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Ameratunga R, Jordan A, Lehnert K, Leung E, Mears ER, Snell R, Steele R, Woon ST. SARS-CoV-2 evolution has increased resistance to monoclonal antibodies and first-generation COVID-19 vaccines: Is there a future therapeutic role for soluble ACE2 receptors for COVID-19? Antiviral Res 2024; 227:105894. [PMID: 38677595 DOI: 10.1016/j.antiviral.2024.105894] [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: 01/24/2024] [Revised: 04/17/2024] [Accepted: 04/22/2024] [Indexed: 04/29/2024]
Abstract
COVID-19 has caused calamitous health, economic and societal consequences. Although several COVID-19 vaccines have received full authorization for use, global deployment has faced political, financial and logistical challenges. The efficacy of first-generation COVID-19 vaccines is waning and breakthrough infections are allowing ongoing transmission and evolution of SARS-CoV-2. Furthermore, COVID-19 vaccine efficacy relies on a functional immune system. Despite receiving three primary doses and three or more heterologous boosters, some immunocompromised patients may not be adequately protected by COVID-19 vaccines and remain vulnerable to severe disease. The evolution of new SARS-CoV-2 variants has also resulted in the rapid obsolescence of monoclonal antibodies. Convalescent plasma from COVID-19 survivors has produced inconsistent results. New drugs such as Paxlovid (nirmatrelvir/ritonavir) are beyond the reach of low- and middle-income countries. With widespread use of Paxlovid, it is likely nirmatrelvir-resistant clades of SARS-CoV-2 will emerge in the future. There is thus an urgent need for new effective anti-SARS-CoV-2 treatments. The in vitro efficacy of soluble ACE2 against multiple SARS-CoV-2 variants including omicron (B.1.1.529), was recently described using a competitive ELISA assay as a surrogate marker for virus neutralization. This indicates soluble wild-type ACE2 receptors are likely to be resistant to viral evolution. Nasal and inhaled treatment with soluble ACE2 receptors has abrogated severe disease in animal models of COVID-19. There is an urgent need for clinical trials of this new class of antiviral therapeutics, which could complement vaccines and Paxlovid.
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Affiliation(s)
- Rohan Ameratunga
- Department of Clinical Immunology, Auckland Hospital, Park Rd, Grafton, 1010, Auckland, New Zealand; Department of Virology and Immunology, Auckland Hospital, Park Rd, Grafton, 1010, Auckland, New Zealand; Department of Molecular Medicine and Pathology, School of Medicine, Faculty of Medical and Health Sciences, University of Auckland, Auckland, New Zealand.
| | - Anthony Jordan
- Department of Clinical Immunology, Auckland Hospital, Park Rd, Grafton, 1010, Auckland, New Zealand
| | - Klaus Lehnert
- Applied Translational Genetics Group, School of Biological Sciences, University of Auckland, Auckland, New Zealand
| | - Euphemia Leung
- Auckland Cancer Society Research Centre, School of Medicine, Faculty of Medical and Health Sciences, University of Auckland, Auckland, New Zealand
| | - Emily R Mears
- Applied Translational Genetics Group, School of Biological Sciences, University of Auckland, Auckland, New Zealand
| | - Russell Snell
- Applied Translational Genetics Group, School of Biological Sciences, University of Auckland, Auckland, New Zealand
| | - Richard Steele
- Department of Virology and Immunology, Auckland Hospital, Park Rd, Grafton, 1010, Auckland, New Zealand
| | - See-Tarn Woon
- Department of Virology and Immunology, Auckland Hospital, Park Rd, Grafton, 1010, Auckland, New Zealand; Department of Molecular Medicine and Pathology, School of Medicine, Faculty of Medical and Health Sciences, University of Auckland, Auckland, New Zealand
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2
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Hernandez-Galicia G, Gomez-Morales L, Lopez-Bailon LU, Valdovinos-Torres H, Contreras-Ochoa CO, Díaz Benítez CE, Martinez-Barnetche J, Alpuche-Aranda C, Ortiz-Navarrete V. Presence of SARS-CoV-2-specific T cells before vaccination in the Mexican population. J Leukoc Biol 2024; 116:95-102. [PMID: 38717738 DOI: 10.1093/jleuko/qiae111] [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: 08/01/2023] [Revised: 04/04/2024] [Accepted: 04/17/2024] [Indexed: 06/30/2024] Open
Abstract
The immune response to SARS-CoV-2 has been extensively studied following the pandemic outbreak in 2020; however, the presence of specific T cells against SARS-CoV-2 before vaccination has not been evaluated in Mexico. In this study, we estimated the frequency of T CD4+ and T CD8+ cells that exhibit a specific response to S (spike) and N (nucleocapsid) proteins in a Mexican population. We collected 78 peripheral blood samples from unvaccinated subjects, and the presence of antibodies against spike (RBD) and N protein was determined. Peripheral blood mononuclear cells were isolated and stimulated with a pool of S or N protein peptides (Wuhan-Hu-1 strain). IL-1β, IL-4, IL-6, IL-10, IL-2, IL-8, TNF-α, IFN-γ, and GM-CSF levels were quantified in the supernatant of the activated cells, and the cells were stained to assess the activation and memory phenotypes. Differential activation frequency dependent on serological status was observed in CD4+ cells but not in CD8+ cells. The predominantly activated population was the central memory T CD4+ cells. Only 10% of the population exhibited the same phenotype with respect to the response to nucleocapsid peptides. The cytokine profile differed between the S and N responses. S peptides induced a more proinflammatory response compared with the N peptides. In conclusion, in a Mexican cohort before vaccination, there was a significant response to the S and N SARS-CoV-2 proteins resulting from previous infections with seasonal coronaviruses or previous undetected exposure to SARS-CoV-2.
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Affiliation(s)
- Gabriela Hernandez-Galicia
- Department of Molecular Biomedicine, Center for Research and Advanced Studies of the National Polytechnic Institute, 2508 Instituto Politécnico Nacional Avenue, 07360, Mexico City, Mexico
| | - Luis Gomez-Morales
- Department of Molecular Biomedicine, Center for Research and Advanced Studies of the National Polytechnic Institute, 2508 Instituto Politécnico Nacional Avenue, 07360, Mexico City, Mexico
- Department of Immunology, National School of Biological Sciences, National Polytechnic Institute, Manuel Carpio and Plan de Ayala St, 11340, Mexico City, Mexico
| | - Luis Uriel Lopez-Bailon
- Department of Molecular Biomedicine, Center for Research and Advanced Studies of the National Polytechnic Institute, 2508 Instituto Politécnico Nacional Avenue, 07360, Mexico City, Mexico
- Department of Immunology, National School of Biological Sciences, National Polytechnic Institute, Manuel Carpio and Plan de Ayala St, 11340, Mexico City, Mexico
| | - Humberto Valdovinos-Torres
- Center for Infectious Diseases Research, National Institute of Public Health, 655 Universidad Avenue, 62100, Cuernavaca, Mexico
| | - Carla O Contreras-Ochoa
- Center for Infectious Diseases Research, National Institute of Public Health, 655 Universidad Avenue, 62100, Cuernavaca, Mexico
| | - Cinthya Estefhany Díaz Benítez
- Center for Infectious Diseases Research, National Institute of Public Health, 655 Universidad Avenue, 62100, Cuernavaca, Mexico
| | - Jesus Martinez-Barnetche
- Center for Infectious Diseases Research, National Institute of Public Health, 655 Universidad Avenue, 62100, Cuernavaca, Mexico
| | - Celia Alpuche-Aranda
- Center for Infectious Diseases Research, National Institute of Public Health, 655 Universidad Avenue, 62100, Cuernavaca, Mexico
| | - Vianney Ortiz-Navarrete
- Department of Molecular Biomedicine, Center for Research and Advanced Studies of the National Polytechnic Institute, 2508 Instituto Politécnico Nacional Avenue, 07360, Mexico City, Mexico
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3
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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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4
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Li Y, Tang Y, Wang X, Zhu A, Liu D, He Y, Guo H, Zheng J, Liu X, Chi F, Wang Y, Zhuang Z, Zhang Z, Liu D, Chen Z, Li F, Ran W, Yu K, Wang D, Wen L, Zhuo J, Zhang Y, Xi Y, Zhao J, Zhao J, Sun J. Characterization of humoral immune responses against SARS-CoV-2 accessory proteins in infected patients and mouse model. Virol Sin 2024:S1995-820X(24)00061-0. [PMID: 38677713 DOI: 10.1016/j.virs.2024.04.005] [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: 11/05/2023] [Accepted: 04/19/2024] [Indexed: 04/29/2024] Open
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the causative agent of COVID-19, encodes several accessory proteins that have been shown to play crucial roles in regulating the innate immune response. However, their expressions in infected cells and immunogenicity in infected humans and mice are still not fully understood. This study utilized various techniques such as luciferase immunoprecipitation system (LIPS), immunofluorescence assay (IFA), and western blot (WB) to detect accessory protein-specific antibodies in sera of COVID-19 patients. Specific antibodies to proteins 3a, 3b, 7b, 8 and 9c can be detected by LIPS, but only protein 3a antibody was detected by IFA or WB. Antibodies against proteins 3a and 7b were only detected in ICU patients, which may serve as a marker for predicting disease progression. Further, we investigated the expression of accessory proteins in SARS-CoV-2-infected cells and identified the expressions of proteins 3a, 6, 7a, 8, and 9b. We also analyzed their ability to induce antibodies in immunized mice and found that only proteins 3a, 6, 7a, 8, 9b and 9c were able to induce measurable antibody productions, but these antibodies lacked neutralizing activities and did not protect mice from SARS-CoV-2 infection. Our findings validate the expression of SARS-CoV-2 accessory proteins and elucidate their humoral immune response, providing a basis for protein detection assays and their role in pathogenesis.
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Affiliation(s)
- Yuming Li
- School of Public Health, Shandong First Medical University & Shandong Academy of Medical Sciences, Ji'nan, 250117, China; Key Laboratory of Emerging Infectious Diseases in Universities of Shandong, Shandong First Medical University & Shandong Academy of Medical Sciences, Ji'nan, 250117, China; State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, National Center for Respiratory Medicine, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, Guangdong, 510182, China
| | - Yanhong Tang
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, National Center for Respiratory Medicine, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, Guangdong, 510182, China; Hunan Provincial People's Hospital, The First Affiliated Hospital of Hunan Normal University, Hunan Normal University, Changsha, 410005, China
| | - Xiaoqian Wang
- School of Public Health, Shandong First Medical University & Shandong Academy of Medical Sciences, Ji'nan, 250117, China; Key Laboratory of Emerging Infectious Diseases in Universities of Shandong, Shandong First Medical University & Shandong Academy of Medical Sciences, Ji'nan, 250117, China
| | - Airu Zhu
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, National Center for Respiratory Medicine, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, Guangdong, 510182, China
| | - Dongdong Liu
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, National Center for Respiratory Medicine, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, Guangdong, 510182, China
| | - Yiyun He
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, National Center for Respiratory Medicine, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, Guangdong, 510182, China
| | - Hu Guo
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, National Center for Respiratory Medicine, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, Guangdong, 510182, China
| | - Jie Zheng
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, National Center for Respiratory Medicine, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, Guangdong, 510182, China
| | - Xinzhuo Liu
- School of Public Health, Shandong First Medical University & Shandong Academy of Medical Sciences, Ji'nan, 250117, China; Key Laboratory of Emerging Infectious Diseases in Universities of Shandong, Shandong First Medical University & Shandong Academy of Medical Sciences, Ji'nan, 250117, China
| | - Fengyu Chi
- School of Public Health, Shandong First Medical University & Shandong Academy of Medical Sciences, Ji'nan, 250117, China; Key Laboratory of Emerging Infectious Diseases in Universities of Shandong, Shandong First Medical University & Shandong Academy of Medical Sciences, Ji'nan, 250117, China
| | - Yanqun Wang
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, National Center for Respiratory Medicine, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, Guangdong, 510182, China
| | - Zhen Zhuang
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, National Center for Respiratory Medicine, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, Guangdong, 510182, China
| | - Zhaoyong Zhang
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, National Center for Respiratory Medicine, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, Guangdong, 510182, China
| | - Donglan Liu
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, National Center for Respiratory Medicine, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, Guangdong, 510182, China
| | - Zhao Chen
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, National Center for Respiratory Medicine, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, Guangdong, 510182, China
| | - Fang Li
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, National Center for Respiratory Medicine, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, Guangdong, 510182, China
| | - Wei Ran
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, National Center for Respiratory Medicine, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, Guangdong, 510182, China
| | - Kuai Yu
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, National Center for Respiratory Medicine, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, Guangdong, 510182, China
| | - Dong Wang
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, National Center for Respiratory Medicine, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, Guangdong, 510182, China
| | - Liyan Wen
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, National Center for Respiratory Medicine, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, Guangdong, 510182, China
| | - Jianfen Zhuo
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, National Center for Respiratory Medicine, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, Guangdong, 510182, China
| | - Yanjun Zhang
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, National Center for Respiratory Medicine, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, Guangdong, 510182, China
| | - Yin Xi
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, National Center for Respiratory Medicine, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, Guangdong, 510182, China.
| | - Jingxian Zhao
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, National Center for Respiratory Medicine, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, Guangdong, 510182, China; Guangzhou National Laboratory, Guangzhou, Guangdong, 510005, China.
| | - Jincun Zhao
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, National Center for Respiratory Medicine, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, Guangdong, 510182, China; Guangzhou National Laboratory, Guangzhou, Guangdong, 510005, China; Shanghai Institute for Advanced Immunochemical Studies, School of Life Science and Technology, Shanghai Tech University, Shanghai, 201210, China; Institute for Hepatology, National Clinical Research Center for Infectious Disease, Shenzhen Third People's Hospital, The Second Affiliated Hospital, School of Medicine, Southern University of Science and Technology, Shenzhen, 518005, China.
| | - Jing Sun
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, National Center for Respiratory Medicine, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, Guangdong, 510182, China.
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Croce G, Bobisse S, Moreno DL, Schmidt J, Guillame P, Harari A, Gfeller D. Deep learning predictions of TCR-epitope interactions reveal epitope-specific chains in dual alpha T cells. Nat Commun 2024; 15:3211. [PMID: 38615042 PMCID: PMC11016097 DOI: 10.1038/s41467-024-47461-8] [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: 09/15/2023] [Accepted: 04/03/2024] [Indexed: 04/15/2024] Open
Abstract
T cells have the ability to eliminate infected and cancer cells and play an essential role in cancer immunotherapy. T cell activation is elicited by the binding of the T cell receptor (TCR) to epitopes displayed on MHC molecules, and the TCR specificity is determined by the sequence of its α and β chains. Here, we collect and curate a dataset of 17,715 αβTCRs interacting with dozens of class I and class II epitopes. We use this curated data to develop MixTCRpred, an epitope-specific TCR-epitope interaction predictor. MixTCRpred accurately predicts TCRs recognizing several viral and cancer epitopes. MixTCRpred further provides a useful quality control tool for multiplexed single-cell TCR sequencing assays of epitope-specific T cells and pinpoints a substantial fraction of putative contaminants in public databases. Analysis of epitope-specific dual α T cells demonstrates that MixTCRpred can identify α chains mediating epitope recognition. Applying MixTCRpred to TCR repertoires from COVID-19 patients reveals enrichment of clonotypes predicted to bind an immunodominant SARS-CoV-2 epitope. Overall, MixTCRpred provides a robust tool to predict TCRs interacting with specific epitopes and interpret TCR-sequencing data from both bulk and epitope-specific T cells.
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Affiliation(s)
- Giancarlo Croce
- Department of Oncology UNIL CHUV, Ludwig Institute for Cancer Research, University of Lausanne, Lausanne, Switzerland
- Swiss Institute of Bioinformatics (SIB), Lausanne, Switzerland
- Agora Cancer Research Centre, Lausanne, Switzerland
- Swiss Cancer Center Leman (SCCL), Lausanne, Switzerland
| | - Sara Bobisse
- Agora Cancer Research Centre, Lausanne, Switzerland
- Swiss Cancer Center Leman (SCCL), Lausanne, Switzerland
- Department of Oncology UNIL CHUV, Ludwig Institute for Cancer Research, University Hospital of Lausanne, Lausanne, Switzerland
| | - Dana Léa Moreno
- Department of Oncology UNIL CHUV, Ludwig Institute for Cancer Research, University of Lausanne, Lausanne, Switzerland
- Swiss Institute of Bioinformatics (SIB), Lausanne, Switzerland
- Agora Cancer Research Centre, Lausanne, Switzerland
- Swiss Cancer Center Leman (SCCL), Lausanne, Switzerland
| | - Julien Schmidt
- Department of Oncology UNIL CHUV, Ludwig Institute for Cancer Research, University of Lausanne, Lausanne, Switzerland
- Swiss Cancer Center Leman (SCCL), Lausanne, Switzerland
- Department of Oncology UNIL CHUV, Ludwig Institute for Cancer Research, University Hospital of Lausanne, Lausanne, Switzerland
| | - Philippe Guillame
- Swiss Cancer Center Leman (SCCL), Lausanne, Switzerland
- Department of Oncology UNIL CHUV, Ludwig Institute for Cancer Research, University Hospital of Lausanne, Lausanne, Switzerland
| | - Alexandre Harari
- Department of Oncology UNIL CHUV, Ludwig Institute for Cancer Research, University of Lausanne, Lausanne, Switzerland
- Agora Cancer Research Centre, Lausanne, Switzerland
- Swiss Cancer Center Leman (SCCL), Lausanne, Switzerland
- Department of Oncology UNIL CHUV, Ludwig Institute for Cancer Research, University Hospital of Lausanne, Lausanne, Switzerland
| | - David Gfeller
- Department of Oncology UNIL CHUV, Ludwig Institute for Cancer Research, University of Lausanne, Lausanne, Switzerland.
- Swiss Institute of Bioinformatics (SIB), Lausanne, Switzerland.
- Agora Cancer Research Centre, Lausanne, Switzerland.
- Swiss Cancer Center Leman (SCCL), Lausanne, Switzerland.
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6
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Coulon PG, Prakash S, Dhanushkodi NR, Srivastava R, Zayou L, Tifrea DF, Edwards RA, Figueroa CJ, Schubl SD, Hsieh L, Nesburn AB, Kuppermann BD, Bahraoui E, Vahed H, Gil D, Jones TM, Ulmer JB, BenMohamed L. High frequencies of alpha common cold coronavirus/SARS-CoV-2 cross-reactive functional CD4 + and CD8 + memory T cells are associated with protection from symptomatic and fatal SARS-CoV-2 infections in unvaccinated COVID-19 patients. Front Immunol 2024; 15:1343716. [PMID: 38605956 PMCID: PMC11007208 DOI: 10.3389/fimmu.2024.1343716] [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: 11/24/2023] [Accepted: 03/08/2024] [Indexed: 04/13/2024] Open
Abstract
Background Cross-reactive SARS-CoV-2-specific memory CD4+ and CD8+ T cells are present in up to 50% of unexposed, pre-pandemic, healthy individuals (UPPHIs). However, the characteristics of cross-reactive memory CD4+ and CD8+ T cells associated with subsequent protection of asymptomatic coronavirus disease 2019 (COVID-19) patients (i.e., unvaccinated individuals who never develop any COVID-19 symptoms despite being infected with SARS-CoV-2) remains to be fully elucidated. Methods This study compares the antigen specificity, frequency, phenotype, and function of cross-reactive memory CD4+ and CD8+ T cells between common cold coronaviruses (CCCs) and SARS-CoV-2. T-cell responses against genome-wide conserved epitopes were studied early in the disease course in a cohort of 147 unvaccinated COVID-19 patients who were divided into six groups based on the severity of their symptoms. Results Compared to severely ill COVID-19 patients and patients with fatal COVID-19 outcomes, the asymptomatic COVID-19 patients displayed significantly: (i) higher rates of co-infection with the 229E alpha species of CCCs (α-CCC-229E); (ii) higher frequencies of cross-reactive functional CD134+CD137+CD4+ and CD134+CD137+CD8+ T cells that cross-recognized conserved epitopes from α-CCCs and SARS-CoV-2 structural, non-structural, and accessory proteins; and (iii) lower frequencies of CCCs/SARS-CoV-2 cross-reactive exhausted PD-1+TIM3+TIGIT+CTLA4+CD4+ and PD-1+TIM3+TIGIT+CTLA4+CD8+ T cells, detected both ex vivo and in vitro. Conclusions These findings (i) support a crucial role of functional, poly-antigenic α-CCCs/SARS-CoV-2 cross-reactive memory CD4+ and CD8+ T cells, induced following previous CCCs seasonal exposures, in protection against subsequent severe COVID-19 disease and (ii) provide critical insights into developing broadly protective, multi-antigen, CD4+, and CD8+ T-cell-based, universal pan-Coronavirus vaccines capable of conferring cross-species protection.
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Affiliation(s)
- Pierre-Gregoire Coulon
- Laboratory of Cellular and Molecular Immunology, Gavin Herbert Eye Institute, University of California Irvine, School of Medicine, Irvine, CA, United States
| | - Swayam Prakash
- Laboratory of Cellular and Molecular Immunology, Gavin Herbert Eye Institute, University of California Irvine, School of Medicine, Irvine, CA, United States
| | - Nisha R. Dhanushkodi
- Laboratory of Cellular and Molecular Immunology, Gavin Herbert Eye Institute, University of California Irvine, School of Medicine, Irvine, CA, United States
| | - Ruchi Srivastava
- Laboratory of Cellular and Molecular Immunology, Gavin Herbert Eye Institute, University of California Irvine, School of Medicine, Irvine, CA, United States
| | - Latifa Zayou
- Laboratory of Cellular and Molecular Immunology, Gavin Herbert Eye Institute, University of California Irvine, School of Medicine, Irvine, CA, United States
| | - Delia F. Tifrea
- Department of Pathology and Laboratory Medicine, School of Medicine, University of California Irvine, Irvine, CA, United States
| | - Robert A. Edwards
- Department of Pathology and Laboratory Medicine, School of Medicine, University of California Irvine, Irvine, CA, United States
| | - Cesar J. Figueroa
- Department of Surgery, Divisions of Trauma, Burns and Critical Care, School of Medicine, University of California Irvine, Irvine, CA, United States
| | - Sebastian D. Schubl
- Department of Surgery, Divisions of Trauma, Burns and Critical Care, School of Medicine, University of California Irvine, Irvine, CA, United States
| | - Lanny Hsieh
- Department of Medicine, Division of Infectious Diseases and Hospitalist Program, School of Medicine, University of California Irvine, Irvine, CA, United States
| | - Anthony B. Nesburn
- Laboratory of Cellular and Molecular Immunology, Gavin Herbert Eye Institute, University of California Irvine, School of Medicine, Irvine, CA, United States
| | - Baruch D. Kuppermann
- Laboratory of Cellular and Molecular Immunology, Gavin Herbert Eye Institute, University of California Irvine, School of Medicine, Irvine, CA, United States
| | | | - Hawa Vahed
- Department of Vaccines and Immunotherapies, TechImmune, LLC, University Lab Partners, Irvine, CA, United States
| | - Daniel Gil
- Department of Vaccines and Immunotherapies, TechImmune, LLC, University Lab Partners, Irvine, CA, United States
| | - Trevor M. Jones
- Department of Vaccines and Immunotherapies, TechImmune, LLC, University Lab Partners, Irvine, CA, United States
| | - Jeffrey B. Ulmer
- Department of Vaccines and Immunotherapies, TechImmune, LLC, University Lab Partners, Irvine, CA, United States
| | - Lbachir BenMohamed
- Laboratory of Cellular and Molecular Immunology, Gavin Herbert Eye Institute, University of California Irvine, School of Medicine, Irvine, CA, United States
- Université Paul Sabatier, Infinity, Inserm, Toulouse, France
- Department of Vaccines and Immunotherapies, TechImmune, LLC, University Lab Partners, Irvine, CA, United States
- Institute for Immunology, The University of California Irvine, School of Medicine, Irvine, CA, United States
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7
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Aoki H, Kitabatake M, Abe H, Xu P, Tsunoda M, Shichino S, Hara A, Ouji-Sageshima N, Motozono C, Ito T, Matsushima K, Ueha S. CD8 + T cell memory induced by successive SARS-CoV-2 mRNA vaccinations is characterized by shifts in clonal dominance. Cell Rep 2024; 43:113887. [PMID: 38458195 DOI: 10.1016/j.celrep.2024.113887] [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: 07/20/2023] [Revised: 12/27/2023] [Accepted: 02/14/2024] [Indexed: 03/10/2024] Open
Abstract
mRNA vaccines against the spike glycoprotein of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) elicit strong T cell responses. However, a clonal-resolution analysis of T cell responses to mRNA vaccination has not been performed. Here, we temporally track the CD8+ T cell repertoire in individuals who received three shots of the BNT162b2 mRNA vaccine through longitudinal T cell receptor sequencing with peptide-human leukocyte antigen (HLA) tetramer analysis. We demonstrate a shift in T cell responses between the clonotypes with different kinetics: from early responders that expand rapidly after the first shot to main responders that greatly expand after the second shot. Although the main responders re-expand after the third shot, their clonal diversity is skewed, and newly elicited third responders partially replace them. Furthermore, this shift in clonal dominance occurs not only between, but also within, clonotypes specific for spike epitopes. Our study will be a valuable resource for understanding vaccine-induced T cell responses in general.
