1
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Faghfuri E. Recent advances in personalized cancer immunotherapy with immune checkpoint inhibitors, T cells and vaccines. Per Med 2024; 21:45-57. [PMID: 38088165 DOI: 10.2217/pme-2023-0054] [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] [Indexed: 01/06/2024]
Abstract
The results of genomic and molecular profiling of cancer patients can be effectively applied to immunotherapy agents, including immune checkpoint inhibitors, to select the most appropriate treatment. In addition, accurate prediction of neoantigens facilitates the development of individualized cancer vaccines and T-cell therapy. This review summarizes the biomarker(s) predicting responses to immune checkpoint inhibitors and focuses on current strategies to identify and isolate neoantigen-reactive T cells as well as the clinical development of neoantigen-based therapeutics. The results suggest that maximal T-cell stimulation and expansion can be achieved with combination therapies that enhance antigen-presenting cells' function and optimal T-cell priming in lymph nodes.
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Affiliation(s)
- Elnaz Faghfuri
- Digestive Disease Research Center, Ardabil University of Medical Sciences, Ardabil, 5613658115, Iran
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2
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Chen Y, Mason GH, Scourfield DO, Greenshields-Watson A, Haigh TA, Sewell AK, Long HM, Gallimore AM, Rizkallah P, MacLachlan BJ, Godkin A. Structural definition of HLA class II-presented SARS-CoV-2 epitopes reveals a mechanism to escape pre-existing CD4 + T cell immunity. Cell Rep 2023; 42:112827. [PMID: 37471227 PMCID: PMC10840515 DOI: 10.1016/j.celrep.2023.112827] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2023] [Revised: 05/21/2023] [Accepted: 06/30/2023] [Indexed: 07/22/2023] Open
Abstract
CD4+ T cells recognize a broad range of peptide epitopes of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), which contribute to immune memory and limit COVID-19 disease. We demonstrate that the immunogenicity of SARS-CoV-2 peptides, in the context of the model allotype HLA-DR1, does not correlate with their binding affinity to the HLA heterodimer. Analyzing six epitopes, some with very low binding affinity, we solve X-ray crystallographic structures of each bound to HLA-DR1. Further structural definitions reveal the precise molecular impact of viral variant mutations on epitope presentation. Omicron escaped ancestral SARS-CoV-2 immunity to two epitopes through two distinct mechanisms: (1) mutations to TCR-facing epitope positions and (2) a mechanism whereby a single amino acid substitution caused a register shift within the HLA binding groove, completely altering the peptide-HLA structure. This HLA-II-specific paradigm of immune escape highlights how CD4+ T cell memory is finely poised at the level of peptide-HLA-II presentation.
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Affiliation(s)
- Yuan Chen
- Division of Infection and Immunity, School of Medicine, Cardiff University, Cardiff CF14 4XN, UK; Systems Immunity University Research Institute, School of Medicine, Cardiff University, Cardiff CF14 4XN, UK
| | - Georgina H Mason
- Division of Infection and Immunity, School of Medicine, Cardiff University, Cardiff CF14 4XN, UK; Systems Immunity University Research Institute, School of Medicine, Cardiff University, Cardiff CF14 4XN, UK
| | - D Oliver Scourfield
- Division of Infection and Immunity, School of Medicine, Cardiff University, Cardiff CF14 4XN, UK; Systems Immunity University Research Institute, School of Medicine, Cardiff University, Cardiff CF14 4XN, UK
| | - Alexander Greenshields-Watson
- Division of Infection and Immunity, School of Medicine, Cardiff University, Cardiff CF14 4XN, UK; Systems Immunity University Research Institute, School of Medicine, Cardiff University, Cardiff CF14 4XN, UK
| | - Tracey A Haigh
- Institute of Immunology and Immunotherapy, University of Birmingham, Birmingham B15 2TT, UK
| | - Andrew K Sewell
- Division of Infection and Immunity, School of Medicine, Cardiff University, Cardiff CF14 4XN, UK; Systems Immunity University Research Institute, School of Medicine, Cardiff University, Cardiff CF14 4XN, UK
| | - Heather M Long
- Institute of Immunology and Immunotherapy, University of Birmingham, Birmingham B15 2TT, UK
| | - Awen M Gallimore
- Division of Infection and Immunity, School of Medicine, Cardiff University, Cardiff CF14 4XN, UK; Systems Immunity University Research Institute, School of Medicine, Cardiff University, Cardiff CF14 4XN, UK
| | - Pierre Rizkallah
- Division of Infection and Immunity, School of Medicine, Cardiff University, Cardiff CF14 4XN, UK; Systems Immunity University Research Institute, School of Medicine, Cardiff University, Cardiff CF14 4XN, UK
| | - Bruce J MacLachlan
- Division of Infection and Immunity, School of Medicine, Cardiff University, Cardiff CF14 4XN, UK; Systems Immunity University Research Institute, School of Medicine, Cardiff University, Cardiff CF14 4XN, UK.
| | - Andrew Godkin
- Division of Infection and Immunity, School of Medicine, Cardiff University, Cardiff CF14 4XN, UK; Systems Immunity University Research Institute, School of Medicine, Cardiff University, Cardiff CF14 4XN, UK; Department of Gastroenterology & Hepatology, University Hospital of Wales, Cardiff CF14 4XW, UK.
