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Cai C, Keoshkerian E, Wing K, Samir J, Effenberger M, Schober K, Bull RA, Lloyd AR, Busch DH, Luciani F. Discovery of a monoclonal, high-affinity CD8 + T-cell clone following natural hepatitis C virus infection. Immunol Cell Biol 2024. [PMID: 38855806 DOI: 10.1111/imcb.12791] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2024] [Revised: 05/20/2024] [Accepted: 05/22/2024] [Indexed: 06/11/2024]
Abstract
CD8+ T cells recognizing their cognate antigen are typically recruited as a polyclonal population consisting of multiple clonotypes with varying T-cell receptor (TCR) affinity to the target peptide-major histocompatibility complex (pMHC) complex. Advances in single-cell sequencing have increased accessibility toward identifying TCRs with matched antigens. Here we present the discovery of a monoclonal CD8+ T-cell population with specificity for a hepatitis C virus (HCV)-derived human leukocyte antigen (HLA) class I epitope (HLA-B*07:02 GPRLGVRAT) which was isolated directly ex vivo from an individual with an episode of acutely resolved HCV infection. This population was absent before infection and underwent expansion and stable maintenance for at least 2 years after infection as measured by HLA-multimer staining. Furthermore, the monoclonal clonotype was characterized by an unusually long dissociation time (half-life = 794 s and koff = 5.73 × 10-4) for its target antigen when compared with previously published results. A comparison with related populations of HCV-specific populations derived from the same individual and a second individual suggested that high-affinity TCR-pMHC interactions may be inherent to epitope identity and shape the phenotype of responses which has implications for rational TCR selection and design in the age of personalized immunotherapies.
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Affiliation(s)
- Curtis Cai
- School of Biomedical Sciences, Faculty of Health and Medicine, UNSW Sydney, Sydney, NSW, Australia
- The Kirby Institute, Faculty of Health and Medicine, UNSW Sydney, Sydney, NSW, Australia
| | - Elizabeth Keoshkerian
- The Kirby Institute, Faculty of Health and Medicine, UNSW Sydney, Sydney, NSW, Australia
| | - Kristof Wing
- School of Medicine and Health, Institute for Medical Microbiology, Immunology and Hygiene, Technical University of Munich, Munich, Germany
| | - Jerome Samir
- School of Biomedical Sciences, Faculty of Health and Medicine, UNSW Sydney, Sydney, NSW, Australia
| | - Manuel Effenberger
- School of Medicine and Health, Institute for Medical Microbiology, Immunology and Hygiene, Technical University of Munich, Munich, Germany
| | - Kilian Schober
- Mikrobiologisches Institut - Klinische Mikrobiologie, Immunologie und Hygiene Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany
| | - Rowena A Bull
- School of Biomedical Sciences, Faculty of Health and Medicine, UNSW Sydney, Sydney, NSW, Australia
- The Kirby Institute, Faculty of Health and Medicine, UNSW Sydney, Sydney, NSW, Australia
| | - Andrew R Lloyd
- The Kirby Institute, Faculty of Health and Medicine, UNSW Sydney, Sydney, NSW, Australia
| | - Dirk H Busch
- School of Medicine and Health, Institute for Medical Microbiology, Immunology and Hygiene, Technical University of Munich, Munich, Germany
- German Center for Infection Research (Deutsches Zentrum für Infektionsforschung), Partner Site Munich, Munich, Germany
| | - Fabio Luciani
- School of Biomedical Sciences, Faculty of Health and Medicine, UNSW Sydney, Sydney, NSW, Australia
- The Kirby Institute, Faculty of Health and Medicine, UNSW Sydney, Sydney, NSW, Australia
- Cellular Genomics Future Institute, UNSW Sydney, Sydney, NSW, Australia
- Department of Physiology and Biophysics, Weill Cornell Medical College, New York City, NY, USA
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2
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Leary AY, Scott D, Gupta NT, Waite JC, Skokos D, Atwal GS, Hawkins PG. Designing meaningful continuous representations of T cell receptor sequences with deep generative models. Nat Commun 2024; 15:4271. [PMID: 38769289 PMCID: PMC11106309 DOI: 10.1038/s41467-024-48198-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2023] [Accepted: 04/24/2024] [Indexed: 05/22/2024] Open
Abstract
T Cell Receptor (TCR) antigen binding underlies a key mechanism of the adaptive immune response yet the vast diversity of TCRs and the complexity of protein interactions limits our ability to build useful low dimensional representations of TCRs. To address the current limitations in TCR analysis we develop a capacity-controlled disentangling variational autoencoder trained using a dataset of approximately 100 million TCR sequences, that we name TCR-VALID. We design TCR-VALID such that the model representations are low-dimensional, continuous, disentangled, and sufficiently informative to provide high-quality TCR sequence de novo generation. We thoroughly quantify these properties of the representations, providing a framework for future protein representation learning in low dimensions. The continuity of TCR-VALID representations allows fast and accurate TCR clustering and is benchmarked against other state-of-the-art TCR clustering tools and pre-trained language models.