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Affiliation(s)
- Hiroyasu Aoki
- Division of Molecular Regulation of Inflammatory and Immune Diseases, Research Institute for Biomedical Sciences, Tokyo University of Science, Noda City, Chiba 2780022, Japan; Department of Preventive Medicine, Graduate School of Medicine, The University of Tokyo, Bunkyo-ku, Tokyo 1130033, Japan
| | - Masahiro Kitabatake
- Department of Immunology, Nara Medical University, Kashihara City, Nara 6348521, Japan
| | - Haruka Abe
- Division of Molecular Regulation of Inflammatory and Immune Diseases, Research Institute for Biomedical Sciences, Tokyo University of Science, Noda City, Chiba 2780022, Japan
| | - Peng Xu
- Division of Molecular Regulation of Inflammatory and Immune Diseases, Research Institute for Biomedical Sciences, Tokyo University of Science, Noda City, Chiba 2780022, Japan
| | - Mikiya Tsunoda
- Division of Molecular Regulation of Inflammatory and Immune Diseases, Research Institute for Biomedical Sciences, Tokyo University of Science, Noda City, Chiba 2780022, Japan
| | - Shigeyuki Shichino
- Division of Molecular Regulation of Inflammatory and Immune Diseases, Research Institute for Biomedical Sciences, Tokyo University of Science, Noda City, Chiba 2780022, Japan
| | - Atsushi Hara
- Department of Immunology, Nara Medical University, Kashihara City, Nara 6348521, Japan
| | - Noriko Ouji-Sageshima
- Department of Immunology, Nara Medical University, Kashihara City, Nara 6348521, Japan
| | - Chihiro Motozono
- Division of Infection and Immunity, Joint Research Center for Human Retrovirus Infection, Kumamoto University, Kumamoto City, Kumamoto 8600811, Japan
| | - Toshihiro Ito
- Department of Immunology, Nara Medical University, Kashihara City, Nara 6348521, Japan
| | - Kouji Matsushima
- Division of Molecular Regulation of Inflammatory and Immune Diseases, Research Institute for Biomedical Sciences, Tokyo University of Science, Noda City, Chiba 2780022, Japan
| | - Satoshi Ueha
- Division of Molecular Regulation of Inflammatory and Immune Diseases, Research Institute for Biomedical Sciences, Tokyo University of Science, Noda City, Chiba 2780022, Japan.
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8
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Peng M, Lin B, Zhang J, Zhou Y, Lin B. scFSNN: a feature selection method based on neural network for single-cell RNA-seq data. BMC Genomics 2024; 25:264. [PMID: 38459442 PMCID: PMC10924397 DOI: 10.1186/s12864-024-10160-1] [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: 07/26/2023] [Accepted: 02/25/2024] [Indexed: 03/10/2024] Open
Abstract
While single-cell RNA sequencing (scRNA-seq) allows researchers to analyze gene expression in individual cells, its unique characteristics like over-dispersion, zero-inflation, high gene-gene correlation, and large data volume with many features pose challenges for most existing feature selection methods. In this paper, we present a feature selection method based on neural network (scFSNN) to solve classification problem for the scRNA-seq data. scFSNN is an embedded method that can automatically select features (genes) during model training, control the false discovery rate of selected features and adaptively determine the number of features to be eliminated. Extensive simulation and real data studies demonstrate its excellent feature selection ability and predictive performance.
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Affiliation(s)
- Minjiao Peng
- School of Mathematical Sciences, Shenzhen University, Nanshan, Shenzhen, 518060, Guangdong, China
- School of Mathematics and Statistics and KLAS, Northeast Normal University, Renmin Street, Changchun, 130000, Jilin, China
| | - Baoqin Lin
- Experimental Center, The First Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangzhou, Guangdong, 510405, China
| | - Jun Zhang
- School of Mathematical Sciences, Shenzhen University, Nanshan, Shenzhen, 518060, Guangdong, China
| | - Yan Zhou
- School of Mathematical Sciences, Shenzhen University, Nanshan, Shenzhen, 518060, Guangdong, China
| | - Bingqing Lin
- School of Mathematical Sciences, Shenzhen University, Nanshan, Shenzhen, 518060, Guangdong, China.
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9
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Malani A, Aiyar J, Sant A, Kamran N, Mohanan M, Taneja S, Woda B, Zhao W, Acharya A. Comparing population-level humoral and cellular immunity to SARS-Cov-2 in Bangalore, India. Sci Rep 2024; 14:5758. [PMID: 38459035 PMCID: PMC10923858 DOI: 10.1038/s41598-024-54922-z] [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: 11/02/2023] [Accepted: 02/18/2024] [Indexed: 03/10/2024] Open
Abstract
Two types of immunity, humoral and cellular, offer protection against COVID. Humoral protection, contributed by circulating neutralizing antibodies, can provide immediate protection but decays more quickly than cellular immunity and can lose effectiveness in the face of mutation and drift in the SARS-CoV-2 spike protein. Therefore, population-level seroprevalence surveys used to estimate population-level immunity may underestimate the degree to which a population is protected against COVID. In early 2021, before India began its vaccination campaign, we tested for humoral and cellular immunity to SARS-Cov-2 in representative samples of slum and non-slum populations in Bangalore, India. We found that 29.7% of samples (unweighted) had IgG antibodies to the spike protein and 15.5% had neutralizing antibodies, but at up to 46% showed evidence of cellular immunity. We also find that prevalence of cellular immunity is significantly higher in slums than in non-slums. These findings suggest (1) that a significantly larger proportion of the population in Bangalore, India, had cellular immunity to SARS-CoV-2 than had humoral immunity, as measured by serological surveys, and (2) that low socio-economic status communities display higher frequency of cellular immunity, likely because of greater exposure to infection due to population density.
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Affiliation(s)
| | | | - Andrea Sant
- Department of Microbiology and Immunology, University of Rochester Medical Center, Rochester, NY, USA
| | | | - Manoj Mohanan
- Sanford School of Public Policy, Duke University, Durham, NC, USA
| | - Saloni Taneja
- University of Southern California, Los Angeles, CA, USA
| | - Bartek Woda
- University of Chicago, Chicago, IL, USA
- Amazon, Chicago, IL, USA
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10
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Collins CP, Longo DL, Murphy WJ. The immunobiology of SARS-CoV-2 infection and vaccine responses: potential influences of cross-reactive memory responses and aging on efficacy and off-target effects. Front Immunol 2024; 15:1345499. [PMID: 38469293 PMCID: PMC10925677 DOI: 10.3389/fimmu.2024.1345499] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2023] [Accepted: 02/12/2024] [Indexed: 03/13/2024] Open
Abstract
Immune responses to both SARS-CoV-2 infection and its associated vaccines have been highly variable within the general population. The increasing evidence of long-lasting symptoms after resolution of infection, called post-acute sequelae of COVID-19 (PASC) or "Long COVID," suggests that immune-mediated mechanisms are at play. Closely related endemic common human coronaviruses (hCoV) can induce pre-existing and potentially cross-reactive immunity, which can then affect primary SARS-CoV-2 infection, as well as vaccination responses. The influence of pre-existing immunity from these hCoVs, as well as responses generated from original CoV2 strains or vaccines on the development of new high-affinity responses to CoV2 antigenic viral variants, needs to be better understood given the need for continuous vaccine adaptation and application in the population. Due in part to thymic involution, normal aging is associated with reduced naïve T cell compartments and impaired primary antigen responsiveness, resulting in a reliance on the pre-existing cross-reactive memory cell pool which may be of lower affinity, restricted in diversity, or of shorter duration. These effects can also be mediated by the presence of down-regulatory anti-idiotype responses which also increase in aging. Given the tremendous heterogeneity of clinical data, utilization of preclinical models offers the greatest ability to assess immune responses under a controlled setting. These models should now involve prior antigen/viral exposure combined with incorporation of modifying factors such as age on immune responses and effects. This will also allow for mechanistic dissection and understanding of the different immune pathways involved in both SARS-CoV-2 pathogen and potential vaccine responses over time and how pre-existing memory responses, including potential anti-idiotype responses, can affect efficacy as well as potential off-target effects in different tissues as well as modeling PASC.
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Affiliation(s)
- Craig P. Collins
- Graduate Program in Immunology, University of California (UC) Davis, Davis, CA, United States
| | - Dan L. Longo
- Harvard Medical School, Brigham and Women’s Hospital, Boston, MA, United States
| | - William J. Murphy
- Departments of Dermatology and Internal Medicine (Hematology/Oncology), University of California (UC) Davis School of Medicine, Sacramento, CA, United States
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11
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Le Bert N, Samandari T. Silent battles: immune responses in asymptomatic SARS-CoV-2 infection. Cell Mol Immunol 2024; 21:159-170. [PMID: 38221577 PMCID: PMC10805869 DOI: 10.1038/s41423-024-01127-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2023] [Revised: 01/03/2024] [Accepted: 01/03/2024] [Indexed: 01/16/2024] Open
Abstract
SARS-CoV-2 infections manifest with a broad spectrum of presentations, ranging from asymptomatic infections to severe pneumonia and fatal outcomes. This review centers on asymptomatic infections, a widely reported phenomenon that has substantially contributed to the rapid spread of the pandemic. In such asymptomatic infections, we focus on the role of innate, humoral, and cellular immunity. Notably, asymptomatic infections are characterized by an early and robust innate immune response, particularly a swift type 1 IFN reaction, alongside a rapid and broad induction of SARS-CoV-2-specific T cells. Often, antibody levels tend to be lower or undetectable after asymptomatic infections, suggesting that the rapid control of viral replication by innate and cellular responses might impede the full triggering of humoral immunity. Even if antibody levels are present in the early convalescent phase, they wane rapidly below serological detection limits, particularly following asymptomatic infection. Consequently, prevalence studies reliant solely on serological assays likely underestimate the extent of community exposure to the virus.
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Affiliation(s)
- Nina Le Bert
- Program in Emerging Infectious Diseases, Duke-NUS Medical School, Singapore, Singapore.
| | - Taraz Samandari
- Program in Emerging Infectious Diseases, Duke-NUS Medical School, Singapore, Singapore
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12
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Dos Santos Alves RP, Timis J, Miller R, Valentine K, Pinto PBA, Gonzalez A, Regla-Nava JA, Maule E, Nguyen MN, Shafee N, Landeras-Bueno S, Olmedillas E, Laffey B, Dobaczewska K, Mikulski Z, McArdle S, Leist SR, Kim K, Baric RS, Ollmann Saphire E, Elong Ngono A, Shresta S. Human coronavirus OC43-elicited CD4 + T cells protect against SARS-CoV-2 in HLA transgenic mice. Nat Commun 2024; 15:787. [PMID: 38278784 PMCID: PMC10817949 DOI: 10.1038/s41467-024-45043-2] [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: 08/18/2023] [Accepted: 01/10/2024] [Indexed: 01/28/2024] Open
Abstract
SARS-CoV-2-reactive T cells are detected in some healthy unexposed individuals. Human studies indicate these T cells could be elicited by the common cold coronavirus OC43. To directly test this assumption and define the role of OC43-elicited T cells that are cross-reactive with SARS-CoV-2, we develop a model of sequential infections with OC43 followed by SARS-CoV-2 in HLA-B*0702 and HLA-DRB1*0101 Ifnar1-/- transgenic mice. We find that OC43 infection can elicit polyfunctional CD8+ and CD4+ effector T cells that cross-react with SARS-CoV-2 peptides. Furthermore, pre-exposure to OC43 reduces subsequent SARS-CoV-2 infection and disease in the lung for a short-term in HLA-DRB1*0101 Ifnar1-/- transgenic mice, and a longer-term in HLA-B*0702 Ifnar1-/- transgenic mice. Depletion of CD4+ T cells in HLA-DRB1*0101 Ifnar1-/- transgenic mice with prior OC43 exposure results in increased viral burden in the lung but no change in virus-induced lung damage following infection with SARS-CoV-2 (versus CD4+ T cell-sufficient mice), demonstrating that the OC43-elicited SARS-CoV-2 cross-reactive T cell-mediated cross-protection against SARS-CoV-2 is partially dependent on CD4+ T cells. These findings contribute to our understanding of the origin of pre-existing SARS-CoV-2-reactive T cells and their effects on SARS-CoV-2 clinical outcomes, and also carry implications for development of broadly protective betacoronavirus vaccines.
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Affiliation(s)
| | - Julia Timis
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology, La Jolla, CA, USA
| | - Robyn Miller
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology, La Jolla, CA, USA
| | - Kristen Valentine
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology, La Jolla, CA, USA
| | | | - Andrew Gonzalez
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology, La Jolla, CA, USA
| | - Jose Angel Regla-Nava
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology, La Jolla, CA, USA
- Department of Microbiology and Pathology, University Center for Health Science (CUCS), University of Guadalajara, Guadalajara, 44340, Mexico
| | - Erin Maule
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology, La Jolla, CA, USA
| | - Michael N Nguyen
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology, La Jolla, CA, USA
| | - Norazizah Shafee
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology, La Jolla, CA, USA
| | - Sara Landeras-Bueno
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology, La Jolla, CA, USA
| | - Eduardo Olmedillas
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology, La Jolla, CA, USA
| | - Brett Laffey
- Microscopy and Histology Core Facility, La Jolla Institute for Immunology, La Jolla, CA, USA
| | - Katarzyna Dobaczewska
- Microscopy and Histology Core Facility, La Jolla Institute for Immunology, La Jolla, CA, USA
| | - Zbigniew Mikulski
- Microscopy and Histology Core Facility, La Jolla Institute for Immunology, La Jolla, CA, USA
| | - Sara McArdle
- Microscopy and Histology Core Facility, La Jolla Institute for Immunology, La Jolla, CA, USA
| | - Sarah R Leist
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Kenneth Kim
- Histopathology Core Facility, La Jolla Institute for Immunology, La Jolla, CA, USA
| | - Ralph S Baric
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- Department of Microbiology and Immunology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Erica Ollmann Saphire
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology, La Jolla, CA, USA
- Department of Medicine, Division of Infectious Diseases and Global Public Health, University of California, San Diego (UCSD), La Jolla, CA, USA
| | - Annie Elong Ngono
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology, La Jolla, CA, USA.
| | - Sujan Shresta
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology, La Jolla, CA, USA.
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13
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Prakash S, Dhanushkodi NR, Zayou L, Ibraim IC, Quadiri A, Coulon PG, Tifrea DF, Suzer B, Shaik AM, Chilukuri A, Edwards RA, Singer M, Vahed H, Nesburn AB, Kuppermann BD, Ulmer JB, Gil D, Jones TM, BenMohamed L. Cross-protection induced by highly conserved human B, CD4 +, and CD8 + T-cell epitopes-based vaccine against severe infection, disease, and death caused by multiple SARS-CoV-2 variants of concern. Front Immunol 2024; 15:1328905. [PMID: 38318166 PMCID: PMC10839970 DOI: 10.3389/fimmu.2024.1328905] [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: 10/27/2023] [Accepted: 01/02/2024] [Indexed: 02/07/2024] Open
Abstract
Background The coronavirus disease 2019 (COVID-19) pandemic has created one of the largest global health crises in almost a century. Although the current rate of Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infections has decreased significantly, the long-term outlook of COVID-19 remains a serious cause of morbidity and mortality worldwide, with the mortality rate still substantially surpassing even that recorded for influenza viruses. The continued emergence of SARS-CoV-2 variants of concern (VOCs), including multiple heavily mutated Omicron sub-variants, has prolonged the COVID-19 pandemic and underscores the urgent need for a next-generation vaccine that will protect from multiple SARS-CoV-2 VOCs. Methods We designed a multi-epitope-based coronavirus vaccine that incorporated B, CD4+, and CD8+ T- cell epitopes conserved among all known SARS-CoV-2 VOCs and selectively recognized by CD8+ and CD4+ T-cells from asymptomatic COVID-19 patients irrespective of VOC infection. The safety, immunogenicity, and cross-protective immunity of this pan-variant SARS-CoV-2 vaccine were studied against six VOCs using an innovative triple transgenic h-ACE-2-HLA-A2/DR mouse model. Results The pan-variant SARS-CoV-2 vaccine (i) is safe , (ii) induces high frequencies of lung-resident functional CD8+ and CD4+ TEM and TRM cells , and (iii) provides robust protection against morbidity and virus replication. COVID-19-related lung pathology and death were caused by six SARS-CoV-2 VOCs: Alpha (B.1.1.7), Beta (B.1.351), Gamma or P1 (B.1.1.28.1), Delta (lineage B.1.617.2), and Omicron (B.1.1.529). Conclusion A multi-epitope pan-variant SARS-CoV-2 vaccine bearing conserved human B- and T- cell epitopes from structural and non-structural SARS-CoV-2 antigens induced cross-protective immunity that facilitated virus clearance, and reduced morbidity, COVID-19-related lung pathology, and death caused by multiple SARS-CoV-2 VOCs.
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Affiliation(s)
- Swayam Prakash
- Laboratory of Cellular and Molecular Immunology, Gavin Herbert Eye Institute, University of California Irvine, School of Medicine, Irvine, CA, United States
| | - Nisha R Dhanushkodi
- Laboratory of Cellular and Molecular Immunology, Gavin Herbert Eye Institute, University of California Irvine, School of Medicine, Irvine, CA, United States
| | - Latifa Zayou
- Laboratory of Cellular and Molecular Immunology, Gavin Herbert Eye Institute, University of California Irvine, School of Medicine, Irvine, CA, United States
| | - Izabela Coimbra Ibraim
- High Containment Facility, University of California Irvine, School of Medicine, Irvine, CA, United States
| | - Afshana Quadiri
- Laboratory of Cellular and Molecular Immunology, Gavin Herbert Eye Institute, University of California Irvine, School of Medicine, Irvine, CA, United States
| | - Pierre Gregoire Coulon
- Laboratory of Cellular and Molecular Immunology, Gavin Herbert Eye Institute, University of California Irvine, School of Medicine, Irvine, CA, United States
| | - Delia F Tifrea
- Department of Pathology and Laboratory Medicine, School of Medicine, the University of California Irvine, Irvine, CA, United States
| | - Berfin Suzer
- Laboratory of Cellular and Molecular Immunology, Gavin Herbert Eye Institute, University of California Irvine, School of Medicine, Irvine, CA, United States
| | - Amin Mohammed Shaik
- Laboratory of Cellular and Molecular Immunology, Gavin Herbert Eye Institute, University of California Irvine, School of Medicine, Irvine, CA, United States
| | - Amruth Chilukuri
- Laboratory of Cellular and Molecular Immunology, Gavin Herbert Eye Institute, University of California Irvine, School of Medicine, Irvine, CA, United States
| | - Robert A Edwards
- Department of Pathology and Laboratory Medicine, School of Medicine, the University of California Irvine, Irvine, CA, United States
| | - Mahmoud Singer
- Laboratory of Cellular and Molecular Immunology, Gavin Herbert Eye Institute, University of California Irvine, School of Medicine, Irvine, CA, United States
| | - Hawa Vahed
- Department of Vaccines and Immunotherapies, TechImmune, LLC, University Lab Partners, Irvine, CA, United States
| | - Anthony B Nesburn
- Laboratory of Cellular and Molecular Immunology, Gavin Herbert Eye Institute, University of California Irvine, School of Medicine, Irvine, CA, United States
| | - Baruch D Kuppermann
- Laboratory of Cellular and Molecular Immunology, Gavin Herbert Eye Institute, University of California Irvine, School of Medicine, Irvine, CA, United States
| | - Jeffrey B Ulmer
- Department of Vaccines and Immunotherapies, TechImmune, LLC, University Lab Partners, Irvine, CA, United States
| | - Daniel Gil
- Department of Vaccines and Immunotherapies, TechImmune, LLC, University Lab Partners, Irvine, CA, United States
| | - Trevor M Jones
- Department of Vaccines and Immunotherapies, TechImmune, LLC, University Lab Partners, Irvine, CA, United States
| | - Lbachir BenMohamed
- Laboratory of Cellular and Molecular Immunology, Gavin Herbert Eye Institute, University of California Irvine, School of Medicine, Irvine, CA, United States
- Department of Vaccines and Immunotherapies, TechImmune, LLC, University Lab Partners, Irvine, CA, United States
- Division of Infectious Diseases and Hospitalist Program, Department of Medicine, School of Medicine, the University of California Irvine, Irvine, CA, United States
- Institute for Immunology; University of California Irvine, School of Medicine, Irvine, CA, United States
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14
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Sattler A, Gamradt S, Proß V, Thole LML, He A, Schrezenmeier EV, Jechow K, Gold SM, Lukassen S, Conrad C, Kotsch K. CD3 downregulation identifies high-avidity, multipotent SARS-CoV-2 vaccine- and recall antigen-specific Th cells with distinct metabolism. JCI Insight 2024; 9:e166833. [PMID: 38206757 PMCID: PMC11143931 DOI: 10.1172/jci.insight.166833] [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: 11/02/2022] [Accepted: 01/09/2024] [Indexed: 01/13/2024] Open
Abstract
Functional avidity is supposed to critically shape the quality of immune responses, thereby influencing host protection against infectious agents including SARS-CoV-2. Here we show that after human SARS-CoV-2 vaccination, a large portion of high-avidity spike-specific CD4+ T cells lost CD3 expression after in vitro activation. The CD3- subset was enriched for cytokine-positive cells, including elevated per-cell expression levels, and showed increased polyfunctionality. Assessment of key metabolic pathways by flow cytometry revealed that superior functionality was accompanied by a shift toward fatty acid synthesis at the expense of their oxidation, whereas glucose transport and glycolysis were similarly regulated in SARS-CoV-2-specific CD3- and CD3+ subsets. As opposed to their CD3+ counterparts, frequencies of vaccine-specific CD3- T cells positively correlated with both the size of the naive CD4+ T cell pool and vaccine-specific IgG levels. Moreover, their frequencies negatively correlated with advancing age and were impaired in patients under immunosuppressive therapy. Typical recall antigen-reactive T cells showed a comparable segregation into functionally and metabolically distinct CD3+ and CD3- subsets but were quantitatively maintained upon aging, likely due to earlier recruitment in life. In summary, our data identify CD3- T helper cells as correlates of high-quality immune responses that are impaired in at-risk populations.
