tabbada K, Andrews S, Corcoran AE. IL-7R signaling activates widespread V H and D H gene usage to drive antibody diversity in bone marrow B cells. Cell Rep 2021; 36:109349. [PMID: 34260907 PMCID: PMC8293627 DOI: 10.1016/j.celrep.2021.109349] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2020] [Revised: 04/05/2021] [Accepted: 06/15/2021] [Indexed: 01/09/2023] Open
Abstract
Generation of the primary antibody repertoire requires V(D)J recombination of hundreds of gene segments in the immunoglobulin heavy chain (Igh) locus. The role of interleukin-7 receptor (IL-7R) signaling in Igh recombination has been difficult to partition from its role in B cell survival and proliferation. With a detailed description of the Igh repertoire in murine IL-7Rα-/- bone marrow B cells, we demonstrate that IL-7R signaling profoundly influences VH gene selection during VH-to-DJH recombination. We find skewing toward 3' VH genes during de novo VH-to-DJH recombination more severe than the fetal liver (FL) repertoire and uncover a role for IL-7R signaling in DH-to-JH recombination. Transcriptome and accessibility analyses suggest reduced expression of B lineage transcription factors (TFs) and targets and loss of DH and VH antisense transcription in IL-7Rα-/- B cells. Thus, in addition to its roles in survival and proliferation, IL-7R signaling shapes the Igh repertoire by activating underpinning mechanisms.
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Affiliation(s)
- Amanda Baizan-Edge
- Nuclear Dynamics Programme, Babraham Institute, Babraham Research Campus, Cambridge CB22 3AT, UK
| | - Bryony A Stubbs
- Nuclear Dynamics Programme, Babraham Institute, Babraham Research Campus, Cambridge CB22 3AT, UK
| | - Michael J T Stubbington
- Nuclear Dynamics Programme, Babraham Institute, Babraham Research Campus, Cambridge CB22 3AT, UK
| | - Daniel J Bolland
- Nuclear Dynamics Programme, Babraham Institute, Babraham Research Campus, Cambridge CB22 3AT, UK; Lymphocyte Signaling and Development Programme, Babraham Institute, Babraham Research Campus, Cambridge CB22 3AT, UK
| | - Kristina Tabbada
- Nuclear Dynamics Programme, Babraham Institute, Babraham Research Campus, Cambridge CB22 3AT, UK; Lymphocyte Signaling and Development Programme, Babraham Institute, Babraham Research Campus, Cambridge CB22 3AT, UK
| | - Simon Andrews
- Bioinformatics Group, Babraham Institute, Babraham Research Campus, Cambridge CB22 3AT, UK
| | - Anne E Corcoran
- Nuclear Dynamics Programme, Babraham Institute, Babraham Research Campus, Cambridge CB22 3AT, UK; Lymphocyte Signaling and Development Programme, Babraham Institute, Babraham Research Campus, Cambridge CB22 3AT, UK.
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19
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Smith M, Abdesselem HB, Mullins M, Tan TM, Nel AJM, Al-Nesf MAY, Bensmail I, Majbour NK, Vaikath NN, Naik A, Ouararhni K, Mohamed-Ali V, Al-Maadheed M, Schell DT, Baros-Steyl SS, Anuar ND, Ismail NH, Morris PE, Mamat RNR, Rosli NSM, Anwar A, Ellan K, Zain RM, Burgers WA, Mayne ES, El-Agnaf OMA, Blackburn JM. Age, Disease Severity and Ethnicity Influence Humoral Responses in a Multi-Ethnic COVID-19 Cohort. Viruses 2021; 13:v13050786. [PMID: 33925055 PMCID: PMC8146997 DOI: 10.3390/v13050786] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2021] [Revised: 04/24/2021] [Accepted: 04/26/2021] [Indexed: 12/16/2022] Open
Abstract
The COVID-19 pandemic has affected all individuals across the globe in some way. Despite large numbers of reported seroprevalence studies, there remains a limited understanding of how the magnitude and epitope utilization of the humoral immune response to SARS-CoV-2 viral anti-gens varies within populations following natural infection. Here, we designed a quantitative, multi-epitope protein microarray comprising various nucleocapsid protein structural motifs, including two structural domains and three intrinsically disordered regions. Quantitative data from the microarray provided complete differentiation between cases and pre-pandemic controls (100% sensitivity and specificity) in a case-control cohort (n = 100). We then assessed the influence of disease severity, age, and ethnicity on the strength and breadth of the humoral response in a multi-ethnic cohort (n = 138). As expected, patients with severe disease showed significantly higher antibody titers and interestingly also had significantly broader epitope coverage. A significant increase in antibody titer and epitope coverage was observed with increasing age, in both mild and severe disease, which is promising for vaccine efficacy in older individuals. Additionally, we observed significant differences in the breadth and strength of the humoral immune response in relation to ethnicity, which may reflect differences in genetic and lifestyle factors. Furthermore, our data enabled localization of the immuno-dominant epitope to the C-terminal structural domain of the viral nucleocapsid protein in two independent cohorts. Overall, we have designed, validated, and tested an advanced serological assay that enables accurate quantitation of the humoral response post natural infection and that has revealed unexpected differences in the magnitude and epitope utilization within a population.
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Affiliation(s)
- Muneerah Smith
- Department of Integrative Biomedical Sciences, Faculty of Health Sciences, University of Cape Town, Cape Town 7925, South Africa; (M.S.); (M.M.); (A.J.M.N.); (D.T.S.); (S.S.B.-S.)
| | - Houari B. Abdesselem
- Neurological Disorders Research Center, Qatar Biomedical Research Institute (QBRI), Hamad Bin Khalifa University, Qatar. Foundation, Doha P.O. Box 34110, Qatar; (H.B.A.); (I.B.); (N.K.M.); (N.N.V.); (A.N.); (K.O.)
- Proteomics Core Facility, Qatar Biomedical Research Institute (QBRI), Hamad Bin Khalifa University, Qatar Foundation, Doha P.O. Box 34110, Qatar
| | - Michelle Mullins
- Department of Integrative Biomedical Sciences, Faculty of Health Sciences, University of Cape Town, Cape Town 7925, South Africa; (M.S.); (M.M.); (A.J.M.N.); (D.T.S.); (S.S.B.-S.)
| | - Ti-Myen Tan
- Sengenics Corporation, Level M, Plaza Zurich, Damansara Heights, Kuala Lumpur 50490, Malaysia; (T.-M.T.); (N.D.A.); (N.H.I.); (P.E.M.); (R.N.R.M.); (N.S.M.R.); (A.A.)
| | - Andrew J. M. Nel
- Department of Integrative Biomedical Sciences, Faculty of Health Sciences, University of Cape Town, Cape Town 7925, South Africa; (M.S.); (M.M.); (A.J.M.N.); (D.T.S.); (S.S.B.-S.)
| | | | - Ilham Bensmail
- Neurological Disorders Research Center, Qatar Biomedical Research Institute (QBRI), Hamad Bin Khalifa University, Qatar. Foundation, Doha P.O. Box 34110, Qatar; (H.B.A.); (I.B.); (N.K.M.); (N.N.V.); (A.N.); (K.O.)
| | - Nour K. Majbour
- Neurological Disorders Research Center, Qatar Biomedical Research Institute (QBRI), Hamad Bin Khalifa University, Qatar. Foundation, Doha P.O. Box 34110, Qatar; (H.B.A.); (I.B.); (N.K.M.); (N.N.V.); (A.N.); (K.O.)
| | - Nishant N. Vaikath
- Neurological Disorders Research Center, Qatar Biomedical Research Institute (QBRI), Hamad Bin Khalifa University, Qatar. Foundation, Doha P.O. Box 34110, Qatar; (H.B.A.); (I.B.); (N.K.M.); (N.N.V.); (A.N.); (K.O.)
| | - Adviti Naik
- Neurological Disorders Research Center, Qatar Biomedical Research Institute (QBRI), Hamad Bin Khalifa University, Qatar. Foundation, Doha P.O. Box 34110, Qatar; (H.B.A.); (I.B.); (N.K.M.); (N.N.V.); (A.N.); (K.O.)
| | - Khalid Ouararhni
- Neurological Disorders Research Center, Qatar Biomedical Research Institute (QBRI), Hamad Bin Khalifa University, Qatar. Foundation, Doha P.O. Box 34110, Qatar; (H.B.A.); (I.B.); (N.K.M.); (N.N.V.); (A.N.); (K.O.)
| | - Vidya Mohamed-Ali
- Anti-Doping Laboratory Qatar, Sports City Road, Aspire Zone, Doha P.O. Box 27775, Qatar; (V.M.-A.); (M.A.-M.)
| | - Mohammed Al-Maadheed
- Anti-Doping Laboratory Qatar, Sports City Road, Aspire Zone, Doha P.O. Box 27775, Qatar; (V.M.-A.); (M.A.-M.)
| | - Darien T. Schell
- Department of Integrative Biomedical Sciences, Faculty of Health Sciences, University of Cape Town, Cape Town 7925, South Africa; (M.S.); (M.M.); (A.J.M.N.); (D.T.S.); (S.S.B.-S.)
| | - Seanantha S. Baros-Steyl
- Department of Integrative Biomedical Sciences, Faculty of Health Sciences, University of Cape Town, Cape Town 7925, South Africa; (M.S.); (M.M.); (A.J.M.N.); (D.T.S.); (S.S.B.-S.)
| | - Nur D. Anuar
- Sengenics Corporation, Level M, Plaza Zurich, Damansara Heights, Kuala Lumpur 50490, Malaysia; (T.-M.T.); (N.D.A.); (N.H.I.); (P.E.M.); (R.N.R.M.); (N.S.M.R.); (A.A.)
| | - Nur H. Ismail
- Sengenics Corporation, Level M, Plaza Zurich, Damansara Heights, Kuala Lumpur 50490, Malaysia; (T.-M.T.); (N.D.A.); (N.H.I.); (P.E.M.); (R.N.R.M.); (N.S.M.R.); (A.A.)
| | - Priscilla E. Morris
- Sengenics Corporation, Level M, Plaza Zurich, Damansara Heights, Kuala Lumpur 50490, Malaysia; (T.-M.T.); (N.D.A.); (N.H.I.); (P.E.M.); (R.N.R.M.); (N.S.M.R.); (A.A.)
