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Omelchenko AA, Siwek JC, Chhibbar P, Arshad S, Nazarali I, Nazarali K, Rosengart A, Rahimikollu J, Tilstra J, Shlomchik MJ, Koes DR, Joglekar AV, Das J. Sliding Window INteraction Grammar (SWING): a generalized interaction language model for peptide and protein interactions. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.01.592062. [PMID: 38746274 PMCID: PMC11092674 DOI: 10.1101/2024.05.01.592062] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/16/2024]
Abstract
The explosion of sequence data has allowed the rapid growth of protein language models (pLMs). pLMs have now been employed in many frameworks including variant-effect and peptide-specificity prediction. Traditionally, for protein-protein or peptide-protein interactions (PPIs), corresponding sequences are either co-embedded followed by post-hoc integration or the sequences are concatenated prior to embedding. Interestingly, no method utilizes a language representation of the interaction itself. We developed an interaction LM (iLM), which uses a novel language to represent interactions between protein/peptide sequences. Sliding Window Interaction Grammar (SWING) leverages differences in amino acid properties to generate an interaction vocabulary. This vocabulary is the input into a LM followed by a supervised prediction step where the LM's representations are used as features. SWING was first applied to predicting peptide:MHC (pMHC) interactions. SWING was not only successful at generating Class I and Class II models that have comparable prediction to state-of-the-art approaches, but the unique Mixed Class model was also successful at jointly predicting both classes. Further, the SWING model trained only on Class I alleles was predictive for Class II, a complex prediction task not attempted by any existing approach. For de novo data, using only Class I or Class II data, SWING also accurately predicted Class II pMHC interactions in murine models of SLE (MRL/lpr model) and T1D (NOD model), that were validated experimentally. To further evaluate SWING's generalizability, we tested its ability to predict the disruption of specific protein-protein interactions by missense mutations. Although modern methods like AlphaMissense and ESM1b can predict interfaces and variant effects/pathogenicity per mutation, they are unable to predict interaction-specific disruptions. SWING was successful at accurately predicting the impact of both Mendelian mutations and population variants on PPIs. This is the first generalizable approach that can accurately predict interaction-specific disruptions by missense mutations with only sequence information. Overall, SWING is a first-in-class generalizable zero-shot iLM that learns the language of PPIs.
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Affiliation(s)
- Alisa A. Omelchenko
- Center for Systems immunology, School of Medicine, University of Pittsburgh, Pittsburgh, PA, USA
- Department of Immunology, School of Medicine, University of Pittsburgh, Pittsburgh, PA, USA
- Department of Computational and Systems Biology, School of Medicine, University of Pittsburgh, PA, USA
- The joint CMU-Pitt PhD program in computational biology, School of Medicine, University of Pittsburgh, PA, USA
| | - Jane C. Siwek
- Center for Systems immunology, School of Medicine, University of Pittsburgh, Pittsburgh, PA, USA
- Department of Immunology, School of Medicine, University of Pittsburgh, Pittsburgh, PA, USA
- Department of Computational and Systems Biology, School of Medicine, University of Pittsburgh, PA, USA
- The joint CMU-Pitt PhD program in computational biology, School of Medicine, University of Pittsburgh, PA, USA
| | - Prabal Chhibbar
- Center for Systems immunology, School of Medicine, University of Pittsburgh, Pittsburgh, PA, USA
- Department of Immunology, School of Medicine, University of Pittsburgh, Pittsburgh, PA, USA
- Integrative systems biology PhD program, School of Medicine, University of Pittsburgh, PA, USA
| | - Sanya Arshad
- Center for Systems immunology, School of Medicine, University of Pittsburgh, Pittsburgh, PA, USA
- Department of Immunology, School of Medicine, University of Pittsburgh, Pittsburgh, PA, USA
| | - Iliyan Nazarali
- Center for Systems immunology, School of Medicine, University of Pittsburgh, Pittsburgh, PA, USA
| | - Kiran Nazarali
- Center for Systems immunology, School of Medicine, University of Pittsburgh, Pittsburgh, PA, USA
| | - AnnaElaine Rosengart
- Center for Systems immunology, School of Medicine, University of Pittsburgh, Pittsburgh, PA, USA
| | - Javad Rahimikollu
- Center for Systems immunology, School of Medicine, University of Pittsburgh, Pittsburgh, PA, USA
- Department of Immunology, School of Medicine, University of Pittsburgh, Pittsburgh, PA, USA
- Department of Computational and Systems Biology, School of Medicine, University of Pittsburgh, PA, USA
- The joint CMU-Pitt PhD program in computational biology, School of Medicine, University of Pittsburgh, PA, USA
| | - Jeremy Tilstra
- Department of Immunology, School of Medicine, University of Pittsburgh, Pittsburgh, PA, USA
- Division of Rheumatology and Clinical Immunology, Department of Medicine, School of Medicine, University of Pittsburgh, PA, USA
| | - Mark J. Shlomchik
- Department of Immunology, School of Medicine, University of Pittsburgh, Pittsburgh, PA, USA
| | - David R. Koes
- Department of Computational and Systems Biology, School of Medicine, University of Pittsburgh, PA, USA
| | - Alok V. Joglekar
- Center for Systems immunology, School of Medicine, University of Pittsburgh, Pittsburgh, PA, USA
- Department of Immunology, School of Medicine, University of Pittsburgh, Pittsburgh, PA, USA
- Department of Computational and Systems Biology, School of Medicine, University of Pittsburgh, PA, USA
| | - Jishnu Das
- Center for Systems immunology, School of Medicine, University of Pittsburgh, Pittsburgh, PA, USA
- Department of Immunology, School of Medicine, University of Pittsburgh, Pittsburgh, PA, USA
- Department of Computational and Systems Biology, School of Medicine, University of Pittsburgh, PA, USA
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Sengupta S, Zhang J, Reed MC, Yu J, Kim A, Boronina TN, Board NL, Wrabl JO, Shenderov K, Welsh RA, Yang W, Timmons AE, Hoh R, Cole RN, Deeks SG, Siliciano JD, Siliciano RF, Sadegh-Nasseri S. A cell-free antigen processing system informs HIV-1 epitope selection and vaccine design. J Exp Med 2023; 220:e20221654. [PMID: 37058141 PMCID: PMC10114365 DOI: 10.1084/jem.20221654] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2022] [Revised: 02/01/2023] [Accepted: 03/23/2023] [Indexed: 04/15/2023] Open
Abstract
Distinct CD4+ T cell epitopes have been associated with spontaneous control of HIV-1 replication, but analysis of antigen-dependent factors that influence epitope selection is lacking. To examine these factors, we used a cell-free antigen processing system that incorporates soluble HLA-DR (DR1), HLA-DM (DM), cathepsins, and full-length protein antigens for epitope identification by LC-MS/MS. HIV-1 Gag, Pol, Env, Vif, Tat, Rev, and Nef were examined using this system. We identified 35 novel epitopes, including glycopeptides. Epitopes from smaller HIV-1 proteins mapped to regions of low protein stability and higher solvent accessibility. HIV-1 antigens associated with limited CD4+ T cell responses were processed efficiently, while some protective epitopes were inefficiently processed. 55% of epitopes obtained from cell-free processing induced memory CD4+ T cell responses in HIV-1+ donors, including eight of 19 novel epitopes tested. Thus, an in vitro processing system utilizing the components of Class II processing reveals factors influencing epitope selection of HIV-1 and represents an approach to understanding epitope selection from non-HIV-1 antigens.
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Affiliation(s)
- Srona Sengupta
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- The Graduate Program in Immunology and Medical Scientist Training Program, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Josephine Zhang
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Madison C. Reed
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Jeanna Yu
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Aeryon Kim
- Department of Inflammation and Oncology and Genome Analysis Unit, Amgen Research, Amgen Inc., South San Francisco, CA, USA
| | - Tatiana N. Boronina
- Department of Biological Chemistry, Mass Spectrometry and Proteomics Facility, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Nathan L. Board
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - James O. Wrabl
- Department of Biology, Johns Hopkins University, Baltimore, MD, USA
| | - Kevin Shenderov
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Robin A. Welsh
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Weiming Yang
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Andrew E. Timmons
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Rebecca Hoh
- Department of Medicine, University of California, San Francisco, San Francisco, CA, USA
| | - Robert N. Cole
- Department of Biological Chemistry, Mass Spectrometry and Proteomics Facility, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Steven G. Deeks
- Department of Medicine, University of California, San Francisco, San Francisco, CA, USA
| | - Janet D. Siliciano
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Robert F. Siliciano
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Howard Hughes Medical Institute, Baltimore, MD, USA
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Liu M, Lau CYJ, Cabello IT, Garssen J, Willemsen LEM, Hennink WE, van Nostrum CF. Live Cell Imaging by Förster Resonance Energy Transfer Fluorescence to Study Trafficking of PLGA Nanoparticles and the Release of a Loaded Peptide in Dendritic Cells. Pharmaceuticals (Basel) 2023; 16:818. [PMID: 37375766 DOI: 10.3390/ph16060818] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2023] [Revised: 05/25/2023] [Accepted: 05/25/2023] [Indexed: 06/29/2023] Open
Abstract
Our previous study demonstrated that a selected β-lactoglobulin-derived peptide (BLG-Pep) loaded in poly(lactic-co-glycolic acid) (PLGA) nanoparticles protected mice against cow's milk allergy development. However, the mechanism(s) responsible for the interaction of the peptide-loaded PLGA nanoparticles with dendritic cells (DCs) and their intracellular fate was/were elusive. Förster resonance energy transfer (FRET), a distance-dependent non-radioactive energy transfer process mediated from a donor to an acceptor fluorochrome, was used to investigate these processes. The ratio of the donor (Cyanine-3)-conjugated peptide and acceptor (Cyanine-5) labeled PLGA nanocarrier was fine-tuned for optimal (87%) FRET efficiency. The colloidal stability and FRET emission of prepared NPs were maintained upon 144 h incubation in PBS buffer and 6 h incubation in biorelevant simulated gastric fluid at 37 °C. A total of 73% of Pep-Cy3 NP was internalized by DCs as quantified using flow cytometry and confirmed using confocal fluorescence microscopy. By real-time monitoring of the change in the FRET signal of the internalized peptide-loaded nanoparticles, we observed prolonged retention (for 96 h) of the nanoparticles-encapsulated peptide as compared to 24 h retention of the free peptide in the DCs. The prolonged retention and intracellular antigen release of the BLG-Pep loaded in PLGA nanoparticles in murine DCs might facilitate antigen-specific tolerance induction.
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Affiliation(s)
- Mengshan Liu
- Department of Pharmaceutics, Utrecht Institute for Pharmaceutical Sciences, Utrecht University, 3584 CG Utrecht, The Netherlands
- Department of Pharmacology, Utrecht Institute for Pharmaceutical Sciences, Utrecht University, 3584 CG Utrecht, The Netherlands
| | - Chun Yin Jerry Lau
- Department of Pharmaceutics, Utrecht Institute for Pharmaceutical Sciences, Utrecht University, 3584 CG Utrecht, The Netherlands
| | - Irene Trillo Cabello
- Department of Pharmaceutics, Utrecht Institute for Pharmaceutical Sciences, Utrecht University, 3584 CG Utrecht, The Netherlands
| | - Johan Garssen
- Department of Pharmacology, Utrecht Institute for Pharmaceutical Sciences, Utrecht University, 3584 CG Utrecht, The Netherlands
- Department of Immunology, Nutricia Research B.V., 3584 CT Utrecht, The Netherlands
| | - Linette E M Willemsen
- Department of Pharmacology, Utrecht Institute for Pharmaceutical Sciences, Utrecht University, 3584 CG Utrecht, The Netherlands
| | - Wim E Hennink
- Department of Pharmaceutics, Utrecht Institute for Pharmaceutical Sciences, Utrecht University, 3584 CG Utrecht, The Netherlands
| | - Cornelus F van Nostrum
- Department of Pharmaceutics, Utrecht Institute for Pharmaceutical Sciences, Utrecht University, 3584 CG Utrecht, The Netherlands
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Huisman BD, Dai Z, Gifford DK, Birnbaum ME. A high-throughput yeast display approach to profile pathogen proteomes for MHC-II binding. eLife 2022; 11:e78589. [PMID: 35781135 PMCID: PMC9292997 DOI: 10.7554/elife.78589] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2022] [Accepted: 07/04/2022] [Indexed: 11/13/2022] Open
Abstract
T cells play a critical role in the adaptive immune response, recognizing peptide antigens presented on the cell surface by major histocompatibility complex (MHC) proteins. While assessing peptides for MHC binding is an important component of probing these interactions, traditional assays for testing peptides of interest for MHC binding are limited in throughput. Here, we present a yeast display-based platform for assessing the binding of tens of thousands of user-defined peptides in a high-throughput manner. We apply this approach to assess a tiled library covering the SARS-CoV-2 proteome and four dengue virus serotypes for binding to human class II MHCs, including HLA-DR401, -DR402, and -DR404. While the peptide datasets show broad agreement with previously described MHC-binding motifs, they additionally reveal experimentally validated computational false positives and false negatives. We therefore present this approach as able to complement current experimental datasets and computational predictions. Further, our yeast display approach underlines design considerations for epitope identification experiments and serves as a framework for examining relationships between viral conservation and MHC binding, which can be used to identify potentially high-interest peptide binders from viral proteins. These results demonstrate the utility of our approach to determine peptide-MHC binding interactions in a manner that can supplement and potentially enhance current algorithm-based approaches.
