1
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Boyd LF, Jiang J, Ahmad J, Natarajan K, Margulies DH. Experimental Structures of Antibody/MHC-I Complexes Reveal Details of Epitopes Overlooked by Computational Prediction. J Immunol 2024; 212:1366-1380. [PMID: 38456672 PMCID: PMC10982845 DOI: 10.4049/jimmunol.2300839] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/06/2023] [Accepted: 02/14/2024] [Indexed: 03/09/2024]
Abstract
mAbs to MHC class I (MHC-I) molecules have proved to be crucial reagents for tissue typing and fundamental studies of immune recognition. To augment our understanding of epitopic sites seen by a set of anti-MHC-I mAb, we determined X-ray crystal structures of four complexes of anti-MHC-I Fabs bound to peptide/MHC-I/β2-microglobulin (pMHC-I). An anti-H2-Dd mAb, two anti-MHC-I α3 domain mAbs, and an anti-β2-microglobulin mAb bind pMHC-I at sites consistent with earlier mutational and functional experiments, and the structures explain allelomorph specificity. Comparison of the experimentally determined structures with computationally derived models using AlphaFold Multimer showed that although predictions of the individual pMHC-I heterodimers were quite acceptable, the computational models failed to properly identify the docking sites of the mAb on pMHC-I. The experimental and predicted structures provide insight into strengths and weaknesses of purely computational approaches and suggest areas that merit additional attention.
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Affiliation(s)
- Lisa F. Boyd
- Molecular Biology Section, Laboratory of Immune System Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD
| | - Jiansheng Jiang
- Molecular Biology Section, Laboratory of Immune System Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD
| | - Javeed Ahmad
- Molecular Biology Section, Laboratory of Immune System Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD
| | - Kannan Natarajan
- Molecular Biology Section, Laboratory of Immune System Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD
| | - David H. Margulies
- Molecular Biology Section, Laboratory of Immune System Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD
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2
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Discepolo V, Kelly CP, Koning F, Schuppan D. How Future Pharmacologic Therapies for Celiac Disease Will Complement the Gluten-Free Diet. Gastroenterology 2024:S0016-5085(24)00416-5. [PMID: 38604542 DOI: 10.1053/j.gastro.2024.02.050] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/13/2023] [Revised: 02/20/2024] [Accepted: 02/22/2024] [Indexed: 04/13/2024]
Abstract
The only proven treatment for celiac disease is adherence to a strict, lifelong, gluten-free diet. However, complete dietary gluten avoidance is challenging and a substantial number of patients do not respond fully, clinically, or histologically, despite their best efforts. As celiac disease is common and its central pathophysiology is well elucidated, it has become attractive for drug development to address the limitations of dietary treatment. Most efforts address nonresponsive celiac disease, defined as continued symptoms and/or signs of disease activity despite a gluten-free diet, including the more severe forms of refractory celiac disease, types I and II. An increasing spectrum of therapeutic approaches target defined mechanisms in celiac disease pathogenesis and some have advanced to current phase 2 and 3 clinical studies. We discuss these approaches in terms of potential efficiency, practicability, safety, and need, as defined by patients, regulatory authorities, health care providers, and payors.
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Affiliation(s)
- Valentina Discepolo
- Department of Translational Medical Science and European Laboratory for the Investigation of Food Induced Diseases, University of Naples Federico II, Naples, Italy.
| | - Ciarán P Kelly
- Celiac Center, Beth Israel Deaconess Medical Center and Harvard Medical School, Boston, Massachusetts
| | - Frits Koning
- Department of Immunology, Leiden University Medical Center, Leiden, The Netherlands
| | - Detlef Schuppan
- Celiac Center, Beth Israel Deaconess Medical Center and Harvard Medical School, Boston, Massachusetts; Institute of Translational Immunology and Research Center for Immunotherapy, Center for Celiac Disease and Autoimmunity, Johannes-Gutenberg University, Mainz, Germany.
