1
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Gibadullin R, Morris RK, Niu J, Sidney J, Sette A, Gellman SH. Thioamide Analogues of MHC I Antigen Peptides. J Am Chem Soc 2023; 145:25559-25569. [PMID: 37968794 PMCID: PMC10782604 DOI: 10.1021/jacs.3c05300] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2023]
Abstract
Short, synthetic peptides that are displayed by major histocompatibility complex I (MHC I) can stimulate CD8 T cells in vivo to destroy virus-infected or cancer cells. The development of such peptides as vaccines that provide protective immunity, however, is limited by rapid proteolytic degradation. Introduction of unnatural amino acid residues can suppress MHC I antigen proteolysis, but the modified peptides typically display lower affinity for MHC I and/or diminished ability to activate CD8 T cells relative to native antigen. Here, we report a new strategy for modifying MHC I antigens to enhance resistance to proteolysis while preserving MHC I affinity and T cell activation properties. This approach, replacing backbone amide groups with thioamides, was evaluated in two well-characterized antigens presented by HLA-A2, a common human MHC I. For each antigen, singly modified thioamide analogues retained affinity for HLA-A2 and activated T cells specific for the native antigen, as measured via interferon-γ secretion. In each system, we identified a highly potent triply substituted thioamide antigen ("thio-antigen") that displayed substantial resistance to proteolytic cleavage. Collectively, our results suggest that thio-antigens may represent a general and readily accessible source of potent vaccine candidates that resist degradation.
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Affiliation(s)
- Ruslan Gibadullin
- Department of Chemistry, University of Wisconsin, 1101 University Avenue, Madison, Wisconsin 53706, United States
- Present address: Department of Chemistry, The Scripps Research Institute, La Jolla, California 92037, United States
| | - Rylie K. Morris
- Department of Chemistry, University of Wisconsin, 1101 University Avenue, Madison, Wisconsin 53706, United States
| | - Jiani Niu
- Department of Chemistry, University of Wisconsin, 1101 University Avenue, Madison, Wisconsin 53706, United States
| | - John Sidney
- Division of Vaccine Discovery, La Jolla Institute for Immunology, La Jolla, California 92037, United States
| | - Alessandro Sette
- Division of Vaccine Discovery, La Jolla Institute for Immunology, La Jolla, California 92037, United States
- Department of Medicine, University of California, San Diego, California 92093, United States
| | - Samuel H. Gellman
- Department of Chemistry, University of Wisconsin, 1101 University Avenue, Madison, Wisconsin 53706, United States
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2
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Kalaitsidou M, Moon OR, Sykorova M, Bao L, Qu Y, Sukumaran S, Valentine M, Zhou X, Pandey V, Foos K, Medvedev S, Powell Jr DJ, Udyavar A, Gschweng E, Rodriguez R, Dudley ME, Hawkins RE, Kueberuwa G, Bridgeman JS. Signaling via a CD28/CD40 chimeric costimulatory antigen receptor (CoStAR™), targeting folate receptor alpha, enhances T cell activity and augments tumor reactivity of tumor infiltrating lymphocytes. Front Immunol 2023; 14:1256491. [PMID: 38022678 PMCID: PMC10664248 DOI: 10.3389/fimmu.2023.1256491] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2023] [Accepted: 10/18/2023] [Indexed: 12/01/2023] Open
Abstract
Transfer of autologous tumor infiltrating lymphocytes (TIL) to patients with refractory melanoma has shown clinical efficacy in a number of trials. However, extending the clinical benefit to patients with other cancers poses a challenge. Inefficient costimulation in the tumor microenvironment can lead to T cell anergy and exhaustion resulting in poor anti-tumor activity. Here, we describe a chimeric costimulatory antigen receptor (CoStAR) comprised of FRα-specific scFv linked to CD28 and CD40 intracellular signaling domains. CoStAR signaling alone does not activate T cells, while the combination of TCR and CoStAR signaling enhances T cell activity resulting in less differentiated T cells, and augmentation of T cell effector functions, including cytokine secretion and cytotoxicity. CoStAR activity resulted in superior T cell proliferation, even in the absence of exogenous IL-2. Using an in vivo transplantable tumor model, CoStAR was shown to improve T cell survival after transfer, enhanced control of tumor growth, and improved host survival. CoStAR could be reliably engineered into TIL from multiple tumor indications and augmented TIL activity against autologous tumor targets both in vitro and in vivo. CoStAR thus represents a general approach to improving TIL therapy with synthetic costimulation.
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Affiliation(s)
| | - Owen R. Moon
- Department of Research, Instil Bio, Dallas, TX, United States
| | | | - Leyuan Bao
- Department of Research, Instil Bio, Dallas, TX, United States
| | - Yun Qu
- Department of Research, Instil Bio, Dallas, TX, United States
| | | | | | - Xingliang Zhou
- Department of Research, Instil Bio, Dallas, TX, United States
| | - Veethika Pandey
- Ovarian Cancer Research Center, Division of Gynecologic Oncology, Department of Obstetrics and Gynecology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, United States
| | - Kay Foos
- Ovarian Cancer Research Center, Division of Gynecologic Oncology, Department of Obstetrics and Gynecology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, United States
| | - Sergey Medvedev
- Ovarian Cancer Research Center, Division of Gynecologic Oncology, Department of Obstetrics and Gynecology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, United States
| | - Daniel J. Powell Jr
- Ovarian Cancer Research Center, Division of Gynecologic Oncology, Department of Obstetrics and Gynecology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, United States
| | - Akshata Udyavar
- Department of Research, Instil Bio, Dallas, TX, United States
| | - Eric Gschweng
- Department of Research, Instil Bio, Dallas, TX, United States
| | - Ruben Rodriguez
- Department of Research, Instil Bio, Dallas, TX, United States
| | - Mark E. Dudley
- Department of Research, Instil Bio, Dallas, TX, United States
| | | | - Gray Kueberuwa
- Department of Research, Instil Bio, Dallas, TX, United States
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3
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Lanfermeijer J, van de Ven K, van Dijken H, Hendriks M, Talavera Ormeño CMP, de Heij F, Roholl P, Borghans JAM, van Baarle D, de Jonge J. Modified influenza M1 58-66 peptide vaccination induces non-relevant T-cells and may enhance pathology after challenge. NPJ Vaccines 2023; 8:116. [PMID: 37573454 PMCID: PMC10423225 DOI: 10.1038/s41541-023-00705-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2022] [Accepted: 07/11/2023] [Indexed: 08/14/2023] Open
Abstract
CD8 + T cells are promising targets for vaccination against influenza A virus (IAV) infection. Their induction via peptide vaccination is not trivial, because peptides are weakly immunogenic. One strategy to overcome this is by vaccination with chemically enhanced altered peptide ligands (CPLs), which have improved MHC-binding and immunogenicity. It remains unknown how peptide-modification affects the resulting immune response. We studied the effect of CPLs derived from the influenza M158-66 epitope (GILGFVFTL) on the T-cell response. In HLA-A2*0201 transgenic mice, CPL-vaccination led to higher T-cell frequencies, but only a small percentage of the induced T cells recognized the GILG-wildtype (WT) peptide. CPL-vaccination resulted in a lower richness of the GILG-WT-specific T-cell repertoire and no improved protection against IAV-infection compared to GILG-WT peptide-vaccination. One CPL even appeared to enhance pathology after IAV-challenge. CPL-vaccination thus induces T cells not targeting the original peptide, which may lead to potential unwanted side effects.
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Affiliation(s)
- Josien Lanfermeijer
- Center for Infectious Disease Control, National Institute for Public Health and the Environment, Bilthoven, the Netherlands
- Center for Translational Immunology, University Medical Center Utrecht, Utrecht, the Netherlands
| | - Koen van de Ven
- Center for Infectious Disease Control, National Institute for Public Health and the Environment, Bilthoven, the Netherlands
| | - Harry van Dijken
- Center for Infectious Disease Control, National Institute for Public Health and the Environment, Bilthoven, the Netherlands
| | - Marion Hendriks
- Center for Infectious Disease Control, National Institute for Public Health and the Environment, Bilthoven, the Netherlands
| | - Cami M P Talavera Ormeño
- Department of Cell and Chemical Biology, Leiden University Medical Centre, Leiden, The Netherlands
| | - Femke de Heij
- Center for Infectious Disease Control, National Institute for Public Health and the Environment, Bilthoven, the Netherlands
| | | | - José A M Borghans
- Center for Translational Immunology, University Medical Center Utrecht, Utrecht, the Netherlands
| | - Debbie van Baarle
- Center for Infectious Disease Control, National Institute for Public Health and the Environment, Bilthoven, the Netherlands
- Center for Translational Immunology, University Medical Center Utrecht, Utrecht, the Netherlands
- Virology & Immunology Research. Dept Medical Microbiology and Infection prevention, University Medical Center Groningen, Groningen, the Netherlands
| | - Jørgen de Jonge
- Center for Infectious Disease Control, National Institute for Public Health and the Environment, Bilthoven, the Netherlands.
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4
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Yue C, Wang P, Tian J, Gao GF, Liu K, Liu WJ. Seeing the T cell Immunity of SARS-CoV-2 and SARS-CoV: Believing the Epitope-Oriented Vaccines. Int J Biol Sci 2023; 19:4052-4060. [PMID: 37705735 PMCID: PMC10496500 DOI: 10.7150/ijbs.80468] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2022] [Accepted: 07/07/2023] [Indexed: 09/15/2023] Open
Abstract
The emergence of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) at the end of 2019 stimulated vigorous research efforts in immunology and vaccinology. In addition to innate immune responses, both virus-specific humoral and cellular immune responses are of importance for viral clearance. T cell epitopes play a central role in T cell-based immune responses. Herein, we summarized the peptide/major histocompatibility complex (pMHC) structures of the SARS-CoV-2-derived T cell epitopes available in the Protein Data Bank (PDB) and proposed the challenge and opportunities for using of T cell epitopes in future vaccine development efforts. A total of 27 SARS-CoV-2 related pMHC structures and five complexes with T cell receptors were retrieved. The peptides are mainly distributed on spike (S), nucleocapsid (N), and ORF1ab proteins. Most peptides are conserved among variants of concerns (VOCs) for SARS-CoV-2, except for several mutated peptides located in the S protein. The structures of human leukocyte antigen (HLA) complexed with seven epitopes derived from SARS-CoV were also retrieved, which showed a potential cross T cell immunity with SARS-CoV-2. Structural studies of antigenic peptides from SARS-CoV-2 and SARS-CoV help to visualize the processes and the mechanisms of cross T cell immunity. T cell epitope-oriented vaccines are potential next-generation vaccines for SARS-CoV-2, which are worthy of further investigation.
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Affiliation(s)
- Can Yue
- CAS Key Laboratory of Infection and Immunity, National Laboratory of Macromolecules, Institute of Biophysics, Chinese Academy of Sciences (CAS), Beijing, China
| | - Pengyan Wang
- Department of Pathogen Biology & Microbiology, School of Medicine, Zhejiang University, Hangzhou, Zhejiang, China
| | - Jinmin Tian
- NHC Key Laboratory of Biosafety, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention (China CDC), Beijing, China
- School of Ophthalmology and Optometry, Eye Hospital, Wenzhou Medical University, Wenzhou, Zhejiang, China
| | - George F. Gao
- NHC Key Laboratory of Biosafety, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention (China CDC), Beijing, China
- CAS Key Laboratory of Pathogen Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences (CAS), Beijing, China
| | - Kefang Liu
- CAS Key Laboratory of Pathogen Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences (CAS), Beijing, China
- Shenzhen Children's Hospital, Shenzhen, Guangdong, China
| | - William J. Liu
- NHC Key Laboratory of Biosafety, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention (China CDC), Beijing, China
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5
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Knezevic L, Wachsmann TLA, Francis O, Dockree T, Bridgeman JS, Wouters A, de Wet B, Cole DK, Clement M, McLaren JE, Gostick E, Ladell K, Llewellyn-Lacey S, Price DA, van den Berg HA, Tabi Z, Sessions RB, Heemskerk MHM, Wooldridge L. High-affinity CD8 variants enhance the sensitivity of pMHCI antigen recognition via low-affinity TCRs. J Biol Chem 2023; 299:104981. [PMID: 37390984 PMCID: PMC10432799 DOI: 10.1016/j.jbc.2023.104981] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2023] [Revised: 06/01/2023] [Accepted: 06/13/2023] [Indexed: 07/02/2023] Open
Abstract
CD8+ T cell-mediated recognition of peptide-major histocompatibility complex class I (pMHCI) molecules involves cooperative binding of the T cell receptor (TCR), which confers antigen specificity, and the CD8 coreceptor, which stabilizes the TCR/pMHCI complex. Earlier work has shown that the sensitivity of antigen recognition can be regulated in vitro by altering the strength of the pMHCI/CD8 interaction. Here, we characterized two CD8 variants with moderately enhanced affinities for pMHCI, aiming to boost antigen sensitivity without inducing non-specific activation. Expression of these CD8 variants in model systems preferentially enhanced pMHCI antigen recognition in the context of low-affinity TCRs. A similar effect was observed using primary CD4+ T cells transduced with cancer-targeting TCRs. The introduction of high-affinity CD8 variants also enhanced the functional sensitivity of primary CD8+ T cells expressing cancer-targeting TCRs, but comparable results were obtained using exogenous wild-type CD8. Specificity was retained in every case, with no evidence of reactivity in the absence of cognate antigen. Collectively, these findings highlight a generically applicable mechanism to enhance the sensitivity of low-affinity pMHCI antigen recognition, which could augment the therapeutic efficacy of clinically relevant TCRs.
