1
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Lu X, Hayashi H, Ishikawa E, Takeuchi Y, Dychiao JVT, Nakagami H, Yamasaki S. Early acquisition of S-specific Tfh clonotypes after SARS-CoV-2 vaccination is associated with the longevity of anti-S antibodies. eLife 2024; 12:RP89999. [PMID: 38716629 PMCID: PMC11078543 DOI: 10.7554/elife.89999] [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] [Indexed: 05/12/2024] Open
Abstract
SARS-CoV-2 vaccines have been used worldwide to combat COVID-19 pandemic. To elucidate the factors that determine the longevity of spike (S)-specific antibodies, we traced the characteristics of S-specific T cell clonotypes together with their epitopes and anti-S antibody titers before and after BNT162b2 vaccination over time. T cell receptor (TCR) αβ sequences and mRNA expression of the S-responded T cells were investigated using single-cell TCR- and RNA-sequencing. Highly expanded 199 TCR clonotypes upon stimulation with S peptide pools were reconstituted into a reporter T cell line for the determination of epitopes and restricting HLAs. Among them, we could determine 78 S epitopes, most of which were conserved in variants of concern (VOCs). After the 2nd vaccination, T cell clonotypes highly responsive to recall S stimulation were polarized to follicular helper T (Tfh)-like cells in donors exhibiting sustained anti-S antibody titers (designated as 'sustainers'), but not in 'decliners'. Even before vaccination, S-reactive CD4+ T cell clonotypes did exist, most of which cross-reacted with environmental or symbiotic microbes. However, these clonotypes contracted after vaccination. Conversely, S-reactive clonotypes dominated after vaccination were undetectable in pre-vaccinated T cell pool, suggesting that highly responding S-reactive T cells were established by vaccination from rare clonotypes. These results suggest that de novo acquisition of memory Tfh-like cells upon vaccination may contribute to the longevity of anti-S antibody titers.
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Affiliation(s)
- Xiuyuan Lu
- Laboratory of Molecular Immunology, Immunology Frontier Research Center, Osaka UniversitySuitaJapan
| | - Hiroki Hayashi
- Department of Health Development and Medicine, Osaka University Graduate School of MedicineSuitaJapan
| | - Eri Ishikawa
- Laboratory of Molecular Immunology, Immunology Frontier Research Center, Osaka UniversitySuitaJapan
- Department of Molecular Immunology, Research Institute for Microbial Diseases, Osaka UniversitySuitaJapan
| | - Yukiko Takeuchi
- Laboratory of Molecular Immunology, Immunology Frontier Research Center, Osaka UniversitySuitaJapan
| | | | - Hironori Nakagami
- Department of Health Development and Medicine, Osaka University Graduate School of MedicineSuitaJapan
| | - Sho Yamasaki
- Laboratory of Molecular Immunology, Immunology Frontier Research Center, Osaka UniversitySuitaJapan
- Department of Molecular Immunology, Research Institute for Microbial Diseases, Osaka UniversitySuitaJapan
- Center for Infectious Disease Education and Research (CiDER), Osaka UniversitySuitaJapan
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2
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Yanagi M, Ikegami I, Kamekura R, Sato T, Sato T, Kamiya S, Murayama K, Jitsukawa S, Ito F, Yorozu A, Kihara M, Abe T, Takaki H, Kawata K, Shigehara K, Miyajima S, Nishikiori H, Sato A, Tohse N, Takano KI, Chiba H, Ichimiya S. Bob1 maintains T follicular helper cells for long-term humoral immunity. Commun Biol 2024; 7:185. [PMID: 38360857 PMCID: PMC10869348 DOI: 10.1038/s42003-024-05827-0] [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: 07/12/2023] [Accepted: 01/16/2024] [Indexed: 02/17/2024] Open
Abstract
Humoral immunity is vital for host protection, yet aberrant antibody responses can trigger harmful inflammation and immune-related disorders. T follicular helper (Tfh) cells, central to humoral immunity, have garnered significant attention for unraveling immune mechanisms. This study shows the role of B-cell Oct-binding protein 1 (Bob1), a transcriptional coactivator, in Tfh cell regulation. Our investigation, utilizing conditional Bob1-deficient mice, suggests that Bob1 plays a critical role in modulating inducible T-cell costimulator expression and cellular respiration in Tfh cells. This regulation maintains the long-term functionality of Tfh cells, enabling their reactivation from central memory T cells to produce antibodies during recall responses. In a bronchial asthma model induced by house dust mite (HDM) inhalation, Bob1 is observed to enhance HDM-specific antibodies, including IgE, highlighting its pivotal function in Tfh cell regulation. Further exploration of Bob1-dependent mechanisms in Tfh cells holds promise for governing protective immunity and addressing immune-related disorders.
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Affiliation(s)
- Masahiro Yanagi
- Department of Human Immunology, Research Institute for Frontier Medicine, Sapporo Medical University School of Medicine, Sapporo, 060-8556, Japan
- Department of Respiratory Medicine and Allergology, Sapporo Medical University School of Medicine, Sapporo, 060-8556, Japan
| | - Ippei Ikegami
- Department of Human Immunology, Research Institute for Frontier Medicine, Sapporo Medical University School of Medicine, Sapporo, 060-8556, Japan
| | - Ryuta Kamekura
- Department of Human Immunology, Research Institute for Frontier Medicine, Sapporo Medical University School of Medicine, Sapporo, 060-8556, Japan
- Department of Otolaryngology-Head and Neck Surgery, Sapporo Medical University School of Medicine, Sapporo, 060-8556, Japan
| | - Tatsuya Sato
- Department of Cellular Physiology and Signal Transduction, Sapporo Medical University School of Medicine, Sapporo, 060-8556, Japan
| | - Taiki Sato
- Department of Human Immunology, Research Institute for Frontier Medicine, Sapporo Medical University School of Medicine, Sapporo, 060-8556, Japan
| | - Shiori Kamiya
- Department of Human Immunology, Research Institute for Frontier Medicine, Sapporo Medical University School of Medicine, Sapporo, 060-8556, Japan
| | - Kosuke Murayama
- Department of Otolaryngology-Head and Neck Surgery, Sapporo Medical University School of Medicine, Sapporo, 060-8556, Japan
| | - Sumito Jitsukawa
- Department of Otolaryngology-Head and Neck Surgery, Sapporo Medical University School of Medicine, Sapporo, 060-8556, Japan
| | - Fumie Ito
- Department of Otolaryngology-Head and Neck Surgery, Sapporo Medical University School of Medicine, Sapporo, 060-8556, Japan
| | - Akira Yorozu
- Department of Human Immunology, Research Institute for Frontier Medicine, Sapporo Medical University School of Medicine, Sapporo, 060-8556, Japan
- Department of Otolaryngology-Head and Neck Surgery, Sapporo Medical University School of Medicine, Sapporo, 060-8556, Japan
| | - Miho Kihara
- Laboratory for Animal Resources and Genetic Engineering, RIKEN Center for Biosystems Dynamics Research, Kobe, 650-0047, Japan
| | - Takaya Abe
- Laboratory for Animal Resources and Genetic Engineering, RIKEN Center for Biosystems Dynamics Research, Kobe, 650-0047, Japan
| | - Hiromi Takaki
- Department of Human Immunology, Research Institute for Frontier Medicine, Sapporo Medical University School of Medicine, Sapporo, 060-8556, Japan
| | - Koji Kawata
- Department of Human Immunology, Research Institute for Frontier Medicine, Sapporo Medical University School of Medicine, Sapporo, 060-8556, Japan
| | - Katsunori Shigehara
- Department of Human Immunology, Research Institute for Frontier Medicine, Sapporo Medical University School of Medicine, Sapporo, 060-8556, Japan
- Department of Respiratory Medicine and Allergology, Sapporo Medical University School of Medicine, Sapporo, 060-8556, Japan
| | - Satsuki Miyajima
- Department of Respiratory Medicine and Allergology, Sapporo Medical University School of Medicine, Sapporo, 060-8556, Japan
| | - Hirotaka Nishikiori
- Department of Respiratory Medicine and Allergology, Sapporo Medical University School of Medicine, Sapporo, 060-8556, Japan
| | - Akinori Sato
- Department of Human Immunology, Research Institute for Frontier Medicine, Sapporo Medical University School of Medicine, Sapporo, 060-8556, Japan
- Department of Rehabilitation, Faculty of Healthcare and Science, Hokkaido Bunkyo University, Eniwa, 061-1449, Japan
| | - Noritsugu Tohse
- Department of Cellular Physiology and Signal Transduction, Sapporo Medical University School of Medicine, Sapporo, 060-8556, Japan
| | - Ken-Ichi Takano
- Department of Otolaryngology-Head and Neck Surgery, Sapporo Medical University School of Medicine, Sapporo, 060-8556, Japan
| | - Hirofumi Chiba
- Department of Respiratory Medicine and Allergology, Sapporo Medical University School of Medicine, Sapporo, 060-8556, Japan
| | - Shingo Ichimiya
- Department of Human Immunology, Research Institute for Frontier Medicine, Sapporo Medical University School of Medicine, Sapporo, 060-8556, Japan.