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3
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Du H, Liu J, Jude KM, Yang X, Li Y, Bell B, Yang H, Kassardjian A, Mobedi A, Parekh U, Sperberg RAP, Julien JP, Mellins ED, Garcia KC, Huang PS. A general platform for targeting MHC-II antigens via a single loop. bioRxiv 2024:2024.01.26.577489. [PMID: 38352315 PMCID: PMC10862749 DOI: 10.1101/2024.01.26.577489] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/21/2024]
Abstract
Class-II major histocompatibility complexes (MHC-IIs) are central to the communications between CD4+ T cells and antigen presenting cells (APCs), but intrinsic structural features associated with MHC-II make it difficult to develop a general targeting system with high affinity and antigen specificity. Here, we introduce a protein platform, Targeted Recognition of Antigen-MHC Complex Reporter for MHC-II (TRACeR-II), to enable the rapid development of peptide-specific MHC-II binders. TRACeR-II has a small helical bundle scaffold and uses an unconventional mechanism to recognize antigens via a single loop. This unique antigen-recognition mechanism renders this platform highly versatile and amenable to direct structural modeling of the interactions with the antigen. We demonstrate that TRACeR-II binders can be rapidly evolved across multiple alleles, while computational protein design can produce specific binding sequences for a SARS-CoV-2 peptide of unknown complex structure. TRACeR-II sheds light on a simple and straightforward approach to address the MHC peptide targeting challenge, without relying on combinatorial selection on complementarity determining region (CDR) loops. It presents a promising basis for further exploration in immune response modulation as well as a broad range of theragnostic applications.
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Affiliation(s)
- Haotian Du
- Department of Chemistry, Stanford University, Stanford, CA, USA
| | - Jingjia Liu
- Department of Bioengineering, Stanford University, CA, USA
| | - Kevin M. Jude
- Departments of Molecular and Cellular Physiology and Structural Biology, Stanford University School of Medicine, Stanford, CA, USA
| | - Xinbo Yang
- Departments of Molecular and Cellular Physiology and Structural Biology, Stanford University School of Medicine, Stanford, CA, USA
| | - Ying Li
- Department of Pediatrics, Divisions of Human Gene Therapy and Allergy, Immunology & Rheumatology, Stanford University School of Medicine, Stanford, CA, USA
- Stanford Program in Immunology, Stanford University School of Medicine, Stanford, CA, USA
| | - Braxton Bell
- Department of Chemistry, Stanford University, Stanford, CA, USA
| | - Hongli Yang
- Department of Bioengineering, Stanford University, CA, USA
| | - Audrey Kassardjian
- Program in Molecular Medicine, The Hospital for Sick Children Research Institute, Toronto, ON M5G 0A4, Canada
- Department of Immunology, University of Toronto, Toronto, ON M5S 1A8, Canada
| | - Ali Mobedi
- Department of Bioengineering, Stanford University, CA, USA
| | - Udit Parekh
- Department of Bioengineering, Stanford University, CA, USA
| | | | - Jean-Philippe Julien
- Program in Molecular Medicine, The Hospital for Sick Children Research Institute, Toronto, ON M5G 0A4, Canada
- Department of Immunology, University of Toronto, Toronto, ON M5S 1A8, Canada
- Department of Biochemistry, University of Toronto, Toronto, ON M5S 1A8, Canada
| | - Elizabeth D. Mellins
- Department of Pediatrics, Divisions of Human Gene Therapy and Allergy, Immunology & Rheumatology, Stanford University School of Medicine, Stanford, CA, USA
- Stanford Program in Immunology, Stanford University School of Medicine, Stanford, CA, USA
| | - K. Christopher Garcia
- Departments of Molecular and Cellular Physiology and Structural Biology, Stanford University School of Medicine, Stanford, CA, USA
- Howard Hughes Medical Institute, Stanford University School of Medicine, Stanford, CA, USA
| | - Po-Ssu Huang
- Department of Bioengineering, Stanford University, CA, USA
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4
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Okura Y, Ikawa-Teranishi Y, Mizoroki A, Takahashi N, Tsushima T, Irie M, Harfuddin Z, Miura-Okuda M, Ito S, Nakamura G, Takesue H, Ozono Y, Nishihara M, Yamada K, Gan SW, Hayasaka A, Ishii S, Wakabayashi T, Muraoka M, Nagaya N, Hino H, Nemoto T, Kuramochi T, Torizawa T, Shimada H, Kitazawa T, Okazaki M, Nezu J, Sollid LM, Igawa T. Characterizations of a neutralizing antibody broadly reactive to multiple gluten peptide:HLA-DQ2.5 complexes in the context of celiac disease. Nat Commun 2023; 14:8502. [PMID: 38135691 PMCID: PMC10746718 DOI: 10.1038/s41467-023-44083-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2023] [Accepted: 11/29/2023] [Indexed: 12/24/2023] Open
Abstract
In human celiac disease (CeD) HLA-DQ2.5 presents gluten peptides to antigen-specific CD4+ T cells, thereby instigating immune activation and enteropathy. Targeting HLA-DQ2.5 with neutralizing antibody for treating CeD may be plausible, yet using pan-HLA-DQ antibody risks affecting systemic immunity, while targeting selected gluten peptide:HLA-DQ2.5 complex (pHLA-DQ2.5) may be insufficient. Here we generate a TCR-like, neutralizing antibody (DONQ52) that broadly recognizes more than twenty-five distinct gluten pHLA-DQ2.5 through rabbit immunization with multi-epitope gluten pHLA-DQ2.5 and multidimensional optimization. Structural analyses show that the proline-rich and glutamine-rich motif of gluten epitopes critical for pathogenesis is flexibly recognized by multiple tyrosine residues present in the antibody paratope, implicating the mechanisms for the broad reactivity. In HLA-DQ2.5 transgenic mice, DONQ52 demonstrates favorable pharmacokinetics with high subcutaneous bioavailability, and blocks immunity to gluten while not affecting systemic immunity. Our results thus provide a rationale for clinical testing of DONQ52 in CeD.
