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Han Y, Yang Y, Tian Y, Fattah FJ, von Itzstein MS, Hu Y, Zhang M, Kang X, Yang DM, Liu J, Xue Y, Liang C, Raman I, Zhu C, Xiao O, Dowell JE, Homsi J, Rashdan S, Yang S, Gwin ME, Hsiehchen D, Gloria-McCutchen Y, Pan K, Wu F, Gibbons D, Wang X, Yee C, Huang J, Reuben A, Cheng C, Zhang J, Gerber DE, Wang T. pan-MHC and cross-Species Prediction of T Cell Receptor-Antigen Binding. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.12.01.569599. [PMID: 38105939 PMCID: PMC10723300 DOI: 10.1101/2023.12.01.569599] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/19/2023]
Abstract
Profiling the binding of T cell receptors (TCRs) of T cells to antigenic peptides presented by MHC proteins is one of the most important unsolved problems in modern immunology. Experimental methods to probe TCR-antigen interactions are slow, labor-intensive, costly, and yield moderate throughput. To address this problem, we developed pMTnet-omni, an Artificial Intelligence (AI) system based on hybrid protein sequence and structure information, to predict the pairing of TCRs of αβ T cells with peptide-MHC complexes (pMHCs). pMTnet-omni is capable of handling peptides presented by both class I and II pMHCs, and capable of handling both human and mouse TCR-pMHC pairs, through information sharing enabled this hybrid design. pMTnet-omni achieves a high overall Area Under the Curve of Receiver Operator Characteristics (AUROC) of 0.888, which surpasses competing tools by a large margin. We showed that pMTnet-omni can distinguish binding affinity of TCRs with similar sequences. Across a range of datasets from various biological contexts, pMTnet-omni characterized the longitudinal evolution and spatial heterogeneity of TCR-pMHC interactions and their functional impact. We successfully developed a biomarker based on pMTnet-omni for predicting immune-related adverse events of immune checkpoint inhibitor (ICI) treatment in a cohort of 57 ICI-treated patients. pMTnet-omni represents a major advance towards developing a clinically usable AI system for TCR-pMHC pairing prediction that can aid the design and implementation of TCR-based immunotherapeutics.
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2
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Shah RK, Cygan E, Kozlik T, Colina A, Zamora AE. Utilizing immunogenomic approaches to prioritize targetable neoantigens for personalized cancer immunotherapy. Front Immunol 2023; 14:1301100. [PMID: 38149253 PMCID: PMC10749952 DOI: 10.3389/fimmu.2023.1301100] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2023] [Accepted: 11/29/2023] [Indexed: 12/28/2023] Open
Abstract
Advancements in sequencing technologies and bioinformatics algorithms have expanded our ability to identify tumor-specific somatic mutation-derived antigens (neoantigens). While recent studies have shown neoantigens to be compelling targets for cancer immunotherapy due to their foreign nature and high immunogenicity, the need for increasingly accurate and cost-effective approaches to rapidly identify neoantigens remains a challenging task, but essential for successful cancer immunotherapy. Currently, gene expression analysis and algorithms for variant calling can be used to generate lists of mutational profiles across patients, but more care is needed to curate these lists and prioritize the candidate neoantigens most capable of inducing an immune response. A growing amount of evidence suggests that only a handful of somatic mutations predicted by mutational profiling approaches act as immunogenic neoantigens. Hence, unbiased screening of all candidate neoantigens predicted by Whole Genome Sequencing/Whole Exome Sequencing may be necessary to more comprehensively access the full spectrum of immunogenic neoepitopes. Once putative cancer neoantigens are identified, one of the largest bottlenecks in translating these neoantigens into actionable targets for cell-based therapies is identifying the cognate T cell receptors (TCRs) capable of recognizing these neoantigens. While many TCR-directed screening and validation assays have utilized bulk samples in the past, there has been a recent surge in the number of single-cell assays that provide a more granular understanding of the factors governing TCR-pMHC interactions. The goal of this review is to provide an overview of existing strategies to identify candidate neoantigens using genomics-based approaches and methods for assessing neoantigen immunogenicity. Additionally, applications, prospects, and limitations of some of the current single-cell technologies will be discussed. Finally, we will briefly summarize some of the recent models that have been used to predict TCR antigen specificity and analyze the TCR receptor repertoire.
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Affiliation(s)
- Ravi K. Shah
- Department of Medicine, Medical College of Wisconsin, Milwaukee, WI, United States
| | - Erin Cygan
- Department of Microbiology and Immunology, Medical College of Wisconsin, Milwaukee, WI, United States
| | - Tanya Kozlik
- Department of Medicine, Medical College of Wisconsin, Milwaukee, WI, United States
| | - Alfredo Colina
- Department of Microbiology and Immunology, Medical College of Wisconsin, Milwaukee, WI, United States
| | - Anthony E. Zamora
- Department of Medicine, Medical College of Wisconsin, Milwaukee, WI, United States
- Department of Microbiology and Immunology, Medical College of Wisconsin, Milwaukee, WI, United States
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3
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Manfredi F, Stasi L, Buonanno S, Marzuttini F, Noviello M, Mastaglio S, Abbati D, Potenza A, Balestrieri C, Cianciotti BC, Tassi E, Feola S, Toffalori C, Punta M, Magnani Z, Camisa B, Tiziano E, Lupo-Stanghellini MT, Branca RM, Lehtiö J, Sikanen TM, Haapala MJ, Cerullo V, Casucci M, Vago L, Ciceri F, Bonini C, Ruggiero E. Harnessing T cell exhaustion and trogocytosis to isolate patient-derived tumor-specific TCR. SCIENCE ADVANCES 2023; 9:eadg8014. [PMID: 38039364 PMCID: PMC10691777 DOI: 10.1126/sciadv.adg8014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/22/2023] [Accepted: 11/02/2023] [Indexed: 12/03/2023]
Abstract
To study and then harness the tumor-specific T cell dynamics after allogeneic hematopoietic stem cell transplant, we typed the frequency, phenotype, and function of lymphocytes directed against tumor-associated antigens (TAAs) in 39 consecutive transplanted patients, for 1 year after transplant. We showed that TAA-specific T cells circulated in 90% of patients but display a limited effector function associated to an exhaustion phenotype, particularly in the subgroup of patients deemed to relapse, where exhausted stem cell memory T cells accumulated. Accordingly, cancer-specific cytolytic functions were relevant only when the TAA-specific T cell receptors (TCRs) were transferred into healthy, genome-edited T cells. We then exploited trogocytosis and ligandome-on-chip technology to unveil the specificities of tumor-specific TCRs retrieved from the exhausted T cell pool. Overall, we showed that harnessing circulating TAA-specific and exhausted T cells allow to isolate TCRs against TAAs and previously not described acute myeloid leukemia antigens, potentially relevant for T cell-based cancer immunotherapy.
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Affiliation(s)
- Francesco Manfredi
- IRCCS San Raffaele Scientific Institute, Division of Immunology, Transplantation, and Infectious Diseases, Experimental Hematology Unit, via Olgettina 60, Milan 20132, Italy
| | - Lorena Stasi
- IRCCS San Raffaele Scientific Institute, Division of Immunology, Transplantation, and Infectious Diseases, Experimental Hematology Unit, via Olgettina 60, Milan 20132, Italy
| | - Silvia Buonanno
- IRCCS San Raffaele Scientific Institute, Division of Immunology, Transplantation, and Infectious Diseases, Experimental Hematology Unit, via Olgettina 60, Milan 20132, Italy
| | - Francesca Marzuttini
- IRCCS San Raffaele Scientific Institute, Division of Immunology, Transplantation, and Infectious Diseases, Experimental Hematology Unit, via Olgettina 60, Milan 20132, Italy
| | - Maddalena Noviello
- IRCCS San Raffaele Scientific Institute, Division of Immunology, Transplantation, and Infectious Diseases, Experimental Hematology Unit, via Olgettina 60, Milan 20132, Italy
| | - Sara Mastaglio
- IRCCS San Raffaele Scientific Institute, Hematology and Hematopoietic Stem Cell Transplantation Unit, via Olgettina 60, Milan 20132, Italy
| | - Danilo Abbati
- IRCCS San Raffaele Scientific Institute, Division of Immunology, Transplantation, and Infectious Diseases, Experimental Hematology Unit, via Olgettina 60, Milan 20132, Italy
| | - Alessia Potenza
- IRCCS San Raffaele Scientific Institute, Division of Immunology, Transplantation, and Infectious Diseases, Experimental Hematology Unit, via Olgettina 60, Milan 20132, Italy
| | - Chiara Balestrieri
- IRCCS San Raffaele Scientific Institute, Division of Immunology, Transplantation, and Infectious Diseases, Experimental Hematology Unit, via Olgettina 60, Milan 20132, Italy
- Center for Omics Sciences, IRCCS San Raffaele Scientific Institute, via Olgettina 60, Milan 20132, Italy
| | - Beatrice Claudia Cianciotti
- IRCCS San Raffaele Scientific Institute, Division of Immunology, Transplantation, and Infectious Diseases, Experimental Hematology Unit, via Olgettina 60, Milan 20132, Italy
| | - Elena Tassi
- IRCCS San Raffaele Scientific Institute, Division of Immunology, Transplantation, and Infectious Diseases, Experimental Hematology Unit, via Olgettina 60, Milan 20132, Italy
| | - Sara Feola
- University of Helsinki, ImmunoVirotherapy Lab, Yliopistonkatu 4, 00100 Helsinki, Finland
| | - Cristina Toffalori
- IRCCS San Raffaele Scientific Institute, Division of Immunology, Transplantation and Infectious Disease, Unit of Immunogenetics, Leukemia Genomics and Immunobiology, via Olgettina 60, Milan 20132, Italy
| | - Marco Punta
- Center for Omics Sciences, IRCCS San Raffaele Scientific Institute, via Olgettina 60, Milan 20132, Italy
- IRCCS San Raffaele Scientific Institute, Division of Immunology, Transplantation and Infectious Disease, Unit of Immunogenetics, Leukemia Genomics and Immunobiology, via Olgettina 60, Milan 20132, Italy
| | - Zulma Magnani
- IRCCS San Raffaele Scientific Institute, Division of Immunology, Transplantation, and Infectious Diseases, Experimental Hematology Unit, via Olgettina 60, Milan 20132, Italy
| | - Barbara Camisa
- IRCCS San Raffaele Scientific Institute, Division of Immunology, Transplantation, and Infectious Diseases, Experimental Hematology Unit, via Olgettina 60, Milan 20132, Italy
| | - Elena Tiziano
- IRCCS San Raffaele Scientific Institute, Division of Immunology, Transplantation, and Infectious Diseases, Experimental Hematology Unit, via Olgettina 60, Milan 20132, Italy
| | - Maria Teresa Lupo-Stanghellini
- IRCCS San Raffaele Scientific Institute, Hematology and Hematopoietic Stem Cell Transplantation Unit, via Olgettina 60, Milan 20132, Italy
| | - Rui Mamede Branca
- Science for Life Laboratory, Department of Oncology-Pathology, Karolinska Institute, 171 65 Solna, Sweden
| | - Janne Lehtiö
- Science for Life Laboratory, Department of Oncology-Pathology, Karolinska Institute, 171 65 Solna, Sweden
| | - Tiina M. Sikanen
- Drug Research Program, Faculty of Pharmacy, Division of Pharmaceutical Chemistry and Technology, Helsinki University,, Viikinkaari 5E, 00014 Helsinki, Finland
| | - Markus J. Haapala
- Drug Research Program, Faculty of Pharmacy, Division of Pharmaceutical Chemistry and Technology, Helsinki University,, Viikinkaari 5E, 00014 Helsinki, Finland
| | - Vincenzo Cerullo
- University of Helsinki, ImmunoVirotherapy Lab, Yliopistonkatu 4, 00100 Helsinki, Finland
| | - Monica Casucci
- IRCCS San Raffaele Scientific Institute, Division of Immunology, Transplantation and Infectious Disease, Innovative Immunotherapies Unit, via Olgettina 60, Milan 20132, Italy
| | - Luca Vago
- IRCCS San Raffaele Scientific Institute, Hematology and Hematopoietic Stem Cell Transplantation Unit, via Olgettina 60, Milan 20132, Italy
- IRCCS San Raffaele Scientific Institute, Division of Immunology, Transplantation and Infectious Disease, Unit of Immunogenetics, Leukemia Genomics and Immunobiology, via Olgettina 60, Milan 20132, Italy
- Vita Salute San Raffaele University, Milan, Italy
| | - Fabio Ciceri
- IRCCS San Raffaele Scientific Institute, Hematology and Hematopoietic Stem Cell Transplantation Unit, via Olgettina 60, Milan 20132, Italy
- IRCCS San Raffaele Scientific Institute, Division of Immunology, Transplantation and Infectious Disease, Innovative Immunotherapies Unit, via Olgettina 60, Milan 20132, Italy
| | - Chiara Bonini
- IRCCS San Raffaele Scientific Institute, Division of Immunology, Transplantation, and Infectious Diseases, Experimental Hematology Unit, via Olgettina 60, Milan 20132, Italy
- IRCCS San Raffaele Scientific Institute, Division of Immunology, Transplantation and Infectious Disease, Innovative Immunotherapies Unit, via Olgettina 60, Milan 20132, Italy
| | - Eliana Ruggiero
- IRCCS San Raffaele Scientific Institute, Division of Immunology, Transplantation, and Infectious Diseases, Experimental Hematology Unit, via Olgettina 60, Milan 20132, Italy
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Mahata D, Mukherjee D, Biswas D, Basak S, Basak AJ, Jamir I, Pandey N, Khatoon H, Samanta D, Basak A, Mukherjee G. Activation and differentiation of cognate T cells by a dextran-based antigen-presenting system for cancer immunotherapy. Eur J Immunol 2023; 53:e2350528. [PMID: 37698527 DOI: 10.1002/eji.202350528] [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: 04/14/2023] [Revised: 08/14/2023] [Accepted: 09/11/2023] [Indexed: 09/13/2023]
Abstract
Immunotherapeutic modulation of antigen-specific T-cell responses instead of the whole repertoire helps avoid immune-related adverse events. We have developed an artificial antigen-presenting system (aAPS) where multiple copies of a multimeric peptide-MHC class I complex presenting a murine class I MHC restricted ovalbumin-derived peptide (signal 1), along with a costimulatory ligand (signal 2) are chemically conjugated to a dextran backbone. Cognate naive CD8+ T cells, when treated with this aAPS underwent significant expansion and showed an activated phenotype. Furthermore, elevated expression of effector cytokines led to the differentiation of these cells to cytotoxic T lymphocytes which resulted in target cell lysis, indicative of the functional efficacy of the aAPS. CD8+ T cells with decreased proliferative potential due to repeated antigenic stimulation could also be re-expanded by the developed aAPS. Thus, the developed aAPS warrants further engineering for future application as a rapidly customizable personalized immunotherapeutic agent, incorporating patient-specific MHC-restricted tumor antigens and different costimulatory signals to modulate both naive and antigen-experienced but exhausted tumor-specific T cells in cancer.