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3
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Dolton G, Rius C, Wall A, Szomolay B, Bianchi V, Galloway SAE, Hasan MS, Morin T, Caillaud ME, Thomas HL, Theaker S, Tan LR, Fuller A, Topley K, Legut M, Attaf M, Hopkins JR, Behiry E, Zabkiewicz J, Alvares C, Lloyd A, Rogers A, Henley P, Fegan C, Ottmann O, Man S, Crowther MD, Donia M, Svane IM, Cole DK, Brown PE, Rizkallah P, Sewell AK. Targeting of multiple tumor-associated antigens by individual T cell receptors during successful cancer immunotherapy. Cell 2023; 186:3333-3349.e27. [PMID: 37490916 DOI: 10.1016/j.cell.2023.06.020] [Citation(s) in RCA: 16] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2022] [Revised: 04/20/2023] [Accepted: 06/24/2023] [Indexed: 07/27/2023]
Abstract
The T cells of the immune system can target tumors and clear solid cancers following tumor-infiltrating lymphocyte (TIL) therapy. We used combinatorial peptide libraries and a proteomic database to reveal the antigen specificities of persistent cancer-specific T cell receptors (TCRs) following successful TIL therapy for stage IV malignant melanoma. Remarkably, individual TCRs could target multiple different tumor types via the HLA A∗02:01-restricted epitopes EAAGIGILTV, LLLGIGILVL, and NLSALGIFST from Melan A, BST2, and IMP2, respectively. Atomic structures of a TCR bound to all three antigens revealed the importance of the shared x-x-x-A/G-I/L-G-I-x-x-x recognition motif. Multi-epitope targeting allows individual T cells to attack cancer in several ways simultaneously. Such "multipronged" T cells exhibited superior recognition of cancer cells compared with conventional T cell recognition of individual epitopes, making them attractive candidates for the development of future immunotherapies.
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Affiliation(s)
- Garry Dolton
- Division of Infection and Immunity, Cardiff University School of Medicine, Cardiff, Wales CF14 4XN, UK
| | - Cristina Rius
- Division of Infection and Immunity, Cardiff University School of Medicine, Cardiff, Wales CF14 4XN, UK
| | - Aaron Wall
- Division of Infection and Immunity, Cardiff University School of Medicine, Cardiff, Wales CF14 4XN, UK
| | - Barbara Szomolay
- Systems Immunology Research Institute, Cardiff, Wales CF14 4XN, UK
| | - Valentina Bianchi
- Division of Infection and Immunity, Cardiff University School of Medicine, Cardiff, Wales CF14 4XN, UK
| | - Sarah A E Galloway
- Division of Infection and Immunity, Cardiff University School of Medicine, Cardiff, Wales CF14 4XN, UK
| | - Md Samiul Hasan
- Division of Infection and Immunity, Cardiff University School of Medicine, Cardiff, Wales CF14 4XN, UK
| | - Théo Morin
- Division of Infection and Immunity, Cardiff University School of Medicine, Cardiff, Wales CF14 4XN, UK
| | - Marine E Caillaud
- Division of Infection and Immunity, Cardiff University School of Medicine, Cardiff, Wales CF14 4XN, UK
| | - Hannah L Thomas
- Division of Infection and Immunity, Cardiff University School of Medicine, Cardiff, Wales CF14 4XN, UK
| | - Sarah Theaker
- Division of Infection and Immunity, Cardiff University School of Medicine, Cardiff, Wales CF14 4XN, UK
| | - Li Rong Tan
- Division of Infection and Immunity, Cardiff University School of Medicine, Cardiff, Wales CF14 4XN, UK
| | - Anna Fuller
- Division of Infection and Immunity, Cardiff University School of Medicine, Cardiff, Wales CF14 4XN, UK
| | - Katie Topley
- Division of Infection and Immunity, Cardiff University School of Medicine, Cardiff, Wales CF14 4XN, UK
| | - Mateusz Legut
- Division of Infection and Immunity, Cardiff University School of Medicine, Cardiff, Wales CF14 4XN, UK
| | - Meriem Attaf
- Division of Infection and Immunity, Cardiff University School of Medicine, Cardiff, Wales CF14 4XN, UK
| | - Jade R Hopkins
- Division of Infection and Immunity, Cardiff University School of Medicine, Cardiff, Wales CF14 4XN, UK
| | - Enas Behiry
- Division of Infection and Immunity, Cardiff University School of Medicine, Cardiff, Wales CF14 4XN, UK
| | - Joanna Zabkiewicz
- Division of Cancer and Genetics, Cardiff University School of Medicine, Cardiff, Wales CF14 4XN, UK
| | - Caroline Alvares
- Division of Cancer and Genetics, Cardiff University School of Medicine, Cardiff, Wales CF14 4XN, UK
| | - Angharad Lloyd
- Division of Infection and Immunity, Cardiff University School of Medicine, Cardiff, Wales CF14 4XN, UK
| | - Amber Rogers
- Division of Infection and Immunity, Cardiff University School of Medicine, Cardiff, Wales CF14 4XN, UK
| | - Peter Henley
- Division of Cancer and Genetics, Cardiff University School of Medicine, Cardiff, Wales CF14 4XN, UK
| | - Christopher Fegan
- Division of Cancer and Genetics, Cardiff University School of Medicine, Cardiff, Wales CF14 4XN, UK
| | - Oliver Ottmann
- Division of Cancer and Genetics, Cardiff University School of Medicine, Cardiff, Wales CF14 4XN, UK
| | - Stephen Man
- Division of Cancer and Genetics, Cardiff University School of Medicine, Cardiff, Wales CF14 4XN, UK
| | - Michael D Crowther
- Division of Infection and Immunity, Cardiff University School of Medicine, Cardiff, Wales CF14 4XN, UK; National Center for Cancer Immune Therapy, Department of Oncology, Copenhagen University Hospital, Herlev, Denmark
| | - Marco Donia
- National Center for Cancer Immune Therapy, Department of Oncology, Copenhagen University Hospital, Herlev, Denmark
| | - Inge Marie Svane
- National Center for Cancer Immune Therapy, Department of Oncology, Copenhagen University Hospital, Herlev, Denmark
| | - David K Cole
- Division of Infection and Immunity, Cardiff University School of Medicine, Cardiff, Wales CF14 4XN, UK
| | - Paul E Brown
- The Zeeman Institute, University of Warwick, Coventry CV4 7AL, UK
| | - Pierre Rizkallah
- Division of Infection and Immunity, Cardiff University School of Medicine, Cardiff, Wales CF14 4XN, UK
| | - Andrew K Sewell
- Division of Infection and Immunity, Cardiff University School of Medicine, Cardiff, Wales CF14 4XN, UK; Systems Immunology Research Institute, Cardiff, Wales CF14 4XN, UK.