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3
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Ito E, Inuki S, Izumi Y, Takahashi M, Dambayashi Y, Ciacchi L, Awad W, Takeyama A, Shibata K, Mori S, Mak JYW, Fairlie DP, Bamba T, Ishikawa E, Nagae M, Rossjohn J, Yamasaki S. Sulfated bile acid is a host-derived ligand for MAIT cells. Sci Immunol 2024; 9:eade6924. [PMID: 38277465 PMCID: PMC11147531 DOI: 10.1126/sciimmunol.ade6924] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2022] [Accepted: 01/03/2024] [Indexed: 01/28/2024]
Abstract
Mucosal-associated invariant T (MAIT) cells are innate-like T cells that recognize bacterial riboflavin-based metabolites as activating antigens. Although MAIT cells are found in tissues, it is unknown whether any host tissue-derived antigens exist. Here, we report that a sulfated bile acid, cholic acid 7-sulfate (CA7S), binds the nonclassical MHC class I protein MR1 and is recognized by MAIT cells. CA7S is a host-derived metabolite whose levels were reduced by more than 98% in germ-free mice. Deletion of the sulfotransferase 2a family of enzymes (Sult2a1-8) responsible for CA7S synthesis reduced the number of thymic MAIT cells in mice. Moreover, recognition of CA7S induced MAIT cell survival and the expression of a homeostatic gene signature. By contrast, recognition of a previously described foreign antigen, 5-(2-oxopropylideneamino)-6-d-ribitylaminouracil (5-OP-RU), drove MAIT cell proliferation and the expression of inflammatory genes. Thus, CA7S is an endogenous antigen for MAIT cells, which promotes their development and function.
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Affiliation(s)
- Emi Ito
- Department of Molecular Immunology, Research Institute for Microbial Diseases, Osaka University, Suita, Osaka 565-0871, Japan
- Laboratory of Molecular Immunology, Immunology Frontier Research Center, Osaka University, Suita, Osaka 565-0871, Japan
| | - Shinsuke Inuki
- Graduate School of Pharmaceutical Sciences, Kyoto University, Kyoto, Kyoto 606-8501, Japan
| | - Yoshihiro Izumi
- Division of Metabolomics, Medical Institute of Bioregulation, Kyushu University, Fukuoka, Fukuoka 812-8582, Japan
| | - Masatomo Takahashi
- Division of Metabolomics, Medical Institute of Bioregulation, Kyushu University, Fukuoka, Fukuoka 812-8582, Japan
| | - Yuki Dambayashi
- Graduate School of Pharmaceutical Sciences, Kyoto University, Kyoto, Kyoto 606-8501, Japan
| | - Lisa Ciacchi
- Infection and Immunity Program and Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, Victoria, Australia
| | - Wael Awad
- Infection and Immunity Program and Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, Victoria, Australia
| | - Ami Takeyama
- Department of Molecular Immunology, Research Institute for Microbial Diseases, Osaka University, Suita, Osaka 565-0871, Japan
- Laboratory of Molecular Immunology, Immunology Frontier Research Center, Osaka University, Suita, Osaka 565-0871, Japan
| | - Kensuke Shibata
- Department of Microbiology and Immunology, Graduate School of Medicine, Yamaguchi University, Ube, Yamaguchi 755-8505, Japan
| | - Shotaro Mori
- Department of Molecular Immunology, Research Institute for Microbial Diseases, Osaka University, Suita, Osaka 565-0871, Japan
- Laboratory of Molecular Immunology, Immunology Frontier Research Center, Osaka University, Suita, Osaka 565-0871, Japan
| | - Jeffrey Y. W. Mak
- Institute for Molecular Bioscience, University of Queensland, Brisbane, Queensland 4072, Australia
| | - David P. Fairlie
- Institute for Molecular Bioscience, University of Queensland, Brisbane, Queensland 4072, Australia
| | - Takeshi Bamba
- Division of Metabolomics, Medical Institute of Bioregulation, Kyushu University, Fukuoka, Fukuoka 812-8582, Japan
| | - Eri Ishikawa
- Department of Molecular Immunology, Research Institute for Microbial Diseases, Osaka University, Suita, Osaka 565-0871, Japan
- Laboratory of Molecular Immunology, Immunology Frontier Research Center, Osaka University, Suita, Osaka 565-0871, Japan
| | - Masamichi Nagae
- Department of Molecular Immunology, Research Institute for Microbial Diseases, Osaka University, Suita, Osaka 565-0871, Japan
- Laboratory of Molecular Immunology, Immunology Frontier Research Center, Osaka University, Suita, Osaka 565-0871, Japan
| | - Jamie Rossjohn
- Infection and Immunity Program and Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, Victoria, Australia
- Institute of Infection and Immunity, Cardiff University, School of Medicine, Heath Park, Cardiff, UK
| | - Sho Yamasaki
- Department of Molecular Immunology, Research Institute for Microbial Diseases, Osaka University, Suita, Osaka 565-0871, Japan
- Laboratory of Molecular Immunology, Immunology Frontier Research Center, Osaka University, Suita, Osaka 565-0871, Japan
- Center for Infectious Disease Education and Research (CiDER), Osaka University, Suita, Osaka, 565-0871, Japan
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4
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Koyama K, Hashimoto K, Nagao C, Mizuguchi K. Attention network for predicting T-cell receptor-peptide binding can associate attention with interpretable protein structural properties. FRONTIERS IN BIOINFORMATICS 2023; 3:1274599. [PMID: 38170146 PMCID: PMC10759225 DOI: 10.3389/fbinf.2023.1274599] [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: 08/08/2023] [Accepted: 11/27/2023] [Indexed: 01/05/2024] Open
Abstract
Understanding how a T-cell receptor (TCR) recognizes its specific ligand peptide is crucial for gaining an insight into biological functions and disease mechanisms. Despite its importance, experimentally determining TCR-peptide-major histocompatibility complex (TCR-pMHC) interactions is expensive and time-consuming. To address this challenge, computational methods have been proposed, but they are typically evaluated by internal retrospective validation only, and few researchers have incorporated and tested an attention layer from language models into structural information. Therefore, in this study, we developed a machine learning model based on a modified version of Transformer, a source-target attention neural network, to predict the TCR-pMHC interaction solely from the amino acid sequences of the TCR complementarity-determining region (CDR) 3 and the peptide. This model achieved competitive performance on a benchmark dataset of the TCR-pMHC interaction, as well as on a truly new external dataset. Additionally, by analyzing the results of binding predictions, we associated the neural network weights with protein structural properties. By classifying the residues into large- and small-attention groups, we identified statistically significant properties associated with the largely attended residues such as hydrogen bonds within CDR3. The dataset that we created and the ability of our model to provide an interpretable prediction of TCR-peptide binding should increase our knowledge about molecular recognition and pave the way for designing new therapeutics.
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Affiliation(s)
- Kyohei Koyama
- Laboratory for Computational Biology, Institute for Protein Research, Osaka University, Osaka, Japan
- National Institutes of Biomedical Innovation, Health and Nutrition, Osaka, Japan
- Graduate School of Frontier Biosciences, Osaka University, Osaka, Japan
| | - Kosuke Hashimoto
- Laboratory for Computational Biology, Institute for Protein Research, Osaka University, Osaka, Japan
| | - Chioko Nagao
- Laboratory for Computational Biology, Institute for Protein Research, Osaka University, Osaka, Japan
| | - Kenji Mizuguchi
- Laboratory for Computational Biology, Institute for Protein Research, Osaka University, Osaka, Japan
- National Institutes of Biomedical Innovation, Health and Nutrition, Osaka, Japan
- Graduate School of Frontier Biosciences, Osaka University, Osaka, Japan
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5
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Mudd P, Borcherding N, Kim W, Quinn M, Han F, Zhou J, Sturtz A, Schmitz A, Lei T, Schattgen S, Klebert M, Suessen T, Middleton W, Goss C, Liu C, Crawford J, Thomas P, Teefey S, Presti R, O'Halloran J, Turner J, Ellebedy A. Antigen-specific CD4 + T cells exhibit distinct transcriptional phenotypes in the lymph node and blood following vaccination in humans. RESEARCH SQUARE 2023:rs.3.rs-3304466. [PMID: 37790414 PMCID: PMC10543502 DOI: 10.21203/rs.3.rs-3304466/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/05/2023]
Abstract
SARS-CoV-2 infection and mRNA vaccination induce robust CD4+ T cell responses that are critical for the development of protective immunity. Here, we evaluated spike-specific CD4+ T cells in the blood and draining lymph node (dLN) of human subjects following BNT162b2 mRNA vaccination using single-cell transcriptomics. We analyze multiple spike-specific CD4+ T cell clonotypes, including novel clonotypes we define here using Trex, a new deep learning-based reverse epitope mapping method integrating single-cell T cell receptor (TCR) sequencing and transcriptomics to predict antigen-specificity. Human dLN spike-specific T follicular helper cells (TFH) exhibited distinct phenotypes, including germinal center (GC)-TFH and IL-10+ TFH, that varied over time during the GC response. Paired TCR clonotype analysis revealed tissue-specific segregation of circulating and dLN clonotypes, despite numerous spike-specific clonotypes in each compartment. Analysis of a separate SARS-CoV-2 infection cohort revealed circulating spike-specific CD4+ T cell profiles distinct from those found following BNT162b2 vaccination. Our findings provide an atlas of human antigen-specific CD4+ T cell transcriptional phenotypes in the dLN and blood following vaccination or infection.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | | | | | | | - Charles Goss
- Division of Biostatistics, Washington University in St.Louis
| | - Chang Liu
- Washington University School of Medicine
| | | | | | | | | | - Jane O'Halloran
- Department of Emergency Medicine, Washington University in St.Louis
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6
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Landry SJ, Mettu RR, Kolls JK, Aberle JH, Norton E, Zwezdaryk K, Robinson J. Structural Framework for Analysis of CD4+ T-Cell Epitope Dominance in Viral Fusion Proteins. Biochemistry 2023; 62:2517-2529. [PMID: 37554055 PMCID: PMC10483696 DOI: 10.1021/acs.biochem.3c00335] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2023] [Revised: 07/31/2023] [Indexed: 08/10/2023]
Abstract
Antigen conformation shapes CD4+ T-cell specificity through mechanisms of antigen processing, and the consequences for immunity may rival those from conformational effects on antibody specificity. CD4+ T cells initiate and control immunity to pathogens and cancer and are at least partly responsible for immunopathology associated with infection, autoimmunity, and allergy. The primary trigger for CD4+ T-cell maturation is the presentation of an epitope peptide in the MHC class II antigen-presenting protein (MHCII), most commonly on an activated dendritic cell, and then the T-cell responses are recalled by subsequent presentations of the epitope peptide by the same or other antigen-presenting cells. Peptide presentation depends on the proteolytic fragmentation of the antigen in an endosomal/lysosomal compartment and concomitant loading of the fragments into the MHCII, a multistep mechanism called antigen processing and presentation. Although the role of peptide affinity for MHCII has been well studied, the role of proteolytic fragmentation has received less attention. In this Perspective, we will briefly summarize evidence that antigen resistance to unfolding and proteolytic fragmentation shapes the specificity of the CD4+ T-cell response to selected viral envelope proteins, identify several remarkable examples in which the immunodominant CD4+ epitopes most likely depend on the interaction of processing machinery with antigen conformation, and outline how knowledge of antigen conformation can inform future efforts to design vaccines.
