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Lapuente D, Winkler TH, Tenbusch M. B-cell and antibody responses to SARS-CoV-2: infection, vaccination, and hybrid immunity. Cell Mol Immunol 2024; 21:144-158. [PMID: 37945737 PMCID: PMC10805925 DOI: 10.1038/s41423-023-01095-w] [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: 09/17/2023] [Accepted: 10/13/2023] [Indexed: 11/12/2023] Open
Abstract
The emergence of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in 2019 prompted scientific, medical, and biotech communities to investigate infection- and vaccine-induced immune responses in the context of this pathogen. B-cell and antibody responses are at the center of these investigations, as neutralizing antibodies (nAbs) are an important correlate of protection (COP) from infection and the primary target of SARS-CoV-2 vaccine modalities. In addition to absolute levels, nAb longevity, neutralization breadth, immunoglobulin isotype and subtype composition, and presence at mucosal sites have become important topics for scientists and health policy makers. The recent pandemic was and still is a unique setting in which to study de novo and memory B-cell (MBC) and antibody responses in the dynamic interplay of infection- and vaccine-induced immunity. It also provided an opportunity to explore new vaccine platforms, such as mRNA or adenoviral vector vaccines, in unprecedented cohort sizes. Combined with the technological advances of recent years, this situation has provided detailed mechanistic insights into the development of B-cell and antibody responses but also revealed some unexpected findings. In this review, we summarize the key findings of the last 2.5 years regarding infection- and vaccine-induced B-cell immunity, which we believe are of significant value not only in the context of SARS-CoV-2 but also for future vaccination approaches in endemic and pandemic settings.
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Affiliation(s)
- Dennis Lapuente
- Institut für klinische und molekulare Virologie, Universitätsklinikum Erlangen und Friedrich-Alexander-Universität (FAU) Erlangen-Nürnberg, Schlossgarten 4, 91054, Erlangen, Germany
| | - Thomas H Winkler
- Department of Biology, Division of Genetics, Nikolaus-Fiebiger-Center for Molecular Medicine, Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU), Erlangen, Germany.
- Medical Immunology Campus Erlangen, Friedrich-Alexander-Universität (FAU) Erlangen-Nürnberg, Schlossplatz 1, 91054, Erlangen, Germany.
| | - Matthias Tenbusch
- Institut für klinische und molekulare Virologie, Universitätsklinikum Erlangen und Friedrich-Alexander-Universität (FAU) Erlangen-Nürnberg, Schlossgarten 4, 91054, Erlangen, Germany
- Medical Immunology Campus Erlangen, Friedrich-Alexander-Universität (FAU) Erlangen-Nürnberg, Schlossplatz 1, 91054, Erlangen, Germany
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Chen Z, Yuan Y, Hu Q, Zhu A, Chen F, Li S, Guan X, Lv C, Tang T, He Y, Cheng J, Zheng J, Hu X, Zhao J, Zhao J, Sun J. SARS-CoV-2 immunity in animal models. Cell Mol Immunol 2024; 21:119-133. [PMID: 38238440 PMCID: PMC10806257 DOI: 10.1038/s41423-023-01122-w] [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: 12/07/2023] [Accepted: 12/18/2023] [Indexed: 01/25/2024] Open
Abstract
The COVID-19 pandemic, which was caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), has become a worldwide health crisis due to its transmissibility. SARS-CoV-2 infection results in severe respiratory illness and can lead to significant complications in affected individuals. These complications encompass symptoms such as coughing, respiratory distress, fever, infectious shock, acute respiratory distress syndrome (ARDS), and even multiple-organ failure. Animal models serve as crucial tools for investigating pathogenic mechanisms, immune responses, immune escape mechanisms, antiviral drug development, and vaccines against SARS-CoV-2. Currently, various animal models for SARS-CoV-2 infection, such as nonhuman primates (NHPs), ferrets, hamsters, and many different mouse models, have been developed. Each model possesses distinctive features and applications. In this review, we elucidate the immune response elicited by SARS-CoV-2 infection in patients and provide an overview of the characteristics of various animal models mainly used for SARS-CoV-2 infection, as well as the corresponding immune responses and applications of these models. A comparative analysis of transcriptomic alterations in the lungs from different animal models revealed that the K18-hACE2 and mouse-adapted virus mouse models exhibited the highest similarity with the deceased COVID-19 patients. Finally, we highlighted the current gaps in related research between animal model studies and clinical investigations, underscoring lingering scientific questions that demand further clarification.
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Affiliation(s)
- Zhao Chen
- State Key Laboratory of Respiratory Disease, National Clinical Research Centre for Respiratory Disease, National Centre for Respiratory Medicine, Guangzhou Institute of Respiratory Health, the First Affiliated Hospital of Guangzhou Medical University, Guangzhou, Guangdong, 510182, China
| | - Yaochang Yuan
- State Key Laboratory of Respiratory Disease, National Clinical Research Centre for Respiratory Disease, National Centre for Respiratory Medicine, Guangzhou Institute of Respiratory Health, the First Affiliated Hospital of Guangzhou Medical University, Guangzhou, Guangdong, 510182, China
| | - Qingtao Hu
- State Key Laboratory of Respiratory Disease, National Clinical Research Centre for Respiratory Disease, National Centre for Respiratory Medicine, Guangzhou Institute of Respiratory Health, the First Affiliated Hospital of Guangzhou Medical University, Guangzhou, Guangdong, 510182, China
- GMU-GIBH Joint School of Life Sciences, Guangzhou Medical University, Guangzhou, 510000, China
| | - Airu Zhu
- State Key Laboratory of Respiratory Disease, National Clinical Research Centre for Respiratory Disease, National Centre for Respiratory Medicine, Guangzhou Institute of Respiratory Health, the First Affiliated Hospital of Guangzhou Medical University, Guangzhou, Guangdong, 510182, China
| | - Fenghua Chen
- State Key Laboratory of Respiratory Disease, National Clinical Research Centre for Respiratory Disease, National Centre for Respiratory Medicine, Guangzhou Institute of Respiratory Health, the First Affiliated Hospital of Guangzhou Medical University, Guangzhou, Guangdong, 510182, China
| | - Shu Li
- State Key Laboratory of Respiratory Disease, National Clinical Research Centre for Respiratory Disease, National Centre for Respiratory Medicine, Guangzhou Institute of Respiratory Health, the First Affiliated Hospital of Guangzhou Medical University, Guangzhou, Guangdong, 510182, China
| | - Xin Guan
- State Key Laboratory of Respiratory Disease, National Clinical Research Centre for Respiratory Disease, National Centre for Respiratory Medicine, Guangzhou Institute of Respiratory Health, the First Affiliated Hospital of Guangzhou Medical University, Guangzhou, Guangdong, 510182, China
| | - Chao Lv
- State Key Laboratory of Respiratory Disease, National Clinical Research Centre for Respiratory Disease, National Centre for Respiratory Medicine, Guangzhou Institute of Respiratory Health, the First Affiliated Hospital of Guangzhou Medical University, Guangzhou, Guangdong, 510182, China
| | - Tian Tang
- State Key Laboratory of Respiratory Disease, National Clinical Research Centre for Respiratory Disease, National Centre 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 Centre for Respiratory Disease, National Centre for Respiratory Medicine, Guangzhou Institute of Respiratory Health, the First Affiliated Hospital of Guangzhou Medical University, Guangzhou, Guangdong, 510182, China
| | - Jinling Cheng
- State Key Laboratory of Respiratory Disease, National Clinical Research Centre for Respiratory Disease, National Centre 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 Centre for Respiratory Disease, National Centre for Respiratory Medicine, Guangzhou Institute of Respiratory Health, the First Affiliated Hospital of Guangzhou Medical University, Guangzhou, Guangdong, 510182, China
| | - Xiaoyu Hu
- State Key Laboratory of Respiratory Disease, National Clinical Research Centre for Respiratory Disease, National Centre 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 Centre for Respiratory Disease, National Centre 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 Centre for Respiratory Disease, National Centre 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, ShanghaiTech 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 Centre for Respiratory Disease, National Centre for Respiratory Medicine, Guangzhou Institute of Respiratory Health, the First Affiliated Hospital of Guangzhou Medical University, Guangzhou, Guangdong, 510182, China.
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Thomas Κ, Grigoropoulos I, Alexopoulou P, Karofylakis E, Galani I, Papadopoulou KK, Tsiavou A, Ntourou A, Mavrou E, Qevani I, Katsimbri P, Koutsianas C, Mavrea E, Vassilopoulos D, Pournaras S, Tsiodras S, Boumpas D, Antoniadou A. Sustained cell-mediated but not humoral responses in rituximab-treated rheumatic patients after vaccination against SARS-CoV-2. Rheumatology (Oxford) 2024; 63:534-541. [PMID: 37228039 PMCID: PMC10836975 DOI: 10.1093/rheumatology/kead236] [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: 12/31/2022] [Revised: 04/18/2023] [Accepted: 05/09/2023] [Indexed: 05/27/2023] Open
Abstract
OBJECTIVES B-cell depleting monoclonal antibodies are associated with increased COVID-19 severity and impaired immune response to vaccination. We aimed to assess the humoral and cell mediated (CMI) immune response after SARS-CoV-2 vaccination in rituximab (RTX)-treated rheumatic patients. METHODS Serum and whole blood samples were collected from RTX-treated rheumatic patients 3-6 months after last vaccination against SARS-CoV-2. Serum was tested by ELISA for quantitative detection of anti-spike SARS-CoV-2 IgG. Cell-mediated variant-specific SARS-CoV-2 immunity (CMI) was assessed by interferon-γ release assay Covi-FERON FIA. Patients were interviewed for breakthrough COVID-19 infection (BTI) 3 months post sampling. RESULTS Sixty patients were studied after a median (IQR) of 179 (117-221.5) days from last vaccine to sampling. Forty (66.7%) patients had positive Covi-FERON and 23 (38.3%) had detectable anti-spike IgG. Covi-FERON positive patients had lower median RTX cumulative dose [6 (4-10.75) vs 11 (6.75-14.75) grams, (P = 0.019)]. Patients with positive anti-spike IgG had received fewer RTX cycles [2 (2-4) vs 6 (4-8), P = 0.002] and cumulative dose [4 (3-7) vs 10 (6.25-13) grams, P = 0.002] and had shorter time from last vaccination to sampling [140 (76-199) vs 192 (128-230) days, P = 0.047]. Thirty-seven percent were positive only for Covi-FERON and 7% only for anti-spike IgG. Twenty (33.3%) BTI occurred post sampling, exclusively during Omicron variant predominance. The proportion of patients with CMI response against Delta variant was lower in patients who experienced BTI (25% vs 55%, P = 0.03). CONCLUSIONS Four out of ten RTX-treated vaccinated patients show lasting cell-mediated immune response despite undetectable anti-spike antibodies. Cumulative RTX dose affects both humoral and cell-mediated responses to SARS-CoV-2 vaccines. Cell-mediated immune responses call for attention as a vaccine efficacy marker against SARS-CoV-2.
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Affiliation(s)
- Κonstantinos Thomas
- 4th Department of Internal Medicine, National and Kapodistrian University of Athens School of Medicine, Attikon University General Hospital, Chaidari, Greece
| | - Ioannis Grigoropoulos
- 4th Department of Internal Medicine, National and Kapodistrian University of Athens School of Medicine, Attikon University General Hospital, Chaidari, Greece
| | - Panagiota Alexopoulou
- 4th Department of Internal Medicine, National and Kapodistrian University of Athens School of Medicine, Attikon University General Hospital, Chaidari, Greece
| | - Emmanouil Karofylakis
- 4th Department of Internal Medicine, National and Kapodistrian University of Athens School of Medicine, Attikon University General Hospital, Chaidari, Greece
| | - Irene Galani
- 4th Department of Internal Medicine, National and Kapodistrian University of Athens School of Medicine, Attikon University General Hospital, Chaidari, Greece
| | - Kyriaki Korina Papadopoulou
- Clinical Microbiology Laboratory, National and Kapodistrian University of Athens School of Medicine, Attikon University General Hospital, Chaidari, Greece
| | - Anastasia Tsiavou
- Clinical Microbiology Laboratory, National and Kapodistrian University of Athens School of Medicine, Attikon University General Hospital, Chaidari, Greece
| | - Aliki Ntourou
- Clinical Immunology-Rheumatology Unit, 4th Department of Internal Medicine, National and Kapodistrian University of Athens School of Medicine, Attikon University General Hospital, Chaidari, Greece
| | - Eleftheria Mavrou
- Clinical Immunology-Rheumatology Unit, 4th Department of Internal Medicine, National and Kapodistrian University of Athens School of Medicine, Attikon University General Hospital, Chaidari, Greece
| | - Irina Qevani
- Clinical Immunology-Rheumatology Unit, 4th Department of Internal Medicine, National and Kapodistrian University of Athens School of Medicine, Attikon University General Hospital, Chaidari, Greece
| | - Pelagia Katsimbri
- Clinical Immunology-Rheumatology Unit, 4th Department of Internal Medicine, National and Kapodistrian University of Athens School of Medicine, Attikon University General Hospital, Chaidari, Greece
| | - Christos Koutsianas
- Clinical Immunology-Rheumatology Unit, 2nd Department of Medicine and Laboratory, National and Kapodistrian University of Athens School of Medicine, Hippokration General Hospital, Athens, Greece
| | - Evgenia Mavrea
- Clinical Immunology-Rheumatology Unit, 2nd Department of Medicine and Laboratory, National and Kapodistrian University of Athens School of Medicine, Hippokration General Hospital, Athens, Greece
| | - Dimitrios Vassilopoulos
- Clinical Immunology-Rheumatology Unit, 2nd Department of Medicine and Laboratory, National and Kapodistrian University of Athens School of Medicine, Hippokration General Hospital, Athens, Greece
| | - Spyros Pournaras
- Clinical Microbiology Laboratory, National and Kapodistrian University of Athens School of Medicine, Attikon University General Hospital, Chaidari, Greece
| | - Sotirios Tsiodras
- 4th Department of Internal Medicine, National and Kapodistrian University of Athens School of Medicine, Attikon University General Hospital, Chaidari, Greece
| | - Dimitrios Boumpas
- 4th Department of Internal Medicine, National and Kapodistrian University of Athens School of Medicine, Attikon University General Hospital, Chaidari, Greece
- Clinical Immunology-Rheumatology Unit, 4th Department of Internal Medicine, National and Kapodistrian University of Athens School of Medicine, Attikon University General Hospital, Chaidari, Greece
| | - Anastasia Antoniadou
- 4th Department of Internal Medicine, National and Kapodistrian University of Athens School of Medicine, Attikon University General Hospital, Chaidari, Greece
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Saito T, Couzinet A, Murakami T, Shimomura M, Suzuki T, Katayama Y, Nakatsura T. Rapid and high throughput assessment of cellular immunity against SARS-CoV-2 based on the ex vivo activation of genes in leukocyte assay with whole blood. Biochem Biophys Res Commun 2024; 694:149398. [PMID: 38134475 DOI: 10.1016/j.bbrc.2023.149398] [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: 10/01/2023] [Revised: 12/05/2023] [Accepted: 12/15/2023] [Indexed: 12/24/2023]
Abstract
During the novel coronavirus outbreak and vaccine development, antibody production garnered major focus as the primary immunogenic response. However, cellular immunity's recent demonstration of comparable or greater significance in controlling infection demands the re-evaluation of the importance of T-cell immunity in SARS-CoV-2 infection. Here, we developed a novel assay, the ex vivo activation of genes in leukocytes (EAGL), which employs short-term whole blood stimulation with the LeukoComplete™ system, to measure ex vivo SARS-CoV-2-specific T cell responses (cellular immunity). This assay measures upregulated mRNA expression related to leukocyte activation 4 h after antigen stimulation. LeukoComplete™ system uses whole blood samples, eliminating the need for pretreatment before analysis. Furthermore, this system's high reproducibility is ensured through a series of operations from mRNA extraction to cDNA synthesis on a 96-well plate. In the performance evaluation using fresh blood from previously SARS-CoV-2-infected and COVID-19-vaccinated individuals, the EAGL assay had a comparable sensitivity and specificity to the ELISpot assay (EAGL: 1.000/1.000; ELISpot: 0.900/0.973). As a simple, high-throughput assay, the EAGL assay is also a quantitative test that is useful in studies with large sample numbers, such as monitoring new vaccine efficacies against novel coronaviruses or epidemiologic studies that require cellular immune testing during viral infection.
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Affiliation(s)
- Taro Saito
- Minaris Medical Co., Ltd, Nagaizumi, Shizuoka, 411-0932, Japan
| | - Arnaud Couzinet
- Division of Cancer Immunotherapy, Exploratory Oncology Research & Clinical Trial Center, National Cancer Center, Kashiwa, Chiba, 277-8577, Japan
| | | | - Manami Shimomura
- Division of Cancer Immunotherapy, Exploratory Oncology Research & Clinical Trial Center, National Cancer Center, Kashiwa, Chiba, 277-8577, Japan
| | - Toshihiro Suzuki
- Division of Cancer Immunotherapy, Exploratory Oncology Research & Clinical Trial Center, National Cancer Center, Kashiwa, Chiba, 277-8577, Japan
| | - Yuki Katayama
- Minaris Medical Co., Ltd, Nagaizumi, Shizuoka, 411-0932, Japan; Resonac Corporation, Minato, Tokyo, 105-7325, Japan.
| | - Tetsuya Nakatsura
- Division of Cancer Immunotherapy, Exploratory Oncology Research & Clinical Trial Center, National Cancer Center, Kashiwa, Chiba, 277-8577, Japan
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55
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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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Mateos-Nozal J, Rodríguez-Domínguez M, San Román J, Candel FJ, Villarrubia N, Pérez-Panizo N, Segura E, Cuñarro JM, Ramírez-Arellano MVM, Rodríguez-Ramos R, Pariente-Rodríguez R, Villar LM, Ramos P, Cantón R, Cruz-Jentoft AJ, Galán JC. Factors Associated with SARS-CoV-2 Infection in Fully Vaccinated Nursing Home Residents and Workers. Viruses 2024; 16:186. [PMID: 38399962 PMCID: PMC10891794 DOI: 10.3390/v16020186] [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: 01/08/2024] [Revised: 01/21/2024] [Accepted: 01/23/2024] [Indexed: 02/25/2024] Open
Abstract
Persons living or working in nursing homes faced a higher risk of SARS-CoV-2 infections during the pandemic, resulting in heightened morbidity and mortality among older adults despite robust vaccination efforts. This prospective study evaluated the humoral and cellular immunity in fully vaccinated residents and workers from two nursing homes in Madrid, Spain, from 2020 to 2021. Measurements of IgG levels were conducted in August 2020 (pre-vaccination) and June and September 2021 (post-vaccination), alongside assessments of neutralizing antibodies and cellular responses in September 2021 among the most vulnerable individuals. Follow-up extended until February 2022 to identify risk factors for SARS-CoV-2 infection or mortality, involving 267 residents (mean age 87.6 years, 81.3% women) and 302 workers (mean age 50.7 years, 82.1% women). Residents exhibited a significantly higher likelihood of experiencing COVID-19 before June 2021 compared with nursing staff (OR [95% CI], 7.2 [3.0 to 17.2], p < 0.01). Participants with a history of previous COVID-19 infection showed more significant increases in IgG levels in August 2020, June 2021 and September 2021, alongside an increased proportion of neutralizing antibodies in the most vulnerable individuals. However, IgG decay remained the same between June and September 2021 based on the previous COVID-19 status. During the Omicron variant wave, residents and staff showed a similar rate of SARS-CoV-2 infection. Notably, preceding clinical or immunological factors before receiving three vaccination doses did not demonstrate associations with COVID-19 infection or overall mortality in our participant cohort.
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Affiliation(s)
- Jesús Mateos-Nozal
- Servicio de Geriatría, Hospital Universitario Ramón y Cajal, IRYCIS, 28034 Madrid, Spain; (N.P.-P.); (M.V.M.R.-A.); (A.J.C.-J.)
| | - Mario Rodríguez-Domínguez
- Servicio de Microbiología, Hospital Universitario Ramón y Cajal, IRYCIS, 28034 Madrid, Spain; (M.R.-D.); (R.C.); (J.C.G.)
- Centro de Investigación Biomédica en Red en Epidemiología y Salud Pública (CIBERESP), Instituto de Salud Carlos III, 28029 Madrid, Spain
| | | | - Francisco Javier Candel
- Servicio de Microbiología Clínica y Enfermedades Infecciosas, Hospital Clínico San Carlos, 28040 Madrid, Spain;
| | - Noelia Villarrubia
- Servicio de Inmunología, Hospital Universitario Ramón y Cajal, IRYCIS, 28034 Madrid, Spain (R.R.-R.); (R.P.-R.); (L.M.V.)
| | - Nuria Pérez-Panizo
- Servicio de Geriatría, Hospital Universitario Ramón y Cajal, IRYCIS, 28034 Madrid, Spain; (N.P.-P.); (M.V.M.R.-A.); (A.J.C.-J.)
| | - Esther Segura
- Residencia de Mayores Manoteras, 28050 Madrid, Spain;
| | | | | | - Rafael Rodríguez-Ramos
- Servicio de Inmunología, Hospital Universitario Ramón y Cajal, IRYCIS, 28034 Madrid, Spain (R.R.-R.); (R.P.-R.); (L.M.V.)
| | - Roberto Pariente-Rodríguez
- Servicio de Inmunología, Hospital Universitario Ramón y Cajal, IRYCIS, 28034 Madrid, Spain (R.R.-R.); (R.P.-R.); (L.M.V.)
| | - Luisa M. Villar
- Servicio de Inmunología, Hospital Universitario Ramón y Cajal, IRYCIS, 28034 Madrid, Spain (R.R.-R.); (R.P.-R.); (L.M.V.)
| | | | - Rafael Cantón
- Servicio de Microbiología, Hospital Universitario Ramón y Cajal, IRYCIS, 28034 Madrid, Spain; (M.R.-D.); (R.C.); (J.C.G.)
- Centro de Investigación Biomédica en Red de Enfermedades Infecciosas (CIBERINFEC), Instituto de Salud Carlos III, 28029 Madrid, Spain
| | - Alfonso J. Cruz-Jentoft
- Servicio de Geriatría, Hospital Universitario Ramón y Cajal, IRYCIS, 28034 Madrid, Spain; (N.P.-P.); (M.V.M.R.-A.); (A.J.C.-J.)
| | - Juan Carlos Galán
- Servicio de Microbiología, Hospital Universitario Ramón y Cajal, IRYCIS, 28034 Madrid, Spain; (M.R.-D.); (R.C.); (J.C.G.)