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4
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Mahajan S, Kortleve D, Debets R, Hammerl D. Detection of Low-Frequency Epitope-Specific T Cells in Blood of Healthy Individuals according to an Optimized In Vitro Amplification System. JOURNAL OF IMMUNOLOGY (BALTIMORE, MD. : 1950) 2022; 209:2239-2247. [PMID: 36426971 DOI: 10.4049/jimmunol.2101122] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/07/2021] [Accepted: 09/26/2022] [Indexed: 11/06/2022]
Abstract
Detection and amplification of epitope-specific T cells hold great promise for diagnosis and therapy of cancer patients. Currently, measurement and retrieval of epitope-specific T cells is hampered by limited availability of patients' biomaterials and lack of sensitive and easy-to-implement T cell priming and expansion. We have developed an in vitro T cell amplification system starting from healthy donor blood and tested different subsets and ratios of autologous T cells and APCs as well as the resting period between amplification cycles. We demonstrated in 10 different donors significantly enhanced frequency of T cells specific for MelanA/HLA-A2, which relied on coculturing of naive T cells and CD11c+ dendritic cells in a 1:1 ratio followed by three weekly amplification cycles using the effluent of the naive T cell sort as APCs, a 24-h rest period prior to every reamplification cycle, and IFN-γ production as a readout for epitope-specific T cells. Using this system, MelanA/HLA-A2-specific T cells were enriched by 200-fold, measuring up to 20-60% of all T cells. We extended this system to enrich NY-ESO-1/HLA-A2- and BMLF-1/HLA-A2-specific T cells, examples of a cancer germline Ag and an oncoviral Ag differing in their ability to bind to HLA-A2 and the presence of specific T cells in the naive and, in case of BMLF-1, also the Ag-experienced repertoire. Collectively, we have developed a sensitive and easy-to-implement in vitro T cell amplification method to enrich epitope-specific T cells that is expected to facilitate research and clinical utility regarding T cell diagnosis and treatments.
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Affiliation(s)
- Shweta Mahajan
- Laboratory of Tumor Immunology, Department of Medical Oncology, Erasmus MC Cancer Institute, Rotterdam, the Netherlands
| | - Dian Kortleve
- Laboratory of Tumor Immunology, Department of Medical Oncology, Erasmus MC Cancer Institute, Rotterdam, the Netherlands
| | - Reno Debets
- Laboratory of Tumor Immunology, Department of Medical Oncology, Erasmus MC Cancer Institute, Rotterdam, the Netherlands
| | - Dora Hammerl
- Laboratory of Tumor Immunology, Department of Medical Oncology, Erasmus MC Cancer Institute, Rotterdam, the Netherlands
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5
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Gene Engineering T Cells with T-Cell Receptor for Adoptive Therapy. METHODS IN MOLECULAR BIOLOGY (CLIFTON, N.J.) 2022; 2453:209-229. [PMID: 35622329 DOI: 10.1007/978-1-0716-2115-8_13] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
Prior to clinical testing of adoptive T-cell therapy with T-cell receptor (TCR)-engineered T cells, TCRs need to be retrieved, annotated, gene-transferred, and extensively tested in vitro to accurately assess specificity and sensitivity of target recognition. Here, we present a fundamental series of protocols that cover critical preclinical parameters, thereby enabling the selection of candidate TCRs for clinical testing.
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6
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CD4 + T Cells Recognize Conserved Influenza A Epitopes through Shared Patterns of V-Gene Usage and Complementary Biochemical Features. Cell Rep 2021; 32:107885. [PMID: 32668259 PMCID: PMC7370177 DOI: 10.1016/j.celrep.2020.107885] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2019] [Revised: 01/20/2020] [Accepted: 06/17/2020] [Indexed: 12/15/2022] Open
Abstract
T cell recognition of peptides presented by human leukocyte antigens (HLAs) is mediated by the highly variable T cell receptor (TCR). Despite this built-in TCR variability, individuals can mount immune responses against viral epitopes by using identical or highly related TCRs expressed on CD8+ T cells. Characterization of these TCRs has extended our understanding of the molecular mechanisms that govern the recognition of peptide-HLA. However, few examples exist for CD4+ T cells. Here, we investigate CD4+ T cell responses to the internal proteins of the influenza A virus that correlate with protective immunity. We identify five internal epitopes that are commonly recognized by CD4+ T cells in five HLA-DR1+ subjects and show conservation across viral strains and zoonotic reservoirs. TCR repertoire analysis demonstrates several shared gene usage biases underpinned by complementary biochemical features evident in a structural comparison. These epitopes are attractive targets for vaccination and other T cell therapies.
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7
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Powlson J, Wright D, Zeltina A, Giza M, Nielsen M, Rampling T, Venkatrakaman N, Bowden TA, Hill AVS, Ewer KJ. Characterization of Antigenic MHC-Class-I-Restricted T Cell Epitopes in the Glycoprotein of Ebolavirus. Cell Rep 2020; 29:2537-2545.e3. [PMID: 31775024 PMCID: PMC6899439 DOI: 10.1016/j.celrep.2019.10.105] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2019] [Revised: 07/20/2019] [Accepted: 10/25/2019] [Indexed: 11/05/2022] Open
Abstract
Ebolavirus causes highly lethal hemorrhagic fever in humans. The envelope-displayed viral glycoprotein (GP) is the primary target of humoral immunity induced by natural exposure and vaccination. No T cell epitopes in the GP have been characterized in humans. A phase I clinical trial of a heterologous prime-boost vaccination regime with viral vectors encoding filovirus antigens elicits humoral and T cell responses in vaccinees. The most frequently recognized peptide pools are deconvoluted to identify the minimal epitopes recognized by antigen-specific T cells. We characterize nine immunogenic epitopes on the Ebolavirus GP. Histocompatibility leukocyte antigen (HLA) typing with in silico epitope analysis determines the likely MHC class I restriction elements. Thirteen HLA-A and -B alleles are predicted to present the identified CD8+ T cell epitopes, suggesting promiscuous recognition and a broad immune response. Delivery of the Ebolavirus GP antigen by using a heterologous prime-boost approach is immunogenic in genetically diverse human populations, with responses against multiple epitopes. Vaccination induces high T cell responses to the Ebola virus glycoprotein in humans Eight CD8+ epitopes were defined, recognized through multiple MHC class I alleles Responses match those observed in Ebola survivors and could boost vaccine efficacy
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Affiliation(s)
- Jonathan Powlson
- The Jenner Institute, Old Road Campus Research Building, University of Oxford, Oxford OX3 7DQ, UK
| | - Daniel Wright
- The Jenner Institute, Old Road Campus Research Building, University of Oxford, Oxford OX3 7DQ, UK
| | - Antra Zeltina
- Division of Structural Biology, Wellcome Centre for Human Genetics, University of Oxford, Oxford OX3 7BN, UK
| | - Mark Giza
- The Jenner Institute, Old Road Campus Research Building, University of Oxford, Oxford OX3 7DQ, UK
| | - Morten Nielsen
- Department of Health Technology, The Technical University of Denmark, Anker Engelunds Vej 1 Bygning 101A, 2800 Kgs Lyngby, Denmark
| | - Tommy Rampling
- The Jenner Institute, Old Road Campus Research Building, University of Oxford, Oxford OX3 7DQ, UK
| | - Navin Venkatrakaman
- The Jenner Institute, Old Road Campus Research Building, University of Oxford, Oxford OX3 7DQ, UK
| | - Thomas A Bowden
- Division of Structural Biology, Wellcome Centre for Human Genetics, University of Oxford, Oxford OX3 7BN, UK
| | - Adrian V S Hill
- The Jenner Institute, Old Road Campus Research Building, University of Oxford, Oxford OX3 7DQ, UK
| | - Katie J Ewer
- The Jenner Institute, Old Road Campus Research Building, University of Oxford, Oxford OX3 7DQ, UK.
