1
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Engelbrecht E, Rodriguez OL, Shields K, Schultze S, Tieri D, Jana U, Yaari G, Lees WD, Smith ML, Watson CT. Resolving haplotype variation and complex genetic architecture in the human immunoglobulin kappa chain locus in individuals of diverse ancestry. Genes Immun 2024; 25:297-306. [PMID: 38844673 PMCID: PMC11327106 DOI: 10.1038/s41435-024-00279-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2023] [Revised: 05/21/2024] [Accepted: 05/24/2024] [Indexed: 08/17/2024]
Abstract
Immunoglobulins (IGs), critical components of the human immune system, are composed of heavy and light protein chains encoded at three genomic loci. The IG Kappa (IGK) chain locus consists of two large, inverted segmental duplications. The complexity of the IG loci has hindered use of standard high-throughput methods for characterizing genetic variation within these regions. To overcome these limitations, we use long-read sequencing to create haplotype-resolved IGK assemblies in an ancestrally diverse cohort (n = 36), representing the first comprehensive description of IGK haplotype variation. We identify extensive locus polymorphism, including novel single nucleotide variants (SNVs) and novel structural variants harboring functional IGKV genes. Among 47 functional IGKV genes, we identify 145 alleles, 67 of which were not previously curated. We report inter-population differences in allele frequencies for 10 IGKV genes, including alleles unique to specific populations within this dataset. We identify haplotypes carrying signatures of gene conversion that associate with SNV enrichment in the IGK distal region, and a haplotype with an inversion spanning the proximal and distal regions. These data provide a critical resource of curated genomic reference information from diverse ancestries, laying a foundation for advancing our understanding of population-level genetic variation in the IGK locus.
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Affiliation(s)
- Eric Engelbrecht
- Department of Biochemistry and Molecular Genetics, University of Louisville, Louisville, KY, USA
| | - Oscar L Rodriguez
- Department of Biochemistry and Molecular Genetics, University of Louisville, Louisville, KY, USA
| | - Kaitlyn Shields
- Department of Biochemistry and Molecular Genetics, University of Louisville, Louisville, KY, USA
| | - Steven Schultze
- Department of Biochemistry and Molecular Genetics, University of Louisville, Louisville, KY, USA
| | - David Tieri
- Department of Biochemistry and Molecular Genetics, University of Louisville, Louisville, KY, USA
| | - Uddalok Jana
- Department of Biochemistry and Molecular Genetics, University of Louisville, Louisville, KY, USA
| | - Gur Yaari
- Faculty of Engineering, Bar Ilan University, Ramat Gan, Israel
- Institute of Nanotechnology and Advanced Materials, Bar Ilan University, Ramat Gan, Israel
| | - William D Lees
- Faculty of Engineering, Bar Ilan University, Ramat Gan, Israel
| | - Melissa L Smith
- Department of Biochemistry and Molecular Genetics, University of Louisville, Louisville, KY, USA.
| | - Corey T Watson
- Department of Biochemistry and Molecular Genetics, University of Louisville, Louisville, KY, USA.
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2
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Abadie V, Han AS, Jabri B, Sollid LM. New Insights on Genes, Gluten, and Immunopathogenesis of Celiac Disease. Gastroenterology 2024; 167:4-22. [PMID: 38670280 PMCID: PMC11283582 DOI: 10.1053/j.gastro.2024.03.042] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/12/2023] [Revised: 03/10/2024] [Accepted: 03/11/2024] [Indexed: 04/28/2024]
Abstract
Celiac disease (CeD) is a gluten-induced enteropathy that develops in genetically susceptible individuals upon consumption of cereal gluten proteins. It is a unique and complex immune disorder to study as the driving antigen is known and the tissue targeted by the immune reaction can be interrogated. This review integrates findings gained from genetic, biochemical, and immunologic studies, which together have revealed mechanisms of gluten peptide modification and HLA binding, thereby enabling a maladapted anti-gluten immune response. Observations in human samples combined with experimental mouse models have revealed that the gluten-induced immune response involves CD4+ T cells, cytotoxic CD8+ T cells, and B cells; their cross-talks are critical for the tissue-damaging response. The emergence of high-throughput technologies is increasing our understanding of the phenotype, location, and presumably function of the gluten-specific cells, which are all required to identify novel therapeutic targets and strategies for CeD.
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Affiliation(s)
- Valérie Abadie
- Department of Medicine, University of Chicago, Chicago, Illinois; Section of Gastroenterology, Nutrition and Hepatology, University of Chicago, Chicago, Illinois; Committee on Immunology, University of Chicago, Chicago, Illinois.
| | - Arnold S Han
- Columbia Center for Translational Immunology, Columbia University, New York, New York; Department of Microbiology and Immunology, Columbia University, New York, New York; Department of Medicine, Digestive and Liver Diseases, Columbia University, New York, New York
| | - Bana Jabri
- Department of Medicine, University of Chicago, Chicago, Illinois; Section of Gastroenterology, Nutrition and Hepatology, University of Chicago, Chicago, Illinois; Committee on Immunology, University of Chicago, Chicago, Illinois; Department of Pathology, University of Chicago, Chicago, Illinois; Department of Pediatrics, University of Chicago, Chicago, Illinois
| | - Ludvig M Sollid
- Norwegian Coeliac Disease Research Centre, Institute of Clinical Medicine, University of Oslo, Oslo, Norway; Department of Immunology, Oslo University Hospital-Rikshospitalet, Oslo, Norway
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3
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Das S, Stamnaes J, Høydahl LS, Skagen C, Lundin KEA, Jahnsen J, Sollid LM, Iversen R. Selective activation of naïve B cells with unique epitope specificity shapes autoantibody formation in celiac disease. J Autoimmun 2024; 146:103241. [PMID: 38754235 DOI: 10.1016/j.jaut.2024.103241] [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: 01/16/2024] [Revised: 03/25/2024] [Accepted: 05/03/2024] [Indexed: 05/18/2024]
Abstract
Many antibody responses induced by infection, vaccination or autoimmunity show signs of convergence across individuals with epitope-dependent selection of particular variable region gene segments and complementarity determining region 3 properties. However, not much is known about the relationship between antigen-specific effector cells and antigen-specific precursors present in the naïve B-cell repertoire. Here, we sought to address this relationship in the context of celiac disease, where there is a stereotyped autoantibody response against the enzyme transglutaminase 2 (TG2). By generating TG2-specific monoclonal antibodies from both duodenal plasma cells and circulating naïve B cells, we demonstrate a discord between the naïve TG2-specific repertoire and the cells that are selected for autoantibody production. Hence, the naïve repertoire does not fully reflect the epitope preference and gene usage observed for memory B cells and plasma cells. Instead, distinct naïve B cells that target particular TG2 epitopes appear to be selectively activated at the expense of TG2-binding B cells targeting other epitopes.
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Affiliation(s)
- Saykat Das
- Norwegian Coeliac Disease Research Centre, Institute of Clinical Medicine, University of Oslo, Oslo, Norway; Department of Immunology, Oslo University Hospital-Rikshospitalet, Oslo, Norway
| | - Jorunn Stamnaes
- Norwegian Coeliac Disease Research Centre, Institute of Clinical Medicine, University of Oslo, Oslo, Norway; Department of Immunology, Oslo University Hospital-Rikshospitalet, Oslo, Norway
| | - Lene S Høydahl
- Norwegian Coeliac Disease Research Centre, Institute of Clinical Medicine, University of Oslo, Oslo, Norway; Department of Immunology, Oslo University Hospital-Rikshospitalet, Oslo, Norway
| | - Christine Skagen
- Department of Immunology, Oslo University Hospital-Rikshospitalet, Oslo, Norway
| | - Knut E A Lundin
- Norwegian Coeliac Disease Research Centre, Institute of Clinical Medicine, University of Oslo, Oslo, Norway; Department of Gastroenterology, Oslo University Hospital-Rikshospitalet, Oslo, Norway
| | - Jørgen Jahnsen
- Department of Gastroenterology, Akershus University Hospital, Lørenskog, Norway
| | - Ludvig M Sollid
- Norwegian Coeliac Disease Research Centre, Institute of Clinical Medicine, University of Oslo, Oslo, Norway; Department of Immunology, Oslo University Hospital-Rikshospitalet, Oslo, Norway
| | - Rasmus Iversen
- Norwegian Coeliac Disease Research Centre, Institute of Clinical Medicine, University of Oslo, Oslo, Norway; Department of Immunology, Oslo University Hospital-Rikshospitalet, Oslo, Norway.
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4
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Lindeman I, Høydahl LS, Christophersen A, Risnes LF, Jahnsen J, Lundin KEA, Sollid LM, Iversen R. Generation of circulating autoreactive pre-plasma cells fueled by naive B cells in celiac disease. Cell Rep 2024; 43:114045. [PMID: 38578826 DOI: 10.1016/j.celrep.2024.114045] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2023] [Revised: 02/22/2024] [Accepted: 03/19/2024] [Indexed: 04/07/2024] Open
Abstract
Autoantibodies against the enzyme transglutaminase 2 (TG2) are characteristic of celiac disease (CeD), and TG2-specific immunoglobulin (Ig) A plasma cells are abundant in gut biopsies of patients. Here, we describe the corresponding population of autoreactive B cells in blood. Circulating TG2-specific IgA cells are present in untreated patients on a gluten-containing diet but not in controls. They are clonally related to TG2-specific small intestinal plasma cells, and they express gut-homing molecules, indicating that they are plasma cell precursors. Unlike other IgA-switched cells, the TG2-specific cells are negative for CD27, placing them in the double-negative (IgD-CD27-) category. They have a plasmablast or activated memory B cell phenotype, and they harbor fewer variable region mutations than other IgA cells. Based on their similarity to naive B cells, we propose that autoreactive IgA cells in CeD are generated mainly through chronic recruitment of naive B cells via an extrafollicular response involving gluten-specific CD4+ T cells.
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Affiliation(s)
- Ida Lindeman
- Norwegian Coeliac Disease Research Centre, Institute of Clinical Medicine, University of Oslo, Oslo, Norway; Department of Immunology, Oslo University Hospital - Rikshospitalet, Oslo, Norway
| | - Lene S Høydahl
- Norwegian Coeliac Disease Research Centre, Institute of Clinical Medicine, University of Oslo, Oslo, Norway; Department of Immunology, Oslo University Hospital - Rikshospitalet, Oslo, Norway
| | - Asbjørn Christophersen
- Norwegian Coeliac Disease Research Centre, Institute of Clinical Medicine, University of Oslo, Oslo, Norway; Department of Immunology, Oslo University Hospital - Rikshospitalet, Oslo, Norway
| | - Louise F Risnes
- Norwegian Coeliac Disease Research Centre, Institute of Clinical Medicine, University of Oslo, Oslo, Norway; Department of Immunology, Oslo University Hospital - Rikshospitalet, Oslo, Norway
| | - Jørgen Jahnsen
- Department of Gastroenterology, Akershus University Hospital, Lørenskog, Norway
| | - Knut E A Lundin
- Norwegian Coeliac Disease Research Centre, Institute of Clinical Medicine, University of Oslo, Oslo, Norway; Department of Gastroenterology, Oslo University Hospital - Rikshospitalet, Oslo, Norway
| | - Ludvig M Sollid
- Norwegian Coeliac Disease Research Centre, Institute of Clinical Medicine, University of Oslo, Oslo, Norway; Department of Immunology, Oslo University Hospital - Rikshospitalet, Oslo, Norway
| | - Rasmus Iversen
- Norwegian Coeliac Disease Research Centre, Institute of Clinical Medicine, University of Oslo, Oslo, Norway; Department of Immunology, Oslo University Hospital - Rikshospitalet, Oslo, Norway.