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Affiliation(s)
- Lea Knezevic
- Faculty of Health Sciences, University of Bristol, Bristol, UK; Department of Haematology, Leiden University Medical Center, Leiden, The Netherlands.
| | - Tassilo L A Wachsmann
- Department of Haematology, Leiden University Medical Center, Leiden, The Netherlands
| | - Ore Francis
- Faculty of Health Sciences, University of Bristol, Bristol, UK
| | - Tamsin Dockree
- Division of Infection and Immunity, Cardiff University School of Medicine, University Hospital of Wales, Cardiff, UK
| | | | - Anne Wouters
- Department of Haematology, Leiden University Medical Center, Leiden, The Netherlands
| | | | - David K Cole
- Division of Infection and Immunity, Cardiff University School of Medicine, University Hospital of Wales, Cardiff, UK; Immunocore, Abingdon, UK
| | - Mathew Clement
- Division of Infection and Immunity, Cardiff University School of Medicine, University Hospital of Wales, Cardiff, UK; Systems Immunity Research Institute, Cardiff University School of Medicine, University Hospital of Wales, Cardiff, UK
| | - James E McLaren
- Division of Infection and Immunity, Cardiff University School of Medicine, University Hospital of Wales, Cardiff, UK
| | - Emma Gostick
- Division of Infection and Immunity, Cardiff University School of Medicine, University Hospital of Wales, Cardiff, UK
| | - Kristin Ladell
- Division of Infection and Immunity, Cardiff University School of Medicine, University Hospital of Wales, Cardiff, UK
| | - Sian Llewellyn-Lacey
- Division of Infection and Immunity, Cardiff University School of Medicine, University Hospital of Wales, Cardiff, UK
| | - David A Price
- Division of Infection and Immunity, Cardiff University School of Medicine, University Hospital of Wales, Cardiff, UK; Systems Immunity Research Institute, Cardiff University School of Medicine, University Hospital of Wales, Cardiff, UK
| | | | - Zsuzsanna Tabi
- Division of Infection and Immunity, Cardiff University School of Medicine, University Hospital of Wales, Cardiff, UK
| | | | - Mirjam H M Heemskerk
- Department of Haematology, Leiden University Medical Center, Leiden, The Netherlands
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6
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Pinilla C, Giulianotti MA, Santos RG, Houghten RA. Identification of B Cell and T Cell Epitopes Using Synthetic Peptide Combinatorial Libraries. Curr Protoc 2022; 2:e378. [PMID: 35263045 DOI: 10.1002/cpz1.378] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
This article presents a combinatorial library method that consists of the synthesis and screening of mixture-based synthetic combinatorial libraries of peptide molecules to identify B and T cell epitopes. The protocols employ peptide libraries to identify peptides recognized by MAbs and T cells. The first protocol uses a positional scanning peptide library made up of hexapeptides to identify antigenic determinants recognized by MAbs. The 120 mixtures in the hexapeptide library are tested for their inhibitory activity in a competitive ELISA. The second protocol uses a decapeptide library to identify T cell peptide ligands. The 200 mixtures of the decapeptide library are tested for their ability to induce T cell activation. Support protocols cover optimization of the assay conditions for each MAb or T cell, to achieve the best level of sensitivity and reproducibility, and preparation of a hexapeptide library, along with deconvolution approaches. © 2022 Wiley Periodicals LLC. Basic Protocol 1: Screening peptide library for antibody inhibition Basic Protocol 2: Screening a peptide library to identify CD4+ Or CD8+ T cell ligands Support Protocol 1: Optimizing antigen and antibody concentrations for screening assay Support Protocol 2: Preparing a positional scanning peptide library.
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Affiliation(s)
- Clemencia Pinilla
- Center for Translational Science, Florida International University, Port St. Lucie, Florida
| | - Marc A Giulianotti
- Center for Translational Science, Florida International University, Port St. Lucie, Florida
| | | | - Richard A Houghten
- Center for Translational Science, Florida International University, Port St. Lucie, Florida
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7
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Zhou W, Chen X, Zhou Y, Shi S, Liang C, Yu X, Chen H, Guo Q, Zhang Y, Liu P, Li C, Chu Y, Luo Y, Wang Y, Zhou Z, Zhao Z, Chen Q, Sun T, Jiang C. Exosomes derived from immunogenically dying tumor cells as a versatile tool for vaccination against pancreatic cancer. Biomaterials 2021; 280:121306. [PMID: 34952381 DOI: 10.1016/j.biomaterials.2021.121306] [Citation(s) in RCA: 36] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2021] [Revised: 11/08/2021] [Accepted: 11/30/2021] [Indexed: 12/15/2022]
Abstract
Despite tremendous progress achieved in immunotherapy, many critical challenges in treating pancreatic ductal adenocarcinoma (PDAC) persist. Considering the poor vascularization of PDAC, after intramuscular administration exosomes can targeted deliver "cargos" to pancreatic tumors and bypass obstructions of the intrinsic overexpressed stroma through lymphatics. Herein, we propose a strategy to derive exosomes from immunogenically dying tumor cells and exploit their properties for several purposes, including antigen presentation, adjuvant supply, and "cargo" delivery of vaccines against pancreatic cancer via intramuscular injection. To enhance the immunostimulatory effects, the MART-1 peptide is modified to the exosomes to expand T-cell-related responses. Furthermore, CCL22 siRNA is electroporated into the exosomes (referred to as spMEXO) to hinder the CCR4/CCL22 axis between DCs and Tregs, thereby suppressing Treg expansion. Both in vitro and in vivo studies demonstrate that spMEXO can serve as an effective prophylactic vaccine to delay tumor growth, whereas combining spMEXO with PDAC first-line chemotherapeutics (co-administration of gemcitabine with albumin-paclitaxel) demonstrated significantly enhanced therapeutic effects in established PANC-02 tumors. Therefore, the present work provides an effective strategy to employ cancer vaccines through intramuscular injection in PDAC and highlights the potential of exosomes derived from immunogenically dying tumor cells as a versatile tool to develop nanovaccines for immunotherapy.
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Affiliation(s)
- Wenxi Zhou
- Key Laboratory of Smart Drug Delivery, Ministry of Education, State Key Laboratory of Medical Neurobiology and MOE Frontiers Center for Brain Science, Department of Pharmaceutics, School of Pharmacy, Fudan University, Shanghai, 201203, China
| | - Xinli Chen
- Key Laboratory of Smart Drug Delivery, Ministry of Education, State Key Laboratory of Medical Neurobiology and MOE Frontiers Center for Brain Science, Department of Pharmaceutics, School of Pharmacy, Fudan University, Shanghai, 201203, China
| | - Yu Zhou
- Department of Interventional Radiology, Ruijin Hospital, Shanghai Jiao Tong University, School of Medicine, Shanghai, 200025, China
| | - Si Shi
- Department of Pancreatic and Hepatobiliary Surgery, Fudan University Shanghai Cancer Center, 270 Dongan Road, Shanghai, 200032, China; Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, 200032, China
| | - Chen Liang
- Department of Pancreatic and Hepatobiliary Surgery, Fudan University Shanghai Cancer Center, 270 Dongan Road, Shanghai, 200032, China; Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, 200032, China
| | - Xianjun Yu
- Department of Pancreatic and Hepatobiliary Surgery, Fudan University Shanghai Cancer Center, 270 Dongan Road, Shanghai, 200032, China; Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, 200032, China
| | - Hongyi Chen
- Key Laboratory of Smart Drug Delivery, Ministry of Education, State Key Laboratory of Medical Neurobiology and MOE Frontiers Center for Brain Science, Department of Pharmaceutics, School of Pharmacy, Fudan University, Shanghai, 201203, China
| | - Qin Guo
- Key Laboratory of Smart Drug Delivery, Ministry of Education, State Key Laboratory of Medical Neurobiology and MOE Frontiers Center for Brain Science, Department of Pharmaceutics, School of Pharmacy, Fudan University, Shanghai, 201203, China
| | - Yiwen Zhang
- Key Laboratory of Smart Drug Delivery, Ministry of Education, State Key Laboratory of Medical Neurobiology and MOE Frontiers Center for Brain Science, Department of Pharmaceutics, School of Pharmacy, Fudan University, Shanghai, 201203, China
| | - Peixin Liu
- Key Laboratory of Smart Drug Delivery, Ministry of Education, State Key Laboratory of Medical Neurobiology and MOE Frontiers Center for Brain Science, Department of Pharmaceutics, School of Pharmacy, Fudan University, Shanghai, 201203, China
| | - Chao Li
- Key Laboratory of Smart Drug Delivery, Ministry of Education, State Key Laboratory of Medical Neurobiology and MOE Frontiers Center for Brain Science, Department of Pharmaceutics, School of Pharmacy, Fudan University, Shanghai, 201203, China
| | - Yongchao Chu
- Key Laboratory of Smart Drug Delivery, Ministry of Education, State Key Laboratory of Medical Neurobiology and MOE Frontiers Center for Brain Science, Department of Pharmaceutics, School of Pharmacy, Fudan University, Shanghai, 201203, China
| | - Yifan Luo
- Key Laboratory of Smart Drug Delivery, Ministry of Education, State Key Laboratory of Medical Neurobiology and MOE Frontiers Center for Brain Science, Department of Pharmaceutics, School of Pharmacy, Fudan University, Shanghai, 201203, China
| | - Yu Wang
- Key Laboratory of Smart Drug Delivery, Ministry of Education, State Key Laboratory of Medical Neurobiology and MOE Frontiers Center for Brain Science, Department of Pharmaceutics, School of Pharmacy, Fudan University, Shanghai, 201203, China
| | - Zheng Zhou
- Key Laboratory of Smart Drug Delivery, Ministry of Education, State Key Laboratory of Medical Neurobiology and MOE Frontiers Center for Brain Science, Department of Pharmaceutics, School of Pharmacy, Fudan University, Shanghai, 201203, China
| | - Zhenhao Zhao
- Key Laboratory of Smart Drug Delivery, Ministry of Education, State Key Laboratory of Medical Neurobiology and MOE Frontiers Center for Brain Science, Department of Pharmaceutics, School of Pharmacy, Fudan University, Shanghai, 201203, China
| | - Qinjun Chen
- Key Laboratory of Smart Drug Delivery, Ministry of Education, State Key Laboratory of Medical Neurobiology and MOE Frontiers Center for Brain Science, Department of Pharmaceutics, School of Pharmacy, Fudan University, Shanghai, 201203, China
| | - Tao Sun
- Key Laboratory of Smart Drug Delivery, Ministry of Education, State Key Laboratory of Medical Neurobiology and MOE Frontiers Center for Brain Science, Department of Pharmaceutics, School of Pharmacy, Fudan University, Shanghai, 201203, China
| | - Chen Jiang
- Key Laboratory of Smart Drug Delivery, Ministry of Education, State Key Laboratory of Medical Neurobiology and MOE Frontiers Center for Brain Science, Department of Pharmaceutics, School of Pharmacy, Fudan University, Shanghai, 201203, China.
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8
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Man S, Redman JE, Cross DL, Cole DK, Can I, Davies B, Hashimdeen SS, Reid R, Llewellyn-Lacey S, Miners KL, Ladell K, Lissina A, Brown PE, Wooldridge L, Price DA, Rizkallah PJ. Synthetic Peptides with Inadvertent Chemical Modifications Can Activate Potentially Autoreactive T Cells. JOURNAL OF IMMUNOLOGY (BALTIMORE, MD. : 1950) 2021; 207:1009-1017. [PMID: 34321228 PMCID: PMC7615501 DOI: 10.4049/jimmunol.2000756] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/24/2020] [Accepted: 05/24/2021] [Indexed: 11/19/2022]
Abstract
The human CD8+ T cell clone 6C5 has previously been shown to recognize the tert-butyl-modified Bax161-170 peptide LLSY(3-tBu)FGTPT presented by HLA-A*02:01. This nonnatural epitope was likely created as a by-product of fluorenylmethoxycarbonyl protecting group peptide synthesis and bound poorly to HLA-A*02:01. In this study, we used a systematic approach to identify and characterize natural ligands for the 6C5 TCR. Functional analyses revealed that 6C5 T cells only recognized the LLSYFGTPT peptide when tBu was added to the tyrosine residue and did not recognize the LLSYFGTPT peptide modified with larger (di-tBu) or smaller chemical groups (Me). Combinatorial peptide library screening further showed that 6C5 T cells recognized a series of self-derived peptides with dissimilar amino acid sequences to LLSY(3-tBu)FGTPT. Structural studies of LLSY(3-tBu)FGTPT and two other activating nonamers (IIGWMWIPV and LLGWVFAQV) in complex with HLA-A*02:01 demonstrated similar overall peptide conformations and highlighted the importance of the position (P) 4 residue for T cell recognition, particularly the capacity of the bulky amino acid tryptophan to substitute for the tBu-modified tyrosine residue in conjunction with other changes at P5 and P6. Collectively, these results indicated that chemical modifications directly altered the immunogenicity of a synthetic peptide via molecular mimicry, leading to the inadvertent activation of a T cell clone with unexpected and potentially autoreactive specificities.