| | - Raja N. R. Mamat
- Sengenics Corporation, Level M, Plaza Zurich, Damansara Heights, Kuala Lumpur 50490, Malaysia; (T.-M.T.); (N.D.A.); (N.H.I.); (P.E.M.); (R.N.R.M.); (N.S.M.R.); (A.A.)
| | - Nurul S. M. Rosli
- Sengenics Corporation, Level M, Plaza Zurich, Damansara Heights, Kuala Lumpur 50490, Malaysia; (T.-M.T.); (N.D.A.); (N.H.I.); (P.E.M.); (R.N.R.M.); (N.S.M.R.); (A.A.)
| | - Arif Anwar
- Sengenics Corporation, Level M, Plaza Zurich, Damansara Heights, Kuala Lumpur 50490, Malaysia; (T.-M.T.); (N.D.A.); (N.H.I.); (P.E.M.); (R.N.R.M.); (N.S.M.R.); (A.A.)
| | - Kavithambigai Ellan
- Virology Lab, Level 2, Block C7, Infectious Disease Research Centre, Institute for Medical Research, Setia Alam, Selangor 40170, Malaysia; (K.E.); (R.M.Z.)
| | - Rozainanee M. Zain
- Virology Lab, Level 2, Block C7, Infectious Disease Research Centre, Institute for Medical Research, Setia Alam, Selangor 40170, Malaysia; (K.E.); (R.M.Z.)
| | - Wendy A. Burgers
- Division of Medical Virology, Department of Pathology, University of Cape Town, Cape Town 7925, South Africa;
- Wellcome Centre for Infectious Diseases Research in Africa, University of Cape Town, Cape Town 7925, South Africa
- Institute of Infectious Disease and Molecular Medicine, Faculty of Health Sciences, University of Cape Town, Cape Town 7925, South Africa
| | - Elizabeth S. Mayne
- Department of Immunology, National Health Laboratory Service (NHLS) and University of the Witwatersrand, Charlotte Maxeke Johannesburg Academic Hospital, Johannesburg 2196, South Africa;
| | - Omar M. A. El-Agnaf
- Neurological Disorders Research Center, Qatar Biomedical Research Institute (QBRI), Hamad Bin Khalifa University, Qatar. Foundation, Doha P.O. Box 34110, Qatar; (H.B.A.); (I.B.); (N.K.M.); (N.N.V.); (A.N.); (K.O.)
- Correspondence: (O.M.A.E.-A.); (J.M.B.); Tel.: +97-455-935-568 (O.M.A.E.-A.); +27-214-066-071 (J.M.B.)
| | - Jonathan M. Blackburn
- Department of Integrative Biomedical Sciences, Faculty of Health Sciences, University of Cape Town, Cape Town 7925, South Africa; (M.S.); (M.M.); (A.J.M.N.); (D.T.S.); (S.S.B.-S.)
- Sengenics Corporation, Level M, Plaza Zurich, Damansara Heights, Kuala Lumpur 50490, Malaysia; (T.-M.T.); (N.D.A.); (N.H.I.); (P.E.M.); (R.N.R.M.); (N.S.M.R.); (A.A.)
- Institute of Infectious Disease and Molecular Medicine, Faculty of Health Sciences, University of Cape Town, Cape Town 7925, South Africa
- Correspondence: (O.M.A.E.-A.); (J.M.B.); Tel.: +97-455-935-568 (O.M.A.E.-A.); +27-214-066-071 (J.M.B.)
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20
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Xie X, Shrimpton J, Doody GM, Conaghan PG, Ponchel F. B-cell capacity for differentiation changes with age. Aging Cell 2021; 20:e13341. [PMID: 33711204 PMCID: PMC8045946 DOI: 10.1111/acel.13341] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2020] [Revised: 01/18/2021] [Accepted: 02/21/2021] [Indexed: 01/17/2023] Open
Abstract
Background Age‐related immune deficiencies are thought to be responsible for increased susceptibility to infection in older adults, with alterations in lymphocyte populations becoming more prevalent over time. The loss of humoral immunity in ageing was attributed to the diminished numbers of B cells and the reduced ability to generate immunoglobulin. Aims To compare the intrinsic B‐cell capacity for differentiation into mature plasma cells (PCs), between young and old donors, using in vitro assays, providing either effective T‐cell help or activation via TLR engagement. Methods B cells were isolated from healthy individuals, in younger (30–38 years) and older (60–64 years) donors. An in vitro model system of B‐cell differentiation was used, analysing 5 differentiation markers by flow cytometry, under T‐dependent (TD: CD40/BCR stimulation) or T‐independent (TI: TLR7/BCR activation) conditions. Antibody secretion was measured by ELISA and gene expression using qPCR. Results TI and TD differentiation resulted in effective proliferation of B cells followed by their differentiation into PC. B‐cell‐executed TI differentiation was faster, all differentiation marker and genes being expressed earlier than under TD differentiation (day 6), although generating less viable cells and lower antibody levels (day 13). Age‐related differences in B‐cell capacity for differentiation were minimal in TD differentiation. In contrast, in TI differentiation age significantly affected proliferation, viability, differentiation, antibody secretion and gene expression, older donors being more efficient. Conclusion Altogether, B‐cell differentiation into PC appeared similar between age groups when provided with T‐cell help, in contrast to TI differentiation, where multiple age‐related changes suggest better capacities in older donors. These new findings may help explain the emergence of autoantibodies in ageing.
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Affiliation(s)
- Xuanxiao Xie
- Leeds Institute of Rheumatic and Musculoskeletal Medicine and NIHR Leeds Biomedical Research Centre University of Leeds Leeds UK
| | - Jennifer Shrimpton
- Division of Haematology and Immunology Leeds Institute of Medical Research University of Leeds Leeds UK
| | - Gina M. Doody
- Division of Haematology and Immunology Leeds Institute of Medical Research University of Leeds Leeds UK
| | - Philip G. Conaghan
- Leeds Institute of Rheumatic and Musculoskeletal Medicine and NIHR Leeds Biomedical Research Centre University of Leeds Leeds UK
| | - Frederique Ponchel
- Leeds Institute of Rheumatic and Musculoskeletal Medicine and NIHR Leeds Biomedical Research Centre University of Leeds Leeds UK
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21
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Stewart A, Ng JCF, Wallis G, Tsioligka V, Fraternali F, Dunn-Walters DK. Single-Cell Transcriptomic Analyses Define Distinct Peripheral B Cell Subsets and Discrete Development Pathways. Front Immunol 2021; 12:602539. [PMID: 33815362 PMCID: PMC8012727 DOI: 10.3389/fimmu.2021.602539] [Citation(s) in RCA: 74] [Impact Index Per Article: 24.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2020] [Accepted: 02/24/2021] [Indexed: 12/17/2022] Open
Abstract
Separation of B cells into different subsets has been useful to understand their different functions in various immune scenarios. In some instances, the subsets defined by phenotypic FACS separation are relatively homogeneous and so establishing the functions associated with them is straightforward. Other subsets, such as the “Double negative” (DN, CD19+CD27-IgD-) population, are more complex with reports of differing functionality which could indicate a heterogeneous population. Recent advances in single-cell techniques enable an alternative route to characterize cells based on their transcriptome. To maximize immunological insight, we need to match prior data from phenotype-based studies with the finer granularity of the single-cell transcriptomic signatures. We also need to be able to define meaningful B cell subsets from single cell analyses performed on PBMCs, where the relative paucity of a B cell signature means that defining B cell subsets within the whole is challenging. Here we provide a reference single-cell dataset based on phenotypically sorted B cells and an unbiased procedure to better classify functional B cell subsets in the peripheral blood, particularly useful in establishing a baseline cellular landscape and in extracting significant changes with respect to this baseline from single-cell datasets. We find 10 different clusters of B cells and applied a novel, geometry-inspired, method to RNA velocity estimates in order to evaluate the dynamic transitions between B cell clusters. This indicated the presence of two main developmental branches of memory B cells. A T-independent branch that involves IgM memory cells and two DN subpopulations, culminating in a population thought to be associated with Age related B cells and the extrafollicular response. The other, T-dependent, branch involves a third DN cluster which appears to be a precursor of classical memory cells. In addition, we identify a novel DN4 population, which is IgE rich and closely linked to the classical/precursor memory branch suggesting an IgE specific T-dependent cell population.
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Affiliation(s)
- Alexander Stewart
- School of Biosciences and Medicine, University of Surrey, Guildford, United Kingdom
| | - Joseph Chi-Fung Ng
- Randall Centre for Cell and Molecular Biophysics, School of Basic and Medical Biosciences, King's College London, London, United Kingdom
| | - Gillian Wallis
- School of Biosciences and Medicine, University of Surrey, Guildford, United Kingdom
| | - Vasiliki Tsioligka
- School of Biosciences and Medicine, University of Surrey, Guildford, United Kingdom
| | - Franca Fraternali
- Randall Centre for Cell and Molecular Biophysics, School of Basic and Medical Biosciences, King's College London, London, United Kingdom
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22
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Hallmarks of aging and immunosenescence: Connecting the dots. Cytokine Growth Factor Rev 2021; 59:9-21. [PMID: 33551332 DOI: 10.1016/j.cytogfr.2021.01.006] [Citation(s) in RCA: 61] [Impact Index Per Article: 20.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2021] [Accepted: 01/24/2021] [Indexed: 12/11/2022]
Abstract
Aging is a natural physiological process that features various and variable challenges, associated with loss of homeostasis within the organism, often leading to negative consequences for health. Cellular senescence occurs when cells exhaust the capacity to renew themselves and their tissue environment as the cell cycle comes to a halt. This process is influenced by genetics, metabolism and extrinsic factors. Immunosenescence, the aging of the immune system, is a result of the aging process, but can also in turn act as a secondary inducer of senescence within other tissues. This review aims to summarize the current state of knowledge regarding hallmarks of aging in relation to immunosenescence, with a focus on aging-related imbalances in the medullary environment, as well as the components of the innate and adaptive immune responses. Aging within the immune system alters its functionality, and has consequences for the person's ability to fight infections, as well as for susceptibility to chronic diseases such as cancer and cardiovascular disease. The senescence-associated secretory phenotype is described, as well as the involvement of this phenomenon in the paracrine induction of senescence in otherwise healthy cells. Inflammaging is discussed in detail, along with the comorbidities associated with this process. A knowledge of these processes is required in order to consider possible targets for the application of senotherapeutic agents - interventions with the potential to modulate the senescence process, thus prolonging the healthy lifespan of the immune system and minimizing the secondary effects of immunosenescence.