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Affiliation(s)
- Yuu Okura
- Translational Research Division, Chugai Pharmaceutical Co., Ltd., Tokyo, Japan
| | | | - Akihiko Mizoroki
- Research Division, Chugai Pharmaceutical Co., Ltd., Kanagawa, Japan
| | | | | | - Machiko Irie
- Research Division, Chugai Pharmaceutical Co., Ltd., Kanagawa, Japan
| | | | | | - Shunsuke Ito
- Translational Research Division, Chugai Pharmaceutical Co., Ltd., Kanagawa, Japan
| | - Genki Nakamura
- Research Division, Chugai Pharmaceutical Co., Ltd., Kanagawa, Japan
| | - Hiroaki Takesue
- Research Division, Chugai Pharmaceutical Co., Ltd., Kanagawa, Japan
| | - Yui Ozono
- Research Division, Chugai Pharmaceutical Co., Ltd., Kanagawa, Japan
| | | | - Kenta Yamada
- Research Division, Chugai Pharmaceutical Co., Ltd., Kanagawa, Japan
| | - Siok Wan Gan
- Chugai Pharmabody Research Pte. Ltd., Singapore, Singapore
| | - Akira Hayasaka
- Research Division, Chugai Pharmaceutical Co., Ltd., Kanagawa, Japan
| | - Shinya Ishii
- Research Division, Chugai Pharmaceutical Co., Ltd., Kanagawa, Japan
| | | | - Masaru Muraoka
- Research Division, Chugai Pharmaceutical Co., Ltd., Kanagawa, Japan
| | - Nishiki Nagaya
- Research Division, Chugai Pharmaceutical Co., Ltd., Kanagawa, Japan
| | - Hiroshi Hino
- Research Division, Chugai Pharmaceutical Co., Ltd., Kanagawa, Japan
| | - Takayuki Nemoto
- Translational Research Division, Chugai Pharmaceutical Co., Ltd., Kanagawa, Japan
| | - Taichi Kuramochi
- Research Division, Chugai Pharmaceutical Co., Ltd., Kanagawa, Japan
| | - Takuya Torizawa
- Research Division, Chugai Pharmaceutical Co., Ltd., Kanagawa, Japan
| | | | | | - Makoto Okazaki
- Chugai Pharmabody Research Pte. Ltd., Singapore, Singapore
| | - Junichi Nezu
- R&D Portfolio Management Department, Chugai Pharmaceutical Co., Ltd., Tokyo, Japan
| | - Ludvig M Sollid
- Department of Immunology, Oslo University Hospital, Oslo, Norway
- Institute of Clinical Medicine, University of Oslo, Oslo, Norway
| | - Tomoyuki Igawa
- Translational Research Division, Chugai Pharmaceutical Co., Ltd., Tokyo, Japan.
