1
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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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2
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Zaslavsky ME, Craig E, Michuda JK, Sehgal N, Ram-Mohan N, Lee JY, Nguyen KD, Hoh RA, Pham TD, Röltgen K, Lam B, Parsons ES, Macwana SR, DeJager W, Drapeau EM, Roskin KM, Cunningham-Rundles C, Moody MA, Haynes BF, Goldman JD, Heath JR, Nadeau KC, Pinsky BA, Blish CA, Hensley SE, Jensen K, Meyer E, Balboni I, Utz PJ, Merrill JT, Guthridge JM, James JA, Yang S, Tibshirani R, Kundaje A, Boyd SD. Disease diagnostics using machine learning of immune receptors. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2022.04.26.489314. [PMID: 35547855 PMCID: PMC9094102 DOI: 10.1101/2022.04.26.489314] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
Clinical diagnosis typically incorporates physical examination, patient history, and various laboratory tests and imaging studies, but makes limited use of the human system's own record of antigen exposures encoded by receptors on B cells and T cells. We analyzed immune receptor datasets from 593 individuals to develop MAchine Learning for Immunological Diagnosis (Mal-ID) , an interpretive framework to screen for multiple illnesses simultaneously or precisely test for one condition. This approach detects specific infections, autoimmune disorders, vaccine responses, and disease severity differences. Human-interpretable features of the model recapitulate known immune responses to SARS-CoV-2, Influenza, and HIV, highlight antigen-specific receptors, and reveal distinct characteristics of Systemic Lupus Erythematosus and Type-1 Diabetes autoreactivity. This analysis framework has broad potential for scientific and clinical interpretation of human immune responses.
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3
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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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4
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Abstract
Among human leukocyte antigen (HLA)-associated disorders, celiac disease has an immunopathogenesis that is particularly well understood. The condition is characterized by hypersensitivity to cereal gluten proteins, and the disease lesion is localized in the gut. Still, the diagnosis can be made by detection of highly disease-specific autoantibodies to transglutaminase 2 in the blood. We now have mechanistic insights into how the disease-predisposing HLA-DQ molecules, via presentation of posttranslationally modified gluten peptides, are connected to the generation of these autoantibodies. This review presents our current understanding of the immunobiology of this common disorder that is positioned in the border zone between food hypersensitivity and autoimmunity.
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Affiliation(s)
- Rasmus Iversen
- KG Jebsen Coeliac Disease Research Centre, Institute of Clinical Medicine, University of Oslo, Oslo, Norway; .,Department of Immunology, Oslo University Hospital-Rikshospitalet, Oslo, Norway
| | - Ludvig M Sollid
- KG 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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5
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Henning AN, Budeebazar M, Boldbaatar D, Yagaanbuyant D, Duger D, Batsukh K, Zhou H, Baumann R, Allison RD, Alter HJ, Dashdorj N, De Giorgi V. Peripheral B cells from patients with hepatitis C virus-associated lymphoma exhibit clonal expansion and an anergic-like transcriptional profile. iScience 2022; 26:105801. [PMID: 36619973 PMCID: PMC9813790 DOI: 10.1016/j.isci.2022.105801] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2022] [Revised: 10/27/2022] [Accepted: 12/09/2022] [Indexed: 12/23/2022] Open
Abstract
Chronic HCV infection remains a global health concern due to its involvement in hepatic and extrahepatic diseases, including B cell non-Hodgkin lymphoma (BNHL). Clinical and epidemiological evidence support a causal role for HCV in BNHL development, although mechanistic insight is lacking. We performed RNA-sequencing on peripheral B cells from patients with HCV alone, BNHL alone, and HCV-associated BNHL to identify unique and shared transcriptional profiles associated with transformation. In patients with HCV-associated BNHL, we observed the enrichment of an anergic-like gene signature and evidence of clonal expansion that was correlated with the expression of epigenetic regulatory genes. Our data support a role for viral-mediated clonal expansion of anergic-like B cells in HCV-associated BNHL development and suggest epigenetic dysregulation as a potential mechanism driving expansion. We propose epigenetic mechanisms may be involved in both HCV-associated lymphoma and regulation of B cell anergy, representing an attractive target for clinical interventions.
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Affiliation(s)
- Amanda N. Henning
- Department of Transfusion Medicine, Clinical Center, National Institutes of Health, Bethesda, MD 20892, USA,Corresponding author
| | - Myagmarjav Budeebazar
- Department of Gastroenterology, Mongolian National University of Medical Sciences, Ulaanbaatar 14210, Mongolia,Liver Center, Ulaanbaatar 14230, Mongolia
| | | | | | - Davaadorj Duger
- Department of Gastroenterology, Mongolian National University of Medical Sciences, Ulaanbaatar 14210, Mongolia
| | - Khishigjargal Batsukh
- Center of Hematology and Bone Marrow Transplantation, First Central Hospital of Mongolia, Ulaanbaatar 14210, Mongolia
| | - Huizhi Zhou
- Department of Transfusion Medicine, Clinical Center, National Institutes of Health, Bethesda, MD 20892, USA
| | - Ryan Baumann
- Department of Transfusion Medicine, Clinical Center, National Institutes of Health, Bethesda, MD 20892, USA
| | - Robert D. Allison
- Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD 21205, USA
| | - Harvey J. Alter
- Department of Transfusion Medicine, Clinical Center, National Institutes of Health, Bethesda, MD 20892, USA
| | - Naranjargal Dashdorj
- Liver Center, Ulaanbaatar 14230, Mongolia,Onom Foundation, Ulaanbaatar 17011, Mongolia
| | - Valeria De Giorgi
- Department of Transfusion Medicine, Clinical Center, National Institutes of Health, Bethesda, MD 20892, USA,Corresponding author
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6
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Kaunisto H, Salmi T, Lindfors K, Kemppainen E. Antibody Responses to Transglutaminase 3 in Dermatitis Herpetiformis: Lessons from Celiac Disease. Int J Mol Sci 2022; 23:ijms23062910. [PMID: 35328331 PMCID: PMC8953297 DOI: 10.3390/ijms23062910] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2022] [Revised: 02/28/2022] [Accepted: 03/01/2022] [Indexed: 12/13/2022] Open
Abstract
Dermatitis herpetiformis (DH) is the skin manifestation of celiac disease, presenting with a blistering rash typically on the knees, elbows, buttocks and scalp. In both DH and celiac disease, exposure to dietary gluten triggers a cascade of events resulting in the production of autoantibodies against the transglutaminase (TG) enzyme, mainly TG2 but often also TG3. The latter is considered to be the primary autoantigen in DH. The dynamics of the development of the TG2-targeted autoimmune response have been studied in depth in celiac disease, but the immunological process underlying DH pathophysiology is incompletely understood. Part of this process is the occurrence of granular deposits of IgA and TG3 in the perilesional skin. While this serves as the primary diagnostic finding in DH, the role of these immunocomplexes in the pathogenesis is unknown. Intriguingly, even though gluten-intolerance likely develops initially in a similar manner in both DH and celiac disease, after the onset of the disease, its manifestations differ widely.