- Centro de Investigación Biomédica en Red en Epidemiología y Salud Pública (CIBERESP), Instituto de Salud Carlos III, 28029 Madrid, Spain
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Kar M, Johnson KEE, Vanderheiden A, Elrod EJ, Floyd K, Geerling E, Stone ET, Salinas E, Banakis S, Wang W, Sathish S, Shrihari S, Davis-Gardner ME, Kohlmeier J, Pinto A, Klein R, Grakoui A, Ghedin E, Suthar MS. CD4+ and CD8+ T cells are required to prevent SARS-CoV-2 persistence in the nasal compartment. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.01.23.576505. [PMID: 38410446 PMCID: PMC10896337 DOI: 10.1101/2024.01.23.576505] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/28/2024]
Abstract
SARS-CoV-2 is the causative agent of COVID-19 and continues to pose a significant public health threat throughout the world. Following SARS-CoV-2 infection, virus-specific CD4+ and CD8+ T cells are rapidly generated to form effector and memory cells and persist in the blood for several months. However, the contribution of T cells in controlling SARS-CoV-2 infection within the respiratory tract are not well understood. Using C57BL/6 mice infected with a naturally occurring SARS-CoV-2 variant (B.1.351), we evaluated the role of T cells in the upper and lower respiratory tract. Following infection, SARS-CoV-2-specific CD4+ and CD8+ T cells are recruited to the respiratory tract and a vast proportion secrete the cytotoxic molecule Granzyme B. Using antibodies to deplete T cells prior to infection, we found that CD4+ and CD8+ T cells play distinct roles in the upper and lower respiratory tract. In the lungs, T cells play a minimal role in viral control with viral clearance occurring in the absence of both CD4+ and CD8+ T cells through 28 days post-infection. In the nasal compartment, depletion of both CD4+ and CD8+ T cells, but not individually, results in persistent and culturable virus replicating in the nasal compartment through 28 days post-infection. Using in situ hybridization, we found that SARS-CoV-2 infection persisted in the nasal epithelial layer of tandem CD4+ and CD8+ T cell-depleted mice. Sequence analysis of virus isolates from persistently infected mice revealed mutations spanning across the genome, including a deletion in ORF6. Overall, our findings highlight the importance of T cells in controlling virus replication within the respiratory tract during SARS-CoV-2 infection.
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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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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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Dallari S, Martinez Pazos V, Munoz Eusse J, Wellens J, Thompson C, Colombel JF, Satsangi J, Cadwell K, Wong SY. Cytokine signature in convalescent SARS-CoV-2 patients with inflammatory bowel disease receiving vedolizumab. Sci Rep 2024; 14:186. [PMID: 38168138 PMCID: PMC10761911 DOI: 10.1038/s41598-023-50035-1] [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: 09/26/2023] [Accepted: 12/14/2023] [Indexed: 01/05/2024] Open
Abstract
While differential antibody responses SARS-CoV-2 in patients with inflammatory bowel disease (IBD) receiving infliximab and vedolizumab are well-characterized, the immune pathways underlying these differences remain unknown. Prior to COVID-19 vaccine development, we screened 235 patients with IBD receiving biological therapy for antibodies to SARS-CoV-2 and measured serum cytokines. In seropositive patients, we prospectively collected clinical data. We found a cytokine signature in patients receiving vedolizumab who are seropositive compared with seronegative for SARS-CoV-2 antibodies that may be linked to repeated SARS-CoV-2 infections. However, there were no differences between seropositive and seronegative patients receiving infliximab. In this single-center cohort of patients with IBD with anti-SARS-CoV-2 antibodies at the onset of the COVID-19 pandemic, and therefore without influence of vaccination, there is a cytokine signature in patients receiving vedolizumab but not infliximab. These findings lay the groundwork for further studies on immune consequences of viral infection in patients with IBD, which is postulated to evolve from aberrant host-microbe responses.
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Affiliation(s)
- Simone Dallari
- Department of Microbiology, New York University Grossman School of Medicine, New York, USA
| | - Vicky Martinez Pazos
- The Henry D. Janowitz Division of Gastroenterology, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, Box 1069, New York, NY, 10029, USA
| | | | - Judith Wellens
- Department of Gastroenterology and Hepatology, Leuven University Hospitals, Leuven, Belgium
| | - Craig Thompson
- Division of Biomedical Sciences, Warwick Medical School, University of Warwick, Warwick, UK
| | - Jean-Frederic Colombel
- The Henry D. Janowitz Division of Gastroenterology, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, Box 1069, New York, NY, 10029, USA
| | - Jack Satsangi
- Nuffield Department of Medicine, Translational Gastroenterology Unit, University of Oxford, Oxford, UK
| | - Ken Cadwell
- Division of Gastroenterology and Hepatology, Department of Medicine, Department of Systems Pharmacology and Translational Therapeutics, Department of Pathology and Laboratory Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - Serre-Yu Wong
- The Henry D. Janowitz Division of Gastroenterology, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, Box 1069, New York, NY, 10029, USA.
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61
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Chen Y, Cao Z, Lu S, Wang Z, Ma C, Zhang G, Chen M, Yang J, Ren Z, Xu J. Pediococcus pentosaceus MIANGUAN Enhances the Immune Response to Vaccination in Mice. Probiotics Antimicrob Proteins 2024:10.1007/s12602-023-10205-z. [PMID: 38169032 DOI: 10.1007/s12602-023-10205-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/10/2023] [Indexed: 01/05/2024]
Abstract
Increasing evidence shows that some probiotics can improve vaccine responses as adjuvants. This study aimed to evaluate the effect of Pediococcus pentosaceus MIANGUAN (PPM) on SARS-CoV-2 vaccine-elicited immune response in mice. Six-week-old female ICR mice were primed and boosted with SARS-CoV-2 vaccine intramuscularly at weeks 0 and 4, respectively. Mice were gavaged with PPM (5 × 109 CFU/mouse) or PBS (control) for 3 days immediately after boosting vaccination. Compared to the control, oral PPM administration resulted in significantly higher levels of RBD-specific IgG binding antibodies (> 2.3-fold) and RBD-specific IgG1 binding antibodies (> 4-fold) in the serum. Additionally, PPM-treated mice had higher titers of RBD-specific IgG binding antibodies (> 2.29-fold) and neutralization antibodies (> 1.6-fold) in the lung compared to the control mice. The transcriptional analyses showed that the B cell receptor (BCR) signaling pathway was upregulated in both splenocytes and BAL cells in the PPM group vs. the control group. In addition, the number of IFN-γ-producing splenocytes (mainly in CD4 + T cells as determined by flow cytometry) in response to restimulation of RBD peptides was significantly increased in the PPM group. RNA sequencing showed that the genes associated with T cell activation and maturation and MHC class II pathway (CD4, H2-DMa, H2-DMb1, H2-Oa, Ctss) were upregulated, suggesting that oral administration of PPM may enhance CD4 + T cell responses through MHC class II pathway. Furthermore, PPM administration could downregulate the expression level of proinflammatory genes. To conclude, oral administration of PPM could boost SARS-CoV-2 vaccine efficacy through enhancing the specific humoral and cellular immunity response and decrease the expression of inflammation pathways.
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Affiliation(s)
- Yulu Chen
- National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Beijing, 102206, China
| | - Zhijie Cao
- National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Beijing, 102206, China
| | - Simin Lu
- National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Beijing, 102206, China
- Research Unite for Unknown Microbe, Chinese Academy of Medical Sciences, Institute of Pathogen Biology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, 100730, China
| | - Zhihuan Wang
- National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Beijing, 102206, China
| | - Caiyun Ma
- National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Beijing, 102206, China
- Department of Epidemiology, School of Public Health, Shanxi Medical University, Taiyuan, 030001, China
| | - Gui Zhang
- Infection Management Office, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, 250021, China
| | - Mengshan Chen
- National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Beijing, 102206, China
- Institute of Public Health, Nankai University, Tianjin, 300071, China
| | - Jing Yang
- National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Beijing, 102206, China
| | - Zhihong Ren
- National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Beijing, 102206, China.
| | - Jianguo Xu
- National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Beijing, 102206, China.
- Institute of Public Health, Nankai University, Tianjin, 300071, China.
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Zeng YC, Young OJ, Si L, Ku MW, Isinelli G, Rajwar A, Jiang A, Wintersinger CM, Graveline AR, Vernet A, Sanchez M, Ryu JH, Kwon IC, Goyal G, Ingber DE, Shih WM. DNA origami vaccine (DoriVac) nanoparticles improve both humoral and cellular immune responses to infectious diseases. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.12.29.573647. [PMID: 38260393 PMCID: PMC10802255 DOI: 10.1101/2023.12.29.573647] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/24/2024]
Abstract
Current SARS-CoV-2 vaccines have demonstrated robust induction of neutralizing antibodies and CD4+ T cell activation, however CD8+ responses are variable, and the duration of immunity and protection against variants are limited. Here we repurposed our DNA origami vaccine platform, DoriVac, for targeting infectious viruses, namely SARS-CoV-2, HIV, and Ebola. The DNA origami nanoparticle, conjugated with infectious-disease-specific HR2 peptides, which act as highly conserved antigens, and CpG adjuvant at precise nanoscale spacing, induced neutralizing antibodies, Th1 CD4+ T cells, and CD8+ T cells in naïve mice, with significant improvement over a bolus control. Pre-clinical studies using lymph-node-on-a-chip systems validated that DoriVac, when conjugated with antigenic peptides or proteins, induced promising cellular immune responses in human cells. These results suggest that DoriVac holds potential as a versatile, modular vaccine platform, capable of inducing both humoral and cellular immunities. The programmability of this platform underscores its potential utility in addressing future pandemics.
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Affiliation(s)
- Yang C. Zeng
- Department of Cancer Biology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts 02115, USA
- Wyss Institute for Biologically Inspired Engineering at Harvard University, Boston, Massachusetts 02115, USA
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Olivia J. Young
- Wyss Institute for Biologically Inspired Engineering at Harvard University, Boston, Massachusetts 02115, USA
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts 02115, USA
- Harvard-Massachusetts Institute of Technology (MIT) Division of Health Sciences and Technology, Massachusetts Institute of Technology, Cambridge, Massachusetts, 02139, USA
| | - Longlong Si
- Wyss Institute for Biologically Inspired Engineering at Harvard University, Boston, Massachusetts 02115, USA
| | - Min Wen Ku
- Wyss Institute for Biologically Inspired Engineering at Harvard University, Boston, Massachusetts 02115, USA
| | - Giorgia Isinelli
- Wyss Institute for Biologically Inspired Engineering at Harvard University, Boston, Massachusetts 02115, USA
| | - Anjali Rajwar
- Wyss Institute for Biologically Inspired Engineering at Harvard University, Boston, Massachusetts 02115, USA
| | - Amanda Jiang
- Wyss Institute for Biologically Inspired Engineering at Harvard University, Boston, Massachusetts 02115, USA
| | - Chris M. Wintersinger
- Department of Cancer Biology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts 02115, USA
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Amanda R. Graveline
- Wyss Institute for Biologically Inspired Engineering at Harvard University, Boston, Massachusetts 02115, USA
| | - Andyna Vernet
- Wyss Institute for Biologically Inspired Engineering at Harvard University, Boston, Massachusetts 02115, USA
| | - Melinda Sanchez
- Wyss Institute for Biologically Inspired Engineering at Harvard University, Boston, Massachusetts 02115, USA
| | - Ju Hee Ryu
- Department of Cancer Biology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts 02115, USA
- Center for Theragnosis, Biomedical Research Institute, Korea Institute of Science and Technology (KIST), Seoul 02792, Republic of Korea
| | - Ick Chan Kwon
- Department of Cancer Biology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts 02115, USA
- Center for Theragnosis, Biomedical Research Institute, Korea Institute of Science and Technology (KIST), Seoul 02792, Republic of Korea
- KU-KIST Graduate School of Converging Science and Technology, Korea University, Seoul 02841, Republic of Korea
| | - Girija Goyal
- Wyss Institute for Biologically Inspired Engineering at Harvard University, Boston, Massachusetts 02115, USA
| | - Donald E. Ingber
- Wyss Institute for Biologically Inspired Engineering at Harvard University, Boston, Massachusetts 02115, USA
- Vascular Biology Program, Department of Surgery, Boston Children’s Hospital and Harvard Medical School, Boston, MA, USA
- Harvard John A. Paulson School of Engineering and Applied Sciences, Cambridge, MA, USA
| | - William M. Shih
- Department of Cancer Biology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts 02115, USA
- Wyss Institute for Biologically Inspired Engineering at Harvard University, Boston, Massachusetts 02115, USA
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts 02115, USA
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63
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Razafimahatratra SL, Andriatefy OH, Mioramalala DJN, Tsatoromila FAM, Randrianarisaona F, Dussart P, Schoenhals M. Multiple SARS-CoV-2 immunizations of an unvaccinated population lead to complex immunity. A T cell reactivity study of blood donors in Antananarivo. J Infect Public Health 2024; 17:175-181. [PMID: 38039861 DOI: 10.1016/j.jiph.2023.11.020] [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: 07/24/2023] [Revised: 11/08/2023] [Accepted: 11/16/2023] [Indexed: 12/03/2023] Open
Abstract
BACKGROUND Madagascar has undergone multiple and robust COVID-19 waves. The resulting immune background developed by its poorly vaccinated population has however not been described. METHODS In this study, serological analysis and specific T cell response descriptions were used to describe the history of exposures of the capital's blood donors to SARS-CoV-2 and its VOCs. Samples were collected early 2022, and pools of multiple immunogenic peptides of SARS-CoV-2 were used in an IFN-γ secretion ELISPOT assay to characterize the specific T-cell immunity developed against these potential epitopes. RESULTS Multiple epidemic waves have led to 92.1% of donors having detectable antibodies, and 94.8% having developed T-cells against SARS-CoV-2. Heterogeneous reactivities to different strain-derived peptides suggested multiple immunological backgrounds in the population including 16.1% of individuals exposed at least once to a unique strain, 27.1% to two strains, 28.5% to three strains, and 23.1% to four distinct strains. CONCLUSIONS Cross-reactivity increased with multiple exposures but did not decrease the risk of re-infection. These results describe the extremely complex immunological background developed following multiple natural immunizations.
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Affiliation(s)
| | | | | | | | | | - Philippe Dussart
- Direction, Institut Pasteur of Madagascar, 101 Antananarivo, Madagascar
| | - Matthieu Schoenhals
- Immunology of Infectious Diseases Unit, Institut Pasteur of Madagascar, 101 Antananarivo, Madagascar.
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Oyaert M, De Scheerder MA, Van Herrewege S, Laureys G, Van Assche S, Cambron M, Naesens L, Hoste L, Claes K, Haerynck F, Kerre T, Van Laecke S, Jacques P, Padalko E. Longevity of the humoral and cellular responses after SARS-CoV-2 booster vaccinations in immunocompromised patients. Eur J Clin Microbiol Infect Dis 2024; 43:177-185. [PMID: 37953413 DOI: 10.1007/s10096-023-04701-x] [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: 07/04/2023] [Accepted: 11/05/2023] [Indexed: 11/14/2023]
Abstract
We assessed the humoral and cellular immune responses after two booster mRNA vaccine administrations [BNT162b2 (Pfizer-BioNTech vaccine)] in cohorts of immunocompromised patients (n = 199) and healthy controls (HC) (n = 54). All patients living with HIV (PLWH) and chronic kidney disease (CKD) patients and almost all (98.2%) of the primary immunodeficiency (PID) patients had measurable antibodies 3 and 6 months after administration of the third and fourth vaccine dose, comparable to the HCs. In contrast, only 53.3% and 83.3% of the multiple sclerosis (MS) and rheumatologic patients, respectively, developed a humoral immune response. Cellular immune response was observed in all PLWH after administration of four vaccine doses. In addition, cellular immune response was positive in 89.6%, 97.8%, 73.3% and 96.9% of the PID, MS, rheumatologic and CKD patients, respectively. Unlike the other groups, only the MS patients had a significantly higher cellular immune response compared to the HC group. Administration of additional vaccine doses results in retained or increased humoral and cellular immune response in patients with acquired or inherited immune disorders.
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Affiliation(s)
- Matthijs Oyaert
- Department of Laboratory Medicine, Ghent University Hospital, Ghent, Belgium.
| | | | - Sophie Van Herrewege
- Department of General Internal Medicine, Ghent University Hospital, Ghent, Belgium
| | - Guy Laureys
- Department of Neurology, Ghent University Hospital, Ghent, Belgium
| | - Sofie Van Assche
- Department of Neurology, Ghent University Hospital, Ghent, Belgium
| | - Melissa Cambron
- Department of Neurology, AZ Sint-Jan Brugge Oostende, Brugge, Belgium
| | - Leslie Naesens
- Department of Internal Medicine and Paediatrics, Ghent University Hospital, Ghent, Belgium
- Primary Immunodeficiency Research Lab, Ghent University, Ghent, Belgium
| | - Levi Hoste
- Department of Internal Medicine and Paediatrics, Ghent University Hospital, Ghent, Belgium
- Primary Immunodeficiency Research Lab, Ghent University, Ghent, Belgium
| | - Karlien Claes
- Department of Internal Medicine and Paediatrics, Ghent University Hospital, Ghent, Belgium
- Primary Immunodeficiency Research Lab, Ghent University, Ghent, Belgium
| | - Filomeen Haerynck
- Department of Internal Medicine and Paediatrics, Ghent University Hospital, Ghent, Belgium
- Primary Immunodeficiency Research Lab, Ghent University, Ghent, Belgium
| | - Tessa Kerre
- Department of Haematology, Ghent University Hospital, Ghent, Belgium
| | | | - Peggy Jacques
- Department of Rheumatology, Ghent University Hospital, Ghent, Belgium
| | - Elizaveta Padalko
- Department of Laboratory Medicine, Ghent University Hospital, Ghent, Belgium
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Barmada A, Handfield LF, Godoy-Tena G, de la Calle-Fabregat C, Ciudad L, Arutyunyan A, Andrés-León E, Hoo R, Porter T, Oszlanczi A, Richardson L, Calero-Nieto FJ, Wilson NK, Marchese D, Sancho-Serra C, Carrillo J, Presas-Rodríguez S, Ramo-Tello C, Ruiz-Sanmartin A, Ferrer R, Ruiz-Rodriguez JC, Martínez-Gallo M, Munera-Campos M, Carrascosa JM, Göttgens B, Heyn H, Prigmore E, Casafont-Solé I, Solanich X, Sánchez-Cerrillo I, González-Álvaro I, Raimondo MG, Ramming A, Martin J, Martínez-Cáceres E, Ballestar E, Vento-Tormo R, Rodríguez-Ubreva J. Single-cell multi-omics analysis of COVID-19 patients with pre-existing autoimmune diseases shows aberrant immune responses to infection. Eur J Immunol 2024; 54:e2350633. [PMID: 37799110 DOI: 10.1002/eji.202350633] [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: 06/28/2023] [Revised: 09/29/2023] [Accepted: 10/03/2023] [Indexed: 10/07/2023]
Abstract
In COVID-19, hyperinflammatory and dysregulated immune responses contribute to severity. Patients with pre-existing autoimmune conditions can therefore be at increased risk of severe COVID-19 and/or associated sequelae, yet SARS-CoV-2 infection in this group has been little studied. Here, we performed single-cell analysis of peripheral blood mononuclear cells from patients with three major autoimmune diseases (rheumatoid arthritis, psoriasis, or multiple sclerosis) during SARS-CoV-2 infection. We observed compositional differences between the autoimmune disease groups coupled with altered patterns of gene expression, transcription factor activity, and cell-cell communication that substantially shape the immune response under SARS-CoV-2 infection. While enrichment of HLA-DRlow CD14+ monocytes was observed in all three autoimmune disease groups, type-I interferon signaling as well as inflammatory T cell and monocyte responses varied widely between the three groups of patients. Our results reveal disturbed immune responses to SARS-CoV-2 in patients with pre-existing autoimmunity, highlighting important considerations for disease treatment and follow-up.
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Affiliation(s)
- Anis Barmada
- Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, United Kingdom
- Department of Medical Genetics, University of Cambridge, Cambridge, United Kingdom
| | | | - Gerard Godoy-Tena
- Epigenetics and Immune Disease Group, Josep Carreras Research Institute (IJC), Barcelona, Spain
| | | | - Laura Ciudad
- Epigenetics and Immune Disease Group, Josep Carreras Research Institute (IJC), Barcelona, Spain
| | - Anna Arutyunyan
- Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, United Kingdom
| | - Eduardo Andrés-León
- Instituto de Parasitología y Biomedicina López-Neyra, Consejo Superior de Investigaciones Científicas (IPBLN-CSIC), Granada, Spain
| | - Regina Hoo
- Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, United Kingdom
| | - Tarryn Porter
- Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, United Kingdom
| | - Agnes Oszlanczi
- Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, United Kingdom
| | - Laura Richardson
- Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, United Kingdom
| | - Fernando J Calero-Nieto
- Department of Haematology and Wellcome & MRC Cambridge Stem Cell Institute, University of Cambridge, Cambridge, United Kingdom
| | - Nicola K Wilson
- Department of Haematology and Wellcome & MRC Cambridge Stem Cell Institute, University of Cambridge, Cambridge, United Kingdom
| | - Domenica Marchese
- CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Barcelona, Spain
| | - Carmen Sancho-Serra
- Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, United Kingdom
| | - Jorge Carrillo
- IrsiCaixa AIDS Research Institute, Hospital Germans Trias i Pujol, Badalona, Spain
| | - Silvia Presas-Rodríguez
- MS Unit, Department of Neurology, Germans Trias i Pujol University Hospital, Barcelona, Spain
| | - Cristina Ramo-Tello
- MS Unit, Department of Neurology, Germans Trias i Pujol University Hospital, Barcelona, Spain
| | - Adolfo Ruiz-Sanmartin
- Department of Intensive Care, Hospital Universitari Vall d'Hebron, Shock, Organ Dysfunction and Resuscitation Research Group, Vall d'Hebron Research Institute (VHIR), Barcelona, Spain
| | - Ricard Ferrer
- Department of Intensive Care, Hospital Universitari Vall d'Hebron, Shock, Organ Dysfunction and Resuscitation Research Group, Vall d'Hebron Research Institute (VHIR), Barcelona, Spain
| | - Juan Carlos Ruiz-Rodriguez
- Department of Intensive Care, Hospital Universitari Vall d'Hebron, Shock, Organ Dysfunction and Resuscitation Research Group, Vall d'Hebron Research Institute (VHIR), Barcelona, Spain
| | - Mónica Martínez-Gallo
- Division of Immunology, Hospital Universitari Vall d'Hebron (HUVH), Vall d'Hebron Research Institute (VHIR), Barcelona, Spain
| | - Mónica Munera-Campos
- Dermatology Service, Germans Trias i Pujol University Hospital, LCMN, Germans Trias i Pujol Research Institute (IGTP), Barcelona, Spain
| | - Jose Manuel Carrascosa
- Dermatology Service, Germans Trias i Pujol University Hospital, LCMN, Germans Trias i Pujol Research Institute (IGTP), Barcelona, Spain
| | - Berthold Göttgens
- Department of Haematology and Wellcome & MRC Cambridge Stem Cell Institute, University of Cambridge, Cambridge, United Kingdom
| | - Holger Heyn
- CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Barcelona, Spain
- Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - Elena Prigmore
- Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, United Kingdom
| | - Ivette Casafont-Solé
- Department of Rheumatology, Germans Trias i Pujol University Hospital, LCMN, Germans Trias i Pujol Research Institute (IGTP), Barcelona, Spain
- Department of Infectious Diseases, Germans Trias i Pujol University Hospital, Barcelona, Spain
| | - Xavier Solanich
- Department of Internal Medicine, Hospital Universitari de Bellvitge, Bellvitge Biomedical Research Institute (IDIBELL), L'Hospitalet de Llobregat, Barcelona, Spain
| | | | | | - Maria Gabriella Raimondo
- Department of Internal Medicine 3, Friedrich-Alexander-University Erlangen-Nürnberg (FAU) and Universitätsklinikum Erlangen, Erlangen, Germany
- Deutsches Zentrum Immuntherapie (DZI), Friedrich-Alexander-University Erlangen-Nürnberg and Universitätsklinikum Erlangen, Erlangen, Germany
| | - Andreas Ramming
- Department of Internal Medicine 3, Friedrich-Alexander-University Erlangen-Nürnberg (FAU) and Universitätsklinikum Erlangen, Erlangen, Germany
- Deutsches Zentrum Immuntherapie (DZI), Friedrich-Alexander-University Erlangen-Nürnberg and Universitätsklinikum Erlangen, Erlangen, Germany
| | - Javier Martin
- Instituto de Parasitología y Biomedicina López-Neyra, Consejo Superior de Investigaciones Científicas (IPBLN-CSIC), Granada, Spain
| | - Eva Martínez-Cáceres
- Division of Immunology, Germans Trias i Pujol University Hospital, LCMN, Germans Trias i Pujol Research Institute (IGTP), Barcelona, Spain
- Department of Cell Biology, Physiology, and Immunology, Universitat Autònoma, Barcelona, Spain
| | - Esteban Ballestar
- Epigenetics and Immune Disease Group, Josep Carreras Research Institute (IJC), Barcelona, Spain
| | - Roser Vento-Tormo
- Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, United Kingdom
| | - Javier Rodríguez-Ubreva
- Epigenetics and Immune Disease Group, Josep Carreras Research Institute (IJC), Barcelona, Spain
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Gabdoulkhakova AG, Mingaleeva RN, Romozanova AM, Sagdeeva AR, Filina YV, Rizvanov AA, Miftakhova RR. Immunology of SARS-CoV-2 Infection. BIOCHEMISTRY. BIOKHIMIIA 2024; 89:65-83. [PMID: 38467546 DOI: 10.1134/s0006297924010048] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/14/2023] [Revised: 11/17/2023] [Accepted: 11/18/2023] [Indexed: 03/13/2024]
Abstract
According to the data from the World Health Organization, about 800 million of the world population had contracted coronavirus infection caused by SARS-CoV-2 by mid-2023. Properties of this virus have allowed it to circulate in the human population for a long time, evolving defense mechanisms against the host immune system. Severity of the disease depends largely on the degree of activation of the systemic immune response, including overstimulation of macrophages and monocytes, cytokine production, and triggering of adaptive T- and B-cell responses, while SARS-CoV-2 evades the immune system actions. In this review, we discuss immune responses triggered in response to the SARS-CoV-2 virus entry into the cell and malfunctions of the immune system that lead to the development of severe disease.
