1
|
Collins AM, Ohlin M, Corcoran M, Heather JM, Ralph D, Law M, Martínez-Barnetche J, Ye J, Richardson E, Gibson WS, Rodriguez OL, Peres A, Yaari G, Watson CT, Lees WD. AIRR-C IG Reference Sets: curated sets of immunoglobulin heavy and light chain germline genes. Front Immunol 2024; 14:1330153. [PMID: 38406579 PMCID: PMC10884231 DOI: 10.3389/fimmu.2023.1330153] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2023] [Accepted: 12/27/2023] [Indexed: 02/27/2024] Open
Abstract
Introduction Analysis of an individual's immunoglobulin (IG) gene repertoire requires the use of high-quality germline gene reference sets. When sets only contain alleles supported by strong evidence, AIRR sequencing (AIRR-seq) data analysis is more accurate and studies of the evolution of IG genes, their allelic variants and the expressed immune repertoire is therefore facilitated. Methods The Adaptive Immune Receptor Repertoire Community (AIRR-C) IG Reference Sets have been developed by including only human IG heavy and light chain alleles that have been confirmed by evidence from multiple high-quality sources. To further improve AIRR-seq analysis, some alleles have been extended to deal with short 3' or 5' truncations that can lead them to be overlooked by alignment utilities. To avoid other challenges for analysis programs, exact paralogs (e.g. IGHV1-69*01 and IGHV1-69D*01) are only represented once in each set, though alternative sequence names are noted in accompanying metadata. Results and discussion The Reference Sets include less than half the previously recognised IG alleles (e.g. just 198 IGHV sequences), and also include a number of novel alleles: 8 IGHV alleles, 2 IGKV alleles and 5 IGLV alleles. Despite their smaller sizes, erroneous calls were eliminated, and excellent coverage was achieved when a set of repertoires comprising over 4 million V(D)J rearrangements from 99 individuals were analyzed using the Sets. The version-tracked AIRR-C IG Reference Sets are freely available at the OGRDB website (https://ogrdb.airr-community.org/germline_sets/Human) and will be regularly updated to include newly observed and previously reported sequences that can be confirmed by new high-quality data.
Collapse
Affiliation(s)
- Andrew M. Collins
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW, Australia
| | - Mats Ohlin
- Department of Immunotechnology, and SciLifeLab, Lund University, Lund, Sweden
| | - Martin Corcoran
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institute, Stockholm, Sweden
| | - James M. Heather
- Mass General Cancer Center, Massachusetts General Hospital, Charlestown, MA, United States
- Department of Medicine, Harvard Medical School, Boston, MA, United States
| | - Duncan Ralph
- Fred Hutchinson Cancer Research Center, Seattle, WA, United States
| | - Mansun Law
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, United States
| | - Jesus Martínez-Barnetche
- Centro de Investigación Sobre Enfermedades Infecciosas, Instituto Nacional de Salud Pública, Cuernavaca, Morelos, Mexico
| | - Jian Ye
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, United States
| | - Eve Richardson
- La Jolla Institute for Immunology, San Diego, CA, United States
| | - William S. Gibson
- Department of Biochemistry and Molecular Genetics, School of Medicine, University of Louisville, Louisville, KY, United States
| | - Oscar L. Rodriguez
- Department of Biochemistry and Molecular Genetics, School of Medicine, University of Louisville, Louisville, KY, United States
| | - Ayelet Peres
- Bioengineering Program, Faculty of Engineering, Bar-Ilan University, Ramat Gan, Israel
| | - Gur Yaari
- Bioengineering Program, Faculty of Engineering, Bar-Ilan University, Ramat Gan, Israel
| | - Corey T. Watson
- Department of Biochemistry and Molecular Genetics, School of Medicine, University of Louisville, Louisville, KY, United States
| | - William D. Lees
- Institute of Structural and Molecular Biology, Birkbeck College, London, United Kingdom
- Human-Centered Computing and Information Science, Institute for Systems and Computer Engineering, Technology and Science, Porto, Portugal
| |
Collapse
|
2
|
Colas L, Magnan A, Brouard S. Immunoglobulin E response in health and disease beyond allergic disorders. Allergy 2022; 77:1700-1718. [PMID: 35073421 DOI: 10.1111/all.15230] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2021] [Revised: 12/13/2021] [Accepted: 01/16/2022] [Indexed: 12/24/2022]
Abstract
Immunoglobulin E is the latest discovered of immunoglobulin family and has been long associated with anaphylaxis and worm expulsion. Immunoglobulin E, along with mast cells, basophils, and eosinophils, is also a hallmark of type 2 immunity which is dysregulated in numerous diseases such as asthma, rhinitis, atopic dermatitis, and eosinophilic esophagitis in addition to anaphylaxis as aforementioned. However, recent advances have shed light on IgE regulation and memory explaining the low level of free IgE, the scarcity of IgE plasma cells that are mainly short live and the absence of IgE memory B cells in homeostatic conditions. Furthermore, IgE was implicated in inflammatory conditions beyond allergic disorders where IgE-mediated facilitated antigen presentation can enhance cellular and humoral response against autoantigens in systemic lupus or chronic urticaria leading to more severe disease and even against neoantigen facilitating tumor cell lysis. At last, IgE was unexpectedly associated with allograft rejection or atheromatous cardiovascular diseases where precise mechanisms remain to be deciphered. The purpose of this review is to summarize these recent advances in IgE regulation, biology, and physiopathology beyond allergic diseases opening whole new fields of IgE biology to explore.
Collapse
Affiliation(s)
- Luc Colas
- Plateforme Transversale d'Allergologie et d'immunologie Clinique PFTA Clinique dermatologique CHU de Nantes Nantes France
- Nantes Université, CHU Nantes, INSERM, Center for Research in Transplantation and Translational Immunology Nantes France
| | - Antoine Magnan
- Hôpital Foch, Suresnes; Université de Versailles Saint‐Quentin Paris‐Saclay; INRAe Paris France
| | - Sophie Brouard
- Nantes Université, CHU Nantes, INSERM, Center for Research in Transplantation and Translational Immunology Nantes France
- Labex IGO Nantes France
- Centre d’Investigation Clinique en Biothérapie Centre de ressources biologiques (CRB) Nantes France
| |
Collapse
|
3
|
Abstract
Coinfection with Plasmodium falciparum and helminths may impact the immune response to these parasites because they induce different immune profiles. We studied the effects of coinfections on the antibody profile in a cohort of 715 Mozambican children and adults using the Luminex technology with a panel of 16 antigens from P. falciparum and 11 antigens from helminths (Ascaris lumbricoides, hookworm, Trichuris trichiura, Strongyloides stercoralis, and Schistosoma spp.) and measured antigen-specific IgG and total IgE responses. We compared the antibody profile between groups defined by P. falciparum and helminth previous exposure (based on serology) and/or current infection (determined by microscopy and/or qPCR). In multivariable regression models adjusted by demographic, socioeconomic, water, and sanitation variables, individuals exposed/infected with P. falciparum and helminths had significantly higher total IgE and antigen-specific IgG levels, magnitude (sum of all levels) and breadth of response to both types of parasites compared to individuals exposed/infected with only one type of parasite (P ≤ 0.05). There was a positive association between exposure/infection with P. falciparum and exposure/infection with helminths or the number of helminth species, and vice versa (P ≤ 0.001). In addition, children coexposed/coinfected tended (P = 0.062) to have higher P. falciparum parasitemia than those single exposed/infected. Our results suggest that an increase in the antibody responses in coexposed/coinfected individuals may reflect higher exposure and be due to a more permissive immune environment to infection in the host. IMPORTANCE Coinfection with Plasmodium falciparum and helminths may impact the immune response to these parasites because they induce different immune profiles. We compared the antibody profile between groups of Mozambican individuals defined by P. falciparum and helminth previous exposure and/or current infection. Our results show a significant increase in antibody responses in individuals coexposed/coinfected with P. falciparum and helminths in comparison with individuals exposed/infected with only one of these parasites, and suggest that this increase is due to a more permissive immune environment to infection in the host. Importantly, this study takes previous exposure into account, which is particularly relevant in endemic areas where continuous infections imprint and shape the immune system. Deciphering the implications of coinfections deserves attention because accounting for the real interactions that occur in nature could improve the design of integrated disease control strategies.