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Affiliation(s)
- Helka Kaunisto
- Celiac Disease Research Center, Faculty of Medicine and Health Technology, Tampere University, FI-33520 Tampere, Finland; (H.K.); (T.S.); (K.L.)
| | - Teea Salmi
- Celiac Disease Research Center, Faculty of Medicine and Health Technology, Tampere University, FI-33520 Tampere, Finland; (H.K.); (T.S.); (K.L.)
- Department of Dermatology, Tampere University Hospital, FI-33520 Tampere, Finland
| | - Katri Lindfors
- Celiac Disease Research Center, Faculty of Medicine and Health Technology, Tampere University, FI-33520 Tampere, Finland; (H.K.); (T.S.); (K.L.)
| | - Esko Kemppainen
- Celiac Disease Research Center, Faculty of Medicine and Health Technology, Tampere University, FI-33520 Tampere, Finland; (H.K.); (T.S.); (K.L.)
- Correspondence:
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7
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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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8
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Kurki A, Kemppainen E, Laurikka P, Kaukinen K, Lindfors K. The use of peripheral blood mononuclear cells in celiac disease diagnosis and treatment. Expert Rev Gastroenterol Hepatol 2021; 15:305-316. [PMID: 33176106 DOI: 10.1080/17474124.2021.1850262] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Introduction: Celiac disease is characterized by an abnormal immune activation driven by the ingestion of gluten from wheat, barley, and rye. Gluten-specific CD4+ T cells play an important role in disease pathogenesis and are detectable among peripheral blood mononuclear cells (PBMCs). Areas covered: This review summarizes the use of celiac disease patient PBMCs in clinical applications focusing on their exploitation in the development of diagnostic approaches and novel drugs to replace or complement gluten-free diet. Expert opinion: The most used PBMC-based methods applied in celiac disease research include ELISpot and HLA-DQ:gluten tetramer technology. ELISpot has been utilized particularly in research aiming to develop a celiac disease vaccine and in studies addressing the toxicity of different grains in celiac disease. HLA-DQ:gluten tetramer technology on the other hand initially focused on improving current diagnostics but in combination with additional markers it is also a useful outcome measure in clinical trials to monitor the efficacy of drug candidates. In addition, the technology serves well in the more detailed characterization of celiac disease-specific T cells, thereby possibly revealing novel therapeutic targets. Future studies may also reveal clinical applications for PBMC microRNAs and/or dendritic cells or monocytes present among PBMCs.
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Affiliation(s)
- Alma Kurki
- Celiac Disease Research Center, Faculty of Medicine and Health Technology, Tampere University , Tampere, Finland
| | - Esko Kemppainen
- Celiac Disease Research Center, Faculty of Medicine and Health Technology, Tampere University , Tampere, Finland
| | - Pilvi Laurikka
- Celiac Disease Research Center, Faculty of Medicine and Health Technology, Tampere University , Tampere, Finland
| | - Katri Kaukinen
- Celiac Disease Research Center, Faculty of Medicine and Health Technology, Tampere University , Tampere, Finland.,Department of Internal Medicine, Tampere University Hospital , Tampere, Finland
| | - Katri Lindfors
- Celiac Disease Research Center, Faculty of Medicine and Health Technology, Tampere University , Tampere, Finland
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9
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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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10
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Omer A, Shemesh O, Peres A, Polak P, Shepherd AJ, Watson C, Boyd SD, Collins AM, Lees W, Yaari G. VDJbase: an adaptive immune receptor genotype and haplotype database. Nucleic Acids Res 2020; 48:D1051-D1056. [PMID: 31602484 PMCID: PMC6943044 DOI: 10.1093/nar/gkz872] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2019] [Revised: 09/19/2019] [Accepted: 10/01/2019] [Indexed: 12/14/2022] Open
Abstract
VDJbase is a publicly available database that offers easy searching of data describing the complete sets of gene sequences (genotypes and haplotypes) inferred from adaptive immune receptor repertoire sequencing datasets. VDJbase is designed to act as a resource that will allow the scientific community to explore the genetic variability of the immunoglobulin (Ig) and T cell receptor (TR) gene loci. It can also assist in the investigation of Ig- and TR-related genetic predispositions to diseases. Our database includes web-based query and online tools to assist in visualization and analysis of the genotype and haplotype data. It enables users to detect those alleles and genes that are significantly over-represented in a particular population, in terms of genotype, haplotype and gene expression. The database website can be freely accessed at https://www.vdjbase.org/, and no login is required. The data and code use creative common licenses and are freely downloadable from https://bitbucket.org/account/user/yaarilab/projects/GPHP.
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Affiliation(s)
- Aviv Omer
- Bioengineering, Faculty of Engineering, Bar-Ilan University, Ramat Gan 5290002, Israel
| | - Or Shemesh
- Bioengineering, Faculty of Engineering, Bar-Ilan University, Ramat Gan 5290002, Israel
| | - Ayelet Peres
- Bioengineering, Faculty of Engineering, Bar-Ilan University, Ramat Gan 5290002, Israel
| | - Pazit Polak
- Bioengineering, Faculty of Engineering, Bar-Ilan University, Ramat Gan 5290002, Israel
| | - Adrian J Shepherd
- Institute of Structural and Molecular Biology, Birkbeck, University of London, London, UK
| | - Corey T Watson
- University of Louisville School of Medicine, Biochemistry and Molecular Genetics, Louisville, KY 40292, USA
| | - Scott D Boyd
- Department of Pathology, Stanford University, Stanford, CA 94305, USA
| | - Andrew M Collins
- School of Biotechnology and Biomolecular Sciences, University of NSW, Kensington, Sydney, NSW 2052, Australia
| | - William Lees
- Institute of Structural and Molecular Biology, Birkbeck, University of London, London, UK
| | - Gur Yaari
- Bioengineering, Faculty of Engineering, Bar-Ilan University, Ramat Gan 5290002, Israel
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11
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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: 31] [Impact Index Per Article: 6.2] [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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12
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Snir O, Kanduri C, Lundin KEA, Sandve GK, Sollid LM. Transcriptional profiling of human intestinal plasma cells reveals effector functions beyond antibody production. United European Gastroenterol J 2019; 7:1399-1407. [PMID: 31839965 DOI: 10.1177/2050640619862461] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/05/2019] [Revised: 06/05/2019] [Indexed: 01/22/2023] Open
Abstract
Background Plasma cells (PCs) are terminally differentiated B-lymphocytes producing antibodies. In coeliac disease (CeD) there is increased density of PCs in the small-intestinal lesion. Many of these PCs produce disease-specific autoantibodies targeting transglutaminase 2 (TG2). Objective The plasmacytosis of CeD motivated us to study the transcriptional programme of PCs from coeliac gut lesions. Methods RNA-seq was performed on the PCs of CeD patients and disease controls, being specific or non-specific for TG2. Results Being antibody-producing cells, 67% of the PCs' transcript was aligned to immunoglobulin genes. Strikingly, genes encoding ligands and receptors of chemokines and cytokines were abundant. Higher transcript levels of genes associated with cell activation and immune responses were observed in PCs of CeD patients compared to controls. TG2-specific compared to non-TG2 specific PCs expressed increased levels of CXCR3, CXCL10 and interleukin-15; factors that have been implicated in the pathogenesis of CeD yet with production attributed to other cells than PCs. The presence of transcripts of HLA class II and T-cell co-stimulatory molecules suggests that PCs may serve as antigen-presenting cells for CD4 + helper T cells. Conclusions Our findings shed new light on the biology of intestinal PCs, implicating functions that go beyond the production of immunoglobulins.