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5
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du Pre MF, Iversen R, Sollid LM. Coeliac disease: the paradox of diagnosing a food hypersensitivity disorder with autoantibodies. Gut 2024; 73:844-853. [PMID: 38378252 DOI: 10.1136/gutjnl-2023-331595] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/11/2023] [Accepted: 01/30/2024] [Indexed: 02/22/2024]
Abstract
Serum antibodies to the autoantigen transglutaminase 2 (TG2) are increasingly harnessed to diagnose coeliac disease. Diagnostic guidelines for children give recommendation for a no-biopsy-based diagnosis through detection of high amounts of IgA anti-TG2 antibodies in serum with confirmation of positivity in a separate blood sample by characteristic autoantibody-staining of tissue. While measurement of IgA anti-TG2 also is important in the diagnostic workup of adults, the adult guidelines still mandate examination of gut biopsies. This requirement might well change in the future, as might the necessity for confirming autoantibody positivity by tissue staining. The key role of autoantibody serology for diagnosis of coeliac disease is paradoxical. Coeliac disease was considered, and still can be considered, a food intolerance disorder where autoantibodies at face value are out of place. The immunological mechanisms underlying the formation of autoantibodies in response to gluten exposure have been dissected. This review presents the current insights demonstrating that the autoantibodies in coeliac disease are intimately integrated in the maladapted immune response to gluten.
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Affiliation(s)
- M Fleur du Pre
- Norwegian Coeliac Disease Research Centre, Institute of Clinical Medicine, University of Oslo, Oslo, Norway
- Department of Immunology, Oslo University Hosptial - Rikshospitalet, Oslo, Norway
| | - Rasmus Iversen
- Norwegian Coeliac Disease Research Centre, Institute of Clinical Medicine, University of Oslo, Oslo, Norway
- Department of Immunology, Oslo University Hosptial - Rikshospitalet, Oslo, Norway
| | - Ludvig M Sollid
- Norwegian Coeliac Disease Research Centre, Institute of Clinical Medicine, University of Oslo, Oslo, Norway
- Department of Immunology, Oslo University Hosptial - Rikshospitalet, Oslo, Norway
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6
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Das S, Stamnaes J, Kemppainen E, Hervonen K, Lundin KEA, Parmar N, Jahnsen FL, Jahnsen J, Lindfors K, Salmi T, Iversen R, Sollid LM. Separate Gut Plasma Cell Populations Produce Auto-Antibodies against Transglutaminase 2 and Transglutaminase 3 in Dermatitis Herpetiformis. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2023; 10:e2300401. [PMID: 37424036 PMCID: PMC10477854 DOI: 10.1002/advs.202300401] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/18/2023] [Revised: 06/23/2023] [Indexed: 07/11/2023]
Abstract
Dermatitis herpetiformis (DH) is an inflammatory skin disorder often considered as an extra intestinal manifestation of celiac disease (CeD). Hallmarks of CeD and DH are auto-antibodies to transglutaminase 2 (TG2) and transglutaminase 3 (TG3), respectively. DH patients have auto-antibodies reactive with both transglutaminase enzymes. Here it is reported that in DH both gut plasma cells and serum auto-antibodies are specific for either TG2 or TG3 with no TG2-TG3 cross reactivity. By generating monoclonal antibodies from TG3-specific duodenal plasma cells of DH patients, three conformational epitope groups are defined. Both TG2-specific and TG3-specific gut plasma cells have few immunoglobulin (Ig) mutations, and the two transglutaminase-reactive populations show distinct selection of certain heavy and light chain V-genes. Mass spectrometry analysis of TG3-specific serum IgA corroborates preferential usage of IGHV2-5 in combination with IGKV4-1. Collectively, these results demonstrate parallel induction of anti-TG2 and anti-TG3 auto-antibody responses involving separate B-cell populations in DH patients.
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Affiliation(s)
- Saykat Das
- Department of ImmunologyOslo University Hospital‐RikshospitaletOslo0372Norway
- KG Jebsen Coeliac Disease Research CentreInstitute of Clinical MedicineUniversity of OsloOslo0372Norway
| | - Jorunn Stamnaes
- Department of ImmunologyOslo University Hospital‐RikshospitaletOslo0372Norway
- KG Jebsen Coeliac Disease Research CentreInstitute of Clinical MedicineUniversity of OsloOslo0372Norway
| | - Esko Kemppainen
- Celiac Disease Research CentreFaculty of Medicine and Health TechnologyTampere UniversityTampere33520Finland
| | - Kaisa Hervonen
- Celiac Disease Research CentreFaculty of Medicine and Health TechnologyTampere UniversityTampere33520Finland
- Department of DermatologyTampere University HospitalTampere33520Finland
| | - Knut E. A. Lundin
- KG Jebsen Coeliac Disease Research CentreInstitute of Clinical MedicineUniversity of OsloOslo0372Norway
- Department of GastroenterologyOslo University Hospital‐RikshospitaletOslo0372Norway
| | - Naveen Parmar
- Department of PathologyUniversity of Oslo and Institute of Clinical MedicineOslo University Hospital‐RikshospitaletOslo0372Norway
| | - Frode L. Jahnsen
- Department of PathologyUniversity of Oslo and Institute of Clinical MedicineOslo University Hospital‐RikshospitaletOslo0372Norway
| | - Jørgen Jahnsen
- Department of GastroenterologyAkershus University HospitalLørenskog1478Norway
| | - Katri Lindfors
- Celiac Disease Research CentreFaculty of Medicine and Health TechnologyTampere UniversityTampere33520Finland
| | - Teea Salmi
- Celiac Disease Research CentreFaculty of Medicine and Health TechnologyTampere UniversityTampere33520Finland
| | - Rasmus Iversen
- Department of ImmunologyOslo University Hospital‐RikshospitaletOslo0372Norway
- KG Jebsen Coeliac Disease Research CentreInstitute of Clinical MedicineUniversity of OsloOslo0372Norway
| | - Ludvig M. Sollid
- Department of ImmunologyOslo University Hospital‐RikshospitaletOslo0372Norway
- KG Jebsen Coeliac Disease Research CentreInstitute of Clinical MedicineUniversity of OsloOslo0372Norway
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7
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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: 15] [Impact Index Per Article: 15.0] [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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8
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Dopico XC, Mandolesi M, Hedestam GBK. Untangling immunoglobulin genotype-function associations. Immunol Lett 2023:S0165-2478(23)00073-1. [PMID: 37209913 DOI: 10.1016/j.imlet.2023.05.003] [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: 01/26/2023] [Revised: 04/19/2023] [Accepted: 05/12/2023] [Indexed: 05/22/2023]
Abstract
Immunoglobulin (IG) genes, encoding B cell receptors (BCRs), are fundamental components of the mammalian immune system, which evolved to recognize the diverse antigenic universe present in nature. To handle these myriad inputs, BCRs are generated through combinatorial recombination of a set of highly polymorphic germline genes, resulting in a vast repertoire of antigen receptors that initiate responses to pathogens and regulate commensals. Following antigen recognition and B cell activation, memory B cells and plasma cells form, allowing for the development of anamnestic antibody (Ab) responses. How inherited variation in IG genes impacts host traits, disease susceptibility, and Ab recall responses is a topic of great interest. Here, we consider approaches to translate emerging knowledge about IG genetic diversity and expressed repertoires to inform our understanding of Ab function in health and disease etiology. As our understanding of IG genetics grows, so will our need for tools to decipher preferences for IG gene or allele usage in different contexts, to better understand antibody responses at the population level.
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Affiliation(s)
- Xaquin Castro Dopico
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm 17177, Sweden.
| | - Marco Mandolesi
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm 17177, Sweden
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9
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Zhang Y, Li Q, Luo L, Duan C, Shen J, Wang Z. Application of germline antibody features to vaccine development, antibody discovery, antibody optimization and disease diagnosis. Biotechnol Adv 2023; 65:108143. [PMID: 37023966 DOI: 10.1016/j.biotechadv.2023.108143] [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: 01/13/2023] [Revised: 03/26/2023] [Accepted: 03/29/2023] [Indexed: 04/08/2023]
Abstract
Although the efficacy and commercial success of vaccines and therapeutic antibodies have been tremendous, designing and discovering new drug candidates remains a labor-, time- and cost-intensive endeavor with high risks. The main challenges of vaccine development are inducing a strong immune response in broad populations and providing effective prevention against a group of highly variable pathogens. Meanwhile, antibody discovery faces several great obstacles, especially the blindness in antibody screening and the unpredictability of the developability and druggability of antibody drugs. These challenges are largely due to poorly understanding of germline antibodies and the antibody responses to pathogen invasions. Thanks to the recent developments in high-throughput sequencing and structural biology, we have gained insight into the germline immunoglobulin (Ig) genes and germline antibodies and then the germline antibody features associated with antigens and disease manifestation. In this review, we firstly outline the broad associations between germline antibodies and antigens. Moreover, we comprehensively review the recent applications of antigen-specific germline antibody features, physicochemical properties-associated germline antibody features, and disease manifestation-associated germline antibody features on vaccine development, antibody discovery, antibody optimization, and disease diagnosis. Lastly, we discuss the bottlenecks and perspectives of current and potential applications of germline antibody features in the biotechnology field.
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Affiliation(s)
- Yingjie Zhang
- National Key Laboratory of Veterinary Public Health Security, Beijing Key Laboratory of Detection Technology for Animal-Derived Food, College of Veterinary Medicine, China Agricultural University, 100193 Beijing, People's Republic of China
| | - Qing Li
- National Key Laboratory of Veterinary Public Health Security, Beijing Key Laboratory of Detection Technology for Animal-Derived Food, College of Veterinary Medicine, China Agricultural University, 100193 Beijing, People's Republic of China
| | - Liang Luo
- National Key Laboratory of Veterinary Public Health Security, Beijing Key Laboratory of Detection Technology for Animal-Derived Food, College of Veterinary Medicine, China Agricultural University, 100193 Beijing, People's Republic of China
| | - Changfei Duan
- National Key Laboratory of Veterinary Public Health Security, Beijing Key Laboratory of Detection Technology for Animal-Derived Food, College of Veterinary Medicine, China Agricultural University, 100193 Beijing, People's Republic of China
| | - Jianzhong Shen
- National Key Laboratory of Veterinary Public Health Security, Beijing Key Laboratory of Detection Technology for Animal-Derived Food, College of Veterinary Medicine, China Agricultural University, 100193 Beijing, People's Republic of China
| | - Zhanhui Wang
- National Key Laboratory of Veterinary Public Health Security, Beijing Key Laboratory of Detection Technology for Animal-Derived Food, College of Veterinary Medicine, China Agricultural University, 100193 Beijing, People's Republic of China.