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Affiliation(s)
- Samuel J. Landry
- Department
of Biochemistry and Molecular Biology, Tulane
University School of Medicine, New Orleans, Louisiana 70112, United States
| | - Ramgopal R. Mettu
- Department
of Computer Science, Tulane University, New Orleans, Louisiana 70118, United States
| | - Jay K. Kolls
- John
W. Deming Department of Internal Medicine, Center for Translational
Research in Infection and Inflammation, Tulane University School of Medicine, New Orleans, Louisiana 70112, United States
| | - Judith H. Aberle
- Center
for Virology, Medical University of Vienna, 1090 Vienna, Austria
| | - Elizabeth Norton
- Department
of Microbiology & Immunology, Tulane
University School of Medicine, New Orleans, Louisiana 70112, United States
| | - Kevin Zwezdaryk
- Department
of Microbiology & Immunology, Tulane
University School of Medicine, New Orleans, Louisiana 70112, United States
| | - James Robinson
- Department
of Pediatrics, Tulane University School
of Medicine, New Orleans, Louisiana 70112, United States
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7
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Yu M, Charles A, Cagigi A, Christ W, Österberg B, Falck-Jones S, Azizmohammadi L, Åhlberg E, Falck-Jones R, Svensson J, Nie M, Warnqvist A, Hellgren F, Lenart K, Arcoverde Cerveira R, Ols S, Lindgren G, Lin A, Maecker H, Bell M, Johansson N, Albert J, Sundling C, Czarnewski P, Klingström J, Färnert A, Loré K, Smed-Sörensen A. Delayed generation of functional virus-specific circulating T follicular helper cells correlates with severe COVID-19. Nat Commun 2023; 14:2164. [PMID: 37061513 PMCID: PMC10105364 DOI: 10.1038/s41467-023-37835-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2022] [Accepted: 04/03/2023] [Indexed: 04/17/2023] Open
Abstract
Effective humoral immune responses require well-orchestrated B and T follicular helper (Tfh) cell interactions. Whether these interactions are impaired and associated with COVID-19 disease severity is unclear. Here, longitudinal blood samples across COVID-19 disease severity are analysed. We find that during acute infection SARS-CoV-2-specific circulating Tfh (cTfh) cells expand with disease severity. SARS-CoV-2-specific cTfh cell frequencies correlate with plasmablast frequencies and SARS-CoV-2 antibody titers, avidity and neutralization. Furthermore, cTfh cells but not other memory CD4 T cells, from severe patients better induce plasmablast differentiation and antibody production compared to cTfh cells from mild patients. However, virus-specific cTfh cell development is delayed in patients that display or later develop severe disease compared to those with mild disease, which correlates with delayed induction of high-avidity neutralizing antibodies. Our study suggests that impaired generation of functional virus-specific cTfh cells delays high-quality antibody production at an early stage, potentially enabling progression to severe disease.
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Affiliation(s)
- Meng Yu
- Division of Immunology and Allergy, Department of Medicine Solna, Center for Molecular Medicine, Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden
| | - Afandi Charles
- Division of Immunology and Allergy, Department of Medicine Solna, Center for Molecular Medicine, Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden
| | - Alberto Cagigi
- Division of Immunology and Allergy, Department of Medicine Solna, Center for Molecular Medicine, Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden
| | - Wanda Christ
- Department of Medicine Huddinge, Karolinska Institutet, Stockholm, Sweden
| | - Björn Österberg
- Division of Immunology and Allergy, Department of Medicine Solna, Center for Molecular Medicine, Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden
| | - Sara Falck-Jones
- Division of Immunology and Allergy, Department of Medicine Solna, Center for Molecular Medicine, Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden
| | - Lida Azizmohammadi
- Division of Immunology and Allergy, Department of Medicine Solna, Center for Molecular Medicine, Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden
| | - Eric Åhlberg
- Division of Immunology and Allergy, Department of Medicine Solna, Center for Molecular Medicine, Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden
| | - Ryan Falck-Jones
- Department of Physiology and Pharmacology, Karolinska Institutet, Stockholm, Sweden
- Department of Perioperative Medicine and Intensive Care, Karolinska University Hospital, Stockholm, Sweden
| | - Julia Svensson
- Division of Immunology and Allergy, Department of Medicine Solna, Center for Molecular Medicine, Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden
| | - Mu Nie
- Division of Immunology and Allergy, Department of Medicine Solna, Center for Molecular Medicine, Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden
| | - Anna Warnqvist
- Division of Biostatistics, Institute of Environmental Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Fredrika Hellgren
- Division of Immunology and Allergy, Department of Medicine Solna, Center for Molecular Medicine, Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden
| | - Klara Lenart
- Division of Immunology and Allergy, Department of Medicine Solna, Center for Molecular Medicine, Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden
| | - Rodrigo Arcoverde Cerveira
- Division of Immunology and Allergy, Department of Medicine Solna, Center for Molecular Medicine, Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden
| | - Sebastian Ols
- Division of Immunology and Allergy, Department of Medicine Solna, Center for Molecular Medicine, Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden
| | - Gustaf Lindgren
- Division of Immunology and Allergy, Department of Medicine Solna, Center for Molecular Medicine, Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden
| | - Ang Lin
- Division of Immunology and Allergy, Department of Medicine Solna, Center for Molecular Medicine, Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden
| | - Holden Maecker
- The Human Immune Monitoring Center, Institute of Immunity, Transplantation and Infection, Stanford University School of Medicine, Stanford, CA, USA
| | - Max Bell
- Department of Physiology and Pharmacology, Karolinska Institutet, Stockholm, Sweden
- Department of Perioperative Medicine and Intensive Care, Karolinska University Hospital, Stockholm, Sweden
| | - Niclas Johansson
- Division of Infectious Diseases, Department of Medicine Solna, Center for Molecular Medicine, Karolinska Institutet, Stockholm, Sweden
- Department of Infectious Diseases, Karolinska University Hospital Solna, Stockholm, Sweden
| | - Jan Albert
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
- Clinical Microbiology, Karolinska University Hospital Solna, Stockholm, Sweden
| | - Christopher Sundling
- Division of Infectious Diseases, Department of Medicine Solna, Center for Molecular Medicine, Karolinska Institutet, Stockholm, Sweden
- Department of Infectious Diseases, Karolinska University Hospital Solna, Stockholm, Sweden
| | - Paulo Czarnewski
- Department of Biochemistry and Biophysics, National Bioinformatics Infrastructure Sweden, Science for Life Laboratory, Stockholm University, Solna, Sweden
| | - Jonas Klingström
- Department of Medicine Huddinge, Karolinska Institutet, Stockholm, Sweden
- Department of Biomedical and Clinical Sciences, Linköping University, Linköping, Sweden
| | - Anna Färnert
- Division of Infectious Diseases, Department of Medicine Solna, Center for Molecular Medicine, Karolinska Institutet, Stockholm, Sweden
- Department of Infectious Diseases, Karolinska University Hospital Solna, Stockholm, Sweden
| | - Karin Loré
- Division of Immunology and Allergy, Department of Medicine Solna, Center for Molecular Medicine, Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden
| | - Anna Smed-Sörensen
- Division of Immunology and Allergy, Department of Medicine Solna, Center for Molecular Medicine, Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden.