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Affiliation(s)
- Dhrubajyoti Mahata
- School of Medical Science and Technology, Indian Institute of Technology Kharagpur, Kharagpur, West Bengal, India
- School of Bioscience, Indian Institute of Technology Kharagpur, Kharagpur, West Bengal, India
| | - Debangshu Mukherjee
- School of Medical Science and Technology, Indian Institute of Technology Kharagpur, Kharagpur, West Bengal, India
| | - Debarati Biswas
- School of Medical Science and Technology, Indian Institute of Technology Kharagpur, Kharagpur, West Bengal, India
| | - Shyam Basak
- Department of Chemistry, Indian Institute of Technology Kharagpur, Kharagpur, West Bengal, India
| | - Aditya Jyoti Basak
- School of Bioscience, Indian Institute of Technology Kharagpur, Kharagpur, West Bengal, India
| | - Imlilong Jamir
- School of Medical Science and Technology, Indian Institute of Technology Kharagpur, Kharagpur, West Bengal, India
| | - Nidhi Pandey
- School of Medical Science and Technology, Indian Institute of Technology Kharagpur, Kharagpur, West Bengal, India
| | - Huma Khatoon
- Department of Chemistry, Indian Institute of Technology Kharagpur, Kharagpur, West Bengal, India
| | - Dibyendu Samanta
- School of Bioscience, Indian Institute of Technology Kharagpur, Kharagpur, West Bengal, India
| | - Amit Basak
- Department of Chemical Sciences, Indian Institute of Science Education and Research Kolkata, Mohanpur, West Bengal, India
| | - Gayatri Mukherjee
- School of Medical Science and Technology, Indian Institute of Technology Kharagpur, Kharagpur, West Bengal, India
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Hammond EM, Olsen KJ, Ram S, Tran GVV, Hall LS, Bradley JE, Lund FE, Samuels DS, Baumgarth N. Antigen-Specific CD4 T Cell and B Cell Responses to Borrelia burgdorferi. JOURNAL OF IMMUNOLOGY (BALTIMORE, MD. : 1950) 2023; 211:994-1005. [PMID: 37556156 PMCID: PMC10530202 DOI: 10.4049/jimmunol.2200890] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/05/2022] [Accepted: 07/18/2023] [Indexed: 08/10/2023]
Abstract
Long-lived T-dependent B cell responses fail to develop during persistent infection of mice with Borrelia burgdorferi, the causative agent of Lyme disease, raising questions about the induction and/or functionality of anti-B. burgdorferi adaptive immune responses. Yet, a lack of reagents has limited investigations into B. burgdorferi-specific T and B cells. We attempted two approaches to track B. burgdorferi-induced CD4 T cells. First, a B. burgdorferi mutant was generated with an influenza hemagglutinin (HA) peptide, HA111-119, inserted into the B. burgdorferi arthritis-related protein (Arp) locus. Although this B. burgdorferi arp::HA strain remained infectious, peptide-specific TCR transgenic CD4 T cells in vitro, or adoptively transferred into B. burgdorferi arp::HA-infected BALB/c mice, did not clonally expand above those of recipients infected with the parental B. burgdorferi strain or a B. burgdorferi mutant containing an irrelevant peptide. Some expansion, however, occurred in B. burgdorferi arp::HA-infected BALB/c SCID mice. Second, a (to our knowledge) newly identified I-Ab-restricted CD4 T cell epitope, Arp152-166, was used to generate Arp MHC class II tetramers. Flow cytometry showed small numbers of Arp-specific CD4 T cells emerging in mice infected with B. burgdorferi but not with Arp-deficient Borrelia afzelii. Although up to 30% of Arp-specific CD4 T cells were ICOS+PD-1+CXCR5+BCL6+ T follicular helper cells, their numbers declined after day 12, before germinal centers (GCs) are prominent. Although some Arp-specific B cells, identified using fluorochrome-labeled rArp proteins, had the phenotype of GC B cells, their frequencies did not correlate with anti-Arp serum IgG. The data suggest a failure not in the induction, but in the maintenance of GC T follicular helper and/or B cells to B. burgdorferi.
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Affiliation(s)
- Elizabeth M. Hammond
- Graduate Group in Immunology, University of California Davis
- Center for Immunology and Infectious Diseases, University of California Davis
- Department of Pathology, Microbiology, and Immunology, University of California Davis
| | - Kimberly J. Olsen
- Center for Immunology and Infectious Diseases, University of California Davis
- Department of Pathology, Microbiology, and Immunology, University of California Davis
| | - Shivneel Ram
- Center for Immunology and Infectious Diseases, University of California Davis
| | - Giang Vu Vi Tran
- Center for Immunology and Infectious Diseases, University of California Davis
- Department of Pathology, Microbiology, and Immunology, University of California Davis
| | - Laura S. Hall
- Division of Biological Sciences, University of Montana
| | - John E. Bradley
- Department of Microbiology, University of Alabama, Birmingham
| | - Frances E. Lund
- Department of Microbiology, University of Alabama, Birmingham
| | | | - Nicole Baumgarth
- Graduate Group in Immunology, University of California Davis
- Center for Immunology and Infectious Diseases, University of California Davis
- Department of Pathology, Microbiology, and Immunology, University of California Davis
- Department of Molecular Microbiology and Immunology and Department of Molecular and Comparative Pathobiology, Johns Hopkins University
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6
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Sugiyarto G, Lau D, Hill SL, Arcia-Anaya D, Boulanger DSM, Parkes EE, James E, Elliott T. Reactivation of low avidity tumor-specific CD8 + T cells associates with immunotherapeutic efficacy of anti-PD-1. J Immunother Cancer 2023; 11:e007114. [PMID: 37586767 PMCID: PMC10432680 DOI: 10.1136/jitc-2023-007114] [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] [Accepted: 07/31/2023] [Indexed: 08/18/2023] Open
Abstract
BACKGROUND CD8+ T cells are a highly diverse population of cells with distinct phenotypic functions that can influence immunotherapy outcomes. Further insights on the roles of CD8+ specificities and TCR avidity of naturally arising tumor-specific T cells, where both high and low avidity T cells recognizing the same peptide-major histocompatibility complex (pMHC) coexist in the same tumor, are crucial for understanding T cell exhaustion and resistance to PD-1 immunotherapy. METHODS CT26 models were treated with anti-PD-1 on days 3, 6 and 9 following subcutaneous tumor implantation generating variable responses during early tumor development. Tetramer staining was performed to determine the frequency and avidity of CD8+ T cells targeting the tumor-specific epitope GSW11 and confirmed with tetramer competition assays. Functional characterization of high and low avidity GSW11-specific CD8+ T cells was conducted using flow cytometry and bulk RNA-seq. In vitro cytotoxicity assays and in vivo adoptive transfer experiments were performed to determine the cytotoxicity of high and low avidity populations. RESULTS Treatment success with anti-PD-1 was associated with the preferential expansion of low avidity (Tetlo) GSW11-specific CD8+ T cells with Vβ TCR expressing clonotypes. High avidity T cells (Tethi), if present, were only found in progressing PD-1 refractory tumors. Tetlo demonstrated precursor exhausted or progenitor T cell phenotypes marked by higher expression of Tcf-1 and T-bet, and lower expression of the exhaustion markers CD39, PD-1 and Eomes compared with Tethi, whereas Tethi cells were terminally exhausted. Transcriptomics analyses showed pathways related to TCR signaling, cytotoxicity and oxidative phosphorylation were significantly enriched in Tetlo found in both regressing and progressing tumors compared with Tethi, whereas genes related to DNA damage, apoptosis and autophagy were downregulated. In vitro studies showed that Tetlo exhibits higher cytotoxicity than Tethi. Adoptive transfer of Tetlo showed more effective tumor control than Tethi, and curative responses were achieved when Tetlo was combined with two doses of anti-PD-1. CONCLUSIONS Targeting subdominant T cell responses with lower avidity against pMHC affinity neoepitopes showed potential for improving PD-1 immunotherapy. Future interventions may consider expanding low avidity populations via vaccination or adoptive transfer.
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Affiliation(s)
- Gessa Sugiyarto
- Centre for Cancer Immunology, Faculty of Medicine, University of Southampton, Southampton, UK
| | - Doreen Lau
- Centre for Immuno-Oncology, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Samuel Luke Hill
- Centre for Cancer Immunology, Faculty of Medicine, University of Southampton, Southampton, UK
| | - David Arcia-Anaya
- Centre for Immuno-Oncology, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Denise S M Boulanger
- Centre for Cancer Immunology, Faculty of Medicine, University of Southampton, Southampton, UK
| | - Eileen E Parkes
- Centre for Immuno-Oncology, Nuffield Department of Medicine, University of Oxford, Oxford, UK
- Department of Oncology, University of Oxford, Oxford, UK
| | - Edward James
- Centre for Cancer Immunology, Faculty of Medicine, University of Southampton, Southampton, UK
| | - Tim Elliott
- Centre for Cancer Immunology, Faculty of Medicine, University of Southampton, Southampton, UK
- Centre for Immuno-Oncology, Nuffield Department of Medicine, University of Oxford, Oxford, UK
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7
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Tippalagama R, Chihab LY, Kearns K, Lewis S, Panda S, Willemsen L, Burel JG, Lindestam Arlehamn CS. Antigen-specificity measurements are the key to understanding T cell responses. Front Immunol 2023; 14:1127470. [PMID: 37122719 PMCID: PMC10140422 DOI: 10.3389/fimmu.2023.1127470] [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: 12/19/2022] [Accepted: 03/30/2023] [Indexed: 05/02/2023] Open
Abstract
Antigen-specific T cells play a central role in the adaptive immune response and come in a wide range of phenotypes. T cell receptors (TCRs) mediate the antigen-specificities found in T cells. Importantly, high-throughput TCR sequencing provides a fingerprint which allows tracking of specific T cells and their clonal expansion in response to particular antigens. As a result, many studies have leveraged TCR sequencing in an attempt to elucidate the role of antigen-specific T cells in various contexts. Here, we discuss the published approaches to studying antigen-specific T cells and their specific TCR repertoire. Further, we discuss how these methods have been applied to study the TCR repertoire in various diseases in order to characterize the antigen-specific T cells involved in the immune control of disease.
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8
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Son ET, Paul-Heng M, Leong M, Wang C, Hill AE, Denkova M, Purcell AW, Mifsud NA, Sharland AF. Screening self-peptides for recognition by mouse alloreactive CD8 + T cells using direct ex vivo multimer staining. STAR Protoc 2023; 4:101943. [PMID: 36525346 PMCID: PMC9792548 DOI: 10.1016/j.xpro.2022.101943] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2022] [Revised: 10/31/2022] [Accepted: 11/24/2022] [Indexed: 12/23/2022] Open
Abstract
Here, we present a protocol to identify immunogenic self-peptide/allogeneic major histocompatibility complex (MHC) epitopes. We describe the generation of enriched alloreactive CD8+ T cells by priming mice with a skin graft expressing the allogeneic MHC class I molecule of interest, followed by boosting with a liver-specific AAV vector encoding the heavy chain of that donor MHC allomorph. We then use a peptide-exchange approach to assemble a range of peptide-MHC (pMHC) multimers for measuring recognition of the various epitopes by these alloreactive T cells. For complete details on the use and execution of this protocol, please refer to Son et al. (2021).1.
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Affiliation(s)
- Eric T Son
- Transplantation Immunobiology Group, University of Sydney Central Clinical School, Charles Perkins Centre, Faculty of Medicine and Health, Sydney, NSW 2006, Australia
| | - Moumita Paul-Heng
- Transplantation Immunobiology Group, University of Sydney Central Clinical School, Charles Perkins Centre, Faculty of Medicine and Health, Sydney, NSW 2006, Australia
| | - Mario Leong
- Transplantation Immunobiology Group, University of Sydney Central Clinical School, Charles Perkins Centre, Faculty of Medicine and Health, Sydney, NSW 2006, Australia
| | - Chuanmin Wang
- Transplantation Immunobiology Group, University of Sydney Central Clinical School, Charles Perkins Centre, Faculty of Medicine and Health, Sydney, NSW 2006, Australia
| | - Alexandra E Hill
- Transplantation Immunobiology Group, University of Sydney Central Clinical School, Charles Perkins Centre, Faculty of Medicine and Health, Sydney, NSW 2006, Australia
| | - Martina Denkova
- Transplantation Immunobiology Group, University of Sydney Central Clinical School, Charles Perkins Centre, Faculty of Medicine and Health, Sydney, NSW 2006, Australia
| | - Anthony W Purcell
- Infection and Immunity Program, Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, VIC 3800, Australia
| | - Nicole A Mifsud
- Infection and Immunity Program, Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, VIC 3800, Australia
| | - Alexandra F Sharland
- Transplantation Immunobiology Group, University of Sydney Central Clinical School, Charles Perkins Centre, Faculty of Medicine and Health, Sydney, NSW 2006, Australia.
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9
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Venema WJ, Hiddingh S, Janssen GMC, Ossewaarde-van Norel J, van Loon ND, de Boer JH, van Veelen PA, Kuiper JJW. Retina-arrestin specific CD8+ T cells are not implicated in HLA-A29-positive birdshot chorioretinitis. Clin Immunol 2023; 247:109219. [PMID: 36581221 DOI: 10.1016/j.clim.2022.109219] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2022] [Revised: 12/21/2022] [Accepted: 12/23/2022] [Indexed: 12/27/2022]
Abstract
BACKGROUND HLA-A29-positive birdshot chorioretinitis (BCR) is an inflammatory eye disorder that is generally assumed to be caused by an autoimmune response to HLA-A29-presented peptides from retinal arrestin (SAG), yet the epitopes recognized by CD8+ T cells from patients remain to be identified. OBJECTIVES The identification of natural ligands of SAG presented by HLA-A29. To quantify CD8+ T cells reactive to antigenic SAG peptides presented by HLA-A29 in patients and controls. METHODS We performed mass-spectrometry based immunopeptidomics of HLA-A29 of antigen-presenting cell lines from patients engineered to express SAG. MHC-I Dextramer technology was utilised to determine expansion of antigen-specific CD8+ T cells reactive to SAG peptides in complex with HLA-A29 in a cohort of BCR patients, HLA-A29-positive controls, and HLA-A29-negative controls. RESULTS We report on the naturally presented antigenic SAG peptides identified by sequencing the HLA-A29 immunopeptidome of antigen-presenting cells of patients. We show that the N-terminally extended SAG peptide precursors can be trimmed in vitro by the antigen-processing aminopeptidases ERAP1 and ERAP2. Unexpectedly, no enhanced antigen engagement by CD8+ T cells upon stimulation with SAG peptides was observed in patients or HLA-A29-positive controls. Multiplexed HLA-A29-peptide dextramer profiling of a case-control cohort revealed that CD8+ T cells specific for these SAG peptides were neither detectable in peripheral blood nor in eye biopsies of patients. CONCLUSIONS Collectively, these findings demonstrate that SAG is not a CD8+ T cell autoantigen and sharply contrast the paradigm in the pathogenesis of BCR. Therefore, the mechanism by which HLA-A29 is associated with BCR does not involve SAG.
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Affiliation(s)
- W J Venema
- Department of Ophthalmology, University Medical Center Utrecht, University of Utrecht, Utrecht, the Netherlands; Center for Translational Immunology, University Medical Center Utrecht, University of Utrecht, Utrecht, the Netherlands
| | - S Hiddingh
- Department of Ophthalmology, University Medical Center Utrecht, University of Utrecht, Utrecht, the Netherlands; Center for Translational Immunology, University Medical Center Utrecht, University of Utrecht, Utrecht, the Netherlands
| | - G M C Janssen
- Center for Proteomics and Metabolomics, Leiden University Medical Center, Leiden, the Netherlands
| | - J Ossewaarde-van Norel
- Department of Ophthalmology, University Medical Center Utrecht, University of Utrecht, Utrecht, the Netherlands
| | - N Dam van Loon
- Department of Ophthalmology, University Medical Center Utrecht, University of Utrecht, Utrecht, the Netherlands
| | - J H de Boer
- Department of Ophthalmology, University Medical Center Utrecht, University of Utrecht, Utrecht, the Netherlands
| | - P A van Veelen
- Center for Proteomics and Metabolomics, Leiden University Medical Center, Leiden, the Netherlands
| | - J J W Kuiper
- Department of Ophthalmology, University Medical Center Utrecht, University of Utrecht, Utrecht, the Netherlands; Center for Translational Immunology, University Medical Center Utrecht, University of Utrecht, Utrecht, the Netherlands.
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10
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Shepherd FR, Davies K, Miners KL, Llewellyn-Lacey S, Kollnberger S, Redman JE, Grant MM, Ladell K, Price DA, McLaren JE. The superantigens SpeC and TSST-1 specifically activate TRBV12-3/12-4 + memory T cells. Commun Biol 2023; 6:78. [PMID: 36670205 PMCID: PMC9854414 DOI: 10.1038/s42003-023-04420-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2021] [Accepted: 01/04/2023] [Indexed: 01/22/2023] Open
Abstract
Severe bacterial or viral infections can induce a state of immune hyperactivation that can culminate in a potentially lethal cytokine storm. The classic example is toxic shock syndrome, a life-threatening complication of Staphylococcus aureus or Streptococcus pyogenes infection, which is driven by potent toxins known as superantigens (SAgs). SAgs are thought to promote immune evasion via the promiscuous activation of T cells, which subsequently become hyporesponsive, and act by cross-linking major histocompatibility complex class II molecules on antigen-presenting cells to particular β-chain variable (TRBV) regions of αβ T cell receptors (TCRs). Although some of these interactions have been defined previously, our knowledge of SAg-responsive TRBV regions is incomplete. In this study, we found that CD4+ and CD8+ T cells expressing TRBV12-3/12-4+ TCRs were highly responsive to streptococcal pyrogenic exotoxin C (SpeC) and toxic shock syndrome toxin-1 (TSST-1). In particular, SpeC and TSST-1 specifically induced effector cytokine production and the upregulation of multiple coinhibitory receptors among TRBV12-3/12-4+ CD4+ and CD8+ memory T cells, and importantly, these biological responses were dependent on human leukocyte antigen (HLA)-DR. Collectively, these data provided evidence of functionally determinative and therapeutically relevant interactions between SpeC and TSST-1 and CD4+ and CD8+ memory T cells expressing TRBV12-3/12-4+ TCRs, mediated via HLA-DR.