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Affiliation(s)
- Allen Y Leary
- Regeneron Pharmaceuticals Inc., 777 Old Saw Mill River Road, Tarrytown, NY, 10591, USA.
| | - Darius Scott
- Regeneron Pharmaceuticals Inc., 777 Old Saw Mill River Road, Tarrytown, NY, 10591, USA
| | - Namita T Gupta
- Regeneron Pharmaceuticals Inc., 777 Old Saw Mill River Road, Tarrytown, NY, 10591, USA
| | - Janelle C Waite
- Regeneron Pharmaceuticals Inc., 777 Old Saw Mill River Road, Tarrytown, NY, 10591, USA
| | - Dimitris Skokos
- Regeneron Pharmaceuticals Inc., 777 Old Saw Mill River Road, Tarrytown, NY, 10591, USA
| | - Gurinder S Atwal
- Regeneron Pharmaceuticals Inc., 777 Old Saw Mill River Road, Tarrytown, NY, 10591, USA
| | - Peter G Hawkins
- Regeneron Pharmaceuticals Inc., 777 Old Saw Mill River Road, Tarrytown, NY, 10591, USA.
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3
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Yossef R, Krishna S, Sindiri S, Lowery FJ, Copeland AR, Gartner JJ, Parkhurst MR, Parikh NB, Hitscherich KJ, Levi ST, Chatani PD, Zacharakis N, Levin N, Vale NR, Nah SK, Dinerman A, Hill VK, Ray S, Bera A, Levy L, Jia L, Kelly MC, Goff SL, Robbins PF, Rosenberg SA. Phenotypic signatures of circulating neoantigen-reactive CD8 + T cells in patients with metastatic cancers. Cancer Cell 2023; 41:2154-2165.e5. [PMID: 38039963 PMCID: PMC10843665 DOI: 10.1016/j.ccell.2023.11.005] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/29/2022] [Revised: 08/07/2023] [Accepted: 11/07/2023] [Indexed: 12/03/2023]
Abstract
Circulating T cells from peripheral blood (PBL) can provide a rich and noninvasive source for antitumor T cells. By single-cell transcriptomic profiling of 36 neoantigen-specific T cell clones from 6 metastatic cancer patients, we report the transcriptional and cell surface signatures of antitumor PBL-derived CD8+ T cells (NeoTCRPBL). Comparison of tumor-infiltrating lymphocyte (TIL)- and PBL-neoantigen-specific T cells revealed that NeoTCRPBL T cells are low in frequency and display less-dysfunctional memory phenotypes relative to their TIL counterparts. Analysis of 100 antitumor TCR clonotypes indicates that most NeoTCRPBL populations target the same neoantigens as TILs. However, NeoTCRPBL TCR repertoire is only partially shared with TIL. Prediction and testing of NeoTCRPBL signature-derived TCRs from PBL of 6 prospective patients demonstrate high enrichment of clonotypes targeting tumor mutations, a viral oncogene, and patient-derived tumor. Thus, the NeoTCRPBL signature provides an alternative source for identifying antitumor T cells from PBL of cancer patients, enabling immune monitoring and immunotherapies.
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Affiliation(s)
- Rami Yossef
- Surgery Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA.
| | - Sri Krishna
- Surgery Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA.
| | - Sivasish Sindiri
- Surgery Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Frank J Lowery
- Surgery Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Amy R Copeland
- Surgery Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Jared J Gartner
- Surgery Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Maria R Parkhurst
- Surgery Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Neilesh B Parikh
- Surgery Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Kyle J Hitscherich
- Surgery Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Shoshana T Levi
- Surgery Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Praveen D Chatani
- Surgery Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Nikolaos Zacharakis
- Surgery Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Noam Levin
- Surgery Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Nolan R Vale
- Surgery Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Shirley K Nah
- Surgery Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Aaron Dinerman
- Surgery Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Victoria K Hill
- Surgery Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Satyajit Ray
- Surgery Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Alakesh Bera
- Surgery Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Lior Levy
- Surgery Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Li Jia
- National Institutes of Health Library, National Institutes of Health, Bethesda, MD 20892, USA
| | - Michael C Kelly
- Single Cell Analysis Facility, Cancer Research Technology Program, Frederick National Laboratory, Bethesda, MD 20892, USA
| | - Stephanie L Goff
- Surgery Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Paul F Robbins
- Surgery Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Steven A Rosenberg
- Surgery Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA.