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5
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Boyd LF, Jiang J, Ahmad J, Natarajan K, Margulies DH. Experimental structures of antibody/MHC-I complexes reveal details of epitopes overlooked by computational prediction. bioRxiv 2023:2023.12.01.569627. [PMID: 38106040 PMCID: PMC10723347 DOI: 10.1101/2023.12.01.569627] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/19/2023]
Abstract
Monoclonal antibodies (mAb) to major histocompatibility complex class I (MHC-I) molecules have proved to be crucial reagents for tissue typing and fundamental studies of immune recognition. To augment our understanding of epitopic sites seen by a set of anti-MHC-I mAb, we determined X-ray crystal structures of four complexes of anti-MHC-I antigen-binding fragments (Fab) bound to peptide/MHC-I/β2m (pMHC-I). An anti-H2-Dd mAb, two anti-MHC-I α3 domain mAb, and an anti-β2-microglobulin (β2m) mAb bind pMHC-I at sites consistent with earlier mutational and functional experiments, and the structures explain allelomorph specificity. Comparison of the experimentally determined structures with computationally derived models using AlphaFold Multimer (AF-M) showed that although predictions of the individual pMHC-I heterodimers were quite acceptable, the computational models failed to properly identify the docking sites of the mAb on pMHC-I. The experimental and predicted structures provide insight into strengths and weaknesses of purely computational approaches and suggest areas that merit additional attention.
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Affiliation(s)
| | | | - Javeed Ahmad
- Molecular Biology Section, Laboratory of Immune System Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda MD, 20892-1892
| | - Kannan Natarajan
- Molecular Biology Section, Laboratory of Immune System Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda MD, 20892-1892
| | - David H. Margulies
- Molecular Biology Section, Laboratory of Immune System Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda MD, 20892-1892
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6
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Abstract
Celiac disease (CeD) is a widespread, gluten-induced, autoimmune disorder that lacks any medicinal therapy. Towards the goal of developing non-dietary treatments for CeD, research has focused on elucidating its molecular and cellular etiology. A model of pathogenesis has emerged centered on interactions between three molecular families: specific class II MHC proteins on antigen-presenting cells (APCs), deamidated gluten-derived peptides, and T cell receptors (TCRs) on inflammatory CD4+ T cells. Growing evidence suggests that this pathogenic axis can be pharmacologically targeted to protect patients from some of the adverse effects of dietary gluten. Further studies have revealed the existence of additional host and environmental contributors to disease initiation and tissue damage. This review summarizes our current understanding of CeD pathogenesis and how it is being harnessed for therapeutic design and development.
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Affiliation(s)
- Harrison A Besser
- Department of Chemistry, Stanford University, Stanford, CA 94305, USA; Stanford Medical Scientist Training Program, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Chaitan Khosla
- Department of Chemistry, Stanford University, Stanford, CA 94305, USA; Department of Chemical Engineering, Stanford University, Stanford, CA 94305, USA; Sarafan ChEM-H (Chemistry, Engineering and Medicine for Human Health), Stanford University, Stanford, CA 94305, USA.
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7
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Ruffolo JA, Chu LS, Mahajan SP, Gray JJ. Fast, accurate antibody structure prediction from deep learning on massive set of natural antibodies. Nat Commun 2023; 14:2389. [PMID: 37185622 PMCID: PMC10129313 DOI: 10.1038/s41467-023-38063-x] [Citation(s) in RCA: 36] [Impact Index Per Article: 36.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2022] [Accepted: 04/14/2023] [Indexed: 05/17/2023] Open
Abstract
Antibodies have the capacity to bind a diverse set of antigens, and they have become critical therapeutics and diagnostic molecules. The binding of antibodies is facilitated by a set of six hypervariable loops that are diversified through genetic recombination and mutation. Even with recent advances, accurate structural prediction of these loops remains a challenge. Here, we present IgFold, a fast deep learning method for antibody structure prediction. IgFold consists of a pre-trained language model trained on 558 million natural antibody sequences followed by graph networks that directly predict backbone atom coordinates. IgFold predicts structures of similar or better quality than alternative methods (including AlphaFold) in significantly less time (under 25 s). Accurate structure prediction on this timescale makes possible avenues of investigation that were previously infeasible. As a demonstration of IgFold's capabilities, we predicted structures for 1.4 million paired antibody sequences, providing structural insights to 500-fold more antibodies than have experimentally determined structures.