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10
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Sollid LM, Iversen R. Tango of B cells with T cells in the making of secretory antibodies to gut bacteria. Nat Rev Gastroenterol Hepatol 2023; 20:120-128. [PMID: 36056203 DOI: 10.1038/s41575-022-00674-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 07/27/2022] [Indexed: 02/03/2023]
Abstract
Polymeric IgA and IgM are transported across the epithelial barrier from plasma cells in the lamina propria to exert a function in the gut lumen as secretory antibodies. Many secretory antibodies are reactive with the gut bacteria, and mounting evidence suggests that these antibodies are important for the host to control gut bacterial communities. However, we have incomplete knowledge of how bacteria-reactive secretory antibodies are formed. Antibodies from gut plasma cells often show bacterial cross-species reactivity, putting the degree of specificity behind anti-bacterial antibody responses into question. Such cross-species reactive antibodies frequently recognize non-genome-encoded membrane glycan structures. On the other hand, the T cell epitopes are peptides encoded in the bacterial genomes, thereby allowing a higher degree of predictable specificity on the T cell side of anti-bacterial immune responses. In this Perspective, we argue that the production of bacteria-reactive secretory antibodies is mainly controlled by the antigen specificity of T cells, which provide help to B cells. To be able to harness this system (for instance, for manipulation with vaccines), we need to obtain insight into the bacterial epitopes recognized by T cells in addition to characterizing the reactivity of the antibodies.
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Affiliation(s)
- Ludvig M Sollid
- K.G. Jebsen Coeliac Disease Research Centre, Institute of Clinical Medicine, University of Oslo, Oslo, Norway. .,Department of Immunology, Oslo University Hospital - Rikshospitalet, Oslo, Norway.
| | - Rasmus Iversen
- K.G. Jebsen Coeliac Disease Research Centre, Institute of Clinical Medicine, University of Oslo, Oslo, Norway. .,Department of Immunology, Oslo University Hospital - Rikshospitalet, Oslo, Norway.
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11
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Jaffe DB, Shahi P, Adams BA, Chrisman AM, Finnegan PM, Raman N, Royall AE, Tsai F, Vollbrecht T, Reyes DS, Hepler NL, McDonnell WJ. Functional antibodies exhibit light chain coherence. Nature 2022; 611:352-357. [PMID: 36289331 PMCID: PMC9607724 DOI: 10.1038/s41586-022-05371-z] [Citation(s) in RCA: 25] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2022] [Accepted: 09/21/2022] [Indexed: 11/08/2022]
Abstract
The vertebrate adaptive immune system modifies the genome of individual B cells to encode antibodies that bind particular antigens1. In most mammals, antibodies are composed of heavy and light chains that are generated sequentially by recombination of V, D (for heavy chains), J and C gene segments. Each chain contains three complementarity-determining regions (CDR1-CDR3), which contribute to antigen specificity. Certain heavy and light chains are preferred for particular antigens2-22. Here we consider pairs of B cells that share the same heavy chain V gene and CDRH3 amino acid sequence and were isolated from different donors, also known as public clonotypes23,24. We show that for naive antibodies (those not yet adapted to antigens), the probability that they use the same light chain V gene is around 10%, whereas for memory (functional) antibodies, it is around 80%, even if only one cell per clonotype is used. This property of functional antibodies is a phenomenon that we call light chain coherence. We also observe this phenomenon when similar heavy chains recur within a donor. Thus, although naive antibodies seem to recur by chance, the recurrence of functional antibodies reveals surprising constraint and determinism in the processes of V(D)J recombination and immune selection. For most functional antibodies, the heavy chain determines the light chain.
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12
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Focused B cell response to recurring gluten motif with implications for epitope spreading in celiac disease. Cell Rep 2022; 41:111541. [DOI: 10.1016/j.celrep.2022.111541] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2022] [Revised: 09/16/2022] [Accepted: 09/29/2022] [Indexed: 11/19/2022] Open
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13
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Aboulaghras S, Piancatelli D, Oumhani K, Balahbib A, Bouyahya A, Taghzouti K. Pathophysiology and immunogenetics of celiac disease. Clin Chim Acta 2022; 528:74-83. [PMID: 35120899 DOI: 10.1016/j.cca.2022.01.022] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2021] [Revised: 01/20/2022] [Accepted: 01/28/2022] [Indexed: 02/08/2023]
Abstract
Celiac disease (CD) is a chronic inflammatory enteropathy caused by gluten (protein from wheat, rye and, barley) in genetically predisposed individuals carrying the HLA-DQ2/HLA-DQ8 genotype. This pathology has a multifactorial etiology in which HLA genes, the microbiome, gluten and, other environmental factors are involved in the development of the disease. Its pathogenesis involves both innate and adaptive immunity as well as upregulation of IL-15. The objective of this review is to examine the results of current studies on genetic and environmental variables to better understand the pathogenesis of this enteropathy. The complex etiology of celiac disease makes our understanding of the pathogenesis of the disease incomplete, and a better knowledge of the many genetic and environmental components would help us better understand the pathophysiology of celiac disease.
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Affiliation(s)
- Sara Aboulaghras
- Physiology and Physiopathology Team, Faculty of Sciences, Genomic of Human Pathologies Research, Mohammed V University in Rabat, Morocco; Laboratoire d'Immunologie, Institut National d'Hygiene, Rabat, Morocco
| | - Daniela Piancatelli
- National Research Council (CNR)-Institute of Translational Pharmacology (IFT), L'Aquila, Italy
| | - Khadija Oumhani
- Laboratoire d'Immunologie, Institut National d'Hygiene, Rabat, Morocco
| | - Abdelaali Balahbib
- Laboratory of Zoology and General Biology, Faculty of Sciences, Mohammed V University in Rabat, Rabat, Morocco
| | - Abdelhakim Bouyahya
- Laboratory of Human Pathologies Biology, Department of Biology, Faculty of Sciences, Genomic Center of Human Pathologies Research, Mohammed V University in Rabat, Rabat, Morocco.
| | - Khalid Taghzouti
- Physiology and Physiopathology Team, Faculty of Sciences, Genomic of Human Pathologies Research, Mohammed V University in Rabat, Morocco
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14
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Lindeman I, Polak J, Qiao S, Holmøy T, Høglund RA, Vartdal F, Berg‐Hansen P, Sollid LM, Lossius A. Stereotyped B‐cell responses are linked to IgG constant region polymorphisms in multiple sclerosis. Eur J Immunol 2022; 52:550-565. [DOI: 10.1002/eji.202149576] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2021] [Revised: 11/19/2021] [Accepted: 01/10/2022] [Indexed: 11/07/2022]
Affiliation(s)
- Ida Lindeman
- Department of Immunology Oslo University Hospital Oslo Norway
- Department of Immunology Institute of Clinical Medicine University of Oslo Norway
- K.G. Jebsen Coeliac Disease Research Centre University of Oslo Norway
| | - Justyna Polak
- Department of Immunology Institute of Clinical Medicine University of Oslo Norway
- K.G. Jebsen Coeliac Disease Research Centre University of Oslo Norway
| | - Shuo‐Wang Qiao
- Department of Immunology Oslo University Hospital Oslo Norway
- Department of Immunology Institute of Clinical Medicine University of Oslo Norway
- K.G. Jebsen Coeliac Disease Research Centre University of Oslo Norway
| | - Trygve Holmøy
- Department of Neurology Akershus University Hospital Lørenskog Norway
- Department of Neurology Institute of Clinical Medicine University of Oslo Norway
| | - Rune A. Høglund
- Department of Neurology Akershus University Hospital Lørenskog Norway
- Department of Neurology Institute of Clinical Medicine University of Oslo Norway
| | - Frode Vartdal
- Department of Immunology Institute of Clinical Medicine University of Oslo Norway
- K.G. Jebsen Coeliac Disease Research Centre University of Oslo Norway
| | - Pål Berg‐Hansen
- Department of Neurology Oslo University Hospital Oslo Norway
| | - Ludvig M. Sollid
- Department of Immunology Oslo University Hospital Oslo Norway
- Department of Immunology Institute of Clinical Medicine University of Oslo Norway
- K.G. Jebsen Coeliac Disease Research Centre University of Oslo Norway
| | - Andreas Lossius
- K.G. Jebsen Coeliac Disease Research Centre University of Oslo Norway
- Department of Neurology Akershus University Hospital Lørenskog Norway
- Department of Molecular Medicine Institute of Basic Medical Sciences University of Oslo Norway
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15
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Unraveling B cell trajectories at single cell resolution. Trends Immunol 2022; 43:210-229. [DOI: 10.1016/j.it.2022.01.003] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2021] [Revised: 01/03/2022] [Accepted: 01/04/2022] [Indexed: 12/31/2022]
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16
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Lindeman I, Sollid LM. Single-cell approaches to dissect adaptive immune responses involved in autoimmunity: the case of celiac disease. Mucosal Immunol 2022; 15:51-63. [PMID: 34531547 DOI: 10.1038/s41385-021-00452-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2021] [Revised: 08/30/2021] [Accepted: 08/31/2021] [Indexed: 02/04/2023]
Abstract
Single-cell analysis is a powerful technology that has found widespread use in recent years. For diseases with involvement of adaptive immunity, single-cell analysis of antigen-specific T cells and B cells is particularly informative. In autoimmune diseases, the adaptive immune system is obviously at play, yet the ability to identify the culprit T and B cells recognizing disease-relevant antigen can be difficult. Celiac disease, a widespread disorder with autoimmune components, is unique in that disease-relevant antigens for both T cells and B cells are well defined. Furthermore, the celiac disease gut lesion is readily accessible allowing for sampling of tissue-resident cells. Thus, disease-relevant T cells and B cells from the gut and blood can be studied at the level of single cells. Here we review single-cell studies providing information on such adaptive immune cells and outline some future perspectives in the area of single-cell analysis in autoimmune diseases.
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Affiliation(s)
- Ida Lindeman
- KG Jebsen Coeliac Disease Research Centre, University of Oslo, Oslo, Norway.,Department of Immunology, Oslo University Hospital, Oslo, Norway
| | - Ludvig M Sollid
- KG Jebsen Coeliac Disease Research Centre, University of Oslo, Oslo, Norway. .,Department of Immunology, Oslo University Hospital, Oslo, Norway. .,Institute of Clinical Medicine, University of Oslo, Oslo, Norway.
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17
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Slabodkin A, Chernigovskaya M, Mikocziova I, Akbar R, Scheffer L, Pavlović M, Bashour H, Snapkov I, Mehta BB, Weber CR, Gutierrez-Marcos J, Sollid LM, Haff IH, Sandve GK, Robert PA, Greiff V. Individualized VDJ recombination predisposes the available Ig sequence space. Genome Res 2021; 31:2209-2224. [PMID: 34815307 PMCID: PMC8647828 DOI: 10.1101/gr.275373.121] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2021] [Accepted: 10/20/2021] [Indexed: 11/25/2022]
Abstract
The process of recombination between variable (V), diversity (D), and joining (J) immunoglobulin (Ig) gene segments determines an individual's naive Ig repertoire and, consequently, (auto)antigen recognition. VDJ recombination follows probabilistic rules that can be modeled statistically. So far, it remains unknown whether VDJ recombination rules differ between individuals. If these rules differed, identical (auto)antigen-specific Ig sequences would be generated with individual-specific probabilities, signifying that the available Ig sequence space is individual specific. We devised a sensitivity-tested distance measure that enables inter-individual comparison of VDJ recombination models. We discovered, accounting for several sources of noise as well as allelic variation in Ig sequencing data, that not only unrelated individuals but also human monozygotic twins and even inbred mice possess statistically distinguishable immunoglobulin recombination models. This suggests that, in addition to genetic, there is also nongenetic modulation of VDJ recombination. We demonstrate that population-wide individualized VDJ recombination can result in orders of magnitude of difference in the probability to generate (auto)antigen-specific Ig sequences. Our findings have implications for immune receptor-based individualized medicine approaches relevant to vaccination, infection, and autoimmunity.
