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Fowler A, FitzPatrick M, Shanmugarasa A, Ibrahim ASF, Kockelbergh H, Yang HC, Williams-Walker A, Luu Hoang KN, Evans S, Provine N, Klenerman P, Soilleux EJ. An Interpretable Classification Model Using Gluten-Specific TCR Sequences Shows Diagnostic Potential in Coeliac Disease. Biomolecules 2023; 13:1707. [PMID: 38136579 PMCID: PMC10742135 DOI: 10.3390/biom13121707] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2023] [Revised: 11/18/2023] [Accepted: 11/21/2023] [Indexed: 12/24/2023] Open
Abstract
Coeliac disease (CeD) is a T-cell mediated enteropathy triggered by dietary gluten which remains substantially under-diagnosed around the world. The diagnostic gold-standard requires histological assessment of intestinal biopsies taken at endoscopy while consuming a gluten-containing diet. However, there is a lack of concordance between pathologists in histological assessment, and both endoscopy and gluten challenge are burdensome and unpleasant for patients. Identification of gluten-specific T-cell receptors (TCRs) in the TCR repertoire could provide a less subjective diagnostic test, and potentially remove the need to consume gluten. We review published gluten-specific TCR sequences, and develop an interpretable machine learning model to investigate their diagnostic potential. To investigate this, we sequenced the TCR repertoires of mucosal CD4+ T cells from 20 patients with and without CeD. These data were used as a training dataset to develop the model, then an independently published dataset of 20 patients was used as the testing dataset. We determined that this model has a training accuracy of 100% and testing accuracy of 80% for the diagnosis of CeD, including in patients on a gluten-free diet (GFD). We identified 20 CD4+ TCR sequences with the highest diagnostic potential for CeD. The sequences identified here have the potential to provide an objective diagnostic test for CeD, which does not require the consumption of gluten.
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Affiliation(s)
- Anna Fowler
- Department of Health Data Science, Institute of Population Health, University of Liverpool, Liverpool L69 3GF, UK
| | - Michael FitzPatrick
- Translational Gastroenterology Unit, Nuffield Department of Medicine, University of Oxford, Oxford OX3 9DU, UK; (M.F.); (P.K.)
| | | | - Amro Sayed Fadel Ibrahim
- Department of Pathology, University of Cambridge, Cambridge CB2 1QP, UK; (A.S.F.I.); (H.-C.Y.); (A.W.-W.); (K.N.L.H.); (S.E.); (E.J.S.)
| | - Hannah Kockelbergh
- Department of Health Data Science, Institute of Population Health, University of Liverpool, Liverpool L69 3GF, UK
| | - Han-Chieh Yang
- Department of Pathology, University of Cambridge, Cambridge CB2 1QP, UK; (A.S.F.I.); (H.-C.Y.); (A.W.-W.); (K.N.L.H.); (S.E.); (E.J.S.)
| | - Amelia Williams-Walker
- Department of Pathology, University of Cambridge, Cambridge CB2 1QP, UK; (A.S.F.I.); (H.-C.Y.); (A.W.-W.); (K.N.L.H.); (S.E.); (E.J.S.)
| | - Kim Ngan Luu Hoang
- Department of Pathology, University of Cambridge, Cambridge CB2 1QP, UK; (A.S.F.I.); (H.-C.Y.); (A.W.-W.); (K.N.L.H.); (S.E.); (E.J.S.)
| | - Shelley Evans
- Department of Pathology, University of Cambridge, Cambridge CB2 1QP, UK; (A.S.F.I.); (H.-C.Y.); (A.W.-W.); (K.N.L.H.); (S.E.); (E.J.S.)
| | - Nicholas Provine
- Translational Gastroenterology Unit, Nuffield Department of Medicine, University of Oxford, Oxford OX3 9DU, UK; (M.F.); (P.K.)
| | - Paul Klenerman
- Translational Gastroenterology Unit, Nuffield Department of Medicine, University of Oxford, Oxford OX3 9DU, UK; (M.F.); (P.K.)
- Peter Medawar Building for Pathogen Research, University of Oxford, Oxford OX1 3SY, UK
| | - Elizabeth J. Soilleux
- Department of Pathology, University of Cambridge, Cambridge CB2 1QP, UK; (A.S.F.I.); (H.-C.Y.); (A.W.-W.); (K.N.L.H.); (S.E.); (E.J.S.)
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2
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Boughter CT, Meier-Schellersheim M. Conserved biophysical compatibility among the highly variable germline-encoded regions shapes TCR-MHC interactions. eLife 2023; 12:e90681. [PMID: 37861280 PMCID: PMC10631762 DOI: 10.7554/elife.90681] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2023] [Accepted: 10/19/2023] [Indexed: 10/21/2023] Open
Abstract
T cells are critically important components of the adaptive immune system primarily responsible for identifying and responding to pathogenic challenges. This recognition of pathogens is driven by the interaction between membrane-bound T cell receptors (TCRs) and antigenic peptides presented on major histocompatibility complex (MHC) molecules. The formation of the TCR-peptide-MHC complex (TCR-pMHC) involves interactions among germline-encoded and hypervariable amino acids. Germline-encoded and hypervariable regions can form contacts critical for complex formation, but only interactions between germline-encoded contacts are likely to be shared across many of all the possible productive TCR-pMHC complexes. Despite this, experimental investigation of these interactions have focused on only a small fraction of the possible interaction space. To address this, we analyzed every possible germline-encoded TCR-MHC contact in humans, thereby generating the first comprehensive characterization of these largely antigen-independent interactions. Our computational analysis suggests that germline-encoded TCR-MHC interactions that are conserved at the sequence level are rare due to the high amino acid diversity of the TCR CDR1 and CDR2 loops, and that such conservation is unlikely to dominate the dynamic protein-protein binding interface. Instead, we propose that binding properties such as the docking orientation are defined by regions of biophysical compatibility between these loops and the MHC surface.