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Affiliation(s)
- Brooke D Huisman
- Koch Institute for Integrative Cancer ResearchCambridgeUnited States
- Department of Biological Engineering, Massachusetts Institute of TechnologyCambridgeUnited States
| | - Zheng Dai
- Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of TechnologyCambridgeUnited States
- Department of Electrical Engineering and Computer Science, Massachusetts Institute of TechnologyCambridgeUnited States
| | - David K Gifford
- Department of Biological Engineering, Massachusetts Institute of TechnologyCambridgeUnited States
- Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of TechnologyCambridgeUnited States
- Department of Electrical Engineering and Computer Science, Massachusetts Institute of TechnologyCambridgeUnited States
| | - Michael E Birnbaum
- Koch Institute for Integrative Cancer ResearchCambridgeUnited States
- Department of Biological Engineering, Massachusetts Institute of TechnologyCambridgeUnited States
- Ragon Institute of MGH, MIT and HarvardCambridgeUnited States
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5
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Patarroyo MA, Patarroyo ME, Pabón L, Alba MP, Bermudez A, Rugeles MT, Díaz-Arevalo D, Zapata-Builes W, Zapata MI, Reyes C, Suarez CF, Agudelo W, López C, Aza-Conde J, Melo M, Escamilla L, Oviedo J, Guzmán F, Silva Y, Forero M, Flórez-Álvarez L, Aguilar-Jimenez W, Moreno-Vranich A, Garry J, Avendaño C. SM-COLSARSPROT: Highly Immunogenic Supramutational Synthetic Peptides Covering the World's Population. Front Immunol 2022; 13:859905. [PMID: 35693819 PMCID: PMC9175637 DOI: 10.3389/fimmu.2022.859905] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2022] [Accepted: 04/19/2022] [Indexed: 12/02/2022] Open
Abstract
Fifty ~20-amino acid (aa)-long peptides were selected from functionally relevant SARS-CoV-2 S, M, and E proteins for trial B-21 and another 53 common ones, plus some new ones derived from the virus' main genetic variants for complementary trial C-21. Peptide selection was based on tremendous SARS-CoV-2 genetic variability for analysing them concerning vast human immunogenetic polymorphism for developing the first supramutational, Colombian SARS-protection (SM-COLSARSPROT), peptide mixture. Specific physicochemical rules were followed, i.e., aa predilection for polyproline type II left-handed (PPIIL) formation, replacing β-branched, aromatic aa, short-chain backbone H-bond-forming residues, π-π interactions (n→π* and π-CH), aa interaction with π systems, and molecular fragments able to interact with them, disrupting PPIIL propensity formation. All these modified structures had PPIIL formation propensity to enable target peptide interaction with human leukocyte antigen-DRβ1* (HLA-DRβ1*) molecules to mediate antigen presentation and induce an appropriate immune response. Such modified peptides were designed for human use; however, they induced high antibody titres against S, M, and E parental mutant peptides and neutralising antibodies when suitably modified and chemically synthesised for immunising 61 major histocompatibility complex class II (MHCII) DNA genotyped Aotus monkeys (matched with their corresponding HLA-DRβ1* molecules), predicted to cover 77.5% to 83.1% of the world's population. Such chemically synthesised peptide mixture represents an extremely pure, stable, reliable, and cheap vaccine for COVID-19 pandemic control, providing a new approach for a logical, rational, and soundly established methodology for other vaccine development.
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Affiliation(s)
- Manuel A. Patarroyo
- Grupos: Síntesis Química, Resonancia Magnética Nuclear y Cálculo Estructural, Biología Molecular e Inmunología e Inmuno-Química, Fundación Instituto de Inmunología de Colombia (FIDIC), Bogotá, Colombia
| | - Manuel E. Patarroyo
- Grupos: Síntesis Química, Resonancia Magnética Nuclear y Cálculo Estructural, Biología Molecular e Inmunología e Inmuno-Química, Fundación Instituto de Inmunología de Colombia (FIDIC), Bogotá, Colombia
| | - Laura Pabón
- Grupos: Síntesis Química, Resonancia Magnética Nuclear y Cálculo Estructural, Biología Molecular e Inmunología e Inmuno-Química, Fundación Instituto de Inmunología de Colombia (FIDIC), Bogotá, Colombia
| | - Martha P. Alba
- Grupos: Síntesis Química, Resonancia Magnética Nuclear y Cálculo Estructural, Biología Molecular e Inmunología e Inmuno-Química, Fundación Instituto de Inmunología de Colombia (FIDIC), Bogotá, Colombia
| | - Adriana Bermudez
- Grupos: Síntesis Química, Resonancia Magnética Nuclear y Cálculo Estructural, Biología Molecular e Inmunología e Inmuno-Química, Fundación Instituto de Inmunología de Colombia (FIDIC), Bogotá, Colombia
| | - María Teresa Rugeles
- Grupo Inmunovirología, Facultad de Medicina, Universidad de Antioquia UdeA, Medellín, Colombia
| | - Diana Díaz-Arevalo
- Grupos: Síntesis Química, Resonancia Magnética Nuclear y Cálculo Estructural, Biología Molecular e Inmunología e Inmuno-Química, Fundación Instituto de Inmunología de Colombia (FIDIC), Bogotá, Colombia
| | - Wildeman Zapata-Builes
- Grupo Inmunovirología, Facultad de Medicina, Universidad de Antioquia UdeA, Medellín, Colombia
| | - María Isabel Zapata
- Grupo Inmunovirología, Facultad de Medicina, Universidad de Antioquia UdeA, Medellín, Colombia
| | - César Reyes
- Grupos: Síntesis Química, Resonancia Magnética Nuclear y Cálculo Estructural, Biología Molecular e Inmunología e Inmuno-Química, Fundación Instituto de Inmunología de Colombia (FIDIC), Bogotá, Colombia
| | - Carlos F. Suarez
- Grupos: Síntesis Química, Resonancia Magnética Nuclear y Cálculo Estructural, Biología Molecular e Inmunología e Inmuno-Química, Fundación Instituto de Inmunología de Colombia (FIDIC), Bogotá, Colombia
| | - William Agudelo
- Grupos: Síntesis Química, Resonancia Magnética Nuclear y Cálculo Estructural, Biología Molecular e Inmunología e Inmuno-Química, Fundación Instituto de Inmunología de Colombia (FIDIC), Bogotá, Colombia
| | - Carolina López
- Grupos: Síntesis Química, Resonancia Magnética Nuclear y Cálculo Estructural, Biología Molecular e Inmunología e Inmuno-Química, Fundación Instituto de Inmunología de Colombia (FIDIC), Bogotá, Colombia
| | - Jorge Aza-Conde
- Grupos: Síntesis Química, Resonancia Magnética Nuclear y Cálculo Estructural, Biología Molecular e Inmunología e Inmuno-Química, Fundación Instituto de Inmunología de Colombia (FIDIC), Bogotá, Colombia
| | - Miguel Melo
- Grupos: Síntesis Química, Resonancia Magnética Nuclear y Cálculo Estructural, Biología Molecular e Inmunología e Inmuno-Química, Fundación Instituto de Inmunología de Colombia (FIDIC), Bogotá, Colombia
| | - Luis Escamilla
- Grupos: Síntesis Química, Resonancia Magnética Nuclear y Cálculo Estructural, Biología Molecular e Inmunología e Inmuno-Química, Fundación Instituto de Inmunología de Colombia (FIDIC), Bogotá, Colombia
| | - Jairo Oviedo
- Grupos: Síntesis Química, Resonancia Magnética Nuclear y Cálculo Estructural, Biología Molecular e Inmunología e Inmuno-Química, Fundación Instituto de Inmunología de Colombia (FIDIC), Bogotá, Colombia
| | - Fanny Guzmán
- Núcleo de Biotecnología, Pontificia U. Católica de Valparaíso, Valparaíso, Chile
| | - Yolanda Silva
- Grupos: Síntesis Química, Resonancia Magnética Nuclear y Cálculo Estructural, Biología Molecular e Inmunología e Inmuno-Química, Fundación Instituto de Inmunología de Colombia (FIDIC), Bogotá, Colombia
| | - Martha Forero
- Grupos: Síntesis Química, Resonancia Magnética Nuclear y Cálculo Estructural, Biología Molecular e Inmunología e Inmuno-Química, Fundación Instituto de Inmunología de Colombia (FIDIC), Bogotá, Colombia
| | - Lizdany Flórez-Álvarez
- Grupo Inmunovirología, Facultad de Medicina, Universidad de Antioquia UdeA, Medellín, Colombia
| | - Wbeimar Aguilar-Jimenez
- Grupo Inmunovirología, Facultad de Medicina, Universidad de Antioquia UdeA, Medellín, Colombia
| | - Armando Moreno-Vranich
- Grupos: Síntesis Química, Resonancia Magnética Nuclear y Cálculo Estructural, Biología Molecular e Inmunología e Inmuno-Química, Fundación Instituto de Inmunología de Colombia (FIDIC), Bogotá, Colombia
| | - Jason Garry
- Grupos: Síntesis Química, Resonancia Magnética Nuclear y Cálculo Estructural, Biología Molecular e Inmunología e Inmuno-Química, Fundación Instituto de Inmunología de Colombia (FIDIC), Bogotá, Colombia
| | - Catalina Avendaño
- Facultad de Ciencias Agropecualrias, Universidad de Ciencias Aplicadas y Ambientales (UDCA), Bogotá, Colombia
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6
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Huisman BD, Grace BE, Holec PV, Birnbaum ME. Yeast Display for the Identification of Peptide-MHC Ligands of Immune Receptors. Methods Mol Biol 2022; 2491:263-291. [PMID: 35482196 DOI: 10.1007/978-1-0716-2285-8_15] [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] [Indexed: 06/14/2023]
Abstract
T cells detect peptide antigens presented by major histocompatibility complex (MHC) proteins via their T cell receptor (TCR). The sequence diversity of possible antigens, with trillions of potential peptide-MHC targets, makes it challenging to study, characterize, and manipulate the peptide repertoire of a given TCR. Yeast display has been utilized to study the interactions between peptide-MHCs and T cell receptors to facilitate high-throughput screening of peptide-MHC libraries. Here we present insights on designing and validating a peptide-MHC yeast display construct, designing and constructing peptide libraries, conducting selections, and preparing, processing, and analyzing peptide library sequencing data. Applications for this approach are broad, including characterizing peptide-MHC recognition profiles for a TCR, screening for high-affinity mimotopes of known TCR-binding peptides, and identifying natural ligands of TCRs from expanded T cells.
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Affiliation(s)
- Brooke D Huisman
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, USA
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Beth E Grace
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, USA
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Patrick V Holec
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, USA
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Michael E Birnbaum
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, USA.
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA.