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Affiliation(s)
- Omri Snir
- Department of Immunology, University of Oslo and Oslo University Hospital-Rikshospitalet, Oslo, Norway.,KG Jebsen Coeliac Disease Research Centre, University of Oslo, Oslo, Norway
| | - Chakravarthi Kanduri
- KG Jebsen Coeliac Disease Research Centre, University of Oslo, Oslo, Norway.,Department of Informatics, University of Oslo, 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
| | - Geir Kjetil Sandve
- KG Jebsen Coeliac Disease Research Centre, University of Oslo, Oslo, Norway.,Department of Informatics, University of Oslo, Oslo, Norway
| | - Ludvig M Sollid
- Department of Immunology, University of Oslo and Oslo University Hospital-Rikshospitalet, Oslo, Norway.,KG Jebsen Coeliac Disease Research Centre, University of Oslo, Oslo, Norway
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13
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Gidoni M, Snir O, Peres A, Polak P, Lindeman I, Mikocziova I, Sarna VK, Lundin KEA, Clouser C, Vigneault F, Collins AM, Sollid LM, Yaari G. Mosaic deletion patterns of the human antibody heavy chain gene locus shown by Bayesian haplotyping. Nat Commun 2019; 10:628. [PMID: 30733445 PMCID: PMC6367474 DOI: 10.1038/s41467-019-08489-3] [Citation(s) in RCA: 56] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2018] [Accepted: 01/10/2019] [Indexed: 12/11/2022] Open
Abstract
Analysis of antibody repertoires by high-throughput sequencing is of major importance in understanding adaptive immune responses. Our knowledge of variations in the genomic loci encoding immunoglobulin genes is incomplete, resulting in conflicting VDJ gene assignments and biased genotype and haplotype inference. Haplotypes can be inferred using IGHJ6 heterozygosity, observed in one third of the people. Here, we propose a robust novel method for determining VDJ haplotypes by adapting a Bayesian framework. Our method extends haplotype inference to IGHD- and IGHV-based analysis, enabling inference of deletions and copy number variations in the entire population. To test this method, we generated a multi-individual data set of naive B-cell repertoires, and found allele usage bias, as well as a mosaic, tiled pattern of deleted IGHD and IGHV genes. The inferred haplotypes may have clinical implications for genetic disease predispositions. Our findings expand the knowledge that can be extracted from antibody repertoire sequencing data.
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Affiliation(s)
- Moriah Gidoni
- Faculty of Engineering, Bar Ilan University, 5290002, Ramat Gan, Israel
| | - Omri Snir
- KG 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, 5290002, Ramat Gan, Israel
| | - Pazit Polak
- Faculty of Engineering, Bar Ilan University, 5290002, Ramat Gan, Israel
| | - Ida Lindeman
- KG Jebsen Centre for Coeliac Disease Research and Department of Immunology, University of Oslo and Oslo University Hospital, 0372, Oslo, Norway
| | - Ivana Mikocziova
- KG Jebsen Centre for Coeliac Disease Research and Department of Immunology, University of Oslo and Oslo University Hospital, 0372, Oslo, Norway
| | - Vikas Kumar Sarna
- KG Jebsen Centre for Coeliac Disease Research and Department of Immunology, University of Oslo and Oslo University Hospital, 0372, Oslo, Norway
| | - Knut E A Lundin
- KG Jebsen Centre for Coeliac Disease Research and Department of Immunology, University of Oslo and Oslo University Hospital, 0372, Oslo, Norway
| | | | | | - Andrew M Collins
- School of Biotechnology and Biomolecular Sciences, University of NSW, Kensington, Sydney, NSW, 2052, Australia
| | - Ludvig M Sollid
- KG 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, 5290002, Ramat Gan, Israel.
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14
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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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15
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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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16
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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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17
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D'Angelo S, Ferrara F, Naranjo L, Erasmus MF, Hraber P, Bradbury ARM. Many Routes to an Antibody Heavy-Chain CDR3: Necessary, Yet Insufficient, for Specific Binding. Front Immunol 2018; 9:395. [PMID: 29568296 PMCID: PMC5852061 DOI: 10.3389/fimmu.2018.00395] [Citation(s) in RCA: 54] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2017] [Accepted: 02/13/2018] [Indexed: 12/11/2022] Open
Abstract
Because of its great potential for diversity, the immunoglobulin heavy-chain complementarity-determining region 3 (HCDR3) is taken as an antibody molecule’s most important component in conferring binding activity and specificity. For this reason, HCDR3s have been used as unique identifiers to investigate adaptive immune responses in vivo and to characterize in vitro selection outputs where display systems were employed. Here, we show that many different HCDR3s can be identified within a target-specific antibody population after in vitro selection. For each identified HCDR3, a number of different antibodies bearing differences elsewhere can be found. In such selected populations, all antibodies with the same HCDR3 recognize the target, albeit at different affinities. In contrast, within unselected populations, the majority of antibodies with the same HCDR3 sequence do not bind the target. In one HCDR3 examined in depth, all target-specific antibodies were derived from the same VDJ rearrangement, while non-binding antibodies with the same HCDR3 were derived from many different V and D gene rearrangements. Careful examination of previously published in vivo datasets reveals that HCDR3s shared between, and within, different individuals can also originate from rearrangements of different V and D genes, with up to 26 different rearrangements yielding the same identical HCDR3 sequence. On the basis of these observations, we conclude that the same HCDR3 can be generated by many different rearrangements, but that specific target binding is an outcome of unique rearrangements and VL pairing: the HCDR3 is necessary, albeit insufficient, for specific antibody binding.