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8
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Ahlmann-Eltze C, Huber W. Comparison of transformations for single-cell RNA-seq data. Nat Methods 2023; 20:665-672. [PMID: 37037999 PMCID: PMC10172138 DOI: 10.1038/s41592-023-01814-1] [Citation(s) in RCA: 20] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2021] [Accepted: 02/11/2023] [Indexed: 04/12/2023]
Abstract
The count table, a numeric matrix of genes × cells, is the basic input data structure in the analysis of single-cell RNA-sequencing data. A common preprocessing step is to adjust the counts for variable sampling efficiency and to transform them so that the variance is similar across the dynamic range. These steps are intended to make subsequent application of generic statistical methods more palatable. Here, we describe four transformation approaches based on the delta method, model residuals, inferred latent expression state and factor analysis. We compare their strengths and weaknesses and find that the latter three have appealing theoretical properties; however, in benchmarks using simulated and real-world data, it turns out that a rather simple approach, namely, the logarithm with a pseudo-count followed by principal-component analysis, performs as well or better than the more sophisticated alternatives. This result highlights limitations of current theoretical analysis as assessed by bottom-line performance benchmarks.
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Affiliation(s)
- Constantin Ahlmann-Eltze
- Genome Biology Unit, EMBL, Heidelberg, Germany.
- Faculty of Biosciences, Heidelberg University, Heidelberg, Germany.
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9
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Shimizu T, Schutt CR, Izumi Y, Tomiyasu N, Omahdi Z, Kano K, Takamatsu H, Aoki J, Bamba T, Kumanogoh A, Takao M, Yamasaki S. Direct activation of microglia by β-glucosylceramide causes phagocytosis of neurons that exacerbates Gaucher disease. Immunity 2023; 56:307-319.e8. [PMID: 36736320 DOI: 10.1016/j.immuni.2023.01.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2022] [Revised: 10/26/2022] [Accepted: 01/11/2023] [Indexed: 02/05/2023]
Abstract
Gaucher disease (GD) is the most common lysosomal storage disease caused by recessive mutations in the degrading enzyme of β-glucosylceramide (β-GlcCer). However, it remains unclear how β-GlcCer causes severe neuronopathic symptoms, which are not fully treated by current therapies. We herein found that β-GlcCer accumulating in GD activated microglia through macrophage-inducible C-type lectin (Mincle) to induce phagocytosis of living neurons, which exacerbated Gaucher symptoms. This process was augmented by tumor necrosis factor (TNF) secreted from activated microglia that sensitized neurons for phagocytosis. This characteristic pathology was also observed in human neuronopathic GD. Blockade of these pathways in mice with a combination of FDA-approved drugs, minocycline (microglia activation inhibitor) and etanercept (TNF blocker), effectively protected neurons and ameliorated neuronopathic symptoms. In this study, we propose that limiting unrestrained microglia activation using drug repurposing provides a quickly applicable therapeutic option for fatal neuronopathic GD.
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Affiliation(s)
- Takashi Shimizu
- Department of Molecular Immunology, Research Institute for Microbial Diseases, Osaka University, Suita, Osaka 565-0871, Japan; Laboratory of Molecular Immunology, Immunology Frontier Research Center (IFReC), Osaka University, Suita, Osaka 565-0871, Japan
| | - Charles R Schutt
- Department of Molecular Immunology, Research Institute for Microbial Diseases, Osaka University, Suita, Osaka 565-0871, Japan
| | - Yoshihiro Izumi
- Division of Metabolomics, Research Center for Transomics Medicine, Medical Institute of Bioregulation, Kyushu University, Fukuoka, Fukuoka 812-8582, Japan
| | - Noriyuki Tomiyasu
- Division of Metabolomics, Research Center for Transomics Medicine, Medical Institute of Bioregulation, Kyushu University, Fukuoka, Fukuoka 812-8582, Japan
| | - Zakaria Omahdi
- Department of Molecular Immunology, Research Institute for Microbial Diseases, Osaka University, Suita, Osaka 565-0871, Japan; Laboratory of Molecular Immunology, Immunology Frontier Research Center (IFReC), Osaka University, Suita, Osaka 565-0871, Japan
| | - Kuniyuki Kano
- Department of Health Chemistry, Graduate School of Pharmaceutical Sciences, The University of Tokyo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Hyota Takamatsu
- Department of Respiratory Medicine and Clinical Immunology, Osaka University Graduate School of Medicine, Suita, Osaka 565-0871, Japan; Department of Immunopathology, Immunology Frontier Research Center (IFReC), Osaka University, Suita, Osaka 565-0871, Japan
| | - Junken Aoki
- Department of Health Chemistry, Graduate School of Pharmaceutical Sciences, The University of Tokyo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Takeshi Bamba
- Division of Metabolomics, Research Center for Transomics Medicine, Medical Institute of Bioregulation, Kyushu University, Fukuoka, Fukuoka 812-8582, Japan
| | - Atsushi Kumanogoh
- Department of Respiratory Medicine and Clinical Immunology, Osaka University Graduate School of Medicine, Suita, Osaka 565-0871, Japan; Department of Immunopathology, Immunology Frontier Research Center (IFReC), Osaka University, Suita, Osaka 565-0871, Japan; Integrated Frontier Research for Medical Science Division, Institute for Open and Transdisciplinary Research Initiatives (OTRI), Osaka University, Suita, Osaka 565-0871, Japan; Center for Infectious Diseases for Education and Research (CiDER), Osaka University, Suita, Osaka 565-0871, Japan
| | - Masaki Takao
- Department of Clinical Laboratory, National Center of Neurology and Psychiatry, Kodaira, Tokyo 187-8551, Japan
| | - Sho Yamasaki
- Department of Molecular Immunology, Research Institute for Microbial Diseases, Osaka University, Suita, Osaka 565-0871, Japan; Laboratory of Molecular Immunology, Immunology Frontier Research Center (IFReC), Osaka University, Suita, Osaka 565-0871, Japan.
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10
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Brown B, Ojha V, Fricke I, Al-Sheboul SA, Imarogbe C, Gravier T, Green M, Peterson L, Koutsaroff IP, Demir A, Andrieu J, Leow CY, Leow CH. Innate and Adaptive Immunity during SARS-CoV-2 Infection: Biomolecular Cellular Markers and Mechanisms. Vaccines (Basel) 2023; 11:408. [PMID: 36851285 PMCID: PMC9962967 DOI: 10.3390/vaccines11020408] [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: 12/18/2022] [Revised: 02/01/2023] [Accepted: 02/04/2023] [Indexed: 02/16/2023] Open
Abstract
The coronavirus 2019 (COVID-19) pandemic was caused by a positive sense single-stranded RNA (ssRNA) severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). However, other human coronaviruses (hCoVs) exist. Historical pandemics include smallpox and influenza, with efficacious therapeutics utilized to reduce overall disease burden through effectively targeting a competent host immune system response. The immune system is composed of primary/secondary lymphoid structures with initially eight types of immune cell types, and many other subtypes, traversing cell membranes utilizing cell signaling cascades that contribute towards clearance of pathogenic proteins. Other proteins discussed include cluster of differentiation (CD) markers, major histocompatibility complexes (MHC), pleiotropic interleukins (IL), and chemokines (CXC). The historical concepts of host immunity are the innate and adaptive immune systems. The adaptive immune system is represented by T cells, B cells, and antibodies. The innate immune system is represented by macrophages, neutrophils, dendritic cells, and the complement system. Other viruses can affect and regulate cell cycle progression for example, in cancers that include human papillomavirus (HPV: cervical carcinoma), Epstein-Barr virus (EBV: lymphoma), Hepatitis B and C (HB/HC: hepatocellular carcinoma) and human T cell Leukemia Virus-1 (T cell leukemia). Bacterial infections also increase the risk of developing cancer (e.g., Helicobacter pylori). Viral and bacterial factors can cause both morbidity and mortality alongside being transmitted within clinical and community settings through affecting a host immune response. Therefore, it is appropriate to contextualize advances in single cell sequencing in conjunction with other laboratory techniques allowing insights into immune cell characterization. These developments offer improved clarity and understanding that overlap with autoimmune conditions that could be affected by innate B cells (B1+ or marginal zone cells) or adaptive T cell responses to SARS-CoV-2 infection and other pathologies. Thus, this review starts with an introduction into host respiratory infection before examining invaluable cellular messenger proteins and then individual immune cell markers.