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Affiliation(s)
- Christopher T Boughter
- Computational Biology Section, Laboratory of Immune System Biology, National Institute of Allergy and Infectious Diseases, National Institutes of HealthBethesdaUnited States
| | - Martin Meier-Schellersheim
- Computational Biology Section, Laboratory of Immune System Biology, National Institute of Allergy and Infectious Diseases, National Institutes of HealthBethesdaUnited States
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3
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CDR3 binding chemistry controls TCR V-domain rotational probability and germline CDR2 scanning of polymorphic MHC. Mol Immunol 2022; 144:138-151. [DOI: 10.1016/j.molimm.2021.11.015] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2021] [Revised: 11/17/2021] [Accepted: 11/21/2021] [Indexed: 11/21/2022]
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4
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Ciacchi L, Reid HH, Rossjohn J. Structural bases of T cell antigen receptor recognition in celiac disease. Curr Opin Struct Biol 2022; 74:102349. [PMID: 35272251 DOI: 10.1016/j.sbi.2022.102349] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2021] [Revised: 01/15/2022] [Accepted: 01/30/2022] [Indexed: 12/16/2022]
Abstract
Celiac disease (CeD) is a human leukocyte antigen (HLA)-linked autoimmune-like disorder that is triggered by the ingestion of gluten or related storage proteins. The majority of CeD patients are HLA-DQ2.5+, with the remainder being either HLA-DQ8+ or HLA-DQ2.2+. Structural studies have shown how deamidation of gluten epitopes engenders binding to HLA-DQ2.5/8, which then triggers an aberrant CD4+ T cell response. HLA tetramer studies, combined with structural investigations, have demonstrated that repeated patterns of TCR usage underpins the immune response to some HLADQ2.5/8 restricted gluten epitopes, with distinct TCR motifs representing common landing pads atop the HLA-gluten complexes. Structural studies have provided insight into TCR specificity and cross-reactivity towards gluten epitopes, as well as cross-reactivity to bacterial homologues of gluten epitopes, suggesting that environmental factors may directly play a role in CeD pathogenesis. Collectively, structural immunology-based studies in the CeD axis may lead to new therapeutics/diagnostics to treat CeD, and also serve as an exemplar for other T cell mediated autoimmune diseases.
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Affiliation(s)
- Laura Ciacchi
- Infection and Immunity Program and Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, Victoria, 3800, Australia
| | - Hugh H Reid
- Infection and Immunity Program and Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, Victoria, 3800, Australia
| | - Jamie Rossjohn
- Infection and Immunity Program and Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, Victoria, 3800, Australia; Institute of Infection and Immunity, School of Medicine, Cardiff University, Cardiff, CF14 4XN, United Kingdom.
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5
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Ciacchi L, Farenc C, Dahal-Koirala S, Petersen J, Sollid LM, Reid HH, Rossjohn J. Structural basis of T cell receptor specificity and cross-reactivity of two HLA-DQ2.5-restricted gluten epitopes in celiac disease. J Biol Chem 2022; 298:101619. [PMID: 35065967 PMCID: PMC8857473 DOI: 10.1016/j.jbc.2022.101619] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2021] [Revised: 01/15/2022] [Accepted: 01/18/2022] [Indexed: 11/17/2022] Open
Abstract
Celiac disease is a T cell-mediated chronic inflammatory condition often characterized by human leukocyte antigen (HLA)-DQ2.5 molecules presenting gluten epitopes derived from wheat, barley, and rye. Although some T cells exhibit cross-reactivity toward distinct gluten epitopes, the structural basis underpinning such cross-reactivity is unclear. Here, we investigated the T-cell receptor specificity and cross-reactivity of two immunodominant wheat gluten epitopes, DQ2.5-glia-α1a (PFPQPELPY) and DQ2.5-glia-ω1 (PFPQPEQPF). We show by surface plasmon resonance that a T-cell receptor alpha variable (TRAV) 4+-T-cell receptor beta variable (TRBV) 29-1+ TCR bound to HLA-DQ2.5-glia-α1a and HLA-DQ2.5-glia-ω1 with similar affinity, whereas a TRAV4- (TRAV9-2+) TCR recognized HLA-DQ2.5-glia-ω1 only. We further determined the crystal structures of the TRAV4+-TRBV29-1+ TCR bound to HLA-DQ2.5-glia-α1a and HLA-DQ2.5-glia-ω1, as well as the structure of an epitope-specific TRAV9-2+-TRBV7-3+ TCR-HLA-DQ2.5-glia-ω1 complex. We found that position 7 (p7) of the DQ2.5-glia-α1a and DQ2.5-glia-ω1 epitopes made very limited contacts with the TRAV4+ TCR, thereby explaining the TCR cross-reactivity across these two epitopes. In contrast, within the TRAV9-2+ TCR-HLA-DQ2.5-glia-ω1 ternary complex, the p7-Gln was situated in an electrostatic pocket formed by the hypervariable CDR3β loop of the TCR and Arg70β from HLA-DQ2.5, a polar network which would not be supported by the p7-Leu residue of DQ2.5-glia-α1a. In conclusion, we provide additional insights into the molecular determinants of TCR specificity and cross-reactivity to two closely-related epitopes in celiac disease.