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4
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Brightman SE, Becker A, Thota RR, Naradikian MS, Chihab L, Zavala KS, Ramamoorthy Premlal AL, Griswold RQ, Dolina JS, Cohen EEW, Miller AM, Peters B, Schoenberger SP. Neoantigen-specific stem cell memory-like CD4 + T cells mediate CD8 + T cell-dependent immunotherapy of MHC class II-negative solid tumors. Nat Immunol 2023; 24:1345-1357. [PMID: 37400675 PMCID: PMC10382322 DOI: 10.1038/s41590-023-01543-9] [Citation(s) in RCA: 17] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2023] [Accepted: 05/22/2023] [Indexed: 07/05/2023]
Abstract
CD4+ T cells play key roles in a range of immune responses, either as direct effectors or through accessory cells, including CD8+ T lymphocytes. In cancer, neoantigen (NeoAg)-specific CD8+ T cells capable of direct tumor recognition have been extensively studied, whereas the role of NeoAg-specific CD4+ T cells is less well understood. We have characterized the murine CD4+ T cell response against a validated NeoAg (CLTCH129>Q) expressed by the MHC-II-deficient squamous cell carcinoma tumor model (SCC VII) at the level of single T cell receptor (TCR) clonotypes and in the setting of adoptive immunotherapy. We find that the natural CLTCH129>Q-specific repertoire is diverse and contains TCRs with distinct avidities as measured by tetramer-binding assays and CD4 dependence. Despite these differences, CD4+ T cells expressing high or moderate avidity TCRs undergo comparable in vivo proliferation to cross-presented antigen from growing tumors and drive similar levels of therapeutic immunity that is dependent on CD8+ T cells and CD40L signaling. Adoptive cellular therapy (ACT) with NeoAg-specific CD4+ T cells is most effective when TCR-engineered cells are differentiated ex vivo with IL-7 and IL-15 rather than IL-2 and this was associated with both increased expansion as well as the acquisition and stable maintenance of a T stem cell memory (TSCM)-like phenotype in tumor-draining lymph nodes (tdLNs). ACT with TSCM-like CD4+ T cells results in lower PD-1 expression by CD8+ T cells in the tumor microenvironment and an increased frequency of PD-1+CD8+ T cells in tdLNs. These findings illuminate the role of NeoAg-specific CD4+ T cells in mediating antitumor immunity via providing help to CD8+ T cells and highlight their therapeutic potential in ACT.
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Affiliation(s)
- Spencer E Brightman
- Division of Developmental Immunology, La Jolla Institute for Immunology, La Jolla, CA, USA
- Biomedical Sciences Program, School of Medicine, University of California San Diego, La Jolla, CA, USA
| | - Angelica Becker
- Division of Developmental Immunology, La Jolla Institute for Immunology, La Jolla, CA, USA
| | - Rukman R Thota
- Division of Developmental Immunology, La Jolla Institute for Immunology, La Jolla, CA, USA
| | - Martin S Naradikian
- Division of Developmental Immunology, La Jolla Institute for Immunology, La Jolla, CA, USA
| | - Leila Chihab
- Division of Vaccine Discovery, La Jolla Institute for Immunology, La Jolla, CA, USA
| | - Karla Soria Zavala
- Division of Developmental Immunology, La Jolla Institute for Immunology, La Jolla, CA, USA
| | | | - Ryan Q Griswold
- Division of Developmental Immunology, La Jolla Institute for Immunology, La Jolla, CA, USA
- Biomedical Sciences Program, School of Medicine, University of California San Diego, La Jolla, CA, USA
| | - Joseph S Dolina
- Division of Developmental Immunology, La Jolla Institute for Immunology, La Jolla, CA, USA
| | - Ezra E W Cohen
- Division of Hematology and Oncology, University of California San Diego Moores Cancer Center, UCSD, La Jolla, CA, USA
| | - Aaron M Miller
- Division of Developmental Immunology, La Jolla Institute for Immunology, La Jolla, CA, USA
- Division of Hematology and Oncology, University of California San Diego Moores Cancer Center, UCSD, La Jolla, CA, USA
| | - Bjoern Peters
- Division of Hematology and Oncology, University of California San Diego Moores Cancer Center, UCSD, La Jolla, CA, USA
- Department of Medicine, University of California San Diego, La Jolla, CA, USA
| | - Stephen P Schoenberger
- Division of Developmental Immunology, La Jolla Institute for Immunology, La Jolla, CA, USA.