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23
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Frasca D, Blomberg BB. Aging induces B cell defects and decreased antibody responses to influenza infection and vaccination. IMMUNITY & AGEING 2020; 17:37. [PMID: 33292323 PMCID: PMC7674578 DOI: 10.1186/s12979-020-00210-z] [Citation(s) in RCA: 52] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 07/01/2020] [Accepted: 11/16/2020] [Indexed: 12/15/2022]
Abstract
Background Aging is characterized by a progressive decline in the capacity of the immune system to fight influenza virus infection and to respond to vaccination. Among the several factors involved, in addition to increased frailty and high-risk conditions, the age-associated decrease in cellular and humoral immune responses plays a relevant role. This is in large part due to inflammaging, the chronic low-grade inflammatory status of the elderly, associated with intrinsic inflammation of the immune cells and decreased immune function. Results Aging is usually associated with reduced influenza virus-specific and influenza vaccine-specific antibody responses but some elderly individuals with higher pre-exposure antibody titers, due to a previous infection or vaccination, have less probability to get infected. Examples of this exception are the elderly individuals infected during the 2009 pandemic season who made antibodies with broader epitope recognition and higher avidity than those made by younger individuals. Several studies have allowed the identification of B cell intrinsic defects accounting for sub-optimal antibody responses of elderly individuals. These defects include 1) reduced class switch recombination, responsible for the generation of a secondary response of class switched antibodies, 2) reduced de novo somatic hypermutation of the antibody variable region, 3) reduced binding and neutralization capacity, as well as binding specificity, of the secreted antibodies, 4) increased epigenetic modifications that are associated with lower antibody responses, 5) increased frequencies of inflammatory B cell subsets, and 6) shorter telomeres. Conclusions Although influenza vaccination represents the most effective way to prevent influenza infection, vaccines with greater immunogenicity are needed to improve the response of elderly individuals. Recent advances in technology have made possible a broad approach to better understand the age-associated changes in immune cells, needed to design tailored vaccines and effective therapeutic strategies that will be able to improve the immune response of vulnerable individuals.
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Affiliation(s)
- Daniela Frasca
- Department of Microbiology and Immunology and Sylvester Comprehensive Cancer Center, University of Miami Miller School of Medicine, RMSB 3146A, 1600 NW 10th Ave, Miami, FL, 33136, USA.
| | - Bonnie B Blomberg
- Department of Microbiology and Immunology and Sylvester Comprehensive Cancer Center, University of Miami Miller School of Medicine, RMSB 3146A, 1600 NW 10th Ave, Miami, FL, 33136, USA
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24
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Ghraichy M, Galson JD, Kovaltsuk A, von Niederhäusern V, Pachlopnik Schmid J, Recher M, Jauch AJ, Miho E, Kelly DF, Deane CM, Trück J. Maturation of the Human Immunoglobulin Heavy Chain Repertoire With Age. Front Immunol 2020; 11:1734. [PMID: 32849618 PMCID: PMC7424015 DOI: 10.3389/fimmu.2020.01734] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2020] [Accepted: 06/29/2020] [Indexed: 01/01/2023] Open
Abstract
B cells play a central role in adaptive immune processes, mainly through the production of antibodies. The maturation of the B cell system with age is poorly studied. We extensively investigated age-related alterations of naïve and antigen-experienced immunoglobulin heavy chain (IgH) repertoires. The most significant changes were observed in the first 10 years of life, and were characterized by altered immunoglobulin gene usage and an increased frequency of mutated antibodies structurally diverging from their germline precursors. Older age was associated with an increased usage of downstream IgH constant region genes and fewer antibodies with self-reactive properties. As mutations accumulated with age, the frequency of germline-encoded self-reactive antibodies decreased, indicating a possible beneficial role of self-reactive B cells in the developing immune system. Our results suggest a continuous process of change through childhood across a broad range of parameters characterizing IgH repertoires and stress the importance of using well-selected, age-appropriate controls in IgH studies.
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Affiliation(s)
- Marie Ghraichy
- Division of Immunology, University Children's Hospital, University of Zurich, Zurich, Switzerland.,Children's Research Center, University of Zurich, Zurich, Switzerland
| | - Jacob D Galson
- Children's Research Center, University of Zurich, Zurich, Switzerland.,Alchemab Therapeutics Ltd, London, United Kingdom
| | | | - Valentin von Niederhäusern
- Division of Immunology, University Children's Hospital, University of Zurich, Zurich, Switzerland.,Children's Research Center, University of Zurich, Zurich, Switzerland
| | - Jana Pachlopnik Schmid
- Division of Immunology, University Children's Hospital, University of Zurich, Zurich, Switzerland.,Children's Research Center, University of Zurich, Zurich, Switzerland
| | - Mike Recher
- Immunodeficiency Laboratory, Department of Biomedicine, University and University Hospital of Basel, Basel, Switzerland
| | - Annaïse J Jauch
- Immunodeficiency Laboratory, Department of Biomedicine, University and University Hospital of Basel, Basel, Switzerland
| | - Enkelejda Miho
- Institute of Medical Engineering and Medical Informatics, University of Applied Sciences and Arts Northwestern Switzerland FHNW, Muttenz, Switzerland.,SIB Swiss Institute of Bioinformatics, Lausanne, Switzerland.,aiNET GmbH, Basel, Switzerland
| | - Dominic F Kelly
- Oxford Vaccine Group, Department of Paediatrics, University of Oxford, Oxford, United Kingdom.,Oxford University Hospitals NHS Foundation Trust, Oxford, United Kingdom
| | - Charlotte M Deane
- Department of Statistics, University of Oxford, Oxford, United Kingdom
| | - Johannes Trück
- Division of Immunology, University Children's Hospital, University of Zurich, Zurich, Switzerland.,Children's Research Center, University of Zurich, Zurich, Switzerland
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25
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Kuri-Cervantes L, Pampena MB, Meng W, Rosenfeld AM, Ittner CAG, Weisman AR, Agyekum RS, Mathew D, Baxter AE, Vella LA, Kuthuru O, Apostolidis SA, Bershaw L, Dougherty J, Greenplate AR, Pattekar A, Kim J, Han N, Gouma S, Weirick ME, Arevalo CP, Bolton MJ, Goodwin EC, Anderson EM, Hensley SE, Jones TK, Mangalmurti NS, Luning Prak ET, Wherry EJ, Meyer NJ, Betts MR. Comprehensive mapping of immune perturbations associated with severe COVID-19. Sci Immunol 2020; 5:eabd7114. [PMID: 32669287 PMCID: PMC7402634 DOI: 10.1126/sciimmunol.abd7114] [Citation(s) in RCA: 561] [Impact Index Per Article: 140.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2020] [Accepted: 07/10/2020] [Indexed: 01/08/2023]
Abstract
Although critical illness has been associated with SARS-CoV-2-induced hyperinflammation, the immune correlates of severe COVID-19 remain unclear. Here, we comprehensively analyzed peripheral blood immune perturbations in 42 SARS-CoV-2 infected and recovered individuals. We identified extensive induction and activation of multiple immune lineages, including T cell activation, oligoclonal plasmablast expansion, and Fc and trafficking receptor modulation on innate lymphocytes and granulocytes, that distinguished severe COVID-19 cases from healthy donors or SARS-CoV-2-recovered or moderate severity patients. We found the neutrophil to lymphocyte ratio to be a prognostic biomarker of disease severity and organ failure. Our findings demonstrate broad innate and adaptive leukocyte perturbations that distinguish dysregulated host responses in severe SARS-CoV-2 infection and warrant therapeutic investigation.
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Affiliation(s)
- Leticia Kuri-Cervantes
- Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
- Institute for Immunology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - M Betina Pampena
- Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
- Institute for Immunology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Wenzhao Meng
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, Philadelphia, PA19104, USA
| | - Aaron M Rosenfeld
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, Philadelphia, PA19104, USA
| | - Caroline A G Ittner
- Division of Pulmonary, Allergy and Critical Care, Center for Translational Lung Biology, Lung Biology Institute, Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Ariel R Weisman
- Division of Pulmonary, Allergy and Critical Care, Center for Translational Lung Biology, Lung Biology Institute, Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Roseline S Agyekum
- Division of Pulmonary, Allergy and Critical Care, Center for Translational Lung Biology, Lung Biology Institute, Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Divij Mathew
- Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
- Department of Systems Pharmacology and Translational Therapeutics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Amy E Baxter
- Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
- Department of Systems Pharmacology and Translational Therapeutics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Laura A Vella
- Institute for Immunology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
- Division of Infectious Diseases, Department of Pediatrics, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, 19104, USA
| | - Oliva Kuthuru
- Institute for Immunology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
- Department of Systems Pharmacology and Translational Therapeutics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Sokratis A Apostolidis
- Institute for Immunology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
- Department of Systems Pharmacology and Translational Therapeutics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
- Division of Rheumatology, Department of Medicine, Hospital of the University of Pennsylvania, Philadelphia, Pennsylvania, 19104, USA
| | - Luanne Bershaw
- Institute for Immunology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
- Department of Systems Pharmacology and Translational Therapeutics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Jeanette Dougherty
- Institute for Immunology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
- Department of Systems Pharmacology and Translational Therapeutics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Allison R Greenplate
- Institute for Immunology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
- Department of Systems Pharmacology and Translational Therapeutics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Ajinkya Pattekar
- Institute for Immunology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
- Division of Gastroenterology, Department of Medicine, Hospital of the University of Pennsylvania, Philadelphia, Pennsylvania, 19104, USA
| | - Justin Kim
- Institute for Immunology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
- Department of Systems Pharmacology and Translational Therapeutics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Nicholas Han
- Institute for Immunology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
- Department of Systems Pharmacology and Translational Therapeutics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Sigrid Gouma
- Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
- Institute for Immunology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Madison E Weirick
- Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
- Institute for Immunology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Claudia P Arevalo
- Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
- Institute for Immunology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Marcus J Bolton
- Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
- Institute for Immunology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Eileen C Goodwin
- Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
- Institute for Immunology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Elizabeth M Anderson
- Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
- Institute for Immunology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Scott E Hensley
- Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
- Institute for Immunology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Tiffanie K Jones
- Division of Pulmonary, Allergy and Critical Care, Center for Translational Lung Biology, Lung Biology Institute, Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Nilam S Mangalmurti
- Institute for Immunology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
- Division of Pulmonary, Allergy and Critical Care, Center for Translational Lung Biology, Lung Biology Institute, Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Eline T Luning Prak
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, Philadelphia, PA19104, USA
| | - E John Wherry
- Institute for Immunology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA.