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Affiliation(s)
- Laura Ciacchi
- Infection and Immunity Program and Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, Victoria, Australia
| | - Carine Farenc
- Infection and Immunity Program and Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, Victoria, Australia
| | - Shiva Dahal-Koirala
- Department of Immunology, University of Oslo and Oslo University Hospital-Rikshospitalet, Oslo, Norway; K. G. Jebsen Centre for Coeliac Disease Research, Institute of Clinical Medicine, University of Oslo, Oslo, Norway
| | - Jan Petersen
- Infection and Immunity Program and Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, Victoria, Australia
| | - Ludvig M Sollid
- Department of Immunology, University of Oslo and Oslo University Hospital-Rikshospitalet, Oslo, Norway; K. G. Jebsen Centre for Coeliac Disease Research, Institute of Clinical Medicine, University of Oslo, Oslo, Norway
| | - Hugh H Reid
- Infection and Immunity Program and Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, Victoria, Australia
| | - Jamie Rossjohn
- Infection and Immunity Program and Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, Victoria, Australia; Institute of Infection and Immunity, School of Medicine, Cardiff University, Cardiff, United Kingdom.
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6
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Frick R, Høydahl LS, Petersen J, du Pré MF, Kumari S, Berntsen G, Dewan AE, Jeliazkov JR, Gunnarsen KS, Frigstad T, Vik ES, Llerena C, Lundin KEA, Yaqub S, Jahnsen J, Gray JJ, Rossjohn J, Sollid LM, Sandlie I, Løset GÅ. A high-affinity human TCR-like antibody detects celiac disease gluten peptide-MHC complexes and inhibits T cell activation. Sci Immunol 2021; 6:6/62/eabg4925. [PMID: 34417258 DOI: 10.1126/sciimmunol.abg4925] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2021] [Accepted: 07/22/2021] [Indexed: 12/12/2022]
Abstract
Antibodies specific for peptides bound to human leukocyte antigen (HLA) molecules are valuable tools for studies of antigen presentation and may have therapeutic potential. Here, we generated human T cell receptor (TCR)-like antibodies toward the immunodominant signature gluten epitope DQ2.5-glia-α2 in celiac disease (CeD). Phage display selection combined with secondary targeted engineering was used to obtain highly specific antibodies with picomolar affinity. The crystal structure of a Fab fragment of the lead antibody 3.C11 in complex with HLA-DQ2.5:DQ2.5-glia-α2 revealed a binding geometry and interaction mode highly similar to prototypic TCRs specific for the same complex. Assessment of CeD biopsy material confirmed disease specificity and reinforced the notion that abundant plasma cells present antigen in the inflamed CeD gut. Furthermore, 3.C11 specifically inhibited activation and proliferation of gluten-specific CD4+ T cells in vitro and in HLA-DQ2.5 humanized mice, suggesting a potential for targeted intervention without compromising systemic immunity.
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Affiliation(s)
- Rahel Frick
- Centre for Immune Regulation and Department of Immunology, University of Oslo and Oslo University Hospital-Rikshospitalet, Oslo, Norway.,Centre for Immune Regulation and Department of Biosciences, University of Oslo, Oslo, Norway
| | - Lene S Høydahl
- Centre for Immune Regulation and Department of Immunology, University of Oslo and Oslo University Hospital-Rikshospitalet, Oslo, Norway.,Centre for Immune Regulation and Department of Biosciences, University of Oslo, Oslo, Norway.,KG Jebsen Coeliac Disease Research Centre, University of Oslo, Oslo, Norway
| | - Jan Petersen
- Infection and Immunity Program, Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, Victoria, Australia.,Australian Research Council Centre of Excellence for Advanced Molecular Imaging, Monash University, Clayton, Victoria, Australia
| | - M Fleur du Pré
- 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
| | | | | | - Alisa E Dewan
- 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
| | | | - Kristin S Gunnarsen
- Centre for Immune Regulation and Department of Immunology, University of Oslo and Oslo University Hospital-Rikshospitalet, Oslo, Norway.,Centre for Immune Regulation and Department of Biosciences, University of Oslo, Oslo, Norway
| | | | | | - Carmen Llerena
- Infection and Immunity Program, Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, Victoria, Australia
| | - Knut E A Lundin
- 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.,Department of Gastroenterology, Oslo University Hospital-Rikshospitalet, Oslo, Norway
| | - Sheraz Yaqub
- Department of Gastrointestinal Surgery, Oslo University Hospital-Rikshospitalet, Oslo, Norway.,Institute of Clinical Medicine, University of Oslo, Oslo, Norway
| | - Jørgen Jahnsen
- Institute of Clinical Medicine, University of Oslo, Oslo, Norway.,Department of Gastroenterology, Akershus University Hospital, Lørenskog, Norway
| | - Jeffrey J Gray