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Affiliation(s)
- Stephen Man
- Division of Cancer and Genetics, School of Medicine, Cardiff University, Cardiff, United Kingdom;
| | - James E Redman
- School of Chemistry, Cardiff University, Cardiff, United Kingdom
| | - Deborah L Cross
- Division of Cancer and Genetics, School of Medicine, Cardiff University, Cardiff, United Kingdom
| | - David K Cole
- Division of Infection and Immunity, School of Medicine, Cardiff University, Cardiff, United Kingdom
| | - Ilona Can
- Division of Cancer and Genetics, School of Medicine, Cardiff University, Cardiff, United Kingdom
| | - Bethan Davies
- Division of Cancer and Genetics, School of Medicine, Cardiff University, Cardiff, United Kingdom
| | - Shaikh Shimaz Hashimdeen
- Division of Cancer and Genetics, School of Medicine, Cardiff University, Cardiff, United Kingdom
| | - Reiss Reid
- Division of Cancer and Genetics, School of Medicine, Cardiff University, Cardiff, United Kingdom
| | - Sian Llewellyn-Lacey
- Division of Infection and Immunity, School of Medicine, Cardiff University, Cardiff, United Kingdom
| | - Kelly L Miners
- Division of Infection and Immunity, School of Medicine, Cardiff University, Cardiff, United Kingdom
| | - Kristin Ladell
- Division of Infection and Immunity, School of Medicine, Cardiff University, Cardiff, United Kingdom
| | - Anya Lissina
- Faculty of Health Sciences, University of Bristol, Bristol, United Kingdom
| | - Paul E Brown
- The Zeeman Institute, University of Warwick, Coventry, United Kingdom; and
| | - Linda Wooldridge
- Faculty of Health Sciences, University of Bristol, Bristol, United Kingdom
| | - David A Price
- Division of Infection and Immunity, School of Medicine, Cardiff University, Cardiff, United Kingdom
- Systems Immunity Research Institute, School of Medicine, Cardiff University, Cardiff, United Kingdom
| | - Pierre J Rizkallah
- Division of Infection and Immunity, School of Medicine, Cardiff University, Cardiff, United Kingdom
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9
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CD8 coreceptor-mediated focusing can reorder the agonist hierarchy of peptide ligands recognized via the T cell receptor. Proc Natl Acad Sci U S A 2021; 118:2019639118. [PMID: 34272276 PMCID: PMC8307375 DOI: 10.1073/pnas.2019639118] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
CD8+ T cells are inherently cross-reactive and recognize numerous peptide antigens in the context of a given major histocompatibility complex class I (MHCI) molecule via the clonotypically expressed T cell receptor (TCR). The lineally expressed coreceptor CD8 interacts coordinately with MHCI at a distinct and largely invariant site to slow the TCR/peptide-MHCI (pMHCI) dissociation rate and enhance antigen sensitivity. However, this biological effect is not necessarily uniform, and theoretical models suggest that antigen sensitivity can be modulated in a differential manner by CD8. We used two intrinsically controlled systems to determine how the relationship between the TCR/pMHCI interaction and the pMHCI/CD8 interaction affects the functional sensitivity of antigen recognition. Our data show that modulation of the pMHCI/CD8 interaction can reorder the agonist hierarchy of peptide ligands across a spectrum of affinities for the TCR.
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10
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Pettmann J, Huhn A, Abu Shah E, Kutuzov MA, Wilson DB, Dustin ML, Davis SJ, van der Merwe PA, Dushek O. The discriminatory power of the T cell receptor. eLife 2021; 10:67092. [PMID: 34030769 PMCID: PMC8219380 DOI: 10.7554/elife.67092] [Citation(s) in RCA: 40] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2021] [Accepted: 05/15/2021] [Indexed: 12/20/2022] Open
Abstract
T cells use their T cell receptors (TCRs) to discriminate between lower-affinity self and higher-affinity non-self peptides presented on major histocompatibility complex (pMHC) antigens. Although the discriminatory power of the TCR is widely believed to be near-perfect, technical difficulties have hampered efforts to precisely quantify it. Here, we describe a method for measuring very low TCR/pMHC affinities and use it to measure the discriminatory power of the TCR and the factors affecting it. We find that TCR discrimination, although enhanced compared with conventional cell-surface receptors, is imperfect: primary human T cells can respond to pMHC with affinities as low as KD ∼ 1 mM. The kinetic proofreading mechanism fit our data, providing the first estimates of both the time delay (2.8 s) and number of biochemical steps (2.67) that are consistent with the extraordinary sensitivity of antigen recognition. Our findings explain why self pMHC frequently induce autoimmune diseases and anti-tumour responses, and suggest ways to modify TCR discrimination.
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Affiliation(s)
- Johannes Pettmann
- Sir William Dunn School of Pathology, University of Oxford, Oxford, United Kingdom.,Radcliffe Department of Medicine, Medical Research Council Human Immunology Unit, Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, United Kingdom
| | - Anna Huhn
- Sir William Dunn School of Pathology, University of Oxford, Oxford, United Kingdom
| | - Enas Abu Shah
- Sir William Dunn School of Pathology, University of Oxford, Oxford, United Kingdom.,Kennedy Institute of Rheumatology, University of Oxford, Oxford, United Kingdom
| | - Mikhail A Kutuzov
- Sir William Dunn School of Pathology, University of Oxford, Oxford, United Kingdom
| | - Daniel B Wilson
- Sir William Dunn School of Pathology, University of Oxford, Oxford, United Kingdom.,Boston University, Department of Mathematics and Statistics, Boston, United States
| | - Michael L Dustin
- Kennedy Institute of Rheumatology, University of Oxford, Oxford, United Kingdom
| | - Simon J Davis
- Radcliffe Department of Medicine, Medical Research Council Human Immunology Unit, Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, United Kingdom
| | | | - Omer Dushek
- Sir William Dunn School of Pathology, University of Oxford, Oxford, United Kingdom
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11
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Gibadullin R, Randall CJ, Sidney J, Sette A, Gellman SH. Backbone Modifications of HLA-A2-Restricted Antigens Induce Diverse Binding and T Cell Activation Outcomes. J Am Chem Soc 2021; 143:6470-6481. [PMID: 33881854 DOI: 10.1021/jacs.1c00016] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
CD8+ T cells express T cell receptors (TCRs) that recognize short peptide antigens in the context of major histocompatibility class I (MHC I) molecules. This recognition process produces an array of cytokine-mediated signals that help to govern immunological responses. Design of biostable MHC I peptide vaccines containing unnatural subunits is desirable, and synthetic antigens in which a native α-amino acid residue is replaced by a homologous β-amino acid residue (native side chain but extended backbone) might be useful in this regard. We have evaluated the impact of α-to-β backbone modification at a single site on T cell-mediated recognition of six clinically important viral and tumor-associated antigens bound to an MHC I. Effects of this modification on MHC I affinity and T cell activation were measured. Many of these modifications diminish or prevent T cell response. However, a number of α/β-peptide antigens were found to mimic the activity of natural antigens or to enhance maximal T cell response, as measured by interferon-γ release. Results from this broad exploratory study advance our understanding of immunological responses to antigens bearing unnatural modifications and suggest that α/β-peptides could be a source of potent and proteolytically stable variants of native antigens.
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Affiliation(s)
- Ruslan Gibadullin
- Department of Chemistry, University of Wisconsin, 1101 University Avenue, Madison, Wisconsin 53706, United States
| | - Caleb J Randall
- Department of Chemistry, University of Wisconsin, 1101 University Avenue, Madison, Wisconsin 53706, United States
| | - John Sidney
- Division of Vaccine Discovery, La Jolla Institute for Immunology, La Jolla, California 92037, United States
| | - Alessandro Sette
- Division of Vaccine Discovery, La Jolla Institute for Immunology, La Jolla, California 92037, United States.,Department of Medicine, University of California, San Diego, California 92093, United States
| | - Samuel H Gellman
- Department of Chemistry, University of Wisconsin, 1101 University Avenue, Madison, Wisconsin 53706, United States
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12
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Lee CH, Salio M, Napolitani G, Ogg G, Simmons A, Koohy H. Predicting Cross-Reactivity and Antigen Specificity of T Cell Receptors. Front Immunol 2020; 11:565096. [PMID: 33193332 PMCID: PMC7642207 DOI: 10.3389/fimmu.2020.565096] [Citation(s) in RCA: 40] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2020] [Accepted: 09/07/2020] [Indexed: 12/13/2022] Open
Abstract
Adaptive immune recognition is mediated by specific interactions between heterodimeric T cell receptors (TCRs) and their cognate peptide-MHC (pMHC) ligands, and the methods to accurately predict TCR:pMHC interaction would have profound clinical, therapeutic and pharmaceutical applications. Herein, we review recent developments in predicting cross-reactivity and antigen specificity of TCR recognition. We discuss current experimental and computational approaches to investigate cross-reactivity and antigen-specificity of TCRs and highlight how integrating kinetic, biophysical and structural features may offer valuable insights in modeling immunogenicity. We further underscore the close inter-relationship of these two interconnected notions and the need to investigate each in the light of the other for a better understanding of T cell responsiveness for the effective clinical applications.
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Affiliation(s)
- Chloe H. Lee
- MRC Human Immunology Unit, Medical Research Council (MRC) Weatherall Institute of Molecular Medicine (WIMM), John Radcliffe Hospital, University of Oxford, Oxford, United Kingdom
- MRC WIMM Centre for Computational Biology, Medical Research Council (MRC) Weatherall Institute of Molecular Medicine, John Radcliffe Hospital, University of Oxford, Oxford, United Kingdom
| | - Mariolina Salio
- MRC Human Immunology Unit, Medical Research Council (MRC) Weatherall Institute of Molecular Medicine (WIMM), John Radcliffe Hospital, University of Oxford, Oxford, United Kingdom
| | - Giorgio Napolitani
- MRC Human Immunology Unit, Medical Research Council (MRC) Weatherall Institute of Molecular Medicine (WIMM), John Radcliffe Hospital, University of Oxford, Oxford, United Kingdom
| | - Graham Ogg
- MRC Human Immunology Unit, Medical Research Council (MRC) Weatherall Institute of Molecular Medicine (WIMM), John Radcliffe Hospital, University of Oxford, Oxford, United Kingdom
| | - Alison Simmons
- MRC Human Immunology Unit, Medical Research Council (MRC) Weatherall Institute of Molecular Medicine (WIMM), John Radcliffe Hospital, University of Oxford, Oxford, United Kingdom
- Translational Gastroenterology Unit, John Radcliffe Hospital, Oxford, United Kingdom
| | - Hashem Koohy
- MRC Human Immunology Unit, Medical Research Council (MRC) Weatherall Institute of Molecular Medicine (WIMM), John Radcliffe Hospital, University of Oxford, Oxford, United Kingdom
- MRC WIMM Centre for Computational Biology, Medical Research Council (MRC) Weatherall Institute of Molecular Medicine, John Radcliffe Hospital, University of Oxford, Oxford, United Kingdom
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13
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Rapid selection and identification of functional CD8 + T cell epitopes from large peptide-coding libraries. Nat Commun 2019; 10:4553. [PMID: 31591401 PMCID: PMC6779888 DOI: 10.1038/s41467-019-12444-7] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2019] [Accepted: 09/10/2019] [Indexed: 12/18/2022] Open
Abstract
Cytotoxic CD8+ T cells recognize and eliminate infected or malignant cells that present peptide epitopes derived from intracellularly processed antigens on their surface. However, comprehensive profiling of specific major histocompatibility complex (MHC)-bound peptide epitopes that are naturally processed and capable of eliciting a functional T cell response has been challenging. Here, we report a method for deep and unbiased T cell epitope profiling, using in vitro co-culture of CD8+ T cells together with target cells transduced with high-complexity, epitope-encoding minigene libraries. Target cells that are subject to cytotoxic attack from T cells in co-culture are isolated prior to apoptosis by fluorescence-activated cell sorting, and characterized by sequencing the encoded minigenes. We then validate this highly parallelized method using known murine T cell receptor/peptide-MHC pairs and diverse minigene-encoded epitope libraries. Our data thus suggest that this epitope profiling method allows unambiguous and sensitive identification of naturally processed and MHC-presented peptide epitopes.
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14
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Sharma P, Harris DT, Stone JD, Kranz DM. T-cell Receptors Engineered De Novo for Peptide Specificity Can Mediate Optimal T-cell Activity without Self Cross-Reactivity. Cancer Immunol Res 2019; 7:2025-2035. [PMID: 31548259 DOI: 10.1158/2326-6066.cir-19-0035] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2019] [Revised: 06/04/2019] [Accepted: 09/17/2019] [Indexed: 12/17/2022]
Abstract
Despite progress in adoptive T-cell therapies, the identification of targets remains a challenge. Although chimeric antigen receptors recognize cell-surface antigens, T-cell receptors (TCR) have the advantage that they can target the array of intracellular proteins by binding to peptides associated with major histocompatibility complex (MHC) products (pepMHC). Although hundreds of cancer-associated peptides have been reported, it remains difficult to identify effective TCRs against each pepMHC complex. Conventional approaches require isolation of antigen-specific CD8+ T cells, followed by TCRαβ gene isolation and validation. To bypass this process, we used directed evolution to engineer TCRs with desired peptide specificity. Here, we compared the activity and cross-reactivity of two affinity-matured TCRs (T1 and RD1) with distinct origins. T1-TCR was isolated from a melanoma-reactive T-cell line specific for MART-1/HLA-A2, whereas RD1-TCR was derived de novo against MART-1/HLA-A2 by in vitro engineering. Despite their distinct origins, both TCRs exhibited similar peptide fine specificities, focused on the center of the MART-1 peptide. In CD4+ T cells, both TCRs mediated activity against MART-1 presented by HLA-A2. However, in CD8+ T cells, T1, but not RD1, demonstrated cross-reactivity with endogenous peptide/HLA-A2 complexes. Based on the fine specificity of these and other MART-1 binding TCRs, we conducted bioinformatics scans to identify structurally similar self-peptides in the human proteome. We showed that the T1-TCR cross-reacted with many of these self-peptides, whereas the RD1-TCR was rarely cross-reactive. Thus, TCRs such as RD1, generated de novo against cancer antigens, can serve as an alternative to TCRs generated from T-cell clones.
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Affiliation(s)
- Preeti Sharma
- Department of Biochemistry and Cancer Center at Illinois, University of Illinois, Urbana, Illinois.
| | - Daniel T Harris
- Department of Biochemistry and Cancer Center at Illinois, University of Illinois, Urbana, Illinois
| | - Jennifer D Stone
- Department of Biochemistry and Cancer Center at Illinois, University of Illinois, Urbana, Illinois
| | - David M Kranz
- Department of Biochemistry and Cancer Center at Illinois, University of Illinois, Urbana, Illinois.
