1
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Drost F, An Y, Bonafonte-Pardàs I, Dratva LM, Lindeboom RGH, Haniffa M, Teichmann SA, Theis F, Lotfollahi M, Schubert B. Multi-modal generative modeling for joint analysis of single-cell T cell receptor and gene expression data. Nat Commun 2024; 15:5577. [PMID: 38956082 PMCID: PMC11220149 DOI: 10.1038/s41467-024-49806-9] [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: 10/10/2023] [Accepted: 05/23/2024] [Indexed: 07/04/2024] Open
Abstract
Recent advances in single-cell immune profiling have enabled the simultaneous measurement of transcriptome and T cell receptor (TCR) sequences, offering great potential for studying immune responses at the cellular level. However, integrating these diverse modalities across datasets is challenging due to their unique data characteristics and technical variations. Here, to address this, we develop the multimodal generative model mvTCR to fuse modality-specific information across transcriptome and TCR into a shared representation. Our analysis demonstrates the added value of multimodal over unimodal approaches to capture antigen specificity. Notably, we use mvTCR to distinguish T cell subpopulations binding to SARS-CoV-2 antigens from bystander cells. Furthermore, when combined with reference mapping approaches, mvTCR can map newly generated datasets to extensive T cell references, facilitating knowledge transfer. In summary, we envision mvTCR to enable a scalable analysis of multimodal immune profiling data and advance our understanding of immune responses.
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Affiliation(s)
- Felix Drost
- Computational Health Center, Helmholtz Munich, Ingolstädter Landstraße 1, 85764, Neuherberg, Germany
- School of Life Sciences Weihenstephan, Technical University of Munich, Alte Akademie 8, 85354, Freising, Germany
| | - Yang An
- Computational Health Center, Helmholtz Munich, Ingolstädter Landstraße 1, 85764, Neuherberg, Germany
- School of Computation, Information and Technology, Technical University of Munich, Boltzmannstraße 3, 85748, Garching bei München, Germany
| | - Irene Bonafonte-Pardàs
- Computational Health Center, Helmholtz Munich, Ingolstädter Landstraße 1, 85764, Neuherberg, Germany
| | - Lisa M Dratva
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Rik G H Lindeboom
- The Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX, Amsterdam, The Netherlands
| | - Muzlifah Haniffa
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
- Biosciences Institute, Newcastle University, Newcastle upon Tyne, NE2 4HH, UK
| | - Sarah A Teichmann
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
- Department of Physics, Cavendish Laboratory, University of Cambridge, 19 JJ Thomson Avenue, Cambridge, UK
| | - Fabian Theis
- Computational Health Center, Helmholtz Munich, Ingolstädter Landstraße 1, 85764, Neuherberg, Germany
- School of Life Sciences Weihenstephan, Technical University of Munich, Alte Akademie 8, 85354, Freising, Germany
- School of Computation, Information and Technology, Technical University of Munich, Boltzmannstraße 3, 85748, Garching bei München, Germany
| | - Mohammad Lotfollahi
- Computational Health Center, Helmholtz Munich, Ingolstädter Landstraße 1, 85764, Neuherberg, Germany.
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK.
| | - Benjamin Schubert
- Computational Health Center, Helmholtz Munich, Ingolstädter Landstraße 1, 85764, Neuherberg, Germany.
- School of Computation, Information and Technology, Technical University of Munich, Boltzmannstraße 3, 85748, Garching bei München, Germany.
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2
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Conte MI, Fuentes-Trillo A, Domínguez Conde C. Opportunities and tradeoffs in single-cell transcriptomic technologies. Trends Genet 2024; 40:83-93. [PMID: 37953195 DOI: 10.1016/j.tig.2023.10.003] [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: 07/11/2023] [Revised: 09/26/2023] [Accepted: 10/03/2023] [Indexed: 11/14/2023]
Abstract
Recent technological and algorithmic advances enable single-cell transcriptomic analysis with remarkable depth and breadth. Nonetheless, a persistent challenge is the compromise between the ability to profile high numbers of cells and the achievement of full-length transcript coverage. Currently, the field is progressing and developing new and creative solutions that improve cellular throughput, gene detection sensitivity and full-length transcript capture. Furthermore, long-read sequencing approaches for single-cell transcripts are breaking frontiers that have previously blocked full transcriptome characterization. We here present a comprehensive overview of available options for single-cell transcriptome profiling, highlighting the key advantages and disadvantages of each approach.
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Affiliation(s)
- Matilde I Conte
- Human Technopole, Viale Rita Levi-Montalcini 1, 20157 Milan, Italy
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3
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Chen HC. A systematic review of the barcoding strategy that contributes to COVID-19 diagnostics at a population level. Front Mol Biosci 2023; 10:1141534. [PMID: 37496777 PMCID: PMC10366608 DOI: 10.3389/fmolb.2023.1141534] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2023] [Accepted: 06/30/2023] [Indexed: 07/28/2023] Open
Abstract
The outbreak of SARS-CoV-2 has made us more alert to the importance of viral diagnostics at a population level to rapidly control the spread of the disease. The critical question would be how to scale up testing capacity and perform a diagnostic test in a high-throughput manner with robust results and affordable costs. Here, the latest 26 articles using barcoding technology for COVID-19 diagnostics and biologically-relevant studies are reviewed. Barcodes are molecular tags, that allow proceeding an array of samples at once. To date, barcoding technology followed by high-throughput sequencing has been made for molecular diagnostics for SARS-CoV-2 infections because it can synchronously analyze up to tens of thousands of clinical samples within a short diagnostic time. Essentially, this technology can also be used together with different biotechnologies, allowing for investigation with resolution of single molecules. In this Mini-Review, I first explain the general principle of the barcoding strategy and then put forward recent studies using this technology to accomplish COVID-19 diagnostics and basic research. In the meantime, I provide the viewpoint to improve the current COVID-19 diagnostic strategy with potential solutions. Finally, and importantly, two practical ideas about how barcodes can be further applied in studying SARS-CoV-2 to accelerate our understanding of this virus are proposed.
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4
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Eser TM, Baranov O, Huth M, Ahmed MIM, Deák F, Held K, Lin L, Pekayvaz K, Leunig A, Nicolai L, Pollakis G, Buggert M, Price DA, Rubio-Acero R, Reich J, Falk P, Markgraf A, Puchinger K, Castelletti N, Olbrich L, Vanshylla K, Klein F, Wieser A, Hasenauer J, Kroidl I, Hoelscher M, Geldmacher C. Nucleocapsid-specific T cell responses associate with control of SARS-CoV-2 in the upper airways before seroconversion. Nat Commun 2023; 14:2952. [PMID: 37225706 DOI: 10.1038/s41467-023-38020-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2022] [Accepted: 04/12/2023] [Indexed: 05/26/2023] Open
Abstract
Despite intensive research since the emergence of SARS-CoV-2, it has remained unclear precisely which components of the early immune response protect against the development of severe COVID-19. Here, we perform a comprehensive immunogenetic and virologic analysis of nasopharyngeal and peripheral blood samples obtained during the acute phase of infection with SARS-CoV-2. We find that soluble and transcriptional markers of systemic inflammation peak during the first week after symptom onset and correlate directly with upper airways viral loads (UA-VLs), whereas the contemporaneous frequencies of circulating viral nucleocapsid (NC)-specific CD4+ and CD8+ T cells correlate inversely with various inflammatory markers and UA-VLs. In addition, we show that high frequencies of activated CD4+ and CD8+ T cells are present in acutely infected nasopharyngeal tissue, many of which express genes encoding various effector molecules, such as cytotoxic proteins and IFN-γ. The presence of IFNG mRNA-expressing CD4+ and CD8+ T cells in the infected epithelium is further linked with common patterns of gene expression among virus-susceptible target cells and better local control of SARS-CoV-2. Collectively, these results identify an immune correlate of protection against SARS-CoV-2, which could inform the development of more effective vaccines to combat the acute and chronic illnesses attributable to COVID-19.