- Department of Systems Pharmacology and Translational Therapeutics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
- Parker Institute for Cancer Immunotherapy at the University of Pennsylvania, Philadelphia, Pennsylvania, 19104, USA
| | - Nuala J Meyer
- Division of Pulmonary, Allergy and Critical Care, Center for Translational Lung Biology, Lung Biology Institute, Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA.
| | - Michael R Betts
- Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA.
- Institute for Immunology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
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26
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Labi V, Derudder E. Cell signaling and the aging of B cells. Exp Gerontol 2020; 138:110985. [PMID: 32504658 DOI: 10.1016/j.exger.2020.110985] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2019] [Revised: 05/17/2020] [Accepted: 05/29/2020] [Indexed: 12/24/2022]
Abstract
The uniqueness of each B cell lies in the structural diversity of the B-cell antigen receptor allowing the virtually limitless recognition of antigens, a necessity to protect individuals against a range of challenges. B-cell development and response to stimulation are exquisitely regulated by a group of cell surface receptors modulating various signaling cascades and their associated genetic programs. The effects of these signaling pathways in optimal antibody-mediated immunity or the aberrant promotion of immune pathologies have been intensely researched in the past in young individuals. In contrast, we are only beginning to understand the contribution of these pathways to the changes in B cells of old organisms. Thus, critical transcription factors such as E2A and STAT5 show differential expression or activity between young and old B cells. As a result, B-cell physiology appears altered, and antibody production is impaired. Here, we discuss selected phenotypic changes during B-cell aging and attempt to relate them to alterations of molecular mechanisms.
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Affiliation(s)
- Verena Labi
- Institute of Developmental Immunology, Biocenter, Medical University of Innsbruck, Innsbruck 6020, Austria.
| | - Emmanuel Derudder
- Institute for Biomedical Aging Research, University of Innsbruck, Innsbruck 6020, Austria.
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27
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Mitsunaga EM, Snyder MP. Deep Characterization of the Human Antibody Response to Natural Infection Using Longitudinal Immune Repertoire Sequencing. Mol Cell Proteomics 2020; 19:278-293. [PMID: 31767621 PMCID: PMC7000125 DOI: 10.1074/mcp.ra119.001633] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2019] [Revised: 10/30/2019] [Indexed: 01/01/2023] Open
Abstract
Human antibody response studies are largely restricted to periods of high immune activity (e.g. vaccination). To comprehensively understand the healthy B cell immune repertoire and how this changes over time and through natural infection, we conducted immune repertoire RNA sequencing on flow cytometry-sorted B cell subsets to profile a single individual's antibodies over 11 months through two periods of natural viral infection. We found that 1) a baseline of healthy variable (V) gene usage in antibodies exists and is stable over time, but antibodies in memory cells consistently have a different usage profile relative to earlier B cell stages; 2) a single complementarity-determining region 3 (CDR3) is potentially generated from more than one VJ gene combination; and 3) IgG and IgA antibody transcripts are found at low levels in early human B cell development, suggesting that class switching may occur earlier than previously realized. These findings provide insight into immune repertoire stability, response to natural infections, and human B cell development.
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Affiliation(s)
- Erin M Mitsunaga
- Department of Genetics, Stanford University School of Medicine, Stanford, California 94305
| | - Michael P Snyder
- Department of Genetics, Stanford University School of Medicine, Stanford, California 94305.
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28
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Omer A, Shemesh O, Peres A, Polak P, Shepherd AJ, Watson C, Boyd SD, Collins AM, Lees W, Yaari G. VDJbase: an adaptive immune receptor genotype and haplotype database. Nucleic Acids Res 2020; 48:D1051-D1056. [PMID: 31602484 PMCID: PMC6943044 DOI: 10.1093/nar/gkz872] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2019] [Revised: 09/19/2019] [Accepted: 10/01/2019] [Indexed: 12/14/2022] Open
Abstract
VDJbase is a publicly available database that offers easy searching of data describing the complete sets of gene sequences (genotypes and haplotypes) inferred from adaptive immune receptor repertoire sequencing datasets. VDJbase is designed to act as a resource that will allow the scientific community to explore the genetic variability of the immunoglobulin (Ig) and T cell receptor (TR) gene loci. It can also assist in the investigation of Ig- and TR-related genetic predispositions to diseases. Our database includes web-based query and online tools to assist in visualization and analysis of the genotype and haplotype data. It enables users to detect those alleles and genes that are significantly over-represented in a particular population, in terms of genotype, haplotype and gene expression. The database website can be freely accessed at https://www.vdjbase.org/, and no login is required. The data and code use creative common licenses and are freely downloadable from https://bitbucket.org/account/user/yaarilab/projects/GPHP.
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Affiliation(s)
- Aviv Omer
- Bioengineering, Faculty of Engineering, Bar-Ilan University, Ramat Gan 5290002, Israel
| | - Or Shemesh
- Bioengineering, Faculty of Engineering, Bar-Ilan University, Ramat Gan 5290002, Israel
| | - Ayelet Peres
- Bioengineering, Faculty of Engineering, Bar-Ilan University, Ramat Gan 5290002, Israel
| | - Pazit Polak
- Bioengineering, Faculty of Engineering, Bar-Ilan University, Ramat Gan 5290002, Israel
| | - Adrian J Shepherd
- Institute of Structural and Molecular Biology, Birkbeck, University of London, London, UK
| | - Corey T Watson
- University of Louisville School of Medicine, Biochemistry and Molecular Genetics, Louisville, KY 40292, USA
| | - Scott D Boyd
- Department of Pathology, Stanford University, Stanford, CA 94305, USA
| | - Andrew M Collins
- School of Biotechnology and Biomolecular Sciences, University of NSW, Kensington, Sydney, NSW 2052, Australia
| | - William Lees
- Institute of Structural and Molecular Biology, Birkbeck, University of London, London, UK
| | - Gur Yaari
- Bioengineering, Faculty of Engineering, Bar-Ilan University, Ramat Gan 5290002, Israel
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29
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Blanco E, Perez-Andres M, Sanoja-Flores L, Wentink M, Pelak O, Martín-Ayuso M, Grigore G, Torres-Canizales J, López-Granados E, Kalina T, van der Burg M, Arriba-Méndez S, Santa Cruz S, Puig N, van Dongen JJ, Orfao A. Selection and validation of antibody clones against IgG and IgA subclasses in switched memory B-cells and plasma cells. J Immunol Methods 2019; 475:112372. [DOI: 10.1016/j.jim.2017.09.008] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2017] [Revised: 07/18/2017] [Accepted: 09/15/2017] [Indexed: 11/27/2022]
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30
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Olson BJ, Moghimi P, Schramm CA, Obraztsova A, Ralph D, Vander Heiden JA, Shugay M, Shepherd AJ, Lees W, Matsen FA. sumrep: A Summary Statistic Framework for Immune Receptor Repertoire Comparison and Model Validation. Front Immunol 2019; 10:2533. [PMID: 31736960 PMCID: PMC6838214 DOI: 10.3389/fimmu.2019.02533] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2019] [Accepted: 10/11/2019] [Indexed: 12/28/2022] Open
Abstract
The adaptive immune system generates an incredible diversity of antigen receptors for B and T cells to keep dangerous pathogens at bay. The DNA sequences coding for these receptors arise by a complex recombination process followed by a series of productivity-based filters, as well as affinity maturation for B cells, giving considerable diversity to the circulating pool of receptor sequences. Although these datasets hold considerable promise for medical and public health applications, the complex structure of the resulting adaptive immune receptor repertoire sequencing (AIRR-seq) datasets makes analysis difficult. In this paper we introduce sumrep, an R package that efficiently performs a wide variety of repertoire summaries and comparisons, and show how sumrep can be used to perform model validation. We find that summaries vary in their ability to differentiate between datasets, although many are able to distinguish between covariates such as donor, timepoint, and cell type for BCR and TCR repertoires. We show that deletion and insertion lengths resulting from V(D)J recombination tend to be more discriminative characterizations of a repertoire than summaries that describe the amino acid composition of the CDR3 region. We also find that state-of-the-art generative models excel at recapitulating gene usage and recombination statistics in a given experimental repertoire, but struggle to capture many physiochemical properties of real repertoires.