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Affiliation(s)
- Aida G Gabdoulkhakova
- Kazan Federal University, Kazan, 420008, Russia.
- Kazan State Medical Academy - Branch Campus of the Federal State Budgetary Educational Institution of Further Professional Education "Russian Medical Academy of Continuous Professional Education" of the Ministry of Health of the Russian Federation, Kazan, 420012, Russia
| | | | | | | | | | - Albert A Rizvanov
- Kazan Federal University, Kazan, 420008, Russia
- Division of Medical and Biological Sciences, Tatarstan Academy of Sciences, Kazan, 420111, Russia
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Mehta P, Chattopadhyay P, Mohite R, D'Rozario R, Bandopadhyay P, Sarif J, Ray Y, Ganguly D, Pandey R. Suppressed transcript diversity and immune response in COVID-19 ICU patients: a longitudinal study. Life Sci Alliance 2024; 7:e202302305. [PMID: 37918965 PMCID: PMC10622646 DOI: 10.26508/lsa.202302305] [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: 08/03/2023] [Revised: 10/21/2023] [Accepted: 10/23/2023] [Indexed: 11/04/2023] Open
Abstract
Understanding the dynamic changes in gene expression during Acute Respiratory Distress Syndrome (ARDS) progression in post-acute infection patients is crucial for unraveling the underlying mechanisms. Study investigates the longitudinal changes in gene/transcript expression patterns in hospital-admitted severe COVID-19 patients with ARDS post-acute SARS-CoV-2 infection. Blood samples were collected at three time points and patients were stratified into severe and mild ARDS, based on their oxygenation saturation (SpO2/FiO2) kinetics over 7 d. Decline in transcript diversity was observed over time, particularly in patients with higher severity, indicating dysregulated transcriptional landscape. Comparing gene/transcript-level analyses highlighted a rather limited overlap. With disease progression, a transition towards an inflammatory state was evident. Strong association was found between antibody response and disease severity, characterized by decreased antibody response and activated B cell population in severe cases. Bayesian network analysis identified various factors associated with disease progression and severity, viz. humoral response, TLR signaling, inflammatory response, interferon response, and effector T cell abundance. The findings highlight dynamic gene/transcript expression changes during ARDS progression, impact on tissue oxygenation and elucidate disease pathogenesis.
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Affiliation(s)
- Priyanka Mehta
- https://ror.org/05ef28661 Division of Immunology and Infectious Disease Biology, INtegrative GENomics of HOst-PathogEn (INGEN-HOPE) Laboratory, CSIR-Institute of Genomics and Integrative Biology (CSIR-IGIB), Delhi, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
| | - Partha Chattopadhyay
- https://ror.org/05ef28661 Division of Immunology and Infectious Disease Biology, INtegrative GENomics of HOst-PathogEn (INGEN-HOPE) Laboratory, CSIR-Institute of Genomics and Integrative Biology (CSIR-IGIB), Delhi, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
| | - Ramakant Mohite
- https://ror.org/05ef28661 Division of Immunology and Infectious Disease Biology, INtegrative GENomics of HOst-PathogEn (INGEN-HOPE) Laboratory, CSIR-Institute of Genomics and Integrative Biology (CSIR-IGIB), Delhi, India
| | - Ranit D'Rozario
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
- https://ror.org/01kh0x418 IICB-Translational Research Unit of Excellence, CSIR-Indian Institute of Chemical Biology, Kolkata, India
| | - Purbita Bandopadhyay
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
- https://ror.org/01kh0x418 IICB-Translational Research Unit of Excellence, CSIR-Indian Institute of Chemical Biology, Kolkata, India
| | - Jafar Sarif
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
- https://ror.org/01kh0x418 IICB-Translational Research Unit of Excellence, CSIR-Indian Institute of Chemical Biology, Kolkata, India
| | - Yogiraj Ray
- Infectious Disease and Beleghata General Hospital, Kolkata, India
- Department of Infectious Diseases, Shambhunath Pandit Hospital, Institute of Postgraduate Medical Education and Research, Kolkata, India
| | - Dipyaman Ganguly
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
- https://ror.org/01kh0x418 IICB-Translational Research Unit of Excellence, CSIR-Indian Institute of Chemical Biology, Kolkata, India
| | - Rajesh Pandey
- https://ror.org/05ef28661 Division of Immunology and Infectious Disease Biology, INtegrative GENomics of HOst-PathogEn (INGEN-HOPE) Laboratory, CSIR-Institute of Genomics and Integrative Biology (CSIR-IGIB), Delhi, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
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68
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O'Neill A, Mantri CK, Tan CW, Saron WAA, Nagaraj SK, Kala MP, Joy CM, Rathore APS, Tripathi S, Wang LF, St John AL. Mucosal SARS-CoV-2 vaccination of rodents elicits superior systemic T central memory function and cross-neutralising antibodies against variants of concern. EBioMedicine 2024; 99:104924. [PMID: 38113758 PMCID: PMC10772395 DOI: 10.1016/j.ebiom.2023.104924] [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: 02/08/2023] [Revised: 11/27/2023] [Accepted: 12/02/2023] [Indexed: 12/21/2023] Open
Abstract
BACKGROUND COVID-19 vaccines used in humans are highly effective in limiting disease and death caused by the SARS-CoV-2 virus, yet improved vaccines that provide greater protection at mucosal surfaces, which could reduce break-through infections and subsequent transmission, are still needed. METHODS Here we tested an intranasal (I.N.) vaccination with the receptor binding domain of Spike antigen of SARS-CoV-2 (S-RBD) in combination with the mucosal adjuvant mastoparan-7 compared with the sub-cutaneous (S.C.) route, adjuvanted by either M7 or the gold-standard adjuvant, alum, in mice, for immunological read-outs. The same formulation delivered I.N. or S.C. was tested in hamsters to assess efficacy. FINDINGS I.N. vaccination improved systemic T cell responses compared to an equivalent dose of antigen delivered S.C. and T cell phenotypes induced by I.N. vaccine administration included enhanced polyfunctionality (combined IFN-γ and TNF expression) and greater numbers of T central memory (TCM) cells. These phenotypes were T cell-intrinsic and could be recalled in the lungs and/or brachial LNs upon antigen challenge after adoptive T cell transfer to naïve recipients. Furthermore, mucosal vaccination induced antibody responses that were similarly effective in neutralising the binding of the parental strain of S-RBD to its ACE2 receptor, but showed greater cross-neutralising capacity against multiple variants of concern (VOC), compared to S.C. vaccination. I.N. vaccination provided significant protection from lung pathology compared to unvaccinated animals upon challenge with homologous and heterologous SARS-CoV-2 strains in a hamster model. INTERPRETATION These results highlight the role of nasal vaccine administration in imprinting an immune profile associated with long-term T cell retention and diversified neutralising antibody responses, which could be applied to improve vaccines for COVID-19 and other infectious diseases. FUNDING This study was funded by Duke-NUS Medical School, the Singapore Ministry of Education, the National Medical Research Council of Singapore and a DBT-BIRAC Grant.
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Affiliation(s)
- Aled O'Neill
- Program in Emerging Infectious Diseases, Duke-National University of Singapore Medical School, 169857, Singapore
| | - Chinmay Kumar Mantri
- Program in Emerging Infectious Diseases, Duke-National University of Singapore Medical School, 169857, Singapore
| | - Chee Wah Tan
- Program in Emerging Infectious Diseases, Duke-National University of Singapore Medical School, 169857, Singapore; Infectious Diseases Translational Research Programme, Department of Microbiology and Immunology, Yong Loo Lin School of Medicine, National University of Singapore, 117545, Singapore
| | - Wilfried A A Saron
- Program in Emerging Infectious Diseases, Duke-National University of Singapore Medical School, 169857, Singapore
| | - Santhosh Kambaiah Nagaraj
- Centre for Infectious Disease Research, Microbiology and Cell Biology Department, Indian Institute of Science, Bengaluru, 560012, India
| | - Monica Palanichamy Kala
- Program in Emerging Infectious Diseases, Duke-National University of Singapore Medical School, 169857, Singapore
| | - Christy Margarat Joy
- Centre for Infectious Disease Research, Microbiology and Cell Biology Department, Indian Institute of Science, Bengaluru, 560012, India
| | - Abhay P S Rathore
- Program in Emerging Infectious Diseases, Duke-National University of Singapore Medical School, 169857, Singapore; Department of Pathology, Duke University Medical Centre, Durham, North Carolina, 27705, USA
| | - Shashank Tripathi
- Centre for Infectious Disease Research, Microbiology and Cell Biology Department, Indian Institute of Science, Bengaluru, 560012, India
| | - Lin-Fa Wang
- Program in Emerging Infectious Diseases, Duke-National University of Singapore Medical School, 169857, Singapore; SingHealth Duke-NUS Global Health Institute, Singapore
| | - Ashley L St John
- Program in Emerging Infectious Diseases, Duke-National University of Singapore Medical School, 169857, Singapore; Department of Pathology, Duke University Medical Centre, Durham, North Carolina, 27705, USA; SingHealth Duke-NUS Global Health Institute, Singapore; Department of Microbiology and Immunology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore.
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69
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Wen Z, Fang C, Liu X, Liu Y, Li M, Yuan Y, Han Z, Wang C, Zhang T, Sun C. A recombinant Mycobacterium smegmatis-based surface display system for developing the T cell-based COVID-19 vaccine. Hum Vaccin Immunother 2023; 19:2171233. [PMID: 36785935 PMCID: PMC10012901 DOI: 10.1080/21645515.2023.2171233] [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: 02/15/2023] Open
Abstract
The immune escape mutations of SARS-CoV-2 variants emerged frequently, posing a new challenge to weaken the protective efficacy of current vaccines. Thus, the development of novel SARS-CoV-2 vaccines is of great significance for future epidemic prevention and control. We herein reported constructing the attenuated Mycobacterium smegmatis (M. smegmatis) as a bacterial surface display system to carry the spike (S) and nucleocapsid (N) of SARS-CoV-2. To mimic the native localization on the surface of viral particles, the S or N antigen was fused with truncated PE_PGRS33 protein, which is a transportation component onto the cell wall of Mycobacterium tuberculosis (M.tb). The sub-cellular fraction analysis demonstrated that S or N protein was exactly expressed onto the surface (cell wall) of the recombinant M. smegmatis. After the immunization of the M. smegmatis-based COVID-19 vaccine candidate in mice, S or N antigen-specific T cell immune responses were effectively elicited, and the subsets of central memory CD4+ T cells and CD8+ T cells were significantly induced. Further analysis showed that there were some potential cross-reactive CTL epitopes between SARS-CoV-2 and M.smegmatis. Overall, our data provided insights that M. smegmatis-based bacterial surface display system could be a suitable vector for developing T cell-based vaccines against SARS-CoV-2 and other infectious diseases.
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Affiliation(s)
- Ziyu Wen
- School of Public Health (Shenzhen), Shenzhen Campus of Sun Yat-sen University, Shenzhen, China
| | - Cuiting Fang
- State Key Laboratory of Respiratory Disease, Guangzhou Institutes of Biomedicine and Health (GIBH), Chinese Academy of Sciences (CAS), Guangzhou, China.,University of Chinese Academy of Sciences (UCAS), Beijing, China.,Guangdong-Hong Kong-Macau Joint Laboratory of Respiratory Infectious Diseases, Guangzhou, China.,China-New Zealand Joint Laboratory on Biomedicine and Health, Guangzhou, China
| | - Xinglai Liu
- School of Public Health (Shenzhen), Shenzhen Campus of Sun Yat-sen University, Shenzhen, China
| | - Yan Liu
- State Key Laboratory of Respiratory Disease, Guangzhou Institutes of Biomedicine and Health (GIBH), Chinese Academy of Sciences (CAS), Guangzhou, China.,University of Chinese Academy of Sciences (UCAS), Beijing, China.,Guangdong-Hong Kong-Macau Joint Laboratory of Respiratory Infectious Diseases, Guangzhou, China
| | - Minchao Li
- School of Public Health (Shenzhen), Shenzhen Campus of Sun Yat-sen University, Shenzhen, China
| | - Yue Yuan
- School of Public Health (Shenzhen), Shenzhen Campus of Sun Yat-sen University, Shenzhen, China
| | - Zirong Han
- School of Public Health (Shenzhen), Shenzhen Campus of Sun Yat-sen University, Shenzhen, China
| | - Congcong Wang
- School of Public Health (Shenzhen), Shenzhen Campus of Sun Yat-sen University, Shenzhen, China
| | - Tianyu Zhang
- State Key Laboratory of Respiratory Disease, Guangzhou Institutes of Biomedicine and Health (GIBH), Chinese Academy of Sciences (CAS), Guangzhou, China.,University of Chinese Academy of Sciences (UCAS), Beijing, China.,Guangdong-Hong Kong-Macau Joint Laboratory of Respiratory Infectious Diseases, Guangzhou, China.,China-New Zealand Joint Laboratory on Biomedicine and Health, Guangzhou, China
| | - Caijun Sun
- School of Public Health (Shenzhen), Shenzhen Campus of Sun Yat-sen University, Shenzhen, China.,Ministry of Education, Key Laboratory of Tropical Disease Control (Sun Yat-sen University), Guangzhou, China
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70
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Wang Y, Yang L, Tang K, Zhang Y, Zhang C, Zhang Y, Jin B, Zhang Y, Zhuang R, Ma Y. Ad5-nCoV Vaccination Could Induce HLA-E Restricted CD8 + T Cell Responses Specific for Epitopes on Severe Acute Respiratory Syndrome Coronavirus 2 Spike Protein. Viruses 2023; 16:52. [PMID: 38257752 PMCID: PMC10820189 DOI: 10.3390/v16010052] [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: 11/08/2023] [Revised: 12/27/2023] [Accepted: 12/27/2023] [Indexed: 01/24/2024] Open
Abstract
We evaluated cellular immune responses induced by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) vaccines in an immunized population based on HLA-E-restricted CD8+ T cell epitope identification. HLA-E-restricted SARS-CoV-2 CD8+ T cell nonamer peptides were predicted with software. An HLA-E-transfected K562 cell binding assay was used to screen for high-affinity peptides. IFN-γ enzyme-linked immunospot assays were used to identify HLA-E-restricted epitopes. An HLA-E/epitope tetramer was employed to detect the frequencies of epitope-specific CD8+ T cells. Four CD8+ T cell epitopes on the spike protein of SARS-CoV-2 restricted by both HLA-E*0101 and E*0103 were identified. HLA-E-restricted epitope-specific IFN-γ-secreting CD8+ T cell responses could be detected in individuals vaccinated with SARS-CoV-2 vaccines. Importantly, the frequencies of epitope-specific CD8+ T cells in Ad5-nCoV vaccinated individuals were higher than in individuals vaccinated with recombinant protein or inactivated vaccines. Moreover, the frequencies of epitope-specific CD8+ T cells could be maintained for at least 120 days after only one dose of Ad5-nCoV vaccine, while the frequencies of epitope-specific CD8+ T cells decreased in individuals after two doses of Ad5-nCoV vaccine. These findings may contribute to a more comprehensive evaluation of the protective effects of vaccines for SARS-CoV-2; meanwhile, they may provide information to characterize HLA-E-restricted CD8+ T cell immunity against SARS-CoV-2 infection.
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Affiliation(s)
| | | | | | | | | | | | | | | | - Ran Zhuang
- Department of Immunology, Air Force Medical University, Xi’an 710032, China; (Y.W.); (L.Y.); (K.T.); (Y.Z.); (C.Z.); (Y.Z.); (B.J.); (Y.Z.)
| | - Ying Ma
- Department of Immunology, Air Force Medical University, Xi’an 710032, China; (Y.W.); (L.Y.); (K.T.); (Y.Z.); (C.Z.); (Y.Z.); (B.J.); (Y.Z.)
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71
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Bar-On L, Dekel H, Aftalion M, Chitlaru T, Erez N. Essential role for Batf3-dependent dendritic cells in regulating CD8 T-cell response during SARS-CoV-2 infection. PLoS One 2023; 18:e0294176. [PMID: 38150441 PMCID: PMC10752548 DOI: 10.1371/journal.pone.0294176] [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: 07/17/2023] [Accepted: 10/26/2023] [Indexed: 12/29/2023] Open
Abstract
SARS-CoV-2 infection elicits robust CD8 T-cell responses, yet the identity of the mechanisms playing dominant roles in initiating the virus-specific CD8 T-cell responses are largely unknown. In the present study, we interrogate the contribution of the cDC1 subset to SARS-CoV-2-specific CD8 T-cell immunity. For this purpose, we used a novel murine line which combines the SARS-CoV-2 susceptible K18-hACE2 transgenic and the Batf3 deficient mice which lack the cDC1 subset. We demonstrate that in the absence of cDC1, viral-specific CD8 T-cell responses were severely impaired both in the draining lymph node as well as in the lungs, during the effector phase of SARS-CoV-2 infection. Furthermore, SARS-CoV-2 specific memory CD8 T-cells in the lungs and spleens were also significantly impacted, whereas humoral responses, as well as CD4 T-cells were not affected. Additionally, we demonstrate that the absence of cDC1 subset, and the consequent impaired CD8 T-cell responses, resulted in significant increase in SARS-CoV-2 viral load in the lungs. The conclusions of the study were further independently corroborated in an additional COVID-19 murine model consisting infection with a mouse-adapted SARS-CoV-2 virus. These results underscore a specific role for Batf3-dependent DC in regulating SARS-CoV-2 specific CD8 T-cell responses and may contribute to future vaccine design and immunization strategies.
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Affiliation(s)
- Liat Bar-On
- Department of Biochemistry and Molecular Genetics, Israel Institute for Biological Research, Ness-Ziona, Israel
| | - Hani Dekel
- Veterinary Center for Preclinical Research, Israel Institute for Biological Research, Ness-Ziona, Israel
| | - Moshe Aftalion
- Department of Biochemistry and Molecular Genetics, Israel Institute for Biological Research, Ness-Ziona, Israel
| | - Theodor Chitlaru
- Department of Biochemistry and Molecular Genetics, Israel Institute for Biological Research, Ness-Ziona, Israel
| | - Noam Erez
- Department of Infectious Diseases, Israel Institute for Biological Research, Ness-Ziona, Israel
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Esteban I, Pastor-Quiñones C, Usero L, Aurrecoechea E, Franceschini L, Esprit A, Gelpí JL, Martínez-Jiménez F, López-Bigas N, Breckpot K, Thielemans K, Leal L, Gómez CE, Sisteré-Oró M, Meyerhans A, Esteban M, Alonso MJ, García F, Plana M. Assessment of Human SARS CoV-2-Specific T-Cell Responses Elicited In Vitro by New Computationally Designed mRNA Immunogens (COVARNA). Vaccines (Basel) 2023; 12:15. [PMID: 38250827 PMCID: PMC10820377 DOI: 10.3390/vaccines12010015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2023] [Revised: 12/12/2023] [Accepted: 12/18/2023] [Indexed: 01/23/2024] Open
Abstract
The COVID-19 pandemic has brought significant changes and advances in the field of vaccination, including the implementation and widespread use of encapsidated mRNA vaccines in general healthcare practice. Here, we present two new mRNAs expressing antigenic parts of the SARS-CoV-2 spike protein and provide data supporting their functionality. The first mRNA, called RBD-mRNA, encodes a trimeric form of the virus spike protein receptor binding domain (RBD). The other mRNA, termed T-mRNA, codes for the relevant HLA I and II spike epitopes. The two mRNAs (COVARNA mRNAs) were designed to be used for delivery to cells in combination, with the RBD-mRNA being the primary source of antigen and the T-mRNA working as an enhancer of immunogenicity by supporting CD4 and CD8 T-cell activation. This innovative approach substantially differs from other available mRNA vaccines, which are largely directed to antibody production by the entire spike protein. In this study, we first show that both mRNAs are functionally transfected into human antigen-presenting cells (APCs). We obtained peripheral blood mononuclear cell (PBMC) samples from three groups of voluntary donors differing in their immunity against SARS-CoV-2: non-infected (naïve), infected-recovered (convalescent), and vaccinated. Using an established method of co-culturing autologous human dendritic cells (hDCs) with T-cells, we detected proliferation and cytokine secretion, thus demonstrating the ability of the COVARNA mRNAs to activate T-cells in an antigen-specific way. Interestingly, important differences in the intensity of the response between the infected-recovered (convalescent) and vaccinated donors were observed, with the levels of T-cell proliferation and cytokine secretion (IFNγ, IL-2R, and IL-13) being higher in the vaccinated group. In summary, our data support the further study of these mRNAs as a combined approach for future use as a vaccine.