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Affiliation(s)
- Jeffrey A Ruffolo
- Program in Molecular Biophysics, The Johns Hopkins University, Baltimore, MD, 21218, USA
| | - Lee-Shin Chu
- Department of Chemical and Biomolecular Engineering, The Johns Hopkins University, Baltimore, MD, 21218, USA
| | - Sai Pooja Mahajan
- Department of Chemical and Biomolecular Engineering, The Johns Hopkins University, Baltimore, MD, 21218, USA
| | - Jeffrey J Gray
- Program in Molecular Biophysics, The Johns Hopkins University, Baltimore, MD, 21218, USA.
- Department of Chemical and Biomolecular Engineering, The Johns Hopkins University, Baltimore, MD, 21218, USA.
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8
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Raybould MIJ, Nissley DA, Kumar S, Deane CM. Computationally profiling peptide:MHC recognition by T-cell receptors and T-cell receptor-mimetic antibodies. Front Immunol 2023; 13:1080596. [PMID: 36700202 PMCID: PMC9868621 DOI: 10.3389/fimmu.2022.1080596] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2022] [Accepted: 12/07/2022] [Indexed: 01/11/2023] Open
Abstract
T-cell receptor-mimetic antibodies (TCRms) targeting disease-associated peptides presented by Major Histocompatibility Complexes (pMHCs) are set to become a major new drug modality. However, we lack a general understanding of how TCRms engage pMHC targets, which is crucial for predicting their specificity and safety. Several new structures of TCRm:pMHC complexes have become available in the past year, providing sufficient initial data for a holistic analysis of TCRms as a class of pMHC binding agents. Here, we profile the complete set of TCRm:pMHC complexes against representative TCR:pMHC complexes to quantify the TCR-likeness of their pMHC engagement. We find that intrinsic molecular differences between antibodies and TCRs lead to fundamentally different roles for their heavy/light chains and Complementarity-Determining Region loops during antigen recognition. The idiotypic properties of antibodies may increase the likelihood of TCRms engaging pMHCs with less peptide selectivity than TCRs. However, the pMHC recognition features of some TCRms, including the two TCRms currently in clinical trials, can be remarkably TCR-like. The insights gained from this study will aid in the rational design and optimisation of next-generation TCRms.
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Affiliation(s)
- Matthew I. J. Raybould
- Oxford Protein Informatics Group, Department of Statistics, University of Oxford, Oxford, United Kingdom
| | - Daniel A. Nissley
- Oxford Protein Informatics Group, Department of Statistics, University of Oxford, Oxford, United Kingdom
| | - Sandeep Kumar
- Biotherapeutics Discovery, Boehringer Ingelheim, Ridgefield, CT, United States
| | - Charlotte M. Deane
- Oxford Protein Informatics Group, Department of Statistics, University of Oxford, Oxford, United Kingdom,*Correspondence: Charlotte M. Deane,
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9
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Li W, Zhang Y, Li R, Wang Y, Chen L, Dai S. A Novel Tolerogenic Antibody Targeting Disulfide-Modified Autoantigen Effectively Prevents Type 1 Diabetes in NOD Mice. Front Immunol 2022; 13:877022. [PMID: 36032077 PMCID: PMC9406144 DOI: 10.3389/fimmu.2022.877022] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2022] [Accepted: 06/06/2022] [Indexed: 11/15/2022] Open
Abstract
Increasing evidence suggested that the islet amyloid polypeptide (IAPP) is an essential autoantigen in the pathogenesis of type 1 diabetes (T1D) in humans and non-obese diabetic (NOD) mice. A unique disulfide containing IAPP-derived peptide KS20 is one of the highly diabetogenic peptides in NOD mice. The KS20-reactive T cells, including prototypic pathogenic BDC5.2.9, accumulate in the pancreas of prediabetic and diabetic mice and contribute to disease development. We generated a monoclonal antibody (LD96.24) that interacts with IAg7-KS20 complexes with high affinity and specificity. LD96.24 recognized the IAg7-KS20 disulfide loop and blocked the interaction between IAg7-KS20 tetramers and cognate T cells but not other autoantigen-reactive T cells. The in vivo LD96.24 studies, at either early or late stages, drastically induced tolerance and delayed the onset of T1D disease in NOD mice by reducing the infiltration of not only IAPP-specific T cells but also chromogranin A and insulin-specific T cells in the pancreas, together with B cells and dendritic cells. LD96.24 can also significantly increase the ratio of Foxp3+ regulatory T cells with Interferon-gamma-secreting effector T cells. Our data suggested the important role of disulfide-modified peptides in the development of T1D. Targeting the complexes of Major histocompatibility complex (MHC)/disulfide modified antigens would influence the thiol redox balance and could be a novel immunotherapy for T1D.