Collapse
|
4
|
Zografou C, Vakrakou AG, Stathopoulos P. Short- and Long-Lived Autoantibody-Secreting Cells in Autoimmune Neurological Disorders. Front Immunol 2021; 12:686466. [PMID: 34220839 PMCID: PMC8248361 DOI: 10.3389/fimmu.2021.686466] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2021] [Accepted: 05/28/2021] [Indexed: 12/24/2022] Open
Abstract
As B cells differentiate into antibody-secreting cells (ASCs), short-lived plasmablasts (SLPBs) are produced by a primary extrafollicular response, followed by the generation of memory B cells and long-lived plasma cells (LLPCs) in germinal centers (GCs). Generation of IgG4 antibodies is T helper type 2 (Th2) and IL-4, -13, and -10-driven and can occur parallel to IgE, in response to chronic stimulation by allergens and helminths. Although IgG4 antibodies are non-crosslinking and have limited ability to mobilize complement and cellular cytotoxicity, when self-tolerance is lost, they can disrupt ligand-receptor binding and cause a wide range of autoimmune disorders including neurological autoimmunity. In myasthenia gravis with predominantly IgG4 autoantibodies against muscle-specific kinase (MuSK), it has been observed that one-time CD20+ B cell depletion with rituximab commonly leads to long-term remission and a marked reduction in autoantibody titer, pointing to a short-lived nature of autoantibody-secreting cells. This is also observed in other predominantly IgG4 autoantibody-mediated neurological disorders, such as chronic inflammatory demyelinating polyneuropathy and autoimmune encephalitis with autoantibodies against the Ranvier paranode and juxtaparanode, respectively, and extends beyond neurological autoimmunity as well. Although IgG1 autoantibody-mediated neurological disorders can also respond well to rituximab induction therapy in combination with an autoantibody titer drop, remission tends to be less long-lasting and cases where titers are refractory tend to occur more often than in IgG4 autoimmunity. Moreover, presence of GC-like structures in the thymus of myasthenic patients with predominantly IgG1 autoantibodies against the acetylcholine receptor and in ovarian teratomas of autoimmune encephalitis patients with predominantly IgG1 autoantibodies against the N‐methyl‐d‐aspartate receptor (NMDAR) confers increased the ability to generate LLPCs. Here, we review available information on the short-and long-lived nature of ASCs in IgG1 and IgG4 autoantibody-mediated neurological disorders and highlight common mechanisms as well as differences, all of which can inform therapeutic strategies and personalized medical approaches.
Collapse
Affiliation(s)
- C Zografou
- Institute of Neuropathology, University of Zurich, Zurich, Switzerland
| | - A G Vakrakou
- First Department of Neurology, National and Kapodistrian University of Athens Medical School, Athens, Greece
| | - P Stathopoulos
- First Department of Neurology, National and Kapodistrian University of Athens Medical School, Athens, Greece
| |
Collapse
|
5
|
Gowthaman U, Chen JS, Eisenbarth SC. Regulation of IgE by T follicular helper cells. J Leukoc Biol 2020; 107:409-418. [PMID: 31965637 DOI: 10.1002/jlb.3ri1219-425r] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2019] [Revised: 12/02/2019] [Accepted: 12/09/2019] [Indexed: 12/24/2022] Open
Abstract
Allergies to food and environmental antigens have steeply grown to epidemic proportions. IgE antibodies are key mediators of allergic disease, including life-threatening anaphylaxis. There is now compelling evidence that one of the hallmarks of anaphylaxis-inducing IgE molecules is their high affinity for allergen, and the cellular pathway to high-affinity IgE is typically through sequential switching of IgG B cells. Further, in contrast to the previously held paradigm that a subset of CD4+ T cells called Th2 cells promotes IgE responses, recent studies suggest that T follicular helper cells are crucial for inducing anaphylactic IgE. Here we discuss recent studies that have enabled us to understand the nature, induction, and regulation of this enigmatic antibody isotype in allergic sensitization.
Collapse
Affiliation(s)
- Uthaman Gowthaman
- Department of Laboratory Medicine, Yale University School of Medicine, New Haven, Connecticut, USA.,Department of Immunobiology, Yale University School of Medicine, New Haven, Connecticut, USA
| | - Jennifer S Chen
- Department of Laboratory Medicine, Yale University School of Medicine, New Haven, Connecticut, USA.,Department of Immunobiology, Yale University School of Medicine, New Haven, Connecticut, USA
| | - Stephanie C Eisenbarth
- Department of Laboratory Medicine, Yale University School of Medicine, New Haven, Connecticut, USA.,Department of Immunobiology, Yale University School of Medicine, New Haven, Connecticut, USA
| |
Collapse
|
6
|
Schwartz GW, Shauli T, Linial M, Hershberg U. Serine substitutions are linked to codon usage and differ for variable and conserved protein regions. Sci Rep 2019; 9:17238. [PMID: 31754132 PMCID: PMC6872785 DOI: 10.1038/s41598-019-53452-3] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2019] [Accepted: 11/01/2019] [Indexed: 11/11/2022] Open
Abstract
Serine is the only amino acid that is encoded by two disjoint codon sets (TCN & AGY) so that a tandem substitution of two nucleotides is required to switch between the two sets. We show that these codon sets underlie distinct substitution patterns at positions subject to purifying and diversifying selections. We found that in humans, positions that are conserved among ~100 vertebrates, and thus subjected to purifying selection, are enriched for substitutions involving serine (TCN, denoted S'), proline, and alanine, (S'PA). In contrast, the less conserved positions are enriched for serine encoded with AGY codons (denoted S″), glycine and asparagine, (GS″N). We tested this phenomenon in the HIV envelope glycoprotein (gp120), and the V-gene that encodes B-cell receptors/antibodies. These fast evolving proteins both have hypervariable positions, which are under diversifying selection, closely adjacent to highly conserved structural regions. In both instances, we identified an opposite abundance of two groups of serine substitutions, with enrichment of S'PA in the conserved positions, and GS″N in the hypervariable regions. Finally, we analyzed the substitutions across 60,000 individual human exomes to show that, when serine has a specific functional constraint of phosphorylation capability, S' codons are 32-folds less prone than S″ to substitutions to Threonine or Tyrosine that could potentially retain the phosphorylation site capacity. Combined, our results, that cover evolutionary signals at different temporal scales, demonstrate that through its encoding by two codon sets, serine allows for the existence of alternating substitution patterns within positions of functional maintenance versus sites of rapid diversification.
Collapse
Affiliation(s)
- Gregory W Schwartz
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, USA
| | - Tair Shauli
- School of Computer Science and Engineering, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Michal Linial
- Department of Biological Chemistry, Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Uri Hershberg
- Drexel School of Biomedical Engineering, Science and Health Systems, Drexel University, Philadelphia, USA.
- Department of Microbiology and Immunology, Drexel College of Medicine, Drexel University, Philadelphia, USA.