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7
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Bell DR, Domeniconi G, Yang CC, Zhou R, Zhang L, Cong G. Dynamics-Based Peptide-MHC Binding Optimization by a Convolutional Variational Autoencoder: A Use-Case Model for CASTELO. J Chem Theory Comput 2021; 17:7962-7971. [PMID: 34793168 DOI: 10.1021/acs.jctc.1c00870] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
An unsolved challenge in the development of antigen-specific immunotherapies is determining the optimal antigens to target. Comprehension of antigen-major histocompatibility complex (MHC) binding is paramount toward achieving this goal. Here, we apply CASTELO, a combined machine learning-molecular dynamics (ML-MD) approach, to identify per-residue antigen binding contributions and then design novel antigens of increased MHC-II binding affinity for a type 1 diabetes-implicated system. We build upon a small-molecule lead optimization algorithm by training a convolutional variational autoencoder (CVAE) on MD trajectories of 48 different systems across four antigens and four HLA serotypes. We develop several new machine learning metrics including a structure-based anchor residue classification model as well as cluster comparison scores. ML-MD predictions agree well with experimental binding results and free energy perturbation-predicted binding affinities. Moreover, ML-MD metrics are independent of traditional MD stability metrics such as contact area and root-mean-square fluctuations (RMSF), which do not reflect binding affinity data. Our work supports the role of structure-based deep learning techniques in antigen-specific immunotherapy design.
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Affiliation(s)
- David R Bell
- IBM Thomas J. Watson Research Center, Yorktown Heights, New York 10598, United States.,Advanced Biomedical Computational Science, Frederick National Laboratory for Cancer Research, Frederick, Maryland 21701, United States
| | - Giacomo Domeniconi
- IBM Thomas J. Watson Research Center, Yorktown Heights, New York 10598, United States
| | - Chih-Chieh Yang
- IBM Thomas J. Watson Research Center, Yorktown Heights, New York 10598, United States
| | - Ruhong Zhou
- IBM Thomas J. Watson Research Center, Yorktown Heights, New York 10598, United States.,Zhejiang University, 688 Yuhangtang Road, Hangzhou 310027, China
| | - Leili Zhang
- IBM Thomas J. Watson Research Center, Yorktown Heights, New York 10598, United States
| | - Guojing Cong
- IBM Thomas J. Watson Research Center, Yorktown Heights, New York 10598, United States.,Oak Ridge National Laboratory, 1 Bethel Valley Road, Oak Ridge, Tennessee 37830, United States
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8
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Repertoire-scale determination of class II MHC peptide binding via yeast display improves antigen prediction. Nat Commun 2020; 11:4414. [PMID: 32887877 PMCID: PMC7473865 DOI: 10.1038/s41467-020-18204-2] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2020] [Accepted: 08/12/2020] [Indexed: 02/03/2023] Open
Abstract
CD4+ helper T cells contribute important functions to the immune response during pathogen infection and tumor formation by recognizing antigenic peptides presented by class II major histocompatibility complexes (MHC-II). While many computational algorithms for predicting peptide binding to MHC-II proteins have been reported, their performance varies greatly. Here we present a yeast-display-based platform that allows the identification of over an order of magnitude more unique MHC-II binders than comparable approaches. These peptides contain previously identified motifs, but also reveal new motifs that are validated by in vitro binding assays. Training of prediction algorithms with yeast-display library data improves the prediction of peptide-binding affinity and the identification of pathogen-associated and tumor-associated peptides. In summary, our yeast-display-based platform yields high-quality MHC-II-binding peptide datasets that can be used to improve the accuracy of MHC-II binding prediction algorithms, and potentially enhance our understanding of CD4+ T cell recognition. Identifying peptides that can bind major histocompatibility complex II (MHC-II) is important for our understanding of T cell immunity and specificity. Here the authors present a yeast-display library screening approach that identifies more potential binders than various reported algorithms to help expand our understanding for antigen presentation.
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9
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Kampstra ASB, van Heemst J, Janssen GM, de Ru AH, van Lummel M, van Veelen PA, Toes REM. Ligandomes obtained from different HLA-class II-molecules are homologous for N- and C-terminal residues outside the peptide-binding cleft. Immunogenetics 2019; 71:519-530. [PMID: 31520135 PMCID: PMC6790208 DOI: 10.1007/s00251-019-01129-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2019] [Accepted: 08/23/2019] [Indexed: 12/31/2022]
Abstract
Human CD4+ T lymphocytes play an important role in inducing potent immune responses. T cells are activated and stimulated by peptides presented in human leucocyte antigen (HLA)-class II molecules. These HLA-class II molecules typically present peptides of between 12 and 20 amino acids in length. The region that interacts with the HLA molecule, designated as the peptide-binding core, is highly conserved in the residues which anchor the peptide to the molecule. In addition, as these peptides are the product of proteolytic cleavages, certain conserved residues may be expected at the N- and C-termini outside the binding core. To study whether similar conserved residues are present in different cell types, potentially harbouring different proteolytic enzymes, the ligandomes of HLA-DRB1*03:01/HLA-DRB > 1 derived from two different cell types (dendritic cells and EBV-transformed B cells) were identified with mass spectrometry and the binding core and N- and C-terminal residues of a total of 16,568 peptides were analysed using the frequencies of the amino acids in the human proteome. Similar binding motifs were found as well as comparable conservations in the N- and C-terminal residues. Furthermore, the terminal conservations of these ligandomes were compared to the N- and C-terminal conservations of the ligandome acquired from dendritic cells homozygous for HLA-DRB1*04:01. Again, comparable conservations were evident with only minor differences. Taken together, these data show that there are conservations in the terminal residues of peptides, presumably the result of the activity of proteases involved in antigen processing.
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Affiliation(s)
- Arieke S B Kampstra
- Department of Rheumatology, Leiden University Medical Center, Leiden, The Netherlands.
| | - Jurgen van Heemst
- Department of Rheumatology, Leiden University Medical Center, Leiden, The Netherlands
| | - George M Janssen
- Center of Proteomics and Metabolomics, Leiden University Medical Center, Leiden, The Netherlands
| | - Arnoud H de Ru
- Center of Proteomics and Metabolomics, Leiden University Medical Center, Leiden, The Netherlands
| | - Menno van Lummel
- Department of Immunohematology and Blood Transfusion, Leiden University Medical Center, Leiden, The Netherlands
| | - Peter A van Veelen
- Center of Proteomics and Metabolomics, Leiden University Medical Center, Leiden, The Netherlands
| | - René E M Toes
- Department of Rheumatology, Leiden University Medical Center, Leiden, The Netherlands
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10
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Footprints of antigen processing boost MHC class II natural ligand predictions. Genome Med 2018; 10:84. [PMID: 30446001 PMCID: PMC6240193 DOI: 10.1186/s13073-018-0594-6] [Citation(s) in RCA: 59] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2018] [Accepted: 10/30/2018] [Indexed: 12/21/2022] Open
Abstract
Background Major histocompatibility complex class II (MHC-II) molecules present peptide fragments to T cells for immune recognition. Current predictors for peptide to MHC-II binding are trained on binding affinity data, generated in vitro and therefore lacking information about antigen processing. Methods We generate prediction models of peptide to MHC-II binding trained with naturally eluted ligands derived from mass spectrometry in addition to peptide binding affinity data sets. Results We show that integrated prediction models incorporate identifiable rules of antigen processing. In fact, we observed detectable signals of protease cleavage at defined positions of the ligands. We also hypothesize a role of the length of the terminal ligand protrusions for trimming the peptide to the MHC presented ligand. Conclusions The results of integrating binding affinity and eluted ligand data in a combined model demonstrate improved performance for the prediction of MHC-II ligands and T cell epitopes and foreshadow a new generation of improved peptide to MHC-II prediction tools accounting for the plurality of factors that determine natural presentation of antigens. Electronic supplementary material The online version of this article (10.1186/s13073-018-0594-6) contains supplementary material, which is available to authorized users.
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11
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Curtidor H, Reyes C, Bermúdez A, Vanegas M, Varela Y, Patarroyo ME. Conserved Binding Regions Provide the Clue for Peptide-Based Vaccine Development: A Chemical Perspective. Molecules 2017; 22:molecules22122199. [PMID: 29231862 PMCID: PMC6149789 DOI: 10.3390/molecules22122199] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2017] [Revised: 11/24/2017] [Accepted: 11/27/2017] [Indexed: 12/17/2022] Open
Abstract
Synthetic peptides have become invaluable biomedical research and medicinal chemistry tools for studying functional roles, i.e., binding or proteolytic activity, naturally-occurring regions’ immunogenicity in proteins and developing therapeutic agents and vaccines. Synthetic peptides can mimic protein sites; their structure and function can be easily modulated by specific amino acid replacement. They have major advantages, i.e., they are cheap, easily-produced and chemically stable, lack infectious and secondary adverse reactions and can induce immune responses via T- and B-cell epitopes. Our group has previously shown that using synthetic peptides and adopting a functional approach has led to identifying Plasmodium falciparumconserved regions binding to host cells. Conserved high activity binding peptides’ (cHABPs) physicochemical, structural and immunological characteristics have been taken into account for properly modifying and converting them into highly immunogenic, protection-inducing peptides (mHABPs) in the experimental Aotus monkey model. This article describes stereo–electron and topochemical characteristics regarding major histocompatibility complex (MHC)-mHABP-T-cell receptor (TCR) complex formation. Some mHABPs in this complex inducing long-lasting, protective immunity have been named immune protection-inducing protein structures (IMPIPS), forming the subunit components in chemically synthesized vaccines. This manuscript summarizes this particular field and adds our recent findings concerning intramolecular interactions (H-bonds or π-interactions) enabling proper IMPIPS structure as well as the peripheral flanking residues (PFR) to stabilize the MHCII-IMPIPS-TCR interaction, aimed at inducing long-lasting, protective immunological memory.
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Affiliation(s)
- Hernando Curtidor
- Colombian Institute of Immunology Foundation (FIDIC Nonprofit-Making Organisation), Bogotá 111321, Colombia.
- School of Medicine and Health Sciences, University of Rosario, Bogotá 111321, Colombia.
| | - César Reyes
- Colombian Institute of Immunology Foundation (FIDIC Nonprofit-Making Organisation), Bogotá 111321, Colombia.
| | - Adriana Bermúdez
- Colombian Institute of Immunology Foundation (FIDIC Nonprofit-Making Organisation), Bogotá 111321, Colombia.
- School of Medicine and Health Sciences, University of Rosario, Bogotá 111321, Colombia.
| | - Magnolia Vanegas
- Colombian Institute of Immunology Foundation (FIDIC Nonprofit-Making Organisation), Bogotá 111321, Colombia.
- School of Medicine and Health Sciences, University of Rosario, Bogotá 111321, Colombia.
| | - Yahson Varela
- Colombian Institute of Immunology Foundation (FIDIC Nonprofit-Making Organisation), Bogotá 111321, Colombia.
- Faculty of Health Sciences, Applied and Environmental Sciences University (UDCA), Bogotá 111321, Colombia.
| | - Manuel E Patarroyo
- Colombian Institute of Immunology Foundation (FIDIC Nonprofit-Making Organisation), Bogotá 111321, Colombia.
- Faculty of Medicine, National University of Colombia, Bogotá 111321, Colombia.