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15
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Bentzen AK, Hadrup SR. T-cell-receptor cross-recognition and strategies to select safe T-cell receptors for clinical translation. IMMUNO-ONCOLOGY AND TECHNOLOGY 2019; 2:1-10. [PMID: 35036898 PMCID: PMC8741623 DOI: 10.1016/j.iotech.2019.06.003] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Adoptive transfer of T-cell-receptor (TCR)-transduced T cells has shown promising results for cancer treatment, but has also produced severe immunotoxicities caused by on-target as well as off-target TCR recognition. Off-target toxicities are related to the ability of a single T cell to cross-recognize and respond to several different peptide–major histocompatibility complex (pMHC) antigens; a property that is essential for providing broad antigenic coverage despite a confined number of unique TCRs in the human body. However, this degeneracy makes it incredibly difficult to account for the range of targets that any TCR might recognize, which represents a major challenge for the clinical development of therapeutic TCRs. The prospect of using affinity-optimized TCRs has been impeded due to observations that affinity enhancement might alter the specificity of a TCR, thereby increasing the risk that it will cross-recognize endogenous tissue. Strategies for selecting safe TCRs for the clinic have included functional assessment after individual incubations with tissue-derived primary cells or with peptides substituted with single amino acids. However, these strategies have not been able to predict cross-recognition sufficiently, leading to fatal cross-reactivity in clinical trials. Novel technologies have emerged that enable extensive characterization of the exact interaction points of a TCR with pMHC, which provides a foundation from which to make predictions of the cross-recognition potential of individual TCRs. This review describes current advances in strategies for dissecting the molecular interaction points of TCRs, focusing on their potential as tools for predicting cross-recognition of TCRs in clinical development. T-cell-receptor (TCR) degeneracy plays a fundamental role in the capacity of our immune systems to recognize foreign antigens. TCR cross-reactivity provides an inherent risk in TCR–gene transfer cell therapies. Advances in description of TCR cross-recognition can guide the selection process for TCRs into clinical use.
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16
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Madura F, Rizkallah PJ, Legut M, Holland CJ, Fuller A, Bulek A, Schauenburg AJ, Trimby A, Hopkins JR, Wells SA, Godkin A, Miles JJ, Sami M, Li Y, Liddy N, Jakobsen BK, Loveridge EJ, Cole DK, Sewell AK. TCR-induced alteration of primary MHC peptide anchor residue. Eur J Immunol 2019; 49:1052-1066. [PMID: 31091334 PMCID: PMC6618058 DOI: 10.1002/eji.201948085] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2019] [Revised: 03/21/2019] [Accepted: 05/14/2019] [Indexed: 12/12/2022]
Abstract
The HLA-A*02:01-restricted decapeptide EAAGIGILTV, derived from melanoma antigen recognized by T-cells-1 (MART-1) protein, represents one of the best-studied tumor associated T-cell epitopes, but clinical results targeting this peptide have been disappointing. This limitation may reflect the dominance of the nonapeptide, AAGIGILTV, at the melanoma cell surface. The decapeptide and nonapeptide are presented in distinct conformations by HLA-A*02:01 and TCRs from clinically relevant T-cell clones recognize the nonapeptide poorly. Here, we studied the MEL5 TCR that potently recognizes the nonapeptide. The structure of the MEL5-HLA-A*02:01-AAGIGILTV complex revealed an induced fit mechanism of antigen recognition involving altered peptide-MHC anchoring. This "flexing" at the TCR-peptide-MHC interface to accommodate the peptide antigen explains previously observed incongruences in this well-studied system and has important implications for future therapeutic approaches. Finally, this study expands upon the mechanisms by which molecular plasticity can influence antigen recognition by T cells.
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Affiliation(s)
| | | | | | | | - Anna Fuller
- School of MedicineCardiff UniversityCardiffUK
| | - Anna Bulek
- School of MedicineCardiff UniversityCardiffUK
| | | | | | | | | | | | - John J. Miles
- School of MedicineCardiff UniversityCardiffUK
- Centre for Biodiscovery and Molecular Development of TherapeuticsAustralian Institute of Tropical Health and MedicineJames Cook UniversityCairnsQueenslandAustralia
| | | | - Yi Li
- Immunocore Ltd.AbingdonUK
| | | | | | - E. Joel Loveridge
- School of ChemistryCardiff UniversityCardiffUK
- Department of ChemistrySwansea UniversitySwanseaUK
| | - David K. Cole
- School of MedicineCardiff UniversityCardiffUK
- Immunocore Ltd.AbingdonUK
| | - Andrew K. Sewell
- School of MedicineCardiff UniversityCardiffUK
- Systems Immunity Research InstituteCardiff UniversityCardiffUK
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17
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Galloway SAE, Dolton G, Attaf M, Wall A, Fuller A, Rius C, Bianchi V, Theaker S, Lloyd A, Caillaud ME, Svane IM, Donia M, Cole DK, Szomolay B, Rizkallah P, Sewell AK. Peptide Super-Agonist Enhances T-Cell Responses to Melanoma. Front Immunol 2019; 10:319. [PMID: 30930889 PMCID: PMC6425991 DOI: 10.3389/fimmu.2019.00319] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2018] [Accepted: 02/06/2019] [Indexed: 12/30/2022] Open
Abstract
Recent immunotherapeutic approaches using adoptive cell therapy, or checkpoint blockade, have demonstrated the powerful anti-cancer potential of CD8 cytotoxic T-lymphocytes (CTL). While these approaches have shown great promise, they are only effective in some patients with some cancers. The potential power, and relative ease, of therapeutic vaccination against tumour associated antigens (TAA) present in different cancers has been a long sought-after approach for harnessing the discriminating sensitivity of CTL to treat cancer and has seen recent renewed interest following cancer vaccination successes using unique tumour neoantigens. Unfortunately, results with TAA-targeted “universal” cancer vaccines (UCV) have been largely disappointing. Infectious disease models have demonstrated that T-cell clonotypes that recognise the same antigen should not be viewed as being equally effective. Extrapolation of this notion to UCV would suggest that the quality of response in terms of the T-cell receptor (TCR) clonotypes induced might be more important than the quantity of the response. Unfortunately, there is little opportunity to assess the effectiveness of individual T-cell clonotypes in vivo. Here, we identified effective, persistent T-cell clonotypes in an HLA A2+ patient following successful tumour infiltrating lymphocyte (TIL) therapy. One such T-cell clone was used to generate super-agonist altered peptide ligands (APLs). Further refinement produced an APL that was capable of inducing T-cells in greater magnitude, and with improved effectiveness, from the blood of all 14 healthy donors tested. Importantly, this APL also induced T-cells from melanoma patient blood that exhibited superior recognition of the patient's own tumour compared to those induced by the natural antigen sequence. These results suggest that use of APL to skew the clonotypic quality of T-cells induced by cancer vaccination could provide a promising avenue in the hunt for the UCV “magic bullet.”
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Affiliation(s)
- Sarah A E Galloway
- T-Cell Modulation Group, Division of Infection and Immunity, Cardiff University School of Medicine, Cardiff, United Kingdom
| | - Garry Dolton
- T-Cell Modulation Group, Division of Infection and Immunity, Cardiff University School of Medicine, Cardiff, United Kingdom
| | - Meriem Attaf
- T-Cell Modulation Group, Division of Infection and Immunity, Cardiff University School of Medicine, Cardiff, United Kingdom
| | - Aaron Wall
- T-Cell Modulation Group, Division of Infection and Immunity, Cardiff University School of Medicine, Cardiff, United Kingdom
| | - Anna Fuller
- T-Cell Modulation Group, Division of Infection and Immunity, Cardiff University School of Medicine, Cardiff, United Kingdom
| | - Cristina Rius
- T-Cell Modulation Group, Division of Infection and Immunity, Cardiff University School of Medicine, Cardiff, United Kingdom
| | - Valentina Bianchi
- T-Cell Modulation Group, Division of Infection and Immunity, Cardiff University School of Medicine, Cardiff, United Kingdom
| | - Sarah Theaker
- T-Cell Modulation Group, Division of Infection and Immunity, Cardiff University School of Medicine, Cardiff, United Kingdom
| | - Angharad Lloyd
- T-Cell Modulation Group, Division of Infection and Immunity, Cardiff University School of Medicine, Cardiff, United Kingdom.,Immunocore LTD, Oxford, United Kingdom
| | - Marine E Caillaud
- T-Cell Modulation Group, Division of Infection and Immunity, Cardiff University School of Medicine, Cardiff, United Kingdom
| | - Inge Marie Svane
- Department of Hematology and Oncology, Center for Cancer Immune Therapy, Herlev Hospital, University of Copenhagen, Herlev, Denmark
| | - Marco Donia
- Department of Hematology and Oncology, Center for Cancer Immune Therapy, Herlev Hospital, University of Copenhagen, Herlev, Denmark
| | - David K Cole
- T-Cell Modulation Group, Division of Infection and Immunity, Cardiff University School of Medicine, Cardiff, United Kingdom.,Immunocore LTD, Oxford, United Kingdom
| | - Barbara Szomolay
- Systems Immunity Research Institute, Cardiff University School of Medicine, Cardiff, United Kingdom
| | - Pierre Rizkallah
- T-Cell Modulation Group, Division of Infection and Immunity, Cardiff University School of Medicine, Cardiff, United Kingdom
| | - Andrew K Sewell
- T-Cell Modulation Group, Division of Infection and Immunity, Cardiff University School of Medicine, Cardiff, United Kingdom.,Systems Immunity Research Institute, Cardiff University School of Medicine, Cardiff, United Kingdom
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18
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Hellman LM, Foley KC, Singh NK, Alonso JA, Riley TP, Devlin JR, Ayres CM, Keller GLJ, Zhang Y, Vander Kooi CW, Nishimura MI, Baker BM. Improving T Cell Receptor On-Target Specificity via Structure-Guided Design. Mol Ther 2018; 27:300-313. [PMID: 30617019 DOI: 10.1016/j.ymthe.2018.12.010] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2018] [Revised: 12/05/2018] [Accepted: 12/08/2018] [Indexed: 12/30/2022] Open
Abstract
T cell receptors (TCRs) have emerged as a new class of immunological therapeutics. However, though antigen specificity is a hallmark of adaptive immunity, TCRs themselves do not possess the high specificity of monoclonal antibodies. Although a necessary function of T cell biology, the resulting cross-reactivity presents a significant challenge for TCR-based therapeutic development, as it creates the potential for off-target recognition and immune toxicity. Efforts to enhance TCR specificity by mimicking the antibody maturation process and enhancing affinity can inadvertently exacerbate TCR cross-reactivity. Here we demonstrate this concern by showing that even peptide-targeted mutations in the TCR can introduce new reactivities against peptides that bear similarity to the original target. To counteract this, we explored a novel structure-guided approach for enhancing TCR specificity independent of affinity. Tested with the MART-1-specific TCR DMF5, our approach had a small but discernible impact on cross-reactivity toward MART-1 homologs yet was able to eliminate DMF5 cross-recognition of more divergent, unrelated epitopes. Our study provides a proof of principle for the use of advanced structure-guided design techniques for improving TCR specificity, and it suggests new ways forward for enhancing TCRs for therapeutic use.
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Affiliation(s)
- Lance M Hellman
- Department of Chemistry and Biochemistry and the Harper Cancer Research Institute, University of Notre Dame, Notre Dame, IN, USA
| | - Kendra C Foley
- Department of Surgery and the Cardinal Bernardin Cancer Center, Loyola University of Chicago, Maywood, IL, USA
| | - Nishant K Singh
- Department of Chemistry and Biochemistry and the Harper Cancer Research Institute, University of Notre Dame, Notre Dame, IN, USA
| | - Jesus A Alonso
- Department of Chemistry and Biochemistry and the Harper Cancer Research Institute, University of Notre Dame, Notre Dame, IN, USA
| | - Timothy P Riley
- Department of Chemistry and Biochemistry and the Harper Cancer Research Institute, University of Notre Dame, Notre Dame, IN, USA
| | - Jason R Devlin
- Department of Chemistry and Biochemistry and the Harper Cancer Research Institute, University of Notre Dame, Notre Dame, IN, USA
| | - Cory M Ayres
- Department of Chemistry and Biochemistry and the Harper Cancer Research Institute, University of Notre Dame, Notre Dame, IN, USA
| | - Grant L J Keller
- Department of Chemistry and Biochemistry and the Harper Cancer Research Institute, University of Notre Dame, Notre Dame, IN, USA
| | - Yuting Zhang
- Department of Chemistry and Biochemistry and the Harper Cancer Research Institute, University of Notre Dame, Notre Dame, IN, USA
| | - Craig W Vander Kooi
- Department of Molecular and Cellular Biochemistry, University of Kentucky, Lexington, KY, USA
| | - Michael I Nishimura
- Department of Surgery and the Cardinal Bernardin Cancer Center, Loyola University of Chicago, Maywood, IL, USA
| | - Brian M Baker
- Department of Chemistry and Biochemistry and the Harper Cancer Research Institute, University of Notre Dame, Notre Dame, IN, USA.
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19
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Venturi V, Thomas PG. The expanding role of systems immunology in decoding the T cell receptor repertoire. ACTA ACUST UNITED AC 2018; 12:37-45. [PMID: 31106281 DOI: 10.1016/j.coisb.2018.09.005] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
T cells play a crucial role in the immune system's defense against many infectious diseases, including persistent infections for which no effective vaccines currently exist. The T cell component of the adaptive immune system is highly complex involving a constantly evolving landscape of various inter-related T cell populations. These T cell populations are characterized by their phenotypic and functional properties as well as the collection, or repertoire, of T cell receptors (TCR) that mediate T cell recognition of antigenic peptides derived from pathogens. Understanding the various processes and factors that impact the development and evolution of the broader T cell repertoire available to recognize and respond to pathogens and the characteristics of antigen-experienced T cell repertoires associated with effective immune control of pathogens is critical to the rational design of T cell-based vaccines and therapies. In this article we discuss, using examples of recent research, the promise that systems immunology approaches, involving quantitative analysis and mathematical and computational modeling of immunological data, hold for decoding the complex TCR repertoire system in the current era of advancing technologies.