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Affiliation(s)
- Arne Sattler
- Charité–Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Department for General and Visceral Surgery, Berlin, Germany
| | - Stefanie Gamradt
- Charité–Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Department of Psychiatry and Neurosciences – Campus Benjamin Franklin, Berlin, Germany
- Charité–Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Department of Psychosomatic Medicine – Campus Benjamin Franklin, Berlin, Germany
| | - Vanessa Proß
- Charité–Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Department for General and Visceral Surgery, Berlin, Germany
| | - Linda Marie Laura Thole
- Charité–Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Department for General and Visceral Surgery, Berlin, Germany
| | - An He
- Charité–Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Department for General and Visceral Surgery, Berlin, Germany
| | - Eva Vanessa Schrezenmeier
- Charité–Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Department of Nephrology and Medical Intensive Care, Berlin, Germany
| | - Katharina Jechow
- Charité–Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Center for Digital Health, Berlin, Germany
| | - Stefan M. Gold
- Charité–Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Department of Psychiatry and Neurosciences – Campus Benjamin Franklin, Berlin, Germany
- Charité–Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Department of Psychosomatic Medicine – Campus Benjamin Franklin, Berlin, Germany
- Universitätsklinikum Hamburg Eppendorf, Institut für Neuroimmunologie und Multiple Sklerose, Hamburg, Germany
| | - Sören Lukassen
- Charité–Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Center for Digital Health, Berlin, Germany
| | - Christian Conrad
- Charité–Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Center for Digital Health, Berlin, Germany
| | - Katja Kotsch
- Charité–Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Department for General and Visceral Surgery, Berlin, Germany
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15
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Proß V, Sattler A, Lukassen S, Tóth L, Thole LML, Siegle J, Stahl C, He A, Damm G, Seehofer D, Götz C, Bayerl C, Jäger P, Macke A, Eggeling S, Kirzinger B, Mayr T, Herbst H, Beyer K, Laue D, Krönke J, Braune J, Rosseck F, Kittner B, Friedersdorff F, Hubatsch M, Weinberger S, Lachmann N, Hofmann VM, Schrezenmeier E, Ludwig C, Schrezenmeier H, Jechow K, Conrad C, Kotsch K. SARS-CoV-2 mRNA vaccination-induced immunological memory in human nonlymphoid and lymphoid tissues. J Clin Invest 2023; 133:e171797. [PMID: 37815874 PMCID: PMC10721158 DOI: 10.1172/jci171797] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2023] [Accepted: 10/05/2023] [Indexed: 10/12/2023] Open
Abstract
Tissue-resident lymphocytes provide organ-adapted protection against invading pathogens. Whereas their biology has been examined in great detail in various infection models, their generation and functionality in response to vaccination have not been comprehensively analyzed in humans. We therefore studied SARS-CoV-2 mRNA vaccine-specific T cells in surgery specimens of kidney, liver, lung, bone marrow, and spleen compared with paired blood samples from largely virus-naive individuals. As opposed to lymphoid tissues, nonlymphoid organs harbored significantly elevated frequencies of spike-specific CD4+ T cells compared with blood showing hallmarks of tissue residency and an expanded memory pool. Organ-derived CD4+ T cells further exhibited increased polyfunctionality over those detected in blood. Single-cell RNA-Seq together with T cell receptor repertoire analysis indicated that the clonotype rather than organ origin is a major determinant of transcriptomic state in vaccine-specific CD4+ T cells. In summary, our data demonstrate that SARS-CoV-2 vaccination entails acquisition of tissue memory and residency features in organs distant from the inoculation site, thereby contributing to our understanding of how local tissue protection might be accomplished.
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Affiliation(s)
- Vanessa Proß
- Department of General and Visceral Surgery, Charité – Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Berlin, Germany
| | - Arne Sattler
- Department of General and Visceral Surgery, Charité – Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Berlin, Germany
| | - Sören Lukassen
- Center of Digital Health, Berlin Institute of Health and Charité – Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
| | - Laura Tóth
- Department of General and Visceral Surgery, Charité – Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Berlin, Germany
| | - Linda Marie Laura Thole
- Department of General and Visceral Surgery, Charité – Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Berlin, Germany
| | - Janine Siegle
- Department of General and Visceral Surgery, Charité – Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Berlin, Germany
| | - Carolin Stahl
- Department of General and Visceral Surgery, Charité – Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Berlin, Germany
| | - An He
- Department of General and Visceral Surgery, Charité – Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Berlin, Germany
| | - Georg Damm
- Department of Hepatobiliary Surgery and Visceral Transplantation, University Hospital, Leipzig University, Leipzig, Germany
| | - Daniel Seehofer
- Department of Hepatobiliary Surgery and Visceral Transplantation, University Hospital, Leipzig University, Leipzig, Germany
| | - Christina Götz
- Department of Hepatobiliary Surgery and Visceral Transplantation, University Hospital, Leipzig University, Leipzig, Germany
| | - Christian Bayerl
- Department of Radiology, Charité – Universitätsmedizin Berlin, Campus Benjamin Franklin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Berlin, Germany
| | - Pia Jäger
- Department of General and Visceral Surgery, Charité – Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Berlin, Germany
| | | | | | | | | | - Hermann Herbst
- Department of Pathology, Vivantes Klinikum Neukölln, Berlin, Germany
| | - Katharina Beyer
- Department of General and Visceral Surgery, Charité – Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Berlin, Germany
| | - Dominik Laue
- Department of Traumatology and Reconstructive Surgery, Campus Benjamin Franklin, Charité – Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Berlin, Germany
| | - Jan Krönke
- Department of Hematology, Oncology and Cancer Immunology, Charité – Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
| | - Jan Braune
- Department of Hematology, Oncology and Cancer Immunology, Charité – Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
| | - Friederike Rosseck
- Institute of Pathology, Charité – Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Berlin, Germany
| | - Beatrice Kittner
- Department of Urology, Evangelisches Krankenhaus Königin Elisabeth Herzberge, Berlin, Germany
| | - Frank Friedersdorff
- Department of Urology, Evangelisches Krankenhaus Königin Elisabeth Herzberge, Berlin, Germany
| | - Mandy Hubatsch
- Department of Urology, Charité – Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Berlin, Germany
| | - Sarah Weinberger
- Department of Urology, Charité – Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Berlin, Germany
| | - Nils Lachmann
- Institute of Transfusion Medicine, Berlin Institute of Health, Charité – Universitätsmedizin Berlin, Humboldt-Universität zu Berlin, Berlin, Germany
| | - Veit Maria Hofmann
- Department of Otolaryngology, Charité – Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Berlin, Germany
| | - Eva Schrezenmeier
- Department of Nephrology and Medical Intensive Care, Charité – Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
- BIH Charité Clinician Scientist Program, BIH Biomedical Innovation Academy, Berlin Institute of Health at Charité – Universitätsmedizin Berlin, Berlin, Germany
| | - Carolin Ludwig
- Institute for Clinical Transfusion Medicine and Immunogenetics, German Red Cross Blood Transfusion Service Baden-Württemberg-Hessen and University Hospital Ulm, Ulm, Germany
| | - Hubert Schrezenmeier
- Institute for Clinical Transfusion Medicine and Immunogenetics, German Red Cross Blood Transfusion Service Baden-Württemberg-Hessen and University Hospital Ulm, Ulm, Germany
| | - Katharina Jechow
- Center of Digital Health, Berlin Institute of Health and Charité – Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
| | - Christian Conrad
- Center of Digital Health, Berlin Institute of Health and Charité – Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
| | - Katja Kotsch
- Department of General and Visceral Surgery, Charité – Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Berlin, Germany
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16
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Markov NS, Ren Z, Senkow KJ, Grant RA, Gao CA, Malsin ES, Sichizya L, Kihshen H, Helmin KA, Jovisic M, Arnold JM, Pérez-Leonor XG, Abdala-Valencia H, Swaminathan S, Nwaezeapu J, Kang M, Rasmussen L, Ozer EA, Lorenzo-Redondo R, Hultquist JF, Simons LM, Rios-Guzman E, Misharin AV, Wunderink RG, Budinger GS, Singer BD, Morales-Nebreda L. A distinctive evolution of alveolar T cell responses is associated with clinical outcomes in unvaccinated patients with SARS-CoV-2 pneumonia. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.12.13.571479. [PMID: 38168346 PMCID: PMC10760069 DOI: 10.1101/2023.12.13.571479] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/05/2024]
Abstract
Pathogen clearance and resolution of inflammation in patients with pneumonia require an effective local T cell response. Nevertheless, local T cell activation may drive lung injury, particularly during prolonged episodes of respiratory failure characteristic of severe SARS-CoV-2 pneumonia. While T cell responses in the peripheral blood are well described, the evolution of T cell phenotypes and molecular signatures in the distal lung of patients with severe pneumonia caused by SARS-CoV-2 or other pathogens is understudied. Accordingly, we serially obtained 432 bronchoalveolar lavage fluid samples from 273 patients with severe pneumonia and respiratory failure, including 74 unvaccinated patients with COVID-19, and performed flow cytometry, transcriptional, and T cell receptor profiling on sorted CD8+ and CD4+ T cell subsets. In patients with COVID-19 but not pneumonia secondary to other pathogens, we found that early and persistent enrichment in CD8+ and CD4+ T cell subsets correlated with survival to hospital discharge. Activation of interferon signaling pathways early after intubation for COVID-19 was associated with favorable outcomes, while activation of NF-κB-driven programs late in disease was associated with poor outcomes. Patients with SARS-CoV-2 pneumonia whose alveolar T cells preferentially targeted the Spike and Nucleocapsid proteins tended to experience more favorable outcomes than patients whose T cells predominantly targeted the ORF1ab polyprotein complex. These results suggest that in patients with severe SARS-CoV-2 pneumonia, alveolar T cell interferon responses targeting structural SARS-CoV-2 proteins characterize patients who recover, yet these responses progress to NF-κB activation against non-structural proteins in patients who go on to experience poor clinical outcomes.
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Affiliation(s)
- Nikolay S. Markov
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL USA
- Simpson Querrey Lung Institute for Translational Science, Northwestern University Feinberg School of Medicine, Chicago, IL USA
| | - Ziyou Ren
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL USA
- Simpson Querrey Lung Institute for Translational Science, Northwestern University Feinberg School of Medicine, Chicago, IL USA
- Department of Dermatology, Northwestern University Feinberg School of Medicine, Chicago, IL USA
| | - Karolina J. Senkow
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL USA
- Simpson Querrey Lung Institute for Translational Science, Northwestern University Feinberg School of Medicine, Chicago, IL USA
| | - Rogan A. Grant
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL USA
- Simpson Querrey Lung Institute for Translational Science, Northwestern University Feinberg School of Medicine, Chicago, IL USA
| | - Catherine A. Gao
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL USA
- Simpson Querrey Lung Institute for Translational Science, Northwestern University Feinberg School of Medicine, Chicago, IL USA
| | - Elizabeth S. Malsin
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL USA
- Simpson Querrey Lung Institute for Translational Science, Northwestern University Feinberg School of Medicine, Chicago, IL USA
| | - Lango Sichizya
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL USA
- Simpson Querrey Lung Institute for Translational Science, Northwestern University Feinberg School of Medicine, Chicago, IL USA
| | - Hermon Kihshen
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL USA
- Simpson Querrey Lung Institute for Translational Science, Northwestern University Feinberg School of Medicine, Chicago, IL USA
| | - Kathryn A. Helmin
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL USA
- Simpson Querrey Lung Institute for Translational Science, Northwestern University Feinberg School of Medicine, Chicago, IL USA
| | - Milica Jovisic
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL USA
- Simpson Querrey Lung Institute for Translational Science, Northwestern University Feinberg School of Medicine, Chicago, IL USA
| | - Jason M. Arnold
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL USA
- Simpson Querrey Lung Institute for Translational Science, Northwestern University Feinberg School of Medicine, Chicago, IL USA
| | | | - Hiam Abdala-Valencia
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL USA
- Simpson Querrey Lung Institute for Translational Science, Northwestern University Feinberg School of Medicine, Chicago, IL USA
| | - Suchitra Swaminathan
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL USA
- Simpson Querrey Lung Institute for Translational Science, Northwestern University Feinberg School of Medicine, Chicago, IL USA
| | - Julu Nwaezeapu
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL USA
- Simpson Querrey Lung Institute for Translational Science, Northwestern University Feinberg School of Medicine, Chicago, IL USA
| | - Mengjia Kang
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL USA
- Simpson Querrey Lung Institute for Translational Science, Northwestern University Feinberg School of Medicine, Chicago, IL USA
| | - Luke Rasmussen
- Division of Health and Biomedical Informatics, Department of Preventive Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL USA
| | - Egon A. Ozer
- Division of Infectious Diseases, Department of Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL USA
- Center for Pathogen Genomics and Microbial Evolution, Institute for Global Health, Northwestern University Feinberg School of Medicine, Chicago, IL USA
| | - Ramon Lorenzo-Redondo
- Division of Infectious Diseases, Department of Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL USA
- Center for Pathogen Genomics and Microbial Evolution, Institute for Global Health, Northwestern University Feinberg School of Medicine, Chicago, IL USA
| | - Judd F. Hultquist
- Division of Infectious Diseases, Department of Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL USA
- Center for Pathogen Genomics and Microbial Evolution, Institute for Global Health, Northwestern University Feinberg School of Medicine, Chicago, IL USA
| | - Lacy M. Simons
- Division of Infectious Diseases, Department of Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL USA
- Center for Pathogen Genomics and Microbial Evolution, Institute for Global Health, Northwestern University Feinberg School of Medicine, Chicago, IL USA
| | - Estefany Rios-Guzman
- Division of Infectious Diseases, Department of Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL USA
- Center for Pathogen Genomics and Microbial Evolution, Institute for Global Health, Northwestern University Feinberg School of Medicine, Chicago, IL USA
| | - Alexander V. Misharin
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL USA
- Simpson Querrey Lung Institute for Translational Science, Northwestern University Feinberg School of Medicine, Chicago, IL USA
| | - Richard G. Wunderink
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL USA
- Simpson Querrey Lung Institute for Translational Science, Northwestern University Feinberg School of Medicine, Chicago, IL USA
| | - G.R. Scott Budinger
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL USA
- Simpson Querrey Lung Institute for Translational Science, Northwestern University Feinberg School of Medicine, Chicago, IL USA
| | - Benjamin D. Singer
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL USA
- Simpson Querrey Lung Institute for Translational Science, Northwestern University Feinberg School of Medicine, Chicago, IL USA
- Department of Biochemistry and Molecular Genetics, Northwestern University Feinberg School of Medicine, Chicago, IL USA
- Simpson Querrey Institute for Epigenetics, Northwestern University Feinberg School of Medicine, Chicago, IL USA
| | - Luisa Morales-Nebreda
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL USA
- Simpson Querrey Lung Institute for Translational Science, Northwestern University Feinberg School of Medicine, Chicago, IL USA
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17
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Muñoz-Ruiz M, Llorian M, D'Antuono R, Pavlova A, Mavrigiannaki AM, McKenzie D, García-Cassani B, Iannitto ML, Wu Y, Dart R, Davies D, Jamal-Hanjani M, Jandke A, Ushakov DS, Hayday AC. IFN-γ-dependent interactions between tissue-intrinsic γδ T cells and tissue-infiltrating CD8 T cells limit allergic contact dermatitis. J Allergy Clin Immunol 2023; 152:1520-1540. [PMID: 37562754 DOI: 10.1016/j.jaci.2023.07.015] [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: 01/16/2023] [Revised: 06/27/2023] [Accepted: 07/21/2023] [Indexed: 08/12/2023]
Abstract
BACKGROUND Elicitation of allergic contact dermatitis (ACD), an inflammatory type 4 hypersensitivity disease, induces skin infiltration by polyclonal effector CD8 αβ T cells and precursors of tissue-resident memory T (TRM) cells. Because TRM have long-term potential to contribute to body-surface immunoprotection and immunopathology, their local regulation needs a fuller understanding. OBJECTIVE We sought to investigate how TRM-cell maturation might be influenced by innate-like T cells pre-existing within many epithelia. METHODS This study examined CD8+ TRM-cell maturation following hapten-induced ACD in wild-type mice and in strains harboring altered compartments of dendritic intraepidermal γδ T cells (DETCs), a prototypic tissue-intrinsic, innate-like T-cell compartment that reportedly regulates ACD, but by no elucidated mechanism. RESULTS In addition to eliciting CD8 TRM, ACD induced DETC activation and an intimate coregulatory association of the 2 cell types. This depended on DETC sensing IFN-γ produced by CD8 cells and involved programmed death-ligand 1 (PD-L1). Thus, in mice lacking DETC or lacking IFN-γ receptor solely on γδ cells, ACD-elicited CD8 T cells showed enhanced proliferative and effector potentials and reduced motility, collectively associated with exaggerated ACD pathology. Comparable dysregulation was elicited by PD-L1 blockade in vitro, and IFN-γ-regulated PD-L1 expression was a trait of human skin-homing and intraepithelial γδ T cells. CONCLUSIONS The size and quality of the tissue-infiltrating CD8 T-cell response during ACD can be profoundly regulated by local innate-like T cells responding to IFN-γ and involving PD-L1. Thus, interindividual and tissue-specific variations in tissue-intrinsic lymphocytes may influence responses to allergens and other challenges and may underpin inflammatory pathologies such as those repeatedly observed in γδ T-cell-deficient settings.
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Affiliation(s)
- Miguel Muñoz-Ruiz
- Immunosurveillance Laboratory, The Francis Crick Institute, London, United Kingdom; Peter Gorer Department of Immunobiology, King's College London, London, United Kingdom; Department of Immunology, Ophthalmology and Ear, Nose and Throat, Complutense University School of Medicine and 12 de Octubre Health Research Institute, Madrid, Spain
| | - Miriam Llorian
- Bioinformatics and Biostatistics science technology platform (STP), The Francis Crick Institute, London, United Kingdom
| | - Rocco D'Antuono
- Light Microscopy STP, The Francis Crick Institute, London, United Kingdom
| | - Anna Pavlova
- Department of Biology, Division of Genetics, Nikolaus-Fiebiger-Center for Molecular Medicine, Erlangen, Germany
| | | | - Duncan McKenzie
- Immunosurveillance Laboratory, The Francis Crick Institute, London, United Kingdom; Peter Gorer Department of Immunobiology, King's College London, London, United Kingdom
| | - Bethania García-Cassani
- Development and Homeostasis of the Nervous System Laboratory, The Francis Crick Institute, London, United Kingdom
| | - Maria Luisa Iannitto
- Peter Gorer Department of Immunobiology, King's College London, London, United Kingdom
| | - Yin Wu
- Immunosurveillance Laboratory, The Francis Crick Institute, London, United Kingdom; Peter Gorer Department of Immunobiology, King's College London, London, United Kingdom; Centre for Inflammation Biology and Cancer Immunology, King's College London, London, United Kingdom
| | - Robin Dart
- Immunosurveillance Laboratory, The Francis Crick Institute, London, United Kingdom; Peter Gorer Department of Immunobiology, King's College London, London, United Kingdom
| | - Daniel Davies
- Immunosurveillance Laboratory, The Francis Crick Institute, London, United Kingdom; Peter Gorer Department of Immunobiology, King's College London, London, United Kingdom
| | - Mariam Jamal-Hanjani
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, United Kingdom
| | - Anett Jandke
- Immunosurveillance Laboratory, The Francis Crick Institute, London, United Kingdom; Peter Gorer Department of Immunobiology, King's College London, London, United Kingdom
| | - Dmitry S Ushakov
- Immunosurveillance Laboratory, The Francis Crick Institute, London, United Kingdom; Peter Gorer Department of Immunobiology, King's College London, London, United Kingdom; Institute of Molecular Virology and Cell Biology, Friedrich-Loeffler-Institut, Federal Research Institute for Animal Health, Greifswald-Insel Riems, Germany
| | - Adrian C Hayday
- Immunosurveillance Laboratory, The Francis Crick Institute, London, United Kingdom; Peter Gorer Department of Immunobiology, King's College London, London, United Kingdom; Centre for Inflammation Biology and Cancer Immunology, King's College London, London, United Kingdom.
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18
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Paniskaki K, Goretzki S, Anft M, Konik MJ, Meister TL, Pfaender S, Lechtenberg K, Vogl M, Dogan B, Dolff S, Westhoff TH, Rohn H, Felderhoff-Mueser U, Stervbo U, Witzke O, Dohna-Schwake C, Babel N. Increased SARS-CoV-2 reactive low avidity T cells producing inflammatory cytokines in pediatric post-acute COVID-19 sequelae (PASC). Pediatr Allergy Immunol 2023; 34:e14060. [PMID: 38146118 DOI: 10.1111/pai.14060] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/22/2023] [Revised: 11/13/2023] [Accepted: 11/29/2023] [Indexed: 12/27/2023]
Abstract
BACKGROUND A proportion of the convalescent SARS-CoV-2 pediatric population presents nonspecific symptoms, mental health problems, and a reduction in quality of life similar to myalgic encephalomyelitis/chronic fatigue syndrome (ME/CFS) and long COVID-19 symptomatic. However, data regarding its clinical manifestation and immune mechanisms are currently scarce. METHODS In this study, we perform a comprehensive clinical and immunological profiling of 17 convalescent COVID-19 children with post-acute COVID-19 sequelae (PASC) manifestation and 13 convalescent children without PASC manifestation. A detailed medical history, blood and instrumental tests, and physical examination were obtained from all patients. SARS-CoV-2 reactive T-cell response was analyzed via multiparametric flow cytometry and the humoral immunity was addressed via pseudovirus neutralization and ELISA assay. RESULTS The most common PASC symptoms were shortness of breath/exercise intolerance, paresthesia, smell/taste disturbance, chest pain, dyspnea, headache, and lack of concentration. Blood count and clinical chemistry showed no statistical differences among the study groups. We detected higher frequencies of spike (S) reactive CD4+ and CD8+ T cells among the PASC study group, characterized by TNFα and IFNγ production and low functional avidity. CRP levels are positively correlated with IFNγ producing reactive CD8+ T cells. CONCLUSIONS Our data might indicate a possible involvement of a persistent cellular inflammatory response triggered by SARS-CoV-2 in the development of the observed sequelae in pediatric PASC. These results may have implications on future therapeutic and prevention strategies.
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Affiliation(s)
- Krystallenia Paniskaki
- Department of Infectious Diseases, West German Centre of Infectious Diseases, University Hospital Essen, University of Duisburg-Essen, Essen, Germany
- Center for Translational Medicine and Immune Diagnostics Laboratory, Medical Department I, Marien Hospital Herne, University Hospital of the Ruhr-University Bochum, Bochum, Germany
| | - Sarah Goretzki
- Department of Infectious Diseases, West German Centre of Infectious Diseases, University Hospital Essen, University of Duisburg-Essen, Essen, Germany
- Department of Pediatrics I, Children's Hospital Essen, University of Duisburg-Essen, Essen, Germany
| | - Moritz Anft
- Center for Translational Medicine and Immune Diagnostics Laboratory, Medical Department I, Marien Hospital Herne, University Hospital of the Ruhr-University Bochum, Bochum, Germany
| | - Margarethe J Konik
- Department of Infectious Diseases, West German Centre of Infectious Diseases, University Hospital Essen, University of Duisburg-Essen, Essen, Germany
| | - Toni L Meister
- Department of Molecular and Medical Virology, Ruhr-University Bochum, Bochum, Germany
| | - Stephanie Pfaender
- Department of Molecular and Medical Virology, Ruhr-University Bochum, Bochum, Germany
| | - Klara Lechtenberg
- Department of Pediatrics I, Children's Hospital Essen, University of Duisburg-Essen, Essen, Germany
| | - Melanie Vogl
- Department of Pediatrics III, Pediatric Pulmonology and Sleep Medicine, Children's Hospital Essen, University of Duisburg-Essen, Essen, Germany
| | - Burcin Dogan
- Department of Pediatrics I, Children's Hospital Essen, University of Duisburg-Essen, Essen, Germany
| | - Sebastian Dolff
- Department of Infectious Diseases, West German Centre of Infectious Diseases, University Hospital Essen, University of Duisburg-Essen, Essen, Germany
| | - Timm H Westhoff
- Medical Department I, Marien Hospital Herne, University Hospital of the Ruhr-University Bochum, Herne, Germany
| | - Hana Rohn
- Department of Infectious Diseases, West German Centre of Infectious Diseases, University Hospital Essen, University of Duisburg-Essen, Essen, Germany
| | - Ursula Felderhoff-Mueser
- Department of Pediatrics I, Children's Hospital Essen, University of Duisburg-Essen, Essen, Germany
- Center for Translational Neuro- and Behavioral Sciences C-TNBS, University of Duisburg-Essen, Essen, Germany
| | - Ulrik Stervbo
- Center for Translational Medicine and Immune Diagnostics Laboratory, Medical Department I, Marien Hospital Herne, University Hospital of the Ruhr-University Bochum, Bochum, Germany
| | - Oliver Witzke
- Department of Infectious Diseases, West German Centre of Infectious Diseases, University Hospital Essen, University of Duisburg-Essen, Essen, Germany
| | - Christian Dohna-Schwake
- Department of Infectious Diseases, West German Centre of Infectious Diseases, University Hospital Essen, University of Duisburg-Essen, Essen, Germany
- Department of Pediatrics I, Children's Hospital Essen, University of Duisburg-Essen, Essen, Germany
- Center for Translational Neuro- and Behavioral Sciences C-TNBS, University of Duisburg-Essen, Essen, Germany
| | - Nina Babel
- Center for Translational Medicine and Immune Diagnostics Laboratory, Medical Department I, Marien Hospital Herne, University Hospital of the Ruhr-University Bochum, Bochum, Germany
- Berlin Institute of Health at Charité - University Clinic Berlin, BIH Center for Regenerative Therapies (BCRT) Berlin, Berlin, Germany
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19
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Wang L, Nicols A, Turtle L, Richter A, Duncan CJA, Dunachie SJ, Klenerman P, Payne RP. T cell immune memory after covid-19 and vaccination. BMJ MEDICINE 2023; 2:e000468. [PMID: 38027416 PMCID: PMC10668147 DOI: 10.1136/bmjmed-2022-000468] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/26/2023] [Accepted: 10/23/2023] [Indexed: 12/01/2023]
Abstract
The T cell memory response is a crucial component of adaptive immunity responsible for limiting or preventing viral reinfection. T cell memory after infection with the SARS-CoV-2 virus or vaccination is broad, and spans multiple viral proteins and epitopes, about 20 in each individual. So far the T cell memory response is long lasting and provides a high level of cross reactivity and hence resistance to viral escape by variants of the SARS-CoV-2 virus, such as the omicron variant. All current vaccine regimens tested produce robust T cell memory responses, and heterologous regimens will probably enhance protective responses through increased breadth. T cell memory could have a major role in protecting against severe covid-19 disease through rapid viral clearance and early presentation of epitopes, and the presence of cross reactive T cells might enhance this protection. T cell memory is likely to provide ongoing protection against admission to hospital and death, and the development of a pan-coronovirus vaccine might future proof against new pandemic strains.