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Affiliation(s)
- Andrei Slabodkin
- Department of Immunology and Oslo University Hospital, University of Oslo, 0372 Oslo, Norway
| | - Maria Chernigovskaya
- Department of Immunology and Oslo University Hospital, University of Oslo, 0372 Oslo, Norway
| | - Ivana Mikocziova
- Department of Immunology and Oslo University Hospital, University of Oslo, 0372 Oslo, Norway
| | - Rahmad Akbar
- Department of Immunology and Oslo University Hospital, University of Oslo, 0372 Oslo, Norway
| | - Lonneke Scheffer
- Department of Informatics, University of Oslo, 0373 Oslo, Norway
| | - Milena Pavlović
- Department of Informatics, University of Oslo, 0373 Oslo, Norway
| | - Habib Bashour
- School of Life Sciences, University of Warwick, Coventry CV4 7AL, United Kingdom
| | - Igor Snapkov
- Department of Immunology and Oslo University Hospital, University of Oslo, 0372 Oslo, Norway
| | - Brij Bhushan Mehta
- Department of Immunology and Oslo University Hospital, University of Oslo, 0372 Oslo, Norway
| | - Cédric R Weber
- Department of Biosystems Science and Engineering, ETH Zurich, 4058 Basel, Switzerland
| | | | - Ludvig M Sollid
- Department of Immunology and Oslo University Hospital, University of Oslo, 0372 Oslo, Norway
| | | | | | - Philippe A Robert
- Department of Immunology and Oslo University Hospital, University of Oslo, 0372 Oslo, Norway
| | - Victor Greiff
- Department of Immunology and Oslo University Hospital, University of Oslo, 0372 Oslo, Norway
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18
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Sun H, Yang HQ, Zhai K, Tong ZH. Signatures of B Cell Receptor Repertoire Following Pneumocystis Infection. Front Microbiol 2021; 12:636250. [PMID: 34135870 PMCID: PMC8202503 DOI: 10.3389/fmicb.2021.636250] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2020] [Accepted: 04/01/2021] [Indexed: 11/13/2022] Open
Abstract
B cells play vital roles in host defense against Pneumocystis infection. However, the features of the B cell receptor (BCR) repertoire in disease progression remain unclear. Here, we integrated single-cell RNA sequencing and single-cell BCR sequencing of immune cells from mouse lungs in an uninfected state and 1–4 weeks post-infection in order to illustrate the dynamic nature of B cell responses during Pneumocystis infection. We identified continuously increased plasma cells and an elevated ratio of (IgA + IgG) to (IgD + IgM) after infection. Moreover, Pneumocystis infection was associated with an increasing naïve B subset characterized by elevated expression of the transcription factor ATF3. The proportion of clonal expanded cells progressively increased, while BCR diversity decreased. Plasma cells exhibited higher levels of somatic hypermutation than naïve B cells. Biased usage of V(D)J genes was observed, and the usage frequency of IGHV9-3 rose. Overall, these results present a detailed atlas of B cell transcriptional changes and BCR repertoire features in the context of Pneumocystis infection, which provides valuable information for finding diagnostic biomarkers and developing potential immunotherapeutic targets.
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Affiliation(s)
- Han Sun
- Department of Respiratory and Critical Care Medicine, Beijing Institute of Respiratory Medicine, Beijing Chao-Yang Hospital, Capital Medical University, Beijing, China
| | - Hu-Qin Yang
- Department of Respiratory and Critical Care Medicine, Beijing Institute of Respiratory Medicine, Beijing Chao-Yang Hospital, Capital Medical University, Beijing, China
| | - Kan Zhai
- Department of Respiratory and Critical Care Medicine, Beijing Institute of Respiratory Medicine, Beijing Chao-Yang Hospital, Capital Medical University, Beijing, China
| | - Zhao-Hui Tong
- Department of Respiratory and Critical Care Medicine, Beijing Institute of Respiratory Medicine, Beijing Chao-Yang Hospital, Capital Medical University, Beijing, China
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19
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Shemesh O, Polak P, Lundin KEA, Sollid LM, Yaari G. Machine Learning Analysis of Naïve B-Cell Receptor Repertoires Stratifies Celiac Disease Patients and Controls. Front Immunol 2021; 12:627813. [PMID: 33790900 PMCID: PMC8006302 DOI: 10.3389/fimmu.2021.627813] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2020] [Accepted: 02/17/2021] [Indexed: 12/13/2022] Open
Abstract
Celiac disease (CeD) is a common autoimmune disorder caused by an abnormal immune response to dietary gluten proteins. The disease has high heritability. HLA is the major susceptibility factor, and the HLA effect is mediated via presentation of deamidated gluten peptides by disease-associated HLA-DQ variants to CD4+ T cells. In addition to gluten-specific CD4+ T cells the patients have antibodies to transglutaminase 2 (autoantigen) and deamidated gluten peptides. These disease-specific antibodies recognize defined epitopes and they display common usage of specific heavy and light chains across patients. Interactions between T cells and B cells are likely central in the pathogenesis, but how the repertoires of naïve T and B cells relate to the pathogenic effector cells is unexplored. To this end, we applied machine learning classification models to naïve B cell receptor (BCR) repertoires from CeD patients and healthy controls. Strikingly, we obtained a promising classification performance with an F1 score of 85%. Clusters of heavy and light chain sequences were inferred and used as features for the model, and signatures associated with the disease were then characterized. These signatures included amino acid (AA) 3-mers with distinct bio-physiochemical characteristics and enriched V and J genes. We found that CeD-associated clusters can be identified and that common motifs can be characterized from naïve BCR repertoires. The results may indicate a genetic influence by BCR encoding genes in CeD. Analysis of naïve BCRs as presented here may become an important part of assessing the risk of individuals to develop CeD. Our model demonstrates the potential of using BCR repertoires and in particular, naïve BCR repertoires, as disease susceptibility markers.
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Affiliation(s)
- Or Shemesh
- Bioengineering, Faculty of Engineering, Bar Ilan University, Ramat Gan, Israel
- Bar Ilan Institute of Nanotechnologies and Advanced Materials, Bar Ilan University, Ramat Gan, 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
| | - Knut E. A. Lundin
- K.G. Jebsen Center for Coeliac Disease Research, Institute of Clinical Medicine, University of Oslo, Oslo, Norway
- Department of Gastroenterology, Oslo University Hospital Rikshopsitalet, Oslo, Norway
| | - Ludvig M. Sollid
- K.G. Jebsen Center for Coeliac Disease Research, Institute of Clinical Medicine, University of Oslo, Oslo, Norway
- Department of Immunology, Oslo University Hospital Rikshospitalet, Oslo, Norway
| | - 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
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20
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Forgacs D, Abreu RB, Sautto GA, Kirchenbaum GA, Drabek E, Williamson KS, Kim D, Emerling DE, Ross TM. Convergent antibody evolution and clonotype expansion following influenza virus vaccination. PLoS One 2021; 16:e0247253. [PMID: 33617543 PMCID: PMC7899375 DOI: 10.1371/journal.pone.0247253] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2020] [Accepted: 02/03/2021] [Indexed: 12/14/2022] Open
Abstract
Recent advances in high-throughput single cell sequencing have opened up new avenues into the investigation of B cell receptor (BCR) repertoires. In this study, PBMCs were collected from 17 human participants vaccinated with the split-inactivated influenza virus vaccine during the 2016-2017 influenza season. A combination of Immune Repertoire Capture (IRCTM) technology and IgG sequencing was performed on ~7,800 plasmablast (PB) cells and preferential IgG heavy-light chain pairings were investigated. In some participants, a single expanded clonotype accounted for ~22% of their PB BCR repertoire. Approximately 60% (10/17) of participants experienced convergent evolution, possessing public PBs that were elicited independently in multiple participants. Binding profiles of one private and three public PBs confirmed they were all subtype-specific, cross-reactive hemagglutinin (HA) head-directed antibodies. Collectively, this high-resolution antibody repertoire analysis demonstrated the impact evolution can have on BCRs in response to influenza virus vaccination, which can guide future universal influenza prophylactic approaches.
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Affiliation(s)
- David Forgacs
- Center for Vaccines and Immunology, University of Georgia, Athens, GA, United States of America
| | - Rodrigo B. Abreu
- Center for Vaccines and Immunology, University of Georgia, Athens, GA, United States of America
| | - Giuseppe A. Sautto
- Center for Vaccines and Immunology, University of Georgia, Athens, GA, United States of America
| | - Greg A. Kirchenbaum
- Center for Vaccines and Immunology, University of Georgia, Athens, GA, United States of America
| | - Elliott Drabek
- Atreca, Inc., South San Francisco, CA, United States of America
| | | | - Dongkyoon Kim
- Atreca, Inc., South San Francisco, CA, United States of America
| | | | - Ted M. Ross
- Center for Vaccines and Immunology, University of Georgia, Athens, GA, United States of America
- Department of Infectious Diseases, University of Georgia, Athens, GA, United States of America
- * E-mail:
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21
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Lindeman I, Zhou C, Eggesbø LM, Miao Z, Polak J, Lundin KE, Jahnsen J, Qiao SW, Iversen R, Sollid LM. Longevity, clonal relationship, and transcriptional program of celiac disease-specific plasma cells. J Exp Med 2021; 218:e20200852. [PMID: 33095260 PMCID: PMC7590513 DOI: 10.1084/jem.20200852] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2020] [Revised: 07/07/2020] [Accepted: 09/30/2020] [Indexed: 12/11/2022] Open
Abstract
Disease-specific plasma cells (PCs) reactive with transglutaminase 2 (TG2) or deamidated gluten peptides (DGPs) are abundant in celiac disease (CeD) gut lesions. Their contribution toward CeD pathogenesis is unclear. We assessed expression of markers associated with PC longevity in 15 untreated and 26 treated CeD patients in addition to 13 non-CeD controls and performed RNA sequencing with clonal inference and transcriptomic analysis of 3,251 single PCs. We observed antigen-dependent V-gene selection and stereotypic antibodies. Generation of recombinant DGP-specific antibodies revealed a key role of a heavy chain residue that displays polymorphism, suggesting that immunoglobulin gene polymorphisms may influence CeD-specific antibody responses. We identified transcriptional differences between CeD-specific and non-disease-specific PCs and between short-lived and long-lived PCs. The short-lived CD19+CD45+ phenotype dominated in untreated and short-term-treated CeD, in particular among disease-specific PCs but also in the general PC population. Thus, the disease lesion of untreated CeD is characterized by massive accumulation of short-lived PCs that are not only directed against disease-specific antigens.