- Program in Molecular Biophysics, Johns Hopkins University, Baltimore, MD, USA.,Department of Chemical and Biomolecular Engineering and Institute of NanoBioTechnology, Johns Hopkins University, Baltimore, MD, USA.,Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins School of Medicine, Baltimore, MD, USA
| | - Jamie Rossjohn
- Infection and Immunity Program, Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, Victoria, Australia.,Australian Research Council Centre of Excellence for Advanced Molecular Imaging, Monash University, Clayton, Victoria, Australia.,Institute of Infection and Immunity, Cardiff University School of Medicine, Heath Park, Cardiff, UK
| | - 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
| | - Inger Sandlie
- Centre for Immune Regulation and Department of Immunology, University of Oslo and Oslo University Hospital-Rikshospitalet, Oslo, Norway.,Centre for Immune Regulation and Department of Biosciences, University of Oslo, Oslo, Norway
| | - Geir Åge Løset
- Centre for Immune Regulation and Department of Immunology, University of Oslo and Oslo University Hospital-Rikshospitalet, Oslo, Norway. .,Centre for Immune Regulation and Department of Biosciences, University of Oslo, Oslo, Norway.,Nextera AS, Oslo, Norway
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7
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CD4 + T Cells Recognize Conserved Influenza A Epitopes through Shared Patterns of V-Gene Usage and Complementary Biochemical Features. Cell Rep 2021; 32:107885. [PMID: 32668259 PMCID: PMC7370177 DOI: 10.1016/j.celrep.2020.107885] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2019] [Revised: 01/20/2020] [Accepted: 06/17/2020] [Indexed: 12/15/2022] Open
Abstract
T cell recognition of peptides presented by human leukocyte antigens (HLAs) is mediated by the highly variable T cell receptor (TCR). Despite this built-in TCR variability, individuals can mount immune responses against viral epitopes by using identical or highly related TCRs expressed on CD8+ T cells. Characterization of these TCRs has extended our understanding of the molecular mechanisms that govern the recognition of peptide-HLA. However, few examples exist for CD4+ T cells. Here, we investigate CD4+ T cell responses to the internal proteins of the influenza A virus that correlate with protective immunity. We identify five internal epitopes that are commonly recognized by CD4+ T cells in five HLA-DR1+ subjects and show conservation across viral strains and zoonotic reservoirs. TCR repertoire analysis demonstrates several shared gene usage biases underpinned by complementary biochemical features evident in a structural comparison. These epitopes are attractive targets for vaccination and other T cell therapies.
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8
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Dahal-Koirala S, Risnes LF, Neumann RS, Christophersen A, Lundin KEA, Sandve GK, Qiao SW, Sollid LM. Comprehensive Analysis of CDR3 Sequences in Gluten-Specific T-Cell Receptors Reveals a Dominant R-Motif and Several New Minor Motifs. Front Immunol 2021; 12:639672. [PMID: 33927715 PMCID: PMC8076556 DOI: 10.3389/fimmu.2021.639672] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2020] [Accepted: 03/17/2021] [Indexed: 12/20/2022] Open
Abstract
Gluten-specific CD4+ T cells are drivers of celiac disease (CeD). Previous studies of gluten-specific T-cell receptor (TCR) repertoires have found public TCRs shared across multiple individuals, biased usage of particular V-genes and conserved CDR3 motifs. The CDR3 motifs within the gluten-specific TCR repertoire, however, have not been systematically investigated. In the current study, we analyzed the largest TCR database of gluten-specific CD4+ T cells studied so far consisting of TCRs of 3122 clonotypes from 63 CeD patients. We established a TCR database from CD4+ T cells isolated with a mix of HLA-DQ2.5:gluten tetramers representing four immunodominant gluten epitopes. In an unbiased fashion we searched by hierarchical clustering for common CDR3 motifs among 2764 clonotypes. We identified multiple CDR3α, CDR3β, and paired CDR3α:CDR3β motif candidates. Among these, a previously known conserved CDR3β R-motif used by TRAV26-1/TRBV7-2 TCRs specific for the DQ2.5-glia-α2 epitope was the most prominent motif. Furthermore, we identified the epitope specificity of altogether 16 new CDR3α:CDR3β motifs by comparing with TCR sequences of 231 T-cell clones with known specificity and TCR sequences of cells sorted with single HLA-DQ2.5:gluten tetramers. We identified 325 public TCRα and TCRβ sequences of which 145, 102 and 78 belonged to TCRα, TCRβ and paired TCRαβ sequences, respectively. While the number of public sequences was depended on the number of clonotypes in each patient, we found that the proportion of public clonotypes from the gluten-specific TCR repertoire of given CeD patients appeared to be stable (median 37%). Taken together, we here demonstrate that the TCR repertoire of CD4+ T cells specific to immunodominant gluten epitopes in CeD is diverse, yet there is clearly biased V-gene usage, presence of public TCRs and existence of conserved motifs of which R-motif is the most prominent.