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Affiliation(s)
- Lulu Wang
- Translational and Clinical Research Institute, Immunity and Inflammation Theme, Newcastle University, Newcastle upon Tyne, UK
| | - Alex Nicols
- Translational and Clinical Research Institute, Immunity and Inflammation Theme, Newcastle University, Newcastle upon Tyne, UK
| | - Lance Turtle
- NIHR Health Protection Research Unit in Emerging and Zoonotic Infections, Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, UK
- Tropical and Infectious Disease Unit, Liverpool University Hospitals NHS Foundation Trust, Liverpool, UK
| | - Alex Richter
- Institute of Immunology and Immunotherapy, College of Medical and Dental Science, University of Birmingham, Birmingham, UK
| | - Christopher JA Duncan
- Translational and Clinical Research Institute, Immunity and Inflammation Theme, Newcastle University, Newcastle upon Tyne, UK
- Department of Infection and Tropical Medicine, Newcastle Upon Tyne Hospitals NHS Foundation Trust, Newcastle Upon Tyne, UK
| | - Susanna J Dunachie
- NDM Centre For Global Health Research, Nuffield Department of Clinical Medicine, University of Oxford, Oxford, UK
- Mahidol-Oxford Tropical Medicine Research Unit, Mahidol University Faculty of Science, Bangkok, Thailand
| | - Paul Klenerman
- Oxford University Hospitals NHS Foundation Trust, Oxford NIHR Biomedical Research Centre, University of Oxford, Oxford, Oxfordshire, UK
- Translational Gastroenterology Unit, University of Oxford, Oxford, UK
| | - Rebecca P Payne
- Translational and Clinical Research Institute, Immunity and Inflammation Theme, Newcastle University, Newcastle upon Tyne, UK
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20
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Paniskaki K, Goretzki S, Anft M, Konik MJ, Lechtenberg K, Vogl M, Meister TL, Pfaender S, Zettler M, Jäger J, Dolff S, Westhoff TH, Rohn H, Felderhoff-Mueser U, Stervbo U, Witzke O, Dohna-Schwake C, Babel N. Fading SARS-CoV-2 humoral VOC cross-reactivity and sustained cellular immunity in convalescent children and adolescents. BMC Infect Dis 2023; 23:818. [PMID: 37993788 PMCID: PMC10664582 DOI: 10.1186/s12879-023-08805-9] [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: 06/16/2023] [Accepted: 11/08/2023] [Indexed: 11/24/2023] Open
Abstract
Cross-reactive cellular and humoral immunity can substantially contribute to antiviral defense against SARS-CoV-2 variants of concern (VOC). While the adult SARS-CoV-2 cellular and humoral immunity and its cross-recognition potential against VOC is broadly analyzed, similar data regarding the pediatric population are missing. In this study, we perform an analysis of the humoral and cellular SARS-CoV-2 response immune of 32 convalescent COVID-19 children (children), 27 convalescent vaccinated adults(C + V+) and 7 unvaccinated convalescent adults (C + V-). Similarly to adults, a significant reduction of cross-reactive neutralizing capacity against delta and omicron VOC was observed 6 months after SARS-CoV-2 infection. While SAR-CoV-2 neutralizing capacity was comparable among children and C + V- against all VOC, children demonstrated as expected an inferior humoral response when compared to C + V+. Nevertheless, children generated SARS-CoV-2 reactive T cells with broad cross-recognition potential. When compared to V + C+, children presented even comparable frequencies of WT-reactive CD4 + and CD8 + T cells with high avidity and functionality. Taking into consideration the limitations of study - unknown disease onset for 53% of the asymptomatic pediatric subjects, serological detection of SARS-CoV-2 infection-, our results suggest that following SARS-CoV-2 infection children generate a humoral SARS-CoV-2 response with neutralizing potential comparable to unvaccinated COVID-19 convalescent adults as well a sustained SARS-CoV-2 cellular response cross-reactive to VOC.
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Affiliation(s)
- Krystallenia Paniskaki
- Department of Infectious Diseases, West German Centre of Infectious Diseases, University Hospital Essen, University Duisburg-Essen, Essen, Germany.
- Center for Translational Medicine and Immune Diagnostics Laboratory, Medical Department I, Marien Hospital Herne, University Hospital of the Ruhr-University Bochum, Bochum, Germany.
| | - Sarah Goretzki
- Department of Pediatrics I, University Hospital Essen, University Duisburg-Essen, Essen, Germany
| | - Moritz Anft
- Center for Translational Medicine and Immune Diagnostics Laboratory, Medical Department I, Marien Hospital Herne, University Hospital of the Ruhr-University Bochum, Bochum, Germany
| | - Margarethe J Konik
- Department of Infectious Diseases, West German Centre of Infectious Diseases, University Hospital Essen, University Duisburg-Essen, Essen, Germany
| | - Klara Lechtenberg
- Department of Pediatrics I, University Hospital Essen, University Duisburg-Essen, Essen, Germany
| | - Melanie Vogl
- Department of Pediatrics III, University Hospital Essen, University Duisburg-Essen, Essen, Germany
| | - Toni L Meister
- Department of Molecular and Medical Virology, Ruhr-University Bochum, Bochum, Germany
| | - Stephanie Pfaender
- Department of Molecular and Medical Virology, Ruhr-University Bochum, Bochum, Germany
| | - Markus Zettler
- Department of Infectious Diseases, West German Centre of Infectious Diseases, University Hospital Essen, University Duisburg-Essen, Essen, Germany
| | - Jasmin Jäger
- Department of Infectious Diseases, West German Centre of Infectious Diseases, University Hospital Essen, University Duisburg-Essen, Essen, Germany
- Center for Translational Medicine and Immune Diagnostics Laboratory, Medical Department I, Marien Hospital Herne, University Hospital of the Ruhr-University Bochum, Bochum, Germany
| | - Sebastian Dolff
- Department of Infectious Diseases, West German Centre of Infectious Diseases, University Hospital Essen, University Duisburg-Essen, Essen, Germany
| | - Timm H Westhoff
- Medical Department I, Marien Hospital Herne, University Hospital of the Ruhr-University Bochum, Herne, Germany
| | - Hana Rohn
- Department of Infectious Diseases, West German Centre of Infectious Diseases, University Hospital Essen, University Duisburg-Essen, Essen, Germany
| | - Ursula Felderhoff-Mueser
- Department of Pediatrics I, University Hospital Essen, University Duisburg-Essen, Essen, Germany
| | - Ulrik Stervbo
- Center for Translational Medicine and Immune Diagnostics Laboratory, Medical Department I, Marien Hospital Herne, University Hospital of the Ruhr-University Bochum, Bochum, Germany
| | - Oliver Witzke
- Department of Infectious Diseases, West German Centre of Infectious Diseases, University Hospital Essen, University Duisburg-Essen, Essen, Germany
| | - Christian Dohna-Schwake
- Department of Pediatrics I, University Hospital Essen, University Duisburg-Essen, Essen, Germany
| | - Nina Babel
- Center for Translational Medicine and Immune Diagnostics Laboratory, Medical Department I, Marien Hospital Herne, University Hospital of the Ruhr-University Bochum, Bochum, Germany
- Berlin Institute of Health at Charité - University Clinic Berlin, BIH Center for Regenerative Therapies (BCRT) Berlin, Berlin, Germany
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21
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Daud M, Dasari P, Adelfinger M, Langenhorst D, Lother J, Slavkovic-Lukic D, Berges C, Kruhm M, Galler A, Schleussner C, Luther CH, Alberter K, Althammer A, Shaikh H, Pallmann N, Bodem J, El-Mowafy M, Beilhack A, Dittrich M, Topp MS, Zipfel PF, Beyersdorf N. Enolase 1 of Candida albicans binds human CD4 + T cells and modulates naïve and memory responses. Eur J Immunol 2023; 53:e2250284. [PMID: 37503840 DOI: 10.1002/eji.202250284] [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: 11/23/2022] [Revised: 06/05/2023] [Accepted: 07/27/2023] [Indexed: 07/29/2023]
Abstract
To obtain a better understanding of the biology behind life-threatening fungal infections caused by Candida albicans, we recently conducted an in silico screening for fungal and host protein interaction partners. We report here that the extracellular domain of human CD4 binds to the moonlighting protein enolase 1 (Eno1) of C. albicans as predicted bioinformatically. By using different anti-CD4 monoclonal antibodies, we determined that C. albicans Eno1 (CaEno1) primarily binds to the extracellular domain 3 of CD4. Functionally, we observed that CaEno1 binding to CD4 activated lymphocyte-specific protein tyrosine kinase (LCK), which was also the case for anti-CD4 monoclonal antibodies tested in parallel. CaEno1 binding to naïve human CD4+ T cells skewed cytokine secretion toward a Th2 profile indicative of poor fungal control. Moreover, CaEno1 inhibited human memory CD4+ T-cell recall responses. Therapeutically, CD4+ T cells transduced with a p41/Crf1-specific T-cell receptor developed for adoptive T-cell therapy were not inhibited by CaEno1 in vitro. Together, the interaction of human CD4+ T cells with CaEno1 modulated host CD4+ T-cell responses in favor of the fungus. Thus, CaEno1 mediates not only immune evasion through its interference with complement regulators but also through the direct modulation of CD4+ T-cell responses.
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Affiliation(s)
- Muhammad Daud
- Institute for Virology and Immunobiology, University of Würzburg, Würzburg, Germany
| | - Prasad Dasari
- Leibniz Institute for Natural Product Research and Infection Biology, Hans-Knöll-Institute, Jena, Germany
| | - Marion Adelfinger
- Department of Internal Medicine II, Division of Hematology, University Hospital Würzburg, Würzburg, Germany
| | - Daniela Langenhorst
- Institute for Virology and Immunobiology, University of Würzburg, Würzburg, Germany
| | - Jasmin Lother
- Department of Internal Medicine II, Division of Hematology, University Hospital Würzburg, Würzburg, Germany
| | - Dragana Slavkovic-Lukic
- Department of Internal Medicine II, Division of Hematology, University Hospital Würzburg, Würzburg, Germany
| | - Carsten Berges
- Department of Internal Medicine II, Division of Hematology, University Hospital Würzburg, Würzburg, Germany
| | - Michaela Kruhm
- Department of Internal Medicine II, Division of Hematology, University Hospital Würzburg, Würzburg, Germany
| | | | | | | | - Karl Alberter
- Institute for Virology and Immunobiology, University of Würzburg, Würzburg, Germany
| | - Anton Althammer
- Institute for Virology and Immunobiology, University of Würzburg, Würzburg, Germany
| | - Haroon Shaikh
- Department of Internal Medicine II, Division of Hematology, University Hospital Würzburg, Würzburg, Germany
| | - Niklas Pallmann
- Institute for Virology and Immunobiology, University of Würzburg, Würzburg, Germany
| | - Jochen Bodem
- Institute for Virology and Immunobiology, University of Würzburg, Würzburg, Germany
| | - Mohammed El-Mowafy
- Institute for Virology and Immunobiology, University of Würzburg, Würzburg, Germany
- Faculty of Pharmacy, Department of Microbiology & Immunology, Mansoura University, Mansoura, Egypt
| | - Andreas Beilhack
- Department of Internal Medicine II, Division of Hematology, University Hospital Würzburg, Würzburg, Germany
| | - Marcus Dittrich
- Chair of Bioinformatics, University of Würzburg, Würzburg, Germany
- Institute of Human Genetics, University of Würzburg, Würzburg, Germany
| | - Max S Topp
- Department of Internal Medicine II, Division of Hematology, University Hospital Würzburg, Würzburg, Germany
| | - Peter F Zipfel
- Leibniz Institute for Natural Product Research and Infection Biology, Hans-Knöll-Institute, Jena, Germany
- Friedrich Schiller University, Jena, Germany
| | - Niklas Beyersdorf
- Institute for Virology and Immunobiology, University of Würzburg, Würzburg, Germany
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22
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Thole LML, Tóth L, Proß V, Siegle J, Stahl C, Hermsdorf G, Knabe A, Winkler A, Schrezenmeier E, Ludwig C, Eckert C, Eggert A, Schrezenmeier H, Sattler A, Schulte JH, Kotsch K. Impact of a booster dose on SARS-CoV2 mRNA vaccine-specific humoral-, B- and T cell immunity in pediatric stem cell transplant recipients. Front Immunol 2023; 14:1239519. [PMID: 37942315 PMCID: PMC10628529 DOI: 10.3389/fimmu.2023.1239519] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2023] [Accepted: 10/09/2023] [Indexed: 11/10/2023] Open
Abstract
Stem cell transplant recipients (SCTR) are imperiled to increased risks after SARS-CoV2 infection, supporting the need for effective vaccination strategies for this vulnerable group. With respect to pediatric patients, data on immunogenicity of SARS-CoV2 mRNA-based vaccination is limited. We therefore comprehensively examined specific humoral, B- and T cell responses in a cohort of 2-19 year old SCTR after the second and third vaccine dose. Only after booster vaccination, transplant recipients reached similar levels of vaccine-specific IgG, IgA and neutralizing antibodies against omicron variant as age-matched controls. Although frequencies of SARS-CoV2 specific B cells increased after the third dose, they were still fourfold reduced in patients compared to controls. Overall, the majority of individuals enrolled mounted SARS-CoV2 Spike protein-specific CD4+ T helper cell responses with patients showing significantly higher portions than controls after the third dose. With respect to functionality, however, SCTR were characterized by reduced frequencies of specific interferon gamma producing CD4+ T cells, along with an increase in IL-2 producers. In summary, our data identify distinct quantitative and qualitative impairments within the SARS-CoV2 vaccination specific B- and CD4+ T cell compartments. More importantly, humoral analyses highlight the need for a booster vaccination of SCTR particularly for development of neutralizing antibodies.
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Affiliation(s)
- Linda Marie Laura Thole
- Department of General and Visceral Surgery, Charite-Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
| | - Laura Tóth
- Department of General and Visceral Surgery, Charite-Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
| | - Vanessa Proß
- Department of General and Visceral Surgery, Charite-Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
| | - Janine Siegle
- Department of General and Visceral Surgery, Charite-Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
| | - Carolin Stahl
- Department of General and Visceral Surgery, Charite-Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
| | - Georg Hermsdorf
- Department of Pediatric Oncology and Hematology, Charite-Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
| | - Annette Knabe
- Department of Pediatric Oncology and Hematology, Charite-Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
| | - Annika Winkler
- Department of Pediatric Oncology and Hematology, Charite-Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
| | - Eva Schrezenmeier
- Department of Nephrology and Medical Intensive Care, Charite-Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
- Berlin Institute of Health at Charité-Universitätsmedizin Berlin, Berlin Institute of Health (BIH) Academy, Clinician Scientist Program Universitätsmedizin Berlin, Berlin, Germany
| | - Carolin Ludwig
- Institute of Transfusion Medicine, Ulm University, Ulm, Germany
- Institute for Clinical Transfusion Medicine and Immunogenetics, German Red Cross Blood Transfusion Service Baden-Württemberg – Hessen and University Hospital Ulm, Ulm, Germany
| | - Cornelia Eckert
- Department of Pediatric Oncology and Hematology, Charite-Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
| | - Angelika Eggert
- Department of Pediatric Oncology and Hematology, Charite-Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
| | - Hubert Schrezenmeier
- Institute of Transfusion Medicine, Ulm University, Ulm, Germany
- Institute for Clinical Transfusion Medicine and Immunogenetics, German Red Cross Blood Transfusion Service Baden-Württemberg – Hessen and University Hospital Ulm, Ulm, Germany
| | - Arne Sattler
- Department of General and Visceral Surgery, Charite-Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
| | - Johannes H. Schulte
- Department of Pediatric Hematology and Oncology, University Children’s Hospital, Eberhard Karls University Tuebingen, Tuebingen, Germany
| | - Katja Kotsch
- Department of General and Visceral Surgery, Charite-Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
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23
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Uhl LFK, Cai H, Oram SL, Mahale JN, MacLean AJ, Mazet JM, Piccirilli T, He AJ, Lau D, Elliott T, Gerard A. Interferon-γ couples CD8 + T cell avidity and differentiation during infection. Nat Commun 2023; 14:6727. [PMID: 37872155 PMCID: PMC10593754 DOI: 10.1038/s41467-023-42455-4] [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: 04/21/2023] [Accepted: 10/11/2023] [Indexed: 10/25/2023] Open
Abstract
Effective responses to intracellular pathogens are characterized by T cell clones with a broad affinity range for their cognate peptide and diverse functional phenotypes. How T cell clones are selected throughout the response to retain a breadth of avidities remains unclear. Here, we demonstrate that direct sensing of the cytokine IFN-γ by CD8+ T cells coordinates avidity and differentiation during infection. IFN-γ promotes the expansion of low-avidity T cells, allowing them to overcome the selective advantage of high-avidity T cells, whilst reinforcing high-avidity T cell entry into the memory pool, thus reducing the average avidity of the primary response and increasing that of the memory response. IFN-γ in this context is mainly provided by virtual memory T cells, an antigen-inexperienced subset with memory features. Overall, we propose that IFN-γ and virtual memory T cells fulfil a critical immunoregulatory role by enabling the coordination of T cell avidity and fate.
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Affiliation(s)
- Lion F K Uhl
- The Kennedy Institute of Rheumatology, University of Oxford, Oxford, UK
| | - Han Cai
- The Kennedy Institute of Rheumatology, University of Oxford, Oxford, UK
| | - Sophia L Oram
- The Kennedy Institute of Rheumatology, University of Oxford, Oxford, UK
| | - Jagdish N Mahale
- The Kennedy Institute of Rheumatology, University of Oxford, Oxford, UK
| | - Andrew J MacLean
- The Kennedy Institute of Rheumatology, University of Oxford, Oxford, UK
| | - Julie M Mazet
- The Kennedy Institute of Rheumatology, University of Oxford, Oxford, UK
| | - Theo Piccirilli
- The Kennedy Institute of Rheumatology, University of Oxford, Oxford, UK
| | - Alexander J He
- The Kennedy Institute of Rheumatology, University of Oxford, Oxford, UK
| | - Doreen Lau
- Centre for Immuno-oncology, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Tim Elliott
- Centre for Immuno-oncology, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Audrey Gerard
- The Kennedy Institute of Rheumatology, University of Oxford, Oxford, UK.
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24
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Soni MK, Migliori E, Fu J, Assal A, Chan HT, Pan J, Khatiwada P, Ciubotariu R, May MS, Pereira MR, De Giorgi V, Sykes M, Mapara MY, Muranski PJ. The prospect of universal coronavirus immunity: characterization of reciprocal and non-reciprocal T cell responses against SARS-CoV2 and common human coronaviruses. Front Immunol 2023; 14:1212203. [PMID: 37901229 PMCID: PMC10612330 DOI: 10.3389/fimmu.2023.1212203] [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: 04/25/2023] [Accepted: 09/25/2023] [Indexed: 10/31/2023] Open
Abstract
T cell immunity plays a central role in clinical outcomes of Coronavirus Infectious Disease 2019 (COVID-19) and T cell-focused vaccination or cellular immunotherapy might provide enhanced protection for some immunocompromised patients. Pre-existing T cell memory recognizing SARS-CoV-2 antigens antedating COVID-19 infection or vaccination, may have developed as an imprint of prior infections with endemic non-SARS human coronaviruses (hCoVs) OC43, HKU1, 229E, NL63, pathogens of "common cold". In turn, SARS-CoV-2-primed T cells may recognize emerging variants or other hCoV viruses and modulate the course of subsequent hCoV infections. Cross-immunity between hCoVs and SARS-CoV-2 has not been well characterized. Here, we systematically investigated T cell responses against the immunodominant SARS-CoV-2 spike, nucleocapsid and membrane proteins and corresponding antigens from α- and β-hCoVs among vaccinated, convalescent, and unexposed subjects. Broad T cell immunity against all tested SARS-CoV-2 antigens emerged in COVID-19 survivors. In convalescent and in vaccinated individuals, SARS-CoV-2 spike-specific T cells reliably recognized most SARS-CoV-2 variants, however cross-reactivity against the omicron variant was reduced by approximately 47%. Responses against spike, nucleocapsid and membrane antigens from endemic hCoVs were significantly more extensive in COVID-19 survivors than in unexposed subjects and displayed cross-reactivity between α- and β-hCoVs. In some, non-SARS hCoV-specific T cells demonstrated a prominent non-reciprocal cross-reactivity with SARS-CoV-2 antigens, whereas a distinct anti-SARS-CoV-2 immunological repertoire emerged post-COVID-19, with relatively limited cross-recognition of non-SARS hCoVs. Based on this cross-reactivity pattern, we established a strategy for in-vitro expansion of universal anti-hCoV T cells for adoptive immunotherapy. Overall, these results have implications for the future design of universal vaccines and cell-based immune therapies against SARS- and non-SARS-CoVs.