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Affiliation(s)
- Vanessa Venturi
- Infection Analytics Program, Kirby Institute for Infection and Immunity, UNSW Australia, Sydney, NSW, Australia
| | - Paul G Thomas
- Department of Immunology, St. Jude Children's Research Hospital, Memphis, TN, USA
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20
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Miles JJ, Tan MP, Dolton G, Edwards ES, Galloway SA, Laugel B, Clement M, Makinde J, Ladell K, Matthews KK, Watkins TS, Tungatt K, Wong Y, Lee HS, Clark RJ, Pentier JM, Attaf M, Lissina A, Ager A, Gallimore A, Rizkallah PJ, Gras S, Rossjohn J, Burrows SR, Cole DK, Price DA, Sewell AK. Peptide mimic for influenza vaccination using nonnatural combinatorial chemistry. J Clin Invest 2018; 128:1569-1580. [PMID: 29528337 PMCID: PMC5873848 DOI: 10.1172/jci91512] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2016] [Accepted: 01/18/2018] [Indexed: 01/11/2023] Open
Abstract
Polypeptide vaccines effectively activate human T cells but suffer from poor biological stability, which confines both transport logistics and in vivo therapeutic activity. Synthetic biology has the potential to address these limitations through the generation of highly stable antigenic "mimics" using subunits that do not exist in the natural world. We developed a platform based on D-amino acid combinatorial chemistry and used this platform to reverse engineer a fully artificial CD8+ T cell agonist that mirrored the immunogenicity profile of a native epitope blueprint from influenza virus. This nonnatural peptide was highly stable in human serum and gastric acid, reflecting an intrinsic resistance to physical and enzymatic degradation. In vitro, the synthetic agonist stimulated and expanded an archetypal repertoire of polyfunctional human influenza virus-specific CD8+ T cells. In vivo, specific responses were elicited in naive humanized mice by subcutaneous vaccination, conferring protection from subsequent lethal influenza challenge. Moreover, the synthetic agonist was immunogenic after oral administration. This proof-of-concept study highlights the power of synthetic biology to expand the horizons of vaccine design and therapeutic delivery.
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Affiliation(s)
- John J. Miles
- Centre for Biodiscovery and Molecular Development of Therapeutics, Australian Institute of Tropical Health and Medicine, James Cook University, Cairns, Queensland, Australia
- QIMR Berghofer Medical Research Institute, Brisbane, Queensland, Australia
- Division of Infection and Immunity, Cardiff University School of Medicine, Cardiff, United Kingdom
- School of Medicine, The University of Queensland, Brisbane, Queensland, Australia
- Griffith University, Brisbane, Queensland, Australia
| | - Mai Ping Tan
- Division of Infection and Immunity, Cardiff University School of Medicine, Cardiff, United Kingdom
| | - Garry Dolton
- Division of Infection and Immunity, Cardiff University School of Medicine, Cardiff, United Kingdom
- Systems Immunity Research Institute, Cardiff University, Cardiff, United Kingdom
| | - Emily S.J. Edwards
- Division of Infection and Immunity, Cardiff University School of Medicine, Cardiff, United Kingdom
| | - Sarah A.E. Galloway
- Division of Infection and Immunity, Cardiff University School of Medicine, Cardiff, United Kingdom
| | - Bruno Laugel
- Division of Infection and Immunity, Cardiff University School of Medicine, Cardiff, United Kingdom
| | - Mathew Clement
- Division of Infection and Immunity, Cardiff University School of Medicine, Cardiff, United Kingdom
| | - Julia Makinde
- Division of Infection and Immunity, Cardiff University School of Medicine, Cardiff, United Kingdom
| | - Kristin Ladell
- Division of Infection and Immunity, Cardiff University School of Medicine, Cardiff, United Kingdom
- Systems Immunity Research Institute, Cardiff University, Cardiff, United Kingdom
| | | | - Thomas S. Watkins
- QIMR Berghofer Medical Research Institute, Brisbane, Queensland, Australia
| | - Katie Tungatt
- Division of Infection and Immunity, Cardiff University School of Medicine, Cardiff, United Kingdom
| | - Yide Wong
- QIMR Berghofer Medical Research Institute, Brisbane, Queensland, Australia
| | - Han Siean Lee
- School of Biomedical Sciences, The University of Queensland, Brisbane, Queensland, Australia
| | - Richard J. Clark
- School of Biomedical Sciences, The University of Queensland, Brisbane, Queensland, Australia
| | - Johanne M. Pentier
- Division of Infection and Immunity, Cardiff University School of Medicine, Cardiff, United Kingdom
| | - Meriem Attaf
- Division of Infection and Immunity, Cardiff University School of Medicine, Cardiff, United Kingdom
| | - Anya Lissina
- Division of Infection and Immunity, Cardiff University School of Medicine, Cardiff, United Kingdom
| | - Ann Ager
- Division of Infection and Immunity, Cardiff University School of Medicine, Cardiff, United Kingdom
| | - Awen Gallimore
- Division of Infection and Immunity, Cardiff University School of Medicine, Cardiff, United Kingdom
| | - Pierre J. Rizkallah
- Division of Infection and Immunity, Cardiff University School of Medicine, Cardiff, United Kingdom
| | - Stephanie Gras
- Infection and Immunity Program and Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, and
- Australian Research Council Centre of Excellence in Advanced Molecular Imaging, Monash University, Clayton, Victoria, Australia
| | - Jamie Rossjohn
- Division of Infection and Immunity, Cardiff University School of Medicine, Cardiff, United Kingdom
- Infection and Immunity Program and Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, and
- Australian Research Council Centre of Excellence in Advanced Molecular Imaging, Monash University, Clayton, Victoria, Australia
| | - Scott R. Burrows
- QIMR Berghofer Medical Research Institute, Brisbane, Queensland, Australia
| | - David K. Cole
- Division of Infection and Immunity, Cardiff University School of Medicine, Cardiff, United Kingdom
| | - David A. Price
- Division of Infection and Immunity, Cardiff University School of Medicine, Cardiff, United Kingdom
- Systems Immunity Research Institute, Cardiff University, Cardiff, United Kingdom
- Human Immunology Section, Vaccine Research Center, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, Maryland, USA
| | - Andrew K. Sewell
- Division of Infection and Immunity, Cardiff University School of Medicine, Cardiff, United Kingdom
- Systems Immunity Research Institute, Cardiff University, Cardiff, United Kingdom
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21
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MacLachlan BJ, Greenshields-Watson A, Mason GH, Schauenburg AJ, Bianchi V, Rizkallah PJ, Sewell AK, Fuller A, Cole DK. Using X-ray Crystallography, Biophysics, and Functional Assays to Determine the Mechanisms Governing T-cell Receptor Recognition of Cancer Antigens. J Vis Exp 2017:54991. [PMID: 28287509 PMCID: PMC5408581 DOI: 10.3791/54991] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023] Open
Abstract
Human CD8+ cytotoxic T lymphocytes (CTLs) are known to play an important role in tumor control. In order to carry out this function, the cell surface-expressed T-cell receptor (TCR) must functionally recognize human leukocyte antigen (HLA)-restricted tumor-derived peptides (pHLA). However, we and others have shown that most TCRs bind sub-optimally to tumor antigens. Uncovering the molecular mechanisms that define this poor recognition could aid in the development of new targeted therapies that circumnavigate these shortcomings. Indeed, present therapies that lack this molecular understanding have not been universally effective. Here, we describe methods that we commonly employ in the laboratory to determine how the nature of the interaction between TCRs and pHLA governs T-cell functionality. These methods include the generation of soluble TCRs and pHLA and the use of these reagents for X-ray crystallography, biophysical analysis, and antigen-specific T-cell staining with pHLA multimers. Using these approaches and guided by structural analysis, it is possible to modify the interaction between TCRs and pHLA and to then test how these modifications impact T-cell antigen recognition. These findings have already helped to clarify the mechanism of T-cell recognition of a number of cancer antigens and could direct the development of altered peptides and modified TCRs for new cancer therapies.
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Affiliation(s)
- Bruce J MacLachlan
- Division of Infection and Immunity and Systems Immunity Research Institute, Cardiff University
| | | | - Georgina H Mason
- Division of Infection and Immunity and Systems Immunity Research Institute, Cardiff University
| | - Andrea J Schauenburg
- Division of Infection and Immunity and Systems Immunity Research Institute, Cardiff University
| | - Valentina Bianchi
- Division of Infection and Immunity and Systems Immunity Research Institute, Cardiff University; Department of Oncology, University Hospital of Lausanne (CHUV); Ludwig Insitutue for Cancer Research, Lausanne Branch, University of Lausanne
| | - Pierre J Rizkallah
- Division of Infection and Immunity and Systems Immunity Research Institute, Cardiff University
| | - Andrew K Sewell
- Division of Infection and Immunity and Systems Immunity Research Institute, Cardiff University
| | - Anna Fuller
- Division of Infection and Immunity and Systems Immunity Research Institute, Cardiff University
| | - David K Cole
- Division of Infection and Immunity and Systems Immunity Research Institute, Cardiff University;
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22
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Blevins SJ, Baker BM. Using Global Analysis to Extend the Accuracy and Precision of Binding Measurements with T cell Receptors and Their Peptide/MHC Ligands. Front Mol Biosci 2017; 4:2. [PMID: 28197404 PMCID: PMC5281623 DOI: 10.3389/fmolb.2017.00002] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2016] [Accepted: 01/11/2017] [Indexed: 11/13/2022] Open
Abstract
In cellular immunity, clonally distributed T cell receptors (TCRs) engage complexes of peptides bound to major histocompatibility complex proteins (pMHCs). In the interactions of TCRs with pMHCs, regions of restricted and variable diversity align in a structurally complex fashion. Many studies have used mutagenesis to attempt to understand the "roles" played by various interface components in determining TCR recognition properties such as specificity and cross-reactivity. However, these measurements are often complicated or even compromised by the weak affinities TCRs maintain toward pMHC. Here, we demonstrate how global analysis of multiple datasets can be used to significantly extend the accuracy and precision of such TCR binding experiments. Application of this approach should positively impact efforts to understand TCR recognition and facilitate the creation of mutational databases to help engineer TCRs with tuned molecular recognition properties. We also show how global analysis can be used to analyze double mutant cycles in TCR-pMHC interfaces, which can lead to new insights into immune recognition.
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Affiliation(s)
- Sydney J Blevins
- Department of Chemistry and Biochemistry and the Harper Cancer Research Institute, University of Notre Dame Notre Dame, IN, USA
| | - Brian M Baker
- Department of Chemistry and Biochemistry and the Harper Cancer Research Institute, University of Notre Dame Notre Dame, IN, USA
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23
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Servín-Blanco R, Zamora-Alvarado R, Gevorkian G, Manoutcharian K. Antigenic variability: Obstacles on the road to vaccines against traditionally difficult targets. Hum Vaccin Immunother 2016; 12:2640-2648. [PMID: 27295540 DOI: 10.1080/21645515.2016.1191718] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
Abstract
Despite the impressive impact of vaccines on public health, the success of vaccines targeting many important pathogens and cancers has to date been limited. The burden of infectious diseases today is mainly caused by antigenically variable pathogens (AVPs), which escape immune responses induced by prior infection or vaccination through changes in molecular structures recognized by antibodies or T cells. Extensive genetic and antigenic variability is the major obstacle for the development of new or improved vaccines against "difficult" targets. Alternative, qualitatively new approaches leading to the generation of disease- and patient-specific vaccine immunogens that incorporate complex permanently changing epitope landscapes of intended targets accompanied by appropriate immunomodulators are urgently needed. In this review, we highlight some of the most critical common issues related to the development of vaccines against many pathogens and cancers that escape protective immune responses owing to antigenic variation, and discuss recent efforts to overcome the obstacles by applying alternative approaches for the rational design of new types of immunogens.
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Affiliation(s)
- R Servín-Blanco
- a Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México (UNAM), AP 70228, Cuidad Universitaria , México DF , México
| | - R Zamora-Alvarado
- a Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México (UNAM), AP 70228, Cuidad Universitaria , México DF , México
| | - G Gevorkian
- a Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México (UNAM), AP 70228, Cuidad Universitaria , México DF , México
| | - K Manoutcharian
- a Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México (UNAM), AP 70228, Cuidad Universitaria , México DF , México
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24
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Cole DK, Bulek AM, Dolton G, Schauenberg AJ, Szomolay B, Rittase W, Trimby A, Jothikumar P, Fuller A, Skowera A, Rossjohn J, Zhu C, Miles JJ, Peakman M, Wooldridge L, Rizkallah PJ, Sewell AK. Hotspot autoimmune T cell receptor binding underlies pathogen and insulin peptide cross-reactivity. J Clin Invest 2016; 126:2191-204. [PMID: 27183389 PMCID: PMC4887163 DOI: 10.1172/jci85679] [Citation(s) in RCA: 83] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2015] [Accepted: 03/10/2016] [Indexed: 12/11/2022] Open
Abstract
The cross-reactivity of T cells with pathogen- and self-derived peptides has been implicated as a pathway involved in the development of autoimmunity. However, the mechanisms that allow the clonal T cell antigen receptor (TCR) to functionally engage multiple peptide–major histocompatibility complexes (pMHC) are unclear. Here, we studied multiligand discrimination by a human, preproinsulin reactive, MHC class-I–restricted CD8+ T cell clone (1E6) that can recognize over 1 million different peptides. We generated high-resolution structures of the 1E6 TCR bound to 7 altered peptide ligands, including a pathogen-derived peptide that was an order of magnitude more potent than the natural self-peptide. Evaluation of these structures demonstrated that binding was stabilized through a conserved lock-and-key–like minimal binding footprint that enables 1E6 TCR to tolerate vast numbers of substitutions outside of this so-called hotspot. Highly potent antigens of the 1E6 TCR engaged with a strong antipathogen-like binding affinity; this engagement was governed though an energetic switch from an enthalpically to entropically driven interaction compared with the natural autoimmune ligand. Together, these data highlight how T cell cross-reactivity with pathogen-derived antigens might break self-tolerance to induce autoimmune disease.