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Affiliation(s)
| | | | | | | | - Peter Hraber
- Los Alamos National Laboratory, Los Alamos, NM, United States
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18
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Tan YG, Wang XF, Zhang M, Yan HP, Lin DD, Wang YQ, Zhang HP, Yu XQ, Liao HY, Wang YP, Lv FD, Gao ZH. Clonal characteristics of paired infiltrating and circulating B lymphocyte repertoire in patients with primary biliary cholangitis. Liver Int 2018; 38:542-552. [PMID: 28834158 DOI: 10.1111/liv.13554] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/10/2016] [Accepted: 08/11/2017] [Indexed: 12/13/2022]
Abstract
BACKGROUND PBC is a prototypical autoimmune liver disease characterized by portal lymphoplasmacyte infiltration. ALD is a prototypical environment-driven disease, featured by mild lymphocyte infiltration. We hypothesize that B cells are more involved in the pathogenesis of PBC. By analysing the infiltrating B cell repertoire, we aimed to unveil greater oligoclonal expansion and active clonal exchange between liver and periphery in PBC than in ALD patients. METHODS Using NGS of Ig H chain genes, we analysed the liver-infiltrating and paired peripheral B lymphocyte repertoire from nine PBC and four ALD patients. RESULTS In the liver of PBC and ALD patients, (i) roughly 10% of the B lymphocytes were clonally related and highly expressed, and there were also lineages that underwent extensive clonal expansion; (ii) there was different use of IGHV/IGHJ segments between PBC and ALD, suggesting distinct Ag exposure backgrounds, but this did not lead to a significant difference in their clonal expansion level. Analysis of data sets from paired samples further revealed, (iii) direct clonal exchange and evolutionally related B cell clones between the infiltrating and peripheral repertoire; (iv) the seeding of the infiltrating clones to periphery, and peripheral ones to the liver, for further extensive evolution. CONCLUSIONS The oligoclonally expanded nature of the infiltrating B cell repertoire implies B cell immunity is involved in the pathogenesis of both diseases. The observed clonal exchange might provide an approach to identify and monitor the infiltrating B cells through the periphery.
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Affiliation(s)
- Yan-Guo Tan
- Department of Clinical Laboratory, FuXing Hospital, Capital Medical University, Beijing, China.,Beijing You An Hospital, Capital Medical University, Beijing, China
| | - Xiao-Feng Wang
- Tianjin Translational Genomics Center, BGI-Tianjin, Tianjin, China.,BGI-Shenzhen, Shenzhen, China
| | - Ming Zhang
- Tianjin Translational Genomics Center, BGI-Tianjin, Tianjin, China.,Tianjin Marvelbio Technology Co. Ltd, Tianjin, China
| | - Hui-Ping Yan
- Beijing You An Hospital, Capital Medical University, Beijing, China
| | - Dong-Dong Lin
- Beijing You An Hospital, Capital Medical University, Beijing, China
| | | | - Hai-Ping Zhang
- Beijing You An Hospital, Capital Medical University, Beijing, China
| | - Xin-Qiu Yu
- Beijing You An Hospital, Capital Medical University, Beijing, China
| | - Hui-Yu Liao
- Beijing You An Hospital, Capital Medical University, Beijing, China
| | - Yi-Peng Wang
- Prenatal Diagnosis Center, Beijing Obstetrics and Gynecology Hospital, Beijing, China
| | - Fu-Dong Lv
- Beijing You An Hospital, Capital Medical University, Beijing, China
| | - Zu-Hua Gao
- Beijing You An Hospital, Capital Medical University, Beijing, China.,Department of Pathology, McGill University, Montreal, QC, Canada
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19
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Miho E, Yermanos A, Weber CR, Berger CT, Reddy ST, Greiff V. Computational Strategies for Dissecting the High-Dimensional Complexity of Adaptive Immune Repertoires. Front Immunol 2018; 9:224. [PMID: 29515569 PMCID: PMC5826328 DOI: 10.3389/fimmu.2018.00224] [Citation(s) in RCA: 116] [Impact Index Per Article: 19.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2017] [Accepted: 01/26/2018] [Indexed: 12/21/2022] Open
Abstract
The adaptive immune system recognizes antigens via an immense array of antigen-binding antibodies and T-cell receptors, the immune repertoire. The interrogation of immune repertoires is of high relevance for understanding the adaptive immune response in disease and infection (e.g., autoimmunity, cancer, HIV). Adaptive immune receptor repertoire sequencing (AIRR-seq) has driven the quantitative and molecular-level profiling of immune repertoires, thereby revealing the high-dimensional complexity of the immune receptor sequence landscape. Several methods for the computational and statistical analysis of large-scale AIRR-seq data have been developed to resolve immune repertoire complexity and to understand the dynamics of adaptive immunity. Here, we review the current research on (i) diversity, (ii) clustering and network, (iii) phylogenetic, and (iv) machine learning methods applied to dissect, quantify, and compare the architecture, evolution, and specificity of immune repertoires. We summarize outstanding questions in computational immunology and propose future directions for systems immunology toward coupling AIRR-seq with the computational discovery of immunotherapeutics, vaccines, and immunodiagnostics.