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12
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Critical role of HLA-DRβ* binding peptides' peripheral flanking residues in fully-protective malaria vaccine development. Biochem Biophys Res Commun 2017; 489:339-345. [DOI: 10.1016/j.bbrc.2017.05.123] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2017] [Accepted: 05/22/2017] [Indexed: 12/15/2022]
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13
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Park YK, Jung S, Park SH. Induction of tolerance against the arthritogenic antigen with type-II collagen peptide-linked soluble MHC class II molecules. BMB Rep 2017; 49:331-6. [PMID: 26779996 PMCID: PMC5070721 DOI: 10.5483/bmbrep.2016.49.6.207] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2015] [Indexed: 11/23/2022] Open
Abstract
In murine collagen-induced arthritis (CIA), self-reactive T cells can recognize peptide antigens derived from type-II collagen (CII). Activation of T cells is an important mediator of autoimmune diseases. Thus, T cells have become a focal point of study to treat autoimmune diseases. In this study, we evaluated the efficacy of recombinant MHC class II molecules in the regulation of antigen-specific T cells by using a self peptide derived from CII (CII260-274; IAGFKGEQGPKGEPG) linked to mouseI-Aq in a murine CIA model. We found that recombinant I-Aq/CII260-274 molecules could be recognized by CII-specific T cells and inhibit the same T cells in vitro. Furthermore, the development of CIA in mice was successfully prevented by in vivo injection of recombinant I-Aq/CII260-274 molecules. Thus, treatment with recombinant soluble MHC class II molecules in complex with an immunodominant self-peptide might offer a potential therapeutic for chronic inflammation in autoimmune disease such as rheumatoid arthritis. [BMB Reports 2016; 49(6): 331-336
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Affiliation(s)
- Yoon-Kyung Park
- Department of Life Sciences, Korea University, Seoul 02841, Korea
| | - Sundo Jung
- Department of Life Sciences, Korea University, Seoul 02841, Korea
| | - Se-Ho Park
- Department of Life Sciences, Korea University, Seoul 02841, Korea
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14
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Jones TD, Hearn AR, Holgate RGE, Kozub D, Fogg MH, Carr FJ, Baker MP, Lacadena J, Gehlsen KR. A deimmunised form of the ribotoxin, α-sarcin, lacking CD4+ T cell epitopes and its use as an immunotoxin warhead. Protein Eng Des Sel 2016; 29:531-540. [PMID: 27578884 PMCID: PMC5081043 DOI: 10.1093/protein/gzw045] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2016] [Revised: 06/30/2016] [Accepted: 07/25/2016] [Indexed: 12/30/2022] Open
Abstract
Fungal ribotoxins that block protein synthesis can be useful warheads in the context of a targeted immunotoxin. α-Sarcin is a small (17 kDa) fungal ribonuclease produced by Aspergillus giganteus that functions by catalytically cleaving a single phosphodiester bond in the sarcin–ricin loop of the large ribosomal subunit, thus making the ribosome unrecognisable to elongation factors and leading to inhibition of protein synthesis. Peptide mapping using an ex vivo human T cell assay determined that α-sarcin contained two T cell epitopes; one in the N-terminal 20 amino acids and the other in the C-terminal 20 amino acids. Various mutations were tested individually within each epitope and then in combination to isolate deimmunised α-sarcin variants that had the desired properties of silencing T cell epitopes and retention of the ability to inhibit protein synthesis (equivalent to wild-type, WT α-sarcin). A deimmunised variant (D9T/Q142T) demonstrated a complete lack of T cell activation in in vitro whole protein human T cell assays using peripheral blood mononuclear cells from donors with diverse HLA allotypes. Generation of an immunotoxin by fusion of the D9T/Q142T variant to a single-chain Fv targeting Her2 demonstrated potent cell killing equivalent to a fusion protein comprising the WT α-sarcin. These results represent the first fungal ribotoxin to be deimmunised with the potential to construct a new generation of deimmunised immunotoxin therapeutics.
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Affiliation(s)
- Tim D Jones
- Abzena plc., Babraham Research Campus, Babraham, CambridgeCB22 3AT, UK
| | - Arron R Hearn
- Abzena plc., Babraham Research Campus, Babraham, CambridgeCB22 3AT, UK
| | | | - Dorota Kozub
- Abzena plc., Babraham Research Campus, Babraham, CambridgeCB22 3AT, UK
| | - Mark H Fogg
- Abzena plc., Babraham Research Campus, Babraham, CambridgeCB22 3AT, UK
| | - Francis J Carr
- Abtelum Biomedical, Inc. 175 Briar Lane, Westwood, MA 02090, USA
| | - Matthew P Baker
- Abzena plc., Babraham Research Campus, Babraham, CambridgeCB22 3AT, UK
| | - Javier Lacadena
- Departamento de Bioquimica y Biologia Molecular I, Facultad de Ciencias Químicas, Universidad Complutense de Madrid, Avenida Complutense s/n, Madrid 28040, Spain
| | - Kurt R Gehlsen
- Research Corporation Technologies Inc., 5210 E. Williams Circle #240, Tucson, AZ 85711, USA
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15
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Stern LJ, Santambrogio L. The melting pot of the MHC II peptidome. Curr Opin Immunol 2016; 40:70-7. [PMID: 27018930 DOI: 10.1016/j.coi.2016.03.004] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2016] [Revised: 03/14/2016] [Accepted: 03/15/2016] [Indexed: 02/07/2023]
Abstract
Recent advances in mass spectrometry technology have facilitated detailed examination of MHC-II immunopeptidomes, for example the repertoires of peptides bound to MHC-II molecules expressed in antigen presenting cells. These studies have deepened our view of MHC-II presentation. Other studies have broadened our view of pathways leading up to peptide loading. Here we review these recent studies in the context of earlier work on conventional and non-conventional MHC-II processing. The message that emerges is that sources of antigen beyond conventional endosomal processing of endocytosed proteins are important for generation of cellular immune responses to pathogens and maintenance of central and peripheral tolerance. The multiplicity of pathways results in a broad MHC II immunopeptidome that conveys the sampled environment to patrolling T cells.
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Affiliation(s)
- Lawrence J Stern
- Department of Pathology, University of Massachusetts Medical School, Worcester, MA 01655, United States; Department of Biochemistry & Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA 01655, United States; Graduate Program in Immunology and Microbiology, University of Massachusetts Medical School, Worcester, MA 01655, United States.
| | - Laura Santambrogio
- Department of Pathology, Albert Einstein College of Medicine, NY 10461, United States; Department of Microbiology & Immunology, Albert Einstein College of Medicine, NY 10461, United States
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Malek Abrahimians E, Vander Elst L, Carlier VA, Saint-Remy JM. Thioreductase-Containing Epitopes Inhibit the Development of Type 1 Diabetes in the NOD Mouse Model. Front Immunol 2016; 7:67. [PMID: 26973647 PMCID: PMC4773585 DOI: 10.3389/fimmu.2016.00067] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2015] [Accepted: 02/12/2016] [Indexed: 01/01/2023] Open
Abstract
Autoreactive CD4+ T cells recognizing islet-derived antigens play a primary role in type 1 diabetes. Specific suppression of such cells therefore represents a strategic target for the cure of the disease. We have developed a methodology by which CD4+ T cells acquire apoptosis-inducing properties on antigen-presenting cells after cognate recognition of natural sequence epitopes. We describe here that inclusion of a thiol-disulfide oxidoreductase (thioreductase) motif within the flanking residues of a single MHC class II-restricted GAD65 epitope induces GAD65-specific cytolytic CD4+ T cells (cCD4+ T). The latter, obtained either in vitro or by active immunization, acquire an effector memory phenotype and lyse APCs by a Fas–FasL interaction. Furthermore, cCD4+ T cells eliminate by apoptosis activated bystander CD4+ T cells recognizing alternative epitopes processed by the same APC. Active immunization with a GAD65 class II-restricted thioreductase-containing T cell epitope protects mice from diabetes and abrogates insulitis. Passive transfer of in vitro-elicited cCD4+ T cells establishes that such cells are efficient in suppressing autoimmunity. These findings provide strong evidence for a new vaccination strategy to prevent type 1 diabetes.
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Affiliation(s)
- Elin Malek Abrahimians
- Center for Molecular and Vascular Biology, University of Leuven, Leuven, Belgium; ImCyse SA, Leuven, Belgium
| | - Luc Vander Elst
- Center for Molecular and Vascular Biology, University of Leuven, Leuven, Belgium; ImCyse SA, Leuven, Belgium
| | - Vincent A Carlier
- Center for Molecular and Vascular Biology, University of Leuven, Leuven, Belgium; ImCyse SA, Leuven, Belgium
| | - Jean-Marie Saint-Remy
- Center for Molecular and Vascular Biology, University of Leuven, Leuven, Belgium; ImCyse SA, Leuven, Belgium
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17
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Kozono H, Matsushita Y, Ogawa N, Kozono Y, Miyabe T, Sekiguchi H, Ichiyanagi K, Okimoto N, Taiji M, Kanagawa O, Sasaki YC. Single-molecule motions of MHC class II rely on bound peptides. Biophys J 2015; 108:350-9. [PMID: 25606683 DOI: 10.1016/j.bpj.2014.12.004] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2014] [Revised: 11/26/2014] [Accepted: 12/02/2014] [Indexed: 11/28/2022] Open
Abstract
The major histocompatibility complex (MHC) class II protein can bind peptides of different lengths in the region outside the peptide-binding groove. Peptide-flanking residues (PFRs) contribute to the binding affinity of the peptide for MHC and change the immunogenicity of the peptide/MHC complex with regard to T cell receptor (TCR). The mechanisms underlying these phenomena are currently unknown. The molecular flexibility of the peptide/MHC complex may be an important determinant of the structures recognized by certain T cells. We used single-molecule x-ray analysis (diffracted x-ray tracking (DXT)) and fluorescence anisotropy to investigate these mechanisms. DXT enabled us to monitor the real-time Brownian motion of the peptide/MHC complex and revealed that peptides without PFRs undergo larger rotational motions than peptides with PFRs. Fluorescence anisotropy further revealed that peptides without PFRs exhibit slightly larger motions on the nanosecond timescale. These results demonstrate that peptides without PFRs undergo dynamic motions in the groove of MHC and consequently are able to assume diverse structures that can be recognized by T cells.
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Affiliation(s)
- Haruo Kozono
- CREST Sasaki Team, Japan Science and Technology Agency, Graduate School of Frontier Sciences, The University of Tokyo, Chiba, Japan; Research Institute for Biomedical Sciences, Tokyo University of Science, Chiba, Japan.
| | - Yufuku Matsushita
- Department of Advanced Materials Science, Graduate School of Frontier Sciences, The University of Tokyo, Chiba, Japan
| | - Naoki Ogawa
- CREST Sasaki Team, Japan Science and Technology Agency, Graduate School of Frontier Sciences, The University of Tokyo, Chiba, Japan; Graduate School for Engineering, Tokyo University of Agriculture and Technology, Tokyo, Japan
| | - Yuko Kozono
- Research Institute for Biomedical Sciences, Tokyo University of Science, Chiba, Japan
| | - Toshihiro Miyabe
- Department of Advanced Materials Science, Graduate School of Frontier Sciences, The University of Tokyo, Chiba, Japan
| | - Hiroshi Sekiguchi
- CREST Sasaki Team, Japan Science and Technology Agency, Graduate School of Frontier Sciences, The University of Tokyo, Chiba, Japan; Japan Synchrotron Radiation Research Institute, Hyogo, Japan
| | - Kouhei Ichiyanagi
- CREST Sasaki Team, Japan Science and Technology Agency, Graduate School of Frontier Sciences, The University of Tokyo, Chiba, Japan; Department of Advanced Materials Science, Graduate School of Frontier Sciences, The University of Tokyo, Chiba, Japan
| | - Noriaki Okimoto
- Computational Biology Research Core, Quantitative Biology Center, RIKEN, Hyogo, Japan
| | - Makoto Taiji
- Computational Biology Research Core, Quantitative Biology Center, RIKEN, Hyogo, Japan
| | - Osami Kanagawa
- CREST Sasaki Team, Japan Science and Technology Agency, Graduate School of Frontier Sciences, The University of Tokyo, Chiba, Japan; Centre International de Recherche en Infectiologie, INSERM U1111, Lyon, France
| | - Yuji C Sasaki
- CREST Sasaki Team, Japan Science and Technology Agency, Graduate School of Frontier Sciences, The University of Tokyo, Chiba, Japan; Department of Advanced Materials Science, Graduate School of Frontier Sciences, The University of Tokyo, Chiba, Japan.
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Malek Abrahimians E, Carlier VA, Vander Elst L, Saint-Remy JMR. MHC Class II-Restricted Epitopes Containing an Oxidoreductase Activity Prompt CD4(+) T Cells with Apoptosis-Inducing Properties. Front Immunol 2015; 6:449. [PMID: 26388872 PMCID: PMC4556975 DOI: 10.3389/fimmu.2015.00449] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2015] [Accepted: 08/18/2015] [Indexed: 12/21/2022] Open
Abstract
Abrogating an unwanted immune response toward a specific antigen without compromising the entire immune system is a hoped-for goal in immunotherapy. Instead of manipulating dendritic cells and suppressive regulatory T cells, depleting effector T cells or blocking their co-stimulatory pathways, we describe a method to specifically inhibit the presentation of an antigen eliciting an unwanted immune reaction. Inclusion of an oxidoreductase motif within the flanking residues of MHC class II epitopes polarizes CD4(+) T cells to cytolytic cells capable of inducing apoptosis in antigen presenting cells (APCs) displaying cognate peptides through MHC class II molecules. This novel function results from an increased synapse formation between both cells. Moreover, these cells eliminate by apoptosis bystander CD4(+) T cells activated at the surface of the APC. We hypothesize that they would thereby block the recruitment of cells of alternative specificity for the same autoantigen or cells specific for another antigen associated with the pathology, providing a system by which response against multiple antigens linked with the same disease can be suppressed. These findings open the way toward a novel form of antigen-specific immunosuppression.