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8
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Li Q, Ding ZY. The Ways of Isolating Neoantigen-Specific T Cells. Front Oncol 2020; 10:1347. [PMID: 32850430 PMCID: PMC7431921 DOI: 10.3389/fonc.2020.01347] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2019] [Accepted: 06/26/2020] [Indexed: 02/05/2023] Open
Abstract
Immunotherapy has revolutionized the standard of care for a range of malignancies. Accumulating evidence suggests that the success of immunotherapy is likely attributable to neoantigen-specific T cells. Thus, adoptive cell therapy with these neoantigen-specific T cells is highly promising. This strategy has proven to successfully elicit tumor regression or even complete remission in metastatic cancer patients. However, a fundamental challenge is to effectively identify and isolate neoantigen-specific T cells or their T cell receptors (TCRs), from either tumor-infiltrating lymphocytes (TILs) or peripheral blood lymphocytes (PBLs), and many methods have been developed to this end. In this review, we focus on the current proposed strategies for identifying and isolating neoantigen-specific T cells.
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Affiliation(s)
- Qing Li
- Department of Biotherapy, Cancer Center, National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, Chengdu, China
| | - Zhen-Yu Ding
- Department of Biotherapy, Cancer Center, National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, Chengdu, China
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9
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Adoptive Cell Therapy-Harnessing Antigen-Specific T Cells to Target Solid Tumours. Cancers (Basel) 2020; 12:cancers12030683. [PMID: 32183246 PMCID: PMC7140076 DOI: 10.3390/cancers12030683] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2020] [Revised: 03/06/2020] [Accepted: 03/10/2020] [Indexed: 12/26/2022] Open
Abstract
In recent years, much research has been focused on the field of adoptive cell therapies (ACT) that use native or genetically modified T cells as therapeutic tools. Immunotherapy with T cells expressing chimeric antigen receptors (CARs) demonstrated great success in the treatment of haematologic malignancies, whereas adoptive transfer of autologous tumour infiltrating lymphocytes (TILs) proved to be highly effective in metastatic melanoma. These encouraging results initiated many studies where ACT was tested as a treatment for various solid tumours. In this review, we provide an overview of the challenges of T cell-based immunotherapies of solid tumours. We describe alternative approaches for choosing the most efficient T cells for cancer treatment in terms of their tumour-specificity and phenotype. Finally, we present strategies for improvement of anti-tumour potential of T cells, including combination therapies.
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10
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Whalley T, Dolton G, Brown PE, Wall A, Wooldridge L, van den Berg H, Fuller A, Hopkins JR, Crowther MD, Attaf M, Knight RR, Cole DK, Peakman M, Sewell AK, Szomolay B. GPU-Accelerated Discovery of Pathogen-Derived Molecular Mimics of a T-Cell Insulin Epitope. Front Immunol 2020; 11:296. [PMID: 32184781 PMCID: PMC7058665 DOI: 10.3389/fimmu.2020.00296] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2019] [Accepted: 02/05/2020] [Indexed: 01/09/2023] Open
Abstract
The strong links between (Human Leukocyte Antigen) HLA, infection and autoimmunity combine to implicate T-cells as primary triggers of autoimmune disease (AD). T-cell crossreactivity between microbially-derived peptides and self-peptides has been shown to break tolerance and trigger AD in experimental animal models. Detailed examination of the potential for T-cell crossreactivity to trigger human AD will require means of predicting which peptides might be recognised by autoimmune T-cell receptors (TCRs). Recent developments in high throughput sequencing and bioinformatics mean that it is now possible to link individual TCRs to specific pathologies for the first time. Deconvolution of TCR function requires knowledge of TCR specificity. Positional Scanning Combinatorial Peptide Libraries (PS-CPLs) can be used to predict HLA-restriction and define antigenic peptides derived from self and pathogen proteins. In silico search of the known terrestrial proteome with a prediction algorithm that ranks potential antigens in order of recognition likelihood requires complex, large-scale computations over several days that are infeasible on a personal computer. We decreased the time required for peptide searching to under 30 min using multiple blocks on graphics processing units (GPUs). This time-efficient, cost-effective hardware accelerator was used to screen bacterial and fungal human pathogens for peptide sequences predicted to activate a T-cell clone, InsB4, that was isolated from a patient with type 1 diabetes and recognised the insulin B-derived epitope HLVEALYLV in the context of disease-risk allele HLA A*0201. InsB4 was shown to kill HLA A*0201+ human insulin producing β-cells demonstrating that T-cells with this specificity might contribute to disease. The GPU-accelerated algorithm and multispecies pathogen proteomic databases were validated to discover pathogen-derived peptide sequences that acted as super-agonists for the InsB4 T-cell clone. Peptide-MHC tetramer binding and surface plasmon resonance were used to confirm that the InsB4 TCR bound to the highest-ranked peptide agonists derived from infectious bacteria and fungi. Adoption of GPU-accelerated prediction of T-cell agonists has the capacity to revolutionise our understanding of AD by identifying potential targets for autoimmune T-cells. This approach has further potential for dissecting T-cell responses to infectious disease and cancer.