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Affiliation(s)
- David K. Cole
- Division of Infection and Immunity and Systems Immunity Research Institute, Cardiff University School of Medicine, Heath Park, Cardiff, United Kingdom
| | - Anna M. Bulek
- Division of Infection and Immunity and Systems Immunity Research Institute, Cardiff University School of Medicine, Heath Park, Cardiff, United Kingdom
| | - Garry Dolton
- Division of Infection and Immunity and Systems Immunity Research Institute, Cardiff University School of Medicine, Heath Park, Cardiff, United Kingdom
| | - Andrea J. Schauenberg
- Division of Infection and Immunity and Systems Immunity Research Institute, Cardiff University School of Medicine, Heath Park, Cardiff, United Kingdom
| | - Barbara Szomolay
- Division of Infection and Immunity and Systems Immunity Research Institute, Cardiff University School of Medicine, Heath Park, Cardiff, United Kingdom
- Mathematics Institute, University of Warwick, Coventry, United Kingdom
| | - William Rittase
- Woodruff School of Mechanical Engineering and Coulter Department of Biomedical Engineering, Georgia Institute of Technology, Atlanta, Georgia, USA
| | - Andrew Trimby
- Division of Infection and Immunity and Systems Immunity Research Institute, Cardiff University School of Medicine, Heath Park, Cardiff, United Kingdom
| | - Prithiviraj Jothikumar
- Woodruff School of Mechanical Engineering and Coulter Department of Biomedical Engineering, Georgia Institute of Technology, Atlanta, Georgia, USA
| | - Anna Fuller
- Division of Infection and Immunity and Systems Immunity Research Institute, Cardiff University School of Medicine, Heath Park, Cardiff, United Kingdom
| | - Ania Skowera
- Department of Immunobiology, King’s College London, London, United Kingdom
- NIHR Biomedical Research Centre at Guy’s and St Thomas’ NHS Foundation Trust and King’s College London, London, United Kingdom
| | - Jamie Rossjohn
- Division of Infection and Immunity and Systems Immunity Research Institute, Cardiff University School of Medicine, Heath Park, Cardiff, United Kingdom
- Department of Biochemistry and Molecular Biology, School of Biomedical Sciences, and
- ARC Centre of Excellence in Advanced Molecular Imaging, Monash University, Clayton, Victoria, Australia
| | - Cheng Zhu
- Woodruff School of Mechanical Engineering and Coulter Department of Biomedical Engineering, Georgia Institute of Technology, Atlanta, Georgia, USA
- Coulter Department of Biomedical Engineering, Georgia Institute of Technology, Atlanta, Georgia, USA
| | - John J. Miles
- Division of Infection and Immunity and Systems Immunity Research Institute, Cardiff University School of Medicine, Heath Park, Cardiff, United Kingdom
- QIMR Berghofer Medical Research Institute, Brisbane, Queensland, Australia
| | - Mark Peakman
- Department of Immunobiology, King’s College London, London, United Kingdom
- NIHR Biomedical Research Centre at Guy’s and St Thomas’ NHS Foundation Trust and King’s College London, London, United Kingdom
| | - Linda Wooldridge
- Faculty of Health Sciences, University of Bristol, Bristol, United Kingdom
| | - Pierre J. Rizkallah
- Division of Infection and Immunity and Systems Immunity Research Institute, Cardiff University School of Medicine, Heath Park, Cardiff, United Kingdom
| | - Andrew K. Sewell
- Division of Infection and Immunity and Systems Immunity Research Institute, Cardiff University School of Medicine, Heath Park, Cardiff, United Kingdom
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25
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Differential scanning fluorimetry based assessments of the thermal and kinetic stability of peptide-MHC complexes. J Immunol Methods 2016; 432:95-101. [PMID: 26906089 DOI: 10.1016/j.jim.2016.02.016] [Citation(s) in RCA: 49] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2015] [Revised: 02/17/2016] [Accepted: 02/17/2016] [Indexed: 11/20/2022]
Abstract
Measurements of thermal stability by circular dichroism (CD) spectroscopy have been widely used to assess the binding of peptides to MHC proteins, particularly within the structural immunology community. Although thermal stability assays offer advantages over other approaches such as IC50 measurements, CD-based stability measurements are hindered by large sample requirements and low throughput. Here we demonstrate that an alternative approach based on differential scanning fluorimetry (DSF) yields results comparable to those based on CD for both class I and class II complexes. As they require much less sample, DSF-based measurements reduce demands on protein production strategies and are amenable for high throughput studies. DSF can thus not only replace CD as a means to assess peptide/MHC thermal stability, but can complement other peptide-MHC binding assays used in screening, epitope discovery, and vaccine design. Due to the physical process probed, DSF can also uncover complexities not observed with other techniques. Lastly, we show that DSF can also be used to assess peptide/MHC kinetic stability, allowing for a single experimental setup to probe both binding equilibria and kinetics.
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26
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Identification of human viral protein-derived ligands recognized by individual MHCI-restricted T-cell receptors. Immunol Cell Biol 2016; 94:573-82. [PMID: 26846725 PMCID: PMC4943067 DOI: 10.1038/icb.2016.12] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2015] [Revised: 12/23/2015] [Accepted: 01/18/2016] [Indexed: 12/12/2022]
Abstract
Evidence indicates that autoimmunity can be triggered by virus-specific CD8+ T cells that crossreact with self-derived peptide epitopes presented on the cell surface by major histocompatibility complex class I (MHCI) molecules. Identification of the associated viral pathogens is challenging because individual T-cell receptors can potentially recognize up to a million different peptides. Here, we generate peptide length-matched combinatorial peptide library (CPL) scan data for a panel of virus-specific CD8+ T-cell clones spanning different restriction elements and a range of epitope lengths. CPL scan data drove a protein database search limited to viruses that infect humans. Peptide sequences were ranked in order of likelihood of recognition. For all anti-viral CD8+ T-cell clones examined in this study, the index peptide was either the top-ranked sequence or ranked as one of the most likely sequences to be recognized. Thus, we demonstrate that anti-viral CD8+ T-cell clones are highly focused on their index peptide sequence and that ‘CPL-driven database searching' can be used to identify the inciting virus-derived epitope for a given CD8+ T-cell clone. Moreover, to augment access to CPL-driven database searching, we have created a publicly accessible webtool. Application of these methodologies in the clinical setting may clarify the role of viral pathogens in the etiology of autoimmune diseases.
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27
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T-cell libraries allow simple parallel generation of multiple peptide-specific human T-cell clones. J Immunol Methods 2016; 430:43-50. [PMID: 26826277 PMCID: PMC4783706 DOI: 10.1016/j.jim.2016.01.014] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2015] [Revised: 01/26/2016] [Accepted: 01/26/2016] [Indexed: 12/29/2022]
Abstract
Isolation of peptide-specific T-cell clones is highly desirable for determining the role of T-cells in human disease, as well as for the development of therapies and diagnostics. However, generation of monoclonal T-cells with the required specificity is challenging and time-consuming. Here we describe a library-based strategy for the simple parallel detection and isolation of multiple peptide-specific human T-cell clones from CD8(+) or CD4(+) polyclonal T-cell populations. T-cells were first amplified by CD3/CD28 microbeads in a 96U-well library format, prior to screening for desired peptide recognition. T-cells from peptide-reactive wells were then subjected to cytokine-mediated enrichment followed by single-cell cloning, with the entire process from sample to validated clone taking as little as 6 weeks. Overall, T-cell libraries represent an efficient and relatively rapid tool for the generation of peptide-specific T-cell clones, with applications shown here in infectious disease (Epstein-Barr virus, influenza A, and Ebola virus), autoimmunity (type 1 diabetes) and cancer.
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28
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Motozono C, Pearson JA, De Leenheer E, Rizkallah PJ, Beck K, Trimby A, Sewell AK, Wong FS, Cole DK. Distortion of the Major Histocompatibility Complex Class I Binding Groove to Accommodate an Insulin-derived 10-Mer Peptide. J Biol Chem 2015; 290:18924-33. [PMID: 26085090 PMCID: PMC4521012 DOI: 10.1074/jbc.m114.622522] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2014] [Revised: 06/12/2015] [Indexed: 01/23/2023] Open
Abstract
The non-obese diabetic mouse model of type 1 diabetes continues to be an important tool for delineating the role of T-cell-mediated destruction of pancreatic β-cells. However, little is known about the molecular mechanisms that enable this disease pathway. We show that insulin reactivity by a CD8(+) T-cell clone, known to induce type 1 diabetes, is characterized by weak T-cell antigen receptor binding to a relatively unstable peptide-MHC. The structure of the native 9- and 10-mer insulin epitopes demonstrated that peptide residues 7 and 8 form a prominent solvent-exposed bulge that could potentially be the main focus of T-cell receptor binding. The C terminus of the peptide governed peptide-MHC stability. Unexpectedly, we further demonstrate a novel mode of flexible peptide presentation in which the MHC peptide-binding groove is able to "open the back door" to accommodate extra C-terminal peptide residues.
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Affiliation(s)
- Chihiro Motozono
- From the Division of Infection and Immunity and the Department of Immunology, Kinki University School of Medicine, Osaka 589-8511, Japan, and
| | - James A Pearson
- the Institute of Molecular and Experimental Medicine, Cardiff University School of Medicine, Heath Park, Cardiff CF14 4XN, United Kingdom
| | - Evy De Leenheer
- the Institute of Molecular and Experimental Medicine, Cardiff University School of Medicine, Heath Park, Cardiff CF14 4XN, United Kingdom
| | | | - Konrad Beck
- the Cardiff University School of Dentistry, Heath Park, Cardiff CF14 4XY, United Kingdom
| | | | | | - F Susan Wong
- the Institute of Molecular and Experimental Medicine, Cardiff University School of Medicine, Heath Park, Cardiff CF14 4XN, United Kingdom,
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29
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He Y, Hong Y, Mizejewski GJ. Engineering α-fetoprotein-based gene vaccines to prevent and treat hepatocellular carcinoma: review and future prospects. Immunotherapy 2015; 6:725-36. [PMID: 25041030 DOI: 10.2217/imt.14.46] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023] Open
Abstract
Activation of a patient's immune system offers an attractive approach to prevent and treat hepatocellular carcinoma (HCC). However, the antitumor efficacy of current HCC vaccines was weak owing to insufficient immune activation of targeting self/tumor antigens. We recently found that epitope-optimized α-fetoprotein effectively activated CD8 T cells and generated potent antitumor effects in the carcinogen-induced autochthonous HCC mouse model. We predict that the same antigen engineering approach of epitope-optimization will enable us to develop effective human vaccines to prevent HCC recurrence after liver resection. The engineered human HCC vaccines may also allow us to identify high-affinity T-cell receptors and antibodies that can be used to reprogram T cells to treat HCC tumors via adoptive transfer.
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Affiliation(s)
- Yukai He
- Georgia Regents University Cancer Center, Cancer Immunology, Inflammation & Tolerance Program, Augusta, GA 30907, USA
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30
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Dyson J. T-cell receptors: tugging on the anchor for a tighter hold on the tumor-associated peptide. Eur J Immunol 2015; 45:380-2. [PMID: 25581444 DOI: 10.1002/eji.201445385] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2015] [Revised: 01/01/2015] [Accepted: 01/07/2015] [Indexed: 11/08/2022]
Abstract
Although it has been shown that human tumor-associated, HLA anchor residue modified "heteroclitic" peptides may induce stronger immune responses than wild-type peptides in cancer vaccine trials, it has also been shown that some T cells primed with these heteroclitic peptides subsequently fail to recognize the natural, tumor-expressed peptide efficiently. This may provide a molecular reason for why clinical trials of these peptides have been thus far unsuccessful. In this issue of the European Journal of Immunology, Madura et al. [Eur. J. Immunol. 2015. 45: 584-591] highlight a novel twist on T-cell receptor (TCR) recognition of HLA-peptide complexes. Tumor-associated peptides often lack canonical anchor residues, which can be substituted for the optimal residue to improve their antigenicity. T-cell cross-reactivity between the natural and modified (heteroclitic) peptides is essential for this approach to work and depends on whether the anchor residue substitution influences peptide conformation. The Melan-A/MART-126-35 peptide epitope is an example where T cells can make this distinction, with the natural peptide stimulating higher affinity CD8(+) T cells than the heteroclitic peptide, despite the heteroclitic peptide's more stable association with HLA-A2. The molecular basis for peptide discrimination is identified through the structure of the TCR bound to the natural peptide; TCR engagement of the natural peptide "lifts" its amino-terminus partly away from the HLA peptide binding groove, forming a higher affinity interface with the TCR than is formed with the anchor residue "optimized" heteroclitic peptide, which cannot be "pulled" from the HLA groove.