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Affiliation(s)
- Mithil K. Soni
- Columbia Center for Translational Immunology, Department of Medicine, Columbia University, New York, NY, United States
| | - Edoardo Migliori
- Columbia Center for Translational Immunology, Department of Medicine, Columbia University, New York, NY, United States
| | - Jianing Fu
- Columbia Center for Translational Immunology, Department of Medicine, Columbia University, New York, NY, United States
| | - Amer Assal
- Department of Medicine, Blood and Marrow Transplantation and Cell Therapy Program, Columbia University Irving Medical Center, New York, NY, United States
- Columbia University Medical Center, Herbert Irving Comprehensive Cancer Center, New York, NY, United States
| | - Hei Ton Chan
- Columbia University Medical Center, Herbert Irving Comprehensive Cancer Center, New York, NY, United States
| | - Jian Pan
- Columbia University Medical Center, Herbert Irving Comprehensive Cancer Center, New York, NY, United States
| | - Prabesh Khatiwada
- Columbia Center for Translational Immunology, Department of Medicine, Columbia University, New York, NY, United States
| | - Rodica Ciubotariu
- Columbia University Medical Center, Herbert Irving Comprehensive Cancer Center, New York, NY, United States
| | - Michael S. May
- Columbia University Medical Center, Herbert Irving Comprehensive Cancer Center, New York, NY, United States
| | - Marcus R. Pereira
- Department of Medicine, Division of Infectious Disease, Columbia University College of Physicians and Surgeons, New York, NY, United States
| | - Valeria De Giorgi
- Department of Transfusion Medicine, National Institutes of Health Clinical Center, Bethesda, MD, United States
| | - Megan Sykes
- Columbia Center for Translational Immunology, Department of Medicine, Columbia University, New York, NY, United States
| | - Markus Y. Mapara
- Columbia Center for Translational Immunology, Department of Medicine, Columbia University, New York, NY, United States
| | - Pawel J. Muranski
- Columbia Center for Translational Immunology, Department of Medicine, Columbia University, New York, NY, United States
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25
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Martini GR, Tikhonova E, Rosati E, DeCelie MB, Sievers LK, Tran F, Lessing M, Bergfeld A, Hinz S, Nikolaus S, Kümpers J, Matysiak A, Hofmann P, Saggau C, Schneiders S, Kamps AK, Jacobs G, Lieb W, Maul J, Siegmund B, Seegers B, Hinrichsen H, Oberg HH, Wesch D, Bereswill S, Heimesaat MM, Rupp J, Kniemeyer O, Brakhage AA, Brunke S, Hube B, Aden K, Franke A, Iliev ID, Scheffold A, Schreiber S, Bacher P. Selection of cross-reactive T cells by commensal and food-derived yeasts drives cytotoxic T H1 cell responses in Crohn's disease. Nat Med 2023; 29:2602-2614. [PMID: 37749331 PMCID: PMC10579100 DOI: 10.1038/s41591-023-02556-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2023] [Accepted: 08/22/2023] [Indexed: 09/27/2023]
Abstract
Aberrant CD4+ T cell reactivity against intestinal microorganisms is considered to drive mucosal inflammation in inflammatory bowel diseases. The disease-relevant microbial species and the corresponding microorganism-specific, pathogenic T cell phenotypes remain largely unknown. In the present study, we identified common gut commensal and food-derived yeasts, as direct activators of altered CD4+ T cell reactions in patients with Crohn's disease (CD). Yeast-responsive CD4+ T cells in CD display a cytotoxic T helper cell (TH1 cell) phenotype and show selective expansion of T cell clones that are highly cross-reactive to several commensal, as well as food-derived, fungal species. This indicates cross-reactive T cell selection by repeated encounter with conserved fungal antigens in the context of chronic intestinal disease. Our results highlighted a role of yeasts as drivers of aberrant CD4+ T cell reactivity in patients with CD and suggest that both gut-resident fungal commensals and daily dietary intake of yeasts might contribute to chronic activation of inflammatory CD4+ T cell responses in patients with CD.
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Affiliation(s)
- Gabriela Rios Martini
- Institute of Immunology, Christian-Albrechts-University of Kiel and University Medical Center Schleswig-Holstein, Kiel, Germany
- Institute of Clinical Molecular Biology, Christian-Albrechts-University of Kiel and University Medical Center Schleswig-Holstein, Kiel, Germany
| | - Ekaterina Tikhonova
- Institute of Immunology, Christian-Albrechts-University of Kiel and University Medical Center Schleswig-Holstein, Kiel, Germany
- Institute of Clinical Molecular Biology, Christian-Albrechts-University of Kiel and University Medical Center Schleswig-Holstein, Kiel, Germany
| | - Elisa Rosati
- Institute of Immunology, Christian-Albrechts-University of Kiel and University Medical Center Schleswig-Holstein, Kiel, Germany
- Institute of Clinical Molecular Biology, Christian-Albrechts-University of Kiel and University Medical Center Schleswig-Holstein, Kiel, Germany
| | - Meghan Bialt DeCelie
- The Jill Roberts Institute for Research in Inflammatory Bowel Disease, Weill Cornell Medicine, Cornell University, New York, NY, USA
- Joan and Sanford I. Weill Department of Medicine, Weill Cornell Medicine, Cornell University, New York, NY, USA
- Department of Microbiology and Immunology, Weill Cornell Medicine, Cornell University, New York, NY, USA
| | - Laura Katharina Sievers
- Institute of Clinical Molecular Biology, Christian-Albrechts-University of Kiel and University Medical Center Schleswig-Holstein, Kiel, Germany
- Department of Internal Medicine I, University Medical Center Schleswig-Holstein, Kiel, Germany
| | - Florian Tran
- Institute of Clinical Molecular Biology, Christian-Albrechts-University of Kiel and University Medical Center Schleswig-Holstein, Kiel, Germany
- Department of Internal Medicine I, University Medical Center Schleswig-Holstein, Kiel, Germany
| | - Matthias Lessing
- Department of Internal Medicine I, University Medical Center Schleswig-Holstein, Kiel, Germany
| | - Arne Bergfeld
- Department of Internal Medicine I, University Medical Center Schleswig-Holstein, Kiel, Germany
| | - Sophia Hinz
- Institute of Clinical Molecular Biology, Christian-Albrechts-University of Kiel and University Medical Center Schleswig-Holstein, Kiel, Germany
- Department of Internal Medicine I, University Medical Center Schleswig-Holstein, Kiel, Germany
| | - Susanna Nikolaus
- Department of Internal Medicine I, University Medical Center Schleswig-Holstein, Kiel, Germany
| | - Julia Kümpers
- Department of Internal Medicine I, University Medical Center Schleswig-Holstein, Kiel, Germany
| | - Anna Matysiak
- Department of Internal Medicine I, University Medical Center Schleswig-Holstein, Kiel, Germany
| | - Philipp Hofmann
- Institute of Immunology, Christian-Albrechts-University of Kiel and University Medical Center Schleswig-Holstein, Kiel, Germany
- Institute of Clinical Molecular Biology, Christian-Albrechts-University of Kiel and University Medical Center Schleswig-Holstein, Kiel, Germany
| | - Carina Saggau
- Institute of Immunology, Christian-Albrechts-University of Kiel and University Medical Center Schleswig-Holstein, Kiel, Germany
| | - Stephan Schneiders
- Institute of Immunology, Christian-Albrechts-University of Kiel and University Medical Center Schleswig-Holstein, Kiel, Germany
- Institute of Clinical Molecular Biology, Christian-Albrechts-University of Kiel and University Medical Center Schleswig-Holstein, Kiel, Germany
| | - Ann-Kristin Kamps
- Institute of Immunology, Christian-Albrechts-University of Kiel and University Medical Center Schleswig-Holstein, Kiel, Germany
- Institute of Clinical Molecular Biology, Christian-Albrechts-University of Kiel and University Medical Center Schleswig-Holstein, Kiel, Germany
| | - Gunnar Jacobs
- Institute of Epidemiology, Christian-Albrechts-University of Kiel and popgen Biobank, University Medical Center Schleswig-Holstein, Kiel, Germany
| | - Wolfgang Lieb
- Institute of Epidemiology, Christian-Albrechts-University of Kiel and popgen Biobank, University Medical Center Schleswig-Holstein, Kiel, Germany
| | - Jochen Maul
- Gastroenterologie am Bayerischen Platz, Berlin, Germany
- Department of Gastroenterology, Rheumatology and Infectious Diseases, Charité-Universitätsmedizin Berlin, Humboldt-Universität zu Berlin and Berlin Institute of Health, Berlin, Germany
| | - Britta Siegmund
- Department of Gastroenterology, Rheumatology and Infectious Diseases, Charité-Universitätsmedizin Berlin, Humboldt-Universität zu Berlin and Berlin Institute of Health, Berlin, Germany
| | | | | | - Hans-Heinrich Oberg
- Institute of Immunology, Christian-Albrechts-University of Kiel and University Medical Center Schleswig-Holstein, Kiel, Germany
| | - Daniela Wesch
- Institute of Immunology, Christian-Albrechts-University of Kiel and University Medical Center Schleswig-Holstein, Kiel, Germany
| | - Stefan Bereswill
- Institute of Microbiology, Infectious Diseases and Immunology, Charité-Universitätsmedizin Berlin, Humboldt-Universität zu Berlin and Berlin Institute of Health, Berlin, Germany
| | - Markus M Heimesaat
- Institute of Microbiology, Infectious Diseases and Immunology, Charité-Universitätsmedizin Berlin, Humboldt-Universität zu Berlin and Berlin Institute of Health, Berlin, Germany
| | - Jan Rupp
- Department of Infectious Diseases and Microbiology, University of Lübeck, Lübeck, Germany
| | - Olaf Kniemeyer
- Department of Molecular and Applied Microbiology, Leibniz Institute for Natural Product Research and Infection Biology-Hans Knoell Institute, Jena, Germany
| | - Axel A Brakhage
- Department of Molecular and Applied Microbiology, Leibniz Institute for Natural Product Research and Infection Biology-Hans Knoell Institute, Jena, Germany
- Friedrich Schiller Universität, Jena, Germany
| | - Sascha Brunke
- Institute of Microbiology, Department of Microbial Pathogenicity Mechanisms, Leibniz Institute for Natural Product Research and Infection Biology-Hans Knoell Institute, Jena, Germany
| | - Bernhard Hube
- Friedrich Schiller Universität, Jena, Germany
- Institute of Microbiology, Department of Microbial Pathogenicity Mechanisms, Leibniz Institute for Natural Product Research and Infection Biology-Hans Knoell Institute, Jena, Germany
| | - Konrad Aden
- Institute of Clinical Molecular Biology, Christian-Albrechts-University of Kiel and University Medical Center Schleswig-Holstein, Kiel, Germany
- Department of Internal Medicine I, University Medical Center Schleswig-Holstein, Kiel, Germany
| | - Andre Franke
- Institute of Clinical Molecular Biology, Christian-Albrechts-University of Kiel and University Medical Center Schleswig-Holstein, Kiel, Germany
| | - Iliyan D Iliev
- The Jill Roberts Institute for Research in Inflammatory Bowel Disease, Weill Cornell Medicine, Cornell University, New York, NY, USA
- Joan and Sanford I. Weill Department of Medicine, Weill Cornell Medicine, Cornell University, New York, NY, USA
- Department of Microbiology and Immunology, Weill Cornell Medicine, Cornell University, New York, NY, USA
| | - Alexander Scheffold
- Institute of Immunology, Christian-Albrechts-University of Kiel and University Medical Center Schleswig-Holstein, Kiel, Germany
| | - Stefan Schreiber
- Institute of Clinical Molecular Biology, Christian-Albrechts-University of Kiel and University Medical Center Schleswig-Holstein, Kiel, Germany
- Department of Internal Medicine I, University Medical Center Schleswig-Holstein, Kiel, Germany
| | - Petra Bacher
- Institute of Immunology, Christian-Albrechts-University of Kiel and University Medical Center Schleswig-Holstein, Kiel, Germany.
- Institute of Clinical Molecular Biology, Christian-Albrechts-University of Kiel and University Medical Center Schleswig-Holstein, Kiel, Germany.
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26
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Goswami A, Kumar M, Ullah S, Gore MM. De novo design of anti-variant COVID-19 vaccine. Biol Methods Protoc 2023; 8:bpad021. [PMID: 37854896 PMCID: PMC10580973 DOI: 10.1093/biomethods/bpad021] [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: 07/28/2023] [Revised: 09/07/2023] [Accepted: 09/21/2023] [Indexed: 10/20/2023] Open
Abstract
Recent studies highlight the effectiveness of hybrid Severe Acute Respiratory Syndrome-Coronavirus-2 (SARS-CoV-2) vaccines combining wild-type nucleocapsid and Spike proteins. We have further enhanced this strategy by incorporating delta and omicron variants' spike protein mutations. Both delta and omicron mark the shifts in viral transmissibility and severity in unvaccinated and vaccinated patients. So their mutations are highly crucial for future viral variants also. Omicron is particularly adept at immune evasion by mutating spike epitopes. The rapid adaptations of Omicron and sub-variants to spike-based vaccines and simultaneous transmissibility underline the urgency for new vaccines in the continuous battle against SARS-CoV-2. Therefore, we have added three persistent T-cell-stimulating nucleocapsid peptides similar to homologous sequences from seasonal Human Coronaviruses (HuCoV) and an envelope peptide that elicits a strong T-cell immune response. These peptides are clustered in the hybrid spike's cytoplasmic region with non-immunogenic linkers, enabling systematic arrangement. AlphaFold (Artificial intelligence-based model building) analysis suggests omitting the transmembrane domain enhances these cytoplasmic epitopes' folding efficiency which can ensure persistent immunity for CD4+ structural epitopes. Further molecular dynamics simulations validate the compact conformation of the modeled structures and a flexible C-terminus region. Overall, the structures show stability and less conformational fluctuation throughout the simulation. Also, the AlphaFold predicted structural epitopes maintained their folds during simulation to ensure the specificity of CD4+ T-cell response after vaccination. Our proposed approach may provide options for incorporating diverse anti-viral T-cell peptides, similar to HuCoV, into linker regions. This versatility can be promising to address outbreaks and challenges posed by various viruses for effective management in this era of innovative vaccines.
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Affiliation(s)
- Arpita Goswami
- Kshamalab, Leo’s Research Services and Suppliers, Mysuru 570016, India
| | - Madan Kumar
- Department of Chemistry-BMC Biochemistry, University of Uppsala, Uppsala 75237, Sweden
| | - Samee Ullah
- National Center for Bioinformatics (NCB), Islamabad 45320, Pakistan
| | - Milind M Gore
- 5/1B, Krutika Co-Op Housing Society, Kothrud, Pune 411039, India
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27
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Beitari S, Duque D, Bavananthasivam J, Hewitt M, Sandhu JK, Hadžisejdić I, Tran A. Cross protection to SARS-CoV-2 variants in hamsters with naturally-acquired immunity. Virol J 2023; 20:167. [PMID: 37507719 PMCID: PMC10386765 DOI: 10.1186/s12985-023-02136-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2023] [Accepted: 07/21/2023] [Indexed: 07/30/2023] Open
Abstract
Since SARS-CoV-2 was first reported in late 2019, multiple variations of the original virus have emerged. Each variant harbors accumulations of mutations, particularly within the spike glycoprotein, that are associated with increased viral transmissibility and escape immunity. The different mutations in the spike protein of different variants shape the subsequent antibody and T cell responses, such that exposure to different spike proteins can result in reduced or enhanced responses to heterologous variants further down the line. Globally, people have been exposed and re-exposed to multiple variations of the Ancestral strain, including the five variants of concerns. Studies have shown that the protective immune response of an individual is influenced by which strain or combination of strains they are exposed to. The initial exposure to a specific strain may also shape their subsequent immune patterns and response to later infections with a heterologous virus. Most immunological observations were carried out early during the pandemic when the Ancestral strain was circulating. However, SARS-CoV-2 variants exhibit varying patterns of disease severity, waning immunity, immune evasion and sensitivity to therapeutics. Here we investigated the cross-protection in hamsters previously infected with a variant of concern (VOC) and subsequently re-infected with a heterologous variant. We also determined if cross-protection and immunity were dependent on the specific virus to which the hamster was first exposed. We further profiled the host cytokine response induced by each SARS-CoV-2 variants as well as subsequent to re-infection. A comparative analysis of the three VOCs revealed that Alpha variant was the most pathogenic VOC to emerge. We showed that naturally acquired immunity protected hamsters from subsequent re-infection with heterologous SARS-CoV-2 variant, regardless which variant the animal was first exposed to. Our study supports observations that heterologous infection of different SARS-CoV-2 variants do not exacerbate disease in subsequent re-infections. The continual emergence of new SARS-CoV-2 variants mandates a better understanding of cross-protection and immune imprinting in infected individuals. Such information is essential to guide vaccine strategy and public policy to emerging SARS-CoV-2 VOCs and future novel pandemic coronaviruses.
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Affiliation(s)
- Saina Beitari
- Infectious Diseases, Human Health Therapeutics Research Centre, National Research Council Canada, ON, Ottawa, Canada
| | - Diana Duque
- Infectious Diseases, Human Health Therapeutics Research Centre, National Research Council Canada, ON, Ottawa, Canada
| | - Jegarubee Bavananthasivam
- Infectious Diseases, Human Health Therapeutics Research Centre, National Research Council Canada, ON, Ottawa, Canada
| | - Melissa Hewitt
- Preclinical Imaging, Human Health Therapeutics Research Centre, National Research Council Canada, ON, Ottawa, Canada
| | - Jagdeep K Sandhu
- Preclinical Imaging, Human Health Therapeutics Research Centre, National Research Council Canada, ON, Ottawa, Canada
| | - Ita Hadžisejdić
- Clinical Department of Pathology and Cytology, University of Rijeka, Rijeka, Croatia
| | - Anh Tran
- Infectious Diseases, Human Health Therapeutics Research Centre, National Research Council Canada, ON, Ottawa, Canada.
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28
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Blyakher MS, Fedorova IM, Tulskaya EA, Kapustin IV, Koteleva SI, Ramazanova ZK, Odintsov EE, Sandalova SV, Novikova LI, Aleshkin AV, Bochkareva SS. [Development and preservation of specific T-cell immunity after COVID-19 or vaccination against this infection]. Vopr Virusol 2023; 68:205-214. [PMID: 37436412 DOI: 10.36233/0507-4088-171] [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: 04/24/2023] [Indexed: 07/13/2023]
Abstract
Aim evaluation of specific T-cell immunity against SARS-CoV-2 in primary and secondary response to virus antigens by screening method. MATERIALS AND METHODS Patients were tested 11.5 months after COVID-19 and 610 months before and after vaccination. Healthy volunteers were screened before, 26 times during the vaccination course, and 68 months after revaccination with the Sputnik V vaccine. IgG and IgM antibodies to SARS-CoV-2 were detected by ELISA using commercially available kits (Vector-Best, Russia). Antigenic (AG) activation of T cells in the fraction of bloods mononuclear cells was assessed by IFN- production after AG stimulation in the wells of plates from ELISA kits intended for detection of antibodies against SARS-CoV-2. Data were processed by MS Excel and Statistica 10.0 software. RESULTS AG-specific T cells were detected in 88.5% of vaccinated healthy volunteers, half of whom were found to have T cells appearing earlier than antibodies to AG. After 6-8 months, the level of AG activation decreases. Following the revaccination, the level of AG activation of memory T cells in vitro increases within six months in 76.9100.0% of vaccinated subjects. On the contrary, after COVID-19, 86.7% of individuals had in their blood the AG-specific T cells with high activity at the time of vaccination. The activity of T cells recognizing the RBD domain of the SARS-CoV-2 S protein and the proportion of individuals who had these cells in their blood increased after the vaccination of reconvalescents. CONCLUSION T-cell immunity against SARS-CoV-2 antigens has been shown to persist for 6 months after illness. In vaccinated individuals without history of COVID-19, such duration of the preservation of AG-specific T cells in blood was only achieved after the revaccination.
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Affiliation(s)
- M S Blyakher
- G.N. Gabrichevsky Moscow Research Institute of Epidemiology and Microbiology
| | - I M Fedorova
- G.N. Gabrichevsky Moscow Research Institute of Epidemiology and Microbiology
| | - E A Tulskaya
- G.N. Gabrichevsky Moscow Research Institute of Epidemiology and Microbiology
| | - I V Kapustin
- G.N. Gabrichevsky Moscow Research Institute of Epidemiology and Microbiology
| | - S I Koteleva
- G.N. Gabrichevsky Moscow Research Institute of Epidemiology and Microbiology
| | - Z K Ramazanova
- G.N. Gabrichevsky Moscow Research Institute of Epidemiology and Microbiology
| | - E E Odintsov
- G.N. Gabrichevsky Moscow Research Institute of Epidemiology and Microbiology
| | - S V Sandalova
- G.N. Gabrichevsky Moscow Research Institute of Epidemiology and Microbiology
| | - L I Novikova
- G.N. Gabrichevsky Moscow Research Institute of Epidemiology and Microbiology
| | - A V Aleshkin
- G.N. Gabrichevsky Moscow Research Institute of Epidemiology and Microbiology
| | - S S Bochkareva
- G.N. Gabrichevsky Moscow Research Institute of Epidemiology and Microbiology
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29
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Becerra-Artiles A, Nanaware PP, Muneeruddin K, Weaver GC, Shaffer SA, Calvo-Calle JM, Stern LJ. Immunopeptidome profiling of human coronavirus OC43-infected cells identifies CD4 T-cell epitopes specific to seasonal coronaviruses or cross-reactive with SARS-CoV-2. PLoS Pathog 2023; 19:e1011032. [PMID: 37498934 PMCID: PMC10409285 DOI: 10.1371/journal.ppat.1011032] [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: 11/30/2022] [Revised: 08/08/2023] [Accepted: 07/06/2023] [Indexed: 07/29/2023] Open
Abstract
Seasonal "common-cold" human coronaviruses are widely spread throughout the world and are mainly associated with mild upper respiratory tract infections. The emergence of highly pathogenic coronaviruses MERS-CoV, SARS-CoV, and most recently SARS-CoV-2 has prompted increased attention to coronavirus biology and immunopathology, but the T-cell response to seasonal coronaviruses remains largely uncharacterized. Here we report the repertoire of viral peptides that are naturally processed and presented upon infection of a model cell line with seasonal coronavirus OC43. We identified MHC-bound peptides derived from each of the viral structural proteins (spike, nucleoprotein, hemagglutinin-esterase, membrane, and envelope) as well as non-structural proteins nsp3, nsp5, nsp6, and nsp12. Eighty MHC-II bound peptides corresponding to 14 distinct OC43-derived epitopes were identified, including many at very high abundance within the overall MHC-II peptidome. Fewer and less abundant MHC-I bound OC43-derived peptides were observed, possibly due to MHC-I downregulation induced by OC43 infection. The MHC-II peptides elicited low-abundance recall T-cell responses in most donors tested. In vitro assays confirmed that the peptides were recognized by CD4+ T cells and identified the presenting HLA alleles. T-cell responses cross-reactive between OC43, SARS-CoV-2, and the other seasonal coronaviruses were confirmed in samples of peripheral blood and peptide-expanded T-cell lines. Among the validated epitopes, spike protein S903-917 presented by DPA1*01:03/DPB1*04:01 and S1085-1099 presented by DRB1*15:01 shared substantial homology to other human coronaviruses, including SARS-CoV-2, and were targeted by cross-reactive CD4 T cells. Nucleoprotein N54-68 and hemagglutinin-esterase HE128-142 presented by DRB1*15:01 and HE259-273 presented by DPA1*01:03/DPB1*04:01 are immunodominant epitopes with low coronavirus homology that are not cross-reactive with SARS-CoV-2. Overall, the set of naturally processed and presented OC43 epitopes comprise both OC43-specific and human coronavirus cross-reactive epitopes, which can be used to follow CD4 T-cell cross-reactivity after infection or vaccination, and to guide selection of epitopes for inclusion in pan-coronavirus vaccines.
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Affiliation(s)
- Aniuska Becerra-Artiles
- Department of Pathology, Department of Biochemistry and Molecular Biotechnology, UMass Chan Medical School, Worcester Massachusetts, United States of America
| | - Padma P. Nanaware
- Department of Pathology, Department of Biochemistry and Molecular Biotechnology, UMass Chan Medical School, Worcester Massachusetts, United States of America
| | - Khaja Muneeruddin
- Mass Spectrometry Facility, UMass Chan Medical School, Shrewsbury Massachusetts, United States of America
| | - Grant C. Weaver
- Department of Pathology, Department of Biochemistry and Molecular Biotechnology, UMass Chan Medical School, Worcester Massachusetts, United States of America
| | - Scott A. Shaffer
- Mass Spectrometry Facility, UMass Chan Medical School, Shrewsbury Massachusetts, United States of America
- Department of Biochemistry and Molecular Biotechnology, UMass Chan Medical School, Worcester, Massachusetts, United States of America
| | - J. Mauricio Calvo-Calle
- Department of Pathology, Department of Biochemistry and Molecular Biotechnology, UMass Chan Medical School, Worcester Massachusetts, United States of America
| | - Lawrence J. Stern
- Department of Pathology, Department of Biochemistry and Molecular Biotechnology, UMass Chan Medical School, Worcester Massachusetts, United States of America
- Department of Biochemistry and Molecular Biotechnology, UMass Chan Medical School, Worcester, Massachusetts, United States of America
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30
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Afroz S, Bartolo L, Su LF. Pre-existing T Cell Memory to Novel Pathogens. Immunohorizons 2023; 7:543-553. [PMID: 37436166 PMCID: PMC10587503 DOI: 10.4049/immunohorizons.2200003] [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: 05/12/2023] [Accepted: 06/22/2023] [Indexed: 07/13/2023] Open
Abstract
Immunological experiences lead to the development of specific T and B cell memory, which readies the host for a later pathogen rechallenge. Currently, immunological memory is best understood as a linear process whereby memory responses are generated by and directed against the same pathogen. However, numerous studies have identified memory cells that target pathogens in unexposed individuals. How "pre-existing memory" forms and impacts the outcome of infection remains unclear. In this review, we discuss differences in the composition of baseline T cell repertoire in mice and humans, factors that influence pre-existing immune states, and recent literature on their functional significance. We summarize current knowledge on the roles of pre-existing T cells in homeostasis and perturbation and their impacts on health and disease.