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Affiliation(s)
| | | | - Ingo Fricke
- Independent Immunologist and Researcher, 311995 Lamspringe, Germany
| | - Suhaila A Al-Sheboul
- Department of Medical Laboratory Sciences, Faculty of Applied Medical Sciences, Jordan University of Science and Technology, Irbid 22110, Jordan
- Department of Medical Microbiology, International School of Medicine, Medipol University-Istanbul, Istanbul 34810, Turkey
| | | | - Tanya Gravier
- Independent Researcher, MPH, San Francisco, CA 94131, USA
| | | | | | | | - Ayça Demir
- Faculty of Medicine, Afyonkarahisar University, Istanbul 03030, Turkey
| | - Jonatane Andrieu
- Faculté de Médecine, Aix–Marseille University, 13005 Marseille, France
| | - Chiuan Yee Leow
- School of Pharmaceutical Sciences, Universiti Sains Malaysia, USM, Penang 11800, Malaysia
| | - Chiuan Herng Leow
- Institute for Research in Molecular Medicine, (INFORMM), Universiti Sains Malaysia, USM, Penang 11800, Malaysia
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11
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Xu Q, Milanez-Almeida P, Martins AJ, Radtke AJ, Hoehn KB, Oguz C, Chen J, Liu C, Tang J, Grubbs G, Stein S, Ramelli S, Kabat J, Behzadpour H, Karkanitsa M, Spathies J, Kalish H, Kardava L, Kirby M, Cheung F, Preite S, Duncker PC, Kitakule MM, Romero N, Preciado D, Gitman L, Koroleva G, Smith G, Shaffer A, McBain IT, McGuire PJ, Pittaluga S, Germain RN, Apps R, Schwartz DM, Sadtler K, Moir S, Chertow DS, Kleinstein SH, Khurana S, Tsang JS, Mudd P, Schwartzberg PL, Manthiram K. Adaptive immune responses to SARS-CoV-2 persist in the pharyngeal lymphoid tissue of children. Nat Immunol 2023; 24:186-199. [PMID: 36536106 PMCID: PMC10777159 DOI: 10.1038/s41590-022-01367-z] [Citation(s) in RCA: 22] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2022] [Accepted: 10/21/2022] [Indexed: 12/24/2022]
Abstract
Most studies of adaptive immunity to SARS-CoV-2 infection focus on peripheral blood, which may not fully reflect immune responses at the site of infection. Using samples from 110 children undergoing tonsillectomy and adenoidectomy during the COVID-19 pandemic, we identified 24 samples with evidence of previous SARS-CoV-2 infection, including neutralizing antibodies in serum and SARS-CoV-2-specific germinal center and memory B cells in the tonsils and adenoids. Single-cell B cell receptor (BCR) sequencing indicated virus-specific BCRs were class-switched and somatically hypermutated, with overlapping clones in the two tissues. Expanded T cell clonotypes were found in tonsils, adenoids and blood post-COVID-19, some with CDR3 sequences identical to previously reported SARS-CoV-2-reactive T cell receptors (TCRs). Pharyngeal tissues from COVID-19-convalescent children showed persistent expansion of germinal center and antiviral lymphocyte populations associated with interferon (IFN)-γ-type responses, particularly in the adenoids, and viral RNA in both tissues. Our results provide evidence for persistent tissue-specific immunity to SARS-CoV-2 in the upper respiratory tract of children after infection.
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Affiliation(s)
- Qin Xu
- Cell Signaling and Immunity Section, Laboratory of Immune System Biology (LISB), National Institute of Allergy and Infectious Diseases (NIAID), National Institutes of Health (NIH), Bethesda, MD, USA
| | | | - Andrew J Martins
- Multiscale Systems Biology Section, LISB, NIAID, NIH, Bethesda, MD, USA
| | - Andrea J Radtke
- Center for Advanced Tissue Imaging, LISB, NIAID, NIH, Bethesda, MD, USA
| | - Kenneth B Hoehn
- Department of Pathology, Yale School of Medicine, New Haven, CT, USA
| | - Cihan Oguz
- NIAID Collaborative Bioinformatics Resource (NCBR), NIAID, NIH, Bethesda, MD, USA
- Axle Informatics, Bethesda, MD, USA
| | - Jinguo Chen
- Center for Human Immunology, NIAID, NIH, Bethesda, MD, USA
| | - Can Liu
- Multiscale Systems Biology Section, LISB, NIAID, NIH, Bethesda, MD, USA
| | - Juanjie Tang
- Division of Viral Products, Center for Biologics Evaluation and Research (CBER), Food and Drug Administration (FDA), Silver Spring, MD, USA
| | - Gabrielle Grubbs
- Division of Viral Products, Center for Biologics Evaluation and Research (CBER), Food and Drug Administration (FDA), Silver Spring, MD, USA
| | - Sydney Stein
- Emerging Pathogens Section, Critical Care Medicine Department, Clinical Center (CC), NIH, Bethesda, MD, USA
- Laboratory of Immunoregulation, NIAID, NIH, Bethesda, MD, USA
| | - Sabrina Ramelli
- Emerging Pathogens Section, Critical Care Medicine Department, Clinical Center (CC), NIH, Bethesda, MD, USA
| | - Juraj Kabat
- Center for Advanced Tissue Imaging, LISB, NIAID, NIH, Bethesda, MD, USA
| | - Hengameh Behzadpour
- Division of Pediatric Otolaryngology, Children's National Hospital, Washington, DC, USA
| | - Maria Karkanitsa
- Laboratory of Immuno-Engineering, National Institute of Biomedical Imaging and Bioengineering (NIBIB), NIH, Bethesda, MD, USA
| | - Jacquelyn Spathies
- Trans-NIH Shared Resource on Biomedical Engineering and Physical Science, NIBIB, NIH, Bethesda, MD, USA
| | - Heather Kalish
- Trans-NIH Shared Resource on Biomedical Engineering and Physical Science, NIBIB, NIH, Bethesda, MD, USA
| | - Lela Kardava
- B-cell Immunology Section, Laboratory of Immunoregulation, NIAID, NIH, Bethesda, MD, USA
| | - Martha Kirby
- National Human Genome Research Institute (NHGRI), NIH, Bethesda, MD, USA
| | - Foo Cheung
- Center for Human Immunology, NIAID, NIH, Bethesda, MD, USA
| | - Silvia Preite
- Cell Signaling and Immunity Section, Laboratory of Immune System Biology (LISB), National Institute of Allergy and Infectious Diseases (NIAID), National Institutes of Health (NIH), Bethesda, MD, USA
| | | | | | - Nahir Romero
- Division of Otolaryngology, Department of Surgery, George Washington University School of Medicine and Health Sciences, Washington, DC, USA
| | - Diego Preciado
- Division of Pediatric Otolaryngology, Children's National Hospital, Washington, DC, USA
- Division of Otolaryngology, Department of Surgery, George Washington University School of Medicine and Health Sciences, Washington, DC, USA
| | - Lyuba Gitman
- Division of Pediatric Otolaryngology, Children's National Hospital, Washington, DC, USA
- Division of Otolaryngology, Department of Surgery, George Washington University School of Medicine and Health Sciences, Washington, DC, USA
| | | | - Grace Smith
- Laboratory of Pathology, Center for Cancer Research, National Cancer Institute (NCI), NIH, Bethesda, MD, USA
| | - Arthur Shaffer
- Lymphoid Malignancies Branch, Center for Cancer Research, NCI, NIH, Bethesda, MD, USA
| | - Ian T McBain
- Cell Signaling and Immunity Section, Laboratory of Immune System Biology (LISB), National Institute of Allergy and Infectious Diseases (NIAID), National Institutes of Health (NIH), Bethesda, MD, USA
| | - Peter J McGuire
- National Human Genome Research Institute (NHGRI), NIH, Bethesda, MD, USA
| | - Stefania Pittaluga
- Laboratory of Pathology, Center for Cancer Research, National Cancer Institute (NCI), NIH, Bethesda, MD, USA
| | - Ronald N Germain
- Center for Advanced Tissue Imaging, LISB, NIAID, NIH, Bethesda, MD, USA
- Lymphocyte Biology Section, LISB, NIAID, NIH, Bethesda, MD, USA
| | - Richard Apps
- Center for Human Immunology, NIAID, NIH, Bethesda, MD, USA
| | | | - Kaitlyn Sadtler
- Laboratory of Immuno-Engineering, National Institute of Biomedical Imaging and Bioengineering (NIBIB), NIH, Bethesda, MD, USA
| | - Susan Moir
- B-cell Immunology Section, Laboratory of Immunoregulation, NIAID, NIH, Bethesda, MD, USA
| | - Daniel S Chertow
- Emerging Pathogens Section, Critical Care Medicine Department, Clinical Center (CC), NIH, Bethesda, MD, USA
- Laboratory of Immunoregulation, NIAID, NIH, Bethesda, MD, USA
| | - Steven H Kleinstein
- Department of Pathology, Yale School of Medicine, New Haven, CT, USA
- Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT, USA
- Department of Immunobiology, Yale School of Medicine, New Haven, CT, USA
| | - Surender Khurana
- Division of Viral Products, Center for Biologics Evaluation and Research (CBER), Food and Drug Administration (FDA), Silver Spring, MD, USA
| | - John S Tsang
- Center for Human Immunology, NIAID, NIH, Bethesda, MD, USA
- Multiscale Systems Biology Section, LISB, NIAID, NIH, Bethesda, MD, USA
| | - Pamela Mudd
- Division of Pediatric Otolaryngology, Children's National Hospital, Washington, DC, USA
- Division of Otolaryngology, Department of Surgery, George Washington University School of Medicine and Health Sciences, Washington, DC, USA
| | - Pamela L Schwartzberg
- Cell Signaling and Immunity Section, Laboratory of Immune System Biology (LISB), National Institute of Allergy and Infectious Diseases (NIAID), National Institutes of Health (NIH), Bethesda, MD, USA.
- National Human Genome Research Institute (NHGRI), NIH, Bethesda, MD, USA.
| | - Kalpana Manthiram
- Cell Signaling and Immunity Section, Laboratory of Immune System Biology (LISB), National Institute of Allergy and Infectious Diseases (NIAID), National Institutes of Health (NIH), Bethesda, MD, USA.