- Department of Human Biology, Faculty of Science, University of Haifa, Haifa, Israel.
| |
Collapse
|
7
|
Gowthaman U, Chen JS, Zhang B, Flynn WF, Lu Y, Song W, Joseph J, Gertie JA, Xu L, Collet MA, Grassmann JDS, Simoneau T, Chiang D, Berin MC, Craft JE, Weinstein JS, Williams A, Eisenbarth SC. Identification of a T follicular helper cell subset that drives anaphylactic IgE. Science 2019; 365:science.aaw6433. [PMID: 31371561 PMCID: PMC6901029 DOI: 10.1126/science.aaw6433] [Citation(s) in RCA: 263] [Impact Index Per Article: 52.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2019] [Accepted: 07/18/2019] [Indexed: 12/15/2022]
Abstract
Cross-linking of high-affinity immunoglobulin E (IgE) results in the life-threatening allergic reaction anaphylaxis. Yet the cellular mechanisms that induce B cells to produce IgE in response to allergens remain poorly understood. T follicular helper (TFH) cells direct the affinity and isotype of antibodies produced by B cells. Although TFH cell-derived interleukin-4 (IL-4) is necessary for IgE production, it is not sufficient. We report a rare population of IL-13-producing TFH cells present in mice and humans with IgE to allergens, but not when allergen-specific IgE was absent or only low-affinity. These "TFH13" cells have an unusual cytokine profile (IL-13hiIL-4hiIL-5hiIL-21lo) and coexpress the transcription factors BCL6 and GATA3. TFH13 cells are required for production of high- but not low-affinity IgE and subsequent allergen-induced anaphylaxis. Blocking TFH13 cells may represent an alternative therapeutic target to ameliorate anaphylaxis.
Collapse
Affiliation(s)
- Uthaman Gowthaman
- Department of Laboratory Medicine, Yale University School of Medicine, New Haven, CT 06520, USA.,Department of Immunobiology, Yale University School of Medicine, New Haven, CT 06520, USA
| | - Jennifer S Chen
- Department of Laboratory Medicine, Yale University School of Medicine, New Haven, CT 06520, USA.,Department of Immunobiology, Yale University School of Medicine, New Haven, CT 06520, USA
| | - Biyan Zhang
- Department of Laboratory Medicine, Yale University School of Medicine, New Haven, CT 06520, USA.,Department of Immunobiology, Yale University School of Medicine, New Haven, CT 06520, USA
| | - William F Flynn
- The Jackson Laboratory for Genomic Medicine, Farmington, CT 06030, USA
| | - Yisi Lu
- Department of Immunobiology, Yale University School of Medicine, New Haven, CT 06520, USA
| | - Wenzhi Song
- Department of Immunobiology, Yale University School of Medicine, New Haven, CT 06520, USA
| | - Julie Joseph
- Department of Laboratory Medicine, Yale University School of Medicine, New Haven, CT 06520, USA
| | - Jake A Gertie
- Department of Laboratory Medicine, Yale University School of Medicine, New Haven, CT 06520, USA.,Department of Immunobiology, Yale University School of Medicine, New Haven, CT 06520, USA
| | - Lan Xu
- Department of Laboratory Medicine, Yale University School of Medicine, New Haven, CT 06520, USA.,Department of Immunobiology, Yale University School of Medicine, New Haven, CT 06520, USA
| | - Magalie A Collet
- The Jackson Laboratory for Genomic Medicine, Farmington, CT 06030, USA
| | | | - Tregony Simoneau
- The Asthma Center, CT Children's Medical Center, Hartford, CT 06106, USA
| | - David Chiang
- Jaffe Food Allergy Institute and Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - M Cecilia Berin
- Jaffe Food Allergy Institute and Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Joseph E Craft
- Department of Immunobiology, Yale University School of Medicine, New Haven, CT 06520, USA
| | - Jason S Weinstein
- Center for Immunity and Inflammation, Rutgers New Jersey Medical School, Newark, NJ 07101, USA
| | - Adam Williams
- The Jackson Laboratory for Genomic Medicine, Farmington, CT 06030, USA. .,The Department of Genetics and Genome Sciences, University of Connecticut Health Center, Farmington, CT 06032, USA
| | - Stephanie C Eisenbarth
- Department of Laboratory Medicine, Yale University School of Medicine, New Haven, CT 06520, USA. .,Department of Immunobiology, Yale University School of Medicine, New Haven, CT 06520, USA
| |
Collapse
|
8
|
Koning MT, Trollmann IJM, van Bergen CAM, Alvarez Saravia D, Navarrete MA, Kiełbasa SM, Veelken H. Peripheral IgE Repertoires of Healthy Donors Carry Moderate Mutation Loads and Do Not Overlap With Other Isotypes. Front Immunol 2019; 10:1543. [PMID: 31333671 PMCID: PMC6617986 DOI: 10.3389/fimmu.2019.01543] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2019] [Accepted: 06/20/2019] [Indexed: 01/04/2023] Open
Abstract
IgE-mediated allergic disease represents an increasing health problem. Although numerous studies have investigated IgE sequences in allergic patients, little information is available on the healthy IgE repertoire. IgM, IgG, IgA, and IgE transcripts from peripheral blood B cells of five healthy, non-atopic individuals were amplified by unbiased, template-switching, isotype-specific PCR. Complete VDJ regions were sequenced to near-exhaustion on the PacBio platform. Sequences were analyzed for clonal relationships, degree of somatic hypermutation, IGHV gene usage, evidence of antigenic selection, and N-linked glycosylation motifs. IgE repertoires appeared to be highly oligoclonal with preferential usage of certain IGHV genes compared to the other isotypes. IgE sequences carried more somatic mutations than IgM, yet fewer than IgG and IgA. Many IgE sequences contained N-linked glycosylation motifs. IgE sequences had no clonal relationship with the other isotypes. The IgE repertoire in healthy individuals is derived from relatively few clonal expansions without apparent relations to immune reactions that give rise to IgG or IgA. The mutational burden of normal IgE suggests an origin through direct class-switching from the IgM repertoire with little evidence of antigenic drive, and hence presumably low affinity for specific antigens. These findings are compatible with a primary function of the healthy IgE repertoire to occupy Fcε receptors for competitive protection against mast cell degranulation induced by allergen-specific, high-affinity IgE. This background knowledge may help to elucidate pathogenic mechanisms in allergic disease and to design improved desensitization strategies.