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Affiliation(s)
- Thomas Whalley
- Cardiff University School of Medicine, Cardiff, United Kingdom.,Systems Immunity Research Institute, Cardiff University, Cardiff, United Kingdom
| | - Garry Dolton
- Cardiff University School of Medicine, Cardiff, United Kingdom
| | - Paul E Brown
- Zeeman Institute for Systems Biology and Infectious Disease Epidemiology Research, University of Warwick Coventry, Coventry, United Kingdom
| | - Aaron Wall
- Cardiff University School of Medicine, Cardiff, United Kingdom
| | - Linda Wooldridge
- Faculty of Health Sciences, University of Bristol, Bristol, United Kingdom
| | - Hugo van den Berg
- Mathematics Institute, University of Warwick, Coventry, United Kingdom
| | - Anna Fuller
- Cardiff University School of Medicine, Cardiff, United Kingdom
| | - Jade R Hopkins
- Cardiff University School of Medicine, Cardiff, United Kingdom
| | | | - Meriem Attaf
- Cardiff University School of Medicine, Cardiff, United Kingdom
| | - Robin R Knight
- Peter Gorer Department of Immunobiology, Guy's Hospital, London, United Kingdom
| | - David K Cole
- Cardiff University School of Medicine, Cardiff, United Kingdom
| | - Mark Peakman
- Peter Gorer Department of Immunobiology, Guy's Hospital, London, United Kingdom
| | - Andrew K Sewell
- Cardiff University School of Medicine, Cardiff, United Kingdom.,Systems Immunity Research Institute, Cardiff University, Cardiff, United Kingdom
| | - Barbara Szomolay
- Cardiff University School of Medicine, Cardiff, United Kingdom.,Systems Immunity Research Institute, Cardiff University, Cardiff, United Kingdom
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11
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MacLachlan BJ, Dolton G, Papakyriakou A, Greenshields-Watson A, Mason GH, Schauenburg A, Besneux M, Szomolay B, Elliott T, Sewell AK, Gallimore A, Rizkallah P, Cole DK, Godkin A. Human leukocyte antigen (HLA) class II peptide flanking residues tune the immunogenicity of a human tumor-derived epitope. J Biol Chem 2019; 294:20246-20258. [PMID: 31619516 PMCID: PMC6937582 DOI: 10.1074/jbc.ra119.009437] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2019] [Revised: 09/18/2019] [Indexed: 01/03/2023] Open
Abstract
CD4+ T-cells recognize peptide antigens, in the context of human leukocyte antigen (HLA) class II molecules (HLA-II), which through peptide-flanking residues (PFRs) can extend beyond the limits of the HLA binding. The role of the PFRs during antigen recognition is not fully understood; however, recent studies have indicated that these regions can influence T-cell receptor (TCR) affinity and pHLA-II stability. Here, using various biochemical approaches including peptide sensitivity ELISA and ELISpot assays, peptide-binding assays and HLA-II tetramer staining, we focused on CD4+ T-cell responses against a tumor antigen, 5T4 oncofetal trophoblast glycoprotein (5T4), which have been associated with improved control of colorectal cancer. Despite their weak TCR-binding affinity, we found that anti-5T4 CD4+ T-cells are polyfunctional and that their PFRs are essential for TCR recognition of the core bound nonamer. The high-resolution (1.95 Å) crystal structure of HLA-DR1 presenting the immunodominant 20-mer peptide 5T4111-130, combined with molecular dynamic simulations, revealed how PFRs explore the HLA-proximal space to contribute to antigen reactivity. These findings advance our understanding of what constitutes an HLA-II epitope and indicate that PFRs can tune weak affinity TCR-pHLA-II interactions.
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Affiliation(s)
- Bruce J MacLachlan
- Division of Infection and Immunity and Systems Immunity Research Institute, Cardiff University, Cardiff CF14 4XN, United Kingdom
| | - Garry Dolton
- Division of Infection and Immunity and Systems Immunity Research Institute, Cardiff University, Cardiff CF14 4XN, United Kingdom
| | - Athanasios Papakyriakou
- Institute of Biosciences and Applications, NCSR "Demokritos," Agia Paraskevi, 15341 Athens, Greece
| | - Alexander Greenshields-Watson
- Division of Infection and Immunity and Systems Immunity Research Institute, Cardiff University, Cardiff CF14 4XN, United Kingdom
| | - Georgina H Mason
- Division of Infection and Immunity and Systems Immunity Research Institute, Cardiff University, Cardiff CF14 4XN, United Kingdom
| | - Andrea Schauenburg
- Division of Infection and Immunity and Systems Immunity Research Institute, Cardiff University, Cardiff CF14 4XN, United Kingdom
| | - Matthieu Besneux
- Division of Infection and Immunity and Systems Immunity Research Institute, Cardiff University, Cardiff CF14 4XN, United Kingdom
| | - Barbara Szomolay
- Division of Infection and Immunity and Systems Immunity Research Institute, Cardiff University, Cardiff CF14 4XN, United Kingdom
| | - Tim Elliott
- Institute for Life Sciences, University of Southampton, Southampton SO17 1BJ, United Kingdom
- Centre for Cancer Immunology, University of Southampton, Faculty of Medicine, University Hospital, Southampton SO16 6YD, United Kingdom
| | - Andrew K Sewell
- Division of Infection and Immunity and Systems Immunity Research Institute, Cardiff University, Cardiff CF14 4XN, United Kingdom
| | - Awen Gallimore