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12
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Ogura H, Gohda J, Lu X, Yamamoto M, Takesue Y, Son A, Doi S, Matsushita K, Isobe F, Fukuda Y, Huang TP, Ueno T, Mambo N, Murakami H, Kawaguchi Y, Inoue JI, Shirai K, Yamasaki S, Hirata JI, Ishido S. Dysfunctional Sars-CoV-2-M protein-specific cytotoxic T lymphocytes in patients recovering from severe COVID-19. Nat Commun 2022; 13:7063. [PMID: 36526616 PMCID: PMC9758236 DOI: 10.1038/s41467-022-34655-1] [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: 07/04/2022] [Accepted: 11/02/2022] [Indexed: 12/23/2022] Open
Abstract
Although the importance of virus-specific cytotoxic T lymphocytes (CTL) in virus clearance is evident in COVID-19, the characteristics of virus-specific CTLs related to disease severity have not been fully explored. Here we show that the phenotype of virus-specific CTLs against immunoprevalent epitopes in COVID-19 convalescents might differ according to the course of the disease. We establish a cellular screening method that uses artificial antigen presenting cells, expressing HLA-A*24:02, the costimulatory molecule 4-1BBL, SARS-CoV-2 structural proteins S, M, and N and non-structural proteins ORF3a and nsp6/ORF1a. The screen implicates SARS-CoV-2 M protein as a frequent target of IFNγ secreting CD8+ T cells, and identifies M198-206 as an immunoprevalent epitope in our cohort of HLA-A*24:02 positive convalescent COVID-19 patients recovering from mild, moderate and severe disease. Further exploration of M198-206-specific CD8+ T cells with single cell RNA sequencing reveals public TCRs in virus-specific CD8+ T cells, and shows an exhausted phenotype with less differentiated status in cells from the severe group compared to cells from the moderate group. In summary, this study describes a method to identify T cell epitopes, indicate that dysfunction of virus-specific CTLs might be an important determinant of clinical outcomes.
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Affiliation(s)
- Hideki Ogura
- grid.272264.70000 0000 9142 153XDepartment of Microbiology, Hyogo Medical University, Hyogo, Japan
| | - Jin Gohda
- grid.26999.3d0000 0001 2151 536XResearch Center for Asian Infectious Diseases, The Institute of Medical Science, The University of Tokyo, Tokyo, Japan
| | - Xiuyuan Lu
- grid.136593.b0000 0004 0373 3971Laboratory of Molecular Immunology, Immunology Frontier Research Center, Osaka University, Suita, Japan
| | - Mizuki Yamamoto
- grid.26999.3d0000 0001 2151 536XResearch Center for Asian Infectious Diseases, The Institute of Medical Science, The University of Tokyo, Tokyo, Japan
| | - Yoshio Takesue
- grid.272264.70000 0000 9142 153XDepartment of Infection Control and Prevention, Hyogo Medical University, Hyogo, Japan ,Tokoname City Hospital, Aichi, Japan
| | - Aoi Son
- grid.272264.70000 0000 9142 153XDepartment of Microbiology, Hyogo Medical University, Hyogo, Japan
| | - Sadayuki Doi
- grid.513274.60000 0004 0569 8532Kawanishi City Hospital, Hyogo, Japan
| | | | - Fumitaka Isobe
- Kyowa Marina Hospital/Wellhouse Nishinomiya, Hyogo, Japan
| | | | | | - Takamasa Ueno
- grid.274841.c0000 0001 0660 6749Joint Research Center for Human Retrovirus Infection, Kumamoto University, Kumamoto, Japan
| | - Naomi Mambo
- grid.272264.70000 0000 9142 153XDepartment of Emergency and Critical Care Medicine, Hyogo Medical University, Hyogo, Japan
| | - Hiromoto Murakami
- grid.272264.70000 0000 9142 153XDepartment of Emergency and Critical Care Medicine, Hyogo Medical University, Hyogo, Japan
| | - Yasushi Kawaguchi
- grid.26999.3d0000 0001 2151 536XResearch Center for Asian Infectious Diseases, The Institute of Medical Science, The University of Tokyo, Tokyo, Japan ,grid.26999.3d0000 0001 2151 536XDivision of Molecular Virology, Department of Microbiology and Immunology, The Institute of Medical Science, The University of Tokyo, Tokyo, Japan
| | - Jun-ichiro Inoue
- grid.26999.3d0000 0001 2151 536XResearch Platform Office, The Institute of Medical Science, The University of Tokyo, Tokyo, Japan
| | - Kunihiro Shirai
- grid.272264.70000 0000 9142 153XDepartment of Emergency and Critical Care Medicine, Hyogo Medical University, Hyogo, Japan
| | - Sho Yamasaki
- grid.136593.b0000 0004 0373 3971Laboratory of Molecular Immunology, Immunology Frontier Research Center, Osaka University, Suita, Japan ,grid.136593.b0000 0004 0373 3971Department of Molecular Immunology, Research Institute for Microbial Diseases, Osaka University, Suita, Japan ,grid.177174.30000 0001 2242 4849Division of Molecular Design, Medical Institute of Bioregulation, Kyushu University, Fukuoka, Japan ,grid.136304.30000 0004 0370 1101Division of Molecular Immunology, Medical Mycology Research Center, Chiba University, Chiba, Japan
| | - Jun-Ichi Hirata
- grid.272264.70000 0000 9142 153XDepartment of Emergency and Critical Care Medicine, Hyogo Medical University, Hyogo, Japan
| | - Satoshi Ishido
- grid.272264.70000 0000 9142 153XDepartment of Microbiology, Hyogo Medical University, Hyogo, Japan
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13
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Lu X, Yamasaki S. Current understanding of T cell immunity against SARS-CoV-2. Inflamm Regen 2022; 42:51. [PMID: 36447270 PMCID: PMC9706904 DOI: 10.1186/s41232-022-00242-6] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2022] [Accepted: 11/17/2022] [Indexed: 11/30/2022] Open
Abstract
As an important part of adaptive immunity, T cells are indispensable in the defense against pathogens including viruses. SARS-CoV-2 is a new human coronavirus that occurred at the end of 2019 and has caused the COVID-19 pandemic. Nevertheless, most of the infected patients recovered without any antiviral therapies, suggesting an effective immunity developed in the bodies. T cell immunity responds upon SARS-CoV-2 infection or vaccination and plays crucial roles in eliminating the viruses and generating T cell memory. Specifically, a subpopulation of CD4+ T cells could support the production of anti-SARS-CoV-2 antibodies, and cytotoxic CD8+ T cells are also protective against the infection. SARS-CoV-2-recognizing T cells could be detected in SARS-CoV-2-unexposed donors, but the role of these cross-reactive T cells is still in debate. T cell responses could be diverse across individuals, mainly due to the polymorphism of HLAs. Thus, compared to antibodies, T cell responses are generally less affected by the mutations of SARS-CoV-2 variants. Up to now, a huge number of studies on SARS-CoV-2-responsive T cells have been published. In this review, we introduced some major findings addressing the questions in the main aspects about T cell responses elicited by SARS-CoV-2, to summarize the current understanding of COVID-19.
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Affiliation(s)
- Xiuyuan Lu
- grid.136593.b0000 0004 0373 3971Laboratory of Molecular Immunology, Immunology Frontier Research Center, Osaka University, Suita, 565-0871 Japan ,grid.136593.b0000 0004 0373 3971Epitope Analysis Team, Center for Advanced Modalities and DDS, Osaka University, Suita, 565-0871 Japan
| | - Sho Yamasaki
- grid.136593.b0000 0004 0373 3971Laboratory of Molecular Immunology, Immunology Frontier Research Center, Osaka University, Suita, 565-0871 Japan ,grid.136593.b0000 0004 0373 3971Epitope Analysis Team, Center for Advanced Modalities and DDS, Osaka University, Suita, 565-0871 Japan ,grid.136593.b0000 0004 0373 3971Department of Molecular Immunology, Research Institute for Microbial Diseases, Osaka University, Suita, 565-0871 Japan ,grid.136593.b0000 0004 0373 3971Center for Infectious Disease Education and Research (CiDER), Osaka University, Suita, 565-0871 Japan ,grid.177174.30000 0001 2242 4849Division of Molecular Design, Research Center for Systems Immunology, Medical Institute of Bioregulation, Kyushu University, Fukuoka, 812-8582 Japan
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14
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Shibata K, Motozono C, Nagae M, Shimizu T, Ishikawa E, Motooka D, Okuzaki D, Izumi Y, Takahashi M, Fujimori N, Wing JB, Hayano T, Asai Y, Bamba T, Ogawa Y, Furutani-Seiki M, Shirai M, Yamasaki S. Symbiotic bacteria-dependent expansion of MR1-reactive T cells causes autoimmunity in the absence of Bcl11b. Nat Commun 2022; 13:6948. [PMID: 36376329 PMCID: PMC9663695 DOI: 10.1038/s41467-022-34802-8] [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: 10/18/2021] [Accepted: 11/08/2022] [Indexed: 11/16/2022] Open
Abstract
MHC class I-related protein 1 (MR1) is a metabolite-presenting molecule that restricts MR1-reactive T cells including mucosal-associated invariant T (MAIT) cells. In contrast to MAIT cells, the function of other MR1-restricted T cell subsets is largely unknown. Here, we report that mice in which a T cell-specific transcription factor, B-cell lymphoma/leukemia 11B (Bcl11b), was ablated in immature thymocytes (Bcl11b∆iThy mice) develop chronic inflammation. Bcl11b∆iThy mice lack conventional T cells and MAIT cells, whereas CD4+IL-18R+ αβ T cells expressing skewed Traj33 (Jα33)+ T cell receptors (TCR) accumulate in the periphery, which are necessary and sufficient for the pathogenesis. The disorders observed in Bcl11b∆iThy mice are ameliorated by MR1-deficiency, transfer of conventional T cells, or germ-free conditions. We further show the crystal structure of the TCR expressed by Traj33+ T cells expanded in Bcl11b∆iThy mice. Overall, we establish that MR1-reactive T cells have pathogenic potential.