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Affiliation(s)
- Tabea M Eser
- Division of Infectious Diseases and Tropical Medicine, University Hospital, LMU Munich, 81377, Munich, Germany
- German Center for Infection Research (DZIF), Partner Site Munich, 81377, Munich, Germany
| | - Olga Baranov
- Division of Infectious Diseases and Tropical Medicine, University Hospital, LMU Munich, 81377, Munich, Germany
- German Center for Infection Research (DZIF), Partner Site Munich, 81377, Munich, Germany
| | - Manuel Huth
- Institute of Computational Biology, Helmholtz Zentrum München, 85764, Neuherberg, Germany
- Center for Mathematics, Technische Universität München, 85748, Garching, Germany
| | - Mohammed I M Ahmed
- Division of Infectious Diseases and Tropical Medicine, University Hospital, LMU Munich, 81377, Munich, Germany
- German Center for Infection Research (DZIF), Partner Site Munich, 81377, Munich, Germany
| | - Flora Deák
- Division of Infectious Diseases and Tropical Medicine, University Hospital, LMU Munich, 81377, Munich, Germany
- German Center for Infection Research (DZIF), Partner Site Munich, 81377, Munich, Germany
| | - Kathrin Held
- Division of Infectious Diseases and Tropical Medicine, University Hospital, LMU Munich, 81377, Munich, Germany
- German Center for Infection Research (DZIF), Partner Site Munich, 81377, Munich, Germany
| | - Luming Lin
- Division of Infectious Diseases and Tropical Medicine, University Hospital, LMU Munich, 81377, Munich, Germany
- German Center for Infection Research (DZIF), Partner Site Munich, 81377, Munich, Germany
| | - Kami Pekayvaz
- Department of Medicine I, University Hospital, LMU Munich, 81377, Munich, Germany
- German Center for Cardiovascular Research (DZHK), Partner Site Munich Heart Alliance, 81377, Munich, Germany
| | - Alexander Leunig
- Department of Medicine I, University Hospital, LMU Munich, 81377, Munich, Germany
- German Center for Cardiovascular Research (DZHK), Partner Site Munich Heart Alliance, 81377, Munich, Germany
| | - Leo Nicolai
- Department of Medicine I, University Hospital, LMU Munich, 81377, Munich, Germany
- German Center for Cardiovascular Research (DZHK), Partner Site Munich Heart Alliance, 81377, Munich, Germany
| | - Georgios Pollakis
- Institute of Infection and Global Health, University of Liverpool, Liverpool, L69 2BE, UK
| | - Marcus Buggert
- Center for Infectious Medicine, Department of Medicine Huddinge, Karolinska Institutet, Karolinska University Hospital Huddinge, 141 86, Stockholm, Sweden
| | - David A Price
- Division of Infection and Immunity, Cardiff University School of Medicine, University Hospital, Heath Park, Cardiff, CF14 4XN, UK
- Systems Immunity Research Institute, Cardiff University School of Medicine, University Hospital, Heath Park, Cardiff, CF14 4XN, UK
| | - Raquel Rubio-Acero
- Division of Infectious Diseases and Tropical Medicine, University Hospital, LMU Munich, 81377, Munich, Germany
| | - Jakob Reich
- Division of Infectious Diseases and Tropical Medicine, University Hospital, LMU Munich, 81377, Munich, Germany
| | - Philine Falk
- Division of Infectious Diseases and Tropical Medicine, University Hospital, LMU Munich, 81377, Munich, Germany
| | - Alissa Markgraf
- Division of Infectious Diseases and Tropical Medicine, University Hospital, LMU Munich, 81377, Munich, Germany
| | - Kerstin Puchinger
- Division of Infectious Diseases and Tropical Medicine, University Hospital, LMU Munich, 81377, Munich, Germany
| | - Noemi Castelletti
- Division of Infectious Diseases and Tropical Medicine, University Hospital, LMU Munich, 81377, Munich, Germany
- German Center for Infection Research (DZIF), Partner Site Munich, 81377, Munich, Germany
| | - Laura Olbrich
- Division of Infectious Diseases and Tropical Medicine, University Hospital, LMU Munich, 81377, Munich, Germany
- German Center for Infection Research (DZIF), Partner Site Munich, 81377, Munich, Germany
| | - Kanika Vanshylla
- Laboratory of Experimental Immunology, Institute of Virology, Faculty of Medicine and University Hospital Cologne, University of Cologne, 50931, Cologne, Germany
| | - Florian Klein
- Laboratory of Experimental Immunology, Institute of Virology, Faculty of Medicine and University Hospital Cologne, University of Cologne, 50931, Cologne, Germany
- German Center for Infection Research (DZIF), Partner Site Bonn-Cologne, 50937, Cologne, Germany
- Center for Molecular Medicine Cologne (CMMC), University of Cologne, 50931, Cologne, Germany
| | - Andreas Wieser
- Division of Infectious Diseases and Tropical Medicine, University Hospital, LMU Munich, 81377, Munich, Germany
- German Center for Infection Research (DZIF), Partner Site Munich, 81377, Munich, Germany
- Max von Pettenkofer Institute for Hygiene and Medical Microbiology, LMU Munich, 81377, Munich, Germany
| | - Jan Hasenauer
- Institute of Computational Biology, Helmholtz Zentrum München, 85764, Neuherberg, Germany
- Center for Mathematics, Technische Universität München, 85748, Garching, Germany
- Faculty of Mathematics and Natural Sciences, University of Bonn, 53113, Bonn, Germany
| | - Inge Kroidl
- Division of Infectious Diseases and Tropical Medicine, University Hospital, LMU Munich, 81377, Munich, Germany
- German Center for Infection Research (DZIF), Partner Site Munich, 81377, Munich, Germany
| | - Michael Hoelscher
- Division of Infectious Diseases and Tropical Medicine, University Hospital, LMU Munich, 81377, Munich, Germany
- German Center for Infection Research (DZIF), Partner Site Munich, 81377, Munich, Germany
| | - Christof Geldmacher
- Division of Infectious Diseases and Tropical Medicine, University Hospital, LMU Munich, 81377, Munich, Germany.
- German Center for Infection Research (DZIF), Partner Site Munich, 81377, Munich, Germany.