- Division of Infection and Immunity and Systems Immunity Research Institute, Cardiff University, Cardiff CF14 4XN, United Kingdom
| | - Pierre Rizkallah
- Division of Infection and Immunity and Systems Immunity Research Institute, Cardiff University, Cardiff CF14 4XN, United Kingdom
| | - David K Cole
- Division of Infection and Immunity and Systems Immunity Research Institute, Cardiff University, Cardiff CF14 4XN, United Kingdom
| | - Andrew Godkin
- Division of Infection and Immunity and Systems Immunity Research Institute, Cardiff University, Cardiff CF14 4XN, United Kingdom
- Department of Gastroenterology and Hepatology, University Hospital of Wales, CF14 4XN Cardiff, United Kingdom
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12
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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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13
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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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14
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Costa-Nunes C, Cachot A, Bobisse S, Arnaud M, Genolet R, Baumgaertner P, Speiser DE, Sousa Alves PM, Sandoval F, Adotévi O, Reith W, Protti MP, Coukos G, Harari A, Romero P, Jandus C. High-throughput Screening of Human Tumor Antigen-specific CD4 T Cells, Including Neoantigen-reactive T Cells. Clin Cancer Res 2019; 25:4320-4331. [PMID: 31015344 DOI: 10.1158/1078-0432.ccr-18-1356] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2018] [Revised: 09/20/2018] [Accepted: 04/17/2019] [Indexed: 11/16/2022]
Abstract
PURPOSE Characterization of tumor antigen-specific CD4 T-cell responses in healthy donors and malignant melanoma patients using an in vitro amplified T-cell library screening procedure. PATIENTS AND METHODS A high-throughput, human leukocyte antigen (HLA)-independent approach was used to estimate at unprecedented high sensitivity level precursor frequencies of tumor antigen- and neoantigen-specific CD4 T cells in healthy donors and patients with cancer. Frequency estimation was combined with isolation and functional characterization of identified tumor-reactive CD4 T-cell clones. RESULTS In healthy donors, we report frequencies of naïve tumor-associated antigen (TAA)-specific CD4 T cells comparable with those of CD4 T cells specific for infectious agents (Tetanus toxoid). Interestingly, we also identified low, but consistent numbers of memory CD4 T cells specific for several TAAs. In patients with melanoma, low frequencies of circulating TAA-specific CD4 T cells were detected that increased after peptide-based immunotherapy. Such antitumor TAA-specific CD4 T-cell responses were also detectable within the tumor-infiltrated tissues. TAA-specific CD4 T cells in patients displayed a highly polyfunctional state, with partial skewing to Type-2 polarization. Finally, we report the applicability of this approach to the detection and amplification of neoantigen-specific CD4 T cells. CONCLUSIONS This simple, noninvasive, high-throughput screening of tumor- and neoantigen-specific CD4 T cells requires little biologic material, is HLA class II independent and allows the concomitant screening for a large number of tumor antigens of interest, including neoantigens. This approach will facilitate the immunomonitoring of preexisting and therapy-induced CD4 T-cell responses, and accelerate the development of CD4 T-cell-based therapies.
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Affiliation(s)
- Carla Costa-Nunes
- Department of Oncology UNIL CHUV, University of Lausanne, Lausanne, Switzerland
| | - Amélie Cachot
- Ludwig Institute for Cancer Research and Department of Oncology, University of Lausanne, Lausanne, Switzerland
| | - Sara Bobisse
- Ludwig Institute for Cancer Research and Department of Oncology, University of Lausanne, Lausanne, Switzerland
| | - Marion Arnaud
- Ludwig Institute for Cancer Research and Department of Oncology, University of Lausanne, Lausanne, Switzerland
| | - Raphael Genolet
- Ludwig Institute for Cancer Research and Department of Oncology, University of Lausanne, Lausanne, Switzerland
| | - Petra Baumgaertner
- Department of Oncology UNIL CHUV, University of Lausanne, Lausanne, Switzerland
| | - Daniel E Speiser
- Department of Oncology UNIL CHUV, University of Lausanne, Lausanne, Switzerland
| | | | | | - Olivier Adotévi
- University Bourgogne Franche-Comté, INSERM, EFS BFC, UMR1098, Besançon, France
| | - Walter Reith
- Department of Pathology and Immunology, Faculty of Medicine, University of Geneva, Geneva, Switzerland
| | - Maria Pia Protti
- Tumor Immunology Unit, Division of Immunology, Transplantation and Infectious Diseases, San Raffaele Scientific Institute, Milan, Italy
| | - George Coukos
- Ludwig Institute for Cancer Research and Department of Oncology, University of Lausanne, Lausanne, Switzerland
| | - Alexandre Harari
- Ludwig Institute for Cancer Research and Department of Oncology, University of Lausanne, Lausanne, Switzerland
| | - Pedro Romero
- Department of Oncology UNIL CHUV, University of Lausanne, Lausanne, Switzerland.
| | - Camilla Jandus
- Ludwig Institute for Cancer Research and Department of Oncology, University of Lausanne, Lausanne, Switzerland.