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Affiliation(s)
- Ignasi Esteban
- Institut d’Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Hospital Clínic, University of Barcelona, 08036 Barcelona, Spain; (I.E.); (C.P.-Q.); (L.U.); (E.A.); or (L.L.); (F.G.)
| | - Carmen Pastor-Quiñones
- Institut d’Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Hospital Clínic, University of Barcelona, 08036 Barcelona, Spain; (I.E.); (C.P.-Q.); (L.U.); (E.A.); or (L.L.); (F.G.)
| | - Lorena Usero
- Institut d’Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Hospital Clínic, University of Barcelona, 08036 Barcelona, Spain; (I.E.); (C.P.-Q.); (L.U.); (E.A.); or (L.L.); (F.G.)
| | - Elena Aurrecoechea
- Institut d’Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Hospital Clínic, University of Barcelona, 08036 Barcelona, Spain; (I.E.); (C.P.-Q.); (L.U.); (E.A.); or (L.L.); (F.G.)
| | - Lorenzo Franceschini
- Laboratory for Molecular and Cellular Therapy, Department of Biomedical Sciences, Vrije Universiteit Brussel, 1090 Brussels, Belgium; (L.F.); (A.E.); (K.B.); (K.T.)
| | - Arthur Esprit
- Laboratory for Molecular and Cellular Therapy, Department of Biomedical Sciences, Vrije Universiteit Brussel, 1090 Brussels, Belgium; (L.F.); (A.E.); (K.B.); (K.T.)
| | - Josep Lluís Gelpí
- Department of Biochemistry and Molecular Biomedicine, University of Barcelona, 08028 Barcelona, Spain;
- Barcelona Supercomputing Center (BSC), 08034 Barcelona, Spain
| | - Francisco Martínez-Jiménez
- Institute for Research in Biomedicine (IRB Barcelona), Barcelona Institute of Science and Technology, 08028 Barcelona, Spain; (F.M.-J.); (N.L.-B.)
| | - Núria López-Bigas
- Institute for Research in Biomedicine (IRB Barcelona), Barcelona Institute of Science and Technology, 08028 Barcelona, Spain; (F.M.-J.); (N.L.-B.)
- Institució Catalana de Recerca i Estudis Avançats (ICREA), 08010 Barcelona, Spain;
- Centro de Investigación Biomédica en Red en Cáncer (CIBERONC), Instituto de Salud Carlos III, 28029 Madrid, Spain
| | - Karine Breckpot
- Laboratory for Molecular and Cellular Therapy, Department of Biomedical Sciences, Vrije Universiteit Brussel, 1090 Brussels, Belgium; (L.F.); (A.E.); (K.B.); (K.T.)
| | - Kris Thielemans
- Laboratory for Molecular and Cellular Therapy, Department of Biomedical Sciences, Vrije Universiteit Brussel, 1090 Brussels, Belgium; (L.F.); (A.E.); (K.B.); (K.T.)
| | - Lorna Leal
- Institut d’Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Hospital Clínic, University of Barcelona, 08036 Barcelona, Spain; (I.E.); (C.P.-Q.); (L.U.); (E.A.); or (L.L.); (F.G.)
- Department of Infectious Diseases, Hospital Clínic, University of Barcelona, 08036 Barcelona, Spain
| | - Carmen Elena Gómez
- Department of Molecular and Cellular Biology, Centro Nacional de Biotecnología (CNB), Consejo Superior de Investigaciones Científicas (CSIC), 28049 Madrid, Spain; (C.E.G.); (M.E.)
- Centro de Investigación Biomédica en Red de Enfermedades Infecciosas (CIBERINFEC), Instituto de Salud Carlos III (ISCIII), 28029 Madrid, Spain
| | - Marta Sisteré-Oró
- Infection Biology Laboratory, Department of Medicine and Life Sciences, Pompeu Fabra University, 08003 Barcelona, Spain;
| | - Andreas Meyerhans
- Institució Catalana de Recerca i Estudis Avançats (ICREA), 08010 Barcelona, Spain;
- Infection Biology Laboratory, Department of Medicine and Life Sciences, Pompeu Fabra University, 08003 Barcelona, Spain;
| | - Mariano Esteban
- Department of Molecular and Cellular Biology, Centro Nacional de Biotecnología (CNB), Consejo Superior de Investigaciones Científicas (CSIC), 28049 Madrid, Spain; (C.E.G.); (M.E.)
| | - María José Alonso
- Center for Research in Molecular Medicine and Chronic Diseases (CiMUS), Campus Vida, Universidade de Santiago de Compostela, 15782 Santiago de Compostela, Spain;
| | - Felipe García
- Institut d’Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Hospital Clínic, University of Barcelona, 08036 Barcelona, Spain; (I.E.); (C.P.-Q.); (L.U.); (E.A.); or (L.L.); (F.G.)
- Department of Infectious Diseases, Hospital Clínic, University of Barcelona, 08036 Barcelona, Spain
| | - Montserrat Plana
- Institut d’Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Hospital Clínic, University of Barcelona, 08036 Barcelona, Spain; (I.E.); (C.P.-Q.); (L.U.); (E.A.); or (L.L.); (F.G.)
- Centro de Investigación Biomédica en Red de Enfermedades Infecciosas (CIBERINFEC), Instituto de Salud Carlos III (ISCIII), 28029 Madrid, Spain
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Almazán NM, Rahbar A, Carlsson M, Hoffman T, Kolstad L, Rönnberg B, Pantalone MR, Fuchs IL, Nauclér A, Ohlin M, Sacharczuk M, Religa P, Amér S, Molnár C, Lundkvist Å, Susrud A, Sörensen B, Söderberg-Nauclér C. Influenza-A mediated pre-existing immunity levels to SARS-CoV-2 could predict early COVID-19 outbreak dynamics. iScience 2023; 26:108441. [PMID: 38144451 PMCID: PMC10746369 DOI: 10.1016/j.isci.2023.108441] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2023] [Revised: 09/14/2023] [Accepted: 11/09/2023] [Indexed: 12/26/2023] Open
Abstract
Susceptibility to severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infections is highly variable and could be mediated by a cross-protective pre-immunity. We identified 14 cross-reactive peptides between SARS-CoV-2 and influenza A H1N1, H3N2, and human herpesvirus (HHV)-6A/B with potential relevance. The H1N1 peptide NGVEGF was identical to a peptide in the most critical receptor binding motif in SARS-CoV-2 spike protein that interacts with the angiotensin converting enzyme 2 receptor. About 62%-73% of COVID-19-negative blood donors in Stockholm had antibodies to this peptide in the early pre-vaccination phase of the pandemic. Seasonal flu vaccination enhanced neutralizing capacity to SARS-CoV-2 and T cell immunity to this peptide. Mathematical modeling taking the estimated pre-immunity levels to flu into account could fully predict pre-Omicron SARS-CoV-2 outbreaks in Stockholm and India. This cross-immunity provides mechanistic explanations to the epidemiological observation that influenza vaccination protected people against early SARS-CoV-2 infections and implies that flu-mediated cross-protective immunity significantly dampened the first SARS-CoV-2 outbreaks.
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Affiliation(s)
- Nerea Martín Almazán
- Department of Medicine, Unit for Microbial Pathogenesis, Karolinska Institutet, 17164 Solna, Stockholm, Sweden
- Department of Neurology, Karolinska University Hospital, 171 76 Solna Stockholm, Sweden
- Department of Laboratory Medicine, Division of Pathology, Karolinska Institutet, 141 86 Huddinge Stockholm, Sweden
| | - Afsar Rahbar
- Department of Medicine, Unit for Microbial Pathogenesis, Karolinska Institutet, 17164 Solna, Stockholm, Sweden
- Department of Neurology, Karolinska University Hospital, 171 76 Solna Stockholm, Sweden
| | - Marcus Carlsson
- Centre for the Mathematical Sciences, Lund University, 223 62 Lund, Sweden
| | - Tove Hoffman
- Zoonosis Science Center (ZSC), Department of Medical Biochemistry and Microbiology (IMBIM), Uppsala University, 1477 Uppsala, Sweden
| | - Linda Kolstad
- Zoonosis Science Center (ZSC), Department of Medical Biochemistry and Microbiology (IMBIM), Uppsala University, 1477 Uppsala, Sweden
| | - Bengt Rönnberg
- Zoonosis Science Center (ZSC), Department of Medical Biochemistry and Microbiology (IMBIM), Uppsala University, 1477 Uppsala, Sweden
| | - Mattia Russel Pantalone
- Department of Medicine, Unit for Microbial Pathogenesis, Karolinska Institutet, 17164 Solna, Stockholm, Sweden
- Department of Neurology, Karolinska University Hospital, 171 76 Solna Stockholm, Sweden
| | - Ilona Lewensohn Fuchs
- Department of Labortory Medicine, Division of Clinical Microbiology, Karolinska Institutet, 141 86 Huddinge Stockholm, Sweden
- Department of Clinical Microbiology, Karolinska University Hospital, 141 86 Huddinge Stockholm, Sweden
| | - Anna Nauclér
- Department of Medicine, Unit for Microbial Pathogenesis, Karolinska Institutet, 17164 Solna, Stockholm, Sweden
| | - Mats Ohlin
- Department of Immunotechnology and SciLifeLab Human Antibody Therapeutics Infrastructure Unit, Lund University, 223 62 Lund, Sweden
| | - Mariusz Sacharczuk
- Faculty of Pharmacy with the Laboratory Medicine Division, Department of Pharmacodynamics, Medical University of Warsaw, Centre for Preclinical Research and Technology, Banacha 1B, 02-091 Warsaw, Poland
- Department of Experimental Genomics, Institute of Genetics and Animal Biotechnology, Polish Academy of Sciences, Postępu 36A, 05-552 Magdalenka, Poland
| | - Piotr Religa
- Department of Medicine, Unit for Microbial Pathogenesis, Karolinska Institutet, 17164 Solna, Stockholm, Sweden
- Department of Neurology, Karolinska University Hospital, 171 76 Solna Stockholm, Sweden
- Department of Experimental Genomics, Institute of Genetics and Animal Biotechnology, Polish Academy of Sciences, Postępu 36A, 05-552 Magdalenka, Poland
| | - Stefan Amér
- Familjeläkarna Saltsjöbaden, 133 34 Saltsjöbaden, Sweden
| | - Christian Molnár
- Familjeläkarna Saltsjöbaden, 133 34 Saltsjöbaden, Sweden
- Department of Neurobiology, Care Sciences and Society, NVS, Karolinska Institutet, 171 77 Stockholm, Sweden
| | - Åke Lundkvist
- Zoonosis Science Center (ZSC), Department of Medical Biochemistry and Microbiology (IMBIM), Uppsala University, 1477 Uppsala, Sweden
| | | | | | - Cecilia Söderberg-Nauclér
- Department of Medicine, Unit for Microbial Pathogenesis, Karolinska Institutet, 17164 Solna, Stockholm, Sweden
- Department of Neurology, Karolinska University Hospital, 171 76 Solna Stockholm, Sweden
- Institute of Biomedicine, Unit for Infection and Immunology, MediCity Research Laboratory, University of Turku, FI-20014 Turku, Finland
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Andrade VM, Maricic I, Kalia R, Jachimowicz L, Bedoya O, Kulp DW, Humeau L, Smith TRF. Delineation of DNA and mRNA COVID-19 vaccine-induced immune responses in preclinical animal models. Hum Vaccin Immunother 2023; 19:2281733. [PMID: 38012018 PMCID: PMC10760386 DOI: 10.1080/21645515.2023.2281733] [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: 07/17/2023] [Accepted: 11/03/2023] [Indexed: 11/29/2023] Open
Abstract
Nucleic acid vaccines are designed based on genetic sequences (DNA or mRNA) of a target antigen to be expressed in vivo to drive a host immune response. In response to the COVID-19 pandemic, mRNA and DNA vaccines based on the SARS-CoV-2 Spike antigen were developed. Surprisingly, head-to-head characterizations of the immune responses elicited by each vaccine type has not been performed to date. Here, we have employed a range of preclinical animal models including the hamster, guinea pig, rabbit, and mouse to compare and delineate the immune response raised by DNA, administered intradermally (ID) with electroporation (EP) and mRNA vaccines (BNT162b2 or mRNA-1273), administered intramuscularly (IM), expressing the SARS-CoV-2 WT spike antigen. The results revealed clear differences in the quality and magnitude of the immune response between the two vaccine platforms. The DNA vaccine immune response was characterized by strong T cell responses, while the mRNA vaccine elicited robust humoral responses. The results may assist in guiding the disease target each vaccine type may be best matched against and suggest mechanisms to further enhance the breadth of each platform's immune response.
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Affiliation(s)
| | - Igor Maricic
- Preclinical R&D, Inovio Pharmaceuticals Inc, San Diego, CA, USA
| | - Richa Kalia
- Preclinical R&D, Inovio Pharmaceuticals Inc, San Diego, CA, USA
| | | | - Olivia Bedoya
- Preclinical R&D, Inovio Pharmaceuticals Inc, San Diego, CA, USA
| | - Daniel W. Kulp
- Vaccine and Immunotherapy Center, The Wistar Institute, Philadelphia, PA, USA
| | - Laurent Humeau
- Preclinical R&D, Inovio Pharmaceuticals Inc, San Diego, CA, USA
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75
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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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Song L, Wang Q, Wen Y, Tan R, Cui Y, Xiong D, Jiao X, Pan Z. Enhanced immunogenicity elicited by a novel DNA vaccine encoding the SARS-CoV-2 S1 protein fused to the optimized flagellin of Salmonella typhimurium in mice. Microbiol Spectr 2023; 11:e0254923. [PMID: 37909745 PMCID: PMC10714832 DOI: 10.1128/spectrum.02549-23] [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: 06/18/2023] [Accepted: 09/08/2023] [Indexed: 11/03/2023] Open
Abstract
IMPORTANCE The development of safe and effective vaccines is needed to control the transmission of coronavirus disease 2019 (COVID-19). Synthetic DNA vaccines represent a promising platform in response to such outbreaks. Here, DNA vaccine candidates were developed using an optimized antibiotic-resistance gene-free asd-pVAX1 vector. An optimized flagellin (FliC) adjuvant was designed by fusion expression to increase the immunogenicity of the S1 antigen. S1 and S1-FliCΔD2D3 proteins were strongly expressed in mammalian cells. The FliCΔD2D3-adjuvanted DNA vaccine induced Th1/Th2-mixed immune responses and high titers of neutralizing antibodies. This study provides crucial information regarding the selection of a safer DNA vector and adjuvant for vaccine development. Our FliCΔD2D3-adjuvanted S1 DNA vaccine is more potent at inducing both humoral and cellular immune responses than S1 alone. This finding provides a new idea for the development of novel DNA vaccines against COVID-19 and could be further applied for the development of other vaccines.
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Affiliation(s)
- Li Song
- Jiangsu Key Laboratory of Zoonosis, Yangzhou University, Yangzhou, Jiangsu, China
- Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou, Jiangsu, China
- Key Laboratory of Prevention and Control of Biological Hazard Factors (Animal Origin) for Agrifood Safety and Quality, Ministry of Agriculture of China, Yangzhou University, Yangzhou, Jiangsu, China
| | - Qiaoju Wang
- Jiangsu Key Laboratory of Zoonosis, Yangzhou University, Yangzhou, Jiangsu, China
- Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou, Jiangsu, China
- Key Laboratory of Prevention and Control of Biological Hazard Factors (Animal Origin) for Agrifood Safety and Quality, Ministry of Agriculture of China, Yangzhou University, Yangzhou, Jiangsu, China
| | - Yaya Wen
- Jiangsu Key Laboratory of Zoonosis, Yangzhou University, Yangzhou, Jiangsu, China
- Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou, Jiangsu, China
- Key Laboratory of Prevention and Control of Biological Hazard Factors (Animal Origin) for Agrifood Safety and Quality, Ministry of Agriculture of China, Yangzhou University, Yangzhou, Jiangsu, China
| | - Ruimeng Tan
- Jiangsu Key Laboratory of Zoonosis, Yangzhou University, Yangzhou, Jiangsu, China
- Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou, Jiangsu, China
- Key Laboratory of Prevention and Control of Biological Hazard Factors (Animal Origin) for Agrifood Safety and Quality, Ministry of Agriculture of China, Yangzhou University, Yangzhou, Jiangsu, China
| | - Yaodan Cui
- Jiangsu Key Laboratory of Zoonosis, Yangzhou University, Yangzhou, Jiangsu, China
- Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou, Jiangsu, China
- Key Laboratory of Prevention and Control of Biological Hazard Factors (Animal Origin) for Agrifood Safety and Quality, Ministry of Agriculture of China, Yangzhou University, Yangzhou, Jiangsu, China
| | - Dan Xiong
- Jiangsu Key Laboratory of Zoonosis, Yangzhou University, Yangzhou, Jiangsu, China
- Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou, Jiangsu, China
- Key Laboratory of Prevention and Control of Biological Hazard Factors (Animal Origin) for Agrifood Safety and Quality, Ministry of Agriculture of China, Yangzhou University, Yangzhou, Jiangsu, China
| | - Xinan Jiao
- Jiangsu Key Laboratory of Zoonosis, Yangzhou University, Yangzhou, Jiangsu, China
- Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou, Jiangsu, China
- Key Laboratory of Prevention and Control of Biological Hazard Factors (Animal Origin) for Agrifood Safety and Quality, Ministry of Agriculture of China, Yangzhou University, Yangzhou, Jiangsu, China
| | - Zhiming Pan
- Jiangsu Key Laboratory of Zoonosis, Yangzhou University, Yangzhou, Jiangsu, China
- Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou, Jiangsu, China
- Key Laboratory of Prevention and Control of Biological Hazard Factors (Animal Origin) for Agrifood Safety and Quality, Ministry of Agriculture of China, Yangzhou University, Yangzhou, Jiangsu, China
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Petersen MS, Pérez-Alós L, í Kongsstovu SK, Eliasen EH, Hansen CB, Larsen S, Hansen JL, Bayarri-Olmos R, Fjallsbak JP, Weihe P, Garred P. Diverging humoral and cellular immune responses due to Omicron-a national study from the Faroe Islands. Microbiol Spectr 2023; 11:e0086523. [PMID: 37909772 PMCID: PMC10714973 DOI: 10.1128/spectrum.00865-23] [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: 02/27/2023] [Accepted: 09/30/2023] [Indexed: 11/03/2023] Open
Abstract
IMPORTANCE The immunity following infection and vaccination with the SARS-CoV-2 Omicron variant is poorly understood. We investigated immunity assessed with antibody and T-cell responses under different scenarios in vaccinated and unvaccinated individuals with and without Omicron infection. We found that the humoral response was higher among vaccinated-naïve than unvaccinated convalescent. Unvaccinated with and without infection had comparable low humoral responses, whereas vaccinated with a second or third dose, independent of infection status, had increasingly higher levels. Only a minor fraction of unvaccinated individuals had detectable humoral responses following Omicron infection, while almost all had positive T-cell responses. In conclusion, primary Omicron infection mounts a low humoral immune response, enhanced by prior vaccination. Omicron infection induced a robust T-cell response in both unvaccinated and vaccinated, demonstrating that immune evasion of primary Omicron infection affects humoral immunity more than T-cell immunity.
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Affiliation(s)
- Maria Skaalum Petersen
- Department of Research, The National Hospital of the Faroe Islands, Tórshavn, Faroe Islands
- Center of Health Science, University of the Faroe Islands, Tórshavn, Faroe Islands
| | - Laura Pérez-Alós
- Laboratory of Molecular Medicine, Department of Clinical Immunology, Section 7631, Copenhagen University Hospital, Rigshospitalet, Copenhagen, Denmark
| | | | - Eina Hansen Eliasen
- Department of Research, The National Hospital of the Faroe Islands, Tórshavn, Faroe Islands
| | - Cecilie Bo Hansen
- Laboratory of Molecular Medicine, Department of Clinical Immunology, Section 7631, Copenhagen University Hospital, Rigshospitalet, Copenhagen, Denmark
| | - Sólrun Larsen
- Chief Medical Officer Office, Tórshavn, Faroe Islands
| | | | - Rafael Bayarri-Olmos
- Laboratory of Molecular Medicine, Department of Clinical Immunology, Section 7631, Copenhagen University Hospital, Rigshospitalet, Copenhagen, Denmark
- Recombinant Protein and Antibody Unit, Copenhagen University Hospital, Rigshospitalet, Copenhagen, Denmark
| | | | - Pál Weihe
- Department of Research, The National Hospital of the Faroe Islands, Tórshavn, Faroe Islands
- Center of Health Science, University of the Faroe Islands, Tórshavn, Faroe Islands
| | - Peter Garred
- Laboratory of Molecular Medicine, Department of Clinical Immunology, Section 7631, Copenhagen University Hospital, Rigshospitalet, Copenhagen, Denmark
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Zhang J, Askenase P, Jaenisch R, Crumpacker CS. Approaches to pandemic prevention - the chromatin vaccine. Front Immunol 2023; 14:1324084. [PMID: 38143744 PMCID: PMC10739501 DOI: 10.3389/fimmu.2023.1324084] [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: 10/18/2023] [Accepted: 11/13/2023] [Indexed: 12/26/2023] Open
Abstract
Developing effective vaccines against viral infections have significant impacts on development, prosperity and well-being of human populations. Thus, successful vaccines such as smallpox and polio vaccines, have promoted global societal well-being. In contrast, ineffective vaccines may fuel arguments that retard scientific progress. We aim to stimulate a multilevel discussion on how to develop effective vaccines against recent and future pandemics by focusing on acquired immunodeficiency syndrome (AIDS), coronavirus disease (COVID) and other viral infections. We appeal to harnessing recent achievements in this field specifically towards a cure for current pandemics and prevention of the next pandemics. Among these, we propose to apply the HIV DNA in chromatin format - an end product of aborted HIV integration in episomal forms, i.e., the chromatin vaccines (cVacc), to elicit the epigenetic silencing and memory that prevent viral replication and infection.