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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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Kang Y, Zhang W, Yu Q, Gao L, Quan J, Gu F, Wu Y, Tian Y, Wu Z, Shao S, Zhou H, Duan S, Zhou Y, Zhang L, Gao X, Tian H, Yao W. Self-assembled nanoparticles based on DNA origami and a nitrated T helper cell epitope as a platform for the development of personalized cancer vaccines. Cancer Immunol Immunother 2023:10.1007/s00262-023-03446-y. [PMID: 37119260 DOI: 10.1007/s00262-023-03446-y] [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: 02/11/2023] [Accepted: 04/03/2023] [Indexed: 05/01/2023]
Abstract
Neoantigen vaccines constitute an emerging and promising cancer immunotherapy. However, not all neoantigens have anti-tumor activity, as poor CD4+ epitope recognition can lead to the lack of greatly limit the persistence of the CD8+ T cell response. Therefore, we designed a self-assembled nanoplatform hereinafter referred to as DNA-coupled nitrated T helper cell epitope nanoparticle (DCNP) based on DNA origami containing a nitrated CD4 + T cell epitope, which can facilitate the effective activation of neoantigen-specific CD8+ T cells. Moreover, we embedded the cytidine-phosphate-guanosine oligonucleotide (CpG ODN) motif sequence in the DNA skeleton to function as a built-in adjuvant to activate Toll-like receptor 9. DCNP can markedly improve adjuvant and neoantigen co-delivery to lymphoid organs and promote neoantigen presentation on dendritic cells. Moreover, DCNP induced robust, and long-lived neoantigen-specific CD8+ T cell responses that significantly delayed tumor growth. Further, these effects were largely dependent on the nitrated T cell epitope. Collectively, our findings indicate that DCNP is a promising platform that could improve the development of personalized therapeutic neoantigen vaccines for cancer immunotherapy.
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Affiliation(s)
- Yanliang Kang
- Jiangsu Key Laboratory of Druggability of Biopharmaceuticals and State Key Laboratory of Natural Medicines, School of Life Science and Technology, China Pharmaceutical University, Nanjing, 211198, China
| | - Wanli Zhang
- Jiangsu Key Laboratory of Druggability of Biopharmaceuticals and State Key Laboratory of Natural Medicines, School of Life Science and Technology, China Pharmaceutical University, Nanjing, 211198, China
| | - Qiumin Yu
- Jiangsu Key Laboratory of Druggability of Biopharmaceuticals and State Key Laboratory of Natural Medicines, School of Life Science and Technology, China Pharmaceutical University, Nanjing, 211198, China
| | - Le Gao
- Jiangsu Key Laboratory of Druggability of Biopharmaceuticals and State Key Laboratory of Natural Medicines, School of Life Science and Technology, China Pharmaceutical University, Nanjing, 211198, China
| | - Jiale Quan
- Jiangsu Key Laboratory of Druggability of Biopharmaceuticals and State Key Laboratory of Natural Medicines, School of Life Science and Technology, China Pharmaceutical University, Nanjing, 211198, China
| | - Fangling Gu
- Jiangsu Key Laboratory of Druggability of Biopharmaceuticals and State Key Laboratory of Natural Medicines, School of Life Science and Technology, China Pharmaceutical University, Nanjing, 211198, China
| | - Yuxin Wu
- Jiangsu Key Laboratory of Druggability of Biopharmaceuticals and State Key Laboratory of Natural Medicines, School of Life Science and Technology, China Pharmaceutical University, Nanjing, 211198, China
| | - Yahong Tian
- Jiangsu Key Laboratory of Druggability of Biopharmaceuticals and State Key Laboratory of Natural Medicines, School of Life Science and Technology, China Pharmaceutical University, Nanjing, 211198, China
| | - Zijie Wu
- Jiangsu Key Laboratory of Druggability of Biopharmaceuticals and State Key Laboratory of Natural Medicines, School of Life Science and Technology, China Pharmaceutical University, Nanjing, 211198, China
| | - Shishuai Shao
- Jiangsu Key Laboratory of Druggability of Biopharmaceuticals and State Key Laboratory of Natural Medicines, School of Life Science and Technology, China Pharmaceutical University, Nanjing, 211198, China
| | - Hongyou Zhou
- Jiangsu Key Laboratory of Druggability of Biopharmaceuticals and State Key Laboratory of Natural Medicines, School of Life Science and Technology, China Pharmaceutical University, Nanjing, 211198, China
| | - Shukang Duan
- Jiangsu Key Laboratory of Druggability of Biopharmaceuticals and State Key Laboratory of Natural Medicines, School of Life Science and Technology, China Pharmaceutical University, Nanjing, 211198, China
| | - Yixiang Zhou
- Jiangsu Key Laboratory of Druggability of Biopharmaceuticals and State Key Laboratory of Natural Medicines, School of Life Science and Technology, China Pharmaceutical University, Nanjing, 211198, China
| | - Li Zhang
- Department of General Internal Medicine, The First Affiliated Hospital of Xinjiang Medical University, Urumqi, 830054, China.
| | - Xiangdong Gao
- Jiangsu Key Laboratory of Druggability of Biopharmaceuticals and State Key Laboratory of Natural Medicines, School of Life Science and Technology, China Pharmaceutical University, Nanjing, 211198, China.
| | - Hong Tian
- Jiangsu Key Laboratory of Druggability of Biopharmaceuticals and State Key Laboratory of Natural Medicines, School of Life Science and Technology, China Pharmaceutical University, Nanjing, 211198, China.
| | - Wenbing Yao
- Jiangsu Key Laboratory of Druggability of Biopharmaceuticals and State Key Laboratory of Natural Medicines, School of Life Science and Technology, China Pharmaceutical University, Nanjing, 211198, China.
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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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Ratnasiri K, Wilk AJ, Lee MJ, Khatri P, Blish CA. Single-cell RNA-seq methods to interrogate virus-host interactions. Semin Immunopathol 2023; 45:71-89. [PMID: 36414692 PMCID: PMC9684776 DOI: 10.1007/s00281-022-00972-2] [Citation(s) in RCA: 18] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2022] [Accepted: 10/31/2022] [Indexed: 11/23/2022]
Abstract
The twenty-first century has seen the emergence of many epidemic and pandemic viruses, with the most recent being the SARS-CoV-2-driven COVID-19 pandemic. As obligate intracellular parasites, viruses rely on host cells to replicate and produce progeny, resulting in complex virus and host dynamics during an infection. Single-cell RNA sequencing (scRNA-seq), by enabling broad and simultaneous profiling of both host and virus transcripts, represents a powerful technology to unravel the delicate balance between host and virus. In this review, we summarize technological and methodological advances in scRNA-seq and their applications to antiviral immunity. We highlight key scRNA-seq applications that have enabled the understanding of viral genomic and host response heterogeneity, differential responses of infected versus bystander cells, and intercellular communication networks. We expect further development of scRNA-seq technologies and analytical methods, combined with measurements of additional multi-omic modalities and increased availability of publicly accessible scRNA-seq datasets, to enable a better understanding of viral pathogenesis and enhance the development of antiviral therapeutics strategies.