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15
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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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16
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Conserved peptide vaccine candidates containing multiple Ebola nucleoprotein epitopes display interactions with diverse HLA molecules. Med Microbiol Immunol 2019; 208:227-238. [DOI: 10.1007/s00430-019-00584-y] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2018] [Accepted: 02/11/2019] [Indexed: 10/27/2022]
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17
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Sauna ZE, Lagassé D, Pedras-Vasconcelos J, Golding B, Rosenberg AS. Evaluating and Mitigating the Immunogenicity of Therapeutic Proteins. Trends Biotechnol 2018; 36:1068-1084. [DOI: 10.1016/j.tibtech.2018.05.008] [Citation(s) in RCA: 45] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2018] [Revised: 05/18/2018] [Accepted: 05/22/2018] [Indexed: 12/19/2022]
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18
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Rius C, Attaf M, Tungatt K, Bianchi V, Legut M, Bovay A, Donia M, Thor Straten P, Peakman M, Svane IM, Ott S, Connor T, Szomolay B, Dolton G, Sewell AK. Peptide-MHC Class I Tetramers Can Fail To Detect Relevant Functional T Cell Clonotypes and Underestimate Antigen-Reactive T Cell Populations. THE JOURNAL OF IMMUNOLOGY 2018; 200:2263-2279. [PMID: 29483360 PMCID: PMC5857646 DOI: 10.4049/jimmunol.1700242] [Citation(s) in RCA: 58] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/16/2017] [Accepted: 01/29/2018] [Indexed: 12/01/2022]
Abstract
Peptide-MHC (pMHC) multimers, usually used as streptavidin-based tetramers, have transformed the study of Ag-specific T cells by allowing direct detection, phenotyping, and enumeration within polyclonal T cell populations. These reagents are now a standard part of the immunology toolkit and have been used in many thousands of published studies. Unfortunately, the TCR-affinity threshold required for staining with standard pMHC multimer protocols is higher than that required for efficient T cell activation. This discrepancy makes it possible for pMHC multimer staining to miss fully functional T cells, especially where low-affinity TCRs predominate, such as in MHC class II–restricted responses or those directed against self-antigens. Several recent, somewhat alarming, reports indicate that pMHC staining might fail to detect the majority of functional T cells and have prompted suggestions that T cell immunology has become biased toward the type of cells amenable to detection with multimeric pMHC. We use several viral- and tumor-specific pMHC reagents to compare populations of human T cells stained by standard pMHC protocols and optimized protocols that we have developed. Our results confirm that optimized protocols recover greater populations of T cells that include fully functional T cell clonotypes that cannot be stained by regular pMHC-staining protocols. These results highlight the importance of using optimized procedures that include the use of protein kinase inhibitor and Ab cross-linking during staining to maximize the recovery of Ag-specific T cells and serve to further highlight that many previous quantifications of T cell responses with pMHC reagents are likely to have considerably underestimated the size of the relevant populations.
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Affiliation(s)
- Cristina Rius
- Division of Infection and Immunity, Cardiff University School of Medicine, University Hospital Wales, Cardiff CF14 4XN, United Kingdom
| | - Meriem Attaf
- Division of Infection and Immunity, Cardiff University School of Medicine, University Hospital Wales, Cardiff CF14 4XN, United Kingdom
| | - Katie Tungatt
- Division of Infection and Immunity, Cardiff University School of Medicine, University Hospital Wales, Cardiff CF14 4XN, United Kingdom
| | - Valentina Bianchi
- Division of Infection and Immunity, Cardiff University School of Medicine, University Hospital Wales, Cardiff CF14 4XN, United Kingdom
| | - Mateusz Legut
- Division of Infection and Immunity, Cardiff University School of Medicine, University Hospital Wales, Cardiff CF14 4XN, United Kingdom
| | - Amandine Bovay
- Division of Infection and Immunity, Cardiff University School of Medicine, University Hospital Wales, Cardiff CF14 4XN, United Kingdom.,Department of Oncology and Ludwig Cancer Research, Lausanne University Hospital, Epalinges VD 1066, Switzerland
| | - Marco Donia
- Centre for Cancer Immune Therapy, Herlev University Hospital, DK-2730 Herlev, Denmark
| | - Per Thor Straten
- Centre for Cancer Immune Therapy, Herlev University Hospital, DK-2730 Herlev, Denmark
| | - Mark Peakman
- Department of Immunobiology, Guy's Hospital, King's College London, London SE1 9RT, United Kingdom
| | - Inge Marie Svane
- Centre for Cancer Immune Therapy, Herlev University Hospital, DK-2730 Herlev, Denmark
| | - Sascha Ott
- Department of Computer Science, University of Warwick, Coventry CV4 7AL, United Kingdom
| | - Tom Connor
- Systems Immunity Research Institute, Cardiff University School of Medicine, University Hospital Wales, Cardiff CF14 4XN, United Kingdom; and.,Cardiff University School of Biosciences, Cardiff CF10 3AX, United Kingdom
| | - Barbara Szomolay
- Division of Infection and Immunity, Cardiff University School of Medicine, University Hospital Wales, Cardiff CF14 4XN, United Kingdom
| | - Garry Dolton
- Division of Infection and Immunity, Cardiff University School of Medicine, University Hospital Wales, Cardiff CF14 4XN, United Kingdom
| | - Andrew K Sewell
- Division of Infection and Immunity, Cardiff University School of Medicine, University Hospital Wales, Cardiff CF14 4XN, United Kingdom; .,Systems Immunity Research Institute, Cardiff University School of Medicine, University Hospital Wales, Cardiff CF14 4XN, United Kingdom; and
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19
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Jones N, Cronin JG, Dolton G, Panetti S, Schauenburg AJ, Galloway SAE, Sewell AK, Cole DK, Thornton CA, Francis NJ. Metabolic Adaptation of Human CD4 + and CD8 + T-Cells to T-Cell Receptor-Mediated Stimulation. Front Immunol 2017; 8:1516. [PMID: 29170670 PMCID: PMC5684100 DOI: 10.3389/fimmu.2017.01516] [Citation(s) in RCA: 56] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2017] [Accepted: 10/26/2017] [Indexed: 02/02/2023] Open
Abstract
Linking immunometabolic adaptation to T-cell function provides insight for the development of new therapeutic approaches in multiple disease settings. T-cell activation and downstream effector functions of CD4+ and CD8+ T-cells are controlled by the strength of interaction between the T-cell receptor (TCR) and peptides presented by human leukocyte antigens (pHLA). The role of TCR–pHLA interactions in modulating T-cell metabolism is unknown. Here, for the first time, we explore the relative contributions of the main metabolic pathways to functional responses in human CD4+ and CD8+ T-cells. Increased expression of hexokinase II accompanied by higher basal glycolysis is demonstrated in CD4+ T-cells; cytokine production in CD8+ T-cells is more reliant on oxidative phosphorylation. Using antigen-specific CD4+ and CD8+ T-cell clones and altered peptide ligands, we demonstrate that binding affinity tunes the underlying metabolic shift. Overall, this study provides important new insight into how metabolic pathways are controlled during antigen-specific activation of human T-cells.