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Affiliation(s)
- Branden J Olson
- Fred Hutchinson Cancer Research Center, Seattle, WA, United States.,Department of Statistics, University of Washington, Seattle, WA, United States
| | - Pejvak Moghimi
- Department of Biological Sciences, Institute of Structural and Molecular Biology, Birkbeck, University of London, London, United Kingdom
| | - Chaim A Schramm
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, United States
| | - Anna Obraztsova
- Center of Life Sciences, Skolkovo Institute of Science and Technology, Moscow, Russia.,Genomics of Adaptive Immunity Department, Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Moscow, Russia
| | - Duncan Ralph
- Fred Hutchinson Cancer Research Center, Seattle, WA, United States
| | - Jason A Vander Heiden
- Department of Bioinformatics and Computational Biology, Genentech, Inc., South San Francisco, CA, United States
| | - Mikhail Shugay
- Center of Life Sciences, Skolkovo Institute of Science and Technology, Moscow, Russia.,Genomics of Adaptive Immunity Department, Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Moscow, Russia.,Department of Molecular Technologies, Pirogov Russian National Research Medical University, Moscow, Russia
| | - Adrian J Shepherd
- Department of Biological Sciences, Institute of Structural and Molecular Biology, Birkbeck, University of London, London, United Kingdom
| | - William Lees
- Department of Biological Sciences, Institute of Structural and Molecular Biology, Birkbeck, University of London, London, United Kingdom
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31
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Hagen M, Derudder E. Inflammation and the Alteration of B-Cell Physiology in Aging. Gerontology 2019; 66:105-113. [PMID: 31553969 DOI: 10.1159/000501963] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2019] [Accepted: 07/08/2019] [Indexed: 11/19/2022] Open
Abstract
Aging results for the immune system in a departure from the optimal homeostatic state seen in young organisms. This divergence regrettably contributes to a higher frequency of compromised responses to infections and inefficient classical vaccination in aged populations. In B cells, the cornerstone of humoral immunity, the development and distribution of the various mature B cell subsets are impacted by aging in both humans and mice. In addition, aged mature B cells demonstrate limited capacity to mount efficient antibody responses. An expected culprit for the decline in effective immunity is the rise of the systemic levels of pro-inflammatory molecules during aging, establishing a chronic low-grade inflammation. Indeed, numerous alterations affecting directly or indirectly B cells in old people and mice are reminiscent of various effects of acute inflammation on this cell type in young adults. The present mini-review will highlight the possible adverse contributions of the persistent low-level inflammation observed in susceptible older organisms to the inadequate B-cell physiology.
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Affiliation(s)
- Magdalena Hagen
- Institute for Biomedical Aging Research, University Innsbruck, Innsbruck, Austria
| | - Emmanuel Derudder
- Institute for Biomedical Aging Research, University Innsbruck, Innsbruck, Austria,
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32
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Margreitter C, Lu HC, Townsend C, Stewart A, Dunn-Walters DK, Fraternali F. BRepertoire: a user-friendly web server for analysing antibody repertoire data. Nucleic Acids Res 2019; 46:W264-W270. [PMID: 29668996 PMCID: PMC6031031 DOI: 10.1093/nar/gky276] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2018] [Accepted: 04/12/2018] [Indexed: 11/18/2022] Open
Abstract
Antibody repertoire analysis by high throughput sequencing is now widely used, but a persisting challenge is enabling immunologists to explore their data to discover discriminating repertoire features for their own particular investigations. Computational methods are necessary for large-scale evaluation of antibody properties. We have developed BRepertoire, a suite of user-friendly web-based software tools for large-scale statistical analyses of repertoire data. The software is able to use data preprocessed by IMGT, and performs statistical and comparative analyses with versatile plotting options. BRepertoire has been designed to operate in various modes, for example analysing sequence-specific V(D)J gene usage, discerning physico-chemical properties of the CDR regions and clustering of clonotypes. Those analyses are performed on the fly by a number of R packages and are deployed by a shiny web platform. The user can download the analysed data in different table formats and save the generated plots as image files ready for publication. We believe BRepertoire to be a versatile analytical tool that complements experimental studies of immune repertoires. To illustrate the server’s functionality, we show use cases including differential gene usage in a vaccination dataset and analysis of CDR3H properties in old and young individuals. The server is accessible under http://mabra.biomed.kcl.ac.uk/BRepertoire.
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Affiliation(s)
- Christian Margreitter
- Randall Centre for Cell & Molecular Biophysics, King’s College London, New Hunt’s House, Guy’s Campus, London SE1 9RT, UK
| | - Hui-Chun Lu
- Cell and Developmental Biology, University College London, Gower Street, Bloomsbury, London WC1E 6BT, UK
| | - Catherine Townsend
- Department of Immunobiology, King’s College London, Guy’s Hospital Great Maze Pond, London SE1 9RT, UK
| | - Alexander Stewart
- Faculty of Health and Medical Sciences, University of Surrey, Guildford GU2 7XH, UK
| | | | - Franca Fraternali
- Randall Centre for Cell & Molecular Biophysics, King’s College London, New Hunt’s House, Guy’s Campus, London SE1 9RT, UK
- To whom correspondence should be addressed. Tel: +44 20 7848 6843;
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33
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Older Human B Cells and Antibodies. HANDBOOK OF IMMUNOSENESCENCE 2019. [PMCID: PMC7121151 DOI: 10.1007/978-3-319-99375-1_21] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
B cells have a number of different roles in the immune response. Their excellent antigen presentation potential can contribute to the activation of other cells of the immune system, and evidence is emerging that specialized subsets of these cells, that may be increased with age, can influence the cell-mediated immune system in antitumor responses. They can also regulate immune responses, to avoid autoreactivity and excessive inflammation. Deficiencies in regulatory B cells may be beneficial in cancer but will only exacerbate the inflammatory environment that is a hallmark of aging. The B cell role as antibody producers is particularly important, since antibodies perform numerous different functions in different environments. Although studying tissue responses in humans is not as easy as in mice, we do know that certain classes of antibodies are more suited to protecting the mucosal tissues (IgA) or responding to T-independent bacterial polysaccharide antigens (IgG2) so we can make some inference with respect to tissue-specific immunity from a study of peripheral blood. We can also make inferences about changes in B cell development with age by looking at the repertoire of different B cell populations to see how age affects the selection events that would normally occur to avoid autoreactivity, or increase specificity, to antigen.
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Matsuzawa S, Isobe M, Kurosawa N. Guinea pig immunoglobulin VH and VL naïve repertoire analysis. PLoS One 2018; 13:e0208977. [PMID: 30543679 PMCID: PMC6292586 DOI: 10.1371/journal.pone.0208977] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2018] [Accepted: 11/28/2018] [Indexed: 12/28/2022] Open
Abstract
The guinea pig has been used as a model to study various human infectious diseases because of its similarity to humans regarding symptoms and immune response, but little is known about the humoral immune response. To better understand the mechanism underlying the generation of the antibody repertoire in guinea pigs, we performed deep sequencing of full-length immunoglobulin variable chains from naïve B and plasma cells. We gathered and analyzed nearly 16,000 full-length VH, Vκ and Vλ genes and analyzed V and J gene segment usage profiles and mutation statuses by annotating recently reported genome data of guinea pig immunoglobulin genes. We found that approximately 70% of heavy, 73% of kappa and 81% of lambda functional germline V gene segments are integrated into the actual V(D)J recombination events. We also found preferential use of a particular V gene segment and accumulated mutation in CDRs 1 and 2 in antigen-specific plasma cells. Our study represents the first attempt to characterize sequence diversity in the expressed guinea pig antibody repertoire and provides significant insight into antibody repertoire generation and Ig-based immunity of guinea pigs.
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Affiliation(s)
- Shun Matsuzawa
- Laboratory of Molecular and Cellular Biology, Graduate School of Science and Engineering for Research, University of Toyama, Toyama-shi, Toyama, Japan
- Medical & Biological Laboratories Co., Ltd., Ina-shi, Nagano, Japan
| | - Masaharu Isobe
- Laboratory of Molecular and Cellular Biology, Graduate School of Science and Engineering for Research, University of Toyama, Toyama-shi, Toyama, Japan
| | - Nobuyuki Kurosawa
- Laboratory of Molecular and Cellular Biology, Graduate School of Science and Engineering for Research, University of Toyama, Toyama-shi, Toyama, Japan
- * E-mail:
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35
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Davydov AN, Obraztsova AS, Lebedin MY, Turchaninova MA, Staroverov DB, Merzlyak EM, Sharonov GV, Kladova O, Shugay M, Britanova OV, Chudakov DM. Comparative Analysis of B-Cell Receptor Repertoires Induced by Live Yellow Fever Vaccine in Young and Middle-Age Donors. Front Immunol 2018; 9:2309. [PMID: 30356675 PMCID: PMC6189279 DOI: 10.3389/fimmu.2018.02309] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2018] [Accepted: 09/17/2018] [Indexed: 12/25/2022] Open
Abstract
Age-related changes can significantly alter the state of adaptive immune system and often lead to attenuated response to novel pathogens and vaccination. In present study we employed 5′RACE UMI-based full length and nearly error-free immunoglobulin profiling to compare plasma cell antibody repertoires in young (19–26 years) and middle-age (45–58 years) individuals vaccinated with a live yellow fever vaccine, modeling a newly encountered pathogen. Our analysis has revealed age-related differences in the responding antibody repertoire ranging from distinct IGH CDR3 repertoire properties to differences in somatic hypermutation intensity and efficiency and antibody lineage tree structure. Overall, our findings suggest that younger individuals respond with a more diverse antibody repertoire and employ a more efficient somatic hypermutation process than elder individuals in response to a newly encountered pathogen.