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Affiliation(s)
- Ida Lindeman
- KG Jebsen Coeliac Disease Research Centre, University of Oslo, Oslo, Norway
- Department of Immunology, University of Oslo and Oslo University Hospital, Oslo, Norway
| | - Chunyan Zhou
- KG Jebsen Coeliac Disease Research Centre, University of Oslo, Oslo, Norway
- State Key Laboratory of Food Science and Technology, Nanchang University, Nanchang, Jiangxi, China
| | - Linn M. Eggesbø
- KG Jebsen Coeliac Disease Research Centre, University of Oslo, Oslo, Norway
- Department of Immunology, University of Oslo and Oslo University Hospital, Oslo, Norway
| | - Zhichao Miao
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Cambridge, UK
- Newcastle Fibrosis Research Group, Institute of Cellular Medicine, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, UK
- Translational Research Institute of Brain and Brain-Like Intelligence and Department of Anesthesiology, Shanghai Fourth People's Hospital (affiliated with Tongji University School of Medicine), Shanghai, China
| | - Justyna Polak
- KG Jebsen Coeliac Disease Research Centre, University of Oslo, Oslo, Norway
- Department of Immunology, University of Oslo and Oslo University Hospital, Oslo, Norway
| | - Knut E.A. Lundin
- KG Jebsen Coeliac Disease Research Centre, University of Oslo, Oslo, Norway
- Department of Immunology, University of Oslo and Oslo University Hospital, Oslo, Norway
- Department of Gastroenterology, Oslo University Hospital-Rikshospitalet, Oslo, Norway
| | - Jørgen Jahnsen
- Department of Gastroenterology, Akershus University Hospital, Lørenskog, Norway
- Institute of Clinical Medicine, University of Oslo, Oslo, Norway
| | - Shuo-Wang Qiao
- KG Jebsen Coeliac Disease Research Centre, University of Oslo, Oslo, Norway
- Department of Immunology, University of Oslo and Oslo University Hospital, Oslo, Norway
| | - Rasmus Iversen
- KG Jebsen Coeliac Disease Research Centre, University of Oslo, Oslo, Norway
- Department of Immunology, University of Oslo and Oslo University Hospital, Oslo, Norway
| | - Ludvig M. Sollid
- KG Jebsen Coeliac Disease Research Centre, University of Oslo, Oslo, Norway
- Department of Immunology, University of Oslo and Oslo University Hospital, Oslo, Norway
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22
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Richardson E, Galson JD, Kellam P, Kelly DF, Smith SE, Palser A, Watson S, Deane CM. A computational method for immune repertoire mining that identifies novel binders from different clonotypes, demonstrated by identifying anti-pertussis toxoid antibodies. MAbs 2021; 13:1869406. [PMID: 33427589 PMCID: PMC7808390 DOI: 10.1080/19420862.2020.1869406] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
Due to their shared genetic history, antibodies from the same clonotype often bind to the same epitope. This knowledge is used in immune repertoire mining, where known binders are used to search bulk sequencing repertoires to identify new binders. However, current computational methods cannot identify epitope convergence between antibodies from different clonotypes, limiting the sequence diversity of antigen-specific antibodies that can be identified. We describe how the antibody binding site, the paratope, can be used to cluster antibodies with common antigen reactivity from different clonotypes. Our method, paratyping, uses the predicted paratope to identify these novel cross clonotype matches. We experimentally validated our predictions on a pertussis toxoid dataset. Our results show that even the simplest abstraction of the antibody binding site, using only the length of the loops involved and predicted binding residues, is sufficient to group antigen-specific antibodies and provide additional information to conventional clonotype analysis. Abbreviations: BCR: B-cell receptor; CDR: complementarity-determining region; PTx: pertussis toxoid
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Affiliation(s)
- Eve Richardson
- Department of Statistics, University of Oxford , Oxford, UK
| | - Jacob D Galson
- Alchemab Therapeutics Ltd , London, UK.,Division of Immunology, University Children's Hospital, University of Zurich, Zurich , Switzerland
| | - Paul Kellam
- Kymab Ltd , Cambridge, UK.,Department of Infectious Diseases, Faculty of Medicine, Imperial College London , London, UK
| | - Dominic F Kelly
- Department of Paediatrics, University of Oxford , Oxford, UK.,Oxford University Hospitals NHS Foundation Trust , Oxford, UK
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23
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Immunoglobulin germline gene variation and its impact on human disease. Genes Immun 2021; 22:205-217. [PMID: 34175903 PMCID: PMC8234759 DOI: 10.1038/s41435-021-00145-5] [Citation(s) in RCA: 46] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2021] [Revised: 06/01/2021] [Accepted: 06/10/2021] [Indexed: 02/06/2023]
Abstract
Immunoglobulins (Ig) play an important role in the immune system both when expressed as antigen receptors on the cell surface of B cells and as antibodies secreted into extracellular fluids. The advent of high-throughput sequencing methods has enabled the investigation of human Ig repertoires at unprecedented depth. This has led to the discovery of many previously unreported germline Ig alleles. Moreover, it is becoming clear that convergent and stereotypic antibody responses are common where different individuals recognise defined antigenic epitopes with the use of the same Ig V genes. Thus, germline V gene variation is increasingly being linked to the differential capacity of generating an effective immune response, which might lead to varying disease susceptibility. Here, we review recent evidence of how germline variation in Ig genes impacts the Ig repertoire and its subsequent effects on the adaptive immune response in vaccination, infection, and autoimmunity.
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24
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Shi B, Dong X, Ma Q, Sun S, Ma L, Yu J, Wang X, Pan J, He X, Su D, Yao X. The Usage of Human IGHJ Genes Follows a Particular Non-random Selection: The Recombination Signal Sequence May Affect the Usage of Human IGHJ Genes. Front Genet 2020; 11:524413. [PMID: 33363565 PMCID: PMC7753069 DOI: 10.3389/fgene.2020.524413] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2020] [Accepted: 11/06/2020] [Indexed: 12/02/2022] Open
Abstract
The formation of the B cell receptor (BCR) heavy chain variable region is derived from the germline V(D)J gene rearrangement according to the “12/23” rule and the “beyond 12/23” rule. The usage frequency of each V(D)J gene in the peripheral BCR repertoires is related to the initial recombination, self-tolerance selection, and the clonal proliferative response. However, their specific differences and possible mechanisms are still unknown. We analyzed in-frame and out-of-frame BCR-H repertoires from human samples with normal physiological and various pathological conditions by high-throughput sequencing. Our results showed that IGHJ gene frequency follows a similar pattern which is previously known, where IGHJ4 is used at high frequency (>40%), IGHJ6/IGHJ3/IGHJ5 is used at medium frequencies (10∼20%), and IGH2/IGHJ1 is used at low frequency (<4%) under whether normal physiological or various pathological conditions. However, our analysis of the recombination signal sequences suggested that the conserved non-amer and heptamer and certain 23 bp spacer length may affect the initial IGHD-IGHJ recombination, which results in different frequencies of IGHJ genes among the initial BCR-H repertoire. Based on this “initial repertoire,” we recommend that re-evaluation and further investigation are needed when analyzing the significance and mechanism of IGHJ gene frequency in self-tolerance selection and the clonal proliferative response.
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Affiliation(s)
- Bin Shi
- Department of Laboratory Medicine, Affiliated Hospital of Zunyi Medical University, Zunyi, China.,School of Laboratory Medicine, Zunyi Medical University, Zunyi, China
| | - Xiaoheng Dong
- Department of Immunology, Center of Immunomolecular Engineering, Innovation & Practice Base for Graduate Students Education, Zunyi Medical University, Zunyi, China
| | - Qingqing Ma
- Department of Immunology, Center of Immunomolecular Engineering, Innovation & Practice Base for Graduate Students Education, Zunyi Medical University, Zunyi, China
| | - Suhong Sun
- Department of Breast Surgery, Affiliated Hospital of Zunyi Medical University, Zunyi, China
| | - Long Ma
- Department of Immunology, Center of Immunomolecular Engineering, Innovation & Practice Base for Graduate Students Education, Zunyi Medical University, Zunyi, China
| | - Jiang Yu
- Department of Immunology, Center of Immunomolecular Engineering, Innovation & Practice Base for Graduate Students Education, Zunyi Medical University, Zunyi, China
| | - Xiaomei Wang
- Department of Immunology, Center of Immunomolecular Engineering, Innovation & Practice Base for Graduate Students Education, Zunyi Medical University, Zunyi, China
| | - Juan Pan
- Department of Immunology, Center of Immunomolecular Engineering, Innovation & Practice Base for Graduate Students Education, Zunyi Medical University, Zunyi, China
| | - Xiaoyan He
- Department of Immunology, Center of Immunomolecular Engineering, Innovation & Practice Base for Graduate Students Education, Zunyi Medical University, Zunyi, China
| | - Danhua Su
- Department of Immunology, Center of Immunomolecular Engineering, Innovation & Practice Base for Graduate Students Education, Zunyi Medical University, Zunyi, China
| | - Xinsheng Yao
- Department of Immunology, Center of Immunomolecular Engineering, Innovation & Practice Base for Graduate Students Education, Zunyi Medical University, Zunyi, China
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25
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Emerging Strategies for Therapeutic Antibody Discovery from Human B Cells. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2020. [PMID: 32949403 DOI: 10.1007/978-981-15-4494-1_18] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register]
Abstract
Monoclonal antibodies from human sources are being increasingly recognized as valuable options in many therapeutic areas. These antibodies can show exquisite specificity and high potency while maintaining a desirable safety profile, having been matured and tolerized within human patients. However, the discovery of these antibodies presents important challenges, since the B cells encoding therapeutic antibodies can be rare in a typical blood draw and are short-lived ex vivo. Furthermore, the unique pairing of VH and VL domains in each B cell contributes to specificity and function; therefore, maintaining antibody chain pairing presents a throughput limitation. This work will review the various approaches aimed at addressing these challenges with an eye to next-generation methods for high-throughput discovery from the human B-cell repertoire.
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26
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du Pré MF, Blazevski J, Dewan AE, Stamnaes J, Kanduri C, Sandve GK, Johannesen MK, Lindstad CB, Hnida K, Fugger L, Melino G, Qiao SW, Sollid LM. B cell tolerance and antibody production to the celiac disease autoantigen transglutaminase 2. J Exp Med 2020; 217:jem.20190860. [PMID: 31727780 PMCID: PMC7041703 DOI: 10.1084/jem.20190860] [Citation(s) in RCA: 37] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2019] [Revised: 09/05/2019] [Accepted: 10/14/2019] [Indexed: 12/18/2022] Open
Abstract
Autoantibodies to transglutaminase 2 (TG2) are hallmarks of celiac disease. To address B cell tolerance and autoantibody formation to TG2, we generated immunoglobulin knock-in (Ig KI) mice that express a prototypical celiac patient-derived anti-TG2 B cell receptor equally reactive to human and mouse TG2. We studied B cell development in the presence/absence of autoantigen by crossing the Ig KI mice to Tgm2-/- mice. Autoreactive B cells in Tgm2+/+ mice were indistinguishable from their naive counterparts in Tgm2-/- mice with no signs of clonal deletion, receptor editing, or B cell anergy. The autoreactive B cells appeared ignorant to their antigen, and they produced autoantibodies when provided T cell help. The findings lend credence to a model of celiac disease where gluten-reactive T cells provide help to autoreactive TG2-specific B cells by involvement of gluten-TG2 complexes, and they outline a general mechanism of autoimmunity with autoantibodies being produced by ignorant B cells on provision of T cell help.