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Affiliation(s)
- Kalani Ratnasiri
- grid.168010.e0000000419368956Stanford Immunology Program, Stanford University School of Medicine, Stanford, CA 94305 USA ,grid.168010.e0000000419368956Department of Medicine, Division of Infectious Diseases and Geographic Medicine, Stanford University School of Medicine, Stanford, CA 94305 USA
| | - Aaron J. Wilk
- grid.168010.e0000000419368956Stanford Immunology Program, Stanford University School of Medicine, Stanford, CA 94305 USA ,grid.168010.e0000000419368956Department of Medicine, Division of Infectious Diseases and Geographic Medicine, Stanford University School of Medicine, Stanford, CA 94305 USA ,grid.168010.e0000000419368956Medical Scientist Training Program, Stanford University School of Medicine, Stanford, CA 94305 USA
| | - Madeline J. Lee
- grid.168010.e0000000419368956Stanford Immunology Program, Stanford University School of Medicine, Stanford, CA 94305 USA ,grid.168010.e0000000419368956Department of Medicine, Division of Infectious Diseases and Geographic Medicine, Stanford University School of Medicine, Stanford, CA 94305 USA
| | - Purvesh Khatri
- Department of Medicine, Division of Infectious Diseases and Geographic Medicine, Stanford University School of Medicine, Stanford, CA, 94305, USA. .,Institute for Immunity, Transplantation and Infection, Stanford University School of Medicine, Stanford, CA, 94305, USA. .,Department of Medicine, Center for Biomedical Informatics Research, Stanford, CA, USA. .,Inflammatix, Inc., Sunnyvale, CA, 94085, USA.
| | - Catherine A. Blish
- grid.168010.e0000000419368956Stanford Immunology Program, Stanford University School of Medicine, Stanford, CA 94305 USA ,grid.168010.e0000000419368956Department of Medicine, Division of Infectious Diseases and Geographic Medicine, Stanford University School of Medicine, Stanford, CA 94305 USA ,grid.168010.e0000000419368956Medical Scientist Training Program, Stanford University School of Medicine, Stanford, CA 94305 USA ,grid.168010.e0000000419368956Institute for Immunity, Transplantation and Infection, Stanford University School of Medicine, Stanford, CA 94305 USA ,grid.499295.a0000 0004 9234 0175Chan Zuckerberg Biohub, San Francisco, CA 94158 USA
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9
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Maliah A, Parikh R, Tayer-Shifman OE, Kimhi O, Gepstein R, Halperin T, Levy Y, Levy C, Basson YPP, Kivity S. Steroid treatment suppresses the CD4 + T-cell response to the third dose of mRNA COVID-19 vaccine in systemic autoimmune rheumatic disease patients. Sci Rep 2022; 12:21056. [PMID: 36474011 PMCID: PMC9727118 DOI: 10.1038/s41598-022-25642-z] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2022] [Accepted: 12/02/2022] [Indexed: 12/12/2022] Open
Abstract
Prolonged steroid treatment has a suppressive effect on the immune system, however, its effect on the cellular response to mRNA vaccine is unknown. Here we assessed the impact of prolonged steroid treatment on the T-cell and humoral response to the SARS-CoV-2 spike (S) peptide following the third dose of the BNT162b2 vaccine in systemic autoimmune rheumatic disease patients. We found that CD4 T-cell response to the S peptide in patients on high-dose long-term steroid treatment showed significantly less S-peptide specific response, compare to low-dose or untreated patients. Remarkably, these results were not reflected in their humoral response, since almost all patients in the cohort had sufficient antibody levels. Moreover, S-peptide activation failed to induce significant mRNA levels of IFNγ and TNFα in patients receiving high-dose steroids. RNA-sequencing datasets analysis implies that steroid treatments' inhibitory effect of nuclear factor kappa-B signaling may interfere with the activation of S-specific CD4 T-cells. This reveals that high-dose steroid treatment inhibits T-cell response to the mRNA vaccine, despite having sufficient antibody levels. Since T-cell immunity is a crucial factor in the immune response to viruses, our findings highlight the need for enhancing the efficiency of vaccines in immune-suppressive patients, by modulation of the T-cell response.
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Affiliation(s)
- Avishai Maliah
- grid.12136.370000 0004 1937 0546Department of Human Genetics and Biochemistry, Sackler Faculty of Medicine, Tel Aviv University, 69978 Tel Aviv, Israel
| | - Roma Parikh
- grid.12136.370000 0004 1937 0546Department of Human Genetics and Biochemistry, Sackler Faculty of Medicine, Tel Aviv University, 69978 Tel Aviv, Israel
| | - Oshrat E. Tayer-Shifman
- grid.415250.70000 0001 0325 0791Rheumatology Unit, Meir Medical Center, Tchernichovsky St 59, Kfar Saba, Israel ,grid.12136.370000 0004 1937 0546Sackler Faculty of Medicine, Tel-Aviv University, Tel-Aviv, Israel
| | - Oded Kimhi
- grid.415250.70000 0001 0325 0791Department of Internal Medicine A, Meir Medical Center, Kfar Saba, Israel
| | - Raz Gepstein
- grid.415250.70000 0001 0325 0791Department of Ophthalmology, Meir Medical Center, Kfar Saba, Israel
| | - Tami Halperin
- grid.12136.370000 0004 1937 0546Department of Infectious Diseases, Tel-Aviv Sourasky Medical Center, Sackler Faculty of Medicine, Tel-Aviv University, Tel-Aviv, Israel
| | - Yair Levy
- grid.12136.370000 0004 1937 0546Sackler Faculty of Medicine, Tel-Aviv University, Tel-Aviv, Israel ,grid.415250.70000 0001 0325 0791Department of Internal Medicine E, Meir Medical Center, Kfar Saba, Israel
| | - Carmit Levy
- grid.12136.370000 0004 1937 0546Department of Human Genetics and Biochemistry, Sackler Faculty of Medicine, Tel Aviv University, 69978 Tel Aviv, Israel
| | - Yael Pri-Paz Basson
- grid.415250.70000 0001 0325 0791Rheumatology Unit, Meir Medical Center, Tchernichovsky St 59, Kfar Saba, Israel
| | - Shaye Kivity
- grid.415250.70000 0001 0325 0791Rheumatology Unit, Meir Medical Center, Tchernichovsky St 59, Kfar Saba, Israel ,grid.12136.370000 0004 1937 0546Sackler Faculty of Medicine, Tel-Aviv University, Tel-Aviv, Israel
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10
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Rood JE, Maartens A, Hupalowska A, Teichmann SA, Regev A. Impact of the Human Cell Atlas on medicine. Nat Med 2022; 28:2486-2496. [PMID: 36482102 DOI: 10.1038/s41591-022-02104-7] [Citation(s) in RCA: 43] [Impact Index Per Article: 21.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2022] [Accepted: 10/24/2022] [Indexed: 12/13/2022]
Abstract
Single-cell atlases promise to provide a 'missing link' between genes, diseases and therapies. By identifying the specific cell types, states, programs and contexts where disease-implicated genes act, we will understand the mechanisms of disease at the cellular and tissue levels and can use this understanding to develop powerful disease diagnostics; identify promising new drug targets; predict their efficacy, toxicity and resistance mechanisms; and empower new kinds of therapies, from cancer therapies to regenerative medicine. Here, we lay out a vision for the potential of cell atlases to impact the future of medicine, and describe how advances over the past decade have begun to realize this potential in common complex diseases, infectious diseases (including COVID-19), rare diseases and cancer.