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Affiliation(s)
- Elin Malek Abrahimians
- Center for Molecular and Vascular Biology, University of Leuven , Leuven , Belgium ; ImCyse SA , Leuven , Belgium
| | - Vincent A Carlier
- Center for Molecular and Vascular Biology, University of Leuven , Leuven , Belgium ; ImCyse SA , Leuven , Belgium
| | - Luc Vander Elst
- Center for Molecular and Vascular Biology, University of Leuven , Leuven , Belgium ; ImCyse SA , Leuven , Belgium
| | - Jean-Marie R Saint-Remy
- Center for Molecular and Vascular Biology, University of Leuven , Leuven , Belgium ; ImCyse SA , Leuven , Belgium
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Barberá A, Lorenzo N, Garrido G, Mazola Y, Falcón V, Torres AM, Hernández MI, Hernández MV, Margry B, de Groot AM, van Roon J, van der Zee R, Broere F, van Eden W, Padrón G, Domínguez MDC. APL-1, an altered peptide ligand derived from human heat-shock protein 60, selectively induces apoptosis in activated CD4+ CD25+ T cells from peripheral blood of rheumatoid arthritis patients. Int Immunopharmacol 2013; 17:1075-83. [PMID: 24177275 DOI: 10.1016/j.intimp.2013.10.010] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2013] [Revised: 09/25/2013] [Accepted: 10/07/2013] [Indexed: 01/05/2023]
Abstract
Rheumatoid arthritis (RA) is a chronic T-cell mediated autoimmune disease that affects primarily the joints. The induction of immune tolerance through antigen-specific therapies for the blockade of pathogenic CD4+ T cells constitutes a current focus of research. In this focus it is attempted to simultaneously activate multiple regulatory mechanisms, such as: apoptosis and regulatory T cells (Tregs). APL-1 is an altered peptide ligand derived from a novel CD4+ T-cell epitope of human heat-shock protein of 60kDa, an autoantigen involved in the pathogenesis of RA. Previously, we have reported that APL-1 induces CD4+ CD25(high)Foxp3+ Tregs in several systems. Here, we investigated the ability of APL-1 in inducing apoptosis in PBMCs from RA patients, who were classified as active or inactive according to their DAS28 score. APL-1 decreased the viability of PBMCs from active but not from inactive patients. DNA fragmentation assays and typical morphological features clearly demonstrated that APL-1 induced apoptosis in these cells. Activated CD4+ CD25+ T cells but not resting CD4+ CD25- T cells were identified as targets of APL-1. Furthermore, CD4+ T-cell responses to APL-1 were found to be dependent on antigen presentation via the HLA-DR molecule. Thus, APL-1 is a regulatory CD4+ T cell epitope which might modulate inflammatory immune responses in PBMCs from RA patients by inducing CD4+ CD25(high)Foxp3+ Tregs and apoptosis in activated CD4+ T cells. These results support further investigation of this candidate drug for the treatment of RA.
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Affiliation(s)
- Ariana Barberá
- Biomedical Research Department, Center for Genetic Engineering and Biotechnology, P.O. Box 6162, Havana 11300, Cuba.
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Braendstrup P, Justesen S, Østerbye T, Nielsen LLB, Mallone R, Vindeløv L, Stryhn A, Buus S. MHC class II tetramers made from isolated recombinant α and β chains refolded with affinity-tagged peptides. PLoS One 2013; 8:e73648. [PMID: 24023895 PMCID: PMC3759463 DOI: 10.1371/journal.pone.0073648] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2013] [Accepted: 07/22/2013] [Indexed: 12/24/2022] Open
Abstract
Targeting CD4+ T cells through their unique antigen-specific, MHC class II-restricted T cell receptor makes MHC class II tetramers an attractive strategy to identify, validate and manipulate these cells at the single cell level. Currently, generating class II tetramers is a specialized undertaking effectively limiting their use and emphasizing the need for improved methods of production. Using class II chains expressed individually in E. coli as versatile recombinant reagents, we have previously generated peptide-MHC class II monomers, but failed to generate functional class II tetramers. Adding a monomer purification principle based upon affinity-tagged peptides, we here provide a robust method to produce class II tetramers and demonstrate staining of antigen-specific CD4+ T cells. We also provide evidence that both MHC class II and T cell receptor molecules largely accept affinity-tagged peptides. As a general approach to class II tetramer generation, this method should support rational CD4+ T cell epitope discovery as well as enable specific monitoring and manipulation of CD4+ T cell responses.
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Affiliation(s)
- Peter Braendstrup
- Laboratory of Experimental Immunology, University of Copenhagen, Copenhagen, Denmark
- Allogeneic Hematopoietic Cell Transplantation Laboratory, Department of Hematology, Rigshospitalet, Copenhagen, Denmark
| | - Sune Justesen
- Laboratory of Experimental Immunology, University of Copenhagen, Copenhagen, Denmark
| | - Thomas Østerbye
- Laboratory of Experimental Immunology, University of Copenhagen, Copenhagen, Denmark
| | | | - Roberto Mallone
- Institut National de la Santé et de la Recherche Médicale, Unité 1016, Cochin Institute, DeAR Lab Avenir, Paris, France
| | - Lars Vindeløv
- Allogeneic Hematopoietic Cell Transplantation Laboratory, Department of Hematology, Rigshospitalet, Copenhagen, Denmark
| | - Anette Stryhn
- Laboratory of Experimental Immunology, University of Copenhagen, Copenhagen, Denmark
| | - Søren Buus
- Laboratory of Experimental Immunology, University of Copenhagen, Copenhagen, Denmark
- * E-mail:
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Pulse-chase analysis for studies of MHC class II biosynthesis, maturation, and peptide loading. Methods Mol Biol 2013; 960:411-432. [PMID: 23329504 DOI: 10.1007/978-1-62703-218-6_31] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Pulse-chase analysis is a commonly used technique for studying the synthesis, processing and transport of proteins. Cultured cells expressing proteins of interest are allowed to take up radioactively labeled amino acids for a brief interval ("pulse"), during which all newly synthesized proteins incorporate the label. The cells are then returned to nonradioactive culture medium for various times ("chase"), during which proteins may undergo conformational changes, trafficking, or degradation. Proteins of interest are isolated (usually by immunoprecipitation) and resolved by sodium dodecyl sulfate polyacrylamide gel electrophoresis (SDS-PAGE), and the fate of radiolabeled molecules is examined by autoradiography. This chapter describes a pulse-chase protocol suitable for studies of major histocompatibility complex (MHC) class II biosynthesis and maturation. We discuss how results are affected by the recognition by certain anti-class II antibodies of distinct class II conformations associated with particular biosynthetic states. Our protocol can be adapted to follow the fate of many other endogenously synthesized proteins, including viral or transfected gene products, in cultured cells.
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22
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Roy BM, Zhukov DV, Maynard JA. Flanking residues are central to DO11.10 T cell hybridoma stimulation by ovalbumin 323-339. PLoS One 2012; 7:e47585. [PMID: 23110081 PMCID: PMC3479146 DOI: 10.1371/journal.pone.0047585] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2012] [Accepted: 09/18/2012] [Indexed: 11/30/2022] Open
Abstract
T cell activation requires formation of a tri-molecular interaction between a major histocompatibility complex (MHC), peptide, and T cell receptor. In a common model system, the ovalbumin epitope 323–339 binds the murine class II MHC, I-Ad, in at least three distinct registers. The DO11.10 T cell recognizes the least stable of these, as determined by peptide-MHC dissociation rates. Using exogenous peptides and peptide insertions into a carrier protein in combination with IL-2 secretion assays, we show that the alternate registers do not competitively inhibit display of the active register four. In contrast, this weakly binding register is stabilized by the presence of n-terminal flanking residues active in MHC binding. The DO11.10 hybridoma is sensitive to the presence of specific wild-type residues extending to at least the P-3 peptide position. Transfer of the P-4 to P-2 flanking residues to a hen egg lysozyme epitope also presented by I-Ad increases the activity of that epitope substantially. These results illustrate the inherent complexity in delineating the interaction of multiple registers based on traditional thermodynamic measurements and demonstrate the potential of flanking residue modification for increasing the activity of weakly bound epitopes. The latter technique represents an alternative to substitution of anchor residues within a weakly bound register, which we show can significantly decrease the activity of the epitope to a responding T cell.
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Affiliation(s)
- Benjamin M. Roy
- Department of Chemical Engineering, University of Minnesota, Minneapolis, Minnesota, United States of America
- Department of Chemical Engineering, University of Texas at Austin, Austin Texas, United States of America
| | - Dmitriy V. Zhukov
- Department of Chemical Engineering, University of Texas at Austin, Austin Texas, United States of America
| | - Jennifer A. Maynard
- Department of Chemical Engineering, University of Texas at Austin, Austin Texas, United States of America
- * E-mail:
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Carlier VA, VanderElst L, Janssens W, Jacquemin MG, Saint-Remy JMR. Increased synapse formation obtained by T cell epitopes containing a CxxC motif in flanking residues convert CD4+ T cells into cytolytic effectors. PLoS One 2012; 7:e45366. [PMID: 23056200 PMCID: PMC3467281 DOI: 10.1371/journal.pone.0045366] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2012] [Accepted: 08/21/2012] [Indexed: 11/25/2022] Open
Abstract
The nature of MHC class II-binding epitopes not only determines the specificity of T cell responses, but may also alter effector cell functions. Cytolytic CD4+ T cells have been observed primarily in anti-viral responses, but very little is known about the conditions under which they can be elicited. Their potential as regulators of immune responses, however, deserves investigations. We describe here that inclusion of a thiol-disulfide oxidoreductase motif within flanking residues of class II-restricted epitopes results, both in vitro and in vivo, in elicitation of antigen-specific cytolytic CD4+ T cells through increased synapse formation. We show that both naïve and polarized CD4+ T cells, including Th17 cells, can be converted by cognate recognition of such modified epitopes. Cytolytic CD4+ T cells induce apoptosis on APCs by Fas-FasL interaction. These findings potentially open the way towards a novel form of antigen-specific immunosuppression.
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24
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Mohan JF, Unanue ER. Unconventional recognition of peptides by T cells and the implications for autoimmunity. Nat Rev Immunol 2012; 12:721-8. [DOI: 10.1038/nri3294] [Citation(s) in RCA: 69] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
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25
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Schlundt A, Günther S, Sticht J, Wieczorek M, Roske Y, Heinemann U, Freund C. Peptide linkage to the α-subunit of MHCII creates a stably inverted antigen presentation complex. J Mol Biol 2012; 423:294-302. [PMID: 22820093 DOI: 10.1016/j.jmb.2012.07.008] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/29/2012] [Revised: 07/05/2012] [Accepted: 07/10/2012] [Indexed: 11/15/2022]
Abstract
Class II proteins of the major histocompatibility complex (MHCII) typically present exogenous antigenic peptides to cognate T cell receptors of CD4-T lymphocytes. The exact conformation of peptide-MHCII complexes (pMHCII) can vary depending on the length, register and orientation of the bound peptide. We have recently found the self-peptide CLIP (class-II-associated invariant chain-derived peptide) to adopt a dynamic bidirectional binding mode with regard to the human MHCII HLA-DR1 (HLA, human leukocyte antigen). We suggested that inversely bound peptides could activate specific T cell clones in the context of autoimmunity. As a first step to prove this hypothesis, pMHC complexes restricted to either the canonical or the inverted peptide orientation have to be constructed. Here, we show that genetically encoded linkage of CLIP and two other antigenic peptides to the HLA-DR1 α-chain results in stable complexes with inversely bound ligands. Two-dimensional NMR and biophysical analyses indicate that the CLIP-bound pMHC(inv) complex (pMHC(inv), inverted MHCII-peptide complex) displays high thermodynamic stability but still allows for the exchange against higher-affinity viral antigen. Complemented by comparable data on a corresponding β-chain-fused canonical HLA-DR1/CLIP complex, we further show that linkage of CLIP leads to a binding mode exactly the same as that of the corresponding unlinked constructs. We suggest that our approach constitutes a general strategy to create pMHC(inv) complexes. Such engineering is needed to create orientation-specific antibodies and raise T cells to study phenomena of autoimmunity caused by isomeric pMHCs.