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Affiliation(s)
- M Fleur du Pré
- K.G. Jebsen Coeliac Disease Research Centre, University of Oslo, Oslo, Norway.,Department of Immunology, Oslo University Hospital, Oslo, Norway
| | - Jana Blazevski
- Department of Immunology, University of Oslo, Oslo, Norway
| | - Alisa E Dewan
- K.G. Jebsen Coeliac Disease Research Centre, University of Oslo, Oslo, Norway.,Department of Immunology, Oslo University Hospital, Oslo, Norway
| | - Jorunn Stamnaes
- K.G. Jebsen Coeliac Disease Research Centre, University of Oslo, Oslo, Norway.,Department of Immunology, Oslo University Hospital, Oslo, Norway.,Department of Immunology, University of Oslo, Oslo, Norway
| | - Chakravarthi Kanduri
- K.G. Jebsen Coeliac Disease Research Centre, University of Oslo, Oslo, Norway.,Department of Informatics, University of Oslo, Oslo, Norway
| | - Geir Kjetil Sandve
- K.G. Jebsen Coeliac Disease Research Centre, University of Oslo, Oslo, Norway.,Department of Informatics, University of Oslo, Oslo, Norway
| | - Marie K Johannesen
- K.G. Jebsen Coeliac Disease Research Centre, University of Oslo, Oslo, Norway.,Department of Immunology, University of Oslo, Oslo, Norway
| | - Christian B Lindstad
- K.G. Jebsen Coeliac Disease Research Centre, University of Oslo, Oslo, Norway.,Department of Immunology, University of Oslo, Oslo, Norway
| | - Kathrin Hnida
- Department of Immunology, University of Oslo, Oslo, Norway
| | - Lars Fugger
- Oxford Centre for Neuroinflammation, Nuffield Department of Clinical Neurosciences, Division of Clinical Neurology and Medical Research Council Human Immunology Unit, Weatherall Institute of Molecular Medicine, John Radcliffe Hospital, University of Oxford, Oxford, UK
| | - Gerry Melino
- Department of Experimental Medicine, TOR, University of Rome "Tor Vergata", Rome, Italy
| | - Shuo-Wang Qiao
- K.G. Jebsen Coeliac Disease Research Centre, University of Oslo, Oslo, Norway.,Department of Immunology, University of Oslo, Oslo, Norway
| | - Ludvig M Sollid
- K.G. Jebsen Coeliac Disease Research Centre, University of Oslo, Oslo, Norway.,Department of Immunology, Oslo University Hospital, Oslo, Norway.,Department of Immunology, University of Oslo, Oslo, Norway
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27
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Mikocziova I, Gidoni M, Lindeman I, Peres A, Snir O, Yaari G, Sollid LM. Polymorphisms in human immunoglobulin heavy chain variable genes and their upstream regions. Nucleic Acids Res 2020; 48:5499-5510. [PMID: 32365177 PMCID: PMC7261178 DOI: 10.1093/nar/gkaa310] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2020] [Accepted: 04/20/2020] [Indexed: 01/13/2023] Open
Abstract
Germline variations in immunoglobulin genes influence the repertoire of B cell receptors and antibodies, and such polymorphisms may impact disease susceptibility. However, the knowledge of the genomic variation of the immunoglobulin loci is scarce. Here, we report 25 potential novel germline IGHV alleles as inferred from rearranged naïve B cell cDNA repertoires of 98 individuals. Thirteen novel alleles were selected for validation, out of which ten were successfully confirmed by targeted amplification and Sanger sequencing of non-B cell DNA. Moreover, we detected a high degree of variability upstream of the V-REGION in the 5′UTR, L-PART1 and L-PART2 sequences, and found that identical V-REGION alleles can differ in upstream sequences. Thus, we have identified a large genetic variation not only in the V-REGION but also in the upstream sequences of IGHV genes. Our findings provide a new perspective for annotating immunoglobulin repertoire sequencing data.
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Affiliation(s)
- Ivana Mikocziova
- K.G.Jebsen Centre for Coeliac Disease Research and Department of Immunology, University of Oslo and Oslo University Hospital, 0372 Oslo, Norway
| | - Moriah Gidoni
- Faculty of Engineering, Bar Ilan University, Ramat Gan 5290002, Israel
| | - Ida Lindeman
- K.G.Jebsen Centre for Coeliac Disease Research and Department of Immunology, University of Oslo and Oslo University Hospital, 0372 Oslo, Norway
| | - Ayelet Peres
- Faculty of Engineering, Bar Ilan University, Ramat Gan 5290002, Israel
| | - Omri Snir
- K.G.Jebsen Centre for Coeliac Disease Research and Department of Immunology, University of Oslo and Oslo University Hospital, 0372 Oslo, Norway
| | - Gur Yaari
- Faculty of Engineering, Bar Ilan University, Ramat Gan 5290002, Israel
| | - Ludvig M Sollid
- K.G.Jebsen Centre for Coeliac Disease Research and Department of Immunology, University of Oslo and Oslo University Hospital, 0372 Oslo, Norway
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28
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Meffre E, O'Connor KC. Impaired B‐cell tolerance checkpoints promote the development of autoimmune diseases and pathogenic autoantibodies. Immunol Rev 2019; 292:90-101. [DOI: 10.1111/imr.12821] [Citation(s) in RCA: 60] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2019] [Accepted: 10/25/2019] [Indexed: 12/13/2022]
Affiliation(s)
- Eric Meffre
- Department of Immunobiology Yale University School of Medicine New Haven CT USA
- Section of Rheumatology, Allergy, and Clinical Immunology Yale University School of Medicine New Haven CT USA
| | - Kevin C. O'Connor
- Department of Immunobiology Yale University School of Medicine New Haven CT USA
- Department of Neurology Yale University School of Medicine New Haven CT USA
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29
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Efficient T cell-B cell collaboration guides autoantibody epitope bias and onset of celiac disease. Proc Natl Acad Sci U S A 2019; 116:15134-15139. [PMID: 31285344 DOI: 10.1073/pnas.1901561116] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
B cells play important roles in autoimmune diseases through autoantibody production, cytokine secretion, or antigen presentation to T cells. In most cases, the contribution of B cells as antigen-presenting cells is not well understood. We have studied the autoantibody response against the enzyme transglutaminase 2 (TG2) in celiac disease patients by generating recombinant antibodies from single gut plasma cells reactive with discrete antigen domains and by undertaking proteomic analysis of anti-TG2 serum antibodies. The majority of the cells recognized epitopes in the N-terminal domain of TG2. Antibodies recognizing C-terminal epitopes interfered with TG2 cross-linking activity, and B cells specific for C-terminal epitopes were inefficient at taking up TG2-gluten complexes for presentation to gluten-specific T cells. The bias toward N-terminal epitopes hence reflects efficient T-B collaboration. Production of antibodies against N-terminal epitopes coincided with clinical onset of disease, suggesting that TG2-reactive B cells with certain epitope specificities could be the main antigen-presenting cells for pathogenic, gluten-specific T cells. The link between B cell epitopes, antigen presentation, and disease onset provides insight into the pathogenic mechanisms of a T cell-mediated autoimmune condition.
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30
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Lai L, Zhou X, Chen H, Luo Y, Sui W, Zhang J, Tang D, Yan Q, Dai Y. Composition and diversity analysis of the B-cell receptor immunoglobulin heavy chain complementarity-determining region 3 repertoire in patients with acute rejection after kidney transplantation using high-throughput sequencing. Exp Ther Med 2019; 17:2206-2220. [PMID: 30867706 PMCID: PMC6395953 DOI: 10.3892/etm.2019.7183] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2018] [Accepted: 11/14/2018] [Indexed: 01/02/2023] Open
Abstract
The aim of the present study was to assess the genetic diversity of the B-cell receptor (BCR) in kidney transplant recipients with acute rejection. A total of three patients with acute rejection after kidney transplantation were examined by performing a composition and diversity analysis of the BCR immunoglobulin heavy chain (IGH) complementarity-determining region 3 (H-CDR3) repertoire. The peripheral blood mononuclear cells of patients were collected at 1 day prior to (Pre1), as well as 1 day (Post1) and 7 days (Post7) after the transplantation, and DNA was extracted. High-throughput sequencing technology was applied to determine the BCR repertoire. Raw sequences in FASTQ format were analyzed with the Basic Local Alignment Search Tool. The diversity of the BCR repertoire was assessed by calculating Shannon entropy, Simpson's diversity index, the Gini coefficient and highly expanded clone distributions. The diversity of the BCR repertoire at Pre1 was greater than that at Post1 or Post7. The diversity of the BCR repertoire was the lowest at Post1 and increased at Post7 but failed to reach the pre-transplantation levels. Patients exhibited the loss of seven IGH variable (IGHV)3 family genes, while five new genes were expressed at a low frequency. Furthermore, five IGHV-IGH joining (IGHJ) gene pairings, including IGHJ6-IGHV3-11, were detected in the patients. Up- and downregulated genes were assessed by calculating the expression frequencies of the IGH diversity and IGHV gene families at Post1 and Post7. The results of the H-CDR3 length distribution and H-CDR3 amino acid (AA) usage analyses indicated that in Case 1 and 2, the AA length was similar at mostly 14–18 AA, while that in Case 3 was relatively stable at 12–16 AA. In conclusion, the present results illustrate the diversity of H-CDR3 in patients with acute rejection after kidney transplantation may provide novel ideas, methods and means of monitoring and analyzing the immune status of patients under physiological and pathological conditions.