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Affiliation(s)
- Freya R. Shepherd
- grid.5600.30000 0001 0807 5670Division of Infection and Immunity, School of Medicine, Cardiff University, Cardiff, UK
| | - Kate Davies
- grid.5600.30000 0001 0807 5670Division of Infection and Immunity, School of Medicine, Cardiff University, Cardiff, UK
| | - Kelly L. Miners
- grid.5600.30000 0001 0807 5670Division of Infection and Immunity, School of Medicine, Cardiff University, Cardiff, UK
| | - Sian Llewellyn-Lacey
- grid.5600.30000 0001 0807 5670Division of Infection and Immunity, School of Medicine, Cardiff University, Cardiff, UK
| | - Simon Kollnberger
- grid.5600.30000 0001 0807 5670Division of Infection and Immunity, School of Medicine, Cardiff University, Cardiff, UK
| | - James E. Redman
- grid.5600.30000 0001 0807 5670School of Chemistry, Cardiff University, Cardiff, UK
| | - Melissa M. Grant
- grid.6572.60000 0004 1936 7486School of Dentistry, Institute of Clinical Sciences, University of Birmingham, Birmingham, UK
| | - Kristin Ladell
- grid.5600.30000 0001 0807 5670Division of Infection and Immunity, School of Medicine, Cardiff University, Cardiff, UK
| | - David A. Price
- grid.5600.30000 0001 0807 5670Division of Infection and Immunity, School of Medicine, Cardiff University, Cardiff, UK ,grid.5600.30000 0001 0807 5670Systems Immunity Research Institute, School of Medicine, Cardiff University, Cardiff, UK
| | - James E. McLaren
- grid.5600.30000 0001 0807 5670Division of Infection and Immunity, School of Medicine, Cardiff University, Cardiff, UK
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11
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Multivalent binding kinetics resolved by fluorescence proximity sensing. Commun Biol 2022; 5:1070. [PMID: 36207490 PMCID: PMC9546861 DOI: 10.1038/s42003-022-03997-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2022] [Accepted: 09/14/2022] [Indexed: 11/12/2022] Open
Abstract
Multivalent protein interactors are an attractive modality for probing protein function and exploring novel pharmaceutical strategies. The throughput and precision of state-of-the-art methodologies and workflows for the effective development of multivalent binders is currently limited by surface immobilization, fluorescent labelling and sample consumption. Using the gephyrin protein, the master regulator of the inhibitory synapse, as benchmark, we exemplify the application of Fluorescence proximity sensing (FPS) for the systematic kinetic and thermodynamic optimization of multivalent peptide architectures. High throughput synthesis of +100 peptides with varying combinatorial dimeric, tetrameric, and octameric architectures combined with direct FPS measurements resolved on-rates, off-rates, and dissociation constants with high accuracy and low sample consumption compared to three complementary technologies. The dataset and its machine learning-based analysis deciphered the relationship of specific architectural features and binding kinetics and thereby identified binders with unprecedented protein inhibition capacity; thus, highlighting the value of FPS for the rational engineering of multivalent inhibitors. Fluorescence proximity sensing enables high throughput determination of binding affinities and kinetics of peptide inhibitors with varying valency and multivalent architecture.
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12
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Hartley GE, Edwards ESJ, O’Hehir RE, van Zelm MC. New insights into human immune memory from SARS-CoV-2 infection and vaccination. Allergy 2022; 77:3553-3566. [PMID: 36048132 PMCID: PMC9538469 DOI: 10.1111/all.15502] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2022] [Revised: 08/13/2022] [Accepted: 08/29/2022] [Indexed: 01/28/2023]
Abstract
Since early 2020, the world has been embroiled in an ongoing viral pandemic with SARS-CoV-2 and emerging variants resulting in mass morbidity and an estimated 6 million deaths globally. The scientific community pivoted rapidly, providing unique and innovative means to identify infected individuals, technologies to evaluate immune responses to infection and vaccination, and new therapeutic strategies to treat infected individuals. Never before has immunology been so critically at the forefront of combatting a global pandemic. It has now become evident that not just antibody responses, but formation and durability of immune memory cells following vaccination are associated with protection against severe disease from SARS-CoV-2 infection. Furthermore, the emergence of variants of concern (VoC) highlight the need for immunological markers to quantify the protective capacity of Wuhan-based vaccines. Thus, harnessing and modulating the immune response is key to successful vaccination and treatment of disease. We here review the latest knowledge about immune memory generation and durability following natural infection and vaccination, and provide insights into the attributes of immune memory that may protect from emerging variants.
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Affiliation(s)
- Gemma E. Hartley
- Allergy and Clinical Immunology Laboratory, Department of Immunology and Pathology, Central Clinical SchoolMonash UniversityMelbourneVictoriaAustralia
| | - Emily S. J. Edwards
- Allergy and Clinical Immunology Laboratory, Department of Immunology and Pathology, Central Clinical SchoolMonash UniversityMelbourneVictoriaAustralia
| | - Robyn E. O’Hehir
- Allergy and Clinical Immunology Laboratory, Department of Immunology and Pathology, Central Clinical SchoolMonash UniversityMelbourneVictoriaAustralia,Allergy, Asthma and Clinical Immunology ServiceAlfred HospitalMelbourneVictoriaAustralia
| | - Menno C. van Zelm
- Allergy and Clinical Immunology Laboratory, Department of Immunology and Pathology, Central Clinical SchoolMonash UniversityMelbourneVictoriaAustralia,Allergy, Asthma and Clinical Immunology ServiceAlfred HospitalMelbourneVictoriaAustralia
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13
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Biomarker correlates with response to NY-ESO-1 TCR T cells in patients with synovial sarcoma. Nat Commun 2022; 13:5296. [PMID: 36075914 PMCID: PMC9458750 DOI: 10.1038/s41467-022-32491-x] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2021] [Accepted: 08/01/2022] [Indexed: 11/16/2022] Open
Abstract
Autologous T cells transduced to express a high affinity T-cell receptor specific to NY-ESO-1 (letetresgene autoleucel, lete-cel) show promise in the treatment of metastatic synovial sarcoma, with 50% overall response rate. The efficacy of lete-cel treatment in 45 synovial sarcoma patients (NCT01343043) has been previously reported, however, biomarkers predictive of response and resistance remain to be better defined. This post-hoc analysis identifies associations of response to lete-cel with lymphodepleting chemotherapy regimen (LDR), product attributes, cell expansion, cytokines, and tumor gene expression. Responders have higher IL-15 levels pre-infusion (p = 0.011) and receive a higher number of transduced effector memory (CD45RA- CCR7-) CD8 + cells per kg (p = 0.039). Post-infusion, responders have increased IFNγ, IL-6, and peak cell expansion (p < 0.01, p < 0.01, and p = 0.016, respectively). Analysis of tumor samples post-treatment illustrates lete-cel infiltration and a decrease in expression of macrophage genes, suggesting remodeling of the tumor microenvironment. Here we report potential predictive and pharmacodynamic markers of lete-cel response that may inform LDR, cell dose, and strategies to enhance anticancer efficacy. Biomarkers predictive of response to T cell therapy remain to be better defined. This study identifies potential predictive and pharmacodynamic markers of response to NY-ESO-1 T-cell therapy in a solid tumor that may inform lymphodepletion, cell dose, and strategies to enhance anticancer efficacy.
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14
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Souter MN, Awad W, Li S, Pediongco TJ, Meehan BS, Meehan LJ, Tian Z, Zhao Z, Wang H, Nelson A, Le Nours J, Khandokar Y, Praveena T, Wubben J, Lin J, Sullivan LC, Lovrecz GO, Mak JY, Liu L, Kostenko L, Kedzierska K, Corbett AJ, Fairlie DP, Brooks AG, Gherardin NA, Uldrich AP, Chen Z, Rossjohn J, Godfrey DI, McCluskey J, Pellicci DG, Eckle SB. CD8 coreceptor engagement of MR1 enhances antigen responsiveness by human MAIT and other MR1-reactive T cells. J Exp Med 2022; 219:213423. [PMID: 36018322 PMCID: PMC9424912 DOI: 10.1084/jem.20210828] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2021] [Revised: 06/24/2022] [Accepted: 07/21/2022] [Indexed: 11/04/2022] Open
Abstract
Mucosal-associated invariant T (MAIT) cells detect microbial infection via recognition of riboflavin-based antigens presented by the major histocompatibility complex class I (MHC-I)-related protein 1 (MR1). Most MAIT cells in human peripheral blood express CD8αα or CD8αβ coreceptors, and the binding site for CD8 on MHC-I molecules is relatively conserved in MR1. Yet, there is no direct evidence of CD8 interacting with MR1 or the functional consequences thereof. Similarly, the role of CD8αα in lymphocyte function remains ill-defined. Here, using newly developed MR1 tetramers, mutated at the CD8 binding site, and by determining the crystal structure of MR1-CD8αα, we show that CD8 engaged MR1, analogous to how it engages MHC-I molecules. CD8αα and CD8αβ enhanced MR1 binding and cytokine production by MAIT cells. Moreover, the CD8-MR1 interaction was critical for the recognition of folate-derived antigens by other MR1-reactive T cells. Together, our findings suggest that both CD8αα and CD8αβ act as functional coreceptors for MAIT and other MR1-reactive T cells.
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Affiliation(s)
- Michael N.T. Souter
- Department of Microbiology and Immunology, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, Australia
| | - Wael Awad
- Infection and Immunity Program and Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Melbourne, Australia
| | - Shihan Li
- Department of Microbiology and Immunology, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, Australia
| | - Troi J. Pediongco
- Department of Microbiology and Immunology, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, Australia
| | - Bronwyn S. Meehan
- Department of Microbiology and Immunology, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, Australia
| | - Lucy J. Meehan
- Department of Microbiology and Immunology, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, Australia
| | - Zehua Tian
- Department of Microbiology and Immunology, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, Australia
| | - Zhe Zhao
- Department of Microbiology and Immunology, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, Australia
| | - Huimeng Wang
- Department of Microbiology and Immunology, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, Australia,State Key Laboratory of Respiratory Disease, Guangzhou Institute of Respiratory Disease, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, Guangdong, China
| | - Adam Nelson
- Department of Microbiology and Immunology, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, Australia
| | - Jérôme Le Nours
- Infection and Immunity Program and Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Melbourne, Australia
| | - Yogesh Khandokar
- Infection and Immunity Program and Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Melbourne, Australia
| | - T. Praveena
- Infection and Immunity Program and Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Melbourne, Australia
| | - Jacinta Wubben
- Infection and Immunity Program and Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Melbourne, Australia
| | - Jie Lin
- Department of Microbiology and Immunology, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, Australia
| | - Lucy C. Sullivan
- Department of Microbiology and Immunology, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, Australia
| | - George O. Lovrecz
- Biomedical Manufacturing, Commonwealth Scientific and Industrial Research Organisation, Melbourne, Australia
| | - Jeffrey Y.W. Mak
- Division of Chemistry and Structural Biology, Institute for Molecular Bioscience, The University of Queensland, Brisbane, Australia
| | - Ligong Liu
- Division of Chemistry and Structural Biology, Institute for Molecular Bioscience, The University of Queensland, Brisbane, Australia
| | - Lyudmila Kostenko
- Department of Microbiology and Immunology, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, Australia
| | - Katherine Kedzierska
- Department of Microbiology and Immunology, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, Australia
| | - Alexandra J. Corbett
- Department of Microbiology and Immunology, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, Australia
| | - David P. Fairlie
- Division of Chemistry and Structural Biology, Institute for Molecular Bioscience, The University of Queensland, Brisbane, Australia
| | - Andrew G. Brooks
- Department of Microbiology and Immunology, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, Australia
| | - Nicholas A. Gherardin
- Department of Microbiology and Immunology, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, Australia
| | - Adam P. Uldrich
- Department of Microbiology and Immunology, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, Australia
| | - Zhenjun Chen
- Department of Microbiology and Immunology, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, Australia
| | - Jamie Rossjohn
- Infection and Immunity Program and Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Melbourne, Australia,Institute of Infection and Immunity, School of Medicine, Cardiff University, Cardiff, UK
| | - Dale I. Godfrey
- Department of Microbiology and Immunology, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, Australia
| | - James McCluskey
- Department of Microbiology and Immunology, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, Australia
| | - Daniel G. Pellicci
- Department of Microbiology and Immunology, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, Australia,Murdoch Children’s Research Institute, Parkville, Melbourne, Australia
| | - Sidonia B.G. Eckle
- Department of Microbiology and Immunology, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, Australia
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15
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Nanoscale organization of two-dimensional multimeric pMHC reagents with DNA origami for CD8 + T cell detection. Nat Commun 2022; 13:3916. [PMID: 35798752 PMCID: PMC9263106 DOI: 10.1038/s41467-022-31684-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2021] [Accepted: 06/23/2022] [Indexed: 11/08/2022] Open
Abstract
Peptide-MHC (pMHC) multimers have excelled in the detection of antigen-specific T cells and have allowed phenotypic analysis using other reagents, but their use for detection of low-affinity T cells remains a challenge. Here we develop a multimeric T cell identifying reagent platform using two-dimensional DNA origami scaffolds to spatially organize pMHCs (termed as dorimers) with nanoscale control. We show that these dorimers enhance the binding avidity for low-affinity antigen-specific T cell receptors (TCRs). The dorimers are able to detect more antigen-specific T cells in mouse CD8+ T cells and early-stage CD4+CD8+ double-positive thymocytes that express less dense TCRs, compared with the equivalent tetramers and dextramers. Moreover, we demonstrate dorimer function in the analysis of autoimmune CD8+ T cells that express low-affinity TCRs, which are difficult to detect using tetramers. We anticipate that dorimers could contribute to the investigation of antigen-specific T cells in immune T cell function or immunotherapy applications. MHC-peptide multimers are important reagents for detecting antigen specific T cells. Here the authors show that DNA scaffolds can be used to make MHC-peptide multimers and the avidity controlled so that low abundance or T cells with low affinity TCR can be detected using these reagents.
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16
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Molvi Z, O'Reilly RJ. Allogeneic Tumor Antigen-Specific T Cells for Broadly Applicable Adoptive Cell Therapy of Cancer. Cancer Treat Res 2022; 183:131-159. [PMID: 35551658 DOI: 10.1007/978-3-030-96376-7_4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
T cells specific for major histocompatibility complex (MHC)-presented tumor antigens are capable of inducing durable remissions when adoptively transferred to patients with refractory cancers presenting such antigens. When such T cells are derived from healthy donors, they can be banked for off-the-shelf administration in appropriately tissue matched patients. Therefore, tumor antigen-specific, donor-derived T cells are expected to be a mainstay in the cancer immunotherapy armamentarium. In this chapter, we analyze clinical evidence that tumor antigen-specific donor-derived T cells can induce tumor regressions when administered to appropriately matched patients whose tumors are refractory to standard therapy. We also delineate the landscape of MHC-presented and unconventional tumor antigens recognized by T cells in healthy individuals that have been targeted for adoptive T cell therapy, as well as emerging antigens for which mounting evidence suggests their utility as targets for adoptive T cell therapy. We discuss the growing technological advancements that have facilitated sequence identification of such antigens and their cognate T cells, and applicability of such technologies in the pre-clinical and clinical settings.
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Affiliation(s)
- Zaki Molvi
- Immunology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA.
| | - Richard J O'Reilly
- Immunology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
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17
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Development of Cancer Immunotherapies. Cancer Treat Res 2022; 183:1-48. [PMID: 35551655 DOI: 10.1007/978-3-030-96376-7_1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
Cancer immunotherapy, or the utilization of components of the immune system to target and eliminate cancer, has become a highly active area of research in the past several decades and a common treatment strategy for several cancer types. The concept of harnessing the immune system for this purpose originated over 100 years ago when a physician by the name of William Coley successfully treated several of his cancer patients with a combination of live and attenuated bacteria, later known as "Coley's Toxins", after observing a subset of prior patients enter remission following their diagnosis with the common bacterial infection, erysipelas. However, it was not until late in the twentieth century that cancer immunotherapies were developed for widespread use, thereby transforming the treatment landscape of numerous cancer types. Pivotal studies elucidating molecular and cellular functions of immune cells, such as the discovery of IL-2 and production of monoclonal antibodies, fostered the development of novel techniques for studying the immune system and ultimately the development and approval of several cancer immunotherapies by the United States Food and Drug Association in the 1980s and 1990s, including the tuberculosis vaccine-Bacillus Calmette-Guérin, IL-2, and the CD20-targeting monoclonal antibody. Approval of the first therapeutic cancer vaccine, Sipuleucel-T, for the treatment of metastatic castration-resistant prostate cancer and the groundbreaking success and approval of immune checkpoint inhibitors and chimeric antigen receptor T cell therapy in the last decade, have driven an explosion of interest in and pursuit of novel cancer immunotherapy strategies. A broad range of modalities ranging from antibodies to adoptive T cell therapies is under investigation for the generalized treatment of a broad spectrum of cancers as well as personalized medicine. This chapter will focus on the recent advances, current strategies, and future outlook of immunotherapy development for the treatment of cancer.