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Affiliation(s)
- Sumbul Afroz
- Division of Rheumatology, Department of Medicine, Perelman School of Medicine, Institute for Immunology, University of Pennsylvania, Philadelphia, PA
| | - Laurent Bartolo
- Division of Rheumatology, Department of Medicine, Perelman School of Medicine, Institute for Immunology, University of Pennsylvania, Philadelphia, PA
| | - Laura F. Su
- Division of Rheumatology, Department of Medicine, Perelman School of Medicine, Institute for Immunology, University of Pennsylvania, Philadelphia, PA
- Corporal Michael J. Crescenz VA Medical Center, Philadelphia, PA
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31
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Tarke A, Zhang Y, Methot N, Narowski TM, Phillips E, Mallal S, Frazier A, Filaci G, Weiskopf D, Dan JM, Premkumar L, Scheuermann RH, Sette A, Grifoni A. Targets and cross-reactivity of human T cell recognition of common cold coronaviruses. Cell Rep Med 2023; 4:101088. [PMID: 37295422 PMCID: PMC10242702 DOI: 10.1016/j.xcrm.2023.101088] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2022] [Revised: 03/17/2023] [Accepted: 05/24/2023] [Indexed: 06/12/2023]
Abstract
The coronavirus (CoV) family includes several viruses infecting humans, highlighting the importance of exploring pan-CoV vaccine strategies to provide broad adaptive immune protection. We analyze T cell reactivity against representative Alpha (NL63) and Beta (OC43) common cold CoVs (CCCs) in pre-pandemic samples. S, N, M, and nsp3 antigens are immunodominant, as shown for severe acute respiratory syndrome 2 (SARS2), while nsp2 and nsp12 are Alpha or Beta specific. We further identify 78 OC43- and 87 NL63-specific epitopes, and, for a subset of those, we assess the T cell capability to cross-recognize sequences from representative viruses belonging to AlphaCoV, sarbecoCoV, and Beta-non-sarbecoCoV groups. We find T cell cross-reactivity within the Alpha and Beta groups, in 89% of the instances associated with sequence conservation >67%. However, despite conservation, limited cross-reactivity is observed for sarbecoCoV, indicating that previous CoV exposure is a contributing factor in determining cross-reactivity. Overall, these results provide critical insights in developing future pan-CoV vaccines.
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Affiliation(s)
- Alison Tarke
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology (LJI), La Jolla, CA 92037, USA; Department of Experimental Medicine and Center of Excellence for Biomedical Research (CEBR), University of Genoa, 16132 Genoa, Italy
| | - Yun Zhang
- J. Craig Venter Institute, La Jolla, CA 92037, USA
| | - Nils Methot
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology (LJI), La Jolla, CA 92037, USA
| | - Tara M Narowski
- Department of Microbiology and Immunology, University of North Carolina School of Medicine, Chapel Hill, NC 27599-7290, USA
| | - Elizabeth Phillips
- Institute for Immunology and Infectious Diseases, Murdoch University, Perth, WA 6150, Australia
| | - Simon Mallal
- Institute for Immunology and Infectious Diseases, Murdoch University, Perth, WA 6150, Australia
| | - April Frazier
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology (LJI), La Jolla, CA 92037, USA
| | - Gilberto Filaci
- Center of Excellence for Biomedical Research, Department of Internal Medicine, University of Genoa, 16132 Genoa, Italy; Biotherapy Unit, IRCCS Ospedale Policlinico San Martino, 16132 Genoa, Italy
| | - Daniela Weiskopf
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology (LJI), La Jolla, CA 92037, USA
| | - Jennifer M Dan
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology (LJI), La Jolla, CA 92037, USA; Department of Medicine, Division of Infectious Diseases and Global Public Health, University of California, San Diego (UCSD), La Jolla, CA 92037, USA
| | - Lakshmanane Premkumar
- Department of Microbiology and Immunology, University of North Carolina School of Medicine, Chapel Hill, NC 27599-7290, USA
| | - Richard H Scheuermann
- J. Craig Venter Institute, La Jolla, CA 92037, USA; Department of Pathology, University of California, San Diego (UCSD), La Jolla, CA 92037, USA.
| | - Alessandro Sette
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology (LJI), La Jolla, CA 92037, USA; Department of Medicine, Division of Infectious Diseases and Global Public Health, University of California, San Diego (UCSD), La Jolla, CA 92037, USA.
| | - Alba Grifoni
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology (LJI), La Jolla, CA 92037, USA.
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Paniskaki K, Konik MJ, Anft M, Heidecke H, Meister TL, Pfaender S, Krawczyk A, Zettler M, Jäger J, Gaeckler A, Dolff S, Westhoff TH, Rohn H, Stervbo U, Scheibenbogen C, Witzke O, Babel N. Low avidity circulating SARS-CoV-2 reactive CD8+ T cells with proinflammatory TEMRA phenotype are associated with post-acute sequelae of COVID-19. Front Microbiol 2023; 14:1196721. [PMID: 37333646 PMCID: PMC10272838 DOI: 10.3389/fmicb.2023.1196721] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2023] [Accepted: 05/16/2023] [Indexed: 06/20/2023] Open
Abstract
The role of adaptive SARS-CoV-2 specific immunity in post-acute sequelae of COVID-19 (PASC) is not well explored, although a growing population of convalescent COVID-19 patients with manifestation of PASC is observed. We analyzed the SARS-CoV-2-specific immune response, via pseudovirus neutralizing assay and multiparametric flow cytometry in 40 post-acute sequelae of COVID-19 patients with non-specific PASC manifestation and 15 COVID-19 convalescent healthy donors. Although frequencies of SARS-CoV-2-reactive CD4+ T cells were similar between the studied cohorts, a stronger SARS-CoV-2 reactive CD8+ T cell response, characterized by IFNγ production and predominant TEMRA phenotype but low functional TCR avidity was detected in PASC patients compared to controls. Of interest, high avidity SARS-CoV-2-reactive CD4+ and CD8+ T cells were comparable between the groups demonstrating sufficient cellular antiviral response in PASC. In line with the cellular immunity, neutralizing capacity in PASC patients was not inferior compared to controls. In conclusion, our data suggest that PASC may be driven by an inflammatory response triggered by an expanded population of low avidity SARS-CoV-2 reactive pro-inflammatory CD8+ T cells. These pro-inflammatory T cells with TEMRA phenotype are known to be activated by a low or even without TCR stimulation and lead to a tissue damage. Further studies including animal models are required for a better understanding of underlying immunopathogensis. Summary: A CD8+ driven persistent inflammatory response triggered by SARS-CoV-2 may be responsible for the observed sequelae in PASC patients.
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Affiliation(s)
- Krystallenia Paniskaki
- Department of Infectious Diseases, West German Centre of Infectious Diseases, University Hospital Essen, University Duisburg-Essen, Essen, Germany
- Center for Translational Medicine and Immune Diagnostics Laboratory, Medical Department I, Marien Hospital Herne, University Hospital of the Ruhr-University Bochum, Bochum, Germany
| | - Margarethe J. Konik
- Department of Infectious Diseases, West German Centre of Infectious Diseases, University Hospital Essen, University Duisburg-Essen, Essen, Germany
| | - Moritz Anft
- Center for Translational Medicine and Immune Diagnostics Laboratory, Medical Department I, Marien Hospital Herne, University Hospital of the Ruhr-University Bochum, Bochum, Germany
| | | | - Toni L. Meister
- Department of Molecular and Medical Virology, Ruhr-University Bochum, Bochum, Germany
| | - Stephanie Pfaender
- Department of Molecular and Medical Virology, Ruhr-University Bochum, Bochum, Germany
| | - Adalbert Krawczyk
- Department of Infectious Diseases, West German Centre of Infectious Diseases, University Hospital Essen, University Duisburg-Essen, Essen, Germany
| | - Markus Zettler
- Department of Infectious Diseases, West German Centre of Infectious Diseases, University Hospital Essen, University Duisburg-Essen, Essen, Germany
| | - Jasmin Jäger
- Department of Infectious Diseases, West German Centre of Infectious Diseases, University Hospital Essen, University Duisburg-Essen, Essen, Germany
- Center for Translational Medicine and Immune Diagnostics Laboratory, Medical Department I, Marien Hospital Herne, University Hospital of the Ruhr-University Bochum, Bochum, Germany
| | - Anja Gaeckler
- Department of Nephrology, University Hospital Essen, University Duisburg-Essen, Essen, Germany
| | - Sebastian Dolff
- Department of Infectious Diseases, West German Centre of Infectious Diseases, University Hospital Essen, University Duisburg-Essen, Essen, Germany
| | - Timm H. Westhoff
- Medical Department I, Marien Hospital Herne, University Hospital of the Ruhr-University Bochum, Herne, Germany
| | - Hana Rohn
- Department of Infectious Diseases, West German Centre of Infectious Diseases, University Hospital Essen, University Duisburg-Essen, Essen, Germany
| | - Ulrik Stervbo
- Center for Translational Medicine and Immune Diagnostics Laboratory, Medical Department I, Marien Hospital Herne, University Hospital of the Ruhr-University Bochum, Bochum, Germany
| | - Carmen Scheibenbogen
- Institute for Medical Immunology, Charité-Universitätsmedizin Berlin, Campus Virchow, Berlin, Germany
| | - Oliver Witzke
- Department of Infectious Diseases, West German Centre of Infectious Diseases, University Hospital Essen, University Duisburg-Essen, Essen, Germany
| | - Nina Babel
- Center for Translational Medicine and Immune Diagnostics Laboratory, Medical Department I, Marien Hospital Herne, University Hospital of the Ruhr-University Bochum, Bochum, Germany
- Berlin Institute of Health at Charité – University Clinic Berlin, BIH Center for Regenerative Therapies (BCRT) Berlin, Berlin, Germany
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Gressier E, Schulte-Schrepping J, Petrov L, Brumhard S, Stubbemann P, Hiller A, Obermayer B, Spitzer J, Kostevc T, Whitney PG, Bachem A, Odainic A, van de Sandt C, Nguyen THO, Ashhurst T, Wilson K, Oates CVL, Gearing LJ, Meischel T, Hochheiser K, Greyer M, Clarke M, Kreutzenbeck M, Gabriel SS, Kastenmüller W, Kurts C, Londrigan SL, Kallies A, Kedzierska K, Hertzog PJ, Latz E, Chen YCE, Radford KJ, Chopin M, Schroeder J, Kurth F, Gebhardt T, Sander LE, Sawitzki B, Schultze JL, Schmidt SV, Bedoui S. CD4 + T cell calibration of antigen-presenting cells optimizes antiviral CD8 + T cell immunity. Nat Immunol 2023; 24:979-990. [PMID: 37188942 DOI: 10.1038/s41590-023-01517-x] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2021] [Accepted: 04/13/2023] [Indexed: 05/17/2023]
Abstract
Antiviral CD8+ T cell immunity depends on the integration of various contextual cues, but how antigen-presenting cells (APCs) consolidate these signals for decoding by T cells remains unclear. Here, we describe gradual interferon-α/interferon-β (IFNα/β)-induced transcriptional adaptations that endow APCs with the capacity to rapidly activate the transcriptional regulators p65, IRF1 and FOS after CD4+ T cell-mediated CD40 stimulation. While these responses operate through broadly used signaling components, they induce a unique set of co-stimulatory molecules and soluble mediators that cannot be elicited by IFNα/β or CD40 alone. These responses are critical for the acquisition of antiviral CD8+ T cell effector function, and their activity in APCs from individuals infected with severe acute respiratory syndrome coronavirus 2 correlates with milder disease. These observations uncover a sequential integration process whereby APCs rely on CD4+ T cells to select the innate circuits that guide antiviral CD8+ T cell responses.
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Affiliation(s)
- Elise Gressier
- Department of Microbiology and Immunology at the Doherty Institute for Infection and Immunity, The University of Melbourne, Melbourne, Victoria, Australia.
| | - Jonas Schulte-Schrepping
- Life and Medical Sciences (LIMES) Institute, University of Bonn, Bonn, Germany
- Systems Medicine, Deutsches Zentrum für Neurodegenerative Erkrankungen (DZNE), Bonn, Germany
| | - Lev Petrov
- Translational Immunology, Berlin Institute of Health (BIH) & Charité University Medicine, Berlin, Germany
| | - Sophia Brumhard
- Infectious Diseases and Respiratory Medicine, Charité, Universitätsmedizin Berlin, Berlin, Germany
| | - Paula Stubbemann
- Infectious Diseases and Respiratory Medicine, Charité, Universitätsmedizin Berlin, Berlin, Germany
| | - Anna Hiller
- Infectious Diseases and Respiratory Medicine, Charité, Universitätsmedizin Berlin, Berlin, Germany
| | - Benedikt Obermayer
- Berlin Institute of Health at Charité, Universitätsmedizin Berlin, Core Unit Bioinformatics, Berlin, Germany
| | - Jasper Spitzer
- Institute of Innate Immunity, University of Bonn, Bonn, Germany
| | - Tomislav Kostevc
- Translational Immunology, Berlin Institute of Health (BIH) & Charité University Medicine, Berlin, Germany
| | - Paul G Whitney
- Department of Microbiology and Immunology at the Doherty Institute for Infection and Immunity, The University of Melbourne, Melbourne, Victoria, Australia
| | - Annabell Bachem
- Department of Microbiology and Immunology at the Doherty Institute for Infection and Immunity, The University of Melbourne, Melbourne, Victoria, Australia
| | - Alexandru Odainic
- Department of Microbiology and Immunology at the Doherty Institute for Infection and Immunity, The University of Melbourne, Melbourne, Victoria, Australia
- Institute of Innate Immunity, University of Bonn, Bonn, Germany
| | - Carolien van de Sandt
- Department of Microbiology and Immunology at the Doherty Institute for Infection and Immunity, The University of Melbourne, Melbourne, Victoria, Australia
| | - Thi H O Nguyen
- Department of Microbiology and Immunology at the Doherty Institute for Infection and Immunity, The University of Melbourne, Melbourne, Victoria, Australia
| | - Thomas Ashhurst
- Sydney Cytometry Core Research Facility, Charles Perkins Centre, Centenary Institute and University of Sydney, Sydney, New South Wales, Australia
| | - Kayla Wilson
- Department of Microbiology and Immunology at the Doherty Institute for Infection and Immunity, The University of Melbourne, Melbourne, Victoria, Australia
| | - Clare V L Oates
- Department of Microbiology and Immunology at the Doherty Institute for Infection and Immunity, The University of Melbourne, Melbourne, Victoria, Australia
| | - Linden J Gearing
- Centre for Innate Immunity and Infectious Diseases, Hudson Institute of Medical Research, Clayton, Victoria, Australia
- Department of Molecular and Translational Science, Monash University, Clayton, Victoria, Australia
| | - Tina Meischel
- Department of Microbiology and Immunology at the Doherty Institute for Infection and Immunity, The University of Melbourne, Melbourne, Victoria, Australia
| | - Katharina Hochheiser
- Department of Microbiology and Immunology at the Doherty Institute for Infection and Immunity, The University of Melbourne, Melbourne, Victoria, Australia
| | - Marie Greyer
- Department of Microbiology and Immunology at the Doherty Institute for Infection and Immunity, The University of Melbourne, Melbourne, Victoria, Australia
| | - Michele Clarke
- Department of Microbiology and Immunology at the Doherty Institute for Infection and Immunity, The University of Melbourne, Melbourne, Victoria, Australia
| | | | - Sarah S Gabriel
- Department of Microbiology and Immunology at the Doherty Institute for Infection and Immunity, The University of Melbourne, Melbourne, Victoria, Australia
| | - Wolfgang Kastenmüller
- Würzburg Institute of Systems Immunology, Max Planck Research Group, Julius-Maximilians-Universität Würzburg, Würzburg, Germany
| | - Christian Kurts
- Institute of Experimental Immunology, University of Bonn, Bonn, Germany
| | - Sarah L Londrigan
- Department of Microbiology and Immunology at the Doherty Institute for Infection and Immunity, The University of Melbourne, Melbourne, Victoria, Australia
| | - Axel Kallies
- Department of Microbiology and Immunology at the Doherty Institute for Infection and Immunity, The University of Melbourne, Melbourne, Victoria, Australia
| | - Katherine Kedzierska
- Department of Microbiology and Immunology at the Doherty Institute for Infection and Immunity, The University of Melbourne, Melbourne, Victoria, Australia
| | - Paul J Hertzog
- Centre for Innate Immunity and Infectious Diseases, Hudson Institute of Medical Research, Clayton, Victoria, Australia
- Department of Molecular and Translational Science, Monash University, Clayton, Victoria, Australia
| | - Eicke Latz
- Institute of Innate Immunity, University of Bonn, Bonn, Germany
| | - Yu-Chen E Chen
- Mater Research Institute, The University of Queensland, Brisbane, Queensland, Australia
| | - Kristen J Radford
- Mater Research Institute, The University of Queensland, Brisbane, Queensland, Australia
| | - Michael Chopin
- Department of Biochemistry, Biomedicine Discovery Institute, Monash University, Clayton, Victoria, Australia
| | - Jan Schroeder
- Department of Microbiology and Immunology at the Doherty Institute for Infection and Immunity, The University of Melbourne, Melbourne, Victoria, Australia
| | - Florian Kurth
- Infectious Diseases and Respiratory Medicine, Charité, Universitätsmedizin Berlin, Berlin, Germany
| | - Thomas Gebhardt
- Department of Microbiology and Immunology at the Doherty Institute for Infection and Immunity, The University of Melbourne, Melbourne, Victoria, Australia
| | - Leif E Sander
- Infectious Diseases and Respiratory Medicine, Charité, Universitätsmedizin Berlin, Berlin, Germany
| | - Birgit Sawitzki
- Translational Immunology, Berlin Institute of Health (BIH) & Charité University Medicine, Berlin, Germany
| | - Joachim L Schultze
- Life and Medical Sciences (LIMES) Institute, University of Bonn, Bonn, Germany
- Systems Medicine, Deutsches Zentrum für Neurodegenerative Erkrankungen (DZNE), Bonn, Germany
- PRECISE Platform for Single Cell Genomics and Epigenomics, DZNE and University of Bonn, Bonn, Germany
| | | | - Sammy Bedoui
- Department of Microbiology and Immunology at the Doherty Institute for Infection and Immunity, The University of Melbourne, Melbourne, Victoria, Australia.
- Institute of Experimental Immunology, University of Bonn, Bonn, Germany.
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Postovskaya A, Vujkovic A, de Block T, van Petersen L, van Frankenhuijsen M, Brosius I, Bottieau E, Van Dijck C, Theunissen C, van Ierssel SH, Vlieghe E, Bartholomeus E, Mullan K, Adriaensen W, Vanham G, Ogunjimi B, Laukens K, Vercauteren K, Meysman P. Leveraging T-cell receptor - epitope recognition models to disentangle unique and cross-reactive T-cell response to SARS-CoV-2 during COVID-19 progression/resolution. Front Immunol 2023; 14:1130876. [PMID: 37325653 PMCID: PMC10264683 DOI: 10.3389/fimmu.2023.1130876] [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: 12/23/2022] [Accepted: 05/15/2023] [Indexed: 06/17/2023] Open
Abstract
Despite the general agreement on the significance of T cells during SARS-CoV-2 infection, the clinical impact of specific and cross-reactive T-cell responses remains uncertain. Understanding this aspect could provide insights for adjusting vaccines and maintaining robust long-term protection against continuously emerging variants. To characterize CD8+ T-cell response to SARS-CoV-2 epitopes unique to the virus (SC2-unique) or shared with other coronaviruses (CoV-common), we trained a large number of T-cell receptor (TCR) - epitope recognition models for MHC-I-presented SARS-CoV-2 epitopes from publicly available data. These models were then applied to longitudinal CD8+ TCR repertoires from critical and non-critical COVID-19 patients. In spite of comparable initial CoV-common TCR repertoire depth and CD8+ T-cell depletion, the temporal dynamics of SC2-unique TCRs differed depending on the disease severity. Specifically, while non-critical patients demonstrated a large and diverse SC2-unique TCR repertoire by the second week of the disease, critical patients did not. Furthermore, only non-critical patients exhibited redundancy in the CD8+ T-cell response to both groups of epitopes, SC2-unique and CoV-common. These findings indicate a valuable contribution of the SC2-unique CD8+ TCR repertoires. Therefore, a combination of specific and cross-reactive CD8+ T-cell responses may offer a stronger clinical advantage. Besides tracking the specific and cross-reactive SARS-CoV-2 CD8+ T cells in any TCR repertoire, our analytical framework can be expanded to more epitopes and assist in the assessment and monitoring of CD8+ T-cell response to other infections.