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Affiliation(s)
- Kensuke Shibata
- grid.268397.10000 0001 0660 7960Department of Microbiology and Immunology, Graduate School of Medicine, Yamaguchi University, Ube, 755-8505 Japan ,grid.177174.30000 0001 2242 4849Department of Ophthalmology, Department of Ocular Pathology and Imaging Science, Graduate School of Medical Sciences, Kyushu University, Fukuoka, 812-8582 Japan ,grid.136593.b0000 0004 0373 3971Department of Molecular Immunology, Research Institute for Microbial Diseases, Osaka University, Suita, 565-0871 Japan
| | - Chihiro Motozono
- grid.136593.b0000 0004 0373 3971Department of Molecular Immunology, Research Institute for Microbial Diseases, Osaka University, Suita, 565-0871 Japan ,grid.274841.c0000 0001 0660 6749Division of Infection and Immunity, Joint Research Center for Human Retrovirus Infection, Kumamoto University, Kumamoto, 860-0871 Japan
| | - Masamichi Nagae
- grid.136593.b0000 0004 0373 3971Department of Molecular Immunology, Research Institute for Microbial Diseases, Osaka University, Suita, 565-0871 Japan ,grid.136593.b0000 0004 0373 3971Laboratory of Molecular Immunology, Immunology Frontier Research Center, Osaka University, Suita, 565-0871 Japan
| | - Takashi Shimizu
- grid.136593.b0000 0004 0373 3971Department of Molecular Immunology, Research Institute for Microbial Diseases, Osaka University, Suita, 565-0871 Japan
| | - Eri Ishikawa
- grid.136593.b0000 0004 0373 3971Department of Molecular Immunology, Research Institute for Microbial Diseases, Osaka University, Suita, 565-0871 Japan ,grid.136593.b0000 0004 0373 3971Laboratory of Molecular Immunology, Immunology Frontier Research Center, Osaka University, Suita, 565-0871 Japan
| | - Daisuke Motooka
- grid.136593.b0000 0004 0373 3971Department of Infection Metagenomics, Genome Information Research Center, Research Institute for Microbial Diseases, Osaka University, Suita, 565-0871 Japan
| | - Daisuke Okuzaki
- grid.136593.b0000 0004 0373 3971Single Cell Genomics, Human Immunology, World Premier International Research Center Initiative Immunology Frontier Research Center, Osaka University, Suita, 565-0871 Japan ,grid.136593.b0000 0004 0373 3971Genome Information Research Center, Research Institute for Microbial Diseases, Osaka University, Suita, 565-0871 Japan
| | - Yoshihiro Izumi
- grid.177174.30000 0001 2242 4849Division of Metabolomics, Medical Institute of Bioregulation, Kyushu University, Fukuoka, 812-8582 Japan
| | - Masatomo Takahashi
- grid.177174.30000 0001 2242 4849Division of Metabolomics, Medical Institute of Bioregulation, Kyushu University, Fukuoka, 812-8582 Japan
| | - Nao Fujimori
- grid.177174.30000 0001 2242 4849Department of Medicine and Bioregulatory Science, Graduate School of Medical Sciences, Kyushu University, Fukuoka, 812-8582 Japan
| | - James B. Wing
- grid.136593.b0000 0004 0373 3971Laboratory of Human Immunology (Single Cell Immunology), World Premier International Immunology Frontier Research Center, Osaka University, Suita, 565-0871 Japan ,grid.136593.b0000 0004 0373 3971Laboratory of Experimental Immunology, World Premier International Immunology Frontier Research Center, Osaka University, Suita, 565-0871 Japan
| | - Takahide Hayano
- grid.268397.10000 0001 0660 7960Department of Systems Bioinformatics, Graduate School of Medicine, Yamaguchi University, Ube, 755-8505 Japan
| | - Yoshiyuki Asai
- grid.268397.10000 0001 0660 7960Department of Systems Bioinformatics, Graduate School of Medicine, Yamaguchi University, Ube, 755-8505 Japan
| | - Takeshi Bamba
- grid.177174.30000 0001 2242 4849Division of Metabolomics, Medical Institute of Bioregulation, Kyushu University, Fukuoka, 812-8582 Japan
| | - Yoshihiro Ogawa
- grid.177174.30000 0001 2242 4849Department of Medicine and Bioregulatory Science, Graduate School of Medical Sciences, Kyushu University, Fukuoka, 812-8582 Japan ,grid.419082.60000 0004 1754 9200Japan Agency for Medical Research and Development, Core Research for Evolutional Science and Technology, Tokyo, 100-0004 Japan ,grid.27476.300000 0001 0943 978XDepartment of Molecular Medicine and Metabolism, Research Institute of Environmental Medicine, Nagoya University, Nagoya, 464-8601 Japan
| | - Makoto Furutani-Seiki
- grid.268397.10000 0001 0660 7960Systems Biochemistry in Pathology and Regeneration, Graduate School of Medicine, Yamaguchi University, Ube, 755-8505 Japan
| | - Mutsunori Shirai
- grid.268397.10000 0001 0660 7960Department of Microbiology and Immunology, Graduate School of Medicine, Yamaguchi University, Ube, 755-8505 Japan
| | - Sho Yamasaki
- grid.136593.b0000 0004 0373 3971Department of Molecular Immunology, Research Institute for Microbial Diseases, Osaka University, Suita, 565-0871 Japan ,grid.136593.b0000 0004 0373 3971Laboratory of Molecular Immunology, Immunology Frontier Research Center, Osaka University, Suita, 565-0871 Japan ,grid.177174.30000 0001 2242 4849Division of Molecular Design, Medical Institute of Bioregulation, Kyushu University, Fukuoka, 812-8582 Japan ,grid.136304.30000 0004 0370 1101Division of Molecular Immunology, Medical Mycology Research Center, Chiba University, Chiba, 260-8673 Japan
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15
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Pogorelyy MV, Rosati E, Minervina AA, Mettelman RC, Scheffold A, Franke A, Bacher P, Thomas PG. Resolving SARS-CoV-2 CD4 + T cell specificity via reverse epitope discovery. Cell Rep Med 2022; 3:100697. [PMID: 35841887 PMCID: PMC9247234 DOI: 10.1016/j.xcrm.2022.100697] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2021] [Revised: 05/08/2022] [Accepted: 06/24/2022] [Indexed: 11/24/2022]
Abstract
The current strategy to detect immunodominant T cell responses focuses on the antigen, employing large peptide pools to screen for functional cell activation. However, these approaches are labor and sample intensive and scale poorly with increasing size of the pathogen peptidome. T cell receptors (TCRs) recognizing the same epitope frequently have highly similar sequences, and thus, the presence of large sequence similarity clusters in the TCR repertoire likely identify the most public and immunodominant responses. Here, we perform a meta-analysis of large, publicly available single-cell and bulk TCR datasets from severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2)-infected individuals to identify public CD4+ responses. We report more than 1,200 αβTCRs forming six prominent similarity clusters and validate histocompatibility leukocyte antigen (HLA) restriction and epitope specificity predictions for five clusters using transgenic T cell lines. Collectively, these data provide information on immunodominant CD4+ T cell responses to SARS-CoV-2 and demonstrate the utility of the reverse epitope discovery approach.
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Affiliation(s)
- Mikhail V Pogorelyy
- Department of Immunology, St. Jude Children's Research Hospital, Memphis, TN 38103, USA
| | - Elisa Rosati
- Institute of Clinical Molecular Biology, Christian-Albrecht University of Kiel, Kiel, Germany; Institute of Immunology, Christian-Albrecht University of Kiel, Kiel, Germany
| | - Anastasia A Minervina
- Department of Immunology, St. Jude Children's Research Hospital, Memphis, TN 38103, USA
| | - Robert C Mettelman
- Department of Immunology, St. Jude Children's Research Hospital, Memphis, TN 38103, USA
| | - Alexander Scheffold
- Institute of Immunology, Christian-Albrecht University of Kiel, Kiel, Germany
| | - Andre Franke
- Institute of Clinical Molecular Biology, Christian-Albrecht University of Kiel, Kiel, Germany
| | - Petra Bacher
- Institute of Clinical Molecular Biology, Christian-Albrecht University of Kiel, Kiel, Germany; Institute of Immunology, Christian-Albrecht University of Kiel, Kiel, Germany.
| | - Paul G Thomas
- Department of Immunology, St. Jude Children's Research Hospital, Memphis, TN 38103, USA.