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Affiliation(s)
- Shiva Dahal-Koirala
- K.G. Jebsen Coeliac Disease Research Centre, Department of Immunology, University of Oslo, Oslo, Norway.,Department of Immunology, University of Oslo and Oslo University Hospital-Rikshospitalet, Oslo, Norway
| | - Louise Fremgaard Risnes
- K.G. Jebsen Coeliac Disease Research Centre, Department of Immunology, University of Oslo, Oslo, Norway.,Department of Immunology, University of Oslo and Oslo University Hospital-Rikshospitalet, Oslo, Norway
| | - Ralf Stefan Neumann
- K.G. Jebsen Coeliac Disease Research Centre, Department of Immunology, University of Oslo, Oslo, Norway
| | - Asbjørn Christophersen
- K.G. Jebsen Coeliac Disease Research Centre, Department of Immunology, University of Oslo, Oslo, Norway.,Department of Immunology, University of Oslo and Oslo University Hospital-Rikshospitalet, Oslo, Norway
| | - Knut E A Lundin
- K.G. Jebsen Coeliac Disease Research Centre, Department of Immunology, University of Oslo, Oslo, Norway.,Department of Immunology, University of Oslo and Oslo University Hospital-Rikshospitalet, Oslo, Norway.,Department of Gastroenterology, Oslo University Hospital-Rikshospitalet, Oslo, Norway
| | - Geir Kjetil Sandve
- Biomedical Informatics, Department of Informatics, University of Oslo, Oslo, Norway
| | - Shuo-Wang Qiao
- K.G. Jebsen Coeliac Disease Research Centre, Department of Immunology, University of Oslo, Oslo, Norway.,Department of Immunology, University of Oslo and Oslo University Hospital-Rikshospitalet, Oslo, Norway
| | - Ludvig M Sollid
- K.G. Jebsen Coeliac Disease Research Centre, Department of Immunology, University of Oslo, Oslo, Norway.,Department of Immunology, University of Oslo and Oslo University Hospital-Rikshospitalet, Oslo, Norway
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9
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Foers AD, Shoukat MS, Welsh OE, Donovan K, Petry R, Evans SC, FitzPatrick ME, Collins N, Klenerman P, Fowler A, Soilleux EJ. Classification of intestinal T-cell receptor repertoires using machine learning methods can identify patients with coeliac disease regardless of dietary gluten status. J Pathol 2021; 253:279-291. [PMID: 33225446 PMCID: PMC7898595 DOI: 10.1002/path.5592] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2020] [Revised: 10/29/2020] [Accepted: 11/12/2020] [Indexed: 12/17/2022]
Abstract
In coeliac disease (CeD), immune-mediated small intestinal damage is precipitated by gluten, leading to variable symptoms and complications, occasionally including aggressive T-cell lymphoma. Diagnosis, based primarily on histopathological examination of duodenal biopsies, is confounded by poor concordance between pathologists and minimal histological abnormality if insufficient gluten is consumed. CeD pathogenesis involves both CD4+ T-cell-mediated gluten recognition and CD8+ and γδ T-cell-mediated inflammation, with a previous study demonstrating a permanent change in γδ T-cell populations in CeD. We leveraged this understanding and explored the diagnostic utility of bulk T-cell receptor (TCR) sequencing in assessing duodenal biopsies in CeD. Genomic DNA extracted from duodenal biopsies underwent sequencing for TCR-δ (TRD) (CeD, n = 11; non-CeD, n = 11) and TCR-γ (TRG) (CeD, n = 33; non-CeD, n = 21). We developed a novel machine learning-based analysis of the TCR repertoire, clustering samples by diagnosis. Leave-one-out cross-validation (LOOCV) was performed to validate the classification algorithm. Using TRD repertoire, 100% (22/22) of duodenal biopsies were correctly classified, with a LOOCV accuracy of 91%. Using TCR-γ (TRG) repertoire, 94.4% (51/54) of duodenal biopsies were correctly classified, with LOOCV of 87%. Duodenal biopsy TRG repertoire analysis permitted accurate classification of biopsies from patients with CeD following a strict gluten-free diet for at least 6 months, who would be misclassified by current tests. This result reflects permanent changes to the duodenal γδ TCR repertoire in CeD, even in the absence of gluten consumption. Our method could complement or replace histopathological diagnosis in CeD and might have particular clinical utility in the diagnostic testing of patients unable to tolerate dietary gluten, and for assessing duodenal biopsies with equivocal features. This approach is generalisable to any TCR/BCR locus and any sequencing platform, with potential to predict diagnosis or prognosis in conditions mediated or modulated by the adaptive immune response. © 2020 The Authors. The Journal of Pathology published by John Wiley & Sons, Ltd. on behalf of The Pathological Society of Great Britain and Ireland.
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Affiliation(s)
- Andrew D Foers
- Department of Pathology, University of Cambridge, Cambridge, UK
| | - M Saad Shoukat
- Department of Pathology, University of Cambridge, Cambridge, UK
| | - Oliver E Welsh
- Department of Pathology, University of Cambridge, Cambridge, UK.,Centre for Mathematical Sciences, University of Cambridge, Cambridge, UK
| | | | - Russell Petry
- Department of Pathology, University of Cambridge, Cambridge, UK.,Centre for Mathematical Sciences, University of Cambridge, Cambridge, UK
| | - Shelley C Evans
- Department of Pathology, University of Cambridge, Cambridge, UK
| | - Michael Eb FitzPatrick
- Translational Gastroenterology Unit, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Nadine Collins
- Department of Molecular Pathology, Royal Surrey NHS Foundation Trust, Guildford, UK
| | - Paul Klenerman
- Translational Gastroenterology Unit, Nuffield Department of Medicine, University of Oxford, Oxford, UK.,Peter Medawar Building for Pathogen Research, University of Oxford, Oxford, UK
| | - Anna Fowler
- Department of Health Data Science, Institute of Population Health, University of Liverpool, Liverpool, UK
| | - Elizabeth J Soilleux
- Department of Pathology, University of Cambridge, Cambridge, UK.,Nuffield Division of Clinical Laboratory Sciences, Radcliffe Department of Medicine, University of Oxford, Oxford, UK
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10
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Frick R, Gunnarsen KS, Dahal-Koirala S, Risnes LF, Sollid LM, Sandlie I, Høydahl LS, Løset GÅ. A TRAV26-1-encoded recognition motif focuses the biased T cell response in celiac disease. Eur J Immunol 2019; 50:142-145. [PMID: 31580480 DOI: 10.1002/eji.201948235] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2019] [Revised: 07/10/2019] [Indexed: 11/08/2022]
Abstract
The semi-public T-cell response towards the gluten epitope DQ2.5-glia-α2 uses a prototypic TCR encoded by the germline segments TRAV26-1 and TRBV7-2. Through mutagenesis experiments, we show that a TRAV26-1encoded recognition motif contacts the MHC β-chain and the TCR CDR3β loop underpinning this conserved T-cell response restricted to the prototypic TCRs.