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Affiliation(s)
- Jielin Zhang
- Department of Medicine, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, United States
| | - Philip Askenase
- Allergy & Clinical Immunology, Yale School of Medicine, New Haven, CT, United States
| | - Rudolf Jaenisch
- Department of Biology, Whitehead Institute, Massachusetts Institute of Technology, Cambridge, MA, United States
| | - Clyde S. Crumpacker
- Department of Medicine, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, United States
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Cai C, Gao Y, Adamo S, Rivera-Ballesteros O, Hansson L, Österborg A, Bergman P, Sandberg JK, Ljunggren HG, Björkström NK, Strålin K, Llewellyn-Lacey S, Price DA, Qin C, Grifoni A, Weiskopf D, Wherry EJ, Sette A, Aleman S, Buggert M. SARS-CoV-2 vaccination enhances the effector qualities of spike-specific T cells induced by COVID-19. Sci Immunol 2023; 8:eadh0687. [PMID: 38064569 PMCID: PMC7615587 DOI: 10.1126/sciimmunol.adh0687] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2023] [Accepted: 10/31/2023] [Indexed: 12/18/2023]
Abstract
T cells are critical for immune protection against severe COVID-19, but it has remained unclear whether repeated exposure to SARS-CoV-2 antigens delivered in the context of vaccination fuels T cell exhaustion or reshapes T cell functionality. Here, we sampled convalescent donors with a history of mild or severe COVID-19 before and after SARS-CoV-2 vaccination to profile the functional spectrum of hybrid T cell immunity. Using combined single-cell technologies and high-dimensional flow cytometry, we found that the frequencies and functional capabilities of spike-specific CD4+ and CD8+ T cells in previously infected individuals were enhanced by vaccination, despite concomitant increases in the expression of inhibitory receptors such as PD-1 and TIM3. In contrast, CD4+ and CD8+ T cells targeting non-spike proteins remained functionally static and waned over time, and only minimal effects were observed in healthy vaccinated donors experiencing breakthrough infections with SARS-CoV-2. Moreover, hybrid immunity was characterized by elevated expression of IFN-γ, which was linked with clonotype specificity in the CD8+ T cell lineage. Collectively, these findings identify a molecular hallmark of hybrid immunity and suggest that vaccination after infection is associated with cumulative immunological benefits over time, potentially conferring enhanced protection against subsequent episodes of COVID-19.
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Affiliation(s)
- Curtis Cai
- Department of Medicine Huddinge, Center for Infectious Medicine, Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden
| | - Yu Gao
- Department of Medicine Huddinge, Center for Infectious Medicine, Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden
| | - Sarah Adamo
- Department of Medicine Huddinge, Center for Infectious Medicine, Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden
| | - Olga Rivera-Ballesteros
- Department of Medicine Huddinge, Center for Infectious Medicine, Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden
| | - Lotta Hansson
- Department of Hematology, Karolinska University Hospital, Stockholm, Sweden
- Department of Oncology-Pathology, Karolinska Institutet, Stockholm, Sweden
| | - Anders Österborg
- Department of Hematology, Karolinska University Hospital, Stockholm, Sweden
- Department of Oncology-Pathology, Karolinska Institutet, Stockholm, Sweden
| | - Peter Bergman
- Department of Laboratory Medicine, Karolinska Institutet, Stockholm, Sweden
- Department of Clinical Immunology and Transfusion Medicine, Karolinska University Hospital, Stockholm, Sweden
| | - Johan K. Sandberg
- Department of Medicine Huddinge, Center for Infectious Medicine, Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden
| | - Hans-Gustaf Ljunggren
- Department of Medicine Huddinge, Center for Infectious Medicine, Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden
| | - Niklas K. Björkström
- Department of Medicine Huddinge, Center for Infectious Medicine, Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden
| | - Kristoffer Strålin
- Department of Infectious Diseases, Karolinska University Hospital, Stockholm, Sweden
- Department of Medicine Huddinge, Infectious Diseases, Karolinska Institutet, Stockholm, Sweden
| | - Sian Llewellyn-Lacey
- Division of Infection and Immunity, Cardiff University School of Medicine, University Hospital of Wales, Cardiff, UK
| | - David A. Price
- Division of Infection and Immunity, Cardiff University School of Medicine, University Hospital of Wales, Cardiff, UK
- Systems Immunity Research Institute, Cardiff University School of Medicine, University Hospital of Wales, Cardiff, UK
| | - Chuan Qin
- Beijing Key Laboratory for Animal Models of Emerging and Reemerging Infectious Diseases, Institute of Laboratory Animal Science, Chinese Academy of Medical Sciences, Beijing, China
- National Health Commission Key Laboratory of Human Disease Comparative Medicine, Comparative Medicine Center, Peking Union Medical College, Beijing, China
| | - Alba Grifoni
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology, La Jolla, California, USA
| | - Daniela Weiskopf
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology, La Jolla, California, USA
- Department of Medicine, Division of Infectious Diseases and Global Public Health, University of California, San Diego, California, USA
| | - E. John Wherry
- Institute for Immunology, Perelman School of Medicine at the University of Pennsylvania, Pennsylvania, USA
- Department of Systems Pharmacology and Translational Therapeutics, Perelman School of Medicine at the University of Pennsylvania, Pennsylvania, USA
- Parker Institute for Cancer Immunotherapy, Perelman School of Medicine at the University of Pennsylvania, Pennsylvania, USA
| | - Alessandro Sette
- National Health Commission Key Laboratory of Human Disease Comparative Medicine, Comparative Medicine Center, Peking Union Medical College, Beijing, China
- Department of Medicine, Division of Infectious Diseases and Global Public Health, University of California, San Diego, California, USA
| | - Soo Aleman
- Department of Infectious Diseases, Karolinska University Hospital, Stockholm, Sweden
- Department of Medicine Huddinge, Infectious Diseases, Karolinska Institutet, Stockholm, Sweden
| | - Marcus Buggert
- Department of Medicine Huddinge, Center for Infectious Medicine, Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden
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Rabenstein M, Thomas OG, Carlin G, Khademi M, Högelin KA, Malmeström C, Axelsson M, Brandt AF, Gafvelin G, Grönlund H, Kockum I, Piehl F, Lycke J, Olsson T, Hessa T. The impact of hybrid immunity on immune responses after SARS-CoV-2 vaccination in persons with multiple sclerosis treated with disease-modifying therapies. Eur J Neurol 2023; 30:3789-3798. [PMID: 37522464 DOI: 10.1111/ene.16015] [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: 11/09/2022] [Revised: 06/22/2023] [Accepted: 07/27/2023] [Indexed: 08/01/2023]
Abstract
BACKGROUND AND PURPOSE Hybrid immunity to severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) develops from a combination of natural infection and vaccine-generated immunity. Multiple sclerosis (MS) disease-modifying therapies (DMTs) have the potential to impact humoral and cellular immunity induced by SARS-CoV-2 vaccination and infection. The aims were to compare antibody and T-cell responses after SARS-CoV-2 mRNA vaccination in persons with MS (pwMS) treated with different DMTs and to assess differences between naïvely vaccinated pwMS and pwMS with hybrid immunity vaccinated following a previous SARS-CoV-2 infection. METHODS Antibody and T-cell responses were determined in pwMS at baseline and 4 and 12 weeks after the second dose of SARS-CoV-2 vaccination in 143 pwMS with or without previous SARS-CoV-2 infection and 40 healthy controls (HCs). The MS cohort comprised natalizumab (n = 22), dimethylfumarate (n = 23), fingolimod (n = 38), cladribine (n = 30), alemtuzumab (n = 17) and teriflunomide (n = 13) treated pwMS. Immunoglobulin G antibody responses to SARS-CoV-2 antigens were measured using a multiplex bead assay and FluoroSpot was used to assess T-cell responses (interferon γ and interleukin 13). RESULTS Humoral and T-cell responses to vaccination were comparable between naïvely vaccinated HCs and pwMS treated with natalizumab, dimethylfumarate, cladribine, alemtuzumab and teriflunomide, but were suppressed in fingolimod-treated pwMS. Both fingolimod-treated pwMS and HCs vaccinated following a previous SARS-CoV-2 infection had higher antibody levels 4 weeks after vaccination compared to naïvely vaccinated individuals. Antibody and interferon γ levels 12 weeks after vaccination were positively correlated with time from last treatment course of cladribine. CONCLUSION These findings are of relevance for infection risk mitigation and for vaccination strategies amongst pwMS undergoing DMT.
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Affiliation(s)
- Monika Rabenstein
- Therapeutic Immune Design, Department of Clinical Neuroscience, Center for Molecular Medicine L8:02, Karolinska Institute, Stockholm, Sweden
- Neuroimmunology Unit, Department of Clinical Neuroscience, Center for Molecular Medicine L8:04, Karolinska Institute, Stockholm, Sweden
- Department of Neurology, Faculty of Medicine and University Hospital, University of Cologne, Cologne, Germany
| | - Olivia G Thomas
- Therapeutic Immune Design, Department of Clinical Neuroscience, Center for Molecular Medicine L8:02, Karolinska Institute, Stockholm, Sweden
- Neuroimmunology Unit, Department of Clinical Neuroscience, Center for Molecular Medicine L8:04, Karolinska Institute, Stockholm, Sweden
| | - Giorgia Carlin
- Neuroimmunology Unit, Department of Clinical Neuroscience, Center for Molecular Medicine L8:04, Karolinska Institute, Stockholm, Sweden
| | - Mohsen Khademi
- Therapeutic Immune Design, Department of Clinical Neuroscience, Center for Molecular Medicine L8:02, Karolinska Institute, Stockholm, Sweden
| | - Klara Asplund Högelin
- Therapeutic Immune Design, Department of Clinical Neuroscience, Center for Molecular Medicine L8:02, Karolinska Institute, Stockholm, Sweden
| | - Clas Malmeström
- Department of Clinical Neuroscience, Institute of Neuroscience and Physiology at Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Markus Axelsson
- Department of Clinical Neuroscience, Institute of Neuroscience and Physiology at Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Anne Frandsen Brandt
- Department of Clinical Neuroscience, Institute of Neuroscience and Physiology at Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Guro Gafvelin
- Neuroimmunology Unit, Department of Clinical Neuroscience, Center for Molecular Medicine L8:04, Karolinska Institute, Stockholm, Sweden
| | - Hans Grönlund
- Neuroimmunology Unit, Department of Clinical Neuroscience, Center for Molecular Medicine L8:04, Karolinska Institute, Stockholm, Sweden
| | - Ingrid Kockum
- Therapeutic Immune Design, Department of Clinical Neuroscience, Center for Molecular Medicine L8:02, Karolinska Institute, Stockholm, Sweden
| | - Fredrik Piehl
- Therapeutic Immune Design, Department of Clinical Neuroscience, Center for Molecular Medicine L8:02, Karolinska Institute, Stockholm, Sweden
| | - Jan Lycke
- Department of Clinical Neuroscience, Institute of Neuroscience and Physiology at Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Tomas Olsson
- Therapeutic Immune Design, Department of Clinical Neuroscience, Center for Molecular Medicine L8:02, Karolinska Institute, Stockholm, Sweden
| | - Tara Hessa
- Therapeutic Immune Design, Department of Clinical Neuroscience, Center for Molecular Medicine L8:02, Karolinska Institute, Stockholm, Sweden
- Neuroimmunology Unit, Department of Clinical Neuroscience, Center for Molecular Medicine L8:04, Karolinska Institute, Stockholm, Sweden
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81
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Mózner O, Moldvay J, Szabó KS, Vaskó D, Domján J, Ács D, Ligeti Z, Fehér C, Hirsch E, Puskás L, Stahl C, Frey M, Sarkadi B. Application of a Receptor-Binding-Domain-Based Simple Immunoassay for Assessing Humoral Immunity against Emerging SARS-CoV-2 Virus Variants. Biomedicines 2023; 11:3193. [PMID: 38137414 PMCID: PMC10740953 DOI: 10.3390/biomedicines11123193] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2023] [Revised: 11/21/2023] [Accepted: 11/21/2023] [Indexed: 12/24/2023] Open
Abstract
We have developed a simple, rapid, high-throughput RBD-based ELISA to assess the humoral immunity against emerging SARS-CoV-2 virus variants. The cDNAs of the His-tagged RBD proteins of the virus variants were stably engineered into HEK cells secreting the protein into the supernatant, and RBD purification was performed by Ni-chromatography and buffer exchange by membrane filtration. The simplified assay uses single dilutions of sera from finger-pricked native blood samples, purified RBD in 96-well plates, and a chromogenic dye for development. The results of this RBD-ELISA were confirmed to correlate with those of a commercial immunoassay measuring antibodies against the Wuhan strain, as well as direct virus neutralization assays assessing the cellular effects of the Wuhan and the Omicron (BA.5) variants. Here, we document the applicability of this ELISA to assess the variant-specific humoral immunity in vaccinated and convalescent patients, as well as to follow the time course of selective vaccination response. This simple and rapid assay, easily modified to detect humoral immunity against emerging SARS-CoV-2 virus variants, may help to assess the level of antiviral protection after vaccination or infection.
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Affiliation(s)
- Orsolya Mózner
- Research Centre for Natural Sciences, 1117 Budapest, Hungary; (O.M.)
- Doctoral School, Semmelweis University, 1085 Budapest, Hungary
- CelluVir Biotechnology Ltd., 1094 Budapest, Hungary
| | - Judit Moldvay
- CelluVir Biotechnology Ltd., 1094 Budapest, Hungary
- I. Department of Pulmonology, National Korányi Institute of Pulmonology, 1121 Budapest, Hungary
| | - Kata Sára Szabó
- Research Centre for Natural Sciences, 1117 Budapest, Hungary; (O.M.)
| | - Dorottya Vaskó
- Department of Organic Chemistry and Technology, Faculty of Chemical Technology and Biotechnology, Budapest University of Technology and Economics, 1111 Budapest, Hungary
| | - Júlia Domján
- Department of Organic Chemistry and Technology, Faculty of Chemical Technology and Biotechnology, Budapest University of Technology and Economics, 1111 Budapest, Hungary
| | - Dorottya Ács
- I. Department of Pulmonology, National Korányi Institute of Pulmonology, 1121 Budapest, Hungary
| | - Zoltán Ligeti
- Research Centre for Natural Sciences, 1117 Budapest, Hungary; (O.M.)
| | - Csaba Fehér
- Biorefinery Research Group, Department of Applied Biotechnology, Faculty of Chemical Technology and Biotechnology, Budapest University of Technology and Economics, 1111 Budapest, Hungary
| | - Edit Hirsch
- Department of Organic Chemistry and Technology, Faculty of Chemical Technology and Biotechnology, Budapest University of Technology and Economics, 1111 Budapest, Hungary
| | | | - Cordula Stahl
- Steinbeis-Innovationszentrum Zellkulturtechnik, c/o University of Applied Sciences Mannheim, Paul-Wittsack-Str. 10, D-68163 Mannheim, Germany
| | - Manfred Frey
- Steinbeis-Innovationszentrum Zellkulturtechnik, c/o University of Applied Sciences Mannheim, Paul-Wittsack-Str. 10, D-68163 Mannheim, Germany
| | - Balázs Sarkadi
- Research Centre for Natural Sciences, 1117 Budapest, Hungary; (O.M.)
- Doctoral School, Semmelweis University, 1085 Budapest, Hungary
- CelluVir Biotechnology Ltd., 1094 Budapest, Hungary
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82
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Aleman A, van Kesteren M, Zajdman AK, Srivastava K, Cognigni C, Mischka J, Chen LY, Upadhyaya B, Serebryakova K, Nardulli JR, Lyttle N, Kappes K, Jackson H, Gleason CR, Oostenink A, Cai GY, Van Oekelen O, van Bakel H, Sordillo EM, Cordon-Cardo C, Merad M, Jagannath S, Wajnberg A, Simon V, Parekh S. Cellular mechanisms associated with sub-optimal immune responses to SARS-CoV-2 bivalent booster vaccination in patients with Multiple Myeloma. EBioMedicine 2023; 98:104886. [PMID: 37995467 PMCID: PMC10708991 DOI: 10.1016/j.ebiom.2023.104886] [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: 08/23/2023] [Revised: 11/06/2023] [Accepted: 11/08/2023] [Indexed: 11/25/2023] Open
Abstract
BACKGROUND The real-world impact of bivalent vaccines for wild type (WA.1) and Omicron variant (BA.5) is largely unknown in immunocompromised patients with Multiple Myeloma (MM). We characterize the humoral and cellular immune responses in patients with MM before and after receiving the bivalent booster, including neutralizing assays to identify patterns associated with continuing vulnerability to current variants (XBB1.16, EG5) in the current post-pandemic era. METHODS We studied the humoral and cellular immune responses before and after bivalent booster immunization in 48 MM patients. Spike binding IgG antibody levels were measured by SARS-CoV-2 spike binding ELISA and neutralization capacity was assessed by a SARS-CoV-2 multi-cycle microneutralization assays to assess inhibition of live virus. We measured spike specific T-cell function using the QuantiFERON SARS-CoV-2 (Qiagen) assay as well as flow-cytometry based T-cell. In a subset of 38 patients, high-dimensional flow cytometry was performed to identify immune cell subsets associated with lack of humoral antibodies. FINDINGS We find that bivalent vaccination provides significant boost in protection to the omicron variant in our MM patients, in a treatment specific manner. MM patients remain vulnerable to newer variants with mutations in the spike portion. Anti-CD38 and anti-BCMA therapies affect the immune machinery needed to produce antibodies. INTERPRETATION Our study highlights varying immune responses observed in MM patients after receiving bivalent COVID-19 vaccination. Specifically, a subgroup of MM patients undergoing anti-CD38 and anti-BCMA therapy experience impairment in immune cells such DCs, B cells, NK cells and TFH cells, leading to an inability to generate adequate humoral and cellular responses to vaccination. FUNDING National Cancer Institute (National Institutes of Health), National Institute of Allergy and Infectious Diseases (National Institutes of Health), NCI Serological Sciences Network for COVID-19 (SeroNet) and The Icahn School of Medicine at Mount Sinai.
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Affiliation(s)
- Adolfo Aleman
- Graduate School of Biomedical Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA; Department of Medicine, Hematology and Medical Oncology, Icahn School of Medicine at Mount Sinai, New York, NY, USA; Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA; Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Morgan van Kesteren
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA; Center for Vaccine Research and Pandemic Preparedness, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Ariel Kogan Zajdman
- Department of Medicine, Hematology and Medical Oncology, Icahn School of Medicine at Mount Sinai, New York, NY, USA; Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Komal Srivastava
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA; Center for Vaccine Research and Pandemic Preparedness, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Christian Cognigni
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA; Center for Vaccine Research and Pandemic Preparedness, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Jacob Mischka
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA; Center for Vaccine Research and Pandemic Preparedness, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Lucia Y Chen
- Department of Medicine, Hematology and Medical Oncology, Icahn School of Medicine at Mount Sinai, New York, NY, USA; Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA; Oxford University Hospitals NHS Foundation Trust, Oxford, UK
| | - Bhaskar Upadhyaya
- Department of Medicine, Hematology and Medical Oncology, Icahn School of Medicine at Mount Sinai, New York, NY, USA; Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Kseniya Serebryakova
- Department of Medicine, Hematology and Medical Oncology, Icahn School of Medicine at Mount Sinai, New York, NY, USA; Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Jessica R Nardulli
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA; Center for Vaccine Research and Pandemic Preparedness, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Neko Lyttle
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA; Center for Vaccine Research and Pandemic Preparedness, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Katerina Kappes
- Department of Medicine, Hematology and Medical Oncology, Icahn School of Medicine at Mount Sinai, New York, NY, USA; Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Hayley Jackson
- Department of Medicine, Hematology and Medical Oncology, Icahn School of Medicine at Mount Sinai, New York, NY, USA; Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Charles R Gleason
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA; Center for Vaccine Research and Pandemic Preparedness, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Annika Oostenink
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA; Center for Vaccine Research and Pandemic Preparedness, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Gianna Y Cai
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA; Center for Vaccine Research and Pandemic Preparedness, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Oliver Van Oekelen
- Department of Medicine, Hematology and Medical Oncology, Icahn School of Medicine at Mount Sinai, New York, NY, USA; Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Harm van Bakel
- Department of Pathology, Molecular and Cell-based Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA; Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, NY, USA
| | - Emilia Mia Sordillo
- Department of Pathology, Molecular and Cell-based Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Carlos Cordon-Cardo
- Department of Pathology, Molecular and Cell-based Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA; Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, NY, USA; Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Miriam Merad
- Department of Medicine, Hematology and Medical Oncology, Icahn School of Medicine at Mount Sinai, New York, NY, USA; Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA; Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA; Human Immune Monitoring Center, Icahn School of Medicine at Mount Sinai, New York, NY, USA; Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Sundar Jagannath
- Department of Medicine, Hematology and Medical Oncology, Icahn School of Medicine at Mount Sinai, New York, NY, USA; Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Ania Wajnberg
- Department of Internal Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA; Department of Geriatrics and Palliative Medicine, Icahn School of Medicine at Mount Sinai, NY, USA
| | - Viviana Simon
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA; Department of Pathology, Molecular and Cell-based Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA; Division of Infectious Disease, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA; Global Health and Emerging Pathogen Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA; Center for Vaccine Research and Pandemic Preparedness, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
| | - Samir Parekh
- Department of Medicine, Hematology and Medical Oncology, Icahn School of Medicine at Mount Sinai, New York, NY, USA; Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA; Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA; Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
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Islas-Vazquez L, Alvarado-Alvarado YC, Cruz-Aguilar M, Velazquez-Soto H, Villalobos-Gonzalez E, Ornelas-Hall G, Perez-Tapia SM, Jimenez-Martinez MC. Evaluation of the Abdala Vaccine: Antibody and Cellular Response to the RBD Domain of SARS-CoV-2. Vaccines (Basel) 2023; 11:1787. [PMID: 38140191 PMCID: PMC10748004 DOI: 10.3390/vaccines11121787] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2023] [Revised: 11/22/2023] [Accepted: 11/24/2023] [Indexed: 12/24/2023] Open
Abstract
Abdala is a recently released RBD protein subunit vaccine against SARS-CoV-2. A few countries, including Mexico, have adopted Abdala as a booster dose in their COVID-19 vaccination schemes. Despite that, most of the Mexican population has received full-scheme vaccination with platforms other than Abdala; little is known regarding Abdala's immunological features, such as its antibody production and T- and B-cell-specific response induction. This work aimed to study antibody production and the adaptive cellular response in the Mexican population that received the Abdala vaccine as a booster. We recruited 25 volunteers and evaluated their RBD-specific antibody production, T- and B-cell-activating profiles, and cytokine production. Our results showed that the Abdala vaccine increases the concentration of RBD IgG-specific antibodies. Regarding the cellular response, after challenging peripheral blood cultures with RBD, the plasmablast (CD19+CD27+CD38High) and transitional B-cell (CD19+CD21+CD38High) percentages increased significantly, while T cells showed an increased activated phenotype (CD3+CD4+CD25+CD69+ and CD3+CD4+CD25+HLA-DR+). Also, IL-2 and IFN-γ increased significantly in the supernatant of the RBD-stimulated cells. Our results suggest that Abdala vaccination, used as a booster, evokes antibody production and the activation of previously generated memory against the SARS-CoV-2 RBD domain.