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Affiliation(s)
- Enkelejda Miho
- Department for Biosystems Science and Engineering, ETH Zürich, Basel, Switzerland
- aiNET GmbH, ETH Zürich, Basel, Switzerland
| | - Alexander Yermanos
- Department for Biosystems Science and Engineering, ETH Zürich, Basel, Switzerland
| | - Cédric R. Weber
- Department for Biosystems Science and Engineering, ETH Zürich, Basel, Switzerland
| | - Christoph T. Berger
- Department of Biomedicine, University Hospital Basel, Basel, Switzerland
- Department of Internal Medicine, Clinical Immunology, University Hospital Basel, Basel, Switzerland
| | - Sai T. Reddy
- Department for Biosystems Science and Engineering, ETH Zürich, Basel, Switzerland
| | - Victor Greiff
- Department for Biosystems Science and Engineering, ETH Zürich, Basel, Switzerland
- Department of Immunology, University of Oslo, Oslo, Norway
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20
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Identification and phenotyping of circulating autoreactive proteinase 3-specific B cells in patients with PR3-ANCA associated vasculitis and healthy controls. J Autoimmun 2017; 84:122-131. [DOI: 10.1016/j.jaut.2017.08.006] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2017] [Revised: 08/17/2017] [Accepted: 08/21/2017] [Indexed: 11/23/2022]
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21
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Snir O, Chen X, Gidoni M, du Pré MF, Zhao Y, Steinsbø Ø, Lundin KE, Yaari G, Sollid LM. Stereotyped antibody responses target posttranslationally modified gluten in celiac disease. JCI Insight 2017; 2:93961. [PMID: 28878138 DOI: 10.1172/jci.insight.93961] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2017] [Accepted: 07/06/2017] [Indexed: 11/17/2022] Open
Abstract
The role of B cells and posttranslational modifications in pathogenesis of organ-specific immune diseases is increasingly envisioned but remains poorly understood, particularly in human disorders. In celiac disease, transglutaminase 2-modified (TG2-modified; deamidated) gluten peptides drive disease-specific T cell and B cell responses, and antibodies to deamidated gluten peptides are excellent diagnostic markers. Here, we substantiate by high-throughput sequencing of IGHV genes that antibodies to a disease-specific, deamidated, and immunodominant B cell epitope of gluten (PLQPEQPFP) have biased and stereotyped usage of IGHV3-23 and IGHV3-15 gene segments with modest somatic mutations. X-ray crystal structures of 2 prototype IGHV3-15/IGKV4-1 and IGHV3-23/IGLV4-69 antibodies reveal peptide interaction mainly via germline-encoded residues. In-depth mutational analysis showed restricted selection and substitution patterns at positions involved in antigen binding. While the IGHV3-15/IGKV4-1 antibody interacts with Glu5 and Gln6, the IGHV3-23/IGLV4-69 antibody interacts with Gln3, Pro4, Pro7, and Phe8 - residues involved in substrate recognition by TG2. Hence, both antibodies, despite different interaction with the epitope, recognize signatures of TG2 processing that facilitates B cell presentation of deamidated gluten peptides to T cells, thereby providing a molecular framework for the generation of these clinically important antibodies. The study provides essential insight into the pathogenic mechanism of celiac disease.
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Affiliation(s)
- Omri Snir
- Centre for Immune Regulation and Department of Immunology, University of Oslo and Oslo University Hospital-Rikshospitalet, Oslo, Norway
| | - Xi Chen
- Centre for Immune Regulation and Department of Immunology, University of Oslo and Oslo University Hospital-Rikshospitalet, Oslo, Norway
| | - Moriah Gidoni
- Bioengineering Faculty of Engineering, Bar-Ilan University, Ramt Gan, Israel
| | - M Fleur du Pré
- Centre for Immune Regulation and Department of Immunology, University of Oslo and Oslo University Hospital-Rikshospitalet, Oslo, Norway
| | - Yuguang Zhao
- Division of Structural Biology, University of Oxford, Wellcome Trust Centre for Human Genetics, Headington, Oxford, United Kingdom
| | - Øyvind Steinsbø
- Centre for Immune Regulation and Department of Immunology, University of Oslo and Oslo University Hospital-Rikshospitalet, Oslo, Norway
| | - Knut Ea Lundin
- Department of Gastroenterology, Oslo University Hospital-Rikshospitalet, Oslo, Norway.,KG Jebsen Coeliac Disease Research Centre, University of Oslo, Oslo, Norway
| | - Gur Yaari
- Bioengineering Faculty of Engineering, Bar-Ilan University, Ramt Gan, Israel
| | - 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
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22
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Roy B, Neumann RS, Snir O, Iversen R, Sandve GK, Lundin KEA, Sollid LM. High-Throughput Single-Cell Analysis of B Cell Receptor Usage among Autoantigen-Specific Plasma Cells in Celiac Disease. THE JOURNAL OF IMMUNOLOGY 2017; 199:782-791. [PMID: 28600290 DOI: 10.4049/jimmunol.1700169] [Citation(s) in RCA: 45] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/01/2017] [Accepted: 05/11/2017] [Indexed: 11/19/2022]
Abstract
Characterization of Ag-specific BCR repertoires is essential for understanding disease mechanisms involving humoral immunity. This is optimally done by interrogation of paired H chain V region (VH) and L chain V region (VL) sequences of individual and Ag-specific B cells. By applying single-cell high-throughput sequencing on gut lesion plasma cells (PCs), we have analyzed the transglutaminase 2 (TG2)-specific VH:VL autoantibody repertoire of celiac disease (CD) patients. Autoantibodies against TG2 are a hallmark of CD, and anti-TG2 IgA-producing gut PCs accumulate in patients upon gluten ingestion. Altogether, we analyzed paired VH and VL sequences of 1482 TG2-specific and 1421 non-TG2-specific gut PCs from 10 CD patients. Among TG2-specific PCs, we observed a striking bias in IGHV and IGKV/IGLV gene usage, as well as pairing preferences with a particular presence of the IGHV5-51:IGKV1-5 pair. Selective and biased VH:VL pairing was particularly evident among expanded clones. In general, TG2-specific PCs had lower numbers of mutations both in VH and VL genes than in non-TG2-specific PCs. TG2-specific PCs using IGHV5-51 had particularly few mutations. Importantly, VL segments paired with IGHV5-51 displayed proportionally low mutation numbers, suggesting that the low mutation rate among IGHV5-51 PCs is dictated by the BCR specificity. Finally, we observed selective amino acid changes in VH and VL and striking CDR3 length and J segment selection among TG2-specific IGHV5-51:IGKV1-5 pairs. Hence this study reveals features of a disease- and Ag-specific autoantibody repertoire with preferred VH:VL usage and pairings, limited mutations, clonal dominance, and selection of particular CDR3 sequences.
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Affiliation(s)
- Bishnudeo Roy
- Department of Immunology, Centre for Immune Regulation, University of Oslo, Oslo University Hospital, 0372 Oslo, Norway
| | - Ralf S Neumann
- Department of Immunology, KG Jebsen Coeliac Disease Research Centre, University of Oslo, Oslo University Hospital, 0372 Oslo, Norway
| | - Omri Snir
- Department of Immunology, Centre for Immune Regulation, University of Oslo, Oslo University Hospital, 0372 Oslo, Norway
| | - Rasmus Iversen
- Department of Immunology, Centre for Immune Regulation, University of Oslo, Oslo University Hospital, 0372 Oslo, Norway
| | - Geir Kjetil Sandve
- Department of Informatics, KG Jebsen Coeliac Disease Research Centre, University of Oslo, 0373 Oslo, Norway; and
| | - Knut E A Lundin
- Department of Gastroenterology, KG Jebsen Coeliac Disease Research Centre, Oslo University Hospital-Rikshospitalet, 0372 Oslo, Norway
| | - Ludvig M Sollid
- Department of Immunology, Centre for Immune Regulation, University of Oslo, Oslo University Hospital, 0372 Oslo, Norway; .,Department of Immunology, KG Jebsen Coeliac Disease Research Centre, University of Oslo, Oslo University Hospital, 0372 Oslo, Norway
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23
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Escudero-Hernández C, Peña AS, Bernardo D. Immunogenetic Pathogenesis of Celiac Disease and Non-celiac Gluten Sensitivity. Curr Gastroenterol Rep 2017; 18:36. [PMID: 27216895 DOI: 10.1007/s11894-016-0512-2] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Celiac disease is the most common oral intolerance in Western countries. It results from an immune response towards gluten proteins from certain cereals in genetically predisposed individuals (HLA-DQ2 and/or HLA-DQ8). Its pathogenesis involves the adaptive (HLA molecules, transglutaminase 2, dendritic cells, and CD4(+) T-cells) and the innate immunity with an IL-15-mediated response elicited in the intraepithelial compartment. At present, the only treatment is a permanent strict gluten-free diet (GFD). Multidisciplinary studies have provided a deeper insight of the genetic and immunological factors and their interaction with the microbiota in the pathogenesis of the disease. Similarly, a better understanding of the composition of the toxic gluten peptides has improved the ways to detect them in food and drinks and how to monitor GFD compliance via non-invasive approaches. This review, therefore, addresses the major findings obtained in the last few years including the re-discovery of non-celiac gluten sensitivity.