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5
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Straub A, Grassmann S, Jarosch S, Richter L, Hilgendorf P, Hammel M, Wagner KI, Buchholz VR, Schober K, Busch DH. Recruitment of epitope-specific T cell clones with a low-avidity threshold supports efficacy against mutational escape upon re-infection. Immunity 2023:S1074-7613(23)00179-6. [PMID: 37164014 DOI: 10.1016/j.immuni.2023.04.010] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2022] [Revised: 02/01/2023] [Accepted: 04/13/2023] [Indexed: 05/12/2023]
Abstract
Repetitive pathogen exposure leads to the dominant outgrowth of T cell clones with high T cell receptor (TCR) affinity to the relevant pathogen-associated antigens. However, low-affinity clones are also known to expand and form immunological memory. While these low-affinity clones contribute less immunity to the original pathogen, their role in protection against pathogens harboring immune escape mutations remains unclear. Based on identification of the TCR repertoire and functionality landscape of naive epitope-specific CD8+ T cells, we reconstructed defined repertoires that could be followed as polyclonal populations during immune responses in vivo. We found that selective clonal expansion is governed by clear TCR avidity thresholds. Simultaneously, initial recruitment of broad TCR repertoires provided a polyclonal niche from which flexible secondary responses to mutant epitopes could be recalled. Elucidating how T cell responses develop "from scratch" is informative for the development of enhanced immunotherapies and vaccines.
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Affiliation(s)
- Adrian Straub
- Institute for Medical Microbiology, Immunology and Hygiene, Technische Universität München (TUM), Munich, Germany
| | - Simon Grassmann
- Institute for Medical Microbiology, Immunology and Hygiene, Technische Universität München (TUM), Munich, Germany; The Joseph Sun Lab, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Sebastian Jarosch
- Institute for Medical Microbiology, Immunology and Hygiene, Technische Universität München (TUM), Munich, Germany
| | - Lena Richter
- Institute for Medical Microbiology, Immunology and Hygiene, Technische Universität München (TUM), Munich, Germany
| | - Philipp Hilgendorf
- Institute for Medical Microbiology, Immunology and Hygiene, Technische Universität München (TUM), Munich, Germany; Mikrobiologisches Institut - Klinische Mikrobiologie, Immunologie und Hygiene, Universitätsklinikum Erlangen, Friedrich-Alexander-Universität (FAU) Erlangen-Nürnberg, Erlangen, Germany
| | - Monika Hammel
- Institute for Medical Microbiology, Immunology and Hygiene, Technische Universität München (TUM), Munich, Germany
| | - Karolin I Wagner
- Institute for Medical Microbiology, Immunology and Hygiene, Technische Universität München (TUM), Munich, Germany
| | - Veit R Buchholz
- Institute for Medical Microbiology, Immunology and Hygiene, Technische Universität München (TUM), Munich, Germany
| | - Kilian Schober
- Institute for Medical Microbiology, Immunology and Hygiene, Technische Universität München (TUM), Munich, Germany; Mikrobiologisches Institut - Klinische Mikrobiologie, Immunologie und Hygiene, Universitätsklinikum Erlangen, Friedrich-Alexander-Universität (FAU) Erlangen-Nürnberg, Erlangen, Germany; Medical Immunology Campus Erlangen, Friedrich-Alexander-Universität (FAU) Erlangen-Nürnberg, Schlossplatz 1, 91054 Erlangen, Germany.
| | - Dirk H Busch
- Institute for Medical Microbiology, Immunology and Hygiene, Technische Universität München (TUM), Munich, Germany; Partner site Munich, German Center for Infection Research (DZIF), Munich, Germany.