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Affiliation(s)
- Julian Dyson
- Section of Molecular Immunology, Imperial College London, Hammersmith Hospital, London, UK
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31
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Neller MA, Ladell K, McLaren JE, Matthews KK, Gostick E, Pentier JM, Dolton G, Schauenburg AJA, Koning D, Fontaine Costa AICA, Watkins TS, Venturi V, Smith C, Khanna R, Miners K, Clement M, Wooldridge L, Cole DK, van Baarle D, Sewell AK, Burrows SR, Price DA, Miles JJ. Naive CD8⁺ T-cell precursors display structured TCR repertoires and composite antigen-driven selection dynamics. Immunol Cell Biol 2015; 93:625-33. [PMID: 25801351 PMCID: PMC4533101 DOI: 10.1038/icb.2015.17] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2014] [Revised: 01/04/2015] [Accepted: 01/22/2015] [Indexed: 02/07/2023]
Abstract
Basic parameters of the naive antigen (Ag)-specific T-cell repertoire in humans remain poorly defined. Systematic characterization of this ‘ground state' immunity in comparison with memory will allow a better understanding of clonal selection during immune challenge. Here, we used high-definition cell isolation from umbilical cord blood samples to establish the baseline frequency, phenotype and T-cell antigen receptor (TCR) repertoire of CD8+ T-cell precursor populations specific for a range of viral and self-derived Ags. Across the board, these precursor populations were phenotypically naive and occurred with hierarchical frequencies clustered by Ag specificity. The corresponding patterns of TCR architecture were highly ordered and displayed partial overlap with adult memory, indicating biased structuring of the T-cell repertoire during Ag-driven selection. Collectively, these results provide new insights into the complex nature and dynamics of the naive T-cell compartment.
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Affiliation(s)
- Michelle A Neller
- Human Immunity Laboratory, Cellular Immunology Laboratory and Tumour Immunology Laboratory, Queensland Institute of Medical Research, Brisbane, QLD, Australia
| | - Kristin Ladell
- Institute of Infection and Immunity, Cardiff University School of Medicine, Heath Park, Cardiff, UK
| | - James E McLaren
- Institute of Infection and Immunity, Cardiff University School of Medicine, Heath Park, Cardiff, UK
| | - Katherine K Matthews
- Human Immunity Laboratory, Cellular Immunology Laboratory and Tumour Immunology Laboratory, Queensland Institute of Medical Research, Brisbane, QLD, Australia
| | - Emma Gostick
- Institute of Infection and Immunity, Cardiff University School of Medicine, Heath Park, Cardiff, UK
| | - Johanne M Pentier
- Institute of Infection and Immunity, Cardiff University School of Medicine, Heath Park, Cardiff, UK
| | - Garry Dolton
- Institute of Infection and Immunity, Cardiff University School of Medicine, Heath Park, Cardiff, UK
| | - Andrea J A Schauenburg
- Institute of Infection and Immunity, Cardiff University School of Medicine, Heath Park, Cardiff, UK
| | - Dan Koning
- Department of Immunology, University Medical Center Utrecht, Utrecht, The Netherlands
| | | | - Thomas S Watkins
- Human Immunity Laboratory, Cellular Immunology Laboratory and Tumour Immunology Laboratory, Queensland Institute of Medical Research, Brisbane, QLD, Australia
| | - Vanessa Venturi
- Computational Biology Unit, Centre for Vascular Research, University of New South Wales, Kensington, NSW, Australia
| | - Corey Smith
- Human Immunity Laboratory, Cellular Immunology Laboratory and Tumour Immunology Laboratory, Queensland Institute of Medical Research, Brisbane, QLD, Australia
| | - Rajiv Khanna
- Human Immunity Laboratory, Cellular Immunology Laboratory and Tumour Immunology Laboratory, Queensland Institute of Medical Research, Brisbane, QLD, Australia
| | - Kelly Miners
- Institute of Infection and Immunity, Cardiff University School of Medicine, Heath Park, Cardiff, UK
| | - Mathew Clement
- Institute of Infection and Immunity, Cardiff University School of Medicine, Heath Park, Cardiff, UK
| | - Linda Wooldridge
- Institute of Infection and Immunity, Cardiff University School of Medicine, Heath Park, Cardiff, UK
| | - David K Cole
- Institute of Infection and Immunity, Cardiff University School of Medicine, Heath Park, Cardiff, UK
| | - Debbie van Baarle
- Department of Immunology, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Andrew K Sewell
- Institute of Infection and Immunity, Cardiff University School of Medicine, Heath Park, Cardiff, UK
| | - Scott R Burrows
- 1] Human Immunity Laboratory, Cellular Immunology Laboratory and Tumour Immunology Laboratory, Queensland Institute of Medical Research, Brisbane, QLD, Australia [2] School of Medicine, The University of Queensland, Brisbane, QLD, Australia
| | - David A Price
- 1] Institute of Infection and Immunity, Cardiff University School of Medicine, Heath Park, Cardiff, UK [2] Human Immunology Section, Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - John J Miles
- 1] Human Immunity Laboratory, Cellular Immunology Laboratory and Tumour Immunology Laboratory, Queensland Institute of Medical Research, Brisbane, QLD, Australia [2] Institute of Infection and Immunity, Cardiff University School of Medicine, Heath Park, Cardiff, UK [3] School of Medicine, The University of Queensland, Brisbane, QLD, Australia
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32
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Madura F, Rizkallah PJ, Holland CJ, Fuller A, Bulek A, Godkin AJ, Schauenburg AJ, Cole DK, Sewell AK. Structural basis for ineffective T-cell responses to MHC anchor residue-improved "heteroclitic" peptides. Eur J Immunol 2015; 45:584-91. [PMID: 25471691 PMCID: PMC4357396 DOI: 10.1002/eji.201445114] [Citation(s) in RCA: 52] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2014] [Revised: 10/03/2014] [Accepted: 11/26/2014] [Indexed: 12/11/2022]
Abstract
MHC anchor residue-modified "heteroclitic" peptides have been used in many cancer vaccine trials and often induce greater immune responses than the wild-type peptide. The best-studied system to date is the decamer MART-1/Melan-A26-35 peptide, EAAGIGILTV, where the natural alanine at position 2 has been modified to leucine to improve human leukocyte antigen (HLA)-A*0201 anchoring. The resulting ELAGIGILTV peptide has been used in many studies. We recently showed that T cells primed with the ELAGIGILTV peptide can fail to recognize the natural tumor-expressed peptide efficiently, thereby providing a potential molecular reason for why clinical trials of this peptide have been unsuccessful. Here, we solved the structure of a TCR in complex with HLA-A*0201-EAAGIGILTV peptide and compared it with its heteroclitic counterpart , HLA-A*0201-ELAGIGILTV. The data demonstrate that a suboptimal anchor residue at position 2 enables the TCR to "pull" the peptide away from the MHC binding groove, facilitating extra contacts with both the peptide and MHC surface. These data explain how a TCR can distinguish between two epitopes that differ by only a single MHC anchor residue and demonstrate how weak MHC anchoring can enable an induced-fit interaction with the TCR. Our findings constitute a novel demonstration of the extreme sensitivity of the TCR to minor alterations in peptide conformation.
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MESH Headings
- Alanine/chemistry
- Alanine/genetics
- Amino Acid Sequence
- Amino Acid Substitution
- Crystallography, X-Ray
- Epitopes, T-Lymphocyte/genetics
- Epitopes, T-Lymphocyte/immunology
- Epitopes, T-Lymphocyte/metabolism
- Escherichia coli/genetics
- Escherichia coli/metabolism
- Gene Expression
- HLA-A2 Antigen/chemistry
- HLA-A2 Antigen/genetics
- HLA-A2 Antigen/immunology
- Humans
- Leucine/chemistry
- Leucine/genetics
- MART-1 Antigen/chemistry
- MART-1 Antigen/genetics
- MART-1 Antigen/immunology
- Models, Molecular
- Molecular Sequence Data
- Peptides/chemistry
- Peptides/genetics
- Peptides/immunology
- Protein Binding
- Protein Interaction Domains and Motifs
- Receptors, Antigen, T-Cell, alpha-beta/chemistry
- Receptors, Antigen, T-Cell, alpha-beta/genetics
- Receptors, Antigen, T-Cell, alpha-beta/immunology
- Recombinant Proteins/chemistry
- Recombinant Proteins/genetics
- Recombinant Proteins/immunology
- T-Lymphocytes, Cytotoxic/cytology
- T-Lymphocytes, Cytotoxic/immunology
- T-Lymphocytes, Cytotoxic/metabolism
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Affiliation(s)
- Florian Madura
- Division of Infection and Immunity, Cardiff University School of MedicineHeath Park, Cardiff, UK
| | - Pierre J Rizkallah
- Division of Infection and Immunity, Cardiff University School of MedicineHeath Park, Cardiff, UK
| | - Christopher J Holland
- Division of Infection and Immunity, Cardiff University School of MedicineHeath Park, Cardiff, UK
| | - Anna Fuller
- Division of Infection and Immunity, Cardiff University School of MedicineHeath Park, Cardiff, UK
| | - Anna Bulek
- Division of Infection and Immunity, Cardiff University School of MedicineHeath Park, Cardiff, UK
| | - Andrew J Godkin
- Division of Infection and Immunity, Cardiff University School of MedicineHeath Park, Cardiff, UK
| | - Andrea J Schauenburg
- Division of Infection and Immunity, Cardiff University School of MedicineHeath Park, Cardiff, UK
| | - David K Cole
- Division of Infection and Immunity, Cardiff University School of MedicineHeath Park, Cardiff, UK
| | - Andrew K Sewell
- Division of Infection and Immunity, Cardiff University School of MedicineHeath Park, Cardiff, UK
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33
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Hoppes R, Oostvogels R, Luimstra JJ, Wals K, Toebes M, Bies L, Ekkebus R, Rijal P, Celie PHN, Huang JH, Emmelot ME, Spaapen RM, Lokhorst H, Schumacher TNM, Mutis T, Rodenko B, Ovaa H. Altered peptide ligands revisited: vaccine design through chemically modified HLA-A2-restricted T cell epitopes. THE JOURNAL OF IMMUNOLOGY 2014; 193:4803-13. [PMID: 25311806 DOI: 10.4049/jimmunol.1400800] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
Virus or tumor Ag-derived peptides that are displayed by MHC class I molecules are attractive starting points for vaccine development because they induce strong protective and therapeutic cytotoxic T cell responses. In thus study, we show that the MHC binding and consequent T cell reactivity against several HLA-A*02 restricted epitopes can be further improved through the incorporation of nonproteogenic amino acids at primary and secondary anchor positions. We screened more than 90 nonproteogenic, synthetic amino acids through a range of epitopes and tested more than 3000 chemically enhanced altered peptide ligands (CPLs) for binding affinity to HLA-A*0201. With this approach, we designed CPLs of viral epitopes, of melanoma-associated Ags, and of the minor histocompatibility Ag UTA2-1, which is currently being evaluated for its antileukemic activity in clinical dendritic cell vaccination trials. The crystal structure of one of the CPLs in complex with HLA-A*0201 revealed the molecular interactions likely responsible for improved binding. The best CPLs displayed enhanced affinity for MHC, increasing MHC stability and prolonging recognition by Ag-specific T cells and, most importantly, they induced accelerated expansion of antitumor T cell frequencies in vitro and in vivo as compared with the native epitope. Eventually, we were able to construct a toolbox of preferred nonproteogenic residues with which practically any given HLA-A*02 restricted epitope can be readily optimized. These CPLs could improve the therapeutic outcome of vaccination strategies or can be used for ex vivo enrichment and faster expansion of Ag-specific T cells for transfer into patients.
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Affiliation(s)
- Rieuwert Hoppes
- Division of Cell Biology, The Netherlands Cancer Institute, 1066 CX Amsterdam, the Netherlands
| | - Rimke Oostvogels
- Department of Clinical Chemistry and Haematology, University Medical Center Utrecht, 3584 CX Utrecht, the Netherlands Department of Haematology, University Medical Center Utrecht, 3584 CX Utrecht, the Netherlands
| | - Jolien J Luimstra
- Division of Cell Biology, The Netherlands Cancer Institute, 1066 CX Amsterdam, the Netherlands
| | - Kim Wals
- Division of Cell Biology, The Netherlands Cancer Institute, 1066 CX Amsterdam, the Netherlands
| | - Mireille Toebes
- Division of Immunology, The Netherlands Cancer Institute, 1066 CX Amsterdam, the Netherlands
| | - Laura Bies
- Division of Immunology, The Netherlands Cancer Institute, 1066 CX Amsterdam, the Netherlands
| | - Reggy Ekkebus
- Division of Cell Biology, The Netherlands Cancer Institute, 1066 CX Amsterdam, the Netherlands
| | - Pramila Rijal
- Division of Cell Biology, The Netherlands Cancer Institute, 1066 CX Amsterdam, the Netherlands
| | - Patrick H N Celie
- Division of Biochemistry, The Netherlands Cancer Institute Protein Facility, 1066 CX Amsterdam, the Netherlands; and
| | - Julie H Huang
- Department of Clinical Chemistry and Haematology, University Medical Center Utrecht, 3584 CX Utrecht, the Netherlands
| | - Maarten E Emmelot
- Department of Clinical Chemistry and Haematology, University Medical Center Utrecht, 3584 CX Utrecht, the Netherlands
| | - Robbert M Spaapen
- Division of Cell Biology, The Netherlands Cancer Institute, 1066 CX Amsterdam, the Netherlands
| | - Henk Lokhorst
- Department of Haematology, University Medical Center Utrecht, 3584 CX Utrecht, the Netherlands
| | - Ton N M Schumacher
- Division of Immunology, The Netherlands Cancer Institute, 1066 CX Amsterdam, the Netherlands
| | - Tuna Mutis
- Department of Clinical Chemistry and Haematology, University Medical Center Utrecht, 3584 CX Utrecht, the Netherlands
| | - Boris Rodenko
- Division of Cell Biology, The Netherlands Cancer Institute, 1066 CX Amsterdam, the Netherlands; Institute of Infection, Immunity and Inflammation, University of Glasgow, Glasgow G12 8TA, United Kingdom
| | - Huib Ovaa
- Division of Cell Biology, The Netherlands Cancer Institute, 1066 CX Amsterdam, the Netherlands
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34
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Sharma G, Holt RA. T-cell epitope discovery technologies. Hum Immunol 2014; 75:514-9. [PMID: 24755351 DOI: 10.1016/j.humimm.2014.03.003] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2013] [Revised: 03/18/2014] [Accepted: 03/27/2014] [Indexed: 01/21/2023]
Abstract
Despite tremendous potential utility in clinical medicine and research, the discovery and characterization of T-cell antigens has lagged behind most other areas of health research in joining the high-throughput '-omics' revolution. Partially responsible for this is the complex nature of the interactions between effector T cells and antigen-presenting cells. Further contributing to the challenge is the vastness of both the T-cell repertoire and the large number of potential T-cell epitopes. In this review, we trace the development of various discovery strategies, the technical platforms used to carry them out, and we assess the level of success achieved in the field today.