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Affiliation(s)
- Celia Escudero-Hernández
- Mucosal Immunology Laboratory, IBGM, Facultad de Medicina, Dpto. Pediatría e Inmunología, University of Valladolid-Consejo Superior de Investigaciones Científicas, (4th floor) Av. Ramón y Cajal 7, 47005, Valladolid, Spain
| | - Amado Salvador Peña
- VU Medical Center Amsterdam, Laboratory of Immunogenetics, Department of Medical Microbiology and Infection Control, VU University Medical Center, De Boelelaan 1108 Room 10E65, 1081 HZ, Amsterdam, The Netherlands
| | - David Bernardo
- Gastroenterology Unit, Hospital Universitario de La Princesa, Instituto de Investigación Sanitaria Princesa (IIS-IP), Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBEREHD), Madrid, 28006, Spain.
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24
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Landsverk OJB, Snir O, Casado RB, Richter L, Mold JE, Réu P, Horneland R, Paulsen V, Yaqub S, Aandahl EM, Øyen OM, Thorarensen HS, Salehpour M, Possnert G, Frisén J, Sollid LM, Baekkevold ES, Jahnsen FL. Antibody-secreting plasma cells persist for decades in human intestine. J Exp Med 2017; 214:309-317. [PMID: 28104812 PMCID: PMC5294861 DOI: 10.1084/jem.20161590] [Citation(s) in RCA: 146] [Impact Index Per Article: 20.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2016] [Revised: 11/28/2016] [Accepted: 12/13/2016] [Indexed: 01/19/2023] Open
Abstract
Plasma cells (PCs) produce antibodies that mediate immunity after infection or vaccination. In contrast to PCs in the bone marrow, PCs in the gut have been considered short lived. In this study, we studied PC dynamics in the human small intestine by cell-turnover analysis in organ transplants and by retrospective cell birth dating measuring carbon-14 in genomic DNA. We identified three distinct PC subsets: a CD19+ PC subset was dynamically exchanged, whereas of two CD19- PC subsets, CD45+ PCs exhibited little and CD45- PCs no replacement and had a median age of 11 and 22 yr, respectively. Accumulation of CD45- PCs during ageing and the presence of rotavirus-specific clones entirely within the CD19- PC subsets support selection and maintenance of protective PCs for life in human intestine.
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Affiliation(s)
- Ole J B Landsverk
- Department of Pathology, Centre for Immune Regulation, Oslo University Hospital-Rikshospitalet and The University of Oslo, 0372 Oslo, Norway
| | - Omri Snir
- Department of Immunology, Centre for Immune Regulation, Oslo University Hospital-Rikshospitalet and The University of Oslo, 0372 Oslo, Norway
| | - Raquel Bartolomé Casado
- Department of Pathology, Centre for Immune Regulation, Oslo University Hospital-Rikshospitalet and The University of Oslo, 0372 Oslo, Norway
| | - Lisa Richter
- Department of Pathology, Centre for Immune Regulation, Oslo University Hospital-Rikshospitalet and The University of Oslo, 0372 Oslo, Norway
| | - Jeff E Mold
- Department of Cell and Molecular Biology, Karolinska Institute, 171 77 Stockholm, Sweden
| | - Pedro Réu
- Department of Cell and Molecular Biology, Karolinska Institute, 171 77 Stockholm, Sweden.,Center for Neuroscience and Cell Biology, University of Coimbra, 3000-213 Coimbra, Portugal
| | - Rune Horneland
- Department of Transplantation Medicine, Oslo University Hospital-Rikshospitalet, 0372 Oslo, Norway
| | - Vemund Paulsen
- Department of Transplantation Medicine, Oslo University Hospital-Rikshospitalet, 0372 Oslo, Norway
| | - Sheraz Yaqub
- Department of Gastrointestinal Surgery, Oslo University Hospital-Rikshospitalet, 0372 Oslo, Norway
| | - Einar Martin Aandahl
- Centre for Molecular Medicine Norway, Nordic European Molecular Biology Laboratory Partnership, Oslo University Hospital-Rikshospitalet and The University of Oslo, 0372 Oslo, Norway.,Department of Transplantation Medicine, Oslo University Hospital-Rikshospitalet, 0372 Oslo, Norway
| | - Ole M Øyen
- Department of Transplantation Medicine, Oslo University Hospital-Rikshospitalet, 0372 Oslo, Norway
| | | | - Mehran Salehpour
- Department of Physics and Astronomy, Ion Physics, Uppsala University, 752 36 Uppsala, Sweden
| | - Göran Possnert
- Department of Physics and Astronomy, Ion Physics, Uppsala University, 752 36 Uppsala, Sweden
| | - Jonas Frisén
- Department of Cell and Molecular Biology, Karolinska Institute, 171 77 Stockholm, Sweden
| | - Ludvig M Sollid
- Department of Immunology, Centre for Immune Regulation and KG Jebsen Coeliac Disease Research Centre, Oslo University Hospital-Rikshospitalet and The University of Oslo, 0372 Oslo, Norway
| | - Espen S Baekkevold
- Department of Pathology, Centre for Immune Regulation, Oslo University Hospital-Rikshospitalet and The University of Oslo, 0372 Oslo, Norway
| | - Frode L Jahnsen
- Department of Pathology, Centre for Immune Regulation, Oslo University Hospital-Rikshospitalet and The University of Oslo, 0372 Oslo, Norway
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25
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Hardy MY, Tye-Din JA. Coeliac disease: a unique model for investigating broken tolerance in autoimmunity. Clin Transl Immunology 2016; 5:e112. [PMID: 27990287 PMCID: PMC5133362 DOI: 10.1038/cti.2016.58] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2016] [Revised: 09/12/2016] [Accepted: 09/12/2016] [Indexed: 01/06/2023] Open
Abstract
Coeliac disease, a prevalent immune-mediated enteropathy driven by dietary gluten, provides an exceptional human model to dissect the genetic, environmental and immunologic factors operating in autoimmunity. Despite the causative antigen being an exogenous food protein, coeliac disease has many features in common with autoimmune disease including a strong HLA class II association and the presence of pathogenic CD4+ T cells and autoantibodies. CD8+ intraepithelial lymphocytes specifically target and destroy intestinal epithelium in response to stress signals and not a specific antigen. A unique feature of coeliac disease is the ability to remove gluten to induce disease remission and reintroduce it to trigger a memory response. This provides an unparalleled opportunity to study disease-relevant CD4+ T cells that have been expanded in vivo. As a result, the causative peptides have been characterised at a level unprecedented for any autoimmune disease. Despite the complexity of the gluten proteome, resistance to gastrointestinal proteolysis and susceptibility to post-translational modification by transglutaminase help shape a restricted repertoire of immunogenic gluten peptides that have high affinity for disease-associated HLA. The critical steps in coeliac disease pathogenesis have been broadly elucidated and provide the basis for experimental therapies in pre-clinical or clinical development. However, little is known about how and why tolerance to gluten sometimes breaks or fails to develop. Understanding the interactions between genes, the environment, gluten immunity and the microbiome may provide novel approaches for the prevention and treatment of disease.