Collapse
Affiliation(s)
- Marvyn T Koning
- Department of Hematology, Leiden University Medical Center, Leiden, Netherlands
| | - Ignis J M Trollmann
- Department of Hematology, Leiden University Medical Center, Leiden, Netherlands
| | | | | | | | - Szymon M Kiełbasa
- Department of Biomedical Data Sciences, Leiden University Medical Center, Leiden, Netherlands
| | - Hendrik Veelken
- Department of Hematology, Leiden University Medical Center, Leiden, Netherlands
| |
Collapse
|
9
|
Ohlin M, Scheepers C, Corcoran M, Lees WD, Busse CE, Bagnara D, Thörnqvist L, Bürckert JP, Jackson KJL, Ralph D, Schramm CA, Marthandan N, Breden F, Scott J, Matsen IV FA, Greiff V, Yaari G, Kleinstein SH, Christley S, Sherkow JS, Kossida S, Lefranc MP, van Zelm MC, Watson CT, Collins AM. Inferred Allelic Variants of Immunoglobulin Receptor Genes: A System for Their Evaluation, Documentation, and Naming. Front Immunol 2019; 10:435. [PMID: 30936866 PMCID: PMC6431624 DOI: 10.3389/fimmu.2019.00435] [Citation(s) in RCA: 45] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2018] [Accepted: 02/19/2019] [Indexed: 11/13/2022] Open
Abstract
Immunoglobulins or antibodies are the main effector molecules of the B-cell lineage and are encoded by hundreds of variable (V), diversity (D), and joining (J) germline genes, which recombine to generate enormous IG diversity. Recently, high-throughput adaptive immune receptor repertoire sequencing (AIRR-seq) of recombined V-(D)-J genes has offered unprecedented insights into the dynamics of IG repertoires in health and disease. Faithful biological interpretation of AIRR-seq studies depends upon the annotation of raw AIRR-seq data, using reference germline gene databases to identify the germline genes within each rearrangement. Existing reference databases are incomplete, as shown by recent AIRR-seq studies that have inferred the existence of many previously unreported polymorphisms. Completing the documentation of genetic variation in germline gene databases is therefore of crucial importance. Lymphocyte receptor genes and alleles are currently assigned by the Immunoglobulins, T cell Receptors and Major Histocompatibility Nomenclature Subcommittee of the International Union of Immunological Societies (IUIS) and managed in IMGT®, the international ImMunoGeneTics information system® (IMGT). In 2017, the IMGT Group reached agreement with a group of AIRR-seq researchers on the principles of a streamlined process for identifying and naming inferred allelic sequences, for their incorporation into IMGT®. These researchers represented the AIRR Community, a network of over 300 researchers whose objective is to promote all aspects of immunoglobulin and T-cell receptor repertoire studies, including the standardization of experimental and computational aspects of AIRR-seq data generation and analysis. The Inferred Allele Review Committee (IARC) was established by the AIRR Community to devise policies, criteria, and procedures to perform this function. Formalized evaluations of novel inferred sequences have now begun and submissions are invited via a new dedicated portal (https://ogrdb.airr-community.org). Here, we summarize recommendations developed by the IARC-focusing, to begin with, on human IGHV genes-with the goal of facilitating the acceptance of inferred allelic variants of germline IGHV genes. We believe that this initiative will improve the quality of AIRR-seq studies by facilitating the description of human IG germline gene variation, and that in time, it will expand to the documentation of TR and IG genes in many vertebrate species.
Collapse
Affiliation(s)
- Mats Ohlin
- Department of Immunotechnology, Lund University, Lund, Sweden
| | - Cathrine Scheepers
- Center for HIV and STIs, National Institute for Communicable Diseases, Johannesburg, South Africa
- Faculty of Health Sciences, School of Pathology, University of the Witwatersrand, Johannesburg, South Africa
| | - Martin Corcoran
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institute, Stockholm, Sweden
| | - William D. Lees
- Institute of Structural and Molecular Biology, Birkbeck College, University of London, London, United Kingdom
| | - Christian E. Busse
- Division of B Cell Immunology, German Cancer Research Center, Heidelberg, Germany
| | - Davide Bagnara
- Department of Experimental Medicine, University of Genoa, Genoa, Italy
| | | | | | | | - Duncan Ralph
- Fred Hutchinson Cancer Research Center, Seattle, WA, United States
| | - Chaim A. Schramm
- Vaccine Research Center, National Institutes of Health, Washington, DC, United States
| | - Nishanth Marthandan
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, BC, Canada
| | - Felix Breden
- Department of Biological Sciences, Simon Fraser University, Burnaby, BC, Canada
| | - Jamie Scott
- Department of Molecular Biology and Biochemistry, Faculty of Health Sciences, Simon Fraser University, Burnaby, BC, Canada
| | | | - Victor Greiff
- Department of Immunology, Institute of Clinical Medicine, University of Oslo, Oslo, Norway
| | - Gur Yaari
- Faculty of Engineering, Bar Ilan University, Ramat Gan, Israel
| | | | - Scott Christley
- Department of Clinical Sciences, University of Texas Southwestern Medical Center, Dallas, TX, United States
| | - Jacob S. Sherkow
- Innovation Center for Law and Technology, New York Law School, New York, NY, United States
| | - Sofia Kossida
- IMGT, The International ImMunoGenetics information system (IMGT), Laboratoire d'ImmunoGénétique Moléculaire (LIGM), CNRS, Institut de Génétique Humaine, Université de Montpellier, Montpellier, France
| | - Marie-Paule Lefranc
- IMGT, The International ImMunoGenetics information system (IMGT), Laboratoire d'ImmunoGénétique Moléculaire (LIGM), CNRS, Institut de Génétique Humaine, Université de Montpellier, Montpellier, France
| | - Menno C. van Zelm
- Department of Immunology and Pathology, Central Clinical School, The Alfred Hospital, Monash University, Melbourne, VIC, Australia
| | - Corey T. Watson
- Department of Biochemistry and Molecular Genetics, University of Louisville, Louisville, KY, United States
| | - Andrew M. Collins
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW, Australia
| |
Collapse
|
10
|
Adaptive antibody diversification through N-linked glycosylation of the immunoglobulin variable region. Proc Natl Acad Sci U S A 2018; 115:1901-1906. [PMID: 29432186 DOI: 10.1073/pnas.1711720115] [Citation(s) in RCA: 81] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
A hallmark of B-cell immunity is the generation of a diverse repertoire of antibodies from a limited set of germline V(D)J genes. This repertoire is usually defined in terms of amino acid composition. However, variable domains may also acquire N-linked glycans, a process conditional on the introduction of consensus amino acid motifs (N-glycosylation sites) during somatic hypermutation. High levels of variable domain glycans have been associated with autoantibodies in rheumatoid arthritis, as well as certain follicular lymphomas. However, the role of these glycans in the humoral immune response remains poorly understood. Interestingly, studies have reported both positive and negative effects on antibody affinity. Our aim was to elucidate the role of variable domain glycans during antigen-specific antibody responses. By analyzing B-cell repertoires by next-generation sequencing, we demonstrate that N-glycosylation sites are introduced at positions in which glycans can affect antigen binding as a result of a specific clustering of progenitor glycosylation sites in the germline sequences of variable domain genes. By analyzing multiple human monoclonal and polyclonal (auto)antibody responses, we subsequently show that this process is subject to selection during antigen-specific antibody responses, skewed toward IgG4, and positively contributes to antigen binding. Together, these results highlight a physiological role for variable domain glycosylation as an additional layer of antibody diversification that modulates antigen binding.