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MESH Headings
- Amino Acid Sequence
- Antigen Presentation
- Antigens, Differentiation, B-Lymphocyte/chemistry
- Antigens, Differentiation, B-Lymphocyte/immunology
- Antigens, Differentiation, B-Lymphocyte/metabolism
- Autoimmunity
- CD4-Positive T-Lymphocytes/immunology
- Crystallography, X-Ray
- Genes, MHC Class II
- HLA-DR1 Antigen/chemistry
- HLA-DR1 Antigen/immunology
- HLA-DR1 Antigen/metabolism
- Histocompatibility Antigens Class II/chemistry
- Histocompatibility Antigens Class II/immunology
- Histocompatibility Antigens Class II/metabolism
- Humans
- Ligands
- Protein Binding
- Protein Conformation
- Receptors, Antigen, T-Cell/immunology
- Receptors, Antigen, T-Cell/metabolism
- Tetanus Toxin/chemistry
- Thermodynamics
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Affiliation(s)
- Andreas Schlundt
- Protein Biochemistry Group, Freie Universität Berlin, Thielallee 63, 14195 Berlin, Germany
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26
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Cole DK, Gallagher K, Lemercier B, Holland CJ, Junaid S, Hindley JP, Wynn KK, Gostick E, Sewell AK, Gallimore AM, Ladell K, Price DA, Gougeon ML, Godkin A. Modification of the carboxy-terminal flanking region of a universal influenza epitope alters CD4⁺ T-cell repertoire selection. Nat Commun 2012; 3:665. [PMID: 22314361 PMCID: PMC3293629 DOI: 10.1038/ncomms1665] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2011] [Accepted: 01/05/2012] [Indexed: 02/01/2023] Open
Abstract
Human CD4(+) αβ T cells are activated via T-cell receptor recognition of peptide epitopes presented by major histocompatibility complex (MHC) class II (MHC-II). The open ends of the MHC-II binding groove allow peptide epitopes to extend beyond a central nonamer core region at both the amino- and carboxy-terminus. We have previously found that these non-bound C-terminal residues can alter T cell activation in an MHC allele-transcending fashion, although the mechanism for this effect remained unclear. Here we show that modification of the C-terminal peptide-flanking region of an influenza hemagglutinin (HA(305-320)) epitope can alter T-cell receptor binding affinity, T-cell activation and repertoire selection of influenza-specific CD4(+) T cells expanded from peripheral blood. These data provide the first demonstration that changes in the C-terminus of the peptide-flanking region can substantially alter T-cell receptor binding affinity, and indicate a mechanism through which peptide flanking residues could influence repertoire selection.
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Affiliation(s)
- David K. Cole
- Institute of Infection and Immunity, Cardiff University School of Medicine, The Henry Wellcome Building, Cardiff CF14 4XN, Wales, UK
- These authors contributed equally to this work
| | - Kathleen Gallagher
- Institute of Infection and Immunity, Cardiff University School of Medicine, The Henry Wellcome Building, Cardiff CF14 4XN, Wales, UK
- These authors contributed equally to this work
| | - Brigitte Lemercier
- Institut Pasteur, Antiviral Immunity, Biotherapy and Vaccine Unit, Department of Infection and Epidemiology, rue du Dr. Roux, 75015 Paris, France
- These authors contributed equally to this work
| | - Christopher J. Holland
- Institute of Infection and Immunity, Cardiff University School of Medicine, The Henry Wellcome Building, Cardiff CF14 4XN, Wales, UK
| | - Sayed Junaid
- Institute of Infection and Immunity, Cardiff University School of Medicine, The Henry Wellcome Building, Cardiff CF14 4XN, Wales, UK
| | - James P. Hindley
- Institute of Infection and Immunity, Cardiff University School of Medicine, The Henry Wellcome Building, Cardiff CF14 4XN, Wales, UK
| | - Katherine K. Wynn
- Institute of Infection and Immunity, Cardiff University School of Medicine, The Henry Wellcome Building, Cardiff CF14 4XN, Wales, UK
| | - Emma Gostick
- Institute of Infection and Immunity, Cardiff University School of Medicine, The Henry Wellcome Building, Cardiff CF14 4XN, Wales, UK
| | - Andrew K. Sewell
- Institute of Infection and Immunity, Cardiff University School of Medicine, The Henry Wellcome Building, Cardiff CF14 4XN, Wales, UK
| | - Awen M. Gallimore
- Institute of Infection and Immunity, Cardiff University School of Medicine, The Henry Wellcome Building, Cardiff CF14 4XN, Wales, UK
| | - Kristin Ladell
- Institute of Infection and Immunity, Cardiff University School of Medicine, The Henry Wellcome Building, Cardiff CF14 4XN, Wales, UK
| | - David A. Price
- Institute of Infection and Immunity, Cardiff University School of Medicine, The Henry Wellcome Building, Cardiff CF14 4XN, Wales, UK
| | - Marie-Lise Gougeon
- Institut Pasteur, Antiviral Immunity, Biotherapy and Vaccine Unit, Department of Infection and Epidemiology, rue du Dr. Roux, 75015 Paris, France
| | - Andrew Godkin
- Institute of Infection and Immunity, Cardiff University School of Medicine, The Henry Wellcome Building, Cardiff CF14 4XN, Wales, UK
- Department of Medicine, University Hospital of Wales, Cardiff CF14 4XW, Wales, UK
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27
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Bozzacco L, Yu H, Zebroski HA, Dengjel J, Deng H, Mojsov S, Steinman RM. Mass spectrometry analysis and quantitation of peptides presented on the MHC II molecules of mouse spleen dendritic cells. J Proteome Res 2011; 10:5016-30. [PMID: 21913724 PMCID: PMC3270889 DOI: 10.1021/pr200503g] [Citation(s) in RCA: 50] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Major histocompatibility complex class II (MHC II) molecules are expressed on the surface of antigen-presenting cells and display short bound peptide fragments derived from self- and nonself antigens. These peptide-MHC complexes function to maintain immunological tolerance in the case of self-antigens and initiate the CD4(+) T cell response in the case of foreign proteins. Here we report the application of LC-MS/MS analysis to identify MHC II peptides derived from endogenous proteins expressed in freshly isolated murine splenic DCs. The cell number was enriched in vivo upon treatment with Flt3L-B16 melanoma cells. In a typical experiment, starting with about 5 × 10(8) splenic DCs, we were able to reliably identify a repertoire of over 100 MHC II peptides originating from about 55 proteins localized in membrane (23%), intracellular (26%), endolysosomal (12%), nuclear (14%), and extracellular (25%) compartments. Using synthetic isotopically labeled peptides corresponding to the sequences of representative bound MHC II peptides, we quantified by LC-MS relative peptide abundance. In a single experiment, peptides were detected in a wide concentration range spanning from 2.5 fmol/μL to 12 pmol/μL or from approximately 13 to 2 × 10(5) copies per DC. These peptides were found in similar amounts on B cells where we detected about 80 peptides originating from 55 proteins distributed homogenously within the same cellular compartments as in DCs. About 90 different binding motifs predicted by the epitope prediction algorithm were found within the sequences of the identified MHC II peptides. These results set a foundation for future studies to quantitatively investigate the MHC II repertoire on DCs generated under different immunization conditions.
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Andreatta M, Schafer-Nielsen C, Lund O, Buus S, Nielsen M. NNAlign: a web-based prediction method allowing non-expert end-user discovery of sequence motifs in quantitative peptide data. PLoS One 2011; 6:e26781. [PMID: 22073191 PMCID: PMC3206854 DOI: 10.1371/journal.pone.0026781] [Citation(s) in RCA: 52] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2011] [Accepted: 10/04/2011] [Indexed: 11/19/2022] Open
Abstract
Recent advances in high-throughput technologies have made it possible to generate both gene and protein sequence data at an unprecedented rate and scale thereby enabling entirely new “omics”-based approaches towards the analysis of complex biological processes. However, the amount and complexity of data that even a single experiment can produce seriously challenges researchers with limited bioinformatics expertise, who need to handle, analyze and interpret the data before it can be understood in a biological context. Thus, there is an unmet need for tools allowing non-bioinformatics users to interpret large data sets. We have recently developed a method, NNAlign, which is generally applicable to any biological problem where quantitative peptide data is available. This method efficiently identifies underlying sequence patterns by simultaneously aligning peptide sequences and identifying motifs associated with quantitative readouts. Here, we provide a web-based implementation of NNAlign allowing non-expert end-users to submit their data (optionally adjusting method parameters), and in return receive a trained method (including a visual representation of the identified motif) that subsequently can be used as prediction method and applied to unknown proteins/peptides. We have successfully applied this method to several different data sets including peptide microarray-derived sets containing more than 100,000 data points. NNAlign is available online at http://www.cbs.dtu.dk/services/NNAlign.
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Affiliation(s)
- Massimo Andreatta
- Center for Biological Sequence Analysis, Technical University of Denmark, Kongens Lyngby, Denmark.
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29
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Hou T, Macmillan H, Chen Z, Keech CL, Jin X, Sidney J, Strohman M, Yoon T, Mellins ED. An insertion mutant in DQA1*0501 restores susceptibility to HLA-DM: implications for disease associations. THE JOURNAL OF IMMUNOLOGY 2011; 187:2442-52. [PMID: 21775680 DOI: 10.4049/jimmunol.1100255] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
HLA-DM (DM) catalyzes CLIP release, stabilizes MHC class II molecules, and edits the peptide repertoire presented by class II. Impaired DM function may have profound effects on Ag presentation events in the thymus and periphery that are critical for maintenance of self-tolerance. The associations of the HLA-DQ2 (DQ2) allele with celiac disease and type 1 diabetes mellitus have been appreciated for a long time. The explanation for these associations, however, remains unknown. We previously found that DQ2 is a poor substrate for DM. In this study, to further characterize DQ2-DM interaction, we introduced point mutations into DQ2 on the proposed DQ2-DM interface to restore the sensitivity of DQ2 to DM. The effects of mutations were investigated by measuring the peptide dissociation and exchange rate in vitro, CLIP and DQ2 expression on the cell surface, and the presentation of α-II-gliadin epitope (residues 62-70) to murine, DQ2-restricted T cell hybridomas. We found that the three α-chain mutations (α+53G, α+53R, or αY22F) decreased the intrinsic stability of peptide-class II complex. More interestingly, the α+53G mutant restored DQ2 sensitivity to DM, likely due to improved interaction with DM. Our data also suggest that α-II-gliadin 62-70 is a DM-suppressed epitope. The DQ2 resistance to DM changes the fate of this peptide from a cryptic to an immunodominant epitope. Our findings elucidate the structural basis for reduced DQ2-DM interaction and have implications for mechanisms underlying disease associations of DQ2.
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Affiliation(s)
- Tieying Hou
- Department of Pediatrics, Program in Immunology, Stanford University, Stanford, CA 94305, USA
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30
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Pezeshki AM, Côté MH, Azar GA, Routy JP, Boulassel MR, Thibodeau J. Forced expression of HLA-DM at the surface of dendritic cells increases loading of synthetic peptides on MHC class II molecules and modulates T cell responses. THE JOURNAL OF IMMUNOLOGY 2011; 187:74-81. [PMID: 21622867 DOI: 10.4049/jimmunol.1002747] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
Adoptive transfer of autologous dendritic cells (DCs) loaded with tumor-associated CD4 and CD8 T cell epitopes represents a promising avenue for the immunotherapy of cancer. In an effort to increase the loading of therapeutic synthetic peptides on MHC II molecules, we used a mutant of HLA-DM (DMY) devoid of its lysosomal sorting motif and that accumulates at the cell surface. Transfection of DMY into HLA-DR(+) cells resulted in increased loading of the exogenously supplied HA(307-318) peptide, as well as increased stimulation of HA-specific T cells. Also, on transduction in mouse and human DCs, DMY increased loading of HEL(48-61) and of the tumor Ag-derived gp100(174-190) peptides, respectively. Interestingly, expression of DMY at the surface of APCs favored Th1 differentiation over Th2. Finally, we found that DMY(-) and DMY(+) mouse APCs differentially stimulated T cell hybridomas sensitive to the fine conformation of peptide-MHC II complexes. Taken together, our results suggest that the overexpression of HLA-DMY at the plasma membrane of DCs may improve quantitatively, but also qualitatively, the presentation of CD4 T cell epitopes in cellular vaccine therapies for cancer.