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Affiliation(s)
- Alexey N Davydov
- Adaptive Immunity Group, Central European Institute of Technology, Brno, Czechia
| | - Anna S Obraztsova
- Faculty of Bioengineering and Bioinformatics, Lomonosov Moscow State University, Moscow, Russia.,Center of Life Sciences, Skolkovo Institute of Science and Technology, Moscow, Russia
| | - Mikhail Y Lebedin
- Genomics of Adaptive Immunity Department, Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Moscow, Russia
| | - Maria A Turchaninova
- Genomics of Adaptive Immunity Department, Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Moscow, Russia.,Department of Molecular Technologies, Pirogov Russian National Research Medical University, Moscow, Russia.,Laboratory of Genomics of Antitumor Adaptive Immunity, Privolzhsky Research Medical University, Nizhny Novgorod, Russia
| | - Dmitriy B Staroverov
- Genomics of Adaptive Immunity Department, Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Moscow, Russia.,Department of Molecular Technologies, Pirogov Russian National Research Medical University, Moscow, Russia
| | - Ekaterina M Merzlyak
- Genomics of Adaptive Immunity Department, Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Moscow, Russia.,Department of Molecular Technologies, Pirogov Russian National Research Medical University, Moscow, Russia
| | - George V Sharonov
- Genomics of Adaptive Immunity Department, Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Moscow, Russia.,Laboratory of Genomics of Antitumor Adaptive Immunity, Privolzhsky Research Medical University, Nizhny Novgorod, Russia
| | - Olga Kladova
- Department of Molecular Technologies, Pirogov Russian National Research Medical University, Moscow, Russia
| | - Mikhail Shugay
- Center of Life Sciences, Skolkovo Institute of Science and Technology, Moscow, Russia.,Genomics of Adaptive Immunity Department, Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Moscow, Russia.,Department of Molecular Technologies, Pirogov Russian National Research Medical University, Moscow, Russia.,Laboratory of Genomics of Antitumor Adaptive Immunity, Privolzhsky Research Medical University, Nizhny Novgorod, Russia
| | - Olga V Britanova
- Genomics of Adaptive Immunity Department, Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Moscow, Russia.,Department of Molecular Technologies, Pirogov Russian National Research Medical University, Moscow, Russia.,Laboratory of Genomics of Antitumor Adaptive Immunity, Privolzhsky Research Medical University, Nizhny Novgorod, Russia
| | - Dmitriy M Chudakov
- Adaptive Immunity Group, Central European Institute of Technology, Brno, Czechia.,Center of Life Sciences, Skolkovo Institute of Science and Technology, Moscow, Russia.,Genomics of Adaptive Immunity Department, Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Moscow, Russia.,Department of Molecular Technologies, Pirogov Russian National Research Medical University, Moscow, Russia.,Laboratory of Genomics of Antitumor Adaptive Immunity, Privolzhsky Research Medical University, Nizhny Novgorod, Russia
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Sheng G, Chen P, Wei Y, Chu J, Cao X, Zhang HL. Better approach for autoimmune pulmonary alveolar proteinosis treatment: inhaled or subcutaneous granulocyte-macrophage colony-stimulating factor: a meta-analyses. Respir Res 2018; 19:163. [PMID: 30165864 PMCID: PMC6117963 DOI: 10.1186/s12931-018-0862-4] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2018] [Accepted: 08/14/2018] [Indexed: 01/10/2023] Open
Abstract
BACKGROUND Autoimmune pulmonary alveolar proteinosis (aPAP) is a rare pulmonary disease caused by functional deficiency of granulocyte-macrophage colony-stimulating factor (GM-CSF). GM-CSF therapy in aPAP has been reported effective in some studies. This meta-analyses aimed to evaluate whether GM-CSF therapy, including inhaled and subcutaneous GM-CSF have therapeutic effect in aPAP patients. METHODS We analyzed 10 studies searched from PubMed, EmBase, Web of Science, Wiley Online Library and Cochrane Collaboration databases to evaluate the pooled effects of GM-CSF treatment in aPAP patients. RESULTS Ten observational studies involving 115 aPAP patients were included. The pooled analyses of response rate (81%, p < 0.001), relapse rate (22%, p = 0.009), PaO2 (13.76 mmHg, p < 0.001) and P(A-a)O2 (19.44 mmHg, p < 0.001) showed that GM-CSF treatment was effective on aPAP patients. Further analyses showed that inhaled GM-CSF treatment was more effective than subcutaneous GM-CSF therapy, including a higher response rate (89% vs. 71%, p = 0.023), more improvements in PaO2 (21.02 mmHg vs. 8.28 mmHg, p < 0.001) and P(A-a)O2 (19.63 mmHg vs. 9.15 mmHg, p < 0.001). CONCLUSIONS As two routes of exogenous GM-CSF treatment, inhaled and subcutaneous were both proven to have effect on aPAP patients. Furthermore, inhaled GM-CSF therapy showed a higher response rate, more improvements on PaO2 and P(A-a)O2 than subcutaneous GM-CSF treatment in aPAP patients, suggesting inhaled GM-CSF therapy could have more benefits on aPAP patients. Therefore, GM-CSF therapy, especially inhaled GM-CSF, might be a promising therapeutic option in treating aPAP.
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Affiliation(s)
- Gaohong Sheng
- Department of Respiratory and Critical Care Medicine, Tongji Hospital of Tongji Medical College, Huazhong University of Science and Technology, No.1095, Jie Fang Road, Han Kou District, Wu Han, 430030, Hu Bei Province, China
| | - Peng Chen
- Division of Cardiology, Departments of Internal Medicine and Genetic Diagnosis Center, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wu Han, China.,Hubei Key Laboratory of Genetics and Molecular Mechanism of Cardiological Disorders, Wuhan, 430030, China
| | - Yanqiu Wei
- Department of Respiratory and Critical Care Medicine, Tongji Hospital of Tongji Medical College, Huazhong University of Science and Technology, No.1095, Jie Fang Road, Han Kou District, Wu Han, 430030, Hu Bei Province, China
| | - Jiaojiao Chu
- Department of Respiratory and Critical Care Medicine, Tongji Hospital of Tongji Medical College, Huazhong University of Science and Technology, No.1095, Jie Fang Road, Han Kou District, Wu Han, 430030, Hu Bei Province, China
| | - Xiaolei Cao
- Division of Respiratory and Critical Care Medicine, the Second Hospital of Huangshi, Huangshi, 435000, China
| | - Hui-Lan Zhang
- Department of Respiratory and Critical Care Medicine, Tongji Hospital of Tongji Medical College, Huazhong University of Science and Technology, No.1095, Jie Fang Road, Han Kou District, Wu Han, 430030, Hu Bei Province, China.
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37
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Weppner G, Ohlei O, Hammers CM, Holl-Ulrich K, Voswinkel J, Bischof J, Hasselbacher K, Riemekasten G, Lamprecht P, Ibrahim S, Iking-Konert C, Recke A, Müller A. In situ detection of PR3-ANCA + B cells and alterations in the variable region of immunoglobulin genes support a role of inflamed tissue in the emergence of auto-reactivity in granulomatosis with polyangiitis. J Autoimmun 2018; 93:89-103. [PMID: 30054207 DOI: 10.1016/j.jaut.2018.07.004] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2018] [Accepted: 07/01/2018] [Indexed: 10/28/2022]
Abstract
Circulating anti-neutrophilic cytoplasmic autoantibodies targeting proteinase 3 (PR3-ANCA) are a diagnostic and pathogenic hallmark of granulomatosis with polyangiitis (GPA). It is, however, incompletely understood if inflamed tissue supports presence or emergence of PR3-ANCA+ B cells. In search of such cells in inflamed tissue of GPA, immunofluorescence staining for IgG and a common PR3-ANCA idiotype (5/7 Id) was undertaken. Few 5/7 Id+/IgG+ B cells were detected in respiratory and kidney tissue of GPA. To gain more insight into surrogate markers possibly indicative of an anti-PR3-response, a meta-analysis comprising IGVH and IGVL genes derived from respiratory tract tissue of GPA (231 clones) was performed. Next generation sequencing-based IGHV genes derived from peripheral blood of healthy donors (244.353 clones) and previously published IGLV genes (148 clones) served as controls. Additionally, Ig genes of three murine and five known human monoclonal anti-PR3 antibodies were analyzed. Primary and probably secondary rearrangements led to altered VDJ usage and an extended complementarity determining region 3 (CDR3) of IGHV clones from GPA tissue. Selection against amino acid exchanges was prominent in the framework region of IGHV clones from GPA tissue. The comparison of V(D)J rearrangements and deduced amino acid sequences of the CDR3 yielded no identities and few similarities between clones derived from respiratory tissue of GPA and anti-PR3 antibodies, arguing against a presence of B cells that carry PR3-ANCA-prone Ig genes among the clones. In line with the scarcity of 5/7 Id+ B lymphocytes in GPA tissue, the results suggest that with respect to a local anti-PR3 response, methods detecting rare clones are required.
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Affiliation(s)
- Gesche Weppner
- Dept. of Rheumatology & Clinical Immunology, University Hospital of Schleswig-Holstein, Campus Lübeck & University of Lübeck, Lübeck, Germany
| | - Olena Ohlei
- Lübeck Interdisciplinary Platform for Genome Analytics, Institute of Neurogenetics, University of Lübeck, Lübeck, Germany
| | - Christoph M Hammers
- Dept. of Dermatology, University Hospital of Schleswig-Holstein, Campus Lübeck & University of Lübeck, Lübeck, Germany
| | | | - Jan Voswinkel
- Medical Faculty, University of Saarland, Saarbrücken, Germany
| | - Julia Bischof
- Dept. of Dermatology, University Hospital of Schleswig-Holstein, Campus Lübeck & University of Lübeck, Lübeck, Germany
| | - Katrin Hasselbacher
- Dept. of Otorhinolaryngology, University Hospital of Schleswig-Holstein, Campus Lübeck & University of Lübeck, Lübeck, Germany
| | - Gabriela Riemekasten
- Dept. of Rheumatology & Clinical Immunology, University Hospital of Schleswig-Holstein, Campus Lübeck & University of Lübeck, Lübeck, Germany
| | - Peter Lamprecht
- Dept. of Rheumatology & Clinical Immunology, University Hospital of Schleswig-Holstein, Campus Lübeck & University of Lübeck, Lübeck, Germany
| | - Saleh Ibrahim
- Dept. of Dermatology, University Hospital of Schleswig-Holstein, Campus Lübeck & University of Lübeck, Lübeck, Germany
| | | | - Andreas Recke
- Dept. of Dermatology, University Hospital of Schleswig-Holstein, Campus Lübeck & University of Lübeck, Lübeck, Germany
| | - Antje Müller
- Dept. of Rheumatology & Clinical Immunology, University Hospital of Schleswig-Holstein, Campus Lübeck & University of Lübeck, Lübeck, Germany.
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38
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Dunn‐Walters D, Townsend C, Sinclair E, Stewart A. Immunoglobulin gene analysis as a tool for investigating human immune responses. Immunol Rev 2018; 284:132-147. [PMID: 29944755 PMCID: PMC6033188 DOI: 10.1111/imr.12659] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
The human immunoglobulin repertoire is a hugely diverse set of sequences that are formed by processes of gene rearrangement, heavy and light chain gene assortment, class switching and somatic hypermutation. Early B cell development produces diverse IgM and IgD B cell receptors on the B cell surface, resulting in a repertoire that can bind many foreign antigens but which has had self-reactive B cells removed. Later antigen-dependent development processes adjust the antigen affinity of the receptor by somatic hypermutation. The effector mechanism of the antibody is also adjusted, by switching the class of the antibody from IgM to one of seven other classes depending on the required function. There are many instances in human biology where positive and negative selection forces can act to shape the immunoglobulin repertoire and therefore repertoire analysis can provide useful information on infection control, vaccination efficacy, autoimmune diseases, and cancer. It can also be used to identify antigen-specific sequences that may be of use in therapeutics. The juxtaposition of lymphocyte development and numerical evaluation of immune repertoires has resulted in the growth of a new sub-speciality in immunology where immunologists and computer scientists/physicists collaborate to assess immune repertoires and develop models of immune action.