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Affiliation(s)
| | - Aidan Maartens
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | | | - Sarah A Teichmann
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK.
- Theory of Condensed Matter, Cavendish Laboratory, Department of Physics, University of Cambridge, Cambridge, UK.
| | - Aviv Regev
- Genentech, South San Francisco, CA, USA.
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11
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Proinflammatory Innate Cytokines and Distinct Metabolomic Signatures Shape the T Cell Response in Active COVID-19. Vaccines (Basel) 2022; 10:vaccines10101762. [PMID: 36298628 PMCID: PMC9609972 DOI: 10.3390/vaccines10101762] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2022] [Revised: 10/07/2022] [Accepted: 10/14/2022] [Indexed: 11/26/2022] Open
Abstract
The underlying factors contributing to the evolution of SARS-CoV-2-specific T cell responses during COVID-19 infection remain unidentified. To address this, we characterized innate and adaptive immune responses with metabolomic profiling longitudinally at three different time points (0–3, 7–9, and 14–16 days post-COVID-19 positivity) from young, mildly symptomatic, active COVID-19 patients infected during the first wave in mid-2020. We observed that anti-RBD IgG and viral neutralization are significantly reduced against the delta variant, compared to the ancestral strain. In contrast, compared to the ancestral strain, T cell responses remain preserved against the delta and omicron variants. We determined innate immune responses during the early stage of active infection, in response to TLR 3/7/8-mediated activation in PBMCs and serum metabolomic profiling. Correlation analysis indicated PBMCs-derived proinflammatory cytokines, IL-18, IL-1β, and IL-23, and the abundance of plasma metabolites involved in arginine biosynthesis were predictive of a robust SARS-CoV-2-specific Th1 response at a later stage (two weeks after PCR positivity). These observations may contribute to designing effective vaccines and adjuvants that promote innate immune responses and metabolites to induce a long-lasting anti-SARS-CoV-2-specific T cell response.
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12
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Morgan DM, Shreffler WG, Love JC. Revealing the heterogeneity of CD4+ T cells through single-cell transcriptomics. J Allergy Clin Immunol 2022; 150:748-755. [DOI: 10.1016/j.jaci.2022.08.010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2022] [Revised: 08/15/2022] [Accepted: 08/19/2022] [Indexed: 11/07/2022]
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13
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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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14
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Liu W, Jia J, Dai Y, Chen W, Pei G, Yan Q, Zhao Z. Delineating COVID-19 immunological features using single-cell RNA sequencing. Innovation (N Y) 2022; 3:100289. [PMID: 35879967 PMCID: PMC9299978 DOI: 10.1016/j.xinn.2022.100289] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2022] [Accepted: 07/16/2022] [Indexed: 11/24/2022] Open
Abstract
Understanding the molecular mechanisms of coronavirus disease 2019 (COVID-19) pathogenesis and immune response is vital for developing therapies. Single-cell RNA sequencing has been applied to delineate the cellular heterogeneity of the host response toward COVID-19 in multiple tissues and organs. Here, we review the applications and findings from over 80 original COVID-19 single-cell RNA sequencing studies as well as many secondary analysis studies. We describe that single-cell RNA sequencing reveals multiple features of COVID-19 patients with different severity, including cell populations with proportional alteration, COVID-19-induced genes and pathways, severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) infection in single cells, and adaptation of immune repertoire. We also collect published single-cell RNA sequencing datasets from original studies. Finally, we discuss the limitations in current studies and perspectives for future advance.
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Affiliation(s)
- Wendao Liu
- The University of Texas MD Anderson Cancer Center UTHealth Graduate School of Biomedical Sciences, Houston, TX 77030, USA
- Center for Precision Health, School of Biomedical Informatics, the University of Texas Health Science Center at Houston, Houston, TX 77030, USA
| | - Johnathan Jia
- The University of Texas MD Anderson Cancer Center UTHealth Graduate School of Biomedical Sciences, Houston, TX 77030, USA
- Center for Precision Health, School of Biomedical Informatics, the University of Texas Health Science Center at Houston, Houston, TX 77030, USA
| | - Yulin Dai
- Center for Precision Health, School of Biomedical Informatics, the University of Texas Health Science Center at Houston, Houston, TX 77030, USA
| | - Wenhao Chen
- Immunobiology and Transplant Science Center, Department of Surgery, Houston Methodist Research Institute and Institute for Academic Medicine, Houston Methodist Hospital, Houston, TX 77030, USA
- Department of Surgery, Weill Cornell Medicine, Cornell University, New York, NY 10065, USA
| | - Guangsheng Pei
- Center for Precision Health, School of Biomedical Informatics, the University of Texas Health Science Center at Houston, Houston, TX 77030, USA
| | - Qiheng Yan
- Center for Precision Health, School of Biomedical Informatics, the University of Texas Health Science Center at Houston, Houston, TX 77030, USA
| | - Zhongming Zhao
- The University of Texas MD Anderson Cancer Center UTHealth Graduate School of Biomedical Sciences, Houston, TX 77030, USA
- Center for Precision Health, School of Biomedical Informatics, the University of Texas Health Science Center at Houston, Houston, TX 77030, USA
- Human Genetics Center, School of Public Health, the University of Texas Health Science Center at Houston, Houston, TX 77030, USA
- Department of Biomedical Informatics, Vanderbilt University Medical Center, Nashville, TN 37203, USA
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15
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Weber S, Kehl V, Erber J, Wagner KI, Jetzlsperger AM, Burrell T, Schober K, Schommers P, Augustin M, Crowell CS, Gerhard M, Winter C, Moosmann A, Spinner CD, Protzer U, Hoffmann D, D’Ippolito E, Busch DH. CMV seropositivity is a potential novel risk factor for severe COVID-19 in non-geriatric patients. PLoS One 2022; 17:e0268530. [PMID: 35613127 PMCID: PMC9132318 DOI: 10.1371/journal.pone.0268530] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2022] [Accepted: 05/02/2022] [Indexed: 12/12/2022] Open
Abstract
BACKGROUND COVID-19 has so far affected more than 250 million individuals worldwide, causing more than 5 million deaths. Several risk factors for severe disease have been identified, most of which coincide with advanced age. In younger individuals, severe COVID-19 often occurs in the absence of obvious comorbidities. Guided by the finding of cytomegalovirus (CMV)-specific T cells with some cross-reactivity to SARS-CoV-2 in a COVID-19 intensive care unit (ICU) patient, we decided to investigate whether CMV seropositivity is associated with severe or critical COVID-19. Herpes simplex virus (HSV) serostatus was investigated as control. METHODS National German COVID-19 bio-sample and data banks were used to retrospectively analyze the CMV and HSV serostatus of patients who experienced mild (n = 101), moderate (n = 130) or severe to critical (n = 80) disease by IgG serology. We then investigated the relationship between disease severity and herpesvirus serostatus via statistical models. RESULTS Non-geriatric patients (< 60 years) with severe COVID-19 were found to have a very high prevalence of CMV-seropositivity, while CMV status distribution in individuals with mild disease was similar to the prevalence in the German population; interestingly, this was not detectable in older patients. Prediction models support the hypothesis that the CMV serostatus, unlike HSV, might be a strong biomarker in identifying younger individuals with a higher risk of developing severe COVID-19, in particular in absence of other co-morbidities. CONCLUSIONS We identified 'CMV-seropositivity' as a potential novel risk factor for severe COVID-19 in non-geriatric individuals in the studied cohorts. More mechanistic analyses as well as confirmation of similar findings in cohorts representing the currently most relevant SARS-CoV-2 variants should be performed shortly.