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Affiliation(s)
- Melinda Y Hardy
- Immunology Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia; Department of Medical Biology, The University of Melbourne, Parkville, Victoria, Australia
| | - Jason A Tye-Din
- Immunology Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia; Department of Medical Biology, The University of Melbourne, Parkville, Victoria, Australia; Centre of Food and Allergy Research, Murdoch Children's Research Institute, Parkville, Victoria, Australia; Department of Gastroenterology, The Royal Melbourne Hospital, Parkville, Victoria, Australia
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26
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Hnida K, Stamnaes J, du Pré MF, Mysling S, Jørgensen TJD, Sollid LM, Iversen R. Epitope-dependent Functional Effects of Celiac Disease Autoantibodies on Transglutaminase 2. J Biol Chem 2016; 291:25542-25552. [PMID: 27784785 DOI: 10.1074/jbc.m116.738161] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2016] [Revised: 10/06/2016] [Indexed: 02/03/2023] Open
Abstract
Transglutaminase 2 (TG2) is a Ca2+-dependent cross-linking enzyme involved in the pathogenesis of CD. We have previously characterized a panel of anti-TG2 mAbs generated from gut plasma cells of celiac patients and identified four epitopes (epitopes 1-4) located in the N-terminal part of TG2. Binding of the mAbs induced allosteric changes in TG2. Thus, we aimed to determine whether these mAbs could influence enzymatic activity through modulation of TG2 susceptibility to oxidative inactivation and Ca2+ affinity. All tested epitope 1 mAbs, as well as 679-14-D04, which recognizes a previously uncharacterized epitope, prevented oxidative inactivation and increased Ca2+ sensitivity of TG2. We have identified crucial residues for binding of 679-14-D04 located within a Ca2+ binding site. Epitope 1 mAbs and 679-14-D04, although recognizing separate epitopes, behaved similarly when assessing their effect on TG2 conformation, suggesting that the shared effects on TG2 function can be explained by induction of the same conformational changes. None of the mAbs targeting other epitopes showed these effects, but epitope 2 mAbs reduced the rate of TG2-catalyzed reactions. Collectively, these effects could be relevant to the pathogenesis of CD. In A20 B cells transduced with TG2-specific B-cell receptor, epitope 2-expressing cells had poorer uptake of TG2-gluten complexes and were less efficient in gluten epitope presentation to T cells than cells expressing an epitope 1 receptor. Thus, the ability of epitope 1-targeting B cells to keep TG2 active and protected from oxidation might explain why generation of epitope 1-targeting plasma cells seems to be favored in celiac patients.
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Affiliation(s)
- Kathrin Hnida
- From the Centre for Immune Regulation and Department of Immunology, University of Oslo and Oslo University Hospital, N-0372 Oslo, Norway and
| | - Jorunn Stamnaes
- From the Centre for Immune Regulation and Department of Immunology, University of Oslo and Oslo University Hospital, N-0372 Oslo, Norway and
| | - M Fleur du Pré
- From the Centre for Immune Regulation and Department of Immunology, University of Oslo and Oslo University Hospital, N-0372 Oslo, Norway and
| | - Simon Mysling
- the Department of Biochemistry and Molecular Biology, University of Southern Denmark, DK-5230 Odense M, Denmark
| | - Thomas J D Jørgensen
- the Department of Biochemistry and Molecular Biology, University of Southern Denmark, DK-5230 Odense M, Denmark
| | - Ludvig M Sollid
- From the Centre for Immune Regulation and Department of Immunology, University of Oslo and Oslo University Hospital, N-0372 Oslo, Norway and
| | - Rasmus Iversen
- From the Centre for Immune Regulation and Department of Immunology, University of Oslo and Oslo University Hospital, N-0372 Oslo, Norway and
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27
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Spencer J, Sollid LM. The human intestinal B-cell response. Mucosal Immunol 2016; 9:1113-24. [PMID: 27461177 DOI: 10.1038/mi.2016.59] [Citation(s) in RCA: 70] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2016] [Accepted: 06/10/2016] [Indexed: 02/04/2023]
Abstract
The intestinal immune system is chronically challenged by a huge plethora of antigens derived from the lumen. B-cell responses in organized gut-associated lymphoid tissues and regional lymph nodes that are driven chronically by gut antigens generate the largest population of antibody-producing cells in the body: the gut lamina propria plasma cells. Although animal studies have provided insights into mechanisms that underpin this dynamic process, some very fundamental differences in this system appear to exist between species. Importantly, this prevents extrapolation from mice to humans to inform translational research questions. Therefore, in this review we will describe the structures and mechanisms involved in the propagation, dissemination, and regulation of this immense plasma cell population in man. Uniquely, we will seek our evidence exclusively from studies of human cells and tissues.