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Affiliation(s)
- Abdul Mohammad Pezeshki
- Laboratoire d'Immunologie Moléculaire, Département de Microbiologie et Immunologie, Université de Montréal, Montréal, Québec H3C 3J7, Canada
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31
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Bidirectional binding of invariant chain peptides to an MHC class II molecule. Proc Natl Acad Sci U S A 2010; 107:22219-24. [PMID: 21115828 DOI: 10.1073/pnas.1014708107] [Citation(s) in RCA: 57] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
T-cell recognition of peptides bound to MHC class II (MHCII) molecules is a central event in cell-mediated adaptive immunity. The current paradigm holds that prebound class II-associated invariant chain peptides (CLIP) and all subsequent antigens maintain a canonical orientation in the MHCII binding groove. Here we provide evidence for MHCII-bound CLIP inversion. NMR spectroscopy demonstrates that the interconversion from the canonical to the inverse alignment is a dynamic process, and X-ray crystallography shows that conserved MHC residues form a hydrogen bond network with the peptide backbone in both orientations. The natural catalyst HLA-DM accelerates peptide reorientation and the exchange of either canonically or inversely bound CLIP against antigenic peptide. Thus, noncanonical MHC-CLIP displays the hallmarks of a structurally and functionally intact antigen-presenting complex.
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32
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Muraille E, Gounon P, Cazareth J, Hoebeke J, Lippuner C, Davalos-Misslitz A, Aebischer T, Muller S, Glaichenhaus N, Mougneau E. Direct visualization of peptide/MHC complexes at the surface and in the intracellular compartments of cells infected in vivo by Leishmania major. PLoS Pathog 2010; 6:e1001154. [PMID: 20976202 PMCID: PMC2954901 DOI: 10.1371/journal.ppat.1001154] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2009] [Accepted: 09/17/2010] [Indexed: 12/22/2022] Open
Abstract
Protozoa and bacteria infect various types of phagocytic cells including macrophages, monocytes, dendritic cells and eosinophils. However, it is not clear which of these cells process and present microbial antigens in vivo and in which cellular compartments parasite peptides are loaded onto Major Histocompatibility Complex molecules. To address these issues, we have infected susceptible BALB/c (H-2d) mice with a recombinant Leishmania major parasite expressing a fluorescent tracer. To directly visualize the antigen presenting cells that present parasite-derived peptides to CD4+ T cells, we have generated a monoclonal antibody that reacts to an antigenic peptide derived from the parasite LACK antigen bound to I-Ad Major Histocompatibility Complex class II molecule. Immunogold electron microscopic analysis of in vivo infected cells showed that intracellular I-Ad/LACK complexes were present in the membrane of amastigote-containing phagosomes in dendritic cells, eosinophils and macrophages/monocytes. In both dendritic cells and macrophages, these complexes were also present in smaller vesicles that did not contain amastigote. The presence of I-Ad/LACK complexes at the surface of dendritic cells, but neither on the plasma membrane of macrophages nor eosinophils was independently confirmed by flow cytometry and by incubating sorted phagocytes with highly sensitive LACK-specific hybridomas. Altogether, our results suggest that peptides derived from Leishmania proteins are loaded onto Major Histocompatibility Complex class II molecules in the phagosomes of infected phagocytes. Although these complexes are transported to the cell surface in dendritic cells, therefore allowing the stimulation of parasite-specific CD4+ T cells, this does not occur in other phagocytic cells. To our knowledge, this is the first study in which Major Histocompatibility Complex class II molecules bound to peptides derived from a parasite protein have been visualized within and at the surface of cells that were infected in vivo.
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Affiliation(s)
- Eric Muraille
- Institut de Pharmacologie Moléculaire et Cellulaire, INSERM U924, Valbonne, France
- Université de Nice Sophia-Antipolis, Nice, France
| | | | - Julie Cazareth
- Institut de Pharmacologie Moléculaire et Cellulaire, INSERM U924, Valbonne, France
- Université de Nice Sophia-Antipolis, Nice, France
- Institut de Pharmacologie Moléculaire et Cellulaire, UMR6097, Valbonne, France
| | - Johan Hoebeke
- UPR 9021 CNRS, Institut de Biologie Moléculaire et Cellulaire, Strasbourg, France
| | | | | | - Toni Aebischer
- Parasitology laboratory, Robert Koch Institute, Berlin, Germany
| | - Sylviane Muller
- UPR 9021 CNRS, Institut de Biologie Moléculaire et Cellulaire, Strasbourg, France
| | - Nicolas Glaichenhaus
- Institut de Pharmacologie Moléculaire et Cellulaire, INSERM U924, Valbonne, France
- Université de Nice Sophia-Antipolis, Nice, France
| | - Evelyne Mougneau
- Institut de Pharmacologie Moléculaire et Cellulaire, INSERM U924, Valbonne, France
- Université de Nice Sophia-Antipolis, Nice, France
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Abstract
SUMMARY Major histocompatibility complex class II (MHC-II) molecules sample peptides from the extracellular space, allowing the immune system to detect the presence of foreign microbes from this compartment. To be able to predict the immune response to given pathogens, a number of methods have been developed to predict peptide-MHC binding. However, few methods other than the pioneering TEPITOPE/ProPred method have been developed for MHC-II. Despite recent progress in method development, the predictive performance for MHC-II remains significantly lower than what can be obtained for MHC-I. One reason for this is that the MHC-II molecule is open at both ends allowing binding of peptides extending out of the groove. The binding core of MHC-II-bound peptides is therefore not known a priori and the binding motif is hence not readily discernible. Recent progress has been obtained by including the flanking residues in the predictions. All attempts to make ab initio predictions based on protein structure have failed to reach predictive performances similar to those that can be obtained by data-driven methods. Thousands of different MHC-II alleles exist in humans. Recently developed pan-specific methods have been able to make reasonably accurate predictions for alleles that were not included in the training data. These methods can be used to define supertypes (clusters) of MHC-II alleles where alleles within each supertype have similar binding specificities. Furthermore, the pan-specific methods have been used to make a graphical atlas such as the MHCMotifviewer, which allows for visual comparison of specificities of different alleles.
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Affiliation(s)
- Morten Nielsen
- Department of Systems Biology, Technical University of Denmark, Centre for Biological Sequence Analysis, Lyngby, Denmark.
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Rinderknecht CH, Roh S, Pashine A, Belmares MP, Patil NS, Lu N, Truong P, Hou T, Macaubas C, Yoon T, Wang N, Busch R, Mellins ED. DM influences the abundance of major histocompatibility complex class II alleles with low affinity for class II-associated invariant chain peptides via multiple mechanisms. Immunology 2010; 131:18-32. [PMID: 20408893 DOI: 10.1111/j.1365-2567.2010.03282.x] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022] Open
Abstract
DM catalyses class II-associated invariant chain peptide (CLIP) release, edits the repertoire of peptides bound to major histocompatibility complex (MHC) class II molecules, affects class II structure, and thereby modulates binding of conformation-sensitive anti-class II antibodies. Here, we investigate the ability of DM to enhance the cell surface binding of monomorphic antibodies. We show that this enhancement reflects increases in cell surface class II expression and total cellular abundance, but notably these effects are selective for particular alleles. Evidence from analysis of cellular class II levels after cycloheximide treatment and from pulse-chase experiments indicates that DM increases the half-life of affected alleles. Unexpectedly, the pulse-chase experiments also revealed an early effect of DM on assembly of these alleles. The allelically variant feature that correlates with susceptibility to these DM effects is low affinity for CLIP; DM-dependent changes in abundance are reduced by invariant chain (CLIP) mutants that enhance CLIP binding to class II. We found evidence that DM mediates rescue of peptide-receptive DR0404 molecules from inactive forms in vitro and evidence suggesting that a similar process occurs in cells. Thus, multiple mechanisms, operating along the biosynthetic pathway of class II molecules, contribute to DM-mediated increases in the abundance of low-CLIP-affinity alleles.
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35
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Limitations of Ab initio predictions of peptide binding to MHC class II molecules. PLoS One 2010; 5:e9272. [PMID: 20174654 PMCID: PMC2822856 DOI: 10.1371/journal.pone.0009272] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2009] [Accepted: 01/21/2010] [Indexed: 11/19/2022] Open
Abstract
Successful predictions of peptide MHC binding typically require a large set of binding data for the specific MHC molecule that is examined. Structure based prediction methods promise to circumvent this requirement by evaluating the physical contacts a peptide can make with an MHC molecule based on the highly conserved 3D structure of peptide:MHC complexes. While several such methods have been described before, most are not publicly available and have not been independently tested for their performance. We here implemented and evaluated three prediction methods for MHC class II molecules: statistical potentials derived from the analysis of known protein structures; energetic evaluation of different peptide snapshots in a molecular dynamics simulation; and direct analysis of contacts made in known 3D structures of peptide:MHC complexes. These methods are ab initio in that they require structural data of the MHC molecule examined, but no specific peptide:MHC binding data. Moreover, these methods retain the ability to make predictions in a sufficiently short time scale to be useful in a real world application, such as screening a whole proteome for candidate binding peptides. A rigorous evaluation of each methods prediction performance showed that these are significantly better than random, but still substantially lower than the best performing sequence based class II prediction methods available. While the approaches presented here were developed independently, we have chosen to present our results together in order to support the notion that generating structure based predictions of peptide:MHC binding without using binding data is unlikely to give satisfactory results.
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36
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Nielsen M, Lund O. NN-align. An artificial neural network-based alignment algorithm for MHC class II peptide binding prediction. BMC Bioinformatics 2009; 10:296. [PMID: 19765293 PMCID: PMC2753847 DOI: 10.1186/1471-2105-10-296] [Citation(s) in RCA: 376] [Impact Index Per Article: 25.1] [Reference Citation Analysis] [Abstract] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2009] [Accepted: 09/18/2009] [Indexed: 01/03/2023] Open
Abstract
BACKGROUND The major histocompatibility complex (MHC) molecule plays a central role in controlling the adaptive immune response to infections. MHC class I molecules present peptides derived from intracellular proteins to cytotoxic T cells, whereas MHC class II molecules stimulate cellular and humoral immunity through presentation of extracellularly derived peptides to helper T cells. Identification of which peptides will bind a given MHC molecule is thus of great importance for the understanding of host-pathogen interactions, and large efforts have been placed in developing algorithms capable of predicting this binding event. RESULTS Here, we present a novel artificial neural network-based method, NN-align that allows for simultaneous identification of the MHC class II binding core and binding affinity. NN-align is trained using a novel training algorithm that allows for correction of bias in the training data due to redundant binding core representation. Incorporation of information about the residues flanking the peptide-binding core is shown to significantly improve the prediction accuracy. The method is evaluated on a large-scale benchmark consisting of six independent data sets covering 14 human MHC class II alleles, and is demonstrated to outperform other state-of-the-art MHC class II prediction methods. CONCLUSION The NN-align method is competitive with the state-of-the-art MHC class II peptide binding prediction algorithms. The method is publicly available at http://www.cbs.dtu.dk/services/NetMHCII-2.0.
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Affiliation(s)
- Morten Nielsen
- Center for Biological Sequence Analysis, Department of Systems Biology, Technical University of Denmark, DK-2800 Lyngby, Denmark.