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Affiliation(s)
- Rahel Frick
- Department of Immunology, University of Oslo and Oslo University Hospital, Oslo, Norway.,Department of Biosciences, University of Oslo, Oslo, Norway
| | - Kristin Støen Gunnarsen
- Department of Immunology, University of Oslo and Oslo University Hospital, Oslo, Norway.,Department of Biosciences, University of Oslo, Oslo, Norway
| | - Shiva Dahal-Koirala
- Department of Immunology, University of Oslo and Oslo University Hospital, Oslo, Norway.,KG Jebsen Coeliac Disease Research Centre, University of Oslo, Oslo, Norway
| | - Louise Fremgaard Risnes
- Department of Immunology, University of Oslo and Oslo University Hospital, Oslo, Norway.,KG Jebsen Coeliac Disease Research Centre, University of Oslo, Oslo, Norway
| | - Ludvig M Sollid
- Department of Immunology, University of Oslo and Oslo University Hospital, Oslo, Norway.,KG Jebsen Coeliac Disease Research Centre, University of Oslo, Oslo, Norway
| | - Inger Sandlie
- Department of Immunology, University of Oslo and Oslo University Hospital, Oslo, Norway.,Department of Biosciences, University of Oslo, Oslo, Norway
| | - Lene Støkken Høydahl
- Department of Immunology, University of Oslo and Oslo University Hospital, Oslo, Norway.,Department of Biosciences, University of Oslo, Oslo, Norway.,KG Jebsen Coeliac Disease Research Centre, University of Oslo, Oslo, Norway
| | - Geir Åge Løset
- Department of Biosciences, University of Oslo, Oslo, Norway.,Nextera AS, Oslo, Norway
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11
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Høydahl LS, Richter L, Frick R, Snir O, Gunnarsen KS, Landsverk OJB, Iversen R, Jeliazkov JR, Gray JJ, Bergseng E, Foss S, Qiao SW, Lundin KEA, Jahnsen J, Jahnsen FL, Sandlie I, Sollid LM, Løset GÅ. Plasma Cells Are the Most Abundant Gluten Peptide MHC-expressing Cells in Inflamed Intestinal Tissues From Patients With Celiac Disease. Gastroenterology 2019; 156:1428-1439.e10. [PMID: 30593798 PMCID: PMC6441630 DOI: 10.1053/j.gastro.2018.12.013] [Citation(s) in RCA: 49] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/24/2017] [Revised: 08/21/2018] [Accepted: 12/20/2018] [Indexed: 12/11/2022]
Abstract
BACKGROUND & AIMS Development of celiac disease is believed to involve the transglutaminase-dependent response of CD4+ T cells toward deamidated gluten peptides in the intestinal mucosa of individuals with specific HLA-DQ haplotypes. We investigated the antigen presentation process during this mucosal immune response. METHODS We generated monoclonal antibodies (mAbs) specific for the peptide-MHC (pMHC) complex of HLA-DQ2.5 and the immunodominant gluten epitope DQ2.5-glia-α1a using phage display. We used these mAbs to assess gluten peptide presentation and phenotypes of presenting cells by flow cytometry and enzyme-linked immune absorbent spot (ELISPOT) in freshly prepared single-cell suspensions from intestinal biopsies from 40 patients with celiac disease (35 untreated and 5 on a gluten-free diet) as well as 18 subjects with confirmed noninflamed gut mucosa (controls, 12 presumed healthy, 5 undergoing pancreatoduodenectomy, and 1 with potential celiac disease). RESULTS Using the mAbs, we detected MHC complexes on cells from intestinal biopsies from patients with celiac disease who consume gluten, but not from patients on gluten-free diets. We found B cells and plasma cells to be the most abundant cells that present DQ2.5-glia-α1a in the inflamed mucosa. We identified a subset of plasma cells that expresses B-cell receptors (BCR) specific for gluten peptides or the autoantigen transglutaminase 2 (TG2). Expression of MHC class II (MHCII) was not restricted to these specific plasma cells in patients with celiac disease but was observed in an average 30% of gut plasma cells from patients and controls. CONCLUSIONS A population of plasma cells from intestinal biopsies of patients with celiac disease express MHCII; this is the most abundant cell type presenting the immunodominant gluten peptide DQ2.5-glia-α1a in the tissues from these patients. These results indicate that plasma cells in the gut can function as antigen-presenting cells and might promote and maintain intestinal inflammation in patients with celiac disease or other inflammatory disorders.