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18
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Patel S, Ramnoruth N, Wehr P, Rossjohn J, Reid HH, Campbell K, Nel HJ, Thomas R. Evaluation of a fit-for-purpose assay to monitor antigen-specific functional CD4+ T-cell subpopulations in rheumatoid arthritis using flow cytometry-based peptide-MHC class-II tetramer staining. Clin Exp Immunol 2022; 207:72-83. [PMID: 35020859 PMCID: PMC8802177 DOI: 10.1093/cei/uxab008] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2021] [Revised: 09/13/2021] [Accepted: 12/01/2021] [Indexed: 12/11/2022] Open
Abstract
Antigen-specific T cells can serve as a response biomarker in non-clinical or clinical immunotherapy studies in autoimmune disease. There are protocols with optimized multimer staining methods to detect peptide (p)MHCII+ CD4+ T cells, and some qualified and validated protocols for pMHCI+ CD8+ T cells. However, no protocol is fully or partially qualified to enumerate and characterize antigen-specific pMHCII+ CD4+ T cells from patient samples. Implementing such an assay requires a desired level of specificity and precision, in terms of assay repeatability and reproducibility. In transgenic type II collagen (CII)-immunized HLA-DR1/DR4 humanized mouse models of collagen-induced arthritis (CIA), CII259-273-specific T cells dominantly expand. Therefore antigen-specific T cells recognizing this epitope presented by rheumatoid arthritis (RA)-associated risk HLA-DR allomorphs are of interest to understand disease progression and responses to immunotherapy in RA patients. Using HLA-DRB1∗04:01 or ∗01:01-collagen type II (CII)259–273 tetramers, we evaluated parameters influencing precision and reproducibility of an optimized flow cytometry–based method for antigen-specific CD4+ T cells and eight specific subpopulations with and without tetramer positivity. We evaluated specificity, precision, and reproducibility for research environments and non-regulated laboratories. The assay has excellent overall precision with %CV<25% for intra-assay repeatability, inter-analyst precision, and inter-assay reproducibility. The precision of the assay correlated negatively with the cell viability after thawing, indicating that post-thaw viability is a critical parameter for reproducibility. This assay is suitable for longitudinal analysis of treatment response and disease activity outcome in RA patients, and adaptable for translational or immunotherapy clinical trial settings.
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Affiliation(s)
- Swati Patel
- The University of Queensland Diamantina Institute, The University of Queensland, Brisbane, QLD, Australia
| | - Nishta Ramnoruth
- The University of Queensland Diamantina Institute, The University of Queensland, Brisbane, QLD, Australia
| | - Pascale Wehr
- The University of Queensland Diamantina Institute, The University of Queensland, Brisbane, QLD, Australia
| | - Jamie Rossjohn
- Infection and Immunity Program and The Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, VIC, Australia.,ARC Centre of Excellence in Advanced Molecular Imaging, Monash University, Clayton, VIC, Australia.,Institute of Infection and Immunity, School of Medicine, Cardiff University, Cardiff, UK
| | - Hugh H Reid
- Infection and Immunity Program and The Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, VIC, Australia.,ARC Centre of Excellence in Advanced Molecular Imaging, Monash University, Clayton, VIC, Australia
| | - Kim Campbell
- Janssen Research & Development, LLC, Spring House, PA, USA.,Janssen Research & Development, LLC, La Jolla, CA, USA
| | - Hendrik J Nel
- The University of Queensland Diamantina Institute, The University of Queensland, Brisbane, QLD, Australia
| | - Ranjeny Thomas
- The University of Queensland Diamantina Institute, The University of Queensland, Brisbane, QLD, Australia
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19
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Abdulhaqq S, Ventura AB, Reed JS, Bashirova AA, Bateman KB, McDonald E, Wu HL, Greene JM, Schell JB, Morrow D, Wisskirchen K, Martin JN, Deeks SG, Carrington M, Protzer U, Früh K, Hansen SG, Picker LJ, Sacha JB, Bimber BN. Identification and Characterization of Antigen-Specific CD8 + T Cells Using Surface-Trapped TNF-α and Single-Cell Sequencing. JOURNAL OF IMMUNOLOGY (BALTIMORE, MD. : 1950) 2021; 207:2913-2921. [PMID: 34810222 PMCID: PMC9124229 DOI: 10.4049/jimmunol.2100535] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/07/2021] [Accepted: 10/15/2021] [Indexed: 12/31/2022]
Abstract
CD8+ T cells are key mediators of antiviral and antitumor immunity. The isolation and study of Ag-specific CD8+ T cells, as well as mapping of their MHC restriction, has practical importance to the study of disease and the development of therapeutics. Unfortunately, most experimental approaches are cumbersome, owing to the highly variable and donor-specific nature of MHC-bound peptide/TCR interactions. Here we present a novel system for rapid identification and characterization of Ag-specific CD8+ T cells, particularly well suited for samples with limited primary cells. Cells are stimulated ex vivo with Ag of interest, followed by live cell sorting based on surface-trapped TNF-α. We take advantage of major advances in single-cell sequencing to generate full-length sequence data from the paired TCR α- and β-chains from these Ag-specific cells. The paired TCR chains are cloned into retroviral vectors and used to transduce donor CD8+ T cells. These TCR transductants provide a virtually unlimited experimental reagent, which can be used for further characterization, such as minimal epitope mapping or identification of MHC restriction, without depleting primary cells. We validated this system using CMV-specific CD8+ T cells from rhesus macaques, characterizing an immunodominant Mamu-A1*002:01-restricted epitope. We further demonstrated the utility of this system by mapping a novel HLA-A*68:02-restricted HIV Gag epitope from an HIV-infected donor. Collectively, these data validate a new strategy to rapidly identify novel Ags and characterize Ag-specific CD8+ T cells, with applications ranging from the study of infectious disease to immunotherapeutics and precision medicine.
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Affiliation(s)
- Shaheed Abdulhaqq
- Vaccine and Gene Therapy Institute, Oregon Health and Science University, Beaverton, OR
| | - Abigail B Ventura
- Vaccine and Gene Therapy Institute, Oregon Health and Science University, Beaverton, OR
| | - Jason S Reed
- Vaccine and Gene Therapy Institute, Oregon Health and Science University, Beaverton, OR
| | - Arman A Bashirova
- Basic Science Program, Frederick National Laboratory for Cancer Research, Frederick, MD
- Laboratory of Integrative Cancer Immunology, Center for Cancer Research, National Cancer Institute, Bethesda, MD
| | - Katherine B Bateman
- Vaccine and Gene Therapy Institute, Oregon Health and Science University, Beaverton, OR
| | - Eric McDonald
- Vaccine and Gene Therapy Institute, Oregon Health and Science University, Beaverton, OR
| | - Helen L Wu
- Vaccine and Gene Therapy Institute, Oregon Health and Science University, Beaverton, OR
| | - Justin M Greene
- Vaccine and Gene Therapy Institute, Oregon Health and Science University, Beaverton, OR
| | - John B Schell
- Vaccine and Gene Therapy Institute, Oregon Health and Science University, Beaverton, OR
| | - David Morrow
- Vaccine and Gene Therapy Institute, Oregon Health and Science University, Beaverton, OR
| | - Karin Wisskirchen
- Institute of Virology, Technical University of Munich/Helmholtz Zentrum Munich, Munich, Germany
| | - Jeffrey N Martin
- Department of Epidemiology and Biostatistics, University of California, San Francisco, San Francisco, CA
| | - Steven G Deeks
- HIV/AIDS Program, Department of Medicine, University of California, San Francisco, San Francisco, CA
| | - Mary Carrington
- Basic Science Program, Frederick National Laboratory for Cancer Research, Frederick, MD
- Laboratory of Integrative Cancer Immunology, Center for Cancer Research, National Cancer Institute, Bethesda, MD
- Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology and Harvard University, Cambridge, MA; and
| | - Ulrike Protzer
- Institute of Virology, Technical University of Munich/Helmholtz Zentrum Munich, Munich, Germany
| | - Klaus Früh
- Vaccine and Gene Therapy Institute, Oregon Health and Science University, Beaverton, OR
| | - Scott G Hansen
- Vaccine and Gene Therapy Institute, Oregon Health and Science University, Beaverton, OR
| | - Louis J Picker
- Vaccine and Gene Therapy Institute, Oregon Health and Science University, Beaverton, OR
| | - Jonah B Sacha
- Vaccine and Gene Therapy Institute, Oregon Health and Science University, Beaverton, OR;
- Oregon National Primate Research Center, Oregon Health and Science University, Beaverton, OR
| | - Benjamin N Bimber
- Oregon National Primate Research Center, Oregon Health and Science University, Beaverton, OR
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20
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Recognition of the antigen-presenting molecule MR1 by a Vδ3 + γδ T cell receptor. Proc Natl Acad Sci U S A 2021; 118:2110288118. [PMID: 34845016 DOI: 10.1073/pnas.2110288118] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/20/2021] [Indexed: 02/05/2023] Open
Abstract
Unlike conventional αβ T cells, γδ T cells typically recognize nonpeptide ligands independently of major histocompatibility complex (MHC) restriction. Accordingly, the γδ T cell receptor (TCR) can potentially recognize a wide array of ligands; however, few ligands have been described to date. While there is a growing appreciation of the molecular bases underpinning variable (V)δ1+ and Vδ2+ γδ TCR-mediated ligand recognition, the mode of Vδ3+ TCR ligand engagement is unknown. MHC class I-related protein, MR1, presents vitamin B metabolites to αβ T cells known as mucosal-associated invariant T cells, diverse MR1-restricted T cells, and a subset of human γδ T cells. Here, we identify Vδ1/2- γδ T cells in the blood and duodenal biopsy specimens of children that showed metabolite-independent binding of MR1 tetramers. Characterization of one Vδ3Vγ8 TCR clone showed MR1 reactivity was independent of the presented antigen. Determination of two Vδ3Vγ8 TCR-MR1-antigen complex structures revealed a recognition mechanism by the Vδ3 TCR chain that mediated specific contacts to the side of the MR1 antigen-binding groove, representing a previously uncharacterized MR1 docking topology. The binding of the Vδ3+ TCR to MR1 did not involve contacts with the presented antigen, providing a basis for understanding its inherent MR1 autoreactivity. We provide molecular insight into antigen-independent recognition of MR1 by a Vδ3+ γδ TCR that strengthens an emerging paradigm of antibody-like ligand engagement by γδ TCRs.
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21
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Baldwin J, Piplani S, Sakala IG, Honda-Okubo Y, Li L, Petrovsky N. Rapid development of analytical methods for evaluating pandemic vaccines: a COVID-19 perspective. Bioanalysis 2021; 13:1805-1826. [PMID: 34645288 PMCID: PMC8516068 DOI: 10.4155/bio-2021-0096] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2021] [Accepted: 09/28/2021] [Indexed: 12/24/2022] Open
Abstract
Vaccines are key in charting a path out of the COVID-19 pandemic. However, development of new vaccines is highly dependent on availability of analytical methods for their design and evaluation. This paper highlights the challenges presented in having to rapidly develop vaccine analytical tools during an ongoing pandemic, including the need to address progressive virus mutation and adaptation which can render initial assays unreliable or redundant. It also discusses the potential of new computational modeling techniques to model and analyze key viral proteins and their attributes to assist vaccine production and assay design. It then reviews the current range of analytical tools available for COVID-19 vaccine application, ranging from in vitro assays for immunogen characterization to assays to measure vaccine responses in vivo. Finally, it provides a future perspective for COVID-19 vaccine analytical tools and attempts to predict how the field might evolve over the next 5-10 years.
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Affiliation(s)
- Jeremy Baldwin
- Vaxine Pty Ltd, 11 Walkley Avenue, Adelaide, 5046, Australia
| | - Sakshi Piplani
- Vaxine Pty Ltd, 11 Walkley Avenue, Adelaide, 5046, Australia
- College of Medicine & Public Health, Flinders University, Adelaide, 5042, Australia
| | - Isaac G Sakala
- Vaxine Pty Ltd, 11 Walkley Avenue, Adelaide, 5046, Australia
- College of Medicine & Public Health, Flinders University, Adelaide, 5042, Australia
| | - Yoshikazu Honda-Okubo
- Vaxine Pty Ltd, 11 Walkley Avenue, Adelaide, 5046, Australia
- College of Medicine & Public Health, Flinders University, Adelaide, 5042, Australia
| | - Lei Li
- Vaxine Pty Ltd, 11 Walkley Avenue, Adelaide, 5046, Australia
- College of Medicine & Public Health, Flinders University, Adelaide, 5042, Australia
| | - Nikolai Petrovsky
- Vaxine Pty Ltd, 11 Walkley Avenue, Adelaide, 5046, Australia
- College of Medicine & Public Health, Flinders University, Adelaide, 5042, Australia
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22
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Hu Y, Cao G, Chen X, Huang X, Asby N, Ankenbruck N, Rahman A, Thusu A, He Y, Riedell PA, Bishop MR, Schreiber H, Kline JP, Huang J. Antigen-Multimers: Specific, Sensitive, Precise, and Multifunctional High-Avidity CAR-Staining Reagents. MATTER 2021; 4:3917-3940. [PMID: 34901832 PMCID: PMC8654235 DOI: 10.1016/j.matt.2021.09.027] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Although chimeric antigen receptor (CAR) T-cell therapy has transformed cancer treatment, high-quality and universal CAR-staining reagents are urgently required to manufacture CAR T cells, predict therapy response, decipher CAR biology, and engineer new CARs. Here, we developed tetrameric and dodecameric forms of a multifunctional and extensible category of high-avidity CAR-staining reagents: antigen-multimers. Antigen-multimers detected CARs against CD19, HER2, and Tn-glycoside with significantly higher specificity, sensitivity, and precision than existing reagents. In addition to accurate CAR T-cell detection by flow cytometry, antigen-multimers also enabled ≥100-fold magnetic enrichment of rare CAR T cells, selective CAR T-cell stimulation, and high-dimensional CAR T-cell profiling by single-cell multi-omics analyses. Finally, antigen-multimers accurately captured clinical anti-CD19 CAR T cells from patients' cellular infusion products, post-infusion peripheral blood, and tumor biopsies. Antigen-multimers can be readily extended to other CAR systems by switching its antigen ligand. As such, antigen-multimers have broad clinical and research applications.
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Affiliation(s)
- Yifei Hu
- Pritzker School of Molecular Engineering, University of Chicago, Chicago, IL 60637, USA
- Pritzker School of Medicine, University of Chicago, Chicago, IL 60637, USA
| | - Guoshuai Cao
- Pritzker School of Molecular Engineering, University of Chicago, Chicago, IL 60637, USA
| | - Xiufen Chen
- Department of Medicine, University of Chicago, Chicago, IL 60637, USA
| | - Xiaodan Huang
- Pritzker School of Molecular Engineering, University of Chicago, Chicago, IL 60637, USA
| | - Nicholas Asby
- Pritzker School of Molecular Engineering, University of Chicago, Chicago, IL 60637, USA
| | - Nicholas Ankenbruck
- Pritzker School of Molecular Engineering, University of Chicago, Chicago, IL 60637, USA
| | - Ali Rahman
- Pritzker School of Molecular Engineering, University of Chicago, Chicago, IL 60637, USA
| | - Ashima Thusu
- Pritzker School of Molecular Engineering, University of Chicago, Chicago, IL 60637, USA
| | - Yanran He
- Committee on Cancer Biology, University of Chicago, Chicago, IL 60637, USA
| | - Peter A. Riedell
- Committee on Cancer Biology, University of Chicago, Chicago, IL 60637, USA
- Department of Medicine, University of Chicago, Chicago, IL 60637, USA
- The David and Etta Jonas Center for Cellular Therapy, University of Chicago, Chicago, IL 60637, USA
| | - Michael R. Bishop
- Department of Medicine, University of Chicago, Chicago, IL 60637, USA
- The David and Etta Jonas Center for Cellular Therapy, University of Chicago, Chicago, IL 60637, USA
| | - Hans Schreiber
- Committee on Immunology, University of Chicago, Chicago, IL 60637, USA
- Committee on Cancer Biology, University of Chicago, Chicago, IL 60637, USA
- The David and Etta Jonas Center for Cellular Therapy, University of Chicago, Chicago, IL 60637, USA
- Department of Pathology, University of Chicago, Chicago, IL 60637, USA
| | - Justin P. Kline
- Committee on Immunology, University of Chicago, Chicago, IL 60637, USA
- Committee on Cancer Biology, University of Chicago, Chicago, IL 60637, USA
- Department of Medicine, University of Chicago, Chicago, IL 60637, USA
- The David and Etta Jonas Center for Cellular Therapy, University of Chicago, Chicago, IL 60637, USA
| | - Jun Huang
- Pritzker School of Molecular Engineering, University of Chicago, Chicago, IL 60637, USA
- Committee on Immunology, University of Chicago, Chicago, IL 60637, USA
- Committee on Cancer Biology, University of Chicago, Chicago, IL 60637, USA
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23
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Balasko A, Graydon C, Fowke KR. Novel in vitro invariant natural killer T cell functional assays. J Immunol Methods 2021; 499:113171. [PMID: 34706265 DOI: 10.1016/j.jim.2021.113171] [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: 08/04/2021] [Revised: 09/16/2021] [Accepted: 10/12/2021] [Indexed: 11/25/2022]
Abstract
BACKGROUND Invariant Natural Killer T (iNKT) cells are innate lymphocytes bridging the innate and adaptive immune systems and are critical first responders against cancer and infectious diseases. iNKT cell phenotype and functionality are studied using in vitro stimulation assays assessing cytokine response and proliferation capabilities. The most common stimulant is the glycolipid α-Galactosyl Ceramide (α-GalCer), which stimulates iNKT cells when presented by CD1d, an MHC class I-like molecule expressed by antigen-presenting cells (APC). Another stimulant used is α-GalCer-loaded DimerX, a CD1d-Ig fusion protein which stimulates iNKT cells in an APC-independent fashion. Here, we demonstrate use of the PBS-57-loaded CD1d-tetramer as an APC-independent stimulant, where PBS-57 is an α-GalCer analogue. METHODS Using healthy fresh (n = 4) and frozen (n = 7) peripheral blood mononuclear cells (PBMCs), 10-h cytokine response (measuring IFN-γ production) and 10-day proliferation assays were performed assessing iNKT functionality using α-GalCer, CD1d-tetramer and DimerX stimulants. RESULTS All stimulants effectively induced IFN-γ production in both fresh and frozen PBMC. After the 10-h activation, CD1d-tetramer was significantly more effective than α-GalCer (p = 0.032) in inducing IFN-γ production in fresh PBMC and significantly more effective than both α-GalCer (p = 0.004) and DimerX (p = 0.021) in frozen PBMC. Similarly, all stimulants induced strong proliferation responses in all samples, although this was only significant in the frozen PBMC. No significant differences in proliferation were observed between stimulants. SIGNIFICANCE This study supports PBS-57-loaded CD1d-tetramer as an effective in vitro APC-independent iNKT cell stimulant, which is comparable to or even more effective than α-GalCer and DimerX. As CD1d is downregulated during infectious disease and cancer as evasion strategies, in vitro assays which are APC-independent can assist in providing objective insight to iNKT activation by not relying on CD1d expression by APCs. Overall, the novel CD1d-tetramer stimulation equips researchers with an expanded "toolkit" to successfully assess iNKT cell function.