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Affiliation(s)
- Nicholas Jones
- Institute of Life Science, Medical School, Swansea University, Swansea, United Kingdom
| | - James G Cronin
- Institute of Life Science, Medical School, Swansea University, Swansea, United Kingdom
| | - Garry Dolton
- Cardiff University School of Medicine, Cardiff, United Kingdom
| | - Silvia Panetti
- Institute of Life Science, Medical School, Swansea University, Swansea, United Kingdom
| | | | | | - Andrew K Sewell
- Cardiff University School of Medicine, Cardiff, United Kingdom
| | - David K Cole
- Cardiff University School of Medicine, Cardiff, United Kingdom
| | - Catherine A Thornton
- Institute of Life Science, Medical School, Swansea University, Swansea, United Kingdom
| | - Nigel J Francis
- Institute of Life Science, Medical School, Swansea University, Swansea, United Kingdom
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20
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Martin SD, Wick DA, Nielsen JS, Little N, Holt RA, Nelson BH. A library-based screening method identifies neoantigen-reactive T cells in peripheral blood prior to relapse of ovarian cancer. Oncoimmunology 2017; 7:e1371895. [PMID: 29296522 PMCID: PMC5739566 DOI: 10.1080/2162402x.2017.1371895] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2017] [Revised: 08/18/2017] [Accepted: 08/19/2017] [Indexed: 12/22/2022] Open
Abstract
Mutated cancer antigens, or neoantigens, represent compelling immunological targets and appear to underlie the success of several forms of immunotherapy. While there are anecdotal reports of neoantigen-specific T cells being present in the peripheral blood and/or tumors of cancer patients, effective adoptive cell therapy (ACT) against neoantigens will require reliable methods to isolate and expand rare, neoantigen-specific T cells from clinically available biospecimens, ideally prior to clinical relapse. Here, we addressed this need using “mini-lines”, large libraries of parallel T cell cultures, each originating from only 2,000 T cells. Using small quantities of peripheral blood from multiple time points in an ovarian cancer patient, we screened over 3.3 × 106 CD8+ T cells by ELISPOT for recognition of peptides corresponding to the full complement of somatic mutations (n = 37) from the patient's tumor. We identified ten T cell lines which collectively recognized peptides encoding five distinct mutations. Six of the ten T cell lines recognized a previously described neoantigen from this patient (HSDL1L25V), whereas the remaining four lines recognized peptides corresponding to four other mutations. Only the HSDL1L25V-specific T cell lines recognized autologous tumor. HSDL1L25V-specific T cells comprised at least three distinct clonotypes and could be identified and expanded from peripheral blood 3–9 months prior to the first tumor recurrence. These T cells became undetectable at later time points, underscoring the dynamic nature of the response. Thus, neoantigen-specific T cells can be expanded from small volumes of blood during tumor remission, making pre-emptive ACT a plausible clinical strategy.
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Affiliation(s)
- Spencer D Martin
- Department of Medical Genetics, University of British Columbia, Vancouver, British Columbia, Canada.,Trev and Joyce Deeley Research Centre, British Columbia Cancer Agency, Victoria, British Columbia, Canada.,Michael Smith's Genome Sciences Centre, British Columbia Cancer Agency, Vancouver, British Columbia, Canada
| | - Darin A Wick
- Trev and Joyce Deeley Research Centre, British Columbia Cancer Agency, Victoria, British Columbia, Canada
| | - Julie S Nielsen
- Trev and Joyce Deeley Research Centre, British Columbia Cancer Agency, Victoria, British Columbia, Canada
| | - Nicole Little
- Trev and Joyce Deeley Research Centre, British Columbia Cancer Agency, Victoria, British Columbia, Canada.,Department of Biochemistry and Microbiology, University of Victoria, Victoria, British Columbia, Canada
| | - Robert A Holt
- Department of Medical Genetics, University of British Columbia, Vancouver, British Columbia, Canada.,Michael Smith's Genome Sciences Centre, British Columbia Cancer Agency, Vancouver, British Columbia, Canada.,Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, British Columbia, Canada
| | - Brad H Nelson
- Department of Medical Genetics, University of British Columbia, Vancouver, British Columbia, Canada.,Trev and Joyce Deeley Research Centre, British Columbia Cancer Agency, Victoria, British Columbia, Canada.,Department of Biochemistry and Microbiology, University of Victoria, Victoria, British Columbia, Canada
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21
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Parvathaneni K, Abdeladhim M, Pratt KP, Scott DW. Hemophilia A inhibitor treatment: the promise of engineered T-cell therapy. Transl Res 2017; 187. [PMID: 28651073 PMCID: PMC5582018 DOI: 10.1016/j.trsl.2017.06.002] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Hemophilia A is a bleeding disorder caused by mutations in the gene encoding factor VIII (FVIII), a cofactor protein that is essential for normal blood clotting. Approximately, 1 in 3 patients with severe hemophilia A produce neutralizing antibodies (inhibitors) that block its biologic function in the clotting cascade. Current efforts to eliminate inhibitors consist of repeated FVIII injections under what is termed an "ITI" protocol (Immune Tolerance Induction). However, this method is extremely costly and approximately 30% of patients undergoing ITI do not achieve peripheral tolerance. Human T regulatory cells (Tregs) have been proposed as a new strategy to treat this antidrug antibody response, as well as other diseases. Polyclonal Tregs are nonspecific and could potentially cause general immunosuppression. Novel approaches to induce tolerance to FVIII include the use of engineered human and mouse antigen-specific Tregs, or alternatively antigen-specific cytotoxic cells, to delete, anergize, or kill FVIII-specific lymphocytes. In this review, we discuss the current state of engineered T-cell therapies, and we describe the recent progress in applying these therapies to induce FVIII-specific tolerance.
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Affiliation(s)
- Kalpana Parvathaneni
- Department of Medicine, Uniformed Services University of Health Sciences, Bethesda, Md
| | - Maha Abdeladhim
- Department of Medicine, Uniformed Services University of Health Sciences, Bethesda, Md
| | - Kathleen P Pratt
- Department of Medicine, Uniformed Services University of Health Sciences, Bethesda, Md
| | - David W Scott
- Department of Medicine, Uniformed Services University of Health Sciences, Bethesda, Md.
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