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Affiliation(s)
- Lorenzo Islas-Vazquez
- Department of Immunology and Research Unit, Institute of Ophthalmology “Conde de Valenciana Foundation”, Mexico City 06800, Mexico; (L.I.-V.)
| | - Yan Carlos Alvarado-Alvarado
- Department of Immunology and Research Unit, Institute of Ophthalmology “Conde de Valenciana Foundation”, Mexico City 06800, Mexico; (L.I.-V.)
| | - Marisa Cruz-Aguilar
- Department of Immunology and Research Unit, Institute of Ophthalmology “Conde de Valenciana Foundation”, Mexico City 06800, Mexico; (L.I.-V.)
| | - Henry Velazquez-Soto
- Department of Immunology and Research Unit, Institute of Ophthalmology “Conde de Valenciana Foundation”, Mexico City 06800, Mexico; (L.I.-V.)
| | - Eduardo Villalobos-Gonzalez
- Unidad de Vigilancia Epidemiológica Hospitalaria, Institute of Ophthalmology “Conde de Valenciana Foundation”, Mexico City 06800, Mexico
| | - Gloria Ornelas-Hall
- Unidad de Vigilancia Epidemiológica Hospitalaria, Institute of Ophthalmology “Conde de Valenciana Foundation”, Mexico City 06800, Mexico
| | - Sonia Mayra Perez-Tapia
- Unidad de Desarrollo e Investigación en Bioterapéuticos (UDIBI), Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Mexico City 11340, Mexico
- Laboratorio Nacional para Servicios Especializados de Investigación, Desarrollo e Innovación (I+D+i) para Farmoquímicos y Biotecnológicos, LANSEIDI-FarBiotec-CONACyT, Mexico City 11340, Mexico
- Departamento de Inmunología, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional (ENCB-IPN), Mexico City 11340, Mexico
| | - Maria C. Jimenez-Martinez
- Department of Immunology and Research Unit, Institute of Ophthalmology “Conde de Valenciana Foundation”, Mexico City 06800, Mexico; (L.I.-V.)
- Department of Biochemistry, Faculty of Medicine, National Autonomous University of Mexico, Mexico City 04510, Mexico
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84
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Zonozi R, Walters LC, Shulkin A, Naranbhai V, Nithagon P, Sauvage G, Kaeske C, Cosgrove K, Nathan A, Tano-Menka R, Gayton AC, Getz MA, Senjobe F, Worrall D, Iafrate AJ, Fromson C, Montesi SB, Rao DA, Sparks JA, Wallace ZS, Farmer JR, Walker BD, Charles RC, Laliberte K, Niles JL, Gaiha GD. T cell responses to SARS-CoV-2 infection and vaccination are elevated in B cell deficiency and reduce risk of severe COVID-19. Sci Transl Med 2023; 15:eadh4529. [PMID: 38019932 DOI: 10.1126/scitranslmed.adh4529] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2023] [Accepted: 11/06/2023] [Indexed: 12/01/2023]
Abstract
Individuals with primary and pharmacologic B cell deficiencies have high rates of severe disease and mortality from coronavirus disease 2019 (COVID-19), but the immune responses and clinical outcomes after severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection and vaccination have yet to be fully defined. Here, we evaluate the cellular immune responses after both SARS-CoV-2 infection and vaccination in patients receiving the anti-CD20 therapy rituximab (RTX) and those with low B cell counts due to common variable immune deficiency (CVID) disease. Assessment of effector and memory CD4+ and CD8+ T cell responses to SARS-CoV-2 revealed elevated reactivity and proliferative capacity after both infection and vaccination in B cell-deficient individuals, particularly within the CD8+ T cell compartment, in comparison with healthy controls. Evaluation of clinical outcomes demonstrates that vaccination of RTX-treated individuals was associated with about 4.8-fold reduced odds of moderate or severe COVID-19 in the absence of vaccine-induced antibodies. Analysis of T cell differentiation demonstrates that RTX administration increases the relative frequency of naïve CD8+ T cells, potentially by depletion of CD8+CD20dim T cells, which are primarily of an effector memory or terminal effector memory (TEMRA) phenotype. However, this also leads to a reduction in preexisting antiviral T cell immunity. Collectively, these data indicate that individuals with B cell deficiencies have enhanced T cell immunity after both SARS-CoV-2 infection and vaccination that potentially accounts for reduced hospitalization and severe disease from subsequent SARS-CoV-2 infection.
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Affiliation(s)
- Reza Zonozi
- Vasculitis and Glomerulonephritis Center, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Lucy C Walters
- Ragon Institute of Mass General, MIT, and Harvard, Cambridge, MA 02139, USA
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
- Koch Institute for Integrative Cancer Research, Cambridge, MA 02139, USA
| | - Aaron Shulkin
- Ragon Institute of Mass General, MIT, and Harvard, Cambridge, MA 02139, USA
| | - Vivek Naranbhai
- Massachusetts General Hospital Cancer Center, Massachusetts General Hospital, Boston, MA 02114, USA
- Center for the AIDS Programme of Research in South Africa, Durban 4001, South Africa
- Monash University, Melbourne, VIC 3022, Australia
| | - Pravarut Nithagon
- Vasculitis and Glomerulonephritis Center, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Gabriel Sauvage
- Vasculitis and Glomerulonephritis Center, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Clarety Kaeske
- Ragon Institute of Mass General, MIT, and Harvard, Cambridge, MA 02139, USA
| | - Katherine Cosgrove
- Vasculitis and Glomerulonephritis Center, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Anusha Nathan
- Ragon Institute of Mass General, MIT, and Harvard, Cambridge, MA 02139, USA
- Program in Health Sciences and Technology, Harvard Medical School and Massachusetts Institute of Technology, Boston, MA 02115, USA
| | - Rhoda Tano-Menka
- Ragon Institute of Mass General, MIT, and Harvard, Cambridge, MA 02139, USA
| | - Alton C Gayton
- Ragon Institute of Mass General, MIT, and Harvard, Cambridge, MA 02139, USA
| | - Matthew A Getz
- Ragon Institute of Mass General, MIT, and Harvard, Cambridge, MA 02139, USA
| | - Fernando Senjobe
- Ragon Institute of Mass General, MIT, and Harvard, Cambridge, MA 02139, USA
| | - Daniel Worrall
- Ragon Institute of Mass General, MIT, and Harvard, Cambridge, MA 02139, USA
| | - A John Iafrate
- Department of Pathology, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Caroline Fromson
- Division of Pulmonary and Critical Care Medicine, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Sydney B Montesi
- Division of Pulmonary and Critical Care Medicine, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Deepak A Rao
- Division of Rheumatology, Inflammation, and Immunity, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Jeffrey A Sparks
- Division of Rheumatology, Inflammation, and Immunity, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Zachary S Wallace
- Division of Rheumatology, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Jocelyn R Farmer
- Ragon Institute of Mass General, MIT, and Harvard, Cambridge, MA 02139, USA
- Division of Allergy and Inflammation, Beth Israel Lahey Health, Boston, MA 02215, USA
| | - Bruce D Walker
- Ragon Institute of Mass General, MIT, and Harvard, Cambridge, MA 02139, USA
- Center for the AIDS Programme of Research in South Africa, Durban 4001, South Africa
- Broad Institute, Cambridge, MA 02142, USA
- Howard Hughes Medical Institute, Chevy Chase, MD 20815, USA
- Institute for Medical Engineering and Science and Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Richelle C Charles
- Division of Infectious Diseases, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Karen Laliberte
- Vasculitis and Glomerulonephritis Center, Massachusetts General Hospital, Boston, MA 02114, USA
| | - John L Niles
- Vasculitis and Glomerulonephritis Center, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Gaurav D Gaiha
- Ragon Institute of Mass General, MIT, and Harvard, Cambridge, MA 02139, USA
- Division of Gastroenterology, Massachusetts General Hospital, Boston, MA 02114, USA
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85
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Lee JS, Karthikeyan D, Fini M, Vincent BG, Rubinsteyn A. ACE configurator for ELISpot: optimizing combinatorial design of pooled ELISpot assays with an epitope similarity model. Brief Bioinform 2023; 25:bbad495. [PMID: 38180831 PMCID: PMC10768796 DOI: 10.1093/bib/bbad495] [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: 08/22/2023] [Revised: 11/16/2023] [Accepted: 12/01/2023] [Indexed: 01/07/2024] Open
Abstract
The enzyme-linked immunosorbent spot (ELISpot) assay is a powerful in vitro immunoassay that enables cost-effective quantification of antigen-specific T-cell reactivity. It is used widely in the context of cancer and infectious diseases to validate the immunogenicity of predicted epitopes. While technological advances have kept pace with the demand for increased throughput, efforts to increase scale are bottlenecked by current assay design and deconvolution methods, which have remained largely unchanged. Current methods for designing pooled ELISpot experiments offer limited flexibility of assay parameters, lack support for high-throughput scenarios and do not consider peptide identity during pool assignment. We introduce the ACE Configurator for ELISpot (ACE) to address these gaps. ACE generates optimized peptide-pool assignments from highly customizable user inputs and handles the deconvolution of positive peptides using assay readouts. In this study, we present a novel sequence-aware pooling strategy, powered by a fine-tuned ESM-2 model that groups immunologically similar peptides, reducing the number of false positives and subsequent confirmatory assays compared to existing combinatorial approaches. To validate ACE's performance on real-world datasets, we conducted a comprehensive benchmark study, contextualizing design choices with their impact on prediction quality. Our results demonstrate ACE's capacity to further increase precision of identified immunogenic peptides, directly optimizing experimental efficiency. ACE is freely available as an executable with a graphical user interface and command-line interfaces at https://github.com/pirl-unc/ace.
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Affiliation(s)
- Jin Seok Lee
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC
- Computational Medicine Program, UNC School of Medicine, Chapel Hill, NC, USA
- Curriculum in Bioinformatics and Computational Biology, UNC School of Medicine, Chapel Hill, NC, USA
| | - Dhuvarakesh Karthikeyan
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC
- Computational Medicine Program, UNC School of Medicine, Chapel Hill, NC, USA
- Curriculum in Bioinformatics and Computational Biology, UNC School of Medicine, Chapel Hill, NC, USA
| | - Misha Fini
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC
- Department of Microbiology and Immunology, UNC School of Medicine, Chapel Hill, NC, USA
| | - Benjamin G Vincent
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC
- Division of Hematology, Department of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC
- Department of Microbiology and Immunology, UNC School of Medicine, Chapel Hill, NC, USA
- Computational Medicine Program, UNC School of Medicine, Chapel Hill, NC, USA
- Curriculum in Bioinformatics and Computational Biology, UNC School of Medicine, Chapel Hill, NC, USA
| | - Alex Rubinsteyn
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC
- Computational Medicine Program, UNC School of Medicine, Chapel Hill, NC, USA
- Curriculum in Bioinformatics and Computational Biology, UNC School of Medicine, Chapel Hill, NC, USA
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599 USA
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86
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Wang K, Khoramjoo M, Srinivasan K, Gordon PMK, Mandal R, Jackson D, Sligl W, Grant MB, Penninger JM, Borchers CH, Wishart DS, Prasad V, Oudit GY. Sequential multi-omics analysis identifies clinical phenotypes and predictive biomarkers for long COVID. Cell Rep Med 2023; 4:101254. [PMID: 37890487 PMCID: PMC10694626 DOI: 10.1016/j.xcrm.2023.101254] [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: 02/17/2023] [Revised: 05/25/2023] [Accepted: 09/29/2023] [Indexed: 10/29/2023]
Abstract
The post-acute sequelae of COVID-19 (PASC), also known as long COVID, is often associated with debilitating symptoms and adverse multisystem consequences. We obtain plasma samples from 117 individuals during and 6 months following their acute phase of infection to comprehensively profile and assess changes in cytokines, proteome, and metabolome. Network analysis reveals sustained inflammatory response, platelet degranulation, and cellular activation during convalescence accompanied by dysregulation in arginine biosynthesis, methionine metabolism, taurine metabolism, and tricarboxylic acid (TCA) cycle processes. Furthermore, we develop a prognostic model composed of 20 molecules involved in regulating T cell exhaustion and energy metabolism that can reliably predict adverse clinical outcomes following discharge from acute infection with 83% accuracy and an area under the curve (AUC) of 0.96. Our study reveals pertinent biological processes during convalescence that differ from acute infection, and it supports the development of specific therapies and biomarkers for patients suffering from long COVID.
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Affiliation(s)
- Kaiming Wang
- Division of Cardiology, Department of Medicine, University of Alberta, Edmonton, AB, Canada; Mazankowski Alberta Heart Institute, University of Alberta, Edmonton, AB, Canada; Cumming School of Medicine, University of Calgary, Calgary, AB, Canada
| | - Mobin Khoramjoo
- Mazankowski Alberta Heart Institute, University of Alberta, Edmonton, AB, Canada; Department of Physiology, University of Alberta, Edmonton, AB, Canada
| | - Karthik Srinivasan
- Department of Chemical and Materials Engineering, University of Alberta, Edmonton, AB, Canada
| | - Paul M K Gordon
- Cumming School of Medicine, University of Calgary, Calgary, AB, Canada
| | - Rupasri Mandal
- The Metabolomics Innovation Center, University of Alberta, Edmonton, AB, Canada
| | - Dana Jackson
- Division of Cardiology, Department of Medicine, University of Alberta, Edmonton, AB, Canada; Mazankowski Alberta Heart Institute, University of Alberta, Edmonton, AB, Canada
| | - Wendy Sligl
- Department of Critical Care Medicine, University of Alberta, Edmonton, AB, Canada; Division of Infectious Diseases, Department of Medicine, University of Alberta, Edmonton, AB, Canada
| | - Maria B Grant
- Department of Ophthalmology and Visual Sciences, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Josef M Penninger
- Department of Medical Genetics, Life Sciences Institute, University of British Columbia, Vancouver, BC, Canada; Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), Vienna, Austria
| | - Christoph H Borchers
- Segal Cancer Proteomics Centre, Lady Davis Institute for Medical Research, Jewish General Hospital, McGill University, Montreal, QC, Canada; Gerald Bronfman Department of Oncology, McGill University, Montreal, QC, Canada
| | - David S Wishart
- The Metabolomics Innovation Center, University of Alberta, Edmonton, AB, Canada
| | - Vinay Prasad
- Department of Chemical and Materials Engineering, University of Alberta, Edmonton, AB, Canada
| | - Gavin Y Oudit
- Division of Cardiology, Department of Medicine, University of Alberta, Edmonton, AB, Canada; Mazankowski Alberta Heart Institute, University of Alberta, Edmonton, AB, Canada; Department of Physiology, University of Alberta, Edmonton, AB, Canada.
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87
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Federico L, Malone B, Tennøe S, Chaban V, Osen JR, Gainullin M, Smorodina E, Kared H, Akbar R, Greiff V, Stratford R, Clancy T, Munthe LA. Experimental validation of immunogenic SARS-CoV-2 T cell epitopes identified by artificial intelligence. Front Immunol 2023; 14:1265044. [PMID: 38045681 PMCID: PMC10691274 DOI: 10.3389/fimmu.2023.1265044] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2023] [Accepted: 11/01/2023] [Indexed: 12/05/2023] Open
Abstract
During the COVID-19 pandemic we utilized an AI-driven T cell epitope prediction tool, the NEC Immune Profiler (NIP) to scrutinize and predict regions of T cell immunogenicity (hotspots) from the entire SARS-CoV-2 viral proteome. These immunogenic regions offer potential for the development of universally protective T cell vaccine candidates. Here, we validated and characterized T cell responses to a set of minimal epitopes from these AI-identified universal hotspots. Utilizing a flow cytometry-based T cell activation-induced marker (AIM) assay, we identified 59 validated screening hits, of which 56% (33 peptides) have not been previously reported. Notably, we found that most of these novel epitopes were derived from the non-spike regions of SARS-CoV-2 (Orf1ab, Orf3a, and E). In addition, ex vivo stimulation with NIP-predicted peptides from the spike protein elicited CD8+ T cell response in PBMC isolated from most vaccinated donors. Our data confirm the predictive accuracy of AI platforms modelling bona fide immunogenicity and provide a novel framework for the evaluation of vaccine-induced T cell responses.
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Affiliation(s)
- Lorenzo Federico
- Department of Immunology, Oslo University Hospital, Oslo, Norway
- KG Jebsen Centre for B cell Malignancies, Institute of Clinical Medicine, University of Oslo, Oslo, Norway
| | | | | | - Viktoriia Chaban
- Department of Immunology, Oslo University Hospital, Oslo, Norway
- KG Jebsen Centre for B cell Malignancies, Institute of Clinical Medicine, University of Oslo, Oslo, Norway
| | - Julie Røkke Osen
- Department of Immunology, Oslo University Hospital, Oslo, Norway
- KG Jebsen Centre for B cell Malignancies, Institute of Clinical Medicine, University of Oslo, Oslo, Norway
| | - Murat Gainullin
- Department of Immunology, Oslo University Hospital, Oslo, Norway
- KG Jebsen Centre for B cell Malignancies, Institute of Clinical Medicine, University of Oslo, Oslo, Norway
| | - Eva Smorodina
- Department of Immunology, Oslo University Hospital, Oslo, Norway
- Institute of Clinical Medicine, Oslo University Hospital, Oslo, Norway
| | - Hassen Kared
- Department of Immunology, Oslo University Hospital, Oslo, Norway
- KG Jebsen Centre for B cell Malignancies, Institute of Clinical Medicine, University of Oslo, Oslo, Norway
| | - Rahmad Akbar
- Department of Immunology, Oslo University Hospital, Oslo, Norway
- Institute of Clinical Medicine, Oslo University Hospital, Oslo, Norway
| | - Victor Greiff
- Department of Immunology, Oslo University Hospital, Oslo, Norway
- Institute of Clinical Medicine, Oslo University Hospital, Oslo, Norway
| | | | | | - Ludvig Andre Munthe
- Department of Immunology, Oslo University Hospital, Oslo, Norway
- KG Jebsen Centre for B cell Malignancies, Institute of Clinical Medicine, University of Oslo, Oslo, Norway
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88
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Hvidt AK, Guo H, Andersen R, Lende SSF, Vibholm LK, Søgaard OS, Schleimann MH, Russell V, Cheung AMW, Paramithiotis E, Olesen R, Tolstrup M. Long-term humoral and cellular immunity after primary SARS-CoV-2 infection: a 20-month longitudinal study. BMC Immunol 2023; 24:45. [PMID: 37974069 PMCID: PMC10652616 DOI: 10.1186/s12865-023-00583-y] [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: 08/29/2023] [Accepted: 11/06/2023] [Indexed: 11/19/2023] Open
Abstract
BACKGROUND SARS-CoV-2 remains a world-wide health issue. SARS-CoV-2-specific immunity is induced upon both infection and vaccination. However, defining the long-term immune trajectory, especially after infection, is limited. In this study, we aimed to further the understanding of long-term SARS-CoV-2-specific immune response after infection. RESULTS We conducted a longitudinal cohort study among 93 SARS-CoV-2 recovered individuals. Immune responses were continuously monitored for up to 20 months after infection. The humoral responses were quantified by Spike- and Nucleocapsid-specific IgG levels. T cell responses to Spike- and non-Spike epitopes were examined using both intercellular cytokine staining (ICS) assay and Activation-Induced marker (AIM) assay with quantification of antigen-specific IFNγ production. During the 20 months follow-up period, Nucleocapsid-specific antibody levels and non-Spike-specific CD4 + and CD8 + T cell frequencies decreased in the blood. However, a majority of participants maintained a durable immune responses 20 months after infection: 59% of the participants were seropositive for Nucleocapsid-specific IgG, and more than 70% had persisting non-Spike-specific T cells. The Spike-specific response initially decreased but as participants were vaccinated against COVID-19, Spike-specific IgG levels and T cell frequencies were boosted reaching similar or higher levels compared to 1 month post-infection. The trajectory of infection-induced SARS-CoV-2-specific immunity decreases, but for the majority of participants it persists beyond 20 months. The T cell response displays a greater durability. Vaccination boosts Spike-specific immune responses to similar or higher levels as seen after primary infection. CONCLUSIONS For most participants, the response persists 20 months after infection, and the cellular response appears to be more long-lived compared to the circulating antibody levels. Vaccination boosts the S-specific response but does not affect the non-S-specific response. Together, these findings support the understanding of immune contraction, and with studies showing the immune levels required for protection, adds to the knowledge of durability of protection against future SARS-CoV-2.
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Affiliation(s)
- Astrid Korning Hvidt
- Department of Infectious Diseases, Aarhus University Hospital, Aarhus, Denmark
- Department of Clinical Medicine, Aarhus University, Aarhus, Denmark
| | | | - Rebecca Andersen
- Department of Infectious Diseases, Aarhus University Hospital, Aarhus, Denmark
- Department of Clinical Medicine, Aarhus University, Aarhus, Denmark
| | - Stine Sofie Frank Lende
- Department of Infectious Diseases, Aarhus University Hospital, Aarhus, Denmark
- Department of Clinical Medicine, Aarhus University, Aarhus, Denmark
| | - Line Khalidan Vibholm
- Department of Infectious Diseases, Aarhus University Hospital, Aarhus, Denmark
- Department of Clinical Medicine, Aarhus University, Aarhus, Denmark
| | - Ole Schmeltz Søgaard
- Department of Infectious Diseases, Aarhus University Hospital, Aarhus, Denmark
- Department of Clinical Medicine, Aarhus University, Aarhus, Denmark
| | - Marianne Hoegsbjerg Schleimann
- Department of Infectious Diseases, Aarhus University Hospital, Aarhus, Denmark
- Department of Clinical Medicine, Aarhus University, Aarhus, Denmark
| | - Victoria Russell
- Toronto General Hospital Research Institute, University Health Network, Toronto, ON, Canada
| | - Angela Man-Wei Cheung
- Toronto General Hospital Research Institute, University Health Network, Toronto, ON, Canada
- Department of Medicine, University Health Network, Toronto, ON, Canada
- Department of Medicine, University of Toronto, Toronto, ON, Canada
- Institute of Health Policy, Management and Evaluation, University of Toronto, Toronto, ON, Canada
| | | | - Rikke Olesen
- Department of Infectious Diseases, Aarhus University Hospital, Aarhus, Denmark.