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Affiliation(s)
- Simone Weber
- Institute for Medical Microbiology, Immunology and Hygiene, Technical University of Munich, Munich, Germany
| | - Victoria Kehl
- Institute for AI and Informatics in Medicine, School of Medicine, Technical University of Munich, Munich, Germany
| | - Johanna Erber
- Department of Internal Medicine II, University Hospital Rechts Der Isar, School of Medicine, Technical University of Munich, Munich, Germany
- German Center for Infection Research (DZIF), Munich, Germany
| | - Karolin I. Wagner
- Institute for Medical Microbiology, Immunology and Hygiene, Technical University of Munich, Munich, Germany
| | | | - Teresa Burrell
- Institute for Medical Microbiology, Immunology and Hygiene, Technical University of Munich, Munich, Germany
| | - Kilian Schober
- Mikrobiologisches Institut–Klinische Mikrobiologie, Immunologie und Hygiene, Universitätsklinikum Erlangen, Friedrich-Alexander-Universität (FAU) Erlangen-Nürnberg, Erlangen, Germany
| | - Philipp Schommers
- Medical Faculty and University Hospital Cologne, Department I of Internal Medicine, University of Cologne, Cologne, Germany
- German Center for Infection Research (DZIF), Bonn-Cologne, Germany
| | - Max Augustin
- Medical Faculty and University Hospital Cologne, Department I of Internal Medicine, University of Cologne, Cologne, Germany
- German Center for Infection Research (DZIF), Bonn-Cologne, Germany
| | - Claudia S. Crowell
- Institute for Medical Microbiology, Immunology and Hygiene, Technical University of Munich, Munich, Germany
- German Center for Infection Research (DZIF), Munich, Germany
| | - Markus Gerhard
- Institute for Medical Microbiology, Immunology and Hygiene, Technical University of Munich, Munich, Germany
- German Center for Infection Research (DZIF), Munich, Germany
| | - Christof Winter
- Institute of Clinicl Chemistry and Pathobiochemistry, School of Medicine, Technical University of Munich, Munich, Germany
| | - Andreas Moosmann
- German Center for Infection Research (DZIF), Munich, Germany
- Department of Medicine III, University Hospital, LMU Munich, Munich, Germany
| | - Christoph D. Spinner
- Department of Internal Medicine II, University Hospital Rechts Der Isar, School of Medicine, Technical University of Munich, Munich, Germany
- German Center for Infection Research (DZIF), Munich, Germany
| | - Ulrike Protzer
- Institute of Virology, School of Medicine, Technical University of Munich, Munich, Germany
| | - Dieter Hoffmann
- Institute of Virology, School of Medicine, Technical University of Munich, Munich, Germany
| | - Elvira D’Ippolito
- Institute for Medical Microbiology, Immunology and Hygiene, Technical University of Munich, Munich, Germany
| | - Dirk H. Busch
- Institute for Medical Microbiology, Immunology and Hygiene, Technical University of Munich, Munich, Germany
- German Center for Infection Research (DZIF), Munich, Germany
- * E-mail:
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16
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Jing L, Wu X, Krist MP, Hsiang TY, Campbell VL, McClurkan CL, Favors SM, Hemingway LA, Godornes C, Tong DQ, Selke S, LeClair AC, Pyo CW, Geraghty DE, Laing KJ, Wald A, Gale M, Koelle DM. T cell response to intact SARS-CoV-2 includes coronavirus cross-reactive and variant-specific components. JCI Insight 2022; 7:e158126. [PMID: 35133988 PMCID: PMC8986086 DOI: 10.1172/jci.insight.158126] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2022] [Accepted: 02/02/2022] [Indexed: 12/03/2022] Open
Abstract
SARS-CoV-2 provokes a robust T cell response. Peptide-based studies exclude antigen processing and presentation biology, which may influence T cell detection studies. To focus on responses to whole virus and complex antigens, we used intact SARS-CoV-2 and full-length proteins with DCs to activate CD8 and CD4 T cells from convalescent people. T cell receptor (TCR) sequencing showed partial repertoire preservation after expansion. Resultant CD8 T cells recognize SARS-CoV-2-infected respiratory tract cells, and CD4 T cells detect inactivated whole viral antigen. Specificity scans with proteome-covering protein/peptide arrays show that CD8 T cells are oligospecific per subject and that CD4 T cell breadth is higher. Some CD4 T cell lines enriched using SARS-CoV-2 cross-recognize whole seasonal coronavirus (sCoV) antigens, with protein, peptide, and HLA restriction validation. Conversely, recognition of some epitopes is eliminated for SARS-CoV-2 variants, including spike (S) epitopes in the Alpha, Beta, Gamma, and Delta variant lineages.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | - Stacy Selke
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, Washington, USA
| | | | - Chu-Woo Pyo
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
| | - Daniel E. Geraghty
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
| | | | - Anna Wald
- Department of Medicine
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, Washington, USA
- Department of Epidemiology, University of Washington, Seattle, Washington, USA
- Vaccine and Infectious Diseases Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
| | - Michael Gale
- Department of Immunology, and
- Center for Innate Immunity of Immune Disease, Department of Immunology, and
- Department of Global Health, University of Washington, Seattle, Washington, USA
| | - David M. Koelle
- Department of Medicine
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, Washington, USA
- Vaccine and Infectious Diseases Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
- Department of Global Health, University of Washington, Seattle, Washington, USA
- Benaroya Research Institute, Seattle, Washington, USA
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17
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Enhanced SARS-CoV-2-Specific CD4 + T Cell Activation and Multifunctionality in Late Convalescent COVID-19 Individuals. Viruses 2022; 14:v14030511. [PMID: 35336918 PMCID: PMC8954911 DOI: 10.3390/v14030511] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2022] [Revised: 02/22/2022] [Accepted: 02/26/2022] [Indexed: 02/04/2023] Open
Abstract
Background: Examination of CD4+ T cell responses during the natural course of severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) infection offers useful information for the improvement of vaccination strategies against this virus and the protective effect of these T cells. Methods: We characterized the SARS-CoV-2-specific CD4+ T cell activation marker, multifunctional cytokine and cytotoxic marker expression in recovered coronavirus disease 2019 (COVID-19) individuals. Results: CD4+ T-cell responses in late convalescent (>6 months of diagnosis) individuals are characterized by elevated frequencies of activated as well as mono, dual- and multi-functional Th1 and Th17 CD4+ T cells in comparison to early convalescent (<1 month of diagnosis) individuals following stimulation with SARS-CoV-2-specific antigens. Similarly, the frequencies of cytotoxic marker expressing CD4+ T cells were also enhanced in late convalescent compared to early convalescent individuals. Conclusion: Our findings from a low-to middle-income country suggest protective adaptive immune responses following natural infection of SARS-CoV-2 are elevated even at six months following initial symptoms, indicating the CD4+ T cell mediated immune protection lasts for six months or more in natural infection.