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Affiliation(s)
- Wei Li
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of Colorado Anschutz Medical Campus, Aurora, CO, United States
- National Health Commission (NHC) Key Laboratory of Pulmonary Immune-Related Diseases, Guizhou Provincial People’s Hospital, Guiyang, China
| | - Yan Zhang
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of Colorado Anschutz Medical Campus, Aurora, CO, United States
| | - Ronghui Li
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of Colorado Anschutz Medical Campus, Aurora, CO, United States
- National Health Commission (NHC) Key Laboratory of Pulmonary Immune-Related Diseases, Guizhou Provincial People’s Hospital, Guiyang, China
| | - Yang Wang
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of Colorado Anschutz Medical Campus, Aurora, CO, United States
| | - Lan Chen
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of Colorado Anschutz Medical Campus, Aurora, CO, United States
| | - Shaodong Dai
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of Colorado Anschutz Medical Campus, Aurora, CO, United States
- Department of Immunology and Microbiology, University of Colorado School of Medicine, Aurora, CO, United States
- *Correspondence: Shaodong Dai,
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10
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Li Y, Jiang W, Mellins ED. TCR-like antibodies targeting autoantigen-mhc complexes: a mini-review. Front Immunol 2022; 13:968432. [PMID: 35967436 PMCID: PMC9363607 DOI: 10.3389/fimmu.2022.968432] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2022] [Accepted: 07/06/2022] [Indexed: 11/13/2022] Open
Abstract
T cell receptors (TCRs) recognize peptide antigens bound to major histocompatibility complex (MHC) molecules (p/MHC) that are expressed on cell surfaces; while B cell-derived antibodies (Abs) recognize soluble or cell surface native antigens of various types (proteins, carbohydrates, etc.). Immune surveillance by T and B cells thus inspects almost all formats of antigens to mount adaptive immune responses against cancer cells, infectious organisms and other foreign insults, while maintaining tolerance to self-tissues. With contributions from environmental triggers, the development of autoimmune disease is thought to be due to the expression of MHC risk alleles by antigen-presenting cells (APCs) presenting self-antigen (autoantigen), breaking through self-tolerance and activating autoreactive T cells, which orchestrate downstream pathologic events. Investigating and treating autoimmune diseases have been challenging, both because of the intrinsic complexity of these diseases and the need for tools targeting T cell epitopes (autoantigen-MHC). Naturally occurring TCRs with relatively low (micromolar) affinities to p/MHC are suboptimal for autoantigen-MHC targeting, whereas the use of engineered TCRs and their derivatives (e.g., TCR multimers and TCR-engineered T cells) are limited by unpredictable cross-reactivity. As Abs generally have nanomolar affinity, recent advances in engineering TCR-like (TCRL) Abs promise advantages over their TCR counterparts for autoantigen-MHC targeting. Here, we compare the p/MHC binding by TCRs and TCRL Abs, review the strategies for generation of TCRL Abs, highlight their application for identification of autoantigen-presenting APCs, and discuss future directions and limitations of TCRL Abs as immunotherapy for autoimmune diseases.