Collapse
|
11
|
Culver EL, Sadler R, Bateman AC, Makuch M, Cargill T, Ferry B, Aalberse R, Barnes E, Rispens T. Increases in IgE, Eosinophils, and Mast Cells Can be Used in Diagnosis and to Predict Relapse of IgG4-Related Disease. Clin Gastroenterol Hepatol 2017; 15:1444-1452.e6. [PMID: 28223204 PMCID: PMC5592233 DOI: 10.1016/j.cgh.2017.02.007] [Citation(s) in RCA: 91] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/07/2016] [Revised: 01/25/2017] [Accepted: 02/01/2017] [Indexed: 12/12/2022]
Abstract
BACKGROUND & AIMS IgG subclass 4-related disease (IgG4-RD) is characterized by increased serum levels of IgG4 and infiltration of biliary, pancreatic, and other tissues by IgG4-positive plasma cells. We assessed the prevalence of allergy and/or atopy, serum, and tissue IgE antibodies, and blood and tissue eosinophils in patients with IgG4-RD. We investigated the association between serum IgE and diagnosis and relapse of this disease. METHODS We performed a prospective study of 48 patients with IgG4-RD, 42 patients with an increased serum level of IgG4 with other inflammatory and autoimmune conditions (disease control subjects), and 51 healthy individuals (healthy control subjects) recruited from Oxford, United Kingdom from March 2010 through March 2014, and followed for a median of 41 months (range, 3-73 months). Serum levels of immunoglobulin were measured at diagnosis, during steroid treatment, and at disease relapse for patients with IgG4-RD; levels at diagnosis were compared with baseline levels of control subjects. Allergen-specific IgEs were measured using the IgE ImmunoCAP. Levels and distribution of IgG4 and IgE antibodies in lymphoid, biliary, and pancreatic tissues from patients with IgG4-RD and disease control subjects were measured by immunohistochemistry. We analyzed data using the Spearman rank correlation and receiver operating characteristic curves. RESULTS Serum levels of IgG4 increased to 1.4 g/L or more, and IgE increased to 125 kIU/L or more, in 81% and 54% of patients with IgG4-RD, respectively, compared with 6% and 16% of healthy control subjects (P < .0001). Peripheral blood eosinophilia was detected in 38% of patients with IgG4-RD versus 9% of healthy control subjects (P = .004). Of patients with IgG4-RD, 63% had a history of allergy and 40% had a history of atopy with an IgE-specific response; these values were 60% and 53% in patients with increased serum levels of IgE (P < .05). Level of IgE at diagnosis >480 kIU/L distinguished patients with IgG4-RD from disease control subjects with 86% specificity, 36% sensitivity, and a likelihood ratio of 3.2. Level of IgE at diagnosis >380 kIU/L identified patients with disease relapse with 88% specificity, 64% sensitivity, and a likelihood ratio of 5.4. IgE-positive mast cells and eosinophilia were observed in lymphoid, biliary, and pancreatic tissue samples from 50% and 86% of patients with IgG4-RD, respectively. CONCLUSIONS In a prospective study, we associated IgG4-RD with allergy, atopy, eosinophilia, increased serum levels of IgE, and IgE-positive mast cells in lymphoid, biliary, and pancreatic tissue. An IgE-mediated allergic response therefore seems to develop in most patients with IgG4-RD; levels of IgE might be used in diagnosis and predicting relapse.
Collapse
Affiliation(s)
- Emma L. Culver
- Translational Gastroenterology Unit, John Radcliffe Hospital, Oxford, United Kingdom,Nuffield Department of Medicine, Oxford University, Oxford, United Kingdom
| | - Ross Sadler
- Clinical Immunology Department, Churchill Hospital, Oxford, United Kingdom
| | - Adrian C. Bateman
- Cellular Pathology Department, Southampton General Hospital, Southampton, United Kingdom
| | - Mateusz Makuch
- Nuffield Department of Medicine, Oxford University, Oxford, United Kingdom,Immunopathology Department, Sanquin, Amsterdam, The Netherlands
| | - Tamsin Cargill
- Translational Gastroenterology Unit, John Radcliffe Hospital, Oxford, United Kingdom,Nuffield Department of Medicine, Oxford University, Oxford, United Kingdom
| | - Berne Ferry
- Clinical Immunology Department, Churchill Hospital, Oxford, United Kingdom
| | - Rob Aalberse
- Immunopathology Department, Sanquin, Amsterdam, The Netherlands
| | - Eleanor Barnes
- Translational Gastroenterology Unit, John Radcliffe Hospital, Oxford, United Kingdom,Nuffield Department of Medicine, Oxford University, Oxford, United Kingdom
| | - Theo Rispens
- Immunopathology Department, Sanquin, Amsterdam, The Netherlands.
| |
Collapse
|
12
|
de Jong BG, IJspeert H, Marques L, van der Burg M, van Dongen JJ, Loos BG, van Zelm MC. Human IgG2- and IgG4-expressing memory B cells display enhanced molecular and phenotypic signs of maturity and accumulate with age. Immunol Cell Biol 2017; 95:744-752. [PMID: 28546550 PMCID: PMC5636940 DOI: 10.1038/icb.2017.43] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2017] [Revised: 05/17/2017] [Accepted: 05/17/2017] [Indexed: 12/28/2022]
Abstract
The mechanisms involved in sequential immunoglobulin G (IgG) class switching are still largely unknown. Sequential IG class switching is linked to higher levels of somatic hypermutation (SHM) in vivo, but it remains unclear if these are generated temporally during an immune response or upon activation in a secondary response. We here aimed to uncouple these processes and to distinguish memory B cells from primary and secondary immune responses. SHM levels and IgG subclasses were studied with 454 pyrosequencing on blood mononuclear cells from young children and adults as models for primary and secondary immunological memory. Additional sequencing and detailed immunophenotyping with IgG subclass-specific antibodies was performed on purified IgG+ memory B-cell subsets. In both children and adults, SHM levels were higher in transcripts involving more downstream-located IGHG genes (esp. IGHG2 and IGHG4). In adults, SHM levels were significantly higher than in children, and downstream IGHG genes were more frequently utilized. This was associated with increased frequencies of CD27+IgG+ memory B cells, which contained higher levels of SHM, more IGHG2 usage, and higher expression levels of activation markers than CD27−IgG+ memory B cells. We conclude that secondary immunological memory accumulates with age and these memory B cells express CD27, high levels of activation markers, and carry high SHM levels and frequent usage of IGHG2. These new insights contribute to our understanding of sequential IgG subclass switching and show a potential relevance of using serum IgG2 levels or numbers of IgG2-expressing B cells as markers for efficient generation of memory responses.
Collapse
Affiliation(s)
- Britt G de Jong
- Department of Immunology, Erasmus MC, Rotterdam, The Netherlands.,Department of Periodontology, ACTA, University of Amsterdam and VU University, Amsterdam, The Netherlands
| | - Hanna IJspeert
- Department of Immunology, Erasmus MC, Rotterdam, The Netherlands
| | | | | | | | - Bruno G Loos
- Department of Periodontology, ACTA, University of Amsterdam and VU University, Amsterdam, The Netherlands
| | - Menno C van Zelm
- Department of Immunology, Erasmus MC, Rotterdam, The Netherlands.,Department of Immunology and Pathology, Monash University and Alfred Hospital, Melbourne, VIC, Australia
| |
Collapse
|
13
|
Collins AM. IgG subclass co-expression brings harmony to the quartet model of murine IgG function. Immunol Cell Biol 2016; 94:949-954. [PMID: 27502143 DOI: 10.1038/icb.2016.65] [Citation(s) in RCA: 94] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2016] [Revised: 07/12/2016] [Accepted: 07/14/2016] [Indexed: 12/24/2022]
Abstract
A model of murine IgG function is presented in which the co-expression of the IgG subclasses is a central feature, class switching occurs before the commencement of somatic hypermutation, and there is little switching between subclasses. It is named the quartet model to emphasize the harmony that comes from the simultaneous presence of the four subclasses. In this model, IgG3 and IgG2b antibodies are particularly important early in the response, when T-cell help may be limiting. IgG3 initiates inflammation through complement fixation, whereas IgG2b provides early FcγR-mediated effector functions. As T-cell help strengthens, IgG2a antibodies increase the power of the response, whereas IgG1 production helps limit the inflammatory drive and limits immunopathology. The model highlights the fact that murine IgG subclasses function quite differently to human IgG subclasses. This allows them to serve the special immunological needs of a species that is vulnerable because of its small size.