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Affiliation(s)
- Anna Postovskaya
- Adrem Data Lab, Department of Computer Science, University of Antwerp, Antwerp, Belgium
- Biomedical Informatics Research Network Antwerp (BIOMINA), University of Antwerp, Antwerp, Belgium
- Antwerp Unit for Data Analysis and Computation in Immunology and Sequencing (AUDACIS), University of Antwerp, Antwerp, Belgium
- Clinical Virology Unit, Department of Clinical Sciences, Institute of Tropical Medicine, Antwerp, Belgium
| | - Alexandra Vujkovic
- Adrem Data Lab, Department of Computer Science, University of Antwerp, Antwerp, Belgium
- Antwerp Unit for Data Analysis and Computation in Immunology and Sequencing (AUDACIS), University of Antwerp, Antwerp, Belgium
- Clinical Virology Unit, Department of Clinical Sciences, Institute of Tropical Medicine, Antwerp, Belgium
| | - Tessa de Block
- Clinical Virology Unit, Department of Clinical Sciences, Institute of Tropical Medicine, Antwerp, Belgium
| | - Lida van Petersen
- Department of Clinical Sciences, Institute of Tropical Medicine, Antwerp, Belgium
| | | | - Isabel Brosius
- Department of Clinical Sciences, Institute of Tropical Medicine, Antwerp, Belgium
| | - Emmanuel Bottieau
- Department of Clinical Sciences, Institute of Tropical Medicine, Antwerp, Belgium
| | - Christophe Van Dijck
- Department of Clinical Sciences, Institute of Tropical Medicine, Antwerp, Belgium
- Centre for Health Economics Research & Modeling Infectious Diseases (CHERMID), Vaccine & Infectious Disease Institute (VAXINFECTIO), University of Antwerp, Antwerp, Belgium
| | - Caroline Theunissen
- Department of Clinical Sciences, Institute of Tropical Medicine, Antwerp, Belgium
| | - Sabrina H. van Ierssel
- Department of General Internal Medicine, Infectious Diseases and Tropical Medicine, Antwerp University Hospital, Edegem, Belgium
- Global Health Institute, University of Antwerp, Antwerp, Belgium
| | - Erika Vlieghe
- Department of General Internal Medicine, Infectious Diseases and Tropical Medicine, Antwerp University Hospital, Edegem, Belgium
| | - Esther Bartholomeus
- Antwerp Unit for Data Analysis and Computation in Immunology and Sequencing (AUDACIS), University of Antwerp, Antwerp, Belgium
- Department of Medical Genetics, University of Antwerp, Antwerp, Belgium
| | - Kerry Mullan
- Adrem Data Lab, Department of Computer Science, University of Antwerp, Antwerp, Belgium
- Biomedical Informatics Research Network Antwerp (BIOMINA), University of Antwerp, Antwerp, Belgium
- Antwerp Unit for Data Analysis and Computation in Immunology and Sequencing (AUDACIS), University of Antwerp, Antwerp, Belgium
| | - Wim Adriaensen
- Clinical Immunology Unit, Department of Clinical Sciences, Institute of Tropical Medicine, Antwerp, Belgium
| | - Guido Vanham
- Global Health Institute, University of Antwerp, Antwerp, Belgium
| | - Benson Ogunjimi
- Antwerp Unit for Data Analysis and Computation in Immunology and Sequencing (AUDACIS), University of Antwerp, Antwerp, Belgium
- Centre for Health Economics Research & Modeling Infectious Diseases (CHERMID), Vaccine & Infectious Disease Institute (VAXINFECTIO), University of Antwerp, Antwerp, Belgium
- Antwerp Center for Translational Immunology and Virology (ACTIV), Vaccine and Infectious Disease Institute, University of Antwerp, Antwerp, Belgium
- Department of Paediatrics, Antwerp University Hospital, Antwerp, Belgium
| | - Kris Laukens
- Adrem Data Lab, Department of Computer Science, University of Antwerp, Antwerp, Belgium
- Biomedical Informatics Research Network Antwerp (BIOMINA), University of Antwerp, Antwerp, Belgium
- Antwerp Unit for Data Analysis and Computation in Immunology and Sequencing (AUDACIS), University of Antwerp, Antwerp, Belgium
| | - Koen Vercauteren
- Clinical Virology Unit, Department of Clinical Sciences, Institute of Tropical Medicine, Antwerp, Belgium
| | - Pieter Meysman
- Adrem Data Lab, Department of Computer Science, University of Antwerp, Antwerp, Belgium
- Biomedical Informatics Research Network Antwerp (BIOMINA), University of Antwerp, Antwerp, Belgium
- Antwerp Unit for Data Analysis and Computation in Immunology and Sequencing (AUDACIS), University of Antwerp, Antwerp, Belgium
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Marcinkevics R, Silva PN, Hankele AK, Dörnte C, Kadelka S, Csik K, Godbersen S, Goga A, Hasenöhrl L, Hirschi P, Kabakci H, LaPierre MP, Mayrhofer J, Title AC, Shu X, Baiioud N, Bernal S, Dassisti L, Saenz-de-Juano MD, Schmidhauser M, Silvestrelli G, Ulbrich SZ, Ulbrich TJ, Wyss T, Stekhoven DJ, Al-Quaddoomi FS, Yu S, Binder M, Schultheiβ C, Zindel C, Kolling C, Goldhahn J, Seighalani BK, Zjablovskaja P, Hardung F, Schuster M, Richter A, Huang YJ, Lauer G, Baurmann H, Low JS, Vaqueirinho D, Jovic S, Piccoli L, Ciesek S, Vogt JE, Sallusto F, Stoffel M, Ulbrich SE. Machine learning analysis of humoral and cellular responses to SARS-CoV-2 infection in young adults. Front Immunol 2023; 14:1158905. [PMID: 37313411 PMCID: PMC10258347 DOI: 10.3389/fimmu.2023.1158905] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2023] [Accepted: 05/09/2023] [Indexed: 06/15/2023] Open
Abstract
The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) induces B and T cell responses, contributing to virus neutralization. In a cohort of 2,911 young adults, we identified 65 individuals who had an asymptomatic or mildly symptomatic SARS-CoV-2 infection and characterized their humoral and T cell responses to the Spike (S), Nucleocapsid (N) and Membrane (M) proteins. We found that previous infection induced CD4 T cells that vigorously responded to pools of peptides derived from the S and N proteins. By using statistical and machine learning models, we observed that the T cell response highly correlated with a compound titer of antibodies against the Receptor Binding Domain (RBD), S and N. However, while serum antibodies decayed over time, the cellular phenotype of these individuals remained stable over four months. Our computational analysis demonstrates that in young adults, asymptomatic and paucisymptomatic SARS-CoV-2 infections can induce robust and long-lasting CD4 T cell responses that exhibit slower decays than antibody titers. These observations imply that next-generation COVID-19 vaccines should be designed to induce stronger cellular responses to sustain the generation of potent neutralizing antibodies.
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Affiliation(s)
| | | | | | - Charlyn Dörnte
- Miltenyi Biotec B.V. & Co. KG, Bergisch Gladbach, Germany
| | - Sarah Kadelka
- Institute of Integrative Biology, ETH Zurich, Zurich, Switzerland
| | - Katharina Csik
- Institute of Molecular Health Sciences, ETH Zurich, Zurich, Switzerland
| | - Svenja Godbersen
- Institute of Molecular Health Sciences, ETH Zurich, Zurich, Switzerland
| | - Algera Goga
- Institute of Molecular Health Sciences, ETH Zurich, Zurich, Switzerland
| | - Lynn Hasenöhrl
- Institute of Molecular Health Sciences, ETH Zurich, Zurich, Switzerland
| | - Pascale Hirschi
- Institute of Molecular Health Sciences, ETH Zurich, Zurich, Switzerland
| | - Hasan Kabakci
- Institute of Molecular Health Sciences, ETH Zurich, Zurich, Switzerland
| | - Mary P. LaPierre
- Institute of Molecular Health Sciences, ETH Zurich, Zurich, Switzerland
| | - Johanna Mayrhofer
- Institute of Molecular Health Sciences, ETH Zurich, Zurich, Switzerland
| | | | - Xuan Shu
- Institute of Molecular Health Sciences, ETH Zurich, Zurich, Switzerland
| | - Nouell Baiioud
- Animal Physiology, Institute of Agricultural Sciences, ETH Zurich, Zurich, Switzerland
| | - Sandra Bernal
- Animal Physiology, Institute of Agricultural Sciences, ETH Zurich, Zurich, Switzerland
| | - Laura Dassisti
- Animal Physiology, Institute of Agricultural Sciences, ETH Zurich, Zurich, Switzerland
| | | | - Meret Schmidhauser
- Animal Physiology, Institute of Agricultural Sciences, ETH Zurich, Zurich, Switzerland
| | - Giulia Silvestrelli
- Animal Physiology, Institute of Agricultural Sciences, ETH Zurich, Zurich, Switzerland
| | - Simon Z. Ulbrich
- Animal Physiology, Institute of Agricultural Sciences, ETH Zurich, Zurich, Switzerland
| | - Thea J. Ulbrich
- Animal Physiology, Institute of Agricultural Sciences, ETH Zurich, Zurich, Switzerland
| | - Tamara Wyss
- Animal Physiology, Institute of Agricultural Sciences, ETH Zurich, Zurich, Switzerland
| | - Daniel J. Stekhoven
- NEXUS Personalized Health Technologies, Zurich & SIB Swiss Institute of Bioinformatics, ETH Zurich, Lausanne, Switzerland
| | - Faisal S. Al-Quaddoomi
- NEXUS Personalized Health Technologies, Zurich & SIB Swiss Institute of Bioinformatics, ETH Zurich, Lausanne, Switzerland
| | - Shuqing Yu
- NEXUS Personalized Health Technologies, Zurich & SIB Swiss Institute of Bioinformatics, ETH Zurich, Lausanne, Switzerland
| | - Mascha Binder
- Department of Internal Medicine IV, Oncology/Hematology, Martin-Luther-University Halle-Wittenberg, Halle (Saale), Germany
| | - Christoph Schultheiβ
- Department of Internal Medicine IV, Oncology/Hematology, Martin-Luther-University Halle-Wittenberg, Halle (Saale), Germany
| | - Claudia Zindel
- Department of Health Science, Translational Medicine, ETH Zurich, Zurich, Switzerland
| | - Christoph Kolling
- Department of Health Science, Translational Medicine, ETH Zurich, Zurich, Switzerland
| | - Jörg Goldhahn
- Department of Health Science, Translational Medicine, ETH Zurich, Zurich, Switzerland
| | | | | | - Frank Hardung
- Miltenyi Biotec B.V. & Co. KG, Bergisch Gladbach, Germany
| | - Marc Schuster
- Miltenyi Biotec B.V. & Co. KG, Bergisch Gladbach, Germany
| | - Anne Richter
- Miltenyi Biotec B.V. & Co. KG, Bergisch Gladbach, Germany
| | - Yi-Ju Huang
- Miltenyi Biotec B.V. & Co. KG, Bergisch Gladbach, Germany
| | - Gereon Lauer
- Miltenyi Biotec B.V. & Co. KG, Bergisch Gladbach, Germany
| | | | - Jun Siong Low
- Institute for Research in Biomedicine, Università della Svizzera Italiana, Bellinzona, Switzerland
| | - Daniela Vaqueirinho
- Institute for Research in Biomedicine, Università della Svizzera Italiana, Bellinzona, Switzerland
| | - Sandra Jovic
- Institute for Research in Biomedicine, Università della Svizzera Italiana, Bellinzona, Switzerland
| | - Luca Piccoli
- Humabs BioMed SA, a Subsidiary of Vir Biotechnology, Bellinzona, Switzerland
| | - Sandra Ciesek
- Institute of Medical Virology, Goethe University Frankfurt, Frankfurt am Main, Germany
| | - Julia E. Vogt
- Department of Computer Science, ETH Zurich, Zurich, Switzerland
| | - Federica Sallusto
- Institute for Research in Biomedicine, Università della Svizzera Italiana, Bellinzona, Switzerland
- Medical Immunology, Institute of Microbiology, ETH Zurich, Zurich, Switzerland
| | - Markus Stoffel
- Institute of Molecular Health Sciences, ETH Zurich, Zurich, Switzerland
- University Hospital Zurich, Zurich, Switzerland
| | - Susanne E. Ulbrich
- Animal Physiology, Institute of Agricultural Sciences, ETH Zurich, Zurich, Switzerland
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36
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Shen J, Fan J, Zhao Y, Jiang D, Niu Z, Zhang Z, Cao G. Innate and adaptive immunity to SARS-CoV-2 and predisposing factors. Front Immunol 2023; 14:1159326. [PMID: 37228604 PMCID: PMC10203583 DOI: 10.3389/fimmu.2023.1159326] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2023] [Accepted: 04/27/2023] [Indexed: 05/27/2023] Open
Abstract
The coronavirus disease 2019 (COVID-19) pandemic, caused by severe acute respiratory syndrome coronavirus (SARS-CoV-2), has affected all countries worldwide. Although some symptoms are relatively mild, others are still associated with severe and even fatal clinical outcomes. Innate and adaptive immunity are important for the control of SARS-CoV-2 infections, whereas a comprehensive characterization of the innate and adaptive immune response to COVID-19 is still lacking and the mechanisms underlying immune pathogenesis and host predisposing factors are still a matter of scientific debate. Here, the specific functions and kinetics of innate and adaptive immunity involved in SARS-CoV-2 recognition and resultant pathogenesis are discussed, as well as their immune memory for vaccinations, viral-mediated immune evasion, and the current and future immunotherapeutic agents. We also highlight host factors that contribute to infection, which may deepen the understanding of viral pathogenesis and help identify targeted therapies that attenuate severe disease and infection.
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Affiliation(s)
- Jiaying Shen
- Tongji University School of Medicine, Tongji University, Shanghai, China
| | - Junyan Fan
- Department of Epidemiology, Shanghai Key Laboratory of Medical Bioprotection, Key Laboratory of Biological Defense, Ministry of Education, Second Military Medical University, Shanghai, China
| | - Yue Zhao
- Department of Epidemiology, Shanghai Key Laboratory of Medical Bioprotection, Key Laboratory of Biological Defense, Ministry of Education, Second Military Medical University, Shanghai, China
| | - Doming Jiang
- Tongji University School of Medicine, Tongji University, Shanghai, China
| | - Zheyun Niu
- Tongji University School of Medicine, Tongji University, Shanghai, China
| | - Zihan Zhang
- Tongji University School of Medicine, Tongji University, Shanghai, China
| | - Guangwen Cao
- Tongji University School of Medicine, Tongji University, Shanghai, China
- Department of Epidemiology, Shanghai Key Laboratory of Medical Bioprotection, Key Laboratory of Biological Defense, Ministry of Education, Second Military Medical University, Shanghai, China
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37
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Zhang S, Li X, Lin J, Lin Q, Wong KC. Review of single-cell RNA-seq data clustering for cell-type identification and characterization. RNA (NEW YORK, N.Y.) 2023; 29:517-530. [PMID: 36737104 PMCID: PMC10158997 DOI: 10.1261/rna.078965.121] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/27/2022] [Accepted: 01/03/2023] [Indexed: 05/06/2023]
Abstract
In recent years, the advances in single-cell RNA-seq techniques have enabled us to perform large-scale transcriptomic profiling at single-cell resolution in a high-throughput manner. Unsupervised learning such as data clustering has become the central component to identify and characterize novel cell types and gene expression patterns. In this study, we review the existing single-cell RNA-seq data clustering methods with critical insights into the related advantages and limitations. In addition, we also review the upstream single-cell RNA-seq data processing techniques such as quality control, normalization, and dimension reduction. We conduct performance comparison experiments to evaluate several popular single-cell RNA-seq clustering approaches on simulated and multiple single-cell transcriptomic data sets.
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Affiliation(s)
- Shixiong Zhang
- School of Computer Science and Technology, Xidian University, Xi'an 710071, China
- Department of Computer Science, City University of Hong Kong, Hong Kong SAR, China
| | - Xiangtao Li
- School of Artificial Intelligence, Jilin University, Jilin 130012, China
| | - Jiecong Lin
- Department of Computer Science, City University of Hong Kong, Hong Kong SAR, China
| | - Qiuzhen Lin
- College of Computer Science and Software Engineering, Shenzhen University, Shenzhen 518060, China
| | - Ka-Chun Wong
- Department of Computer Science, City University of Hong Kong, Hong Kong SAR, China
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38
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Murray SM, Ansari AM, Frater J, Klenerman P, Dunachie S, Barnes E, Ogbe A. The impact of pre-existing cross-reactive immunity on SARS-CoV-2 infection and vaccine responses. Nat Rev Immunol 2023; 23:304-316. [PMID: 36539527 PMCID: PMC9765363 DOI: 10.1038/s41577-022-00809-x] [Citation(s) in RCA: 55] [Impact Index Per Article: 55.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/08/2022] [Indexed: 12/24/2022]
Abstract
Pre-existing cross-reactive immune responses to severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) proteins in infection-naive subjects have been described by several studies. In particular, regions of high homology between SARS-CoV-2 and common cold coronaviruses have been highlighted as a likely source of this cross-reactivity. However, the role of such cross-reactive responses in the outcome of SARS-CoV-2 infection and vaccination is currently unclear. Here, we review evidence regarding the impact of pre-existing humoral and T cell immune responses to outcomes of SARS-CoV-2 infection and vaccination. Furthermore, we discuss the importance of conserved coronavirus epitopes for the rational design of pan-coronavirus vaccines and consider cross-reactivity of immune responses to ancestral SARS-CoV-2 and SARS-CoV-2 variants, as well as their impact on COVID-19 vaccination.
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Affiliation(s)
- Sam M Murray
- Peter Medawar Building for Pathogen Research, Nuffield Department of Clinical Medicine, University of Oxford, Oxford, UK
| | - Azim M Ansari
- Peter Medawar Building for Pathogen Research, Nuffield Department of Clinical Medicine, University of Oxford, Oxford, UK
| | - John Frater
- Peter Medawar Building for Pathogen Research, Nuffield Department of Clinical Medicine, University of Oxford, Oxford, UK
- Oxford University Hospitals NHS Foundation Trust, Oxford, UK
- NIHR Oxford Biomedical Research Centre, University of Oxford, Oxford, UK
| | - Paul Klenerman
- Peter Medawar Building for Pathogen Research, Nuffield Department of Clinical Medicine, University of Oxford, Oxford, UK
- Oxford University Hospitals NHS Foundation Trust, Oxford, UK
- NIHR Oxford Biomedical Research Centre, University of Oxford, Oxford, UK
| | - Susanna Dunachie
- Peter Medawar Building for Pathogen Research, Nuffield Department of Clinical Medicine, University of Oxford, Oxford, UK
- Oxford University Hospitals NHS Foundation Trust, Oxford, UK
- NIHR Oxford Biomedical Research Centre, University of Oxford, Oxford, UK
- Centre for Tropical Medicine and Global Health, Nuffield Department of Clinical Medicine, University of Oxford, Oxford, UK
- Mahidol-Oxford Tropical Medicine Research Unit, Mahidol University, Bangkok, Thailand
| | - Eleanor Barnes
- Peter Medawar Building for Pathogen Research, Nuffield Department of Clinical Medicine, University of Oxford, Oxford, UK.
- Oxford University Hospitals NHS Foundation Trust, Oxford, UK.
- NIHR Oxford Biomedical Research Centre, University of Oxford, Oxford, UK.
| | - Ane Ogbe
- Peter Medawar Building for Pathogen Research, Nuffield Department of Clinical Medicine, University of Oxford, Oxford, UK.
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39
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Clever S, Volz A. Mouse models in COVID-19 research: analyzing the adaptive immune response. Med Microbiol Immunol 2023; 212:165-183. [PMID: 35661253 PMCID: PMC9166226 DOI: 10.1007/s00430-022-00735-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2022] [Accepted: 03/15/2022] [Indexed: 11/29/2022]
Abstract
The emergence of SARS-CoV-2, the severe acute respiratory syndrome coronavirus type 2 causing the COVID-19 pandemic, resulted in a major necessity for scientific countermeasures. Investigations revealing the exact mechanisms of the SARS-CoV-2 pathogenesis provide the basis for the development of therapeutic measures and protective vaccines against COVID-19. Animal models are inevitable for infection and pre-clinical vaccination studies as well as therapeutic testing. A well-suited animal model, mimicking the pathology seen in human COVID-19 patients, is an important basis for these investigations. Several animal models were already used during SARS-CoV-2 studies with different clinical outcomes after SARS-CoV-2 infection. Here, we give an overview of different animal models used in SARS-CoV-2 infection studies with a focus on the mouse model. Mice provide a well-established animal model for laboratory use and several different mouse models have been generated and are being used in SARS-CoV-2 studies. Furthermore, the analysis of SARS-CoV-2-specific T cells during infection and in vaccination studies in mice is highlighted.
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Affiliation(s)
- Sabrina Clever
- Institute of Virology, University of Veterinary Medicine Hannover, Hannover, Germany
- Research Center for Emerging Infections and Zoonoses, University of Veterinary Medicine Hannover, Hannover, Germany
| | - Asisa Volz
- Institute of Virology, University of Veterinary Medicine Hannover, Hannover, Germany
- Research Center for Emerging Infections and Zoonoses, University of Veterinary Medicine Hannover, Hannover, Germany
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40
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Pacheco-García U, Serafín-López J. Indirect Dispersion of SARS-CoV-2 Live-Attenuated Vaccine and Its Contribution to Herd Immunity. Vaccines (Basel) 2023; 11:655. [PMID: 36992239 PMCID: PMC10055900 DOI: 10.3390/vaccines11030655] [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: 12/29/2022] [Revised: 03/03/2023] [Accepted: 03/07/2023] [Indexed: 03/16/2023] Open
Abstract
It has been 34 months since the beginning of the SARS-CoV-2 coronavirus pandemic, which causes the COVID-19 disease. In several countries, immunization has reached a proportion near what is required to reach herd immunity. Nevertheless, infections and re-infections have been observed even in vaccinated persons. That is because protection conferred by vaccines is not entirely effective against new virus variants. It is unknown how often booster vaccines will be necessary to maintain a good level of protective immunity. Furthermore, many individuals refuse vaccination, and in developing countries, a large proportion of the population has not yet been vaccinated. Some live-attenuated vaccines against SARS-CoV-2 are being developed. Here, we analyze the indirect dispersion of a live-attenuated virus from vaccinated individuals to their contacts and the contribution that this phenomenon could have to reaching Herd Immunity.
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Affiliation(s)
- Ursino Pacheco-García
- Department of Cardio-Renal Pathophysiology, Instituto Nacional de Cardiología “Ignacio Chávez”, Mexico City 14080, Mexico
| | - Jeanet Serafín-López
- Department of Immunology, Escuela Nacional de Ciencias Biológicas (ENCB), Instituto Politécnico Nacional (IPN), Mexico City 11340, Mexico
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41
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Yang G, Wang J, Sun P, Qin J, Yang X, Chen D, Zhang Y, Zhong N, Wang Z. SARS-CoV-2 epitope-specific T cells: Immunity response feature, TCR repertoire characteristics and cross-reactivity. Front Immunol 2023; 14:1146196. [PMID: 36969254 PMCID: PMC10036809 DOI: 10.3389/fimmu.2023.1146196] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2023] [Accepted: 03/01/2023] [Indexed: 03/12/2023] Open
Abstract
The devastating COVID-19 pandemic caused by SARS-CoV-2 and multiple variants or subvariants remains an ongoing global challenge. SARS-CoV-2-specific T cell responses play a critical role in early virus clearance, disease severity control, limiting the viral transmission and underpinning COVID-19 vaccine efficacy. Studies estimated broad and robust T cell responses in each individual recognized at least 30 to 40 SARS-CoV-2 antigen epitopes and associated with COVID-19 clinical outcome. Several key immunodominant viral proteome epitopes, including S protein- and non-S protein-derived epitopes, may primarily induce potent and long-lasting antiviral protective effects. In this review, we summarized the immune response features of immunodominant epitope-specific T cells targeting different SRAS-CoV-2 proteome structures after infection and vaccination, including abundance, magnitude, frequency, phenotypic features and response kinetics. Further, we analyzed the epitopes immunodominance hierarchy in combination with multiple epitope-specific T cell attributes and TCR repertoires characteristics, and discussed the significant implications of cross-reactive T cells toward HCoVs, SRAS-CoV-2 and variants of concern, especially Omicron. This review may be essential for mapping the landscape of T cell responses toward SARS-CoV-2 and optimizing the current vaccine strategy.
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Affiliation(s)
- Gang Yang
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming, China
- Guangzhou Laboratory, Guangzhou, China
- Department of Pulmonary and Critical Care Medicine, The First People’s Hospital of Yunnan Province, Kunming, China
| | - Junxiang Wang
- State Key Laboratory of Respiratory Disease & National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou Medical University, Guangzhou, China
| | - Ping Sun
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming, China
| | - Jian Qin
- Department of Pulmonary and Critical Care Medicine, The First People’s Hospital of Yunnan Province, Kunming, China
| | - Xiaoyun Yang
- Guangzhou Laboratory, Guangzhou, China
- State Key Laboratory of Respiratory Disease & National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou Medical University, Guangzhou, China
| | - Daxiang Chen
- Guangzhou Laboratory, Guangzhou, China
- State Key Laboratory of Respiratory Disease & National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou Medical University, Guangzhou, China
| | - Yunhui Zhang
- Department of Pulmonary and Critical Care Medicine, The First People’s Hospital of Yunnan Province, Kunming, China
- *Correspondence: Zhongfang Wang, ; Nanshan Zhong, ; Yunhui Zhang,
| | - Nanshan Zhong
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming, China
- Guangzhou Laboratory, Guangzhou, China
- State Key Laboratory of Respiratory Disease & National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou Medical University, Guangzhou, China
- *Correspondence: Zhongfang Wang, ; Nanshan Zhong, ; Yunhui Zhang,
| | - Zhongfang Wang
- Guangzhou Laboratory, Guangzhou, China
- State Key Laboratory of Respiratory Disease & National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou Medical University, Guangzhou, China
- *Correspondence: Zhongfang Wang, ; Nanshan Zhong, ; Yunhui Zhang,
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Cable J, Balachandran S, Daley-Bauer LP, Rustagi A, Antony F, Frere JJ, Strampe J, Kedzierska K, Cannon JL, McGargill MA, Weiskopf D, Mettelman RC, Niessl J, Thomas PG, Briney B, Valkenburg SA, Bloom JD, Bjorkman PJ, Iketani S, Rappazzo CG, Crooks CM, Crofts KF, Pöhlmann S, Krammer F, Sant AJ, Nabel GJ, Schultz-Cherry S. Viral immunity: Basic mechanisms and therapeutic applications-a Keystone Symposia report. Ann N Y Acad Sci 2023; 1521:32-45. [PMID: 36718537 DOI: 10.1111/nyas.14960] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
Viruses infect millions of people each year. Both endemic viruses circulating throughout the population as well as novel epidemic and pandemic viruses pose ongoing threats to global public health. Developing more effective tools to address viruses requires not only in-depth knowledge of the virus itself but also of our immune system's response to infection. On June 29 to July 2, 2022, researchers met for the Keystone symposium "Viral Immunity: Basic Mechanisms and Therapeutic Applications." This report presents concise summaries from several of the symposium presenters.