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Reipert BM, Steinitz KN, van Helden PM, Unterthurner S, Schuster M, Ahmad RU, Ilas J, Schwarz HP. Opportunities and limitations of mouse models humanized for HLA class II antigens. J Thromb Haemost 2009; 7 Suppl 1:92-7. [PMID: 19630777 DOI: 10.1111/j.1538-7836.2009.03403.x] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
MHC class II molecules are essential for shaping the CD4+ T-cell repertoire in the thymus and for selecting antigenic peptides that are presented to CD4+ T cells in the periphery. A range of different mouse models humanized for HLA class II antigens have been developed to study the regulation of MHC-class II restricted immune responses. These mouse models have been used to identify immunodominant peptides that trigger diseases and to characterize the interactions of T-cell receptors with disease-associated peptides and MHC class II molecules. Peptides presented to CD4+ T cells in these mouse models were shown to be similar to peptides presented to CD4+ T cells in patients who carry the same MHC class II haplotype. Opportunities and limitations associated with these mouse models will be discussed and the potential application of these models for understanding the regulation of antibody responses against factor VIII in hemophilia A will be indicated.
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38
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Dustin ML. Multiscale analysis of T cell activation: correlating in vitro and in vivo analysis of the immunological synapse. Curr Top Microbiol Immunol 2009; 334:47-70. [PMID: 19521681 DOI: 10.1007/978-3-540-93864-4_3] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Recently implemented fluorescence imaging techniques, such as total internal reflection fluorescence microscopy and two-photon laser scanning microscopy, have made possible multiscale analysis of the immune response from single molecules in an interface to cells moving in lymphoid tissues and tumors. In this review, we consider components of T cell sensitivity: the immunological synapse, the coordination of migration, and antigen recognition in vivo. Potency, dose, and detection threshold for peptide-MHC determine T cell sensitivity. The immunological synapse incorporates T cell receptor microclusters that initiate and sustain signaling, and it also determines the positional stability of the T cells through symmetry and symmetry breaking. In vivo decisions by T cells on stopping or migration are based on antigen stop signals and environmental go signals that can sometimes prevent arrest of T cells altogether, and thus can change the outcome of antigen encounters.
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Affiliation(s)
- Michael L Dustin
- Department of Pathology, Program of Molecular Pathogenesis, Skirball Institute of BioMolecular Medicine, NYU School of Medicine, 540 First Avenue, New York, NY 10016, USA
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39
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Fallang LE, Roh S, Holm A, Bergseng E, Yoon T, Fleckenstein B, Bandyopadhyay A, Mellins ED, Sollid LM. Complexes of two cohorts of CLIP peptides and HLA-DQ2 of the autoimmune DR3-DQ2 haplotype are poor substrates for HLA-DM. THE JOURNAL OF IMMUNOLOGY 2008; 181:5451-5461. [PMID: 18832702 DOI: 10.4049/jimmunol.181.8.5451] [Citation(s) in RCA: 52] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
Atypical invariant chain (Ii) CLIP fragments (CLIP2) have been found in association with HLA-DQ2 (DQ2) purified from cell lysates. We mapped the binding register of CLIP2 (Ii 96-104) to DQ2 and found proline at the P1 position, in contrast to the canonical CLIP1 (Ii 83-101) register with methionine at P1. CLIP1/2 peptides are the predominant peptide species, even for DQ2 from HLA-DM (DM)-expressing cells. We hypothesized that DQ2-CLIP1/2 might be poor substrates for DM. We measured DM-mediated exchange of CLIP and other peptides for high-affinity indicator peptides and found it is inefficient for DQ2. DM-DQ-binding and DM chaperone effects on conformation and levels of DQ are also reduced for DQ2, compared with DQ1. We suggest that the unusual interaction of DQ2 with Ii and DM may provide a basis for the known disease associations of DQ2.
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Affiliation(s)
- Lars-Egil Fallang
- Centre for Immune Regulation and Institute of Immunology, University of Oslo, Rikshospitalet, N-0027 Oslo, Norway
| | - Sujin Roh
- Department of Pediatrics, Stanford University, Stanford, CA 94305, USA
| | - Anders Holm
- Centre for Immune Regulation and Institute of Immunology, University of Oslo, Rikshospitalet, N-0027 Oslo, Norway
| | - Elin Bergseng
- Centre for Immune Regulation and Institute of Immunology, Rikshospitalet University Hospital, N-0027 Oslo, Norway
| | - Taejin Yoon
- Department of Pediatrics, Stanford University, Stanford, CA 94305, USA
| | - Burkhard Fleckenstein
- Centre for Immune Regulation and Institute of Immunology, University of Oslo, Rikshospitalet, N-0027 Oslo, Norway
| | | | | | - Ludvig M Sollid
- Centre for Immune Regulation and Institute of Immunology, University of Oslo, Rikshospitalet, N-0027 Oslo, Norway.,Centre for Immune Regulation and Institute of Immunology, Rikshospitalet University Hospital, N-0027 Oslo, Norway
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40
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Muixí L, Alvarez I, Jaraquemada D. Peptides presented in vivo by HLA-DR in thyroid autoimmunity. Adv Immunol 2008; 99:165-209. [PMID: 19117535 DOI: 10.1016/s0065-2776(08)00606-8] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
The association of the major histocompatibility complex (MHC) genes with autoimmune diseases together with the ectopic expression of class II molecules by epithelial cells of the target tissue gives to these molecules a central role in the pathogenesis of the disease, in its regulation and in the persistence of the immune response in situ. HLA-DR molecules expressed by thyroid follicular cells in thyroid autoimmune diseases are compact molecules stably associated with peptides. The nature of these peptides is of vital importance in the understanding of the disease, since these MHC-II-peptide complexes are going to be recognized by both effector and regulatory T cells in situ. In this chapter, we review the current state of the analysis of naturally processed peptides presented by MHC class II molecules in the context of autoimmunity and we discuss our data of natural HLA-DR ligands eluted from Graves' disease affected thyroid glands, from where autoantigen-derived peptides have been identified.
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Affiliation(s)
- Laia Muixí
- Immunology Unit, Institut de Biotechnologia i Biomedicina, Universitat Autònoma de Barcelona, Campus de Bellaterra, Barcelona, Spain
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41
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Abstract
Heterogeneous intracellular pathways and biochemical mechanisms are responsible for generating the glycoprotein complexes of peptide and major histocompatibility complex that are displayed on the surfaces of antigen-presenting cells for recognition by T lymphocytes. These pathways have a profound influence on the specificity of adaptive immunity and tolerance, as well as the context and consequences of antigen recognition by T cells in the thymus and periphery. The field of antigen processing and presentation has continued to advance since the publication of a focus issue on the topic in Nature Immunology in July 2004. Progress has been made on many fronts, including advances in understanding how proteases, accessory molecules and intracellular pathways influence peptide loading and antigen presentation in various cell types.
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Affiliation(s)
- Peter E Jensen
- Department of Pathology, University of Utah, Salt Lake City, Utah 84112, USA.
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42
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Voutsas IF, Gritzapis AD, Mahaira LG, Salagianni M, Hofe EV, Kallinteris NL, Baxevanis CN. Induction of potent CD4+ T cell-mediated antitumor responses by a helper HER-2/neu peptide linked to the Ii-Key moiety of the invariant chain. Int J Cancer 2007; 121:2031-2041. [PMID: 17634957 DOI: 10.1002/ijc.22936] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
The Ii-Key fragment from the MHC class II-associated invariant chain (or Ii protein) has been shown to facilitate direct charging of MHC class II epitopes to the peptide binding groove. The purpose of the present study was to test the potential of a series of Ii-Key/HER-2/neu776-790 hybrid peptides to generate increased frequencies of peptide-specific CD4+ T cells over the native peptide in mice transgenic (Tg) for a chimeric human mouse class II molecule (DR4-IE) (H-2b) as well as their antitumor potency. Following in vivo priming, such hybrid peptides induced increased proliferation and frequencies of IFN-gamma producing CD4+ T cells in response to either syngeneic dendritic cells pulsed with native peptide, or HLA-DR4+ human tumor cell lines expressing HER-2/neu. Hybrid peptides were more stable in an off-rate kinetics assay compared to the native peptide. In addition, antigen-specific CD4+ T cells from hybrid peptide immunized DR4-IE Tg mice synergized with HER-2/neu(435-443)-specific CD8+ T cells from HLA-A2.1 Tg HHD (H-2b) mice in producing antitumor immunity into SCID mice xenografted with the HER-2/neu+, HLA-A2.1+ and HLA-DR4+ FM3 human melanoma cell line. High proportions of these adoptively transferred HER-2/neu peptide-specific CD4+ and CD8+ T cells infiltrated FM3-induced tumors (tumor infiltrating lymphocytes; TIL) in SCID mice. CD8+ TIL exhibited long-lasting antitumor activity when cotransferred with CD4+ TIL, inducing regression of FM3 tumors in a group of untreated, tumor-bearing SCID mice, following adoptive transfer. Our data show that Ii-Key modified HER-2/neu776-790 hybrid peptides are sufficiently potent to provide antigen-specific CD4+ TH cells with therapeutic antitumor activity.
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MESH Headings
- Animals
- Antigens, Differentiation, B-Lymphocyte/chemistry
- Antigens, Differentiation, B-Lymphocyte/genetics
- Antigens, Differentiation, B-Lymphocyte/immunology
- Antigens, Differentiation, B-Lymphocyte/metabolism
- CD4-Positive T-Lymphocytes/cytology
- CD4-Positive T-Lymphocytes/immunology
- CD4-Positive T-Lymphocytes/metabolism
- Cell Proliferation
- Cells, Cultured
- Dendritic Cells/immunology
- Dendritic Cells/metabolism
- Histocompatibility Antigens Class II/chemistry
- Histocompatibility Antigens Class II/genetics
- Histocompatibility Antigens Class II/immunology
- Histocompatibility Antigens Class II/metabolism
- Humans
- Kinetics
- Mice
- Mice, SCID
- Mice, Transgenic
- Neoplasms/immunology
- Neoplasms/metabolism
- Neoplasms/pathology
- Peptide Fragments/genetics
- Peptide Fragments/immunology
- Peptide Fragments/metabolism
- Protein Binding
- Receptor, ErbB-2/genetics
- Receptor, ErbB-2/immunology
- Receptor, ErbB-2/metabolism
- T-Lymphocytes, Cytotoxic/cytology
- T-Lymphocytes, Cytotoxic/immunology
- T-Lymphocytes, Cytotoxic/metabolism
- Xenograft Model Antitumor Assays
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Affiliation(s)
- Ioannis F Voutsas
- Cancer Immunology and Immunotherapy Center, Saint Savas Cancer Hospital, Athens, Greece
| | - Angelos D Gritzapis
- Cancer Immunology and Immunotherapy Center, Saint Savas Cancer Hospital, Athens, Greece
| | - Louisa G Mahaira
- Cancer Immunology and Immunotherapy Center, Saint Savas Cancer Hospital, Athens, Greece
| | - Maria Salagianni
- Cancer Immunology and Immunotherapy Center, Saint Savas Cancer Hospital, Athens, Greece
| | - Eric von Hofe
- Antigen Express Inc., Biotech III, One Innovation Drive, Worcester, MA
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Lovitch SB, Esparza TJ, Schweitzer G, Herzog J, Unanue ER. Activation of Type B T Cells after Protein Immunization Reveals Novel Pathways of In Vivo Presentation of Peptides. THE JOURNAL OF IMMUNOLOGY 2006; 178:122-33. [PMID: 17182547 DOI: 10.4049/jimmunol.178.1.122] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
Type B T cells recognize a peptide-MHC conformer generated in recycling endosomes and eliminated by H2-DM in late endosomes; as a result, they recognize exogenous peptide, but fail to respond to the identical epitope generated from the native protein. To investigate the behavior of these cells in vivo, we generated mice transgenic for a type B TCR recognizing the 48-62 epitope of hen egg white lysozyme (HEL) presented by I-A(k). Type B T cells responded only to peptide ex vivo, but responded in vivo to immunization with either protein or peptide in the presence of Freund's adjuvant or LPS. Presentation of the type B conformer was MyD88-independent, evident within 24 h after HEL immunization, and restricted to the CD11b/c(+) APC subset. Immunization with listeriolysin O, a potent inducer of cell death, also primed type B T cells in vivo, and transfer of HEL-bearing allogeneic dendritic cells activated type B T cells. We conclude that a number of conditions in vivo, some of which induce inflammation and cell death, lead to peptide presentation through mechanisms distinct from the classical pathways involving H-2DM molecules.
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Affiliation(s)
- Scott B Lovitch
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO 63110, USA
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