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18
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Jing L, Wu X, Krist MP, Hsiang TY, Campbell VL, McClurkan CL, Favors SM, Hemingway LA, Godornes C, Tong DQ, Selke S, LeClair AC, Pyo CW, Geraghty DE, Laing KJ, Wald A, Gale M, Koelle DM. T cell response to intact SARS-CoV-2 includes coronavirus cross-reactive and variant-specific components. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2022:2022.01.23.22269497. [PMID: 35118477 PMCID: PMC8811910 DOI: 10.1101/2022.01.23.22269497] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
SARS-CoV-2 provokes a brisk T cell response. Peptide-based studies exclude antigen processing and presentation biology and may influence T cell detection studies. To focus on responses to whole virus and complex antigens, we used intact SARS-CoV-2 and full-length proteins with DC to activate CD8 and CD4 T cells from convalescent persons. T cell receptor (TCR) sequencing showed partial repertoire preservation after expansion. Resultant CD8 T cells recognize SARS-CoV-2-infected respiratory cells, and CD4 T cells detect inactivated whole viral antigen. Specificity scans with proteome-covering protein/peptide arrays show that CD8 T cells are oligospecific per subject and that CD4 T cell breadth is higher. Some CD4 T cell lines enriched using SARS-CoV-2 cross-recognize whole seasonal coronavirus (sCoV) antigens, with protein, peptide, and HLA restriction validation. Conversely, recognition of some epitopes is eliminated for SARS-CoV-2 variants, including spike (S) epitopes in the alpha, beta, gamma, and delta variant lineages.
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19
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Wagner KI, Mateyka LM, Jarosch S, Grass V, Weber S, Schober K, Hammel M, Burrell T, Kalali B, Poppert H, Beyer H, Schambeck S, Holdenrieder S, Strötges-Achatz A, Haselmann V, Neumaier M, Erber J, Priller A, Yazici S, Roggendorf H, Odendahl M, Tonn T, Dick A, Witter K, Mijočević H, Protzer U, Knolle PA, Pichlmair A, Crowell CS, Gerhard M, D'Ippolito E, Busch DH. Recruitment of highly cytotoxic CD8 + T cell receptors in mild SARS-CoV-2 infection. Cell Rep 2021; 38:110214. [PMID: 34968416 PMCID: PMC8677487 DOI: 10.1016/j.celrep.2021.110214] [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: 08/27/2021] [Revised: 11/07/2021] [Accepted: 12/13/2021] [Indexed: 01/12/2023] Open
Abstract
T cell immunity is crucial for control of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection and has been studied widely on a quantitative level. However, the quality of responses, in particular of CD8+ T cells, has only been investigated marginally so far. Here, we isolate T cell receptor (TCR) repertoires specific for immunodominant SARS-CoV-2 epitopes restricted to common human Leukocyte antigen (HLA) class I molecules in convalescent individuals. SARS-CoV-2-specific CD8+ T cells are detected up to 12 months after infection. TCR repertoires are diverse, with heterogeneous functional avidity and cytotoxicity toward virus-infected cells, as demonstrated for TCR-engineered T cells. High TCR functionality correlates with gene signatures that, remarkably, could be retrieved for each epitope:HLA combination analyzed. Overall, our data demonstrate that polyclonal and highly functional CD8+ TCRs—classic features of protective immunity—are recruited upon mild SARS-CoV-2 infection, providing tools to assess the quality of and potentially restore functional CD8+ T cell immunity.
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Affiliation(s)
- Karolin I Wagner
- Institute for Medical Microbiology, Immunology and Hygiene, Technical University of Munich (TUM), 81675 Munich, Germany
| | - Laura M Mateyka
- 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
| | - Vincent Grass
- Institute of Virology, School of Medicine, Technical University of Munich (TUM), 81675 Munich, Germany
| | - Simone Weber
- Institute for Medical Microbiology, Immunology and Hygiene, Technical University of Munich (TUM), 81675 Munich, Germany
| | - Kilian Schober
- Institute for Medical Microbiology, Immunology and Hygiene, Technical University of Munich (TUM), 81675 Munich, Germany; Mikrobiologisches Institut - Klinische Mikrobiologie, Immunologie und Hygiene, Universitätsklinikum Erlangen, Friedrich-Alexander-Universität (FAU) Erlangen-Nürnberg, 91054 Erlangen, Germany
| | - Monika Hammel
- Institute for Medical Microbiology, Immunology and Hygiene, Technical University of Munich (TUM), 81675 Munich, Germany
| | - Teresa Burrell
- Institute for Medical Microbiology, Immunology and Hygiene, Technical University of Munich (TUM), 81675 Munich, Germany
| | - Behnam Kalali
- Institute for Medical Microbiology, Immunology and Hygiene, Technical University of Munich (TUM), 81675 Munich, Germany
| | - Holger Poppert
- Department of Neurology, Helios Klinikum München West, 81241 Munich, Germany; Neurologische Klinik, University Hospital Rechts der Isar, Technical University of Munich (TUM), 81675 Munich, Germany
| | - Henriette Beyer
- Department of Neurology, Helios Klinikum München West, 81241 Munich, Germany
| | - Sophia Schambeck
- Institute for Medical Microbiology, Immunology and Hygiene, Technical University of Munich (TUM), 81675 Munich, Germany; Department of Neurology, Helios Klinikum München West, 81241 Munich, Germany
| | - Stefan Holdenrieder
- Institute of Laboratory Medicine, Munich Biomarker Research Center, Deutsches Herzzentrum München, Technical University of Munich (TUM), 80636 Munich, Germany
| | - Andrea Strötges-Achatz
- Institute of Laboratory Medicine, Munich Biomarker Research Center, Deutsches Herzzentrum München, Technical University of Munich (TUM), 80636 Munich, Germany
| | - Verena Haselmann
- Department of Clinical Chemistry, University Medicine Mannheim, Medical Faculty Mannheim of the University of Heidelberg, 68167 Mannheim, Germany
| | - Michael Neumaier
- Department of Clinical Chemistry, University Medicine Mannheim, Medical Faculty Mannheim of the University of Heidelberg, 68167 Mannheim, Germany
| | - Johanna Erber
- Department of Internal Medicine II, University Hospital rechts der Isar, Technical University of Munich, School of Medicine, Munich, Germany
| | - Alina Priller
- Institute of Molecular Immunology and Experimental Oncology, School of Medicine, Technical University of Munich (TUM), 81675 Munich, Germany
| | - Sarah Yazici
- Institute of Molecular Immunology and Experimental Oncology, School of Medicine, Technical University of Munich (TUM), 81675 Munich, Germany
| | - Hedwig Roggendorf
- Institute of Molecular Immunology and Experimental Oncology, School of Medicine, Technical University of Munich (TUM), 81675 Munich, Germany
| | - Marcus Odendahl
- Experimental Transfusion Medicine, Medical Faculty Carl Gustav Carus, TU Dresden, 01307 Dresden, Germany; Institute for Transfusion Medicine Dresden, German Red Cross Blood Donation Service North-East, 01307 Dresden, Germany
| | - Torsten Tonn