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Affiliation(s)
| | - Siddharth Balachandran
- Blood Cell Development and Function Program, Fox Chase Cancer Center, Philadelphia, Pennsylvania, USA
| | - Lisa P Daley-Bauer
- Department of Microbiology and Immunology, Emory Vaccine Center, Emory University School of Medicine, Atlanta, Georgia, USA
| | - Arjun Rustagi
- Division of Infectious Diseases and Geographic Medicine, Department of Medicine, Stanford University, Stanford, California, USA
| | - Ferrin Antony
- Department of Pathobiology, College of Veterinary Medicine, Auburn University, Auburn, Alabama, USA
| | - Justin J Frere
- East Harlem Health Outreach Partnership; Department of Medical Education; and Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Jamie Strampe
- Bioinformatics Program, Boston University and National Emerging Infectious Diseases Laboratories, Boston, Massachusetts, USA
| | - Katherine Kedzierska
- Department of Microbiology and Immunology, University of Melbourne at The Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia
| | - Judy L Cannon
- Department of Molecular Genetics and Microbiology, University of New Mexico School of Medicine, Albuquerque, New Mexico, USA
| | - Maureen A McGargill
- Department of Immunology, St. Jude Children's Research Hospital, Memphis, Tennessee, USA
| | - Daniela Weiskopf
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology (LJI), La Jolla, California, USA
| | - Robert C Mettelman
- Department of Immunology, St. Jude Children's Research Hospital, Memphis, Tennessee, USA
| | - Julia Niessl
- Department of Medicine, Center for Infectious Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Paul G Thomas
- Department of Immunology, St. Jude Children's Research Hospital, Memphis, Tennessee, USA
- Department of Microbiology, Immunology, and Biochemistry, University of Tennessee Health Science Center, Memphis, Tennessee, USA
| | - Bryan Briney
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, California, USA
| | - Sophie A Valkenburg
- HKU-Pasteur Research Pole, School of Public Health, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, PR China
| | - Jesse D Bloom
- Basic Sciences Division and Howard Hughes Medical Institute, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
- Department of Microbiology and Department of Genome Sciences, University of Washington, Seattle, Washington, USA
| | - Pamela J Bjorkman
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, California, USA
| | - Sho Iketani
- Aaron Diamond AIDS Research Center, Columbia University Vagelos College of Physicians and Surgeons, New York, New York, USA
| | | | - Chelsea M Crooks
- Department of Pathobiological Sciences, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Kali F Crofts
- Department of Microbiology and Immunology, Wake Forest School of Medicine, Winston-Salem, North Carolina, USA
| | - Stefan Pöhlmann
- Infection Biology Unit, German Primate Center and Faculty of Biology and Psychology, University Medical Center Göttingen, Georg-August-University Göttingen, Göttingen, Germany
| | - Florian Krammer
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Andrea J Sant
- Department of Infectious Diseases, St. Jude Children's Research Hospital, Memphis, Tennessee, USA
| | - Gary J Nabel
- Modex Therapeutics Inc., an OPKO Health Company, Natick, Massachusetts, USA
| | - Stacey Schultz-Cherry
- Department of Laboratory Medicine and Department of Immunology, Yale University School of Medicine, New Haven, Connecticut, USA
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43
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Zheng Z, Chang L, Mu J, Ni Q, Bing Z, Zou QH, Wan Y, Wu Y, Li J, Zou L. Database of synovial T cell repertoire of rheumatoid arthritis patients identifies cross-reactive potential against pathogens including unencountered SARS-CoV-2. Ann Rheum Dis 2023; 82:438-440. [PMID: 36261250 PMCID: PMC9933155 DOI: 10.1136/ard-2022-222763] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2022] [Accepted: 10/08/2022] [Indexed: 11/04/2022]
Affiliation(s)
- Zihan Zheng
- Institute of Immunology, Army Medical University, Chongqing, Chongqing, China,Department of Autoimmune Diseases, Chongqing International Institute for Immunology, Chongqing, Chongqing, China
| | - Ling Chang
- Institute of Immunology, Army Medical University, Chongqing, Chongqing, China
| | - Jie Mu
- Biomedical Analysis Center, Army Medical University, Chongqing, Chongqing, China
| | - Qingshan Ni
- Biomedical Analysis Center, Army Medical University, Chongqing, Chongqing, China
| | - Zhong Bing
- Department of Rheumatology and Immunology, First Affiliated Hospital (Southwest Hospital) of Army Medical University, Chongqing, Chongqing, China
| | - Qing-Hua Zou
- Department of Rheumatology and Immunology, First Affiliated Hospital (Southwest Hospital) of Army Medical University, Chongqing, Chongqing, China
| | - Ying Wan
- Biomedical Analysis Center, Army Medical University, Chongqing, Chongqing, China
| | - Yuzhang Wu
- Institute of Immunology, Army Medical University, Chongqing, Chongqing, China
| | - Jingyi Li
- Department of Rheumatology and Immunology, First Affiliated Hospital (Southwest Hospital) of Army Medical University, Chongqing, Chongqing, China
| | - Liyun Zou
- Institute of Immunology, Army Medical University, Chongqing, Chongqing, China
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44
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Schwarz C, Eschenhagen P, Schmidt H, Hohnstein T, Iwert C, Grehn C, Roehmel J, Steinke E, Stahl M, Lozza L, Tikhonova E, Rosati E, Stervbo U, Babel N, Mainz JG, Wisplinghoff H, Ebel F, Jia LJ, Blango MG, Hortschansky P, Brunke S, Hube B, Brakhage AA, Kniemeyer O, Scheffold A, Bacher P. Antigen specificity and cross-reactivity drive functionally diverse anti-Aspergillus fumigatus T cell responses in cystic fibrosis. J Clin Invest 2023; 133:161593. [PMID: 36701198 PMCID: PMC9974102 DOI: 10.1172/jci161593] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2022] [Accepted: 01/19/2023] [Indexed: 01/27/2023] Open
Abstract
BACKGROUNDThe fungus Aspergillus fumigatus causes a variety of clinical phenotypes in patients with cystic fibrosis (pwCF). Th cells orchestrate immune responses against fungi, but the types of A. fumigatus-specific Th cells in pwCF and their contribution to protective immunity or inflammation remain poorly characterized.METHODSWe used antigen-reactive T cell enrichment (ARTE) to investigate fungus-reactive Th cells in peripheral blood of pwCF and healthy controls.RESULTSWe show that clonally expanded, high-avidity A. fumigatus-specific effector Th cells, which were absent in healthy donors, developed in pwCF. Individual patients were characterized by distinct Th1-, Th2-, or Th17-dominated responses that remained stable over several years. These different Th subsets target different A. fumigatus proteins, indicating that differential antigen uptake and presentation directs Th cell subset development. Patients with allergic bronchopulmonary aspergillosis (ABPA) are characterized by high frequencies of Th2 cells that cross-recognize various filamentous fungi.CONCLUSIONOur data highlight the development of heterogenous Th responses targeting different protein fractions of a single fungal pathogen and identify the development of multispecies cross-reactive Th2 cells as a potential risk factor for ABPA.FUNDINGGerman Research Foundation (DFG), under Germany's Excellence Strategy (EXC 2167-390884018 "Precision Medicine in Chronic Inflammation" and EXC 2051-390713860 "Balance of the Microverse"); Oskar Helene Heim Stiftung; Christiane Herzog Stiftung; Mukoviszidose Institut gGmb; German Cystic Fibrosis Association Mukoviszidose e.V; German Federal Ministry of Education and Science (BMBF) InfectControl 2020 Projects AnDiPath (BMBF 03ZZ0838A+B).
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Affiliation(s)
- Carsten Schwarz
- Klinikum Westbrandenburg, Campus Potsdam, Cystic Fibrosis Section, Potsdam, Germany
| | - Patience Eschenhagen
- Klinikum Westbrandenburg, Campus Potsdam, Cystic Fibrosis Section, Potsdam, Germany
| | - Henrijette Schmidt
- Institute of Clinical Molecular Biology, Christian-Albrecht University of Kiel, Kiel, Germany.,Institute of Immunology, Christian-Albrecht University of Kiel and UKSH Schleswig-Holstein, Kiel, Germany
| | - Thordis Hohnstein
- Department of Microbiology, Infectious Diseases and Immunology, Charité – Universitätsmedizin Berlin, Berlin, Germany
| | - Christina Iwert
- Berlin Institute of Health at Charité – Universitätsmedizin Berlin, Translational Immunology, Berlin, Germany
| | - Claudia Grehn
- Berlin Institute of Health at Charité – Universitätsmedizin Berlin, Berlin, Germany
| | - Jobst Roehmel
- Department of Pediatric Respiratory Medicine, Immunology and Critical Care Medicine and Cystic Fibrosis Center, Charité – Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt – Universität zu Berlin, Berlin, Germany
| | - Eva Steinke
- Berlin Institute of Health at Charité – Universitätsmedizin Berlin, Berlin, Germany.,Department of Pediatric Respiratory Medicine, Immunology and Critical Care Medicine and Cystic Fibrosis Center, Charité – Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt – Universität zu Berlin, Berlin, Germany.,German Center for Lung Research (DZL), associated partner site, Berlin, Germany
| | - Mirjam Stahl
- Berlin Institute of Health at Charité – Universitätsmedizin Berlin, Berlin, Germany.,Department of Pediatric Respiratory Medicine, Immunology and Critical Care Medicine and Cystic Fibrosis Center, Charité – Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt – Universität zu Berlin, Berlin, Germany.,German Center for Lung Research (DZL), associated partner site, Berlin, Germany
| | - Laura Lozza
- Cell Biology Laboratory, Precision for Medicine GmbH, Berlin, Germany
| | - Ekaterina Tikhonova
- Institute of Clinical Molecular Biology, Christian-Albrecht University of Kiel, Kiel, Germany.,Institute of Immunology, Christian-Albrecht University of Kiel and UKSH Schleswig-Holstein, Kiel, Germany
| | - Elisa Rosati
- Institute of Clinical Molecular Biology, Christian-Albrecht University of Kiel, Kiel, Germany.,Institute of Immunology, Christian-Albrecht University of Kiel and UKSH Schleswig-Holstein, Kiel, Germany
| | - Ulrik Stervbo
- Center for Translational Medicine and Immune Diagnostics Laboratory, Marien Hospital Herne, University Hospital of the Ruhr University Bochum, Herne, Germany
| | - Nina Babel
- Berlin Institute of Health at Charité – Universitätsmedizin Berlin, Berlin, Germany.,Center for Translational Medicine and Immune Diagnostics Laboratory, Marien Hospital Herne, University Hospital of the Ruhr University Bochum, Herne, Germany
| | - Jochen G. Mainz
- Brandenburg Medical School/Medizinische Hochschule Brandenburg (MHB), University, Pediatric Pulmonology/Cystic Fibrosis, Klinikum Westbrandenburg, Brandenburg an der Havel, Germany
| | - Hilmar Wisplinghoff
- Labor Dr. Wisplinghoff, Cologne, Germany.,Institute for Virology and Microbiology, Witten/Herdecke University, Witten, Germany
| | - Frank Ebel
- Institute for Infectious Diseases and Zoonoses, LMU, Munich, Germany
| | - Lei-Jie Jia
- Department of Molecular and Applied Microbiology, Leibniz Institute for Natural Product Research and Infection Biology (Leibniz-HKI), Jena, Germany
| | - Matthew G. Blango
- Department of Molecular and Applied Microbiology, Leibniz Institute for Natural Product Research and Infection Biology (Leibniz-HKI), Jena, Germany
| | - Peter Hortschansky
- Department of Molecular and Applied Microbiology, Leibniz Institute for Natural Product Research and Infection Biology (Leibniz-HKI), Jena, Germany
| | - Sascha Brunke
- Department of Microbial Pathogenicity Mechanisms, Leibniz Institute for Natural Product Research and Infection Biology (Leibniz-HKI), Jena, Germany
| | - Bernhard Hube
- Department of Microbial Pathogenicity Mechanisms, Leibniz Institute for Natural Product Research and Infection Biology (Leibniz-HKI), Jena, Germany.,Institute of Microbiology, Friedrich Schiller University, Jena, Germany
| | - Axel A. Brakhage
- Department of Molecular and Applied Microbiology, Leibniz Institute for Natural Product Research and Infection Biology (Leibniz-HKI), Jena, Germany.,Institute of Microbiology, Friedrich Schiller University, Jena, Germany
| | - Olaf Kniemeyer
- Department of Molecular and Applied Microbiology, Leibniz Institute for Natural Product Research and Infection Biology (Leibniz-HKI), Jena, Germany
| | - Alexander Scheffold
- Institute of Immunology, Christian-Albrecht University of Kiel and UKSH Schleswig-Holstein, Kiel, Germany
| | - Petra Bacher
- Institute of Clinical Molecular Biology, Christian-Albrecht University of Kiel, Kiel, Germany.,Institute of Immunology, Christian-Albrecht University of Kiel and UKSH Schleswig-Holstein, Kiel, Germany
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45
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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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46
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del Molino del Barrio I, Hayday TS, Laing AG, Hayday AC, Di Rosa F. COVID-19: Using high-throughput flow cytometry to dissect clinical heterogeneity. Cytometry A 2023; 103:117-126. [PMID: 34811890 PMCID: PMC9011838 DOI: 10.1002/cyto.a.24516] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2021] [Revised: 10/18/2021] [Accepted: 11/11/2021] [Indexed: 12/22/2022]
Abstract
Here we consider how high-content flow cytometric methodology at appropriate scale and throughput rapidly provided meaningful biological data in our recent studies of COVID-19, which we discuss in the context of other similar investigations. In our work, high-throughput flow cytometry was instrumental to identify a consensus immune signature in COVID-19 patients, and to investigate the impact of SARS-CoV-2 exposure on patients with either solid or hematological cancers. We provide here some examples of our 'holistic' approach, in which flow cytometry data generated by lymphocyte and myelomonocyte panels were integrated with other analytical metrics, including SARS-CoV-2-specific serum antibody titers, plasma cytokine/chemokine levels, and in-depth clinical annotation. We report how selective differences between T cell subsets were revealed by a newly described flow cytometric TDS assay to distinguish actively cycling T cells in the peripheral blood. By such approaches, our and others' high-content flow cytometry studies collectively identified overt abnormalities and subtle but critical changes that discriminate the immuno-signature of COVID-19 patients from those of healthy donors and patients with non-COVID respiratory infections. Thereby, these studies offered several meaningful biomarkers of COVID-19 severity that have the potential to improve the management of patients and of hospital resources. In sum, flow cytometry provides an important means for rapidly obtaining data that can guide clinical decision-making without requiring highly expensive, sophisticated equipment, and/or "-omics" capabilities. We consider how this approach might be further developed.
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Affiliation(s)
- Irene del Molino del Barrio
- Peter Gorer Department of ImmunobiologyKing's College LondonLondonUK
- University College LondonLondonUK
- Cancer Research UK Cancer Immunotherapy AcceleratorLondonUK
| | - Thomas S. Hayday
- Peter Gorer Department of ImmunobiologyKing's College LondonLondonUK
| | - Adam G. Laing
- Peter Gorer Department of ImmunobiologyKing's College LondonLondonUK
| | - Adrian C. Hayday
- Peter Gorer Department of ImmunobiologyKing's College LondonLondonUK
- Cancer Research UK Cancer Immunotherapy AcceleratorLondonUK
- Immunosurveillance LaboratoryThe Francis Crick InstituteLondonUK
| | - Francesca Di Rosa
- Institute of Molecular Biology and PathologyNational Research Council of ItalyRomeItaly
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47
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Gao CA, Pickens CI, Morales-Nebreda L, Wunderink RG. Clinical Features of COVID-19 and Differentiation from Other Causes of CAP. Semin Respir Crit Care Med 2023; 44:8-20. [PMID: 36646082 DOI: 10.1055/s-0042-1759889] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
Community-acquired pneumonia (CAP) is a significant cause of morbidity and mortality, one of the most common reasons for infection-related death worldwide. Causes of CAP include numerous viral, bacterial, and fungal pathogens, though frequently no specific organism is found. Beginning in 2019, the COVID-19 pandemic has caused incredible morbidity and mortality. COVID-19 has many features typical of CAP such as fever, respiratory distress, and cough, and can be difficult to distinguish from other types of CAP. Here, we highlight unique clinical features of COVID-19 pneumonia such as olfactory and gustatory dysfunction, lymphopenia, and distinct imaging appearance.
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Affiliation(s)
- Catherine A Gao
- Division of Pulmonary and Critical Care, Northwestern University Feinberg School of Medicine, Chicago, Illinois
| | - Chiagozie I Pickens
- Division of Pulmonary and Critical Care, Northwestern University Feinberg School of Medicine, Chicago, Illinois
| | - Luisa Morales-Nebreda
- Division of Pulmonary and Critical Care, Northwestern University Feinberg School of Medicine, Chicago, Illinois
| | - Richard G Wunderink
- Division of Pulmonary and Critical Care, Northwestern University Feinberg School of Medicine, Chicago, Illinois
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Almendro-Vázquez P, Laguna-Goya R, Paz-Artal E. Defending against SARS-CoV-2: The T cell perspective. Front Immunol 2023; 14:1107803. [PMID: 36776863 PMCID: PMC9911802 DOI: 10.3389/fimmu.2023.1107803] [Citation(s) in RCA: 20] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2022] [Accepted: 01/16/2023] [Indexed: 01/28/2023] Open
Abstract
SARS-CoV-2-specific T cell response has been proven essential for viral clearance, COVID-19 outcome and long-term memory. Impaired early T cell-driven immunity leads to a severe form of the disease associated with lymphopenia, hyperinflammation and imbalanced humoral response. Analyses of acute SARS-CoV-2 infection have revealed that mild COVID-19 course is characterized by an early induction of specific T cells within the first 7 days of symptoms, coordinately followed by antibody production for an effective control of viral infection. In contrast, patients who do not develop an early specific cellular response and initiate a humoral immune response with subsequent production of high levels of antibodies, develop severe symptoms. Yet, delayed and persistent bystander CD8+ T cell activation has been also reported in hospitalized patients and could be a driver of lung pathology. Literature supports that long-term maintenance of T cell response appears more stable than antibody titters. Up to date, virus-specific T cell memory has been detected 22 months post-symptom onset, with a predominant IL-2 memory response compared to IFN-γ. Furthermore, T cell responses are conserved against the emerging variants of concern (VoCs) while these variants are mostly able to evade humoral responses. This could be partly explained by the high HLA polymorphism whereby the viral epitope repertoire recognized could differ among individuals, greatly decreasing the likelihood of immune escape. Current COVID-19-vaccination has been shown to elicit Th1-driven spike-specific T cell response, as does natural infection, which provides substantial protection against severe COVID-19 and death. In addition, mucosal vaccination has been reported to induce strong adaptive responses both locally and systemically and to protect against VoCs in animal models. The optimization of vaccine formulations by including a variety of viral regions, innovative adjuvants or diverse administration routes could result in a desirable enhanced cellular response and memory, and help to prevent breakthrough infections. In summary, the increasing evidence highlights the relevance of monitoring SARS-CoV-2-specific cellular immune response, and not only antibody levels, as a correlate for protection after infection and/or vaccination. Moreover, it may help to better identify target populations that could benefit most from booster doses and to personalize vaccination strategies.
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Affiliation(s)
- Patricia Almendro-Vázquez
- Instituto de Investigación Sanitaria Hospital 12 de Octubre (imas12), Madrid, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Infecciosas (CIBERINFEC), Instituto de Salud Carlos III, Madrid, Spain
| | - Rocío Laguna-Goya
- Instituto de Investigación Sanitaria Hospital 12 de Octubre (imas12), Madrid, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Infecciosas (CIBERINFEC), Instituto de Salud Carlos III, Madrid, Spain
- Department of Immunology, Hospital Universitario 12 de Octubre, Madrid, Spain
| | - Estela Paz-Artal
- Instituto de Investigación Sanitaria Hospital 12 de Octubre (imas12), Madrid, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Infecciosas (CIBERINFEC), Instituto de Salud Carlos III, Madrid, Spain
- Department of Immunology, Hospital Universitario 12 de Octubre, Madrid, Spain
- Department of Immunology, Ophthalmology and ENT, Complutense University School of Medicine, Madrid, Spain
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49
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High titers of neutralizing SARS-CoV-2 antibodies six months after symptom onset are associated with increased severity in COVID-19 hospitalized patients. Virol J 2023; 20:14. [PMID: 36698135 PMCID: PMC9875770 DOI: 10.1186/s12985-023-01974-8] [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: 07/01/2022] [Accepted: 01/20/2023] [Indexed: 01/26/2023] Open
Abstract
BACKGROUND Viral shedding and neutralizing antibody (NAb) dynamics among patients hospitalized with severe coronavirus disease 2019 (COVID-19) and immune correlates of protection have been key questions throughout the pandemic. We investigated the duration of reverse transcriptase-polymerase chain reaction (RT-PCR) positivity, infectious viral shedding and NAb titers as well as the association between NAb titers and disease severity in hospitalized COVID-19 patients in Denmark 2020-2021. MATERIALS AND METHODS Prospective single-center observational cohort study of 47 hospitalized COVID-19 patients. Oropharyngeal swabs were collected at eight time points during the initial 30 days of inclusion. Serum samples were collected after a median time of 7 (IQR 5 - 10), 37 (IQR 35 - 38), 97 (IQR 95 - 100), and 187 (IQR 185 - 190) days after symptom onset. NAb titers were determined by an in-house live virus microneutralization assay. Viral culturing was performed in Vero E6 cells. RESULTS Patients with high disease severity had higher mean log2 NAb titers at day 37 (1.58, 95% CI [0.34 -2.81]), 97 (2.07, 95% CI [0.53-3.62]) and 187 (2.49, 95% CI [0.20- 4.78]) after symptom onset, compared to patients with low disease severity. Peak viral load (0.072, 95% CI [- 0.627 - 0.728]), expressed as log10 SARS-CoV-2 copies/ml, was not associated with disease severity. Virus cultivation attempts were unsuccessful in almost all (60/61) oropharyngeal samples collected shortly after hospital admission. CONCLUSIONS We document an association between high disease severity and high mean NAb titers at days 37, 97 and 187 after symptom onset. However, peak viral load during admission was not associated with disease severity. TRIAL REGISTRATION The study is registered at https://clinicaltrials.gov/ (NCT05274373).
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50
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Measures of epitope binding degeneracy from T cell receptor repertoires. Proc Natl Acad Sci U S A 2023; 120:e2213264120. [PMID: 36649423 PMCID: PMC9942805 DOI: 10.1073/pnas.2213264120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Abstract
Adaptive immunity is driven by specific binding of hypervariable receptors to diverse molecular targets. The sequence diversity of receptors and targets are both individually known but because multiple receptors can recognize the same target, a measure of the effective "functional" diversity of the human immune system has remained elusive. Here, we show that sequence near-coincidences within T cell receptors that bind specific epitopes provide a new window into this problem and allow the quantification of how binding probability covaries with sequence. We find that near-coincidence statistics within epitope-specific repertoires imply a measure of binding degeneracy to amino acid changes in receptor sequence that is consistent across disparate experiments. Paired data on both chains of the heterodimeric receptor are particularly revealing since simultaneous near-coincidences are rare and we show how they can be exploited to estimate the number of epitope responses that created the memory compartment. In addition, we find that paired-chain coincidences are strongly suppressed across donors with different human leukocyte antigens, evidence for a central role of antigen-driven selection in making paired chain receptors public. These results demonstrate the power of coincidence analysis to reveal the sequence determinants of epitope binding in receptor repertoires.
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