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Affiliation(s)
- Liusheng Lai
- Department of Nephrology, Guilin No. 924 Hospital, Guangxi Key Laboratory of Metabolic Disease Research, Guilin Key Laboratory of Kidney Disease Research, Guilin, Guangxi 541002, P.R. China
| | - Xianqing Zhou
- Department of Nephrology, Guilin No. 924 Hospital, Guangxi Key Laboratory of Metabolic Disease Research, Guilin Key Laboratory of Kidney Disease Research, Guilin, Guangxi 541002, P.R. China
| | - Huaizhou Chen
- Department of Nephrology, Guilin No. 924 Hospital, Guangxi Key Laboratory of Metabolic Disease Research, Guilin Key Laboratory of Kidney Disease Research, Guilin, Guangxi 541002, P.R. China
| | - Yadan Luo
- Department of Nephrology, Guilin No. 924 Hospital, Guangxi Key Laboratory of Metabolic Disease Research, Guilin Key Laboratory of Kidney Disease Research, Guilin, Guangxi 541002, P.R. China
| | - Weiguo Sui
- Department of Nephrology, Guilin No. 924 Hospital, Guangxi Key Laboratory of Metabolic Disease Research, Guilin Key Laboratory of Kidney Disease Research, Guilin, Guangxi 541002, P.R. China
| | - Jiaxing Zhang
- Department of Nephrology, Guilin No. 924 Hospital, Guangxi Key Laboratory of Metabolic Disease Research, Guilin Key Laboratory of Kidney Disease Research, Guilin, Guangxi 541002, P.R. China
| | - Donge Tang
- Clinical Medical Research Center of The Second Clinical Medical College, Jinan University, Shenzhen People's Hospital, Shenzhen, Guangdong 518020, P.R. China
| | - Qiang Yan
- Department of Nephrology, Guilin No. 924 Hospital, Guangxi Key Laboratory of Metabolic Disease Research, Guilin Key Laboratory of Kidney Disease Research, Guilin, Guangxi 541002, P.R. China
| | - Yong Dai
- Clinical Medical Research Center of The Second Clinical Medical College, Jinan University, Shenzhen People's Hospital, Shenzhen, Guangdong 518020, P.R. China
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31
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Quaglia S, Ferrara F, De Leo L, Ziberna F, Vatta S, Marchiò S, Sblattero D, Ventura A, Not T. A Functional Idiotype/Anti-Idiotype Network Is Active in Genetically Gluten-Intolerant Individuals Negative for Both Celiac Disease-Related Intestinal Damage and Serum Autoantibodies. THE JOURNAL OF IMMUNOLOGY 2019; 202:1079-1087. [PMID: 30635394 DOI: 10.4049/jimmunol.1800819] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/12/2018] [Accepted: 12/10/2018] [Indexed: 11/19/2022]
Abstract
An unbalance between Abs that recognize an autoantigen (idiotypes; IDs) and Igs that bind such Abs (anti-IDs) is considered a functional event in autoimmune disorders. We investigated the presence of an ID/anti-ID network in celiac disease (CD), a condition in which antitissue transglutaminase 2 (TG2) Abs are suspected to contribute to CD pathogenesis. To characterize the ID side, we reproduced by in vitro yeast display the intestine-resident Abs from CD and control patients. These TG2-specific IDs were used to identify potential anti-IDs in the serum. We observed elevated titers of anti-IDs in asymptomatic patients with predisposition to CD and demonstrated that anti-ID depletion from the serum restores a detectable humoral response against TG2. Our study provides an alternative approach to quantify CD-related autoantibodies in cases that would be defined "negative serology" with current diagnostic applications. Therefore, we suggest that developments of this technology could be designed for perspective routine tests.
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Affiliation(s)
- Sara Quaglia
- Institute for Maternal and Child Health, Istituto di Ricerca e Cura a Carattere Scientifico Burlo Garofolo, Trieste 34137, Italy
| | | | - Luigina De Leo
- Institute for Maternal and Child Health, Istituto di Ricerca e Cura a Carattere Scientifico Burlo Garofolo, Trieste 34137, Italy
| | - Fabiana Ziberna
- Institute for Maternal and Child Health, Istituto di Ricerca e Cura a Carattere Scientifico Burlo Garofolo, Trieste 34137, Italy
| | - Serena Vatta
- Institute for Maternal and Child Health, Istituto di Ricerca e Cura a Carattere Scientifico Burlo Garofolo, Trieste 34137, Italy
| | - Serena Marchiò
- Candiolo Cancer Institute-Fondazione del Piemonte per l'Oncologia, Istituto di Ricerca e Cura a Carattere Scientifico, Candiolo, Turin 10060, Italy.,Department of Oncology, University of Turin School of Medicine, Candiolo, Turin 10060, Italy; and
| | - Daniele Sblattero
- University of Trieste, Department of Life Science, Trieste 34128, Italy
| | - Alessandro Ventura
- Institute for Maternal and Child Health, Istituto di Ricerca e Cura a Carattere Scientifico Burlo Garofolo, Trieste 34137, Italy.,University of Trieste, Department of Life Science, Trieste 34128, Italy
| | - Tarcisio Not
- Institute for Maternal and Child Health, Istituto di Ricerca e Cura a Carattere Scientifico Burlo Garofolo, Trieste 34137, Italy; .,University of Trieste, Department of Life Science, Trieste 34128, Italy
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32
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Davidsen K, Matsen FA. Benchmarking Tree and Ancestral Sequence Inference for B Cell Receptor Sequences. Front Immunol 2018; 9:2451. [PMID: 30429847 PMCID: PMC6220437 DOI: 10.3389/fimmu.2018.02451] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2018] [Accepted: 10/04/2018] [Indexed: 12/13/2022] Open
Abstract
B cell receptor sequences evolve during affinity maturation according to a Darwinian process of mutation and selection. Phylogenetic tools are used extensively to reconstruct ancestral sequences and phylogenetic trees from affinity-matured sequences. In addition to using general-purpose phylogenetic methods, researchers have developed new tools to accommodate the special features of B cell sequence evolution. However, the performance of classical phylogenetic techniques in the presence of B cell-specific features is not well understood, nor how much the newer generation of B cell specific tools represent an improvement over classical methods. In this paper we benchmark the performance of classical phylogenetic and new B cell-specific tools when applied to B cell receptor sequences simulated from a forward-time model of B cell receptor affinity maturation toward a mature receptor. We show that the currently used tools vary substantially in terms of tree structure and ancestral sequence inference accuracy. Furthermore, we show that there are still large performance gains to be achieved by modeling the special mutation process of B cell receptors. These conclusions are further strengthened with real data using the rules of isotype switching to count possible violations within each inferred phylogeny.
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Affiliation(s)
| | - Frederick A. Matsen
- Computational Biology Program, Fred Hutchinson Cancer Research Center, Seattle, WA, United States
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33
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Breden F, Watson CT. Using High-Throughput Sequencing to Characterize the Development of the Antibody Repertoire During Infections: A Case Study of HIV-1. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2018; 1053:245-263. [PMID: 29549643 DOI: 10.1007/978-3-319-72077-7_12] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
High throughput sequencing (HTS) approaches have only recently been applied to describing the antibody/B-cell repertoire in fine detail, but these data sets have already become critical to the design of vaccines and therapeutics, and monitoring of cancer immunotherapy. As a case study, we describe the potential and present limitations of HTS studies of the Ab repertoire during infection with HIV-1. Most of the present studies restrict their analyses to lineages of specific bnAbs. We discuss future initiatives to expand this type of analysis to more complete repertoires and to improve comparing and sharing of these Ab repertoire data across studies and institutions.
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Affiliation(s)
- Felix Breden
- Department of Biological Sciences, Simon Fraser University, Burnaby, BC, Canada.
| | - Corey T Watson
- Department of Biochemistry and Molecular Genetics, University of Louisville School of Medicine, Louisville, KY, USA
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34
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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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35
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Iversen R, Snir O, Stensland M, Kroll JE, Steinsbø Ø, Korponay-Szabó IR, Lundin KEA, de Souza GA, Sollid LM. Strong Clonal Relatedness between Serum and Gut IgA despite Different Plasma Cell Origins. Cell Rep 2018; 20:2357-2367. [PMID: 28877470 PMCID: PMC5603730 DOI: 10.1016/j.celrep.2017.08.036] [Citation(s) in RCA: 57] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2017] [Revised: 07/14/2017] [Accepted: 08/07/2017] [Indexed: 01/02/2023] Open
Abstract
Mucosal antigens induce generation of lamina propria plasma cells (PCs) that secrete dimeric immunoglobulin A (IgA) destined for transport across the epithelium. In addition, blood contains monomeric IgA. To study the relationship between mucosal and systemic antibody responses, we took advantage of celiac disease patient samples for isolation of gut PCs as well as serum IgA and IgG reactive with a gluten-derived peptide or the autoantigen transglutaminase 2. Proteomic analysis of serum IgA revealed antigen-specific V-gene preferences, which matched those found in gut PCs. Further, gut PC CDR-H3 sequences were abundant in serum IgA but also detectable in serum IgG. Our data indicate that the same B cell clones that give rise to gut PCs also contribute to the serum antibody pool. However, serum IgA antibodies had a molecular composition distinct from that of IgA antibodies secreted in the gut, suggesting that individual B cell clones give rise to different PC populations.
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Affiliation(s)
- Rasmus Iversen
- Centre for Immune Regulation and Department of Immunology, University of Oslo and Oslo University Hospital-Rikshospitalet, NO-0372 Oslo, Norway
| | - Omri Snir
- Centre for Immune Regulation and Department of Immunology, University of Oslo and Oslo University Hospital-Rikshospitalet, NO-0372 Oslo, Norway
| | - Maria Stensland
- Centre for Immune Regulation and Department of Immunology, University of Oslo and Oslo University Hospital-Rikshospitalet, NO-0372 Oslo, Norway; Proteomics Core Facility, Oslo University Hospital-Rikshospitalet, NO-0372 Oslo, Norway
| | - José E Kroll
- Brain Institute, Federal University of Rio Grande do Norte, RN 59056-450 Natal, Brazil
| | - Øyvind Steinsbø
- Centre for Immune Regulation and Department of Immunology, University of Oslo and Oslo University Hospital-Rikshospitalet, NO-0372 Oslo, Norway
| | | | - Knut E A Lundin
- Centre for Immune Regulation and Department of Immunology, University of Oslo and Oslo University Hospital-Rikshospitalet, NO-0372 Oslo, Norway; Department of Gastroenterology, Oslo University Hospital-Rikshospitalet, NO-0372 Oslo, Norway; KG Jebsen Coeliac Disease Research Centre, University of Oslo, NO-0372 Oslo, Norway
| | - Gustavo A de Souza
- Centre for Immune Regulation and Department of Immunology, University of Oslo and Oslo University Hospital-Rikshospitalet, NO-0372 Oslo, Norway; Proteomics Core Facility, Oslo University Hospital-Rikshospitalet, NO-0372 Oslo, Norway; Brain Institute, Federal University of Rio Grande do Norte, RN 59056-450 Natal, Brazil
| | - Ludvig M Sollid
- Centre for Immune Regulation and Department of Immunology, University of Oslo and Oslo University Hospital-Rikshospitalet, NO-0372 Oslo, Norway; KG Jebsen Coeliac Disease Research Centre, University of Oslo, NO-0372 Oslo, Norway.
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36
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Tutturen AEV, Dørum S, Clancy T, Reims HM, Christophersen A, Lundin KEA, Sollid LM, de Souza GA, Stamnaes J. Characterization of the Small Intestinal Lesion in Celiac Disease by Label-Free Quantitative Mass Spectrometry. THE AMERICAN JOURNAL OF PATHOLOGY 2018; 188:1563-1579. [PMID: 29684362 DOI: 10.1016/j.ajpath.2018.03.017] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/21/2017] [Revised: 02/08/2018] [Accepted: 03/13/2018] [Indexed: 12/16/2022]
Abstract
Global characterization of tissue proteomes from small amounts of biopsy material has become feasible because of advances in mass spectrometry and bioinformatics tools. In celiac disease (CD), dietary gluten induces an immune response that is accompanied by pronounced remodeling of the small intestine. Removal of gluten from the diet abrogates the immune response, and the tissue architecture normalizes. In this study, differences in global protein expression of small intestinal biopsy specimens from CD patients were quantified by analyzing formalin-fixed, paraffin-embedded material using liquid chromatography-mass spectrometry and label-free protein quantitation. Protein expression was compared in biopsy specimens collected from the same patients before and after 1-year treatment with gluten-free diet (n = 10) or before and after 3-day gluten provocation (n = 4). Differential expression of proteins in particular from mature enterocytes, neutrophils, and plasma cells could distinguish untreated from treated CD mucosa, and Ig variable region IGHV5-51 expression was found to serve as a CD-specific marker of ongoing immune activation. In patients who had undergone gluten challenge, coordinated up-regulation of wound response proteins, including the CD autoantigen transglutaminase 2, was observed. Our study provides a global and unbiased assessment of antigen-driven changes in protein expression in the celiac intestinal mucosa.