- Department of Clinical Medicine, Aarhus University, Aarhus, Denmark.
| | - Martin Tolstrup
- Department of Infectious Diseases, Aarhus University Hospital, Aarhus, Denmark
- Department of Clinical Medicine, Aarhus University, Aarhus, Denmark
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89
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Pathakumari B, Marty PK, Shah M, Van Keulen VP, Erskine CL, Block MS, Arias-Sanchez P, Escalante P, Peikert T. Convalescent Adaptive Immunity Is Highly Heterogenous after SARS-CoV-2 Infection. J Clin Med 2023; 12:7136. [PMID: 38002748 PMCID: PMC10672050 DOI: 10.3390/jcm12227136] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2023] [Revised: 11/03/2023] [Accepted: 11/14/2023] [Indexed: 11/26/2023] Open
Abstract
The optimal detection strategies for effective convalescent immunity after SARS-CoV-2 infection and vaccination remain unclear. The objective of this study was to characterize convalescent immunity targeting the SARS-CoV-2 spike protein using a multiparametric approach. At the beginning of the pandemic, we recruited 30 unvaccinated convalescent donors who had previously been infected with COVID-19 and 7 unexposed asymptomatic controls. Peripheral blood mononuclear cells (PBMCs) were obtained from leukapheresis cones. The humoral immune response was assessed by measuring serum anti-SARS-CoV-2 spike S1 subunit IgG via semiquantitative ELISA, and T-cell immunity against S1 and S2 subunits were studied via IFN-γ enzyme-linked immunosorbent spot (ELISpot) and flow cytometric (FC) activation-induced marker (AIM) assays and the assessment of cytotoxic CD8+ T-cell function (in the subset of HLA-A2-positive patients). No single immunoassay was sufficient in identifying anti-spike convalescent immunity among all patients. There was no consistent correlation between adaptive humoral and cellular anti-spike responses. Our data indicate that the magnitude of anti-spike convalescent humoral and cellular immunity is highly heterogeneous and highlights the need for using multiple assays to comprehensively measure SARS-CoV-2 convalescent immunity. These observations might have implications for COVID-19 surveillance, and the determination of optimal vaccination strategies for emerging variants. Further studies are needed to determine the optimal assessment of adaptive humoral and cellular immunity following SARS-CoV-2 infection, especially in the context of emerging variants and unclear vaccination schedules.
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Affiliation(s)
- Balaji Pathakumari
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Mayo Clinic, Rochester, MN 55905, USA; (B.P.); (P.K.M.); (M.S.); (V.P.V.K.); (P.A.-S.); (P.E.)
| | - Paige K. Marty
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Mayo Clinic, Rochester, MN 55905, USA; (B.P.); (P.K.M.); (M.S.); (V.P.V.K.); (P.A.-S.); (P.E.)
| | - Maleeha Shah
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Mayo Clinic, Rochester, MN 55905, USA; (B.P.); (P.K.M.); (M.S.); (V.P.V.K.); (P.A.-S.); (P.E.)
| | - Virginia P. Van Keulen
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Mayo Clinic, Rochester, MN 55905, USA; (B.P.); (P.K.M.); (M.S.); (V.P.V.K.); (P.A.-S.); (P.E.)
- Department of Immunology, Mayo Clinic, Rochester, MN 55905, USA; (C.L.E.); (M.S.B.)
| | - Courtney L. Erskine
- Department of Immunology, Mayo Clinic, Rochester, MN 55905, USA; (C.L.E.); (M.S.B.)
| | - Matthew S. Block
- Department of Immunology, Mayo Clinic, Rochester, MN 55905, USA; (C.L.E.); (M.S.B.)
- Department of Oncology, Mayo Clinic, Rochester, MN 55905, USA
| | - Pedro Arias-Sanchez
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Mayo Clinic, Rochester, MN 55905, USA; (B.P.); (P.K.M.); (M.S.); (V.P.V.K.); (P.A.-S.); (P.E.)
| | - Patricio Escalante
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Mayo Clinic, Rochester, MN 55905, USA; (B.P.); (P.K.M.); (M.S.); (V.P.V.K.); (P.A.-S.); (P.E.)
| | - Tobias Peikert
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Mayo Clinic, Rochester, MN 55905, USA; (B.P.); (P.K.M.); (M.S.); (V.P.V.K.); (P.A.-S.); (P.E.)
- Department of Immunology, Mayo Clinic, Rochester, MN 55905, USA; (C.L.E.); (M.S.B.)
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90
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Kushwaha ND, Mohan J, Kushwaha B, Ghazi T, Nwabuife JC, Koorbanally N, Chuturgoon AA. A comprehensive review on the global efforts on vaccines and repurposed drugs for combating COVID-19. Eur J Med Chem 2023; 260:115719. [PMID: 37597435 DOI: 10.1016/j.ejmech.2023.115719] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2023] [Revised: 07/31/2023] [Accepted: 08/09/2023] [Indexed: 08/21/2023]
Abstract
The recently discovered coronavirus, known as SARS-CoV-2, is a highly contagious and potentially lethal viral infection that was declared a pandemic by the World Health Organization on March 11, 2020. Since the beginning of the pandemic, an unprecedented number of COVID-19 vaccine candidates have been investigated for their potential to manage the pandemic. Herein, we reviewed vaccine development and the associated research effort, both traditional and forward-looking, to demonstrate the advantages and disadvantages of their technology, in addition to their efficacy limitations against mutant SARS-CoV-2. Moreover, we report repurposed drug discovery, which mainly focuses on virus-based and host-based targets, as well as their inhibitors. SARS-CoV-2 targets include the main protease (Mpro), and RNA-dependent RNA-polymerase (RdRp), which are the most well-studied and conserved across coronaviruses, enabling the development of broad-spectrum inhibitors of these enzymes.
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Affiliation(s)
- Narva Deshwar Kushwaha
- Discipline of Medical Biochemistry, School of Laboratory Medicine and Medical Science, College of Health Sciences, University of KwaZulu-Natal, Durban, South Africa; Department of Pharmaceutical Sciences, Eugene Applebaum College of Pharmacy and Health Sciences, Wayne State University, Detroit, MI, 48201, USA.
| | - Jivanka Mohan
- Discipline of Medical Biochemistry, School of Laboratory Medicine and Medical Science, College of Health Sciences, University of KwaZulu-Natal, Durban, South Africa
| | - Babita Kushwaha
- Discipline of Medical Biochemistry, School of Laboratory Medicine and Medical Science, College of Health Sciences, University of KwaZulu-Natal, Durban, South Africa
| | - Terisha Ghazi
- Discipline of Medical Biochemistry, School of Laboratory Medicine and Medical Science, College of Health Sciences, University of KwaZulu-Natal, Durban, South Africa
| | - Joshua C Nwabuife
- Discipline of Pharmaceutical Sciences, College of Health Sciences, University of KwaZulu-Natal, Durban, 4000, South Africa
| | - Neil Koorbanally
- School of Chemistry, College of Agriculture, Engineering and Science, University of KwaZulu-Natal, Durban, 4000, South Africa
| | - Anil A Chuturgoon
- Discipline of Medical Biochemistry, School of Laboratory Medicine and Medical Science, College of Health Sciences, University of KwaZulu-Natal, Durban, South Africa.
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Al Saihati HA, Hussein HAM, Thabet AA, Wardany AA, Mahmoud SY, Farrag ES, Mohamed TIA, Fathy SM, Elnosary ME, Sobhy A, Ahmed AE, El-Adly AM, El-Shenawy FS, Elsadek AA, Rayan A, Zahran ZAM, El-Badawy O, El-Naggar MGM, Afifi MM, Zahran AM. Memory T Cells Discrepancies in COVID-19 Patients. Microorganisms 2023; 11:2737. [PMID: 38004749 PMCID: PMC10673271 DOI: 10.3390/microorganisms11112737] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2023] [Revised: 10/24/2023] [Accepted: 11/03/2023] [Indexed: 11/26/2023] Open
Abstract
The immune response implicated in Coronavirus disease 2019 (COVID-19) pathogenesis remains to be fully understood. The present study aimed to clarify the alterations in CD4+ and CD8+ memory T cells' compartments in SARS-CoV-2-infected patients, with an emphasis on various comorbidities affecting COVID-19 patients. Peripheral blood samples were collected from 35 COVID-19 patients, 16 recovered individuals, and 25 healthy controls, and analyzed using flow cytometry. Significant alterations were detected in the percentage of CD8+ T cells and effector memory-expressing CD45RA CD8+ T cells (TEMRA) in COVID-19 patients compared to healthy controls. Interestingly, altered percentages of CD4+ T cells, CD8+ T cells, T effector (TEff), T naïve cells (TNs), T central memory (TCM), T effector memory (TEM), T stem cell memory (TSCM), and TEMRA T cells were significantly associated with the disease severity. Male patients had more CD8+ TSCMs and CD4+ TNs cells, while female patients had a significantly higher percentage of effector CD8+CD45RA+ T cells. Moreover, altered percentages of CD8+ TNs and memory CD8+CD45RO+ T cells were detected in diabetic and non-diabetic COVID-19 patients, respectively. In summary, this study identified alterations in memory T cells among COVID-19 patients, revealing a sex bias in the percentage of memory T cells. Moreover, COVID-19 severity and comorbidities have been linked to specific subsets of T memory cells which could be used as therapeutic, diagnostic, and protective targets for severe COVID-19.
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Affiliation(s)
- Hajir A. Al Saihati
- Department of Clinical Laboratory Sciences, College of Applied Medical Science, University of Hafr Al Batin, P.O. Box 1803, Hafar Al Batin 31991, Saudi Arabia; (H.A.A.S.); (E.S.F.)
| | - Hosni A. M. Hussein
- Department of Botany and Microbiology, Faculty of Science, Al-Azhar University, Assiut 71524, Egypt; (A.A.W.); (T.I.A.M.); (A.M.E.-A.); (F.S.E.-S.)
| | - Ali A. Thabet
- Department of Zoology, Faculty of Science, Al-Azhar University, Assiut 71524, Egypt;
| | - Ahmed A. Wardany
- Department of Botany and Microbiology, Faculty of Science, Al-Azhar University, Assiut 71524, Egypt; (A.A.W.); (T.I.A.M.); (A.M.E.-A.); (F.S.E.-S.)
| | - Sabry Y. Mahmoud
- Biology Department, College of Sciences, University of Hafr Al-Batin, Hafr Al-Batin 31991, Saudi Arabia;
- Department of Microbiology, Sohag University, Sohag 82524, Egypt
| | - Eman S. Farrag
- Department of Clinical Laboratory Sciences, College of Applied Medical Science, University of Hafr Al Batin, P.O. Box 1803, Hafar Al Batin 31991, Saudi Arabia; (H.A.A.S.); (E.S.F.)
- Department of Microbiology, South Valley University, Qena 83523, Egypt
| | - Taha I. A. Mohamed
- Department of Botany and Microbiology, Faculty of Science, Al-Azhar University, Assiut 71524, Egypt; (A.A.W.); (T.I.A.M.); (A.M.E.-A.); (F.S.E.-S.)
| | - Samah M. Fathy
- Department of Zoology, Faculty of Science, Fayoum University, Fayoum 63514, Egypt;
| | - Mohamed E. Elnosary
- Department of Botany and Microbiology, Faculty of Science, Al-Azhar University, Nasr City 11884, Egypt; (M.E.E.); (M.M.A.)
| | - Ali Sobhy
- Department of Clinical Pathology, Faculty of Medicine, Al-Azhar University, Assiut 71524, Egypt; (A.S.); (A.E.A.)
| | - Abdelazeem E. Ahmed
- Department of Clinical Pathology, Faculty of Medicine, Al-Azhar University, Assiut 71524, Egypt; (A.S.); (A.E.A.)
| | - Ahmed M. El-Adly
- Department of Botany and Microbiology, Faculty of Science, Al-Azhar University, Assiut 71524, Egypt; (A.A.W.); (T.I.A.M.); (A.M.E.-A.); (F.S.E.-S.)
| | - Fareed S. El-Shenawy
- Department of Botany and Microbiology, Faculty of Science, Al-Azhar University, Assiut 71524, Egypt; (A.A.W.); (T.I.A.M.); (A.M.E.-A.); (F.S.E.-S.)
| | | | - Amal Rayan
- Department of Clinical Oncology, Faculty of Medicine, Assiut University, Assiut 71515, Egypt;
| | | | - Omnia El-Badawy
- Department of Medical Microbiology and Immunology, Faculty of Medicine, Assiut University, Assiut 71515, Egypt;
| | - Mohamed G. M. El-Naggar
- Department of Clinical Pathology, South Egypt Cancer Institute, Assiut University, Assiut 71515, Egypt; (M.G.M.E.-N.); (A.M.Z.)
| | - Magdy M. Afifi
- Department of Botany and Microbiology, Faculty of Science, Al-Azhar University, Nasr City 11884, Egypt; (M.E.E.); (M.M.A.)
| | - Asmaa M. Zahran
- Department of Clinical Pathology, South Egypt Cancer Institute, Assiut University, Assiut 71515, Egypt; (M.G.M.E.-N.); (A.M.Z.)
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92
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Algu P, Hameed N, DeAngelis T, Stern J, Harel A. Post-vaccination SARS-Cov-2 T-cell receptor repertoires in patients with multiple sclerosis and related disorders. Mult Scler Relat Disord 2023; 79:104965. [PMID: 37657307 DOI: 10.1016/j.msard.2023.104965] [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: 04/27/2023] [Revised: 07/21/2023] [Accepted: 08/28/2023] [Indexed: 09/03/2023]
Abstract
BACKGROUND Attenuation in post-vaccination SARS-CoV-2 humoral responses has been demonstrated in people treated with either anti-CD20 therapies or sphingosine-1-phosphate (S1P) receptor modulators. In the setting of disease modifying therapy (DMT) use, humoral response may not correlate with effective immunity, and analysis of vaccine-mediated SARS-CoV-2-specific memory T-cell responses is crucial. While vaccination in patients treated with anti-CD20 agents leads to deficient antibody production, emerging data from live cell assays suggests intact T-cell responses to vaccination. We evaluated post-vaccination SARS-CoV-2 T-cell receptor (TCR) repertoires in DMT-treated patients using the ImmunoSeqR assay, an assay that does not require live cells. METHODS Adults 18-80 years old without prior COVID-19, with neuroimmune conditions, who had been vaccinated with two doses of Pfizer-BioNTech or Moderna mRNA vaccines at least 3 weeks and up to 6 months prior, were recruited. Whole blood was obtained for immunosequencing, and matched serum was obtained for humoral analysis. Immunosequencing of the CDR3 regions of human TCRβ chains was completed using the immunoSEQR Assay (Adaptive Biotechnologies). TCR sequences were mapped across a set of TCR sequences reactive to SARS-CoV-2. Clonal diversity (breadth) and frequency (depth) of TCRs specific to SARS-CoV-2 spike protein were calculated and relationships with clinical variables were assessed. RESULTS Forty patients were recruited into the study, aged 25-77, and 27 female. 37 had MS, 2 had neuromyelitis optica spectrum disorder (NMOSD), and 1 had hypophysitis. Subjects treated with anti-CD20 agents and S1P receptor modulators had severely attenuated humoral responses, but SARS-CoV-2-spike-specific TCR clonal depth and breadth were robust across all treatment classes except S1P modulators. No spike-specific or non-spike-specific SARS-CoV-2-associated TCRs were found in those treated with S1P modulators (p = 0.002 for both breadth and depth). Subjects treated with fumarates exhibited somewhat lower spike TCR breadth than subjects treated with other or no DMTs (median 2.27 × 10^-5 for fumarates and 4.96 × 10^-5 for all others, p = 0.008), but no statistically significant difference was demonstrated with spike TCR depth. No other significant associations with DMT type were found. We found no significant correlations between depth or breadth and age, duration of treatment, type of vaccination, or time interval since vaccination. CONCLUSION This is the first study to characterize post-vaccination SARS-CoV-2 TCR repertoires in DMT-treated individuals. We demonstrated a dichotomous response to SARS-CoV-2 vaccination in anti-CD20-treated patients, with severely attenuated humoral response but intact TCR depth and breadth. It is unclear to what degree each arm of the adaptive immune system impacts post-vaccine immunity, both from the standpoint of incidence of post-vaccine infections and that of infection severity, and further clinical studies are necessary. S1P modulator-treated subjects exhibited both severely attenuated humoral responses and absent spike-specific TCR depth and breadth, information which is crucial for counseling of patients on these agents. Our methodology can be used in larger studies to determine the benefit of repeated vaccination doses, including those that are modified to better target modern or seasonal variants, without the use of live cell assays.
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Affiliation(s)
- Priyanka Algu
- Zucker School of Medicine at Hofstra/Northwell, 173 Lawrence St., New Hyde Park, NY 11040, United States
| | - Natasha Hameed
- Northwell Multiple Sclerosis Center, 611 Northern Blvd, Great Neck, NY 11021, United States
| | - Tracy DeAngelis
- Neurological Associates of Long Island, 1991 Marcus Ave, New Hyde Park, NY 11042, United States
| | - Joel Stern
- Northwell Multiple Sclerosis Center, 350 Community Drive, Manhasset NY 11030, United States
| | - Asaff Harel
- Northwell Multiple Sclerosis Center, 130 East 77th Street, 8 Black Hall, NY 10075, United States.
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93
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Taylor JV, Callery EL, Rowbottom A. Optimisation of SARS-CoV-2 peptide stimulation and measurement of cytokine output by intracellular flow cytometry and bio-plex analysis. J Immunol Methods 2023; 522:113556. [PMID: 37683822 DOI: 10.1016/j.jim.2023.113556] [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: 07/21/2023] [Revised: 09/02/2023] [Accepted: 09/05/2023] [Indexed: 09/10/2023]
Abstract
Our study was conducted to optimise a peptide stimulation and an intracellular cytokine staining protocol, alongside Bio-Plex supernatant analysis, for use in patients who had previously contracted SARS-CoV-2 or received vaccination against this virus in a clinical laboratory setting. Peripheral Blood Mononuclear Cell extraction and cryopreservation allowed for cells to be stored long term and enhanced logistical processing of samples. Viability and functionality of cells were analysed by flow cytometric methodology using viability staining monoclonal antibodies conjugated to fluorochromes. Antibiotics and Benzonase Nuclease did not impact lymphocyte viability and so cell culture conditions were optimised in terms of retaining viability and functionality. Optimisation of peptide stimulation with Influenza and SARS-CoV-2 peptide pools was conducted through stimulation experiments assessing peptide concentration, peptide stimulation time and enrichment studies to increase precursor frequency. Cytokine output was measured by flow cytometry and Bio-Plex methodologies, with positive cytokine readings predominantly detected in the cell culture supernatant. Analysis of both intracellular and extracellular compartments allowed for detection of cytokines and established the retained cellular functionality post cryopreservation. These results also indicated that our peptide stimulation method can generate antigen-specific T lymphocytes upon exposure to SARS-CoV-2 peptide pools. Moreover, the measurement of specific cytokines could be applied to an array of conditions, such as chronic inflammatory diseases, but to also offer an alternative method of measuring vaccine responses. This platform is easily adaptable and can remain relevant alongside changing vaccine composition, thus ensuring its applicability to future vaccination programmes.
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Affiliation(s)
| | | | - Anthony Rowbottom
- Immunology Department at Lancashire Teaching Hospitals, United Kingdom
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94
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Guan X, Huang Q, Dong M, Li M, Xie H, Wei X, Kang L, Wang X, Li A, Wang Q, Huang F, Wang Q. SARS-CoV-2-specific antibody and T-cell immunity in convalescents after infection wave in Beijing in late 2022. J Infect 2023; 87:413-419. [PMID: 37652314 DOI: 10.1016/j.jinf.2023.08.010] [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: 07/19/2023] [Revised: 08/24/2023] [Accepted: 08/27/2023] [Indexed: 09/02/2023]
Abstract
OBJECTIVES To evaluate SARS-CoV-2-specific antibody and T-cell responses in convalescents 5 months after infection wave in Beijing from December 2022 to January 2023 to prevent reinfection and severe disease. METHODS Convalescents and uninfected individuals vaccinated with different doses were enrolled to assess the IFNγ T-cell responses against SARS-CoV-2 prototype strain, BF.7, BQ.1, and XBB. Neutralizing antibodies against prototype strain, BF.7, BA.5, and XBB and immunoglobulin G antibody were further analyzed. RESULTS In convalescents, the IFNγ T-cell response was significantly higher than that of uninfected individuals (all P < 0.001), and the T-cell response against XBB had no significant difference from that of SARS-CoV-2 prototype strain and BF.7 and BQ.1 (all P > 0.05). The seropositive rates of IgG antibodies were 100% (303/303) with a median concentration of 90.52 (95% CI, 82.52-99.37). The neutralizing antibodies titers of convalescents against BF.7 and BA.5 were higher than that against the prototype strain (both P < 0.001), while XBB.1.5 was lower (P < 0.001). T-cell response, IgG and neutralizing antibodies had no significant difference in convalescents vaccinated with different doses (all P > 0.05). CONCLUSIONS The immunities may have some protective effect against possible future outbreaks and severe diseases of COVID-19.
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Affiliation(s)
- Xuejiao Guan
- Beijing Center for Disease Prevention and Control, Beijing Academy for Preventive Medicine, Beijing Institute of Tuberculosis Control Research and Prevention, Beijing 100013, People's Republic of China
| | - Qi Huang
- Beijing Center for Disease Prevention and Control, Beijing Academy for Preventive Medicine, Beijing Institute of Tuberculosis Control Research and Prevention, Beijing 100013, People's Republic of China; School of Public Health, Capital Medical University, Beijing 100069, People's Republic of China
| | - Mei Dong
- Beijing Center for Disease Prevention and Control, Beijing Academy for Preventive Medicine, Beijing Institute of Tuberculosis Control Research and Prevention, Beijing 100013, People's Republic of China
| | - Maozhong Li
- Beijing Center for Disease Prevention and Control, Beijing Academy for Preventive Medicine, Beijing Institute of Tuberculosis Control Research and Prevention, Beijing 100013, People's Republic of China
| | - Hui Xie
- Beijing Center for Disease Prevention and Control, Beijing Academy for Preventive Medicine, Beijing Institute of Tuberculosis Control Research and Prevention, Beijing 100013, People's Republic of China
| | - Xiaofeng Wei
- Beijing Center for Disease Prevention and Control, Beijing Academy for Preventive Medicine, Beijing Institute of Tuberculosis Control Research and Prevention, Beijing 100013, People's Republic of China; School of Public Health, Capital Medical University, Beijing 100069, People's Republic of China
| | - Lu Kang
- Beijing Center for Disease Prevention and Control, Beijing Academy for Preventive Medicine, Beijing Institute of Tuberculosis Control Research and Prevention, Beijing 100013, People's Republic of China
| | - Xue Wang
- Beijing Center for Disease Prevention and Control, Beijing Academy for Preventive Medicine, Beijing Institute of Tuberculosis Control Research and Prevention, Beijing 100013, People's Republic of China
| | - Aihua Li
- Beijing Center for Disease Prevention and Control, Beijing Academy for Preventive Medicine, Beijing Institute of Tuberculosis Control Research and Prevention, Beijing 100013, People's Republic of China
| | - Qing Wang
- Beijing Center for Disease Prevention and Control, Beijing Academy for Preventive Medicine, Beijing Institute of Tuberculosis Control Research and Prevention, Beijing 100013, People's Republic of China; School of Public Health, Capital Medical University, Beijing 100069, People's Republic of China
| | - Fang Huang
- Beijing Center for Disease Prevention and Control, Beijing Academy for Preventive Medicine, Beijing Institute of Tuberculosis Control Research and Prevention, Beijing 100013, People's Republic of China; Beijing Research Center for Respiratory Infectious Diseases, People's Republic of China.
| | - Quanyi Wang
- Beijing Center for Disease Prevention and Control, Beijing Academy for Preventive Medicine, Beijing Institute of Tuberculosis Control Research and Prevention, Beijing 100013, People's Republic of China; Beijing Research Center for Respiratory Infectious Diseases, People's Republic of China.