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Affiliation(s)
- Allison Balasko
- Department of Medical Microbiology and Infectious Diseases, University of Manitoba, Winnipeg, Canada.
| | - Colin Graydon
- Department of Medical Microbiology and Infectious Diseases, University of Manitoba, Winnipeg, Canada
| | - Keith R Fowke
- Department of Medical Microbiology and Infectious Diseases, University of Manitoba, Winnipeg, Canada; Department of Medical Microbiology, University of Nairobi, Nairobi, Kenya; Department of Community Health Sciences, University of Manitoba, Winnipeg, Canada; Partners for Health and Development in Africa, Nairobi, Kenya.
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24
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Almeida CF, Smith DGM, Cheng TY, Harpur CM, Batleska E, Nguyen-Robertson CV, Nguyen T, Thelemann T, Reddiex SJJ, Li S, Eckle SBG, Van Rhijn I, Rossjohn J, Uldrich AP, Moody DB, Williams SJ, Pellicci DG, Godfrey DI. Benzofuran sulfonates and small self-lipid antigens activate type II NKT cells via CD1d. Proc Natl Acad Sci U S A 2021; 118:e2104420118. [PMID: 34417291 PMCID: PMC8403964 DOI: 10.1073/pnas.2104420118] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Natural killer T (NKT) cells detect lipids presented by CD1d. Most studies focus on type I NKT cells that express semi-invariant αβ T cell receptors (TCR) and recognize α-galactosylceramides. However, CD1d also presents structurally distinct lipids to NKT cells expressing diverse TCRs (type II NKT cells), but our knowledge of the antigens for type II NKT cells is limited. An early study identified a nonlipidic NKT cell agonist, phenyl pentamethyldihydrobenzofuransulfonate (PPBF), which is notable for its similarity to common sulfa drugs, but its mechanism of NKT cell activation remained unknown. Here, we demonstrate that a range of pentamethylbenzofuransulfonates (PBFs), including PPBF, activate polyclonal type II NKT cells from human donors. Whereas these sulfa drug-like molecules might have acted pharmacologically on cells, here we demonstrate direct contact between TCRs and PBF-treated CD1d complexes. Further, PBF-treated CD1d tetramers identified type II NKT cell populations expressing αβTCRs and γδTCRs, including those with variable and joining region gene usage (TRAV12-1-TRAJ6) that was conserved across donors. By trapping a CD1d-type II NKT TCR complex for direct mass-spectrometric analysis, we detected molecules that allow the binding of CD1d to TCRs, finding that both selected PBF family members and short-chain sphingomyelin lipids are present in these complexes. Furthermore, the combination of PPBF and short-chain sphingomyelin enhances CD1d tetramer staining of PPBF-reactive T cell lines over either molecule alone. This study demonstrates that nonlipidic small molecules, which resemble sulfa drugs implicated in systemic hypersensitivity and drug allergy reactions, are targeted by a polyclonal population of type II NKT cells in a CD1d-restricted manner.
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Affiliation(s)
- Catarina F Almeida
- Department of Microbiology and Immunology, The Peter Doherty Institute for Infection and Immunity, The University of Melbourne, Melbourne, VIC 3000, Australia;
- Australian Research Council Centre of Excellence in Advanced Molecular Imaging, The University of Melbourne, Melbourne, VIC 3010, Australia
| | - Dylan G M Smith
- School of Chemistry, The University of Melbourne, Melbourne, VIC 3052, Australia
- Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Melbourne, VIC 3052, Australia
| | - Tan-Yun Cheng
- Division of Rheumatology, Immunity and Inflammation, Brigham and Women's Hospital, Boston, MA 02115
| | - Chris M Harpur
- Department of Microbiology and Immunology, The Peter Doherty Institute for Infection and Immunity, The University of Melbourne, Melbourne, VIC 3000, Australia
| | - Elena Batleska
- Department of Microbiology and Immunology, The Peter Doherty Institute for Infection and Immunity, The University of Melbourne, Melbourne, VIC 3000, Australia
| | - Catriona V Nguyen-Robertson
- Department of Microbiology and Immunology, The Peter Doherty Institute for Infection and Immunity, The University of Melbourne, Melbourne, VIC 3000, Australia
- Australian Research Council Centre of Excellence in Advanced Molecular Imaging, The University of Melbourne, Melbourne, VIC 3010, Australia
| | - Tram Nguyen
- School of Chemistry, The University of Melbourne, Melbourne, VIC 3052, Australia
- Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Melbourne, VIC 3052, Australia
| | - Tamara Thelemann
- Department of Microbiology and Immunology, The Peter Doherty Institute for Infection and Immunity, The University of Melbourne, Melbourne, VIC 3000, Australia
| | - Scott J J Reddiex
- Department of Microbiology and Immunology, The Peter Doherty Institute for Infection and Immunity, The University of Melbourne, Melbourne, VIC 3000, Australia
- Australian Research Council Centre of Excellence in Advanced Molecular Imaging, The University of Melbourne, Melbourne, VIC 3010, Australia
| | - Shihan Li
- Department of Microbiology and Immunology, The Peter Doherty Institute for Infection and Immunity, The University of Melbourne, Melbourne, VIC 3000, Australia
- Australian Research Council Centre of Excellence in Advanced Molecular Imaging, The University of Melbourne, Melbourne, VIC 3010, Australia
| | - Sidonia B G Eckle
- Department of Microbiology and Immunology, The Peter Doherty Institute for Infection and Immunity, The University of Melbourne, Melbourne, VIC 3000, Australia
| | - Ildiko Van Rhijn
- Division of Rheumatology, Immunity and Inflammation, Brigham and Women's Hospital, Boston, MA 02115
- Department of Infectious Diseases and Immunology, Faculty of Veterinary Medicine, University Utrecht, 3584CL Utrecht, Netherlands
| | - Jamie Rossjohn
- Infection and Immunity Program, Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, VIC 3800, Australia
- Australian Research Council Centre of Excellence in Advanced Molecular Imaging, Monash University, Clayton, VIC 3800, Australia
- Institute of Infection and Immunity, Cardiff University School of Medicine, Cardiff CF14 4XN, United Kingdom
| | - Adam P Uldrich
- Department of Microbiology and Immunology, The Peter Doherty Institute for Infection and Immunity, The University of Melbourne, Melbourne, VIC 3000, Australia
- Australian Research Council Centre of Excellence in Advanced Molecular Imaging, The University of Melbourne, Melbourne, VIC 3010, Australia
| | - D Branch Moody
- Division of Rheumatology, Immunity and Inflammation, Brigham and Women's Hospital, Boston, MA 02115;
| | - Spencer J Williams
- Australian Research Council Centre of Excellence in Advanced Molecular Imaging, The University of Melbourne, Melbourne, VIC 3010, Australia;
- School of Chemistry, The University of Melbourne, Melbourne, VIC 3052, Australia
- Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Melbourne, VIC 3052, Australia
| | - Daniel G Pellicci
- Department of Microbiology and Immunology, The Peter Doherty Institute for Infection and Immunity, The University of Melbourne, Melbourne, VIC 3000, Australia;
- Australian Research Council Centre of Excellence in Advanced Molecular Imaging, The University of Melbourne, Melbourne, VIC 3010, Australia
- Murdoch Children's Research Institute, Parkville, VIC 3052, Australia
- Department of Paediatrics, The University of Melbourne, Parkville, VIC 3052, Australia
| | - Dale I Godfrey
- Department of Microbiology and Immunology, The Peter Doherty Institute for Infection and Immunity, The University of Melbourne, Melbourne, VIC 3000, Australia;
- Australian Research Council Centre of Excellence in Advanced Molecular Imaging, The University of Melbourne, Melbourne, VIC 3010, Australia
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25
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Dahotre SN, Romanov AM, Su FY, Kwong GA. Synthetic Antigen-Presenting Cells for Adoptive T Cell Therapy. ADVANCED THERAPEUTICS 2021; 4:2100034. [PMID: 34541300 PMCID: PMC8447293 DOI: 10.1002/adtp.202100034] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2021] [Indexed: 11/06/2022]
Abstract
Adoptive T cell therapies are transforming the treatment of solid and liquid tumors, yet their widespread adoption is limited in part by the challenge of generating functional cells. T cell activation and expansion using conventional antigen-presenting cells (APCs) is unreliable due to the variable quality of donor-derived APCs. As a result, engineered approaches using nanomaterials presenting T cell activation signals are a promising alternative due to their ability to be robustly manufactured with precise control over stimulation cues. In this work, we design synthetic APCs that consist of liposomes surface-functionalized with peptide-major histocompatibility complexes (pMHC). Synthetic APCs selectively target and activate antigen-specific T cell populations to levels similar to conventional protocols using non-specific αCD3 and αCD28 antibodies without the need for costimulation signals. T cells treated with synthetic APCs produce effector cytokines and demonstrate cytotoxic activity when co-cultured with tumor cells presenting target antigen in vitro. Following adoptive transfer into tumor-bearing mice, activated cells control tumor growth and improve overall survival compared to untreated mice. Synthetic APCs could potentially be used in the future to improve the accessibility of adoptive T cell therapies by removing the need for conventional APCs during manufacturing.
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Affiliation(s)
- Shreyas N Dahotre
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Tech and Emory University, Atlanta, GA 30332, USA
| | - Anna M Romanov
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Tech and Emory University, Atlanta, GA 30332, USA
| | - Fang-Yi Su
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Tech and Emory University, Atlanta, GA 30332, USA
| | - Gabriel A Kwong
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Tech and Emory University, Atlanta, GA 30332, USA
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26
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Cannarile MA, Gomes B, Canamero M, Reis B, Byrd A, Charo J, Yadav M, Karanikas V. Biomarker Technologies to Support Early Clinical Immuno-oncology Development: Advances and Interpretation. Clin Cancer Res 2021; 27:4147-4159. [PMID: 33766813 DOI: 10.1158/1078-0432.ccr-20-2345] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2020] [Revised: 02/02/2021] [Accepted: 03/08/2021] [Indexed: 11/16/2022]
Abstract
Today, there is a huge effort to develop cancer immunotherapeutics capable of combating cancer cells as well as the biological environment in which they can grow, adapt, and survive. For such treatments to benefit more patients, there is a great need to dissect the complex interplays between tumor cells and the host's immune system. Monitoring mechanisms of resistance to immunotherapeutics can delineate the evolution of key players capable of driving an efficacious antitumor immune response. In doing so, simultaneous and systematic interrogation of multiple biomarkers beyond single biomarker approaches needs to be undertaken. Zooming into cell-to-cell interactions using technological advancements with unprecedented cellular resolution such as single-cell spatial transcriptomics, advanced tissue histology approaches, and new molecular immune profiling tools promises to provide a unique level of molecular granularity of the tumor environment and may support better decision-making during drug development. This review will focus on how such technological tools are applied in clinical settings, to inform the underlying tumor-immune biology of patients and offer a deeper understanding of cancer immune responsiveness to immuno-oncology treatments.
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Affiliation(s)
- Michael A Cannarile
- F. Hoffmann-La Roche AG, Pharmaceutical Research and Early Development Oncology, Roche Innovation Center Munich, Munich, Germany
| | - Bruno Gomes
- F. Hoffmann-La Roche AG, Pharmaceutical Research and Early Development Oncology, Roche Innovation Center Basel, Basel, Switzerland
| | - Marta Canamero
- F. Hoffmann-La Roche AG, Pharmaceutical Research and Early Development Oncology, Roche Innovation Center Munich, Munich, Germany
| | - Bernhard Reis
- F. Hoffmann-La Roche AG, Pharmaceutical Research and Early Development Oncology, Roche Innovation Center Basel, Basel, Switzerland
| | | | - Jehad Charo
- F. Hoffmann-La Roche AG, Pharmaceutical Research and Early Development Oncology, Roche Innovation Center Zurich, Zurich, Switzerland
| | | | - Vaios Karanikas
- F. Hoffmann-La Roche AG, Pharmaceutical Research and Early Development Oncology, Roche Innovation Center Zurich, Zurich, Switzerland.
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27
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This S, Valbon SF, Lebel MÈ, Melichar HJ. Strength and Numbers: The Role of Affinity and Avidity in the 'Quality' of T Cell Tolerance. Cells 2021; 10:1530. [PMID: 34204485 PMCID: PMC8234061 DOI: 10.3390/cells10061530] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2021] [Revised: 06/13/2021] [Accepted: 06/14/2021] [Indexed: 11/17/2022] Open
Abstract
The ability of T cells to identify foreign antigens and mount an efficient immune response while limiting activation upon recognition of self and self-associated peptides is critical. Multiple tolerance mechanisms work in concert to prevent the generation and activation of self-reactive T cells. T cell tolerance is tightly regulated, as defects in these processes can lead to devastating disease; a wide variety of autoimmune diseases and, more recently, adverse immune-related events associated with checkpoint blockade immunotherapy have been linked to a breakdown in T cell tolerance. The quantity and quality of antigen receptor signaling depend on a variety of parameters that include T cell receptor affinity and avidity for peptide. Autoreactive T cell fate choices (e.g., deletion, anergy, regulatory T cell development) are highly dependent on the strength of T cell receptor interactions with self-peptide. However, less is known about how differences in the strength of T cell receptor signaling during differentiation influences the 'function' and persistence of anergic and regulatory T cell populations. Here, we review the literature on this subject and discuss the clinical implications of how T cell receptor signal strength influences the 'quality' of anergic and regulatory T cell populations.
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Affiliation(s)
- Sébastien This
- Centre de Recherche de l’Hôpital Maisonneuve-Rosemont, Montréal, QC H1T 2M4, Canada; (S.T.); (S.F.V.); (M.-È.L.)
- Département de Microbiologie, Immunologie et Infectiologie, Université de Montréal, Montréal, QC H3C 3J7, Canada
| | - Stefanie F. Valbon
- Centre de Recherche de l’Hôpital Maisonneuve-Rosemont, Montréal, QC H1T 2M4, Canada; (S.T.); (S.F.V.); (M.-È.L.)
- Département de Microbiologie, Immunologie et Infectiologie, Université de Montréal, Montréal, QC H3C 3J7, Canada
| | - Marie-Ève Lebel
- Centre de Recherche de l’Hôpital Maisonneuve-Rosemont, Montréal, QC H1T 2M4, Canada; (S.T.); (S.F.V.); (M.-È.L.)
| | - Heather J. Melichar
- Centre de Recherche de l’Hôpital Maisonneuve-Rosemont, Montréal, QC H1T 2M4, Canada; (S.T.); (S.F.V.); (M.-È.L.)