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Affiliation(s)
- Ying Li
- Department of Pediatrics, Divisions of Human Gene Therapy and Allergy, Immunology & Rheumatology, Stanford University School of Medicine, Stanford, CA, United States
- Stanford Program in Immunology, Stanford University School of Medicine, Stanford, CA, United States
| | - Wei Jiang
- Department of Pediatrics, Divisions of Human Gene Therapy and Allergy, Immunology & Rheumatology, Stanford University School of Medicine, Stanford, CA, United States
- Stanford Program in Immunology, Stanford University School of Medicine, Stanford, CA, United States
- *Correspondence: Wei Jiang, ; Elizabeth D. Mellins,
| | - Elizabeth D. Mellins
- Department of Pediatrics, Divisions of Human Gene Therapy and Allergy, Immunology & Rheumatology, Stanford University School of Medicine, Stanford, CA, United States
- Stanford Program in Immunology, Stanford University School of Medicine, Stanford, CA, United States
- *Correspondence: Wei Jiang, ; Elizabeth D. Mellins,
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11
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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Minton AR, Smith LD, Bryant DJ, Strefford JC, Forconi F, Stevenson FK, Tumbarello DA, James E, Løset GÅ, Munthe LA, Steele AJ, Packham G. B-cell receptor dependent phagocytosis and presentation of particulate antigen by chronic lymphocytic leukemia cells. Explor Target Antitumor Ther 2022; 3:37-49. [PMID: 35309250 PMCID: PMC7612515 DOI: 10.37349/etat.2022.00070] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2021] [Accepted: 01/28/2022] [Indexed: 11/28/2022] Open
Abstract
Aim T-helper cells could play an important role in the pathogenesis of chronic lymphocytic leukemia (CLL), a common B-cell neoplasm. Although CLL cells can present soluble antigens targeted from the B-cell receptor to T-helper cells via major histocompatibility complex (MHC) class II, antigens recognized by some CLL cells may be encountered in a particulate form. Here the ability of CLL cells to internalize and present anti-immunoglobulin M (IgM) beads as a model for the interaction of CLL cells with particulate antigens was investigated. Methods The effect of anti-IgM beads on antigen presentation pathways was analyzed using RNA-seq and internalization of anti-IgM beads by primary CLL cells was investigated using confocal microscopy and flow cytometry. Antigen presentation was investigated by analyzing activation of a T-cell line expressing a T-cell receptor specific for a peptide derived from mouse κ light chains after incubating CLL cells with a mouse κ light chain-containing anti-IgM monoclonal antibody. Kinase inhibitors were used to characterize the pathways mediating internalization and antigen presentation. Results Stimulation of surface IgM of CLL cells increased expression of the antigen presentation machinery and CLL cells were able to phagocytose anti-IgM beads. Internalization of anti-IgM beads was associated with MHC class II-restricted activation of cognate T-helper cells. Antigen presentation by CLL cells was dependent on activity of spleen tyrosine kinase (SYK) and phosphatidylinositol 3-kinase delta (PI3Kδ) but was unaffected by inhibitors of Bruton's tyrosine kinase (BTK). Conclusions CLL cells can internalize and present antigen from anti-IgM beads. This capacity of CLL cells may be particularly important for recruitment of T-cell help in vivo in response to particulate antigens.
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Affiliation(s)
- Annabel R. Minton
- Cancer Research UK Centre, Cancer Sciences, Faculty of Medicine, University of Southampton, SO16 6YD Southampton, UK
| | - Lindsay D. Smith
- Cancer Research UK Centre, Cancer Sciences, Faculty of Medicine, University of Southampton, SO16 6YD Southampton, UK
- Current address: Ploughshare Innovations Limited, Porton Science Park, Porton Down, SP4 0BF Wiltshire, UK
| | - Dean J. Bryant
- Cancer Research UK Centre, Cancer Sciences, Faculty of Medicine, University of Southampton, SO16 6YD Southampton, UK
| | - Jonathan C. Strefford
- Cancer Research UK Centre, Cancer Sciences, Faculty of Medicine, University of Southampton, SO16 6YD Southampton, UK
| | - Francesco Forconi
- Cancer Research UK Centre, Cancer Sciences, Faculty of Medicine, University of Southampton, SO16 6YD Southampton, UK
| | - Freda K. Stevenson
- Cancer Research UK Centre, Cancer Sciences, Faculty of Medicine, University of Southampton, SO16 6YD Southampton, UK
| | - David A. Tumbarello
- Biological Sciences, Faculty of Environmental and Life Sciences, University of Southampton, SO17 1BJ Southampton, UK
| | - Edd James
- Cancer Research UK Centre, Cancer Sciences, Faculty of Medicine, University of Southampton, SO16 6YD Southampton, UK
| | | | - Ludvig A. Munthe
- KG Jebsen Centre for B cell Malignancies, Institute of Clinical Medicine, University of Oslo, NO-0424 Oslo, Norway
| | - Andrew J. Steele
- Cancer Research UK Centre, Cancer Sciences, Faculty of Medicine, University of Southampton, SO16 6YD Southampton, UK
- Current address: Janssen R&D, 1400 McKean Road, Spring House, Ambler, PA 19477, USA
| | - Graham Packham
- Cancer Research UK Centre, Cancer Sciences, Faculty of Medicine, University of Southampton, SO16 6YD Southampton, UK
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Frick R, Høydahl LS, Hodnebrug I, Vik ES, Dalhus B, Sollid LM, Gray JJ, Sandlie I, Løset GÅ. Affinity maturation of TCR-like antibodies using phage display guided by structural modeling. Protein Eng Des Sel 2022; 35:6649134. [PMID: 35871543 PMCID: PMC9536190 DOI: 10.1093/protein/gzac005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2022] [Revised: 07/02/2022] [Accepted: 07/05/2022] [Indexed: 12/01/2022] Open
Abstract
TCR-like antibodies represent a unique type of engineered antibodies with specificity toward pHLA, a ligand normally restricted to the sensitive recognition by T cells. Here, we report a phage display-based sequential development path of such antibodies. The strategy goes from initial lead identification through in silico informed CDR engineering in combination with framework engineering for affinity and thermostability optimization, respectively. The strategy allowed the identification of HLA-DQ2.5 gluten peptide-specific TCR-like antibodies with low picomolar affinity. Our method outlines an efficient and general method for development of this promising class of antibodies, which should facilitate their utility including translation to human therapy.