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Affiliation(s)
- Lene Støkken Høydahl
- Centre for Immune Regulation and Department of Immunology, University of Oslo and Oslo University Hospital, Oslo, Norway; Centre for Immune Regulation and Department of Biosciences, University of Oslo, Oslo, Norway; KG Jebsen Coeliac Disease Research Centre, University of Oslo, Oslo, Norway.
| | - Lisa Richter
- Centre for Immune Regulation and Department of Pathology, University of Oslo and Oslo University Hospital, Oslo, Norway.,Present address: Core Facility Flow Cytometry, Biomedical Center Munich, Ludwig-Maximilians-Universität Munich, Planegg-Martinsried, Germany
| | - Rahel Frick
- Centre for Immune Regulation and Department of Immunology, University of Oslo and Oslo University Hospital, Oslo, Norway.,Centre for Immune Regulation and Department of Biosciences, University of Oslo, Oslo, Norway
| | - Omri Snir
- Centre for Immune Regulation and Department of Immunology, University of Oslo and Oslo University Hospital, Oslo, Norway
| | - Kristin Støen Gunnarsen
- Centre for Immune Regulation and Department of Immunology, University of Oslo and Oslo University Hospital, Oslo, Norway.,Centre for Immune Regulation and Department of Biosciences, University of Oslo, Oslo, Norway
| | - Ole JB Landsverk
- Centre for Immune Regulation and Department of Pathology, University of Oslo and Oslo University Hospital, Oslo, Norway
| | - Rasmus Iversen
- Centre for Immune Regulation and Department of Immunology, University of Oslo and Oslo University Hospital, Oslo, Norway
| | - Jeliazko R Jeliazkov
- Program in Molecular Biophysics, Johns Hopkins University, Baltimore, Maryland, USA
| | - Jeffrey J Gray
- Program in Molecular Biophysics, Johns Hopkins University, Baltimore, Maryland, USA.,Department of Chemical and Biomolecular Engineering and Institute of NanoBioTechnology, Johns Hopkins University, Baltimore, Maryland, USA.,Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins School of Medicine, Baltimore, Maryland, USA
| | - Elin Bergseng
- Centre for Immune Regulation and Department of Immunology, University of Oslo and Oslo University Hospital, Oslo, Norway
| | - Stian Foss
- Centre for Immune Regulation and Department of Immunology, University of Oslo and Oslo University Hospital, Oslo, Norway.,Centre for Immune Regulation and Department of Biosciences, University of Oslo, Oslo, Norway
| | - Shuo-Wang Qiao
- Centre for Immune Regulation and Department of Immunology, University of Oslo and Oslo University Hospital, Oslo, Norway.,KG Jebsen Coeliac Disease Research Centre and Department of Immunology, University of Oslo, Oslo, Norway
| | - Knut EA Lundin
- Centre for Immune Regulation and Department of Immunology, University of Oslo and Oslo University Hospital, Oslo, Norway.,Dept 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
| | - Frode L Jahnsen
- Centre for Immune Regulation and Department of Pathology, University of Oslo and Oslo University Hospital, Oslo, Norway
| | - Inger Sandlie
- Centre for Immune Regulation and Department of Immunology, University of Oslo and Oslo University Hospital, Oslo, Norway.,Centre for Immune Regulation and Department of Biosciences, University of Oslo, Oslo, Norway
| | - Ludvig M Sollid
- Centre for Immune Regulation and Department of Immunology, University of Oslo and Oslo University Hospital, Oslo, Norway.,KG Jebsen Coeliac Disease Research Centre and Department of Immunology, University of Oslo, Oslo, Norway
| | - Geir Åge Løset
- Centre for Immune Regulation and Department of Immunology, University of Oslo and Oslo University Hospital, Oslo, Norway; Centre for Immune Regulation and Department of Biosciences, University of Oslo, Oslo, Norway; Nextera AS, Oslo, Norway.
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12
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Corrie BD, Marthandan N, Zimonja B, Jaglale J, Zhou Y, Barr E, Knoetze N, Breden FMW, Christley S, Scott JK, Cowell LG, Breden F. iReceptor: A platform for querying and analyzing antibody/B-cell and T-cell receptor repertoire data across federated repositories. Immunol Rev 2019; 284:24-41. [PMID: 29944754 DOI: 10.1111/imr.12666] [Citation(s) in RCA: 86] [Impact Index Per Article: 17.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Next-generation sequencing allows the characterization of the adaptive immune receptor repertoire (AIRR) in exquisite detail. These large-scale AIRR-seq data sets have rapidly become critical to vaccine development, understanding the immune response in autoimmune and infectious disease, and monitoring novel therapeutics against cancer. However, at present there is no easy way to compare these AIRR-seq data sets across studies and institutions. The ability to combine and compare information for different disease conditions will greatly enhance the value of AIRR-seq data for improving biomedical research and patient care. The iReceptor Data Integration Platform (gateway.ireceptor.org) provides one implementation of the AIRR Data Commons envisioned by the AIRR Community (airr-community.org), an initiative that is developing protocols to facilitate sharing and comparing AIRR-seq data. The iReceptor Scientific Gateway links distributed (federated) AIRR-seq repositories, allowing sequence searches or metadata queries across multiple studies at multiple institutions, returning sets of sequences fulfilling specific criteria. We present a review of the development of iReceptor, and how it fits in with the general trend toward sharing genomic and health data, and the development of standards for describing and reporting AIRR-seq data. Researchers interested in integrating their repositories of AIRR-seq data into the iReceptor Platform are invited to contact support@ireceptor.org.