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Affiliation(s)
- J Spencer
- Peter Gorer Department of Immunobiology, King's College London, London, UK
| | - L M Sollid
- Centre for Immune Regulation and Department of Immunology, University of Oslo and Oslo University Hospital-Rikshospitalet, Oslo, Norway
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28
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Tan YG, Wang YQ, Zhang M, Han YX, Huang CY, Zhang HP, Li ZM, Wu XL, Wang XF, Dong Y, Zhu HM, Zhu SD, Li HM, Li N, Yan HP, Gao ZH. Clonal Characteristics of Circulating B Lymphocyte Repertoire in Primary Biliary Cholangitis. THE JOURNAL OF IMMUNOLOGY 2016; 197:1609-20. [DOI: 10.4049/jimmunol.1600096] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/21/2016] [Accepted: 06/17/2016] [Indexed: 12/27/2022]
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29
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Yaari G, Kleinstein SH. Practical guidelines for B-cell receptor repertoire sequencing analysis. Genome Med 2015; 7:121. [PMID: 26589402 PMCID: PMC4654805 DOI: 10.1186/s13073-015-0243-2] [Citation(s) in RCA: 152] [Impact Index Per Article: 16.9] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
High-throughput sequencing of B-cell immunoglobulin repertoires is increasingly being applied to gain insights into the adaptive immune response in healthy individuals and in those with a wide range of diseases. Recent applications include the study of autoimmunity, infection, allergy, cancer and aging. As sequencing technologies continue to improve, these repertoire sequencing experiments are producing ever larger datasets, with tens- to hundreds-of-millions of sequences. These data require specialized bioinformatics pipelines to be analyzed effectively. Numerous methods and tools have been developed to handle different steps of the analysis, and integrated software suites have recently been made available. However, the field has yet to converge on a standard pipeline for data processing and analysis. Common file formats for data sharing are also lacking. Here we provide a set of practical guidelines for B-cell receptor repertoire sequencing analysis, starting from raw sequencing reads and proceeding through pre-processing, determination of population structure, and analysis of repertoire properties. These include methods for unique molecular identifiers and sequencing error correction, V(D)J assignment and detection of novel alleles, clonal assignment, lineage tree construction, somatic hypermutation modeling, selection analysis, and analysis of stereotyped or convergent responses. The guidelines presented here highlight the major steps involved in the analysis of B-cell repertoire sequencing data, along with recommendations on how to avoid common pitfalls.
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Affiliation(s)
- Gur Yaari
- Bioengineering Program, Faculty of Engineering, Bar-Ilan University, 5290002, Ramat Gan, Israel.
| | - Steven H Kleinstein
- Interdepartmental Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT, 06511, USA. .,Departments of Pathology and Immunobiology, Yale University School of Medicine, New Haven, CT, 06520, USA.
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30
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Celiac disease: Autoimmunity in response to food antigen. Semin Immunol 2015; 27:343-52. [PMID: 26603490 DOI: 10.1016/j.smim.2015.11.001] [Citation(s) in RCA: 92] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/16/2015] [Revised: 11/02/2015] [Accepted: 11/02/2015] [Indexed: 02/06/2023]
Abstract
Celiac disease (CD) is an increasingly common disease of the small intestine that occurs in genetically susceptible subjects by ingestion of cereal gluten proteins. Gluten is highly abundant in the modern diet and well tolerated by most individuals. In CD, however, an erroneous but highly specific, adaptive immune response is mounted toward certain parts of the gluten proteome. The resulting intestinal destruction is reversible and resolved upon removal of gluten from the diet. Post-translational modification (deamidation) of gluten peptides by transglutaminase 2 (TG2) is essential for the peptides to act as HLA-DQ-restricted T-cell antigens. Characteristically, deamidated gluten and the self-protein TG2 both become targets of highly disease specific B-cell responses. These antibodies share several peculiar characteristics despite being directed against vastly different antigens, which suggests a common mechanism of development. Importantly, no clear function has been ascribed to the antibodies and their contribution to disease may relate to their function as antigen receptors of the B cells rather than as soluble immunoglobulins. Adaptive immunity against gluten and TG2 appears not to be sufficient for establishment of the disease lesion, and it has been suggested that stress responses in the intestinal epithelium are essential for the development of full-blown disease and tissue damage. In this review we will summarize current concepts of the immune pathology of CD with particular focus on recent advances in our understanding of disease specific B-cell responses.
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31
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Bioinformatic and Statistical Analysis of Adaptive Immune Repertoires. Trends Immunol 2015; 36:738-749. [DOI: 10.1016/j.it.2015.09.006] [Citation(s) in RCA: 138] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2015] [Revised: 09/15/2015] [Accepted: 09/15/2015] [Indexed: 01/16/2023]
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32
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Iversen R, Fleur du Pré M, Di Niro R, Sollid LM. Igs as Substrates for Transglutaminase 2: Implications for Autoantibody Production in Celiac Disease. THE JOURNAL OF IMMUNOLOGY 2015; 195:5159-68. [PMID: 26503953 DOI: 10.4049/jimmunol.1501363] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/17/2015] [Accepted: 10/05/2015] [Indexed: 01/19/2023]
Abstract
Autoantibodies specific for the enzyme transglutaminase 2 (TG2) are a hallmark of the gluten-sensitive enteropathy celiac disease. Production of the Abs is strictly dependent on exposure to dietary gluten proteins, thus raising the question how a foreign Ag (gluten) can induce an autoimmune response. It has been suggested that TG2-reactive B cells are activated by gluten-reactive T cells following receptor-mediated uptake of TG2-gluten complexes. In this study, we propose a revised model that is based on the ability of the BCR to serve as a substrate to TG2 and become cross-linked to gluten-derived peptides. We show that TG2-specific IgD molecules are preferred in the reaction and that binding of TG2 via a common epitope targeted by cells using the IgH variable gene segment (IGHV)5-51 results in more efficient cross-linking. Based on these findings we hypothesize that IgD-expressing B cells using IGHV5-51 are preferentially activated, and we suggest that this property can explain the previously reported low number of somatic mutations as well as the overrepresentation of IGHV5-51 among TG2-specific plasma cells in the celiac lesion. The model also couples gluten peptide uptake by TG2-reactive B cells directly to peptide deamidation, which is necessary for the activation of gluten-reactive T cells. It thereby provides a link between gluten deamidation, T cell activation, and the production of TG2-specific Abs. These are all key events in the development of celiac disease, and by connecting them the model may explain why the same enzyme that catalyzes gluten deamidation is also an autoantigen, something that is hardly coincidental.
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Affiliation(s)
- Rasmus Iversen
- Centre for Immune Regulation and Department of Immunology, University of Oslo and Oslo University Hospital, N-0372 Oslo, Norway
| | - M Fleur du Pré
- Centre for Immune Regulation and Department of Immunology, University of Oslo and Oslo University Hospital, N-0372 Oslo, Norway
| | - Roberto Di Niro
- Centre for Immune Regulation and Department of Immunology, University of Oslo and Oslo University Hospital, N-0372 Oslo, Norway
| | - Ludvig M Sollid
- Centre for Immune Regulation and Department of Immunology, University of Oslo and Oslo University Hospital, N-0372 Oslo, Norway
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