- Département de Médecine, Université de Montréal, Montréal, QC H3T 1J4, Canada
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28
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Kumar ARK, Shou Y, Chan B, L K, Tay A. Materials for Improving Immune Cell Transfection. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2021; 33:e2007421. [PMID: 33860598 DOI: 10.1002/adma.202007421] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/30/2020] [Revised: 12/08/2020] [Indexed: 06/12/2023]
Abstract
Chimeric antigen receptor T cell (CAR-T) therapy holds great promise for preventing and treating deadly diseases such as cancer. However, it remains challenging to transfect and engineer primary immune cells for clinical cell manufacturing. Conventional tools using viral vectors and bulk electroporation suffer from low efficiency while posing risks like viral transgene integration and excessive biological perturbations. Emerging techniques using microfluidics, nanoparticles, and high-aspect-ratio nanostructures can overcome these challenges, and on top of that, provide universal and high-throughput cargo delivery. Herein, the strengths and limitations of traditional and emerging materials for immune cell transfection, and commercial development of these tools, are discussed. To enhance the characterization of transfection techniques and uptake by the clinical community, a list of in vitro and in vivo assays to perform, along with relevant protocols, is recommended. The overall aim, herein, is to motivate the development of novel materials to meet rising demand in transfection for clinical CAR-T cell manufacturing.
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Affiliation(s)
- Arun R K Kumar
- Department of Biomedical Engineering, National University of Singapore, Singapore, 117583, Singapore
- Institute for Health Innovation & Technology, National University of Singapore, Singapore, 117599, Singapore
| | - Yufeng Shou
- Department of Biomedical Engineering, National University of Singapore, Singapore, 117583, Singapore
| | - Brian Chan
- Department of Biomedical Engineering, National University of Singapore, Singapore, 117583, Singapore
| | - Krishaa L
- Department of Biomedical Engineering, National University of Singapore, Singapore, 117583, Singapore
| | - Andy Tay
- Department of Biomedical Engineering, National University of Singapore, Singapore, 117583, Singapore
- Institute for Health Innovation & Technology, National University of Singapore, Singapore, 117599, Singapore
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29
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Adair K, Meng X, Naisbitt DJ. Drug hapten-specific T-cell activation: Current status and unanswered questions. Proteomics 2021; 21:e2000267. [PMID: 33651918 DOI: 10.1002/pmic.202000267] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2020] [Revised: 02/14/2021] [Accepted: 02/16/2021] [Indexed: 11/07/2022]
Abstract
Drug haptens are formed from the irreversible, covalent binding of drugs to nucleophilic moieties on proteins, which can warrant adverse reactions in the body including severe delayed-type, T-cell mediated, drug hypersensitivity reactions (DHRs). While three main pathways exist for the activation of T-cells in DHRs, namely the hapten model, the pharmacological interaction model and the altered peptide repertoire model, the exact antigenic determinants responsible have not yet been defined. In recent years, progress has been made using advanced mass spectrometry-based proteomic methods to identify protein carriers and characterise the structure of drug-haptenated proteins. Since genome-wide association studies discovered a link between human leukocyte antigens (HLA) and an individual's susceptibility to DHRs, much effort has been made to define the drug-associated HLA ligands driving T-cell activation, including the elution of natural HLA peptides from HLA molecules and the generation of HLA-binding peptides. In this review, we discuss our current methodology used to design and synthesise drug-modified HLA ligands to investigate their immunogenicity using T-cell models, and thus their implication in drug hypersensitivity.
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Affiliation(s)
- Kareena Adair
- Department of Molecular and Clinical Pharmacology, MRC Centre for Drug Safety Science, University of Liverpool, Liverpool, UK
| | - Xiaoli Meng
- Department of Molecular and Clinical Pharmacology, MRC Centre for Drug Safety Science, University of Liverpool, Liverpool, UK
| | - Dean J Naisbitt
- Department of Molecular and Clinical Pharmacology, MRC Centre for Drug Safety Science, University of Liverpool, Liverpool, UK
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30
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Sugata K, Matsunaga Y, Yamashita Y, Nakatsugawa M, Guo T, Halabelian L, Ohashi Y, Saso K, Rahman MA, Anczurowski M, Wang CH, Murata K, Saijo H, Kagoya Y, Ly D, Burt BD, Butler MO, Mak TW, Hirano N. Affinity-matured HLA class II dimers for robust staining of antigen-specific CD4 + T cells. Nat Biotechnol 2021; 39:958-967. [PMID: 33649568 DOI: 10.1038/s41587-021-00836-4] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2019] [Accepted: 01/15/2021] [Indexed: 01/08/2023]
Abstract
Peptide-major histocompatibility complex (pMHC) multimers enable the detection of antigen-specific T cells in studies ranging from vaccine efficacy to cancer immunotherapy. However, this technology is unreliable when applied to pMHC class II for the detection of CD4+ T cells. Here, using a combination of molecular biological and immunological techniques, we cloned sequences encoding human leukocyte antigen (HLA)-DP, HLA-DQ and HLA-DR molecules with enhanced CD4 binding affinity (with a Kd of 8.9 ± 1.1 µM between CD4 and affinity-matured HLA-DP4) and produced affinity-matured class II dimers that stain antigen-specific T cells better than conventional multimers in both in vitro and ex vivo analyses. Using a comprehensive library of dimers for HLA-DP4, which is the most frequent HLA allele in many ancestry groups, we mapped 103 HLA-DP4-restricted epitopes derived from diverse tumor-associated antigens and cloned the cognate T-cell antigen receptor (TCR) genes from in vitro-stimulated CD4+ T cells. The availability of affinity-matured class II dimers across HLA-DP, HLA-DQ and HLA-DR alleles will aid in the investigation of human CD4+ T-cell responses.
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Affiliation(s)
- Kenji Sugata
- Tumor Immunotherapy Program, Campbell Family Institute for Breast Cancer Research, Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Yukiko Matsunaga
- Tumor Immunotherapy Program, Campbell Family Institute for Breast Cancer Research, Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Yuki Yamashita
- Tumor Immunotherapy Program, Campbell Family Institute for Breast Cancer Research, Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Munehide Nakatsugawa
- Tumor Immunotherapy Program, Campbell Family Institute for Breast Cancer Research, Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Tingxi Guo
- Tumor Immunotherapy Program, Campbell Family Institute for Breast Cancer Research, Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Levon Halabelian
- Structural Genomics Consortium, University of Toronto, Toronto, Ontario, Canada
| | - Yota Ohashi
- Tumor Immunotherapy Program, Campbell Family Institute for Breast Cancer Research, Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada.,Department of Immunology, University of Toronto, Toronto, Ontario, Canada
| | - Kayoko Saso
- Tumor Immunotherapy Program, Campbell Family Institute for Breast Cancer Research, Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Muhammed A Rahman
- Tumor Immunotherapy Program, Campbell Family Institute for Breast Cancer Research, Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Mark Anczurowski
- Tumor Immunotherapy Program, Campbell Family Institute for Breast Cancer Research, Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada.,Department of Immunology, University of Toronto, Toronto, Ontario, Canada
| | - Chung-Hsi Wang
- Tumor Immunotherapy Program, Campbell Family Institute for Breast Cancer Research, Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada.,Department of Immunology, University of Toronto, Toronto, Ontario, Canada
| | - Kenji Murata
- Tumor Immunotherapy Program, Campbell Family Institute for Breast Cancer Research, Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Hiroshi Saijo
- Tumor Immunotherapy Program, Campbell Family Institute for Breast Cancer Research, Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Yuki Kagoya
- Tumor Immunotherapy Program, Campbell Family Institute for Breast Cancer Research, Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Dalam Ly
- Tumor Immunotherapy Program, Campbell Family Institute for Breast Cancer Research, Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Brian D Burt
- Tumor Immunotherapy Program, Campbell Family Institute for Breast Cancer Research, Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Marcus O Butler
- Tumor Immunotherapy Program, Campbell Family Institute for Breast Cancer Research, Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada.,Department of Immunology, University of Toronto, Toronto, Ontario, Canada.,Department of Medicine, University of Toronto, Toronto, Ontario, Canada
| | - Tak W Mak
- Tumor Immunotherapy Program, Campbell Family Institute for Breast Cancer Research, Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada.,Department of Immunology, University of Toronto, Toronto, Ontario, Canada
| | - Naoto Hirano
- Tumor Immunotherapy Program, Campbell Family Institute for Breast Cancer Research, Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada. .,Department of Immunology, University of Toronto, Toronto, Ontario, Canada.
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31
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Stark FC, Dudani R, Agbayani G, McCluskie MJ. A Method to Evaluate In Vivo CD8 + T Cell Cytotoxicity in a Murine Model. Methods Mol Biol 2021; 2183:549-558. [PMID: 32959267 DOI: 10.1007/978-1-0716-0795-4_32] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Herein, a method to measure in vivo CD8+ T cell cytotoxicity in a murine model is presented. The activation of a strong CD8+ T cell response is paramount when designing vaccines to tackle intracellular infections and for cancer therapy. CD8+ T cells can directly kill infected and transformed cells and are directly associated with beneficial protection in many disease models. CD8+ T cell cytotoxicity can be measured using multiple methods including measuring IFNγ production by ELISPOT or measuring intracellular cytokines or cytotoxic granules by flow cytometry. However, to determine the ability of CD8+ T cells to kill their target in the context of its cognate receptor and in their native environment, the in vivo cytotoxic T cell assay (in vivo CTL) is ideal. The in vivo CTL assay provides a snapshot of the whole ability of the host to kill "Target" cells by measuring the loss of injected target cells relative to "Non-target" cells. The assay involves isolating splenocytes from donor mice, forming "Target" and "Non-target" cellular samples and injecting them intravenously into naïve and experimental mice at a chosen time-point in the experiment. Mice are humanely sacrificed 20 h later, and their spleens are excised and processed for flow cytometric analysis. The extent of "Target" cell killing relative to "Non-target" cells is determined by comparing the surviving proportions of these cells among experimental mice relative to naïve mice. The in vivo CTL assay is a rapid, sensitive, and reliable method to measure the potency of CD8+ T cells in their host to kill their target.
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Affiliation(s)
- Felicity C Stark
- Human Health Therapeutics, National Research Council Canada, Ottawa, ON, Canada
| | - Renu Dudani
- Human Health Therapeutics, National Research Council Canada, Ottawa, ON, Canada
| | - Gerard Agbayani
- Human Health Therapeutics, National Research Council Canada, Ottawa, ON, Canada
| | - Michael J McCluskie
- Human Health Therapeutics, National Research Council Canada, Ottawa, ON, Canada.
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32
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Kolawole EM, Lamb TJ, Evavold BD. Relationship of 2D Affinity to T Cell Functional Outcomes. Int J Mol Sci 2020; 21:ijms21217969. [PMID: 33120989 PMCID: PMC7662510 DOI: 10.3390/ijms21217969] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2020] [Revised: 10/14/2020] [Accepted: 10/23/2020] [Indexed: 12/11/2022] Open
Abstract
T cells are critical for a functioning adaptive immune response and a strong correlation exists between T cell responses and T cell receptor (TCR): peptide-loaded MHC (pMHC) binding. Studies that utilize pMHC tetramer, multimers, and assays of three-dimensional (3D) affinity have provided advancements in our understanding of T cell responses across different diseases. However, these technologies focus on higher affinity and avidity T cells while missing the lower affinity responders. Lower affinity TCRs in expanded polyclonal populations almost always constitute a significant proportion of the response with cells mediating different effector functions associated with variation in the proportion of high and low affinity T cells. Since lower affinity T cells expand and are functional, a fully inclusive view of T cell responses is required to accurately interpret the role of affinity for adaptive T cell immunity. For example, low affinity T cells are capable of inducing autoimmune disease and T cells with an intermediate affinity have been shown to exhibit an optimal anti-tumor response. Here, we focus on how affinity of the TCR may relate to T cell phenotype and provide examples where 2D affinity influences functional outcomes.
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33
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Keeble AH, Howarth M. Power to the protein: enhancing and combining activities using the Spy toolbox. Chem Sci 2020; 11:7281-7291. [PMID: 33552459 PMCID: PMC7844731 DOI: 10.1039/d0sc01878c] [Citation(s) in RCA: 82] [Impact Index Per Article: 20.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2020] [Accepted: 06/30/2020] [Indexed: 12/27/2022] Open
Abstract
Proteins span an extraordinary range of shapes, sizes and functionalities. Therefore generic approaches are needed to overcome this diversity and stream-line protein analysis or application. Here we review SpyTag technology, now used in hundreds of publications or patents, and its potential for detecting and controlling protein behaviour. SpyTag forms a spontaneous and irreversible isopeptide bond upon binding its protein partner SpyCatcher, where both parts are genetically-encoded. New variants of this pair allow reaction at a rate approaching the diffusion limit, while reversible versions allow purification of SpyTagged proteins or tuned dynamic interaction inside cells. Anchoring of SpyTag-linked proteins has been established to diverse nanoparticles or surfaces, including gold, graphene and the air/water interface. SpyTag/SpyCatcher is mechanically stable, so is widely used for investigating protein folding and force sensitivity. A toolbox of scaffolds allows SpyTag-fusions to be assembled into defined multimers, from dimers to 180-mers, or unlimited 1D, 2D or 3D networks. Icosahedral multimers are being evaluated for vaccination against malaria, HIV and cancer. For enzymes, Spy technology has increased resilience, promoted substrate channelling, and assembled hydrogels for continuous flow biocatalysis. Combinatorial increase in functionality has been achieved through modular derivatisation of antibodies, light-emitting diodes or viral vectors. In living cells, SpyTag allowed imaging of protein trafficking, retargeting of CAR-T cell killing, investigation of heart contraction, and control of nucleosome position. The simple genetic encoding and rapid irreversible reaction provide diverse opportunities to enhance protein function. We describe limitations as well as future directions.
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Affiliation(s)
- Anthony H Keeble
- Department of Biochemistry , University of Oxford , South Parks Road , Oxford , OX1 3QU , UK . ; Tel: +44 (0)1865 613200
| | - Mark Howarth
- Department of Biochemistry , University of Oxford , South Parks Road , Oxford , OX1 3QU , UK . ; Tel: +44 (0)1865 613200
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34
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Identification of a superagonist variant of the immunodominant Yellow fever virus epitope NS4b 214-222 by combinatorial peptide library screening. Mol Immunol 2020; 125:43-50. [PMID: 32645549 DOI: 10.1016/j.molimm.2020.06.025] [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: 01/27/2020] [Revised: 05/27/2020] [Accepted: 06/24/2020] [Indexed: 11/22/2022]
Abstract
The CD8 T cell response to the HLA-A2-restricted epitope LLWNGPMAV (LLW) of the non-structural protein 4b of Yellow Fever Virus (YFV) is remarkably immunodominant, highly prevalent and powerful in YFV-vaccinated humans. Here we used a combinatorial peptide library screening in the context of an A2/LLW-specific CD8 T cell clone to identify a superagonist that features a methionine to isoleucine substitution at position 7. Based on in silico modeling, the functional enhancement of this LLW-7I mutation was associated with alterations in the structural dynamics of the peptide in the major histocompatibility complex (pMHC) binding with the T cell receptor (TCR). While the TCR off-rate of LLW-7I pMHC is comparable to the wild type peptide, the rigidity of the 7I peptide seems to confer less entropy loss upon TCR binding. This LLW-7I superagonist is an example of improved functionality in human CD8 T cells associated with optimized ligand rigidity for TCR binding and not with changes in TCR:pMHC off-rate kinetics.