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Affiliation(s)
- Govinda Sharma
- Michael Smith Genome Sciences Centre, BC Cancer Agency, 675 W 10th Avenue, Vancouver, British Columbia V5Z 1L3, Canada; Department of Medical Genetics, University of British Columbia, C201 - 4500 Oak Street, Vancouver, British Columbia V6H 3N1, Canada.
| | - Robert A Holt
- Michael Smith Genome Sciences Centre, BC Cancer Agency, 675 W 10th Avenue, Vancouver, British Columbia V5Z 1L3, Canada; Department of Medical Genetics, University of British Columbia, C201 - 4500 Oak Street, Vancouver, British Columbia V6H 3N1, Canada; Department of Molecular Biology and Biochemistry, Simon Fraser University, 8888 University Drive, Burnaby, British Columbia V5A 1S6, Canada.
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35
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Hong Y, Peng Y, Guo ZS, Guevara-Patino J, Pang J, Butterfield LH, Mivechi N, Munn DH, Bartlett DL, He Y. Epitope-optimized alpha-fetoprotein genetic vaccines prevent carcinogen-induced murine autochthonous hepatocellular carcinoma. Hepatology 2014; 59:1448-58. [PMID: 24122861 PMCID: PMC4151349 DOI: 10.1002/hep.26893] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/08/2013] [Revised: 09/25/2013] [Accepted: 10/06/2013] [Indexed: 12/12/2022]
Abstract
UNLABELLED Immunization with effective cancer vaccines can offer a much needed adjuvant therapy to fill the treatment gap after liver resection to prevent relapse of hepatocellular carcinoma (HCC). However, current HCC cancer vaccines are mostly based on native shared-self/tumor antigens that are only able to induce weak immune responses. In this study we investigated whether the HCC-associated self/tumor antigen of alpha-fetoprotein (AFP) could be engineered to create an effective vaccine to break immune tolerance and potently activate CD8 T cells to prevent clinically relevant carcinogen-induced autochthonous HCC in mice. We found that the approach of computer-guided methodical epitope-optimization created a highly immunogenic AFP and that immunization with lentivector expressing the epitope-optimized AFP, but not wild-type AFP, potently activated CD8 T cells. Critically, the activated CD8 T cells not only cross-recognized short synthetic wild-type AFP peptides, but also recognized and killed tumor cells expressing wild-type AFP protein. Immunization with lentivector expressing optimized AFP, but not native AFP, completely protected mice from tumor challenge and reduced the incidence of carcinogen-induced autochthonous HCC. In addition, prime-boost immunization with the optimized AFP significantly increased the frequency of AFP-specific memory CD8 T cells in the liver that were highly effective against emerging HCC tumor cells, further enhancing the tumor prevention of carcinogen-induced autochthonous HCC. CONCLUSIONS Epitope-optimization is required to break immune tolerance and potently activate AFP-specific CD8 T cells, generating effective antitumor effect to prevent clinically relevant carcinogen-induced autochthonous HCC in mice. Our study provides a practical roadmap to develop effective human HCC vaccines that may result in an improved outcome compared to the current HCC vaccines based on wild-type AFP.
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Affiliation(s)
- Yuan Hong
- Cancer Immunology, Inflammation, and Tolerance Program, Georgia Regents University Cancer Center, Augusta, GA
| | - Yibing Peng
- Cancer Immunology, Inflammation, and Tolerance Program, Georgia Regents University Cancer Center, Augusta, GA
| | - Z. Sheng Guo
- Department of Surgery and University of Pittsburgh Cancer Institute, Pittsburgh, PA
| | - Jose Guevara-Patino
- Depart of Surgery, Cardinal Bernardin Cancer Center, Loyola University, Maywood, IL
| | - Junfeng Pang
- Department of Radiology and Molecular Chaperone Program, Georgia Regents University Cancer Center, Augusta, GA
| | - Lisa H. Butterfield
- Department of Medicine, Surgery, and Immunology, University of Pittsburgh Cancer Institute, Pittsburgh, PA
| | - Nahid Mivechi
- Department of Radiology and Molecular Chaperone Program, Georgia Regents University Cancer Center, Augusta, GA
| | - David H Munn
- Cancer Immunology, Inflammation, and Tolerance Program, Georgia Regents University Cancer Center, Augusta, GA,Department of Pediatrics, Medical College of Georgia, Augusta, GA
| | - David L Bartlett
- Department of Surgery and University of Pittsburgh Cancer Institute, Pittsburgh, PA
| | - Yukai He
- Cancer Immunology, Inflammation, and Tolerance Program, Georgia Regents University Cancer Center, Augusta, GA,Department of Medicine, Medical College of Georgia, Augusta, GA
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36
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Robert-Tissot C, Nguyen LT, Ohashi PS, Speiser DE. Mobilizing and evaluating anticancer T cells: pitfalls and solutions. Expert Rev Vaccines 2013; 12:1325-40. [PMID: 24127850 DOI: 10.1586/14760584.2013.843456] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Immunotherapy is a promising means to fight cancer, prompting a steady increase in clinical trials and correlative laboratory studies in this field. As antitumor T cells play central roles in immunity against malignant diseases, most immunotherapeutic protocols aim to induce and/or strengthen their function. Various treatment strategies have elicited encouraging clinical responses; however, major challenges have been uncovered that should be addressed in order to fully exploit the potential of immunotherapy. Here, we outline pitfalls for the mobilization of antitumor T cells and offer solutions to improve their therapeutic efficacy. We provide a critical perspective on the main methodologies used to characterize T-cell responses to cancer therapies, with a focus on discrepancies between T-cell attributes measured in vitro and protective responses in vivo. This review altogether provides recommendations to optimize the design of future clinical trials and highlights important considerations for the proficient analysis of clinical specimens available for research.
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Affiliation(s)
- Céline Robert-Tissot
- Campbell Family Institute for Breast Cancer Research, Princess Margaret Cancer Centre, University Health Network, Toronto, ON, M5G 2C1, Canada
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37
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Buhrman JD, Jordan KR, Munson DJ, Moore BL, Kappler JW, Slansky JE. Improving antigenic peptide vaccines for cancer immunotherapy using a dominant tumor-specific T cell receptor. J Biol Chem 2013; 288:33213-25. [PMID: 24106273 PMCID: PMC3829168 DOI: 10.1074/jbc.m113.509554] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
Vaccines that incorporate peptide mimics of tumor antigens, or mimotope vaccines, are commonly used in cancer immunotherapy and function by eliciting increased numbers of T cells that cross-react with the native tumor antigen. Unfortunately, they often elicit T cells that do not cross-react with or that have low affinity for the tumor antigen. Using a high affinity tumor-specific T cell clone, we identified a panel of mimotope vaccines for the dominant peptide antigen from a mouse colon tumor that elicits a range of tumor protection following vaccination. The TCR from this high affinity T cell clone was rarely identified in ex vivo evaluation of tumor-specific T cells elicited by mimotope vaccination. Conversely, a low affinity clone found in the tumor and following immunization was frequently identified. Using peptide libraries, we determined if this frequently identified TCR improved the discovery of efficacious mimotopes. We demonstrated that the representative TCR identified more protective mimotopes than the high affinity TCR. These results suggest that targeting a dominant fraction of tumor-specific T cells generates potent immunity and that consideration of the available T cell repertoire is necessary for targeted T cell therapy. These results have important implications when optimizing mimotope vaccines for cancer immunotherapy.
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38
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Wooldridge L. Individual MHCI-Restricted T-Cell Receptors are Characterized by a Unique Peptide Recognition Signature. Front Immunol 2013; 4:199. [PMID: 23888160 PMCID: PMC3719040 DOI: 10.3389/fimmu.2013.00199] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2013] [Accepted: 07/03/2013] [Indexed: 11/13/2022] Open
Abstract
Effective immunity requires that a limited TCR repertoire is able to recognize a vast number of foreign peptide-MHCI (peptide-major histocompatibility complex class I) molecules. This challenge is overcome by the ability of individual TCRs to recognize large numbers of peptides. Recently, it was demonstrated that MHCI-restricted TCRs can recognize up to 106 peptides of a defined length. Astonishingly, this remarkable level of promiscuity does not extend to peptides of different lengths, a fundamental observation that has broad implications for CD8+ T-cell immunity. In particular, the findings suggest that effective immunity can only be achieved by mobilization of “length-matched” CD8+ T-cell clonotypes. Overall, recent findings suggest that every TCR is specific for a unique set of peptides, which can be described as a unique “peptide recognition signature” (PRS) and consists of three components: (1) peptide length preference, (2) number of peptides recognized; and, (3) sequence identity (e.g., self versus pathogen derived). In future, the ability to de-convolute peptide recognition signatures across the normal and pathogenic repertoire will be essential for understanding the system requirements for effective CD8+ T-cell immunity and elucidating mechanisms which underlie CD8+ T-cell mediated disease.
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Affiliation(s)
- Linda Wooldridge
- Institute of Infection and Immunity, Cardiff University School of Medicine , Heath Park, Cardiff , UK
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39
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Motozono C, Miles JJ, Hasan Z, Gatanaga H, Meribe SC, Price DA, Oka S, Sewell AK, Ueno T. CD8(+) T cell cross-reactivity profiles and HIV-1 immune escape towards an HLA-B35-restricted immunodominant Nef epitope. PLoS One 2013; 8:e66152. [PMID: 23799076 PMCID: PMC3684606 DOI: 10.1371/journal.pone.0066152] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2013] [Accepted: 05/01/2013] [Indexed: 11/23/2022] Open
Abstract
Antigen cross-reactivity is an inbuilt feature of the T cell compartment. However, little is known about the flexibility of T cell recognition in the context of genetically variable pathogens such as HIV-1. In this study, we used a combinatorial library containing 24 billion octamer peptides to characterize the cross-reactivity profiles of CD8+ T cells specific for the immunodominant HIV-1 subtype B Nef epitope VY8 (VPLRPMTY) presented by HLA-B*35∶01. In conjunction, we examined naturally occurring antigenic variations within the VY8 epitope. Sequence analysis of plasma viral RNA isolated from 336 HIV-1-infected individuals revealed variability at position (P) 3 and P8 of VY8; Phe at P8, but not Val at P3, was identified as an HLA-B*35∶01-associated polymorphism. VY8-specific T cells generated from several different HIV-1-infected patients showed unique and clonotype-dependent cross-reactivity footprints. Nonetheless, all T cells recognized both the index Leu and mutant Val at P3 equally well. In contrast, competitive titration assays revealed that the Tyr to Phe substitution at P8 reduced T cell recognition by 50–130 fold despite intact peptide binding to HLA-B*35∶01. These findings explain the preferential selection of Phe at the C-terminus of VY8 in HLA-B*35∶01+ individuals and demonstrate that HIV-1 can exploit the limitations of T cell recognition in vivo.
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Affiliation(s)
- Chihiro Motozono
- Institute of Infection and Immunity, Cardiff University School of Medicine, Heath Park, Cardiff, United Kingdom
- Center for AIDS Research, Kumamoto University, Kumamoto, Japan
| | - John J. Miles
- Institute of Infection and Immunity, Cardiff University School of Medicine, Heath Park, Cardiff, United Kingdom
- Australian Centre for Vaccine Development, Human Immunity Laboratory, Queensland Institute of Medical Research, Brisbane, Australia
- School of Medicine, The University of Queensland, Brisbane, Australia
| | - Zafrul Hasan
- Center for AIDS Research, Kumamoto University, Kumamoto, Japan
| | - Hiroyuki Gatanaga
- Center for AIDS Research, Kumamoto University, Kumamoto, Japan
- AIDS Clinical Center, National Center for Global Health and Medicine, Tokyo, Japan
| | | | - David A. Price
- Institute of Infection and Immunity, Cardiff University School of Medicine, Heath Park, Cardiff, United Kingdom
| | - Shinichi Oka
- Center for AIDS Research, Kumamoto University, Kumamoto, Japan
- AIDS Clinical Center, National Center for Global Health and Medicine, Tokyo, Japan
| | - Andrew K. Sewell
- Institute of Infection and Immunity, Cardiff University School of Medicine, Heath Park, Cardiff, United Kingdom
- * E-mail: (TU); (AKS)
| | - Takamasa Ueno
- Center for AIDS Research, Kumamoto University, Kumamoto, Japan
- * E-mail: (TU); (AKS)
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40
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Pentier JM, Sewell AK, Miles JJ. Advances in T-cell epitope engineering. Front Immunol 2013; 4:133. [PMID: 23761792 PMCID: PMC3672776 DOI: 10.3389/fimmu.2013.00133] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2013] [Accepted: 05/21/2013] [Indexed: 12/11/2022] Open
Affiliation(s)
- Johanne M Pentier
- Institute of Infection and Immunity, Cardiff University School of Medicine Heath Park, Cardiff, Wales, UK
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