- Experimental Transfusion Medicine, Medical Faculty Carl Gustav Carus, TU Dresden, 01307 Dresden, Germany; Institute for Transfusion Medicine Dresden, German Red Cross Blood Donation Service North-East, 01307 Dresden, Germany
| | - Andrea Dick
- Laboratory of Immunogenetics and Molecular Diagnostics, Department of Transfusion Medicine, Cellular Therapeutics and Hemostaseology, LMU University Hospital, 81377 Munich, Germany
| | - Klaus Witter
- Laboratory of Immunogenetics and Molecular Diagnostics, Department of Transfusion Medicine, Cellular Therapeutics and Hemostaseology, LMU University Hospital, 81377 Munich, Germany
| | - Hrvoje Mijočević
- Institute of Virology, School of Medicine, Technical University of Munich (TUM), 81675 Munich, Germany
| | - Ulrike Protzer
- Institute of Virology, School of Medicine, Technical University of Munich (TUM), 81675 Munich, Germany; German Center for Infection Research (DZIF), Partner Site Munich, Munich, Germany
| | - Percy A Knolle
- Institute of Molecular Immunology and Experimental Oncology, School of Medicine, Technical University of Munich (TUM), 81675 Munich, Germany; German Center for Infection Research (DZIF), Partner Site Munich, Munich, Germany
| | - Andreas Pichlmair
- Institute of Virology, School of Medicine, Technical University of Munich (TUM), 81675 Munich, Germany; German Center for Infection Research (DZIF), Partner Site Munich, Munich, Germany
| | - Claudia S Crowell
- Institute for Medical Microbiology, Immunology and Hygiene, Technical University of Munich (TUM), 81675 Munich, Germany; German Center for Infection Research (DZIF), Partner Site Munich, Munich, Germany
| | - Markus Gerhard
- Institute for Medical Microbiology, Immunology and Hygiene, Technical University of Munich (TUM), 81675 Munich, Germany; German Center for Infection Research (DZIF), Partner Site Munich, Munich, Germany
| | - Elvira D'Ippolito
- 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, Munich, Germany.
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20
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Dogra N, Ledesma-Feliciano C, Sen R. Developmental Aspects of SARS-CoV-2, Potential Role of Exosomes and Their Impact on the Human Transcriptome. J Dev Biol 2021; 9:54. [PMID: 34940501 PMCID: PMC8708617 DOI: 10.3390/jdb9040054] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2021] [Revised: 11/12/2021] [Accepted: 11/23/2021] [Indexed: 12/21/2022] Open
Abstract
With over 4.8 million deaths within 2 years, time is of the essence in combating COVID-19. The infection now shows devastating impacts on the younger population, who were not previously predicted to be vulnerable, such as in the older population. COVID-19-related complications have been reported in neonates whose mothers were infected with SARS-CoV-2 during pregnancy, and in children who get infected. Hence, a deeper understanding of the pathophysiology of COVID-19 during various developmental stages and placental transmission is essential. Although a connection has not yet been established between exosomal trafficking and the placental transmission of COVID-19, reports indicate that SARS-CoV-2 components may be trafficked between cells through exosomes. As the infection spreads, the transcriptome of cells is drastically perturbed, e.g., through the severe upregulation of several immune-related genes. Consequently, a major outcome of COVID-19 is an elevated immune response and the detection of viral RNA transcripts in host tissue. In this direction, this review focuses on SARS-CoV-2 virology, its in utero transmission from infected pregnant mothers to fetuses, SARS-CoV-2 and exosomal cellular trafficking, transcriptomic impacts, and RNA-mediated therapeutics against COVID-19. Future research will establish stronger connections between the above processes to develop diagnostic and therapeutic solutions towards COVID-19 and similar viral outbreaks.
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Affiliation(s)
- Navneet Dogra
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Department of Pathology, Molecular and Cell-Based Medicine, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Carmen Ledesma-Feliciano
- Division of Infectious Diseases, School of Medicine, Anschutz Medical Campus, University of Colorado, Aurora, CO 80045, USA;
| | - Rwik Sen
- Active Motif, Incorporated, Carlsbad, CA 92008, USA
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21
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Serr I, Drost F, Schubert B, Daniel C. Antigen-Specific Treg Therapy in Type 1 Diabetes - Challenges and Opportunities. Front Immunol 2021; 12:712870. [PMID: 34367177 PMCID: PMC8341764 DOI: 10.3389/fimmu.2021.712870] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2021] [Accepted: 07/06/2021] [Indexed: 01/16/2023] Open
Abstract
Regulatory T cells (Tregs) are key mediators of peripheral self-tolerance and alterations in their frequencies, stability, and function have been linked to autoimmunity. The antigen-specific induction of Tregs is a long-envisioned goal for the treatment of autoimmune diseases given reduced side effects compared to general immunosuppressive therapies. However, the translation of antigen-specific Treg inducing therapies for the treatment or prevention of autoimmune diseases into the clinic remains challenging. In this mini review, we will discuss promising results for antigen-specific Treg therapies in allergy and specific challenges for such therapies in autoimmune diseases, with a focus on type 1 diabetes (T1D). We will furthermore discuss opportunities for antigen-specific Treg therapies in T1D, including combinatorial strategies and tissue-specific Treg targeting. Specifically, we will highlight recent advances in miRNA-targeting as a means to foster Tregs in autoimmunity. Additionally, we will discuss advances and perspectives of computational strategies for the detailed analysis of tissue-specific Tregs on the single-cell level.
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Affiliation(s)
- Isabelle Serr
- Group Immune Tolerance in Type 1 Diabetes, Helmholtz Diabetes Center at Helmholtz Zentrum München, Institute of Diabetes Research, Munich, Germany
- Deutsches Zentrum für Diabetesforschung (DZD), Neuherberg, Germany
| | - Felix Drost
- School of Life Sciences Weihenstephan, Technische Universität München, Garching bei München, Germany
| | - Benjamin Schubert
- Institute of Computational Biology, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany
- Department of Mathematics, Technische Universität München, Garching bei München, Germany
| | - Carolin Daniel
- Group Immune Tolerance in Type 1 Diabetes, Helmholtz Diabetes Center at Helmholtz Zentrum München, Institute of Diabetes Research, Munich, Germany
- Deutsches Zentrum für Diabetesforschung (DZD), Neuherberg, Germany
- Division of Clinical Pharmacology, Department of Medicine IV, Ludwig-Maximilians-Universität München, Munich, Germany
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