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35
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Souter MNT, Loh L, Li S, Meehan BS, Gherardin NA, Godfrey DI, Rossjohn J, Fairlie DP, Kedzierska K, Pellicci DG, Chen Z, Kjer-Nielsen L, Corbett AJ, McCluskey J, Eckle SBG. Characterization of Human Mucosal-associated Invariant T (MAIT) Cells. ACTA ACUST UNITED AC 2020; 127:e90. [PMID: 31763790 DOI: 10.1002/cpim.90] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Mucosal-associated invariant T (MAIT) cells are a subset of unconventional T cells restricted by the major histocompatibility complex (MHC) class I-like molecule MHC-related protein 1 (MR1). MAIT cells are found throughout the body, especially in human blood and liver. Unlike conventional T cells, which are stimulated by peptide antigens presented by MHC molecules, MAIT cells recognize metabolite antigens derived from an intermediate in the microbial biosynthesis of riboflavin. MAIT cells mediate protective immunity to infections by riboflavin-producing microbes via the production of cytokines and cytotoxicity. The discovery of stimulating MAIT cell antigens allowed for the development of an analytical tool, the MR1 tetramer, that binds specifically to the MAIT T cell receptor (TCR) and is becoming the gold standard for identification of MAIT cells by flow cytometry. This article describes protocols to characterize the phenotype of human MAIT cells in blood and tissues by flow cytometry using fluorescently labeled human MR1 tetramers alongside antibodies specific for MAIT cell markers. © 2019 by John Wiley & Sons, Inc. The main protocols include: Basic Protocol 1: Determining the frequency and steady-state surface phenotype of human MAIT cells Basic Protocol 2: Determining the activation phenotype of human MAIT cells in blood Basic Protocol 3: Characterizing MAIT cell TCRs using TCR-positive reporter cell lines Alternate protocols are provided for determining the absolute number, transcription factor phenotype, and TCR usage of human MAIT cells; and determining activation phenotype by staining for intracellular markers, measuring secreted cytokines, and measuring fluorescent dye dilution due to proliferation. Additional methods are provided for determining the capacity of MAIT cells to produce cytokine independently of antigen using plate-bound or bead-immobilized CD3/CD28 stimulation; and determining the MR1-Ag dependence of MAIT cell activation using MR1-blocking antibody or competitive inhibition. For TCR-positive reporter cell lines, methods are also provided for evaluating the MAIT TCR-mediated MR1-Ag response, determining the capacity of the reporter lines to produce cytokine independently of antigen, determining the MR1-Ag dependence of the reporter lines, and evaluating the MR1-Ag response of the reporter lines using IL-2 secretion. Support Protocols describe the preparation of PBMCs from human blood, the preparation of single-cell suspensions from tissue, the isolation of MAIT cells by FACS and MACS, cloning MAIT TCRα and β chain genes and MR1 genes for transduction, generating stably and transiently transfected cells lines, generating a stable MR1 knockout antigen-presenting cell line, and generating monocyte-derived dendritic cells.
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Affiliation(s)
- Michael N T Souter
- Department of Microbiology and Immunology, Peter Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, Australia.,Australian Research Council Centre of Excellence in Advanced Molecular Imaging, University of Melbourne, Parkville, Australia
| | - Liyen Loh
- Department of Microbiology and Immunology, Peter Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, Australia
| | - Shihan Li
- Department of Microbiology and Immunology, Peter Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, Australia.,Australian Research Council Centre of Excellence in Advanced Molecular Imaging, University of Melbourne, Parkville, Australia
| | - Bronwyn S Meehan
- Department of Microbiology and Immunology, Peter Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, Australia
| | - Nicholas A Gherardin
- Department of Microbiology and Immunology, Peter Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, Australia.,Australian Research Council Centre of Excellence in Advanced Molecular Imaging, University of Melbourne, Parkville, Australia
| | - Dale I Godfrey
- Department of Microbiology and Immunology, Peter Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, Australia.,Australian Research Council Centre of Excellence in Advanced Molecular Imaging, University of Melbourne, Parkville, Australia
| | - Jamie Rossjohn
- Infection and Immunity Program and Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, Australia.,Australian Research Council Centre of Excellence in Advanced Molecular Imaging, Monash University, Clayton, Australia.,Institute of Infection and Immunity, Cardiff University School of Medicine, Heath Park, Wales, United Kingdom
| | - David P Fairlie
- Division of Chemistry and Structural Biology, Institute for Molecular Bioscience, University of Queensland, Brisbane, Australia.,Australian Research Council Centre of Excellence in Advanced Molecular Imaging, University of Queensland, Brisbane, Australia
| | - Katherine Kedzierska
- Department of Microbiology and Immunology, Peter Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, Australia
| | - Daniel G Pellicci
- Department of Microbiology and Immunology, Peter Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, Australia.,Murdoch Children's Research Institute, Parkville, Australia
| | - Zhenjun Chen
- Department of Microbiology and Immunology, Peter Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, Australia
| | - Lars Kjer-Nielsen
- Department of Microbiology and Immunology, Peter Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, Australia
| | - Alexandra J Corbett
- Department of Microbiology and Immunology, Peter Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, Australia
| | - James McCluskey
- Department of Microbiology and Immunology, Peter Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, Australia
| | - Sidonia B G Eckle
- Department of Microbiology and Immunology, Peter Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, Australia
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36
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Abstract
T cells respond to threats in an antigen-specific manner using T cell receptors (TCRs) that recognize short peptide antigens presented on major histocompatibility complex (MHC) proteins. The TCR-peptide-MHC interaction mediated between a T cell and its target cell dictates its function and thereby influences its role in disease. A lack of approaches for antigen discovery has limited the fundamental understanding of the antigenic landscape of the overall T cell response. Recent advances in high-throughput sequencing, mass cytometry, microfluidics and computational biology have led to a surge in approaches to address the challenge of T cell antigen discovery. Here, we summarize the scope of this challenge, discuss in depth the recent exciting work and highlight the outstanding questions and remaining technical hurdles in this field.
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37
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Christophersen A. Peptide-MHC class I and class II tetramers: From flow to mass cytometry. HLA 2020; 95:169-178. [PMID: 31891448 DOI: 10.1111/tan.13789] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2019] [Revised: 11/26/2019] [Accepted: 12/30/2019] [Indexed: 12/31/2022]
Abstract
To develop better vaccines and more targeted treatments for cancer and autoimmune disorders, the disease-specific T cells and their cognate antigens need to be better characterized. For more than two decades, peptide-major histocompatibility complex (pMHC) tetramers and flow cytometry have been the gold standard for detection of CD8+ and CD4+ T cells specific to antigens in the context of MHC class I and class II, respectively. Nonetheless, more recent studies combining such reagents with mass cytometry, that is, cytometry by time of flight (CyTOF), have offered far more comprehensive profiling of antigen-specific T-cell responses. In addition, mass cytometry has enabled ex vivo screening of CD8+ T-cell reactivities against hundreds of MHC class I restricted candidate epitopes. MHC class II molecules, on the other hand, have been challenging to combine with mass cytometry as they are more complex and bind with lower affinities to cognate T-cell receptors than MHC class I molecules. In this review, I discuss how techniques originally developed to improve the staining capacity of pMHC tetramers in flow cytometry led to the successful combination of such reagents with mass cytometry. Especially, I will highlight very recent advances facilitating the combination with pMHC class II tetramers. Together, these mass cytometry-based studies can help develop more targeted treatments for cancer and autoimmune disorders.
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Affiliation(s)
- Asbjørn Christophersen
- KG Jebsen Coeliac Disease Research Centre, University of Oslo, Oslo, Norway.,Institute of Clinical Medicine, University of Oslo, Norway.,Department of Immunology, University of Oslo, Oslo, Norway
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38
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Abstract
T cells can be controllably stimulated through antigen-specific or nonspecific protocols. Accompanying functional hallmarks of T cell activation can include cytoskeletal reorganization, cell size increase, and cytokine secretion. Photon-induced near-field electron microscopy (PINEM) is used to image and quantify evanescent electric fields at the surface of T cells as a function of various stimulation conditions. While PINEM signal strength scales with multiple of the biophysical changes associated with T cell functional activation, it mostly strongly correlates with antigen-engagement of the T cell receptors, even under conditions that do not lead to functional T cell activation. PINEM image analysis suggests that a stimulation-induced reorganization of T cell surface structure, especially over length scales of a few hundred nanometers, is the dominant contributor to these PINEM signal changes. These experiments reveal that PINEM can provide a sensitive label-free probe of nanoscale cellular surface structures.
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39
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Roesner LM, Werfel T. Autoimmunity (or Not) in Atopic Dermatitis. Front Immunol 2019; 10:2128. [PMID: 31552053 PMCID: PMC6746887 DOI: 10.3389/fimmu.2019.02128] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2019] [Accepted: 08/23/2019] [Indexed: 12/18/2022] Open
Abstract
Atopic dermatitis (AD), one of the most frequent inflammatory skin diseases worldwide, is believed to result from a disturbed skin barrier as well as aberrant immune reactions against per se harmless allergens. Starting mostly during childhood with a chronic, remitting relapsing course, the disease can persist into adulthood in about one fifth of patients. Immune reactions to self-proteins have been observed in AD patients already in the beginning of the Twentieth century, when human cellular extracts were shown to provoke skin lesions. However, the term “autoimmunity” has never been claimed, since AD is first and foremost an atopic disease. In contrast, this IgE-hallmarked autoreactivity was termed “autoallergy” and is ongoing discussed regarding its impact on the disease. Since severely affected patients tend to develop IgE-hypersensitivity reactions to numerous environmental allergens, the impact of immune responses to self-proteins is difficult to determine. On the other hand: any autoreactivity, irrespective of the magnitude, implicates the potential of driving the chronification of the disease while shaping the immune response. This review article revisits the observations made on autoallergy from an actual point of view and tries to approach the question whether these still point to a contribution to the disease.
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Affiliation(s)
- Lennart M Roesner
- Division of Immunodermatology and Allergy Research, Department of Dermatology and Allergy, Hannover Medical School, Hanover, Germany
| | - Thomas Werfel
- Division of Immunodermatology and Allergy Research, Department of Dermatology and Allergy, Hannover Medical School, Hanover, Germany
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40
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Magnin M, Guillaume P, Coukos G, Harari A, Schmidt J. High-throughput identification of human antigen-specific CD8 + and CD4 + T cells using soluble pMHC multimers. Methods Enzymol 2019; 631:21-42. [PMID: 31948548 DOI: 10.1016/bs.mie.2019.05.019] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
Peptide major histocompatibility complex (pMHC) multimers have been used since decades to identify, isolate and analyze antigen-specific T cells by flow (and more recently mass) cytometry. Yet well established as a standard technology, improvements are still required to face the growing needs of personalized immune monitoring. Here we review the latest developments about (i) the quality of pMHC class I and II monomers, (ii) the importance of the multimeric scaffold, (iii) the staining conditions and (iv) the high-throughput synthesis of pMHC monomers. Finally, innovative multiplexed, combinatorial strategies for parallel detection of antigen-specific T cells in a single sample are discussed.
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Affiliation(s)
- Morgane Magnin
- Ludwig Institute for Cancer Research, University of Lausanne, Lausanne, Switzerland; Department of Oncology, University Hospital of Lausanne, Lausanne, Switzerland
| | - Philippe Guillaume
- Ludwig Institute for Cancer Research, University of Lausanne, Lausanne, Switzerland; Department of Oncology, University Hospital of Lausanne, Lausanne, Switzerland
| | - George Coukos
- Ludwig Institute for Cancer Research, University of Lausanne, Lausanne, Switzerland; Department of Oncology, University Hospital of Lausanne, Lausanne, Switzerland.
| | - Alexandre Harari
- Ludwig Institute for Cancer Research, University of Lausanne, Lausanne, Switzerland; Department of Oncology, University Hospital of Lausanne, Lausanne, Switzerland
| | - Julien Schmidt
- Ludwig Institute for Cancer Research, University of Lausanne, Lausanne, Switzerland; Department of Oncology, University Hospital of Lausanne, Lausanne, Switzerland
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41
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Binan L, Bélanger F, Uriarte M, Lemay JF, Pelletier De Koninck JC, Roy J, Affar EB, Drobetsky E, Wurtele H, Costantino S. Opto-magnetic capture of individual cells based on visual phenotypes. eLife 2019; 8:e45239. [PMID: 30969169 PMCID: PMC6499596 DOI: 10.7554/elife.45239] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2019] [Accepted: 04/09/2019] [Indexed: 12/19/2022] Open
Abstract
The ability to isolate rare live cells within a heterogeneous population based solely on visual criteria remains technically challenging, due largely to limitations imposed by existing sorting technologies. Here, we present a new method that permits labeling cells of interest by attaching streptavidin-coated magnetic beads to their membranes using the lasers of a confocal microscope. A simple magnet allows highly specific isolation of the labeled cells, which then remain viable and proliferate normally. As proof of principle, we tagged, isolated, and expanded individual cells based on three biologically relevant visual characteristics: i) presence of multiple nuclei, ii) accumulation of lipid vesicles, and iii) ability to resolve ionizing radiation-induced DNA damage foci. Our method constitutes a rapid, efficient, and cost-effective approach for isolation and subsequent characterization of rare cells based on observable traits such as movement, shape, or location, which in turn can generate novel mechanistic insights into important biological processes.
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Affiliation(s)
- Loïc Binan
- Research CenterMaisonneuve-Rosemont HospitalMontrealCanada
- Department of OphthalmologyUniversity of MontrealMontrealCanada
| | - François Bélanger
- Research CenterMaisonneuve-Rosemont HospitalMontrealCanada
- Department of Medicine and Molecular Biology ProgramUniversity of MontrealMontrealCanada
| | - Maxime Uriarte
- Research CenterMaisonneuve-Rosemont HospitalMontrealCanada
- Department of Medicine and Molecular Biology ProgramUniversity of MontrealMontrealCanada
| | | | | | - Joannie Roy
- Research CenterMaisonneuve-Rosemont HospitalMontrealCanada
| | - El Bachir Affar
- Research CenterMaisonneuve-Rosemont HospitalMontrealCanada
- Department of Medicine and Molecular Biology ProgramUniversity of MontrealMontrealCanada
| | - Elliot Drobetsky
- Research CenterMaisonneuve-Rosemont HospitalMontrealCanada
- Department of Medicine and Molecular Biology ProgramUniversity of MontrealMontrealCanada
| | - Hugo Wurtele
- Research CenterMaisonneuve-Rosemont HospitalMontrealCanada
| | - Santiago Costantino
- Research CenterMaisonneuve-Rosemont HospitalMontrealCanada
- Department of OphthalmologyUniversity of MontrealMontrealCanada
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42
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Goyette J, Nieves DJ, Ma Y, Gaus K. How does T cell receptor clustering impact on signal transduction? J Cell Sci 2019; 132:132/4/jcs226423. [DOI: 10.1242/jcs.226423] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
ABSTRACT
The essential function of the T cell receptor (TCR) is to translate the engagement of peptides on the major histocompatibility complex (pMHC) into appropriate intracellular signals through the associated cluster of differentiation 3 (CD3) complex. The spatial organization of the TCR–CD3 complex in the membrane is thought to be a key regulatory element of signal transduction, raising the question of how receptor clustering impacts on TCR triggering. How signal transduction at the TCR–CD3 complex encodes the quality and quantity of pMHC molecules is not fully understood. This question can be approached by reconstituting T cell signaling in model and cell membranes and addressed by single-molecule imaging of endogenous proteins in T cells. We highlight such methods and further discuss how TCR clustering could affect pMHC rebinding rates, the local balance between kinase and phosphatase activity and/or the lipid environment to regulate the signal efficiency of the TCR–CD3 complex. We also examine whether clustering could affect the conformation of cytoplasmic CD3 tails through a biophysical mechanism. Taken together, we highlight how the spatial organization of the TCR–CD3 complex – addressed by reconstitution approaches – has emerged as a key regulatory element in signal transduction of this archetypal immune receptor.
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Affiliation(s)
- Jesse Goyette
- EMBL Australia Node in Single Molecule Science, University of New South Wales, Sydney 2052, Australia
- ARC Centre of Excellence in Advanced Molecular imaging, University of New South Wales, Sydney 2052, Australia
| | - Daniel J. Nieves
- EMBL Australia Node in Single Molecule Science, University of New South Wales, Sydney 2052, Australia
- ARC Centre of Excellence in Advanced Molecular imaging, University of New South Wales, Sydney 2052, Australia
| | - Yuanqing Ma
- EMBL Australia Node in Single Molecule Science, University of New South Wales, Sydney 2052, Australia
- ARC Centre of Excellence in Advanced Molecular imaging, University of New South Wales, Sydney 2052, Australia
| | - Katharina Gaus
- EMBL Australia Node in Single Molecule Science, University of New South Wales, Sydney 2052, Australia
- ARC Centre of Excellence in Advanced Molecular imaging, University of New South Wales, Sydney 2052, Australia
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43
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Kong YY, Kwok WW. Identification of Human Antigen-Specific CD4 + T-Cells with Peptide-MHC Multimer Technologies. Methods Mol Biol 2019; 1988:375-386. [PMID: 31147953 DOI: 10.1007/978-1-4939-9450-2_26] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
The development of peptide-MHC class II multimers has provided a novel approach in studying antigen-specific CD4+ T-cells and extended the knowledge of these T cells in various disease settings, including infectious diseases, autoimmune diseases, cancer, and allergies. This chapter discusses the various applications of the peptide-MHC class II multimer technologies, specifically their uses in the evaluation of antigen-specific CD4+ T-cells ex vivo, and their uses in epitope identification.
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Affiliation(s)
- Ying Ying Kong
- Benaroya Research Institute at Virginia Mason, Seattle, WA, USA
| | - William W Kwok
- Benaroya Research Institute at Virginia Mason, Seattle, WA, USA.
- Department of Medicine, University of Washington, Seattle, WA, USA.