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Affiliation(s)
| | | | - Emma Sinclair
- Faculty of Health and Medical SciencesUniversity of SurreyGuildfordUK
| | - Alex Stewart
- Faculty of Health and Medical SciencesUniversity of SurreyGuildfordUK
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39
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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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40
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Imkeller K, Wardemann H. Assessing human B cell repertoire diversity and convergence. Immunol Rev 2018; 284:51-66. [DOI: 10.1111/imr.12670] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Affiliation(s)
| | - Hedda Wardemann
- German Cancer Research Center; B Cell Immunology; Heidelberg Germany
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41
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Abstract
Somatic assembly of T cell receptor and B cell receptor (BCR) genes produces a vast diversity of lymphocyte antigen recognition capacity. The advent of efficient high-throughput sequencing of lymphocyte antigen receptor genes has recently generated unprecedented opportunities for exploration of adaptive immune responses. With these opportunities have come significant challenges in understanding the analysis techniques that most accurately reflect underlying biological phenomena. In this regard, sample preparation and sequence analysis techniques, which have largely been borrowed and adapted from other fields, continue to evolve. Here, we review current methods and challenges of library preparation, sequencing and statistical analysis of lymphocyte receptor repertoire studies. We discuss the general steps in the process of immune repertoire generation including sample preparation, platforms available for sequencing, processing of sequencing data, measurable features of the immune repertoire, and the statistical tools that can be used for analysis and interpretation of the data. Because BCR analysis harbors additional complexities, such as immunoglobulin (Ig) (i.e., antibody) gene somatic hypermutation and class switch recombination, the emphasis of this review is on Ig/BCR sequence analysis.
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Affiliation(s)
- Neha Chaudhary
- Division of Rheumatology, Department of Medicine, Immunology and Allergy, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, United States
| | - Duane R. Wesemann
- Division of Rheumatology, Department of Medicine, Immunology and Allergy, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, United States
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42
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Abstract
Broad changes in human innate and adaptive immunity are associated with advanced age. The age-related alteration of gene expression was reported for both T and B lymphocytes. We analysed the genome-wide expression profiles (n=20) of naive and whole B cell populations from young and early aged healthy donors under 60 years. We revealed large homogeneity of all analysed genome-wide expression profiles but did not identified any significant gene deregulation between young (30-45 years) and early aged healthy donors (50-60 years). We argue that B cells avoid the aging program on molecular level until 60 years of age. Our results demonstrate the potential of hematopoietic stem cells to generate uncompromised lymphocytes in early elderly. These are very encouraging findings for the general health and the immunity maintenance would not need any intervention to naive B cells. Rather, a suitable immune stimulation in healthy body environment warrants further research into aging of older elderly.
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43
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Vergani S, Korsunsky I, Mazzarello AN, Ferrer G, Chiorazzi N, Bagnara D. Novel Method for High-Throughput Full-Length IGHV-D-J Sequencing of the Immune Repertoire from Bulk B-Cells with Single-Cell Resolution. Front Immunol 2017; 8:1157. [PMID: 28959265 PMCID: PMC5603803 DOI: 10.3389/fimmu.2017.01157] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2017] [Accepted: 09/01/2017] [Indexed: 11/13/2022] Open
Abstract
Efficient and accurate high-throughput DNA sequencing of the adaptive immune receptor repertoire (AIRR) is necessary to study immune diversity in healthy subjects and disease-related conditions. The high complexity and diversity of the AIRR coupled with the limited amount of starting material, which can compromise identification of the full biological diversity makes such sequencing particularly challenging. AIRR sequencing protocols often fail to fully capture the sampled AIRR diversity, especially for samples containing restricted numbers of B lymphocytes. Here, we describe a library preparation method for immunoglobulin sequencing that results in an exhaustive full-length repertoire where virtually every sampled B-cell is sequenced. This maximizes the likelihood of identifying and quantifying the entire IGHV-D-J repertoire of a sample, including the detection of rearrangements present in only one cell in the starting population. The methodology establishes the importance of circumventing genetic material dilution in the preamplification phases and incorporates the use of certain described concepts: (1) balancing the starting material amount and depth of sequencing, (2) avoiding IGHV gene-specific amplification, and (3) using Unique Molecular Identifier. Together, this methodology is highly efficient, in particular for detecting rare rearrangements in the sampled population and when only a limited amount of starting material is available.
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Affiliation(s)
- Stefano Vergani
- Karches Centre for Chronic Lymphocytic Leukemia Research, The Feinstein Institute for Medical Research, Northwell Health, Manhasset, NY, United States.,Hofstra-Northwell Health School of Medicine, Hempstead, NY, United States
| | - Ilya Korsunsky
- Robert S. Boas Center for Genomics & Human Genetics, The Feinstein Institute for Medical Research, Northwell Health, Manhasset, NY, United States
| | - Andrea Nicola Mazzarello
- Karches Centre for Chronic Lymphocytic Leukemia Research, The Feinstein Institute for Medical Research, Northwell Health, Manhasset, NY, United States
| | - Gerardo Ferrer
- Karches Centre for Chronic Lymphocytic Leukemia Research, The Feinstein Institute for Medical Research, Northwell Health, Manhasset, NY, United States
| | - Nicholas Chiorazzi
- Karches Centre for Chronic Lymphocytic Leukemia Research, The Feinstein Institute for Medical Research, Northwell Health, Manhasset, NY, United States
| | - Davide Bagnara
- Karches Centre for Chronic Lymphocytic Leukemia Research, The Feinstein Institute for Medical Research, Northwell Health, Manhasset, NY, United States.,Department of Experimental Medicine, University of Genoa, Genoa, Italy
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44
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Moody S, Escudero-Ibarz L, Wang M, Clipson A, Ochoa Ruiz E, Dunn-Walters D, Xue X, Zeng N, Robson A, Chuang SS, Cogliatti S, Liu H, Goodlad J, Ashton-Key M, Raderer M, Bi Y, Du MQ. Significant association between TNFAIP3
inactivation and biased immunoglobulin heavy chain variable region 4-34 usage in mucosa-associated lymphoid tissue lymphoma. J Pathol 2017; 243:3-8. [DOI: 10.1002/path.4933] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2017] [Revised: 06/05/2017] [Accepted: 06/23/2017] [Indexed: 12/17/2022]
Affiliation(s)
- Sarah Moody
- Division of Cellular and Molecular Pathology, Department of Pathology; University of Cambridge; Cambridge UK
| | - Leire Escudero-Ibarz
- Division of Cellular and Molecular Pathology, Department of Pathology; University of Cambridge; Cambridge UK
| | - Ming Wang
- Division of Cellular and Molecular Pathology, Department of Pathology; University of Cambridge; Cambridge UK
| | - Alexandra Clipson
- Division of Cellular and Molecular Pathology, Department of Pathology; University of Cambridge; Cambridge UK
| | - Eguzkine Ochoa Ruiz
- Division of Cellular and Molecular Pathology, Department of Pathology; University of Cambridge; Cambridge UK
| | - Deborah Dunn-Walters
- Division of Infection, Immunity and Inflammatory Disease; King's College London Faculty of Life Sciences & Medicine; London UK
| | - Xuemin Xue
- Division of Cellular and Molecular Pathology, Department of Pathology; University of Cambridge; Cambridge UK
| | - Naiyan Zeng
- Division of Cellular and Molecular Pathology, Department of Pathology; University of Cambridge; Cambridge UK
| | - Alistair Robson
- Department of Dermatopathology; St John's Institute of Dermatology; London UK
| | | | - Sergio Cogliatti
- Institute of Pathology; State Hospital St Gallen; St Gallen Switzerland
| | - Hongxiang Liu
- Molecular Malignancy Laboratory, Addenbrooke's Hospital; Cambridge University Hospitals NHS Foundation Trust; Cambridge UK
| | - John Goodlad
- Department of Pathology, Western General Hospital; NHS Lothian University Hospitals Trust; Edinburgh UK
| | - Margaret Ashton-Key
- Department of Cellular Pathology; Southampton University Hospitals National Health Service Trust; Southampton UK
| | - Markus Raderer
- Department of Medicine I, Clinical Division of Oncology; Medical University of Vienna; Vienna Austria
| | - Yingwen Bi
- Division of Cellular and Molecular Pathology, Department of Pathology; University of Cambridge; Cambridge UK
- Department of Pathology, Eye & ENT Hospital; Fudan University; Shanghai PR China
| | - Ming-Qing Du
- Division of Cellular and Molecular Pathology, Department of Pathology; University of Cambridge; Cambridge UK
- Molecular Malignancy Laboratory, Addenbrooke's Hospital; Cambridge University Hospitals NHS Foundation Trust; Cambridge UK
- Department of Histopathology, Addenbrooke's Hospital; Cambridge University Hospitals NHS Foundation Trust; Cambridge UK
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45
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Novel Approaches to Analyze Immunoglobulin Repertoires. Trends Immunol 2017; 38:471-482. [PMID: 28566130 DOI: 10.1016/j.it.2017.05.003] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2017] [Revised: 04/25/2017] [Accepted: 05/04/2017] [Indexed: 11/21/2022]
Abstract
Analysis of immunoglobulin (Ig) repertoires aims to comprehend Ig diversity with the goal of predicting humoral immune responses in the context of infection, vaccination, autoimmunity, and malignancies. The first next-generation sequencing (NGS) analyses of bulk B cell populations dramatically advanced sampling depth over previous low-throughput single-cell-based protocols, albeit at the expense of accuracy and loss of chain-pairing information. In recent years the field has substantially differentiated, with bulk analyses becoming more accurate while single-cell approaches have gained in throughput. Additionally, new platforms striving to combine high throughput and chain pairing have been developed as well as various computational tools for analysis. Here we review the developments of the past 4-5 years and discuss the open challenges.