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Affiliation(s)
- Brian D Corrie
- The IRMACS Centre, Simon Fraser University, Burnaby, BC, Canada
| | - Nishanth Marthandan
- The IRMACS Centre, Simon Fraser University, Burnaby, BC, Canada.,Deptartment of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, BC, Canada
| | - Bojan Zimonja
- The IRMACS Centre, Simon Fraser University, Burnaby, BC, Canada
| | - Jerome Jaglale
- The IRMACS Centre, Simon Fraser University, Burnaby, BC, Canada
| | - Yang Zhou
- The IRMACS Centre, Simon Fraser University, Burnaby, BC, Canada
| | - Emily Barr
- The IRMACS Centre, Simon Fraser University, Burnaby, BC, Canada
| | - Nicole Knoetze
- The IRMACS Centre, Simon Fraser University, Burnaby, BC, Canada
| | | | - Scott Christley
- Department of Clinical Sciences, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Jamie K Scott
- Deptartment of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, BC, Canada.,Faculty of Health Sciences, Simon Fraser University, Burnaby, BC, Canada
| | - Lindsay G Cowell
- Department of Clinical Sciences, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Felix Breden
- The IRMACS Centre, Simon Fraser University, Burnaby, BC, Canada.,Department of Biological Sciences, Simon Fraser University, Burnaby, BC, Canada
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13
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Gunnarsen KS, Høydahl LS, Neumann RS, Bjerregaard-Andersen K, Nilssen NR, Sollid LM, Sandlie I, Løset GÅ. Soluble T-cell receptor design influences functional yield in an E. coli chaperone-assisted expression system. PLoS One 2018; 13:e0195868. [PMID: 29649333 PMCID: PMC5897000 DOI: 10.1371/journal.pone.0195868] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2018] [Accepted: 03/30/2018] [Indexed: 11/29/2022] Open
Abstract
There is a quest for production of soluble protein of high quality for the study of T-cell receptors (TCRs), but expression often results in low yields of functional molecules. In this study, we used an E. coli chaperone-assisted periplasmic production system and compared expression of 4 different soluble TCR formats: single-chain TCR (scTCR), two different disulfide-linked TCR (dsTCR) formats, and chimeric Fab (cFab). A stabilized version of scTCR was also included. Additionally, we evaluated the influence of host (XL1-Blue or RosettaBlueTM) and the effect of IPTG induction on expression profiles. A celiac disease patient-derived TCR with specificity for gluten was used, and we achieved detectable expression for all formats and variants. We found that expression in RosettaBlueTM without IPTG induction resulted in the highest periplasmic yields. Moreover, after large-scale expression and protein purification, only the scTCR format was obtained in high yields. Importantly, stability engineering of the scTCR was a prerequisite for obtaining reliable biophysical characterization of the TCR-pMHC interaction. The scTCR format is readily compatible with high-throughput screening approaches that may enable both development of reagents allowing for defined peptide MHC (pMHC) characterization and discovery of potential novel therapeutic leads.
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Affiliation(s)
- Kristin Støen Gunnarsen
- Centre for Immune Regulation, University of Oslo and Oslo University Hospital-Rikshospitalet, Oslo, Norway
- Department of Immunology, University of Oslo and Oslo University Hospital-Rikshospitalet, Oslo, Norway
- Department of Biosciences, University of Oslo, Oslo, Norway
| | - Lene Støkken Høydahl
- Centre for Immune Regulation, University of Oslo and Oslo University Hospital-Rikshospitalet, Oslo, Norway
- Department of Immunology, University of Oslo and Oslo University Hospital-Rikshospitalet, Oslo, Norway
- Department of Biosciences, University of Oslo, Oslo, Norway
| | - Ralf Stefan Neumann
- Centre for Immune Regulation, University of Oslo and Oslo University Hospital-Rikshospitalet, Oslo, Norway
- Department of Immunology, University of Oslo and Oslo University Hospital-Rikshospitalet, Oslo, Norway
| | | | - Nicolay Rustad Nilssen
- Centre for Immune Regulation, University of Oslo and Oslo University Hospital-Rikshospitalet, Oslo, Norway
- Department of Immunology, University of Oslo and Oslo University Hospital-Rikshospitalet, Oslo, Norway
- Department of Biosciences, University of Oslo, Oslo, Norway
| | - Ludvig Magne Sollid
- Centre for Immune Regulation, University of Oslo and Oslo University Hospital-Rikshospitalet, Oslo, Norway
- Department of Immunology, University of Oslo and Oslo University Hospital-Rikshospitalet, Oslo, Norway
- KG Jebsen Coeliac Disease Research Centre and Department of Immunology, University of Oslo, Oslo, Norway
| | - Inger Sandlie
- Centre for Immune Regulation, University of Oslo and Oslo University Hospital-Rikshospitalet, Oslo, Norway
- Department of Immunology, University of Oslo and Oslo University Hospital-Rikshospitalet, Oslo, Norway
- Department of Biosciences, University of Oslo, Oslo, Norway
| | - Geir Åge Løset
- Centre for Immune Regulation, University of Oslo and Oslo University Hospital-Rikshospitalet, Oslo, Norway
- Department of Immunology, University of Oslo and Oslo University Hospital-Rikshospitalet, Oslo, Norway
- Department of Biosciences, University of Oslo, Oslo, Norway
- Nextera AS, Oslo, Norway
- * E-mail:
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