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16
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Wang A, Tian Y, Liu H, Ding P, Chen Y, Liang C, Du Y, Jiang D, Zhu X, Yin J, Zhang G. Identification of three conserved linear B cell epitopes on the SARS-CoV-2 spike protein. Emerg Microbes Infect 2022; 11:2120-2131. [PMID: 35916768 PMCID: PMC9487943 DOI: 10.1080/22221751.2022.2109515] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Spike (S) glycoproteins is the most significant structural protein of SARS-CoV-2 and a key target for neutralizing antibodies. In light of the ongoing SARS-CoV-2 pandemic, identification and screening of epitopes of spike glycoproteins will provide vital progress in the development of sensitive and specific diagnostic tools. In the present study, NTD, RBD and S2 gene were inserted to the pcDNA3.1(+) vector and designed with N-terminal 6×His-tag for fusion expression in HEK293F cells by transient transfection. Six monoclonal antibodies (4G, 9E, 4B, 7D, 8F, 3D) were prepared using the expressed proteins by cell fusion technique. The characterization of mAbs were performed by indirect -ELISA, western blot and IFA. We designed 49 overlapping synthetized peptides cover the extracellular region of S protein which 6 amino acid residues were offset between adjacent (S1-S49). Peptides S12, S19 and S49 were identified as the immunodominant epitopes regions by the mAbs. These regions were further truncated and the peptides S12.2 286TDAVDCALDPLS297, S19.2 464FERDISTEIYQA475 and S49.4 1202ELGKYEQYIKWP1213 were identified as B- cell linear epitopes for the first time. Alanine scans showed that, the D467, I468, E471, Q474, A475 of the epitope S19.2 and K1205, Q1208, Y1209 of the epitope S49.4 were the core sites involved in the mAbs binding. Multiple sequence alignment analysis showed that these three epitopes were highly conserved among the variants of concern (VOCs) and variants of interest (VOIs). Taken together, the findings provide a potential material for rapid diagnosis methods of COVID-19.
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Affiliation(s)
- Aiping Wang
- School of Life Sciences, Zhengzhou University, Zhengzhou 450001, P.R. China.,Longhu laboratory of advanced immunology, Zhengzhou 450002, P.R. China.,Henan Key Laboratory of Immunobiology, Zhengzhou 450001, P.R. China
| | - Yuanyuan Tian
- School of Life Sciences, Zhengzhou University, Zhengzhou 450001, P.R. China.,Longhu laboratory of advanced immunology, Zhengzhou 450002, P.R. China.,Henan Key Laboratory of Immunobiology, Zhengzhou 450001, P.R. China
| | - Hongliang Liu
- School of Life Sciences, Zhengzhou University, Zhengzhou 450001, P.R. China.,Longhu laboratory of advanced immunology, Zhengzhou 450002, P.R. China.,Henan Key Laboratory of Immunobiology, Zhengzhou 450001, P.R. China
| | - Peiyang Ding
- School of Life Sciences, Zhengzhou University, Zhengzhou 450001, P.R. China.,Longhu laboratory of advanced immunology, Zhengzhou 450002, P.R. China.,Henan Key Laboratory of Immunobiology, Zhengzhou 450001, P.R. China
| | - Yumei Chen
- School of Life Sciences, Zhengzhou University, Zhengzhou 450001, P.R. China.,Longhu laboratory of advanced immunology, Zhengzhou 450002, P.R. China.,Henan Key Laboratory of Immunobiology, Zhengzhou 450001, P.R. China
| | - Chao Liang
- School of Life Sciences, Zhengzhou University, Zhengzhou 450001, P.R. China.,Longhu laboratory of advanced immunology, Zhengzhou 450002, P.R. China.,Henan Key Laboratory of Immunobiology, Zhengzhou 450001, P.R. China
| | - Yongkun Du
- College of Veterinary Medicine, Henan Agricultural University, Zhengzhou 450002, P.R. China
| | - Dawei Jiang
- College of Veterinary Medicine, Henan Agricultural University, Zhengzhou 450002, P.R. China
| | - Xifang Zhu
- School of Life Sciences, Zhengzhou University, Zhengzhou 450001, P.R. China.,Longhu laboratory of advanced immunology, Zhengzhou 450002, P.R. China.,Henan Key Laboratory of Immunobiology, Zhengzhou 450001, P.R. China
| | - Jiajia Yin
- School of Life Sciences, Zhengzhou University, Zhengzhou 450001, P.R. China.,Longhu laboratory of advanced immunology, Zhengzhou 450002, P.R. China.,Henan Key Laboratory of Immunobiology, Zhengzhou 450001, P.R. China
| | - Gaiping Zhang
- School of Life Sciences, Zhengzhou University, Zhengzhou 450001, P.R. China.,Longhu laboratory of advanced immunology, Zhengzhou 450002, P.R. China.,Henan Key Laboratory of Immunobiology, Zhengzhou 450001, P.R. China.,College of Veterinary Medicine, Henan Agricultural University, Zhengzhou 450002, P.R. China
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17
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Mettelman RC, Allen EK, Thomas PG. Mucosal immune responses to infection and vaccination in the respiratory tract. Immunity 2022; 55:749-780. [PMID: 35545027 PMCID: PMC9087965 DOI: 10.1016/j.immuni.2022.04.013] [Citation(s) in RCA: 58] [Impact Index Per Article: 29.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2022] [Revised: 04/12/2022] [Accepted: 04/15/2022] [Indexed: 01/25/2023]
Abstract
The lungs are constantly exposed to inhaled debris, allergens, pollutants, commensal or pathogenic microorganisms, and respiratory viruses. As a result, innate and adaptive immune responses in the respiratory tract are tightly regulated and are in continual flux between states of enhanced pathogen clearance, immune-modulation, and tissue repair. New single-cell-sequencing techniques are expanding our knowledge of airway cellular complexity and the nuanced connections between structural and immune cell compartments. Understanding these varied interactions is critical in treatment of human pulmonary disease and infections and in next-generation vaccine design. Here, we review the innate and adaptive immune responses in the lung and airways following infection and vaccination, with particular focus on influenza virus and severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). The ongoing SARS-CoV-2 pandemic has put pulmonary research firmly into the global spotlight, challenging previously held notions of respiratory immunity and helping identify new populations at high risk for respiratory distress.
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Affiliation(s)
- Robert C Mettelman
- Department of Immunology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - E Kaitlynn Allen
- Department of Immunology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Paul G Thomas
- Department of Immunology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA.
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18
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Abstract
Robust T cell responses have been associated with milder outcomes in many infections. T cells also establish long-term memory pools and, as they are predominantly directed toward epitopes encompassing conserved peptides, can respond to SARS-CoV-2 variants, including Omicron. Here, we discuss epitope-specific CD8+ and CD4+ T cell responses toward SARS-CoV-2 infection and vaccination, their subsequent persistence into long-term memory, and ongoing work to determine their role in limiting disease severity.
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Affiliation(s)
- Katherine Kedzierska
- Department of Microbiology and Immunology at Peter Doherty Institute for Infection and Immunity, University of Melbourne, VIC 3000, Australia
| | - Paul G. Thomas
- Department of Immunology, St. Jude Children’s Research Hospital, Memphis, TN, USA
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19
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Rosati E, Pogorelyy MV, Minervina AA, Scheffold A, Franke A, Bacher P, Thomas PG. Characterization of SARS-CoV-2 public CD4+ αβ T cell clonotypes through reverse epitope discovery. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2021:2021.11.19.469229. [PMID: 34845450 PMCID: PMC8629193 DOI: 10.1101/2021.11.19.469229] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
UNLABELLED The amount of scientific data and level of public sharing produced as a consequence of the COVID-19 pandemic, as well as the speed at which these data were produced, far exceeds any previous effort against a specific disease condition. This unprecedented situation allows for development and application of new research approaches. One of the major technical hurdles in immunology is the characterization of HLA-antigen-T cell receptor (TCR) specificities. Most approaches aim to identify reactive T cells starting from known antigens using functional assays. However, the need for a reverse approach identifying the antigen specificity of orphan TCRs is increasing. Utilizing large public single-cell gene expression and TCR datasets, we identified highly public CD4 + T cell responses to SARS-CoV-2, covering >75% of the analysed population. We performed an integrative meta-analysis to deeply characterize these clonotypes by TCR sequence, gene expression, HLA-restriction, and antigen-specificity, identifying strong and public CD4 + immunodominant responses with confirmed specificity. CD4 + COVID-enriched clonotypes show T follicular helper functional features, while clonotypes depleted in SARS-CoV-2 individuals preferentially had a central memory phenotype. In total we identify more than 1200 highly public CD4+ T cell clonotypes reactive to SARS-CoV-2. TCR similarity analysis showed six prominent TCR clusters, for which we predicted both HLA-restriction and cognate SARS-CoV-2 immunodominant epitopes. To validate our predictions we used an independent cohort of TCR repertoires before and after vaccination with ChAdOx1 , a replication-deficient simian adenovirus-vectored vaccine, encoding the SARS-CoV-2 spike protein. We find statistically significant enrichment of the predicted spike-reactive TCRs after vaccination with ChAdOx1 , while the frequency of TCRs specific to other SARS-CoV-2 proteins remains stable. Thus, the CD4-associated TCR repertoire differentiates vaccination from natural infection. In conclusion, our study presents a novel reverse epitope discovery approach that can be used to infer HLA- and antigen-specificity of orphan TCRs in any context, such as viral infections, antitumor immune responses, or autoimmune disease. HIGHLIGHTS Identification of highly public CD4+ T cell responses to SARS-CoV-2Systematic prediction of exact immunogenic HLA class II epitopes for CD4+ T cell responseMethodological framework for reverse epitope discovery, which can be applied to other disease contexts and may provide essential insights for future studies and clinical applications.
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