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44
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Bunse L, Green EW, Platten M. High-throughput discovery of cancer-targeting TCRs. Methods Enzymol 2019; 629:401-417. [DOI: 10.1016/bs.mie.2019.10.009] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
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45
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Dey S, Kamil Reza K, Wuethrich A, Korbie D, Ibn Sina AA, Trau M. Tracking antigen specific T-cells: Technological advancement and limitations. Biotechnol Adv 2018; 37:145-153. [PMID: 30508573 DOI: 10.1016/j.biotechadv.2018.11.010] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2018] [Revised: 10/30/2018] [Accepted: 11/20/2018] [Indexed: 11/18/2022]
Abstract
Assessing T-cell mediated immune status can help to understand the body's response to disease and also provide essential diagnostic information. However, detection and characterization of immune response are challenging due to the rarity of signature biomolecules in biological fluid and require highly sensitive and specific assay technique for the analysis. Until now, several techniques spanning from flow cytometry to microsensors have been developed or under investigation for T-cell mediated immune response monitoring. Most of the current assays are designed to estimate average immune responses, i.e., total functional protein analysis and detection of total T-cells irrespective of their antigen specificity. Although potential, immune response analysis without detecting and characterizing the rare subset of T-cell population could lead to over or underestimation of patient's immune status. Addressing this limitation, recently a number of technological advancements in biosensing have been developed for this. The potential of simple and precise micro-technologies including microarray and microfluidic platforms for assessing antigen-specific T-cells will be highlighted in this review, together with a discussion on existing challenges and future aspects of immune-sensor development.
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Affiliation(s)
- Shuvashis Dey
- Centre for Personalised Nanomedicine, Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, QLD 4072, Australia
| | - K Kamil Reza
- Centre for Personalised Nanomedicine, Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, QLD 4072, Australia
| | - Alain Wuethrich
- Centre for Personalised Nanomedicine, Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, QLD 4072, Australia
| | - Darren Korbie
- Centre for Personalised Nanomedicine, Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, QLD 4072, Australia
| | - Abu Ali Ibn Sina
- Centre for Personalised Nanomedicine, Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, QLD 4072, Australia.
| | - Matt Trau
- Centre for Personalised Nanomedicine, Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, QLD 4072, Australia; School of Chemistry and Molecular Biosciences, The University of Queensland, QLD 4072, Australia.
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46
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García-Guerrero E, Sánchez-Abarca LI, Domingo E, Ramos TL, Bejarano-García JA, Gonzalez-Campos JA, Caballero-Velázquez T, Pérez-Simón JA. Selection of Tumor-Specific Cytotoxic T Lymphocytes in Acute Myeloid Leukemia Patients Through the Identification of T-Cells Capable to Establish Stable Interactions With the Leukemic Cells: "Doublet Technology". Front Immunol 2018; 9:1971. [PMID: 30233577 PMCID: PMC6129592 DOI: 10.3389/fimmu.2018.01971] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2018] [Accepted: 08/10/2018] [Indexed: 01/28/2023] Open
Abstract
The relevance of the immune system in cancer has long been studied. Autologous adoptive T cell therapies, based on the use of tumor infiltrating lymphocytes (TILs), have made great progress in recent years for the treatment of solid tumors, especially melanoma. However, further work is needed to isolate tumor-reactive T cells among patients diagnosed with hematologic malignancies. The dynamics of the interaction between T cells and antigen presenting cells (APC) dictate the quality of the immune responses. While stable joints between target cells and T lymphocytes lead to the induction of T cell activation and immune response, brief contacts contribute to the induction of immune-tolerance. Taking advantage of the strong interaction between target cell and activated T-cells, we show the feasibility to identify and isolate tumor-specific cytotoxic T lymphocytes (CTLs) from acute myeloid leukemia (AML) patients by flow cytometry. Using this technology, CTLs bound through T cell receptor (TCR) to tumor cells can be identified in peripheral blood and bone marrow and subsequently selected and isolated by FACS-based cell sorting. These CTLs display higher percentage of effector cells and marked cytotoxic activity against AML blasts. In conclusion, we have developed a new procedure to identify and select specific cytotoxic T cells in patients diagnosed with acute myeloid leukemia.
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Affiliation(s)
- Estefanía García-Guerrero
- Instituto de Biomedicina de Sevilla, UGC de Hematología, Hospital Universitario Virgen del Rocío and Consejo Superior de Investigaciones Científicas (CSIC) and Centro de Investigación Biomédica en Red Cáncer (CIBERONC), Universidad de Sevilla, Seville, Spain
| | - Luís I Sánchez-Abarca
- Servicio de Hematología, Instituto de Investigación Biomédica de Salamanca (IBSAL) - Hospital Universitario de Salamanca, Salamanca, Spain
| | - Esther Domingo
- Instituto de Biomedicina de Sevilla, UGC de Hematología, Hospital Universitario Virgen del Rocío and Consejo Superior de Investigaciones Científicas (CSIC) and Centro de Investigación Biomédica en Red Cáncer (CIBERONC), Universidad de Sevilla, Seville, Spain
| | - Teresa L Ramos
- Instituto de Biomedicina de Sevilla, UGC de Hematología, Hospital Universitario Virgen del Rocío and Consejo Superior de Investigaciones Científicas (CSIC) and Centro de Investigación Biomédica en Red Cáncer (CIBERONC), Universidad de Sevilla, Seville, Spain
| | - Jose A Bejarano-García
- Instituto de Biomedicina de Sevilla, UGC de Hematología, Hospital Universitario Virgen del Rocío and Consejo Superior de Investigaciones Científicas (CSIC) and Centro de Investigación Biomédica en Red Cáncer (CIBERONC), Universidad de Sevilla, Seville, Spain
| | - Jose A Gonzalez-Campos
- Instituto de Biomedicina de Sevilla, UGC de Hematología, Hospital Universitario Virgen del Rocío and Consejo Superior de Investigaciones Científicas (CSIC) and Centro de Investigación Biomédica en Red Cáncer (CIBERONC), Universidad de Sevilla, Seville, Spain
| | - Teresa Caballero-Velázquez
- Instituto de Biomedicina de Sevilla, UGC de Hematología, Hospital Universitario Virgen del Rocío and Consejo Superior de Investigaciones Científicas (CSIC) and Centro de Investigación Biomédica en Red Cáncer (CIBERONC), Universidad de Sevilla, Seville, Spain
| | - Jose A Pérez-Simón
- Instituto de Biomedicina de Sevilla, UGC de Hematología, Hospital Universitario Virgen del Rocío and Consejo Superior de Investigaciones Científicas (CSIC) and Centro de Investigación Biomédica en Red Cáncer (CIBERONC), Universidad de Sevilla, Seville, Spain
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47
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Dolton G, Zervoudi E, Rius C, Wall A, Thomas HL, Fuller A, Yeo L, Legut M, Wheeler S, Attaf M, Chudakov DM, Choy E, Peakman M, Sewell AK. Optimized Peptide-MHC Multimer Protocols for Detection and Isolation of Autoimmune T-Cells. Front Immunol 2018; 9:1378. [PMID: 30008714 PMCID: PMC6034003 DOI: 10.3389/fimmu.2018.01378] [Citation(s) in RCA: 49] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2018] [Accepted: 06/04/2018] [Indexed: 12/14/2022] Open
Abstract
Peptide–MHC (pMHC) multimers have become the “gold standard” for the detection and isolation of antigen-specific T-cells but recent evidence shows that normal use of these reagents can miss fully functional T-cells that bear T-cell receptors (TCRs) with low affinity for cognate antigen. This issue is particularly pronounced for anticancer and autoimmune T-cells as self-reactive T-cell populations are enriched for low-affinity TCRs due to the removal of cells with higher affinity receptors by immune tolerance mechanisms. Here, we stained a wide variety of self-reactive human T-cells using regular pMHC staining and an optimized technique that included: (i) protein kinase inhibitor (PKI), to prevent TCR triggering and internalization, and (ii) anti-fluorochrome antibody, to reduce reagent dissociation during washing steps. Lymphocytes derived from the peripheral blood of type 1 diabetes patients were stained with pMHC multimers made with epitopes from preproinsulin (PPI), insulin-β chain, glutamic acid decarboxylase 65 (GAD65), or glucose-6-phospate catalytic subunit-related protein (IGRP) presented by disease-risk allelles HLA A*02:01 or HLA*24:02. Samples from ankylosing spondylitis patients were stained with a multimerized epitope from vasoactive intestinal polypeptide receptor 1 (VIPR1) presented by HLA B*27:05. Optimized procedures stained an average of 40.5-fold (p = 0.01, range between 1.4 and 198) more cells than could be detected without the inclusion of PKI and cross-linking anti-fluorochrome antibody. Higher order pMHC dextramers recovered more cells than pMHC tetramers in parallel assays, and standard staining protocols with pMHC tetramers routinely recovered less cells than functional assays. HLA A*02:01-restricted PPI-specific and HLA B*27:05-restricted VIPR1-specific T-cell clones generated using the optimized procedure could not be stained by standard pMHC tetramer staining. However, these clones responded well to exogenously supplied peptide and endogenously processed and presented epitopes. We also showed that anti-fluorochrome antibody-conjugated magnetic beads enhanced staining of self-reactive T-cells that could not be stained using standard protocols, thus enabling rapid ex vivo isolation of autoimmune T-cells. We, therefore, conclude that regular pMHC tetramer staining is generally unsuitable for recovering self-reactive T-cells from clinical samples and recommend the use of the optimized protocols described herein.
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Affiliation(s)
- Garry Dolton
- Division of Infection and Immunity, Cardiff University School of Medicine, Cardiff, United Kingdom
| | - Efthalia Zervoudi
- Division of Infection and Immunity, Cardiff University School of Medicine, Cardiff, United Kingdom
| | - Cristina Rius
- Division of Infection and Immunity, Cardiff University School of Medicine, Cardiff, United Kingdom
| | - Aaron Wall
- Division of Infection and Immunity, Cardiff University School of Medicine, Cardiff, United Kingdom
| | - Hannah L Thomas
- Division of Infection and Immunity, Cardiff University School of Medicine, Cardiff, United Kingdom
| | - Anna Fuller
- Division of Infection and Immunity, Cardiff University School of Medicine, Cardiff, United Kingdom
| | - Lorraine Yeo
- Department of Immunobiology, Faculty of Life Sciences and Medicine, 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
| | - Mateusz Legut
- Division of Infection and Immunity, Cardiff University School of Medicine, Cardiff, United Kingdom
| | - Sophie Wheeler
- 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
| | - Dmitriy M Chudakov
- Pirogov Russian National Research Medical University, Moscow, Russia.,Centre for Data-Intensive Biomedicine and Biotechnology, Skolkovo Institute of Science and Technology, Skolkovo, Russia.,Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Moscow, Russia
| | - Ernest Choy
- Division of Infection and Immunity, Cardiff University School of Medicine, Cardiff, United Kingdom.,Systems Immunity Research Institute, Cardiff University, Cardiff, United Kingdom
| | - Mark Peakman
- Department of Immunobiology, Faculty of Life Sciences and Medicine, 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
| | - 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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48
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A simple and enzyme-free method for processing infiltrating lymphocytes from small mouse tumors for ELISpot analysis. J Immunol Methods 2018; 459:90-93. [PMID: 29859231 DOI: 10.1016/j.jim.2018.05.015] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2018] [Revised: 05/23/2018] [Accepted: 05/29/2018] [Indexed: 11/21/2022]
Abstract
The ELISpot assay prevails as one of the most sensitive and meaningful assays for the detection of antigen-specific, effector immune responses. Acquisition of cellular analyte for ELISpot analysis is typically not problematic when derived from tissues enriched in lymphocytes (e.g., lymphoid organs and blood); however, cell processing becomes more difficult when lymphocytes represent only a very minor population relative to the source tissue, especially when the source tissue is in limited supply (e.g., small mouse tumors). Traditional enzymatic-based methods for dissociating tumors often result in poor yields, inconsistent lymphocyte enrichment, and can have deleterious effects on lymphocyte phenotype and function. To address these limitations, we have developed an enzyme-free protocol for processing tumor infiltrating lymphocytes (TILs) from small mouse tumors, which enables the enumeration of antigen-specific effector lymphocytes using ELISpot analysis. This procedure is predicated on the dissociation of tumor tissue using gentle agitation with a paddle blender followed by a brief in vitro culture period to remove adherent cells, as well as to revive lymphocytes from a non-responsive state. Although this method is demonstrated with mouse intracerebral tumors, we have found that this protocol is applicable to peripheral tumors and may likely extend to alternative tissue sources wherein lymphocytes exist in low numbers.
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49
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Andargachew R, Martinez RJ, Kolawole EM, Evavold BD. CD4 T Cell Affinity Diversity Is Equally Maintained during Acute and Chronic Infection. THE JOURNAL OF IMMUNOLOGY 2018; 201:19-30. [PMID: 29777029 DOI: 10.4049/jimmunol.1800295] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/27/2018] [Accepted: 04/30/2018] [Indexed: 12/31/2022]
Abstract
TCR affinity for peptide MHC dictates the functional efficiency of T cells and their propensity to differentiate into effectors and form memory. However, in the context of chronic infections, it is unclear what the overall profile of TCR affinity for Ag is and if it differs from acute infections. Using the comprehensive affinity analysis provided by the two-dimensional micropipette adhesion frequency assay and the common indirect affinity evaluation methods of MHC class II tetramer and functional avidity, we tracked IAb GP61-80-specific cells in the mouse model of acute (Armstrong) and chronic (clone 13) lymphocytic choriomeningitis virus infection. In each response, we show CD4 T cell population affinity peaks at the effector phase and declines with memory. Of interest, the range and average relative two-dimensional affinity was equivalent between acute and chronic infection, indicating chronic Ag exposure did not skew TCR affinity. In contrast, functional and tetramer avidity measurements revealed divergent results and lacked a consistent correlation with TCR affinity. Our findings highlight that the immune system maintains a diverse range in TCR affinity even under the pressures of chronic Ag stimulation.
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Affiliation(s)
- Rakieb Andargachew
- Department of Microbiology and Immunology, Emory University, Atlanta, GA 30322
| | - Ryan J Martinez
- School of Medicine, Emory University, Atlanta, GA 30322; and
| | - Elizabeth M Kolawole
- Division of Microbiology and Immunology, Department of Pathology, University of Utah, Salt Lake City, UT 84112
| | - Brian D Evavold
- Division of Microbiology and Immunology, Department of Pathology, University of Utah, Salt Lake City, UT 84112
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50
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Induction of influenza-specific local CD8 T-cells in the respiratory tract after aerosol delivery of vaccine antigen or virus in the Babraham inbred pig. PLoS Pathog 2018; 14:e1007017. [PMID: 29772011 PMCID: PMC5957346 DOI: 10.1371/journal.ppat.1007017] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2017] [Accepted: 04/10/2018] [Indexed: 12/04/2022] Open
Abstract
There is increasing evidence that induction of local immune responses is a key component of effective vaccines. For respiratory pathogens, for example tuberculosis and influenza, aerosol delivery is being actively explored as a method to administer vaccine antigens. Current animal models used to study respiratory pathogens suffer from anatomical disparity with humans. The pig is a natural and important host of influenza viruses and is physiologically more comparable to humans than other animal models in terms of size, respiratory tract biology and volume. It may also be an important vector in the birds to human infection cycle. A major drawback of the current pig model is the inability to analyze antigen-specific CD8+ T-cell responses, which are critical to respiratory immunity. Here we address this knowledge gap using an established in-bred pig model with a high degree of genetic identity between individuals, including the MHC (Swine Leukocyte Antigen (SLA)) locus. We developed a toolset that included long-term in vitro pig T-cell culture and cloning and identification of novel immunodominant influenza-derived T-cell epitopes. We also generated structures of the two SLA class I molecules found in these animals presenting the immunodominant epitopes. These structures allowed definition of the primary anchor points for epitopes in the SLA binding groove and established SLA binding motifs that were used to successfully predict other influenza-derived peptide sequences capable of stimulating T-cells. Peptide-SLA tetramers were constructed and used to track influenza-specific T-cells ex vivo in blood, the lungs and draining lymph nodes. Aerosol immunization with attenuated single cycle influenza viruses (S-FLU) induced large numbers of CD8+ T-cells specific for conserved NP peptides in the respiratory tract. Collectively, these data substantially increase the utility of pigs as an effective model for studying protective local cellular immunity against respiratory pathogens. Influenza virus infection in pigs represents a significant problem to industry and also carries substantial risks to human health. Pigs can be infected with both bird and human forms of influenza where these viruses can mix with swine influenza viruses to generate new pandemic strains that can spread quickly and kill many millions of people across the globe. To date, the study of immunology and vaccination against flu in pigs has been hampered by a lack of suitable tools and reagents. Here, we have built a complete molecular toolset that allows such study. These tools could also be applied to other important infections in pigs such as foot-and-mouth disease and the normally fatal African Swine Fever virus. Finally, pigs are set to become an important model organism for study of influenza A virus infection. Here, we make use of a new research toolset to study a Broadly Protective Influenza Vaccine (BPIV) candidate, S-FLU, which could offer protection against all influenza A viruses. These new tools have been used to demonstrate the induction of large numbers of antigen specific CD8+ T cells to conserved NP epitopes in the respiratory tract after aerosol immunization.
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