Collapse
Affiliation(s)
- Andrew M Collins
- School of Biotechnology and Biomolecular Sciences, The University of New South Wales, Sydney, NSW, Australia
| |
Collapse
|
14
|
Steinke JW, Platts-Mills TAE, Commins SP. The alpha-gal story: lessons learned from connecting the dots. J Allergy Clin Immunol 2015; 135:589-96; quiz 597. [PMID: 25747720 DOI: 10.1016/j.jaci.2014.12.1947] [Citation(s) in RCA: 174] [Impact Index Per Article: 19.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2014] [Revised: 11/21/2014] [Accepted: 12/10/2014] [Indexed: 10/23/2022]
Abstract
Anaphylaxis is a severe allergic reaction that can be rapidly progressing and fatal, and therefore establishing its cause is pivotal to long-term risk management. Our recent work has identified a novel IgE antibody response to a mammalian oligosaccharide epitope, galactose-alpha-1,3-galactose (alpha-gal). IgE to alpha-gal has been associated with 2 distinct forms of anaphylaxis: (1) immediate-onset anaphylaxis during first exposure to intravenous cetuximab and (2) delayed-onset anaphylaxis 3 to 6 hours after ingestion of mammalian food products (eg, beef and pork). Results of our studies and those of others strongly suggest that tick bites are a cause, if not the only significant cause, of IgE antibody responses to alpha-gal in the southern, eastern, and central United States; Europe; Australia; and parts of Asia. Typical immune responses to carbohydrates are considered to be T-cell independent, whereas IgE antibody production is thought to involve sequential class-switching that requires input from T cells. Therefore, establishing the mechanism of the specific IgE antibody response to alpha-gal will be an important aspect to address as this area of research continues.
Collapse
Affiliation(s)
- John W Steinke
- Asthma and Allergic Diseases Center, Carter Immunology Center, Department of Medicine, University of Virginia Health System, Charlottesville, Va
| | - Thomas A E Platts-Mills
- Asthma and Allergic Diseases Center, Carter Immunology Center, Department of Medicine, University of Virginia Health System, Charlottesville, Va.
| | - Scott P Commins
- Asthma and Allergic Diseases Center, Carter Immunology Center, Department of Medicine, University of Virginia Health System, Charlottesville, Va
| |
Collapse
|
15
|
Wong KJ, Timbrell V, Xi Y, Upham JW, Collins AM, Davies JM. IgE+ B cells are scarce, but allergen-specific B cells with a memory phenotype circulate in patients with allergic rhinitis. Allergy 2015; 70:420-8. [PMID: 25556717 DOI: 10.1111/all.12563] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/19/2014] [Indexed: 01/28/2023]
Abstract
BACKGROUND Despite the critical role of immunoglobulin E (IgE) in allergy, circulating IgE+ B cells are scarce. Here, we describe in patients with allergic rhinitis B cells with a memory phenotype responding to a prototypic aeroallergen. METHODS Fifteen allergic rhinitis patients with grass pollen allergy and 13 control subjects were examined. Blood mononuclear cells stained with carboxyfluorescein diacetate succinimidyl ester (CFSE) were cultured with Bahia grass pollen. Proliferation and phenotype were assessed by multicolour flow cytometry. RESULTS In blood of allergic rhinitis patients with high serum IgE to grass pollen, most IgE(hi) cells were CD123+ HLA-DR(-) basophils, with IgE for the major pollen allergen (Pas n 1). Both B and T cells from pollen-allergic donors showed higher proliferation to grass pollen than nonallergic donors (P = 0.002, and 0.010, respectively), whereas responses to vaccine antigens and mitogen did not differ between groups. Allergen-driven B cells that divided rapidly (CD19(mid) CD3(-) CFSE(lo) ) showed higher CD27 (P = 0.008) and lower CD19 (P = 0.004) and CD20 (P = 0.004) expression than B cells that were slow to respond to allergen (CD19(hi) CD3(-) CFSE(mid) ). Moreover, rapidly dividing allergen-driven B cells (CD19(mid) CFSE(lo) CD27(hi) ) showed higher expression of the plasmablast marker CD38 compared with B cells (CD19(hi) CFSE(mid) CD27(lo) ) that were slow to divide. CONCLUSION Patients with pollen allergy but not control donors have a population of circulating allergen-specific B cells with the phenotype and functional properties of adaptive memory B-cell responses. These cells could provide precursors for allergen-specific IgE production upon allergen re-exposure.
Collapse
Affiliation(s)
- K. J. Wong
- Lung and Allergy Research Centre; School of Medicine; The University of Queensland; Woolloongabba Qld Australia
| | - V. Timbrell
- Lung and Allergy Research Centre; School of Medicine; The University of Queensland; Woolloongabba Qld Australia
| | - Y. Xi
- Lung and Allergy Research Centre; School of Medicine; The University of Queensland; Woolloongabba Qld Australia
| | - J. W. Upham
- Lung and Allergy Research Centre; School of Medicine; The University of Queensland; Woolloongabba Qld Australia
- Department of Respiratory Medicine; Princess Alexandra Hospital; Woolloongabba Qld Australia
| | - A. M. Collins
- School of Biotechnology and Biomolecular Sciences; University of New South Wales; Kensington NSW Australia
| | - J. M. Davies
- Lung and Allergy Research Centre; School of Medicine; The University of Queensland; Woolloongabba Qld Australia
| |
Collapse
|
16
|
Saini J, Hershberg U. B cell variable genes have evolved their codon usage to focus the targeted patterns of somatic mutation on the complementarity determining regions. Mol Immunol 2015; 65:157-67. [PMID: 25660968 DOI: 10.1016/j.molimm.2015.01.001] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2014] [Revised: 11/29/2014] [Accepted: 01/02/2015] [Indexed: 01/19/2023]
Abstract
The exceptional ability of B cells to diversify through somatic mutation and improve affinity of the repertoire toward the antigens is the cornerstone of adaptive immunity. Somatic mutation is not evenly distributed and exhibits certain micro-sequence specificities. We show here that the combination of somatic mutation targeting and the codon usage in human B cell receptor (BCR) Variable (V) genes create expected patterns of mutation and post mutation changes that are focused on their complementarity determining regions (CDR). T cell V genes are also skewed in targeting mutations but to a lesser extent and are lacking the codon usage bias observed in BCRs. This suggests that the observed skew in T cell receptors is due to their amino acid usage, which is similar to that of BCRs. The mutation targeting and the codon bias allow B cell CDRs to diversify by specifically accumulating nonconservative changes. We counted the distribution of mutations to CDR in 4 different human datasets. In all four cases we found that the number of actual mutations in the CDR correlated significantly with the V gene mutation biases to the CDR predicted by our models. Finally, it appears that the mutation bias in V genes indeed relates to their long-term survival in actual human repertoires. We observed that resting repertoires of B cells overexpressed V genes that were especially biased toward focused mutation and change in the CDR. This bias in V gene usage was somewhat relaxed at the height of the immune response to a vaccine, presumably because of the need for a wider diversity in a primary response. However, older patients did not retain this flexibility and were biased toward using only highly skewed V genes at all stages of their response.