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Affiliation(s)
- Rahel Frick
- Centre for Immune Regulation and Department of Immunology, University of Oslo and Oslo University Hospital , Sognsvannsveien 20, 0372 Oslo, Norway
- Centre for Immune Regulation and Department of Biosciences, University of Oslo , Blindernveien 31, 0371 Oslo, Norway
- Department of Chemical and Biomolecular Engineering, Johns Hopkins University , 3400 N. Charles Street, Baltimore, MD 21218, USA
| | - Lene S Høydahl
- Centre for Immune Regulation and Department of Immunology, University of Oslo and Oslo University Hospital , Sognsvannsveien 20, 0372 Oslo, Norway
- Centre for Immune Regulation and Department of Biosciences, University of Oslo , Blindernveien 31, 0371 Oslo, Norway
- KG Jebsen Coeliac Disease Research Centre, University of Oslo , Sognsvannsveien 20, 0372 Oslo, Norway
| | - Ina Hodnebrug
- Centre for Immune Regulation and Department of Immunology, University of Oslo and Oslo University Hospital , Sognsvannsveien 20, 0372 Oslo, Norway
- Centre for Immune Regulation and Department of Biosciences, University of Oslo , Blindernveien 31, 0371 Oslo, Norway
| | - Erik S Vik
- Nextera AS , Gaustadalléen 21, 0349 Oslo, Norway
| | - Bjørn Dalhus
- Department for Medical Biochemistry , Institute for Clinical Medicine, , Sognsvannsveien 20, 0372 Oslo, Norway
- University of Oslo , Institute for Clinical Medicine, , Sognsvannsveien 20, 0372 Oslo, Norway
- Department for Microbiology , Clinic for Laboratory Medicine, , Sognsvannsveien 20, 0372 Oslo, Norway
- Oslo University Hospital , Clinic for Laboratory Medicine, , Sognsvannsveien 20, 0372 Oslo, Norway
| | - Ludvig M Sollid
- Centre for Immune Regulation and Department of Immunology, University of Oslo and Oslo University Hospital , Sognsvannsveien 20, 0372 Oslo, Norway
- KG Jebsen Coeliac Disease Research Centre, University of Oslo , Sognsvannsveien 20, 0372 Oslo, Norway
| | - Jeffrey J Gray
- Program in Molecular Biophysics, Johns Hopkins University , 3400 N. Charles Street, Baltimore, MD 21218, USA
- Department of Chemical and Biomolecular Engineering and Institute of NanoBioTechnology, Johns Hopkins University , 3400 N. Charles Street, Baltimore, MD 21218, USA
- Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins School of Medicine , 733 N Broadway, Baltimore, MD 21205, USA
| | - Inger Sandlie
- Centre for Immune Regulation and Department of Immunology, University of Oslo and Oslo University Hospital , Sognsvannsveien 20, 0372 Oslo, Norway
- Centre for Immune Regulation and Department of Biosciences, University of Oslo , Blindernveien 31, 0371 Oslo, Norway
| | - Geir Åge Løset
- Centre for Immune Regulation and Department of Immunology, University of Oslo and Oslo University Hospital , Sognsvannsveien 20, 0372 Oslo, Norway
- Centre for Immune Regulation and Department of Biosciences, University of Oslo , Blindernveien 31, 0371 Oslo, Norway
- Nextera AS , Gaustadalléen 21, 0349 Oslo, Norway
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