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6
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Jang HJ, Caron C, Lee CK, Wang L, Jama B, Bui JD, Morris GP. Dual receptor T cells mediate effective antitumor immune responses via increased recognition of tumor antigens. J Immunother Cancer 2023; 11:e006472. [PMID: 37188395 PMCID: PMC10186424 DOI: 10.1136/jitc-2022-006472] [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: 04/30/2023] [Indexed: 05/17/2023] Open
Abstract
BACKGROUND Discovery that ~16% of T cells naturally co-express two T-cell receptor (TCR) clonotypes prompts examining the role of dual TCR cells in immune functions. METHODS Using TCRα-reporter transgenic mice, enabling unambiguous identification of single-TCR and dual-TCR cells, we tested the role of dual TCR cells in antitumor immune responses against immune-responsive syngeneic 6727 sarcoma and immune-resistant B16F10 melanoma. RESULTS Dual TCR cells were specifically increased among tumor-infiltrating lymphocytes (TILs) in both models, indicating selective advantage in antitumor responses. Phenotype and single-cell gene expression analyses identified dual TCR are predominant during the effective antitumor response, demonstrating selectively increased activation in the TIL compartment and skewing toward an effector memory phenotype. Absence of dual TCR cells impaired immune response to B16F10 but not 6727, suggesting that dual TCR cells may be more influential in responses against poorly immunogenic tumors. Dual TCR cells demonstrated an advantage in recognition of B16F10-derived neoantigens in vitro, providing a mechanistic basis for their antitumor reactivity. CONCLUSIONS These results discover an unrecognized role for dual TCR cells in protective immune function and identify these cells and their TCRs as a potential resource for antitumor immunotherapy.
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Affiliation(s)
- Hyun J Jang
- Department of Pathology, University of California San Diego, La Jolla, California, USA
| | - Christine Caron
- Department of Pathology, University of California San Diego, La Jolla, California, USA
| | - Calvin K Lee
- Department of Pathology, University of California San Diego, La Jolla, California, USA
| | - Lu Wang
- Department of Pathology, University of California San Diego, La Jolla, California, USA
| | - Burhan Jama
- Department of Pathology, University of California San Diego, La Jolla, California, USA
| | - Jack D Bui
- Department of Pathology, University of California San Diego, La Jolla, California, USA
| | - Gerald P Morris
- Department of Pathology, University of California San Diego, La Jolla, California, USA
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7
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Mateyka LM, Strobl PM, Jarosch S, Scheu SJC, Busch DH, D'Ippolito E. Gene Signatures of T-Cell Activation Can Serve as Predictors of Functionality for SARS-CoV-2-Specific T-Cell Receptors. Vaccines (Basel) 2022; 10:vaccines10101617. [PMID: 36298482 PMCID: PMC9611811 DOI: 10.3390/vaccines10101617] [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: 08/15/2022] [Revised: 09/15/2022] [Accepted: 09/23/2022] [Indexed: 11/16/2022] Open
Abstract
The importance of T cells in controlling SARS-CoV-2 infections has been demonstrated widely, but insights into the quality of these responses are still limited due to technical challenges. Indeed, understanding the functionality of the T-cell receptor (TCR) repertoire of a polyclonal antigen-specific population still requires the tedious work of T-cell cloning or TCR re-expression and subsequent characterization. In this work, we show that it is possible to discriminate highly functional and bystander TCRs based on gene signatures of T-cell activation induced by recent peptide stimulation. SARS-CoV-2-specific TCRs previously identified by cytokine release after peptide restimulation and subsequent single-cell RNA sequencing were re-expressed via CRISPR-Cas9-mediated gene editing into a Jurkat-based reporter cell line system suitable for high-throughput screening. We could observe differences in SARS-CoV-2 epitope recognition as well as a wide range of functional avidities. By correlating these in vitro TCR engineered functional data with the transcriptomic profiles of the corresponding TCR-expressing parental T cells, we could validate that gene signatures of recent T-cell activation accurately identify and predict truly SARS-CoV-2-specific TCRs. In summary, this work paves the way for alternative approaches useful for the functional analysis of global antigen-specific TCR repertoires with largely improved throughput.
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Affiliation(s)
- Laura M Mateyka
- Institute for Medical Microbiology, Immunology and Hygiene, Technical University of Munich (TUM), 81675 Munich, Germany
| | - Philipp M Strobl
- Institute for Medical Microbiology, Immunology and Hygiene, Technical University of Munich (TUM), 81675 Munich, Germany
| | - Sebastian Jarosch
- Institute for Medical Microbiology, Immunology and Hygiene, Technical University of Munich (TUM), 81675 Munich, Germany
| | - Sebastian J C Scheu
- Institute for Medical Microbiology, Immunology and Hygiene, Technical University of Munich (TUM), 81675 Munich, Germany
| | - Dirk H Busch
- Institute for Medical Microbiology, Immunology and Hygiene, Technical University of Munich (TUM), 81675 Munich, Germany
- German Center for Infection Research (DZIF), Partner Site Munich, 81675 Munich, Germany
| | - Elvira D'Ippolito
- Institute for Medical Microbiology, Immunology and Hygiene, Technical University of Munich (TUM), 81675 Munich, Germany
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