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46
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Martin VG, Wu YCB, Townsend CL, Lu GHC, O'Hare JS, Mozeika A, Coolen ACC, Kipling D, Fraternali F, Dunn-Walters DK. Transitional B Cells in Early Human B Cell Development - Time to Revisit the Paradigm? Front Immunol 2016; 7:546. [PMID: 27994589 PMCID: PMC5133252 DOI: 10.3389/fimmu.2016.00546] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2016] [Accepted: 11/16/2016] [Indexed: 01/08/2023] Open
Abstract
The B cell repertoire is generated in the adult bone marrow by an ordered series of gene rearrangement processes that result in massive diversity of immunoglobulin (Ig) genes and consequently an equally large number of potential specificities for antigen. As the process is essentially random, the cells exhibiting excess reactivity with self-antigens are generated and need to be removed from the repertoire before the cells are fully mature. Some of the cells are deleted, and some will undergo receptor editing to see if changing the light chain can rescue an autoreactive antibody. As a consequence, the binding properties of the B cell receptor are changed as development progresses through pre-B ≫ immature ≫ transitional ≫ naïve phenotypes. Using long-read, high-throughput, sequencing we have produced a unique set of sequences from these four cell types in human bone marrow and matched peripheral blood, and our results describe the effects of tolerance selection on the B cell repertoire at the Ig gene level. Most strong effects of selection are seen within the heavy chain repertoire and can be seen both in gene usage and in CDRH3 characteristics. Age-related changes are small, and only the size of the CDRH3 shows constant and significant change in these data. The paucity of significant changes in either kappa or lambda light chain repertoires implies that either the heavy chain has more influence over autoreactivity than light chain and/or that switching between kappa and lambda light chains, as opposed to switching within the light chain loci, may effect a more successful autoreactive rescue by receptor editing. Our results show that the transitional cell population contains cells other than those that are part of the pre-B ≫ immature ≫ transitional ≫ naïve development pathway, since the population often shows a repertoire that is outside the trajectory of gene loss/gain between pre-B and naïve stages.
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Affiliation(s)
- Victoria G Martin
- Division of Infection, Immunity and Inflammatory Disease, Faculty of Life Sciences & Medicine, King's College London , London , UK
| | - Yu-Chang Bryan Wu
- Randall Division of Cell and Molecular Biophysics, Faculty of Life Sciences & Medicine, King's College London , London , UK
| | - Catherine L Townsend
- Division of Infection, Immunity and Inflammatory Disease, Faculty of Life Sciences & Medicine, King's College London , London , UK
| | - Grace H C Lu
- Randall Division of Cell and Molecular Biophysics, Faculty of Life Sciences & Medicine, King's College London , London , UK
| | - Joselli Silva O'Hare
- Faculty of Health and Medical Sciences, School of Biosciences and Medicine, University of Surrey , Guildford, Surrey , UK
| | - Alexander Mozeika
- Faculty of Life Sciences & Medicine, Institute for Mathematical and Molecular Biomedicine, King's College London , London , UK
| | - Anthonius C C Coolen
- Faculty of Life Sciences & Medicine, Institute for Mathematical and Molecular Biomedicine, King's College London , London , UK
| | - David Kipling
- Institute of Cancer and Genetics, School of Medicine, Cardiff University , Cardiff , UK
| | - Franca Fraternali
- Randall Division of Cell and Molecular Biophysics, Faculty of Life Sciences & Medicine, King's College London, London, UK; Faculty of Life Sciences & Medicine, Institute for Mathematical and Molecular Biomedicine, King's College London, London, UK
| | - Deborah K Dunn-Walters
- Division of Infection, Immunity and Inflammatory Disease, Faculty of Life Sciences & Medicine, King's College London, London, UK; Faculty of Health and Medical Sciences, School of Biosciences and Medicine, University of Surrey, Guildford, Surrey, UK
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47
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IJspeert H, van Schouwenburg PA, van Zessen D, Pico-Knijnenburg I, Driessen GJ, Stubbs AP, van der Burg M. Evaluation of the Antigen-Experienced B-Cell Receptor Repertoire in Healthy Children and Adults. Front Immunol 2016; 7:410. [PMID: 27799928 PMCID: PMC5066086 DOI: 10.3389/fimmu.2016.00410] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2016] [Accepted: 09/22/2016] [Indexed: 12/03/2022] Open
Abstract
Upon antigen recognition via their B cell receptor (BR), B cells migrate to the germinal center where they undergo somatic hypermutation (SHM) to increase their affinity for the antigen, and class switch recombination (CSR) to change the effector function of the secreted antibodies. These steps are essential to create an antigen-experienced BR repertoire that efficiently protects the body against pathogens. At the same time, the BR repertoire should be selected to protect against responses to self-antigen or harmless antigens. Insights into the processes of SHM, selection, and CSR can be obtained by studying the antigen-experienced BR repertoire. Currently, a large reference data set of healthy children and adults, which ranges from neonates to the elderly, is not available. In this study, we analyzed the antigen-experienced repertoire of 38 healthy donors (HD), ranging from cord blood to 74 years old, by sequencing IGA and IGG transcripts using next generation sequencing. This resulted in a large, freely available reference data set containing 412,890 IGA and IGG transcripts. We used this data set to study mutation levels, SHM patterns, antigenic selection, and CSR from birth to elderly HD. Only small differences were observed in SHM patterns, while the mutation levels increase in early childhood and stabilize at 6 years of age at around 7%. Furthermore, comparison of the antigen-experienced repertoire with sequences from the naive immune repertoire showed that features associated with autoimmunity such as long CDR3 length and IGHV4-34 usage are reduced in the antigen-experienced repertoire. Moreover, IGA2 and IGG2 usage was increased in HD in higher age categories, while IGG1 usage was decreased. In addition, we studied clonal relationship in the different samples. Clonally related sequences were found with different subclasses. Interestingly, we found transcripts with the same CDR1–CDR3 sequence, but different subclasses. Together, these data suggest that a single antigen can provoke a B-cell response with BR of different subclasses and that, during the course of an immune response, some B cells change their isotype without acquiring additional SHM or can directly switch to different isotypes.
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Affiliation(s)
- Hanna IJspeert
- 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
| | - Ingrid Pico-Knijnenburg
- Department of Immunology, Erasmus MC, University Medical Center Rotterdam , Rotterdam , Netherlands
| | - Gertjan J Driessen
- Department of Pediatrics, Erasmus MC-Sophia Children's Hospital, 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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48
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Bischof J, Ibrahim SM. bcRep: R Package for Comprehensive Analysis of B Cell Receptor Repertoire Data. PLoS One 2016; 11:e0161569. [PMID: 27551775 PMCID: PMC4995022 DOI: 10.1371/journal.pone.0161569] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2016] [Accepted: 08/08/2016] [Indexed: 01/11/2023] Open
Abstract
Immunoglobulins, as well as T cell receptors, play a key role in adaptive immune responses because of their ability to recognize antigens. Recent advances in next generation sequencing improved also the quality and quantity of individual B cell receptors repertoire sequencing. Unfortunately, appropriate software to exhaustively analyze repertoire data from NGS platforms without limitations of the number of sequences are lacking. Here we introduce a new R package, bcRep, which offers a platform for comprehensive analyses of B cell receptor repertoires, using IMGT/HighV-QUEST formatted data. Methods for gene usage statistics, clonotype classification, as well as diversity measures, are included. Furthermore, functions to filter datasets, to do summary statistics about mutations, as well as visualization methods, are available. To compare samples in respect of gene usage, diversity, amino acid proportions, similar sequences or clones, several functions including also distance measurements, as well as multidimensional scaling methods, are provided.
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Affiliation(s)
- Julia Bischof
- Institute of Experimental Dermatology, University of Lübeck, Lübeck, Germany
- * E-mail:
| | - Saleh M. Ibrahim
- Institute of Experimental Dermatology, University of Lübeck, Lübeck, Germany
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49
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Abstract
Human immune system aging results in impaired responses to pathogens or vaccines. In the innate immune system, which mediates the earliest pro-inflammatory responses to immunologic challenge, processes ranging from Toll-like Receptor function to Neutrophil Extracellular Trap formation are generally diminished in older adults. Dysregulated, enhanced basal inflammation with age reflecting activation by endogenous damage-associated ligands contributes to impaired innate immune responses. In the adaptive immune system, T and B cell subsets and function alter with age. The control of cytomegalovirus infection, particularly in the T lineage, plays a dominant role in the differentiation and diversity of the T cell compartment.
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Affiliation(s)
- Thilinie Bandaranayake
- Section of Infectious Diseases, Department of Internal Medicine, Yale School of Medicine, New Haven, CT 06520, USA
| | - Albert C Shaw
- Section of Infectious Diseases, Department of Internal Medicine, Yale School of Medicine, New Haven, CT 06520, USA.
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50
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Frasca D, Blomberg BB. B Cell-Specific Biomarkers for Optimal Antibody Responses to Influenza Vaccination and Molecular Pathways That Reduce B Cell Function with Aging. Crit Rev Immunol 2016; 36:523-537. [PMID: 28845758 DOI: 10.1615/critrevimmunol.2017020113] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
This review highlights recent findings on the effects of aging on influenza vaccine responses, with major emphasis on T and B cells, which are significantly impaired by aging. We discuss changes in T cell production and thymic output; T cell subsets; and TCR repertoire, function, and response to latent persistent infection. We also discuss changes in B cell subsets, repertoire, and function, and how function is impaired by increased intrinsic B cell inflammation and reduced signal transduction. This review presents age-related effects on antigen-presenting cells, summarizes recent studies, including our own, aimed at the identification of biomarkers of protective vaccine responses, and provides examples of recent technical advances and insights into human vaccine responses that are helping to define the features associated with successful vaccination and that may enable a more predictive vaccinology in the future.
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Affiliation(s)
- Daniela Frasca
- Department of Microbiology and Immunology, University of Miami Miller School of Medicine, Miami, FL 33101, USA
| | - Bonnie B Blomberg
- Department of Microbiology and Immunology, University of Miami Miller School of Medicine, Miami, FL 33101, USA
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