Collapse
Affiliation(s)
- Jasmine Saini
- School of Biomedical Engineering Sciences and Health Systems, Drexel University, Philadelphia, PA 19104, United States
| | - Uri Hershberg
- School of Biomedical Engineering Sciences and Health Systems, Drexel University, Philadelphia, PA 19104, United States; Department of Microbiology and Immunology, College of Medicine, Drexel University, Philadelphia, PA 19104, United States.
| |
Collapse
|
17
|
Rogosch T, Kerzel S, Dey F, Wagner JJ, Zhang Z, Maier RF, Zemlin M. IgG4 and IgE transcripts in childhood allergic asthma reflect divergent antigen-driven selection. THE JOURNAL OF IMMUNOLOGY 2014; 193:5801-8. [PMID: 25385824 DOI: 10.4049/jimmunol.1401409] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
The physiologic function of the "odd" Ab IgG4 remains enigmatic. IgG4 mediates immunotolerance, as, for example, during specific immunotherapy of allergies, but it mediates tissue damage in autoimmune pemphigus vulgaris and "IgG4-related disease." Approximately half of the circulating IgG4 molecules are bispecific owing to their unique ability to exchange half-molecules. Better understanding of the interrelation between IgG4 and IgE repertoires may yield insight into the pathogenesis of allergies and into potential novel therapies that modulate IgG4 responses. We aimed to compare the selective forces that forge the IgG4 and IgE repertoires in allergic asthma. Using an IgG4-specific RT-PCR, we amplified, cloned, and sequenced IgG4 H chain transcripts of PBMCs from 10 children with allergic asthma. We obtained 558 functional IgG4 sequences, of which 286 were unique. Compared with previously published unique IgE transcripts from the same blood samples, the somatic mutation rate was significantly enhanced in IgG4 transcripts (62 versus 83%; p < 0.001), whereas fewer IgG4 sequences displayed statistical evidence of Ag-driven selection (p < 0.001). On average, the hypervariable CDRH3 region was four nucleotides shorter in IgG4 than in IgE transcripts (p < 0.001). IgG4 transcripts in the circulation of children with allergic asthma reflect some characteristics of classical Ag-driven B2 immune responses but display less indication of Ag selection than do IgE transcripts. Although allergen-specific IgG4 can block IgE-mediated allergen presentation and degranulation of mast cells, key factors that influence the Ag-binding properties of the Ab differ between the overall repertoires of circulating IgG4- and IgE-expressing cells.
Collapse
Affiliation(s)
- Tobias Rogosch
- Department of Pediatrics, Philipps-University Marburg, D-35033 Marburg, Germany
| | - Sebastian Kerzel
- Department of Pediatric Pneumology and Allergy, University Children's Hospital Regensburg, St. Hedwig Campus, 93053 Regensburg, Germany; and
| | - Friederike Dey
- Department of Pediatrics, Philipps-University Marburg, D-35033 Marburg, Germany
| | | | - Zhixin Zhang
- Department of Pathology and Microbiology, Eppley Institute for Research in Cancer, University of Nebraska Medical Center, Omaha, NE 68198
| | - Rolf F Maier
- Department of Pediatrics, Philipps-University Marburg, D-35033 Marburg, Germany
| | - Michael Zemlin
- Department of Pediatrics, Philipps-University Marburg, D-35033 Marburg, Germany;
| |
Collapse
|
18
|
Levin M, Davies AM, Liljekvist M, Carlsson F, Gould HJ, Sutton BJ, Ohlin M. Human IgE against the major allergen Bet v 1--defining an epitope with limited cross-reactivity between different PR-10 family proteins. Clin Exp Allergy 2014; 44:288-99. [PMID: 24447087 PMCID: PMC4215112 DOI: 10.1111/cea.12230] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2013] [Revised: 09/24/2013] [Accepted: 10/25/2013] [Indexed: 02/05/2023]
Abstract
Background The interaction between IgE and allergen is a key event at the initiation of an allergic response, and its characteristics have substantial effects on the clinical manifestation. Despite this, the molecular details of the interaction between human IgE and the major birch allergen Bet v 1, one of the most potent tree allergens, still remain poorly investigated. Objective To isolate Bet v 1-specific human monoclonal IgE and characterize their interaction with the allergen. Methods Recombinant human IgE were isolated from a combinatorial antibody fragment library and their interaction with Bet v 1 assessed using various immunological assays. The structure of one such IgE in the single-chain fragment variable format was determined using X-ray crystallography. Results We present four novel Bet v 1-specific IgE, for one of which we solve the structure, all with their genetic origin in the IGHV5 germline gene, and demonstrate that they target two non-overlapping epitopes on the surface of Bet v 1, thereby fulfilling the basic criteria for FcεRI cross-linkage. We further define these epitopes and for one epitope pinpoint single amino acid residues important for the interaction with human IgE. This provides a potential explanation, at the molecular level, for the differences in recognition of isoforms of Bet v 1 and other allergens in the PR-10 protein family displayed by IgE targeting this epitope. Finally, we present the first high-resolution structure of a human allergen-specific IgE fragment in the single-chain fragment variable (scFv) format. Conclusions and Clinical Relevance We here display the usefulness of allergen-specific human monoclonal IgE as a tool in studies of the crucial molecular interaction taking place at the initiation of an allergic response. Such studies may aid us in development of better diagnostic tools and guide us in the development of new therapeutic compounds.
Collapse
Affiliation(s)
- M Levin
- Department of Immunotechnology, Lund University, Lund, Sweden
| | | | | | | | | | | | | |
Collapse
|
19
|
Pontes-de-Carvalho L, Mengel J. A Question of Nature: Some Antigens are Bound to be Allergens. Front Immunol 2014; 5:373. [PMID: 25140169 PMCID: PMC4122158 DOI: 10.3389/fimmu.2014.00373] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Key Words] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2014] [Accepted: 07/21/2014] [Indexed: 01/11/2023] Open
Affiliation(s)
- Lain Pontes-de-Carvalho
- Centro de Pesquisas Gonçalo Moniz, Fundação Oswaldo Cruz , Salvador , Brazil ; Social Changes, Asthma and Allergy in Latin America - SCAALA - Program , Salvador , Brazil
| | - José Mengel
- Instituto Oswaldo Cruz, Fundação Oswaldo Cruz , Rio de Janeiro , Brazil ; Faculty of Medicine of Petropolis, FMP-FASE , Petrópolis , Brazil
| |
Collapse
|
20
|
Human immunoglobulin classes and subclasses show variability in VDJ gene mutation levels. Immunol Cell Biol 2014; 92:729-33. [DOI: 10.1038/icb.2014.44] [Citation(s) in RCA: 70] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2014] [Revised: 04/30/2014] [Accepted: 04/30/2014] [Indexed: 01/30/2023]
|
21
|
Wu LC, Zarrin AA. The production and regulation of IgE by the immune system. Nat Rev Immunol 2014; 14:247-59. [PMID: 24625841 DOI: 10.1038/nri3632] [Citation(s) in RCA: 184] [Impact Index Per Article: 18.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
IgE not only provides protective immunity against helminth parasites but can also mediate the type I hypersensitivity reactions that contribute to the pathogenesis of allergic diseases such as asthma, allergic rhinitis and atopic dermatitis. Despite the importance of IgE in immune biology and allergic pathogenesis, the cells and the pathways that produce and regulate IgE are poorly understood. In this Review, we summarize recent advances in our understanding of the production and the regulation of IgE in vivo, as revealed by studies in mice, and we discuss how these findings compare to what is known about human IgE biology.