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95
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Misra P, Garg PK, Awasthi A, Kant S, Rai SK, Ahmad M, Guleria R, Deori TJ, Mandal S, Jaiswal A, Gongal G, Vishwakarma S, Bairwa M, Kumar R, Haldar P, Binayke A. Cell-Mediated Immunity (CMI) for SARS-CoV-2 Infection Among the General Population of North India: A Cross-Sectional Analysis From a Sub-sample of a Large Sero-Epidemiological Study. Cureus 2023; 15:e48824. [PMID: 38106811 PMCID: PMC10722242 DOI: 10.7759/cureus.48824] [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] [Accepted: 11/13/2023] [Indexed: 12/19/2023] Open
Abstract
Background Cell-mediated immunity (CMI), or specifically T-cell-mediated immunity, is proven to remain largely preserved against the variants of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), including Omicron. The persistence of cell-mediated immune response in individuals longitudinally followed up for an extended period remains largely unelucidated. To address this, the current study was planned to study whether the effect of cell-mediated immunity persists after an extended period of convalescence or vaccination. Methods Whole blood specimens of 150 selected participants were collected and tested for Anti-SARS-CoV-2 Interferon-gamma (IFN-γ) response. Ex vivo SARS-CoV-2-specific interferon-gamma Enzyme-linked Immunospot (IFN-γ ELISpot) assay was carried out to determine the levels of virus-specific IFN-γ producing cells in individual samples. Findings Out of all the samples tested for anti-SARS-CoV-2 T-cell-mediated IFN-γ response, 78.4% of samples were positive. The median (interquartile range) spots forming units (SFU) per million levels of SARS-CoV-2-specific IFN-γ producing cells of the vaccinated and diagnosed participants was 336 (138-474) while those who were vaccinated but did not have the disease diagnosis was 18 (0-102); the difference between the groups was statistically significant. Since almost all the participants were vaccinated, a similar pattern of significance was observed when the diagnosed and the never-diagnosed participants were compared, irrespective of their vaccination status. Interpretations Cell-mediated immunity against SARS-CoV-2 persisted, irrespective of age and sex of the participant, for more than six months of previous exposure. Participants who had a history of diagnosed COVID-19 infection had better T-cell response compared to those who had never been diagnosed, in spite of being vaccinated.
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Affiliation(s)
- Puneet Misra
- Epidemiology and Public Health, Centre for Community Medicine, All India Institute of Medical Sciences, New Delhi, New Delhi, IND
| | - Pramod K Garg
- Gastroenterology, All India Institute of Medical Sciences, New Delhi, New Delhi, IND
| | - Amit Awasthi
- Allergy and Immunology, Centre for Immunobiology and Immunotherapy, Translational Health Science and Technology Institute, Faridabad, IND
| | - Shashi Kant
- Epidemiology and Public Health, Centre for Community Medicine, All India Institute of Medical Sciences, New Delhi, New Delhi, IND
| | - Sanjay K Rai
- Epidemiology and Public Health, Centre for Community Medicine, All India Institute of Medical Sciences, New Delhi, New Delhi, IND
| | - Mohammad Ahmad
- Epidemiology and Public Health, World Health Organization, New Delhi, IND
| | - Randeep Guleria
- Pulmonary, Critical Care, and Sleep Medicine, All India Institute of Medical Sciences, New Delhi, New Delhi, IND
| | - Trideep J Deori
- Epidemiology and Public Health, Centre for Community Medicine, All India Institute of Medical Sciences, New Delhi, New Delhi, IND
| | - Suprakash Mandal
- Epidemiology and Public Health, Centre for Community Medicine, All India Institute of Medical Sciences, New Delhi, New Delhi, IND
| | - Abhishek Jaiswal
- Community Medicine, All India Institute of Medical Sciences, New Delhi, New Delhi, IND
| | - Gaurav Gongal
- Epidemiology and Public Health, Centre for Community Medicine, All India Institute of Medical Sciences, New Delhi, New Delhi, IND
| | - Siddhesh Vishwakarma
- Allergy and Immunology, Immunology Core Laboratory, Translational Health Science and Technology Institute, Faridabad, IND
| | - Mohan Bairwa
- Epidemiology and Public Health, Centre for Community Medicine, All India Institute of Medical Sciences, New Delhi, New Delhi, IND
| | - Rakesh Kumar
- Epidemiology and Public Health, Centre for Community Medicine, All India Institute of Medical Sciences, New Delhi, New Delhi, IND
| | - Partha Haldar
- Preventive Medicine, Centre for Community Medicine, All India Institute of Medical Sciences, New Delhi, New Delhi, IND
| | - Akshay Binayke
- Allergy and Immunology, Centre for Immunobiology and Immunotherapy, Translational Health Science and Technology Institute, Faridabad, IND
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96
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Ssali I, Mugaba S, Watelo AK, Bemanzi J, Katende JS, Oluka GK, Ankunda V, Baine C, Kato L, Onyachi N, Muwanga M, Jjuuko M, Kayiwa J, Nsereko C, Auma BO, Weiskopf D, Sette A, Lutalo T, Musenero M, Kaleebu P, Serwanga J. Spike protein is a key target for stronger and more persistent T-cell responses-a study of mild and asymptomatic SARS-CoV-2 infection. Int J Infect Dis 2023; 136:49-56. [PMID: 37683720 DOI: 10.1016/j.ijid.2023.09.001] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2023] [Revised: 08/08/2023] [Accepted: 09/02/2023] [Indexed: 09/10/2023] Open
Abstract
OBJECTIVES Understanding the immune response in very mild and asymptomatic COVID-19 is crucial for developing effective vaccines and immunotherapies, yet remains poorly characterized. This longitudinal study examined the evolution of interferon (IFN)-γ responses to SARS-CoV-2 peptides in 109 asymptomatic or mildly symptomatic Ugandan COVID-19 patients across 365 days and explored their association with antibody generation. METHODS T-cell responses to spike-containing clusters of differentiation (CD4)-S and CD8 nCoV-A (CD8-A) megapools, and the non-spike CD4-R and CD8 nCoV-B (CD8-B) megapools, were assessed and correlated with demographic and temporal variables. RESULTS SARS-CoV-2-specific IFN-γ responses were consistently detected in all peptide pools and time points, with the spike-targeted response exhibiting higher potency and durability than the non-spike responses. Throughout the entire 365-day infection timeline, a robust positive correlation was observed between CD4 T-cell responses to the spike-derived peptides and anti-spike immunoglobulin G antibody levels, underscoring their interdependent dynamics in the immune response against SARS-CoV-2; in contrast, CD8 T-cell responses exhibited no such correlation, highlighting their distinctive, autonomous role in defense. No meaningful variations in complete blood count parameters were observed between individuals with COVID-19 infection and those without, indicating clinical insignificance. CONCLUSIONS This study highlights the dominant role of spike-directed T-cell responses in mild and asymptomatic disease and provides crucial longitudinal data from Sub-Saharan African settings. The findings provide valuable insights into the dynamics of T-cell responses and their potential significance in developing effective strategies for combating COVID-19.
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Affiliation(s)
- Ivan Ssali
- Pathogen Genomics, Phenotype, and Immunity Program, Medical Research Council, Uganda Virus Research Institute and London School of Hygiene and Tropical Medicine, Uganda Research Unit, Entebbe, Uganda
| | - Susan Mugaba
- Pathogen Genomics, Phenotype, and Immunity Program, Medical Research Council, Uganda Virus Research Institute and London School of Hygiene and Tropical Medicine, Uganda Research Unit, Entebbe, Uganda
| | | | - Juliana Bemanzi
- Department of Immunology, Uganda Virus Research Institute, Entebbe, Uganda
| | - Joseph Ssebwana Katende
- Pathogen Genomics, Phenotype, and Immunity Program, Medical Research Council, Uganda Virus Research Institute and London School of Hygiene and Tropical Medicine, Uganda Research Unit, Entebbe, Uganda; Department of Immunology, Uganda Virus Research Institute, Entebbe, Uganda
| | - Gerald Kevin Oluka
- Pathogen Genomics, Phenotype, and Immunity Program, Medical Research Council, Uganda Virus Research Institute and London School of Hygiene and Tropical Medicine, Uganda Research Unit, Entebbe, Uganda; Department of Immunology, Uganda Virus Research Institute, Entebbe, Uganda
| | - Violet Ankunda
- Pathogen Genomics, Phenotype, and Immunity Program, Medical Research Council, Uganda Virus Research Institute and London School of Hygiene and Tropical Medicine, Uganda Research Unit, Entebbe, Uganda
| | - Claire Baine
- Department of Immunology, Uganda Virus Research Institute, Entebbe, Uganda
| | - Laban Kato
- Pathogen Genomics, Phenotype, and Immunity Program, Medical Research Council, Uganda Virus Research Institute and London School of Hygiene and Tropical Medicine, Uganda Research Unit, Entebbe, Uganda
| | - Nathan Onyachi
- Department of Internal Medicine, Masaka Regional Referral Hospital, Masaka, Uganda
| | - Moses Muwanga
- Department of Internal Medicine, Entebbe Regional Referral Hospital, Entebbe, Uganda
| | - Mark Jjuuko
- Department of Internal Medicine, Masaka Regional Referral Hospital, Masaka, Uganda
| | - John Kayiwa
- Department of Immunology, Uganda Virus Research Institute, Entebbe, Uganda
| | - Christopher Nsereko
- Department of Internal Medicine, Entebbe Regional Referral Hospital, Entebbe, Uganda
| | - Betty Oliver Auma
- Pathogen Genomics, Phenotype, and Immunity Program, Medical Research Council, Uganda Virus Research Institute and London School of Hygiene and Tropical Medicine, Uganda Research Unit, Entebbe, Uganda
| | - Daniela Weiskopf
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology, La Jolla, USA
| | - Alessandro Sette
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology, La Jolla, USA; Department of Medicine, Division of Infectious Diseases and Global Public Health, University of California, San Diego (UCSD), La Jolla, USA
| | - Tom Lutalo
- Department of Immunology, Uganda Virus Research Institute, Entebbe, Uganda
| | - Monica Musenero
- Science, Technology, and Innovation Secretariat, Office of the President, Government of Uganda, Kampala, Uganda
| | - Pontiano Kaleebu
- Pathogen Genomics, Phenotype, and Immunity Program, Medical Research Council, Uganda Virus Research Institute and London School of Hygiene and Tropical Medicine, Uganda Research Unit, Entebbe, Uganda; Department of Immunology, Uganda Virus Research Institute, Entebbe, Uganda
| | - Jennifer Serwanga
- Pathogen Genomics, Phenotype, and Immunity Program, Medical Research Council, Uganda Virus Research Institute and London School of Hygiene and Tropical Medicine, Uganda Research Unit, Entebbe, Uganda; Department of Immunology, Uganda Virus Research Institute, Entebbe, Uganda.
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97
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Diniz MO, Maini MK, Swadling L. T cell control of SARS-CoV-2: When, which, and where? Semin Immunol 2023; 70:101828. [PMID: 37651850 DOI: 10.1016/j.smim.2023.101828] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/18/2023] [Accepted: 08/13/2023] [Indexed: 09/02/2023]
Abstract
Efficient immune protection against viruses such as SARS-CoV-2 requires the coordinated activity of innate immunity, B and T cells. Accumulating data point to a critical role for T cells not only in the clearance of established infection, but also for aborting viral replication independently of humoral immunity. Here we review the evidence supporting the contribution of antiviral T cells and consider which of their qualitative features favour efficient control of infection. We highlight how studies of SARS-CoV-2 and other coronaviridae in animals and humans have provided important lessons on the optimal timing (When), functionality and specificity (Which), and location (Where) of antiviral T cells. We discuss the clinical implications, particularly for the development of next-generation vaccines, and emphasise areas requiring further study.
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Affiliation(s)
- Mariana O Diniz
- Division of Infection and Immunity, Institute of Immunity and Transplantation, University College London, Pears Building, London WC1E 6BT, UK
| | - Mala K Maini
- Division of Infection and Immunity, Institute of Immunity and Transplantation, University College London, Pears Building, London WC1E 6BT, UK.
| | - Leo Swadling
- Division of Infection and Immunity, Institute of Immunity and Transplantation, University College London, Pears Building, London WC1E 6BT, UK.
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98
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Schmidt F, Fields HF, Purwanti Y, Milojkovic A, Salim S, Wu KX, Simoni Y, Vitiello A, MacLeod DT, Nardin A, Newell EW, Fink K, Wilm A, Fehlings M. In-depth analysis of human virus-specific CD8 + T cells delineates unique phenotypic signatures for T cell specificity prediction. Cell Rep 2023; 42:113250. [PMID: 37837618 DOI: 10.1016/j.celrep.2023.113250] [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: 03/10/2023] [Revised: 07/21/2023] [Accepted: 09/26/2023] [Indexed: 10/16/2023] Open
Abstract
Following viral infection, the human immune system generates CD8+ T cell responses to virus antigens that differ in specificity, abundance, and phenotype. A characterization of virus-specific T cell responses allows one to assess infection history and to understand its contribution to protective immunity. Here, we perform in-depth profiling of CD8+ T cells binding to CMV-, EBV-, influenza-, and SARS-CoV-2-derived antigens in peripheral blood samples from 114 healthy donors and 55 cancer patients using high-dimensional mass cytometry and single-cell RNA sequencing. We analyze over 500 antigen-specific T cell responses across six different HLA alleles and observed unique phenotypes of T cells specific for antigens from different virus categories. Using machine learning, we extract phenotypic signatures of antigen-specific T cells, predict virus specificity for bulk CD8+ T cells, and validate these predictions, suggesting that machine learning can be used to accurately predict antigen specificity from T cell phenotypes.
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Affiliation(s)
| | | | | | | | | | - Kan Xing Wu
- ImmunoScape Pte Ltd, Singapore 228208, Singapore
| | | | | | | | | | - Evan W Newell
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | - Katja Fink
- ImmunoScape Pte Ltd, Singapore 228208, Singapore
| | - Andreas Wilm
- ImmunoScape Pte Ltd, Singapore 228208, Singapore
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99
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Yin S, Klaeger S, Chea VA, Carulli IP, Rachimi S, Black KE, Filbin M, Hariri LP, Knipe RS, Padera RF, Stevens JD, Lane WJ, Carr SA, Wu CJ, Kim EY, Keskin DB. Integrated Immunopeptidomic and Proteomic Analysis of COVID-19 lung biopsies. Front Immunol 2023; 14:1269335. [PMID: 37942334 PMCID: PMC10628763 DOI: 10.3389/fimmu.2023.1269335] [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: 07/31/2023] [Accepted: 10/09/2023] [Indexed: 11/10/2023] Open
Abstract
Introduction Severe respiratory illness is the most prominent manifestation of patients infected with SARS-CoV-2, and yet the molecular mechanisms underlying severe lung disease in COVID-19 affected patients still require elucidation. Human leukocyte antigen class I (HLA-I) expression is crucial for antigen presentation and the host's response to SARS-CoV-2. Methods To gain insights into the immune response and molecular pathways involved in severe lung disease, we performed immunopeptidomic and proteomic analyses of lung tissues recovered at four COVID-19 autopsy and six non-COVID-19 transplants. Results We found signals of tissue injury and regeneration in lung fibroblast and alveolar type I/II cells, resulting in the production of highly immunogenic self-antigens within the lungs of COVID-19 patients. We also identified immune activation of the M2c macrophage as the primary source of HLA-I presentation and immunogenicity in this context. Additionally, we identified 28 lung signatures that can serve as early plasma markers for predicting infection and severe COVID-19 disease. These protein signatures were predominantly expressed in macrophages and epithelial cells and were associated with complement and coagulation cascades. Discussion Our findings emphasize the significant role of macrophage-mediated immunity in the development of severe lung disease in COVID-19 patients.
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Affiliation(s)
- Shanye Yin
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, United States
- Harvard Medical School, Boston, MA, United States
| | - Susan Klaeger
- Broad Institute of MIT and Harvard, Cambridge, MA, United States
| | - Vipheaviny A. Chea
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, United States
- Translational Immunogenomics Laboratory, Dana-Farber Cancer Institute, Boston, MA, United States
| | - Isabel P. Carulli
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, United States
- Translational Immunogenomics Laboratory, Dana-Farber Cancer Institute, Boston, MA, United States
| | - Suzanna Rachimi
- Broad Institute of MIT and Harvard, Cambridge, MA, United States
| | - Katharine E. Black
- Harvard Medical School, Boston, MA, United States
- Division of Pulmonary and Critical Care Medicine, Massachusetts General Hospital, Boston, MA, United States
| | - Michael Filbin
- Harvard Medical School, Boston, MA, United States
- Department of Emergency Medicine, Massachusetts General Hospital, Boston, MA, United States
| | - Lida P. Hariri
- Harvard Medical School, Boston, MA, United States
- Division of Pulmonary and Critical Care Medicine, Massachusetts General Hospital, Boston, MA, United States
- Department of Pathology, Massachusetts General Hospital, Boston, MA, United States
| | - Rachel S. Knipe
- Harvard Medical School, Boston, MA, United States
- Division of Pulmonary and Critical Care Medicine, Massachusetts General Hospital, Boston, MA, United States
| | - Robert F. Padera
- Harvard Medical School, Boston, MA, United States
- Department of Pathology, Brigham and Women’s Hospital, Boston, MA, United States
| | - Jonathan D. Stevens
- Department of Pathology, Brigham and Women’s Hospital, Boston, MA, United States
| | - William J. Lane
- Harvard Medical School, Boston, MA, United States
- Department of Pathology, Brigham and Women’s Hospital, Boston, MA, United States
| | - Steven A. Carr
- Broad Institute of MIT and Harvard, Cambridge, MA, United States
| | - Catherine J. Wu
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, United States
- Harvard Medical School, Boston, MA, United States
- Broad Institute of MIT and Harvard, Cambridge, MA, United States
- Department of Medicine, Brigham and Women’s Hospital, Boston, MA, United States
| | - Edy Yong Kim
- Harvard Medical School, Boston, MA, United States
- Division of Pulmonary and Critical Care Medicine, Brigham and Women’s Hospital, Boston, MA, United States
| | - Derin B. Keskin
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, United States
- Harvard Medical School, Boston, MA, United States
- Broad Institute of MIT and Harvard, Cambridge, MA, United States
- Translational Immunogenomics Laboratory, Dana-Farber Cancer Institute, Boston, MA, United States
- Section for Bioinformatics, Department of Health Technology, Technical University of Denmark, Lyngby, Denmark
- Department of Computer Science, Metropolitan College, Boston University, Boston, MA, United States
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100
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Ashokkumar C, Rohan V, Kroemer AH, Rao S, Mazariegos G, Higgs BW, Nadig S, Almeda J, Dhani H, Khan K, Yazigi N, Ekong U, Kaufman S, Betancourt-Garcia MM, Mukund K, Sethi P, Mehrotra S, Soltys K, Singh MS, Bond G, Khanna A, Ningappa M, Spishock B, Sindhi E, Atale N, Saunders M, Baliga P, Fishbein T, Subramaniam S, Sindhi R. Impaired Cellular and Antibody immunity after COVID-19 in Chronically Immunosuppressed Transplant Recipients. JOURNAL OF SURGERY AND RESEARCH 2023; 6:348-363. [PMID: 38606317 PMCID: PMC11007760 DOI: 10.26502/jsr.10020321] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/13/2024]
Abstract
Assessment of cellular immunity to the SARS-CoV-2 coronavirus is of great interest in chronically immunosuppressed transplant recipients (Tr), who are predisposed to infections and vaccination failures. We evaluated CD154-expressing T-cells induced by spike (S) antigenic peptides in 204 subjects-103 COVID-19 patients and 101 healthy unexposed subjects. S-reactive CD154+T-cell frequencies were a) higher in 42 healthy unexposed Tr who were sampled pre-pandemic, compared with healthy NT (p=0.02), b) lower in Tr COVID-19 patients compared with healthy Tr (p<0.0001) and were accompanied by lower S-reactive B-cell frequencies (p<0.05), c) lower in Tr with severe COVID-19 (p<0.0001), or COVID-19 requiring hospitalization (p<0.05), compared with healthy Tr. Among Tr with COVID-19, cytomegalovirus co-infection occurred in 34%; further, incidence of anti-receptor-binding-domain IgG (p=0.011) was lower compared with NT COVID-19 patients. Healthy unexposed Tr exhibit pre-existing T-cell immunity to SARS-CoV-2. COVID-19 impairs anti-S T-cell and antibody and predisposes to CMV co-infection in transplant recipients.
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Affiliation(s)
- Chethan Ashokkumar
- Plexision Inc., Pittsburgh, PA, USA
- Hillman Center for Pediatric Transplantation, University of Pittsburgh, PA, USA
| | - Vinayak Rohan
- Medical University of South Carolina, Charleston, SC, USA
| | | | - Sohail Rao
- DHR Health and DHR Health Institute for Research and Development, Edinburg, Tx, University of Houston, Houston, TX, USA
| | - George Mazariegos
- Hillman Center for Pediatric Transplantation, University of Pittsburgh, PA, USA
| | - Brandon W Higgs
- Hillman Center for Pediatric Transplantation, University of Pittsburgh, PA, USA
| | - Satish Nadig
- Medical University of South Carolina, Charleston, SC, USA
| | - Jose Almeda
- DHR Health and DHR Health Institute for Research and Development, Edinburg, Tx, University of Houston, Houston, TX, USA
| | - Harmeet Dhani
- Medstar Georgetown Transplant Institute, Washington, DC, USA
| | - Khalid Khan
- Medstar Georgetown Transplant Institute, Washington, DC, USA
| | - Nada Yazigi
- Medstar Georgetown Transplant Institute, Washington, DC, USA
| | - Udeme Ekong
- Medstar Georgetown Transplant Institute, Washington, DC, USA
| | - Stuart Kaufman
- Medstar Georgetown Transplant Institute, Washington, DC, USA
| | - Monica M Betancourt-Garcia
- DHR Health and DHR Health Institute for Research and Development, Edinburg, Tx, University of Houston, Houston, TX, USA
| | | | | | | | - Kyle Soltys
- Hillman Center for Pediatric Transplantation, University of Pittsburgh, PA, USA
| | - Manasi S Singh
- Medical University of South Carolina, Charleston, SC, USA
| | - Geoffrey Bond
- Hillman Center for Pediatric Transplantation, University of Pittsburgh, PA, USA
| | - Ajai Khanna
- Hillman Center for Pediatric Transplantation, University of Pittsburgh, PA, USA
| | - Mylarappa Ningappa
- Hillman Center for Pediatric Transplantation, University of Pittsburgh, PA, USA
| | | | | | | | | | | | - Thomas Fishbein
- Medstar Georgetown Transplant Institute, Washington, DC, USA
| | | | - Rakesh Sindhi
- Plexision Inc., Pittsburgh, PA, USA
- Hillman Center for Pediatric Transplantation, University of Pittsburgh, PA, USA
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