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Affiliation(s)
- Astrid E V Tutturen
- Centre for Immune Regulation and Department of Immunology, University of Oslo and Oslo University Hospital-Rikshospitalet, Oslo, Norway; Proteomics Core Facility, Oslo University Hospital-Rikshospitalet, Oslo, Norway
| | - Siri Dørum
- Centre for Immune Regulation and Department of Immunology, University of Oslo and Oslo University Hospital-Rikshospitalet, Oslo, Norway
| | - Trevor Clancy
- Department of Immunology, Institute for Cancer Research, Oslo University Hospital-Radiumhospitalet, Oslo, Norway
| | - Henrik M Reims
- Department of Pathology, Oslo University Hospital, Oslo, Norway
| | | | - Knut E A Lundin
- KG Jebsen Coeliac Disease Research Centre, University of Oslo, Oslo, Norway; Department of Gastroenterology, Oslo University Hospital-Rikshospitalet, Oslo, Norway
| | - Ludvig M Sollid
- Centre for Immune Regulation and Department of Immunology, University of Oslo and Oslo University Hospital-Rikshospitalet, Oslo, Norway; KG Jebsen Coeliac Disease Research Centre, University of Oslo, Oslo, Norway
| | - Gustavo A de Souza
- Proteomics Core Facility, Oslo University Hospital-Rikshospitalet, Oslo, Norway; The Brain Institute, Universidade Federal do Rio Grande do Norte, Natal-RN, Brazil
| | - Jorunn Stamnaes
- Centre for Immune Regulation and Department of Immunology, University of Oslo and Oslo University Hospital-Rikshospitalet, Oslo, Norway.
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37
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Correa I, Ilieva KM, Crescioli S, Lombardi S, Figini M, Cheung A, Spicer JF, Tutt ANJ, Nestle FO, Karagiannis P, Lacy KE, Karagiannis SN. Evaluation of Antigen-Conjugated Fluorescent Beads to Identify Antigen-Specific B Cells. Front Immunol 2018; 9:493. [PMID: 29628923 PMCID: PMC5876289 DOI: 10.3389/fimmu.2018.00493] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2017] [Accepted: 02/26/2018] [Indexed: 11/30/2022] Open
Abstract
Selection of single antigen-specific B cells to identify their expressed antibodies is of considerable interest for evaluating human immune responses. Here, we present a method to identify single antibody-expressing cells using antigen-conjugated fluorescent beads. To establish this, we selected Folate Receptor alpha (FRα) as a model antigen and a mouse B cell line, expressing both the soluble and the membrane-bound forms of a human/mouse chimeric antibody (MOv18 IgG1) specific for FRα, as test antibody-expressing cells. Beads were conjugated to FRα using streptavidin/avidin-biotin bridges and used to select single cells expressing the membrane-bound form of anti-FRα. Bead-bound cells were single cell-sorted and processed for single cell RNA retrotranscription and PCR to isolate antibody heavy and light chain variable regions. Variable regions were then cloned and expressed as human IgG1/k antibodies. Like the original clone, engineered antibodies from single cells recognized native FRα. To evaluate whether antigen-coated beads could identify specific antibody-expressing cells in mixed immune cell populations, human peripheral blood mononuclear cells (PBMCs) were spiked with test antibody-expressing cells. Antigen-specific cells could comprise up to 75% of cells selected with antigen-conjugated beads when the frequency of the antigen-positive cells was 1:100 or higher. In PBMC pools, beads conjugated to recombinant antigens FRα and HER2 bound antigen-specific anti-FRα MOv18 and anti-HER2 Trastuzumab antibody-expressing cells, respectively. From melanoma patient-derived B cells selected with melanoma cell line-derived protein-coated fluorescent beads, we generated a monoclonal antibody that recognized melanoma antigen-coated beads. This approach may be further developed to facilitate analysis of B cells and their antibody profiles at the single cell level and to help unravel humoral immune repertoires.
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Affiliation(s)
- Isabel Correa
- St. John's Institute of Dermatology, School of Basic & Medical Biosciences, King's College London, Guy's Hospital, London, United Kingdom.,NIHR Biomedical Research Centre at Guy's and St. Thomas's Hospitals and King's College London, King's College London, London, United Kingdom
| | - Kristina M Ilieva
- St. John's Institute of Dermatology, School of Basic & Medical Biosciences, King's College London, Guy's Hospital, London, United Kingdom.,NIHR Biomedical Research Centre at Guy's and St. Thomas's Hospitals and King's College London, King's College London, London, United Kingdom.,Breast Cancer Now Research Unit, School of Cancer & Pharmaceutical Sciences, King's College London, Guy's Cancer Centre, London, United Kingdom
| | - Silvia Crescioli
- St. John's Institute of Dermatology, School of Basic & Medical Biosciences, King's College London, Guy's Hospital, London, United Kingdom.,NIHR Biomedical Research Centre at Guy's and St. Thomas's Hospitals and King's College London, King's College London, London, United Kingdom
| | - Sara Lombardi
- St. John's Institute of Dermatology, School of Basic & Medical Biosciences, King's College London, Guy's Hospital, London, United Kingdom
| | - Mariangela Figini
- Department of Applied Research and Technology Development, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy
| | - Anthony Cheung
- St. John's Institute of Dermatology, School of Basic & Medical Biosciences, King's College London, Guy's Hospital, London, United Kingdom.,Breast Cancer Now Research Unit, School of Cancer & Pharmaceutical Sciences, King's College London, Guy's Cancer Centre, London, United Kingdom
| | - James F Spicer
- School of Cancer & Pharmaceutical Sciences, King's College London, Guy's Hospital, London, United Kingdom
| | - Andrew N J Tutt
- Breast Cancer Now Research Unit, School of Cancer & Pharmaceutical Sciences, King's College London, Guy's Cancer Centre, London, United Kingdom.,Breast Cancer Now Toby Robins Research Centre, Institute of Cancer Research, London, United Kingdom
| | - Frank O Nestle
- St. John's Institute of Dermatology, School of Basic & Medical Biosciences, King's College London, Guy's Hospital, London, United Kingdom.,NIHR Biomedical Research Centre at Guy's and St. Thomas's Hospitals and King's College London, King's College London, London, United Kingdom.,Immunology and Inflammation Therapeutic Research Area, Sanofi US, Cambridge, MA, United States
| | - Panagiotis Karagiannis
- St. John's Institute of Dermatology, School of Basic & Medical Biosciences, King's College London, Guy's Hospital, London, United Kingdom.,NIHR Biomedical Research Centre at Guy's and St. Thomas's Hospitals and King's College London, King's College London, London, United Kingdom.,Department of Oncology, Haematology and Stem Cell Transplantation, University Hospital of Hamburg Eppendorf, Hamburg, Germany
| | - Katie E Lacy
- St. John's Institute of Dermatology, School of Basic & Medical Biosciences, King's College London, Guy's Hospital, London, United Kingdom
| | - Sophia N Karagiannis
- St. John's Institute of Dermatology, School of Basic & Medical Biosciences, King's College London, Guy's Hospital, London, United Kingdom.,NIHR Biomedical Research Centre at Guy's and St. Thomas's Hospitals and King's College London, King's College London, London, United Kingdom.,Breast Cancer Now Research Unit, School of Cancer & Pharmaceutical Sciences, King's College London, Guy's Cancer Centre, London, United Kingdom
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38
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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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39
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Stathopoulos P, Kumar A, Vander Heiden JA, Pascual-Goñi E, Nowak RJ, O’Connor KC. Mechanisms underlying B cell immune dysregulation and autoantibody production in MuSK myasthenia gravis. Ann N Y Acad Sci 2018; 1412:154-165. [PMID: 29381221 PMCID: PMC5793885 DOI: 10.1111/nyas.13535] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2017] [Revised: 09/20/2017] [Accepted: 09/26/2017] [Indexed: 12/16/2022]
Abstract
Pathogenic autoantibodies to muscle-specific tyrosine kinase (MuSK) can be found in patients with myasthenia gravis (MG) who do not have detectable antibodies to the acetylcholine receptor. Although the autoantibody-mediated pathology is well understood, much remains to be learned about the cellular immunology that contributes to autoantibody production. To that end, our laboratory has investigated particular components associated with the cellular immunopathology of MuSK MG. First, we found that B cell tolerance defects contribute to the abnormal development of the naive repertoire, which indicates that dysregulation occurs before the production of autoantibodies. Second, both the naive and antigen-experienced memory B cell repertoire, which we examined through the application of high-throughput adaptive immune receptor repertoire sequencing, include abnormalities not found in healthy controls. This highlights a broad immune dysregulation. Third, using complementary approaches, including production of human monoclonal antibodies, we determined that circulating plasmablasts directly contribute to the production of MuSK-specific autoantibodies in patients experiencing relapse following B cell depletion therapy. These collective findings contribute to defining a mechanistic model that describes MuSK MG immunopathogenesis.
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Affiliation(s)
- Panos Stathopoulos
- Department of Neurology, Yale School of Medicine, New Haven, Connecticut
| | - Aditya Kumar
- Department of Neurology, Yale School of Medicine, New Haven, Connecticut
| | | | - Elba Pascual-Goñi
- Neurology Department, Hospital de la Santa Creu i Sant Pau, Barcelona, Spain
| | - Richard J. Nowak
- Department of Neurology, Yale School of Medicine, New Haven, Connecticut
| | - Kevin C. O’Connor
- Department of Neurology, Yale School of Medicine, New Haven, Connecticut
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40
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De Re V, Magris R, Cannizzaro R. New Insights into the Pathogenesis of Celiac Disease. Front Med (Lausanne) 2017; 4:137. [PMID: 28913337 PMCID: PMC5583152 DOI: 10.3389/fmed.2017.00137] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2017] [Accepted: 07/27/2017] [Indexed: 12/12/2022] Open
Abstract
Celiac disease (CD) is an autoimmune and multisystem gluten-related disorder that causes symptoms involving the gastrointestinal tract and other organs. Pathogenesis of CD is only partially known. It had been established that ingestion of gluten proteins present in wheat and other cereals are necessary for the disease and develops in individuals genetically predisposed carrying the DQ2 or DQ8 human leukocyte antigen haplotypes. In this review, we had pay specific attention on the last discoveries regarding the three cellular components mainly involved in the development and maintenance of CD: T-cells, B-cells, and microbioma. All of them had been showed critical for the interaction between inflammatory immune response and gluten peptides. Although the mechanisms of interaction among overall these components are not yet fully understood, recent proteomics and molecular studies had shed some lights in the pathogenic role of tissue transglutaminase 2 in CD and in the alteration of the intestinal barrier function induced by host microbiota.
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Affiliation(s)
- Valli De Re
- Immunopatologia e Biomarcatori Oncologici/Bio-Proteomics Facility, CRO Aviano National Cancer Institute, Aviano, Italy
| | - Raffaella Magris
- Oncological Gastroenterology, CRO Aviano National Cancer Institute, Aviano, Italy
| | - Renato Cannizzaro
- Oncological Gastroenterology, CRO Aviano National Cancer Institute, Aviano, Italy
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