Collapse
Affiliation(s)
- Lawren C Wu
- Department of Immunology, Genentech Inc., 1 DNA Way, South San Francisco, California 94080, USA
| | - Ali A Zarrin
- Department of Immunology, Genentech Inc., 1 DNA Way, South San Francisco, California 94080, USA
| |
Collapse
|
22
|
The promise and challenge of high-throughput sequencing of the antibody repertoire. Nat Biotechnol 2014; 32:158-68. [PMID: 24441474 PMCID: PMC4113560 DOI: 10.1038/nbt.2782] [Citation(s) in RCA: 465] [Impact Index Per Article: 46.5] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2013] [Accepted: 12/04/2013] [Indexed: 12/16/2022]
Abstract
Georgiou and colleagues discuss rapidly evolving methods for high-throughput sequencing of the antibody repertoire, and how the resulting data may be applied to answer basic and translational research questions. Efforts to determine the antibody repertoire encoded by B cells in the blood or lymphoid organs using high-throughput DNA sequencing technologies have been advancing at an extremely rapid pace and are transforming our understanding of humoral immune responses. Information gained from high-throughput DNA sequencing of immunoglobulin genes (Ig-seq) can be applied to detect B-cell malignancies with high sensitivity, to discover antibodies specific for antigens of interest, to guide vaccine development and to understand autoimmunity. Rapid progress in the development of experimental protocols and informatics analysis tools is helping to reduce sequencing artifacts, to achieve more precise quantification of clonal diversity and to extract the most pertinent biological information. That said, broader application of Ig-seq, especially in clinical settings, will require the development of a standardized experimental design framework that will enable the sharing and meta-analysis of sequencing data generated by different laboratories.
Collapse
|
23
|
Gadermaier E, Levin M, Flicker S, Ohlin M. The human IgE repertoire. Int Arch Allergy Immunol 2013; 163:77-91. [PMID: 24296690 DOI: 10.1159/000355947] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
IgE is a key mediator in allergic diseases. However, in strong contrast to other antibody isotypes, many details of the composition of the human IgE repertoire are poorly defined. The low levels of human IgE in the circulation and the rarity of IgE-producing B cells are important reasons for this lack of knowledge. In this review, we summarize the current knowledge on these repertoires both in terms of their complexity and activity, i.e. knowledge which despite the difficulties encountered when studying the molecular details of human IgE has been acquired in recent years. We also take a look at likely future developments, for instance through improvements in sequencing technology and methodology that allow the isolation of additional allergen-specific human antibodies mimicking IgE, as this certainly will support our understanding of human IgE in the context of human disease in the years to come.
Collapse
Affiliation(s)
- Elisabeth Gadermaier
- Division of Immunopathology, Department of Pathophysiology, Center for Pathophysiology, Infectiology and Immunology, Medical University of Vienna, Vienna, Austria
| | | | | | | |
Collapse
|
24
|
Collins AM, Jackson KJL. A Temporal Model of Human IgE and IgG Antibody Function. Front Immunol 2013; 4:235. [PMID: 23950757 PMCID: PMC3738878 DOI: 10.3389/fimmu.2013.00235] [Citation(s) in RCA: 103] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2013] [Accepted: 07/29/2013] [Indexed: 12/18/2022] Open
Abstract
The diversity of the human antibody repertoire that is generated by V(D)J gene rearrangement is extended by nine constant region genes that give antibodies their complex array of effector functions. The application of high throughput sequencing to the study of V(D)J gene rearrangements has led to significant recent advances in our understanding of the antigen-binding repertoire. In contrast, our understanding of antibody function has changed little, and mystery still surrounds the existence of four distinctive IgG subclasses. Recent observations from murine models and from human studies of VDJ somatic point mutations suggest that the timing of emergence of cells from the germinal center may vary as a consequence of class switching. This should lead to predictable differences in affinity between isotypes. These differences, and varying abilities of the isotypes to fix complement and bind FcRs, could help coordinate the humoral defenses over the time course of a response. We therefore propose a Temporal Model of human IgE and IgG function in which early emergence of IgE sensitizes sentinel mast cells while switching to IgG3 recruits FcγR-mediated functions to the early response. IgG1 then emerges as the major effector of antigen clearance, and subsequently IgG2 competes with IgG1 to produce immune complexes that slow the inflammatory drive. Persisting antigen may finally stimulate high affinity IgG4 that outcompetes other isotypes and can terminate IgG1/FcγR-mediated activation via the inhibitory FcγRIIB. In this way, IgG antibodies of different subclasses, at different concentrations and with sometimes opposing functions deliver cohesive, protective immune function.
Collapse
Affiliation(s)
- Andrew M Collins
- School of Biotechnology and Biomolecular Sciences, University of New South Wales , Sydney, NSW , Australia
| | | |
Collapse
|
25
|
Davies JM, Platts-Mills TA, Aalberse RC. The enigma of IgE+ B-cell memory in human subjects. J Allergy Clin Immunol 2013; 131:972-6. [DOI: 10.1016/j.jaci.2012.12.1569] [Citation(s) in RCA: 53] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2012] [Revised: 12/21/2012] [Accepted: 12/27/2012] [Indexed: 01/09/2023]
|
26
|
Levin M, Ohlin M. Inconclusive evidence for or against positive antigen selection in the shaping of human immunoglobulin E repertoires: a call for new approaches. Int Arch Allergy Immunol 2013; 161:122-6. [PMID: 23343692 DOI: 10.1159/000345421] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2012] [Accepted: 10/24/2012] [Indexed: 11/19/2022] Open
Abstract
BACKGROUND The mechanisms driving the development of immunoglobulin E (IgE) antibody repertoires are a matter of debate. Alternatives to the classical view on antibody development, involving somatic mutation and antigen-driven selection of high-affinity variants in germinal centers, have been proposed. METHODS We have re-analyzed the pattern of mutations in previously isolated and characterized human clonally unrelated IgE-encoding transcripts using the validated focused binomial methodology to find evidence in such genes of antigen-specific selection. RESULTS As expected there is a selection against replacement mutations in IgE framework regions. In contrast, in all examined cases but one (assessing IgE repertoires of parasite-infected individuals) there was no evidence in favor of either positive or negative selection in complementarity determining regions. Importantly, however, the validated method also failed to detect selection for replacement mutations in two, non-IgE, hypermutated antibody populations targeting tetanus toxoid and vaccinia virus, respectively. CONCLUSIONS Current methodology is unable to define with certainty, using commonly assessed IgE repertoire sizes, whether antigen selection is or is not a major driving force in the establishment of human IgE. New approaches are needed to address this matter.
Collapse
Affiliation(s)
- Mattias Levin
- Department of Immunotechnology, Lund University, Lund, Sweden
| | | |
Collapse
|
27
|
|
28
|
Yang Z, Sullivan BM, Allen CDC. Fluorescent in vivo detection reveals that IgE(+) B cells are restrained by an intrinsic cell fate predisposition. Immunity 2012; 36:857-72. [PMID: 22406270 DOI: 10.1016/j.immuni.2012.02.009] [Citation(s) in RCA: 155] [Impact Index Per Article: 12.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2011] [Revised: 01/30/2012] [Accepted: 02/09/2012] [Indexed: 10/28/2022]
Abstract
IgE antibodies may be protective in parasite immunity, but their aberrant production can lead to allergic disease and life-threatening anaphylaxis. Despite the importance of IgE regulation, few studies have directly examined the B cells that express IgE, because these cells are rare and difficult to detect. Here, we describe fluorescent IgE reporter mice and validate a flow cytometry procedure to allow sensitive and specific identification of IgE-expressing B cells in vivo. Similar to IgG1(+) cells, IgE(+) B cells differentiated into germinal center (GC) B cells and plasma cells (PCs) during primary immune responses to a T cell-dependent hapten-protein conjugate and the helminth Nippostrongylus brasiliensis. However, the participation of IgE(+) B cells in GCs was transient. IgE(+) B cells had an atypical propensity to upregulate the transcription factor Blimp-1 and undergo PC differentiation. Most IgE(+) PCs were short lived and showed reduced affinity maturation, revealing intrinsic mechanisms that restrict the IgE antibody response.
Collapse
Affiliation(s)
- Zhiyong Yang
- Sandler Asthma Basic Research Center, University of California, San Francisco, San Francisco, CA 94143, USA
| | | | | |
Collapse
|