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Trabelsi K, Ben Khalaf N, Ramadan AR, Elsharkawy A, Ashoor D, Chlif S, Boussoffara T, Ben-Ahmed M, Kumar M, Fathallah MD. A novel approach to designing viral precision vaccines applied to SARS-CoV-2. Front Cell Infect Microbiol 2024; 14:1346349. [PMID: 38628551 PMCID: PMC11018900 DOI: 10.3389/fcimb.2024.1346349] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2023] [Accepted: 03/08/2024] [Indexed: 04/19/2024] Open
Abstract
Efficient precision vaccines against several highly pathogenic zoonotic viruses are currently lacking. Proteolytic activation is instrumental for a number of these viruses to gain host-cell entry and develop infectivity. For SARS-CoV-2, this process is enhanced by the insertion of a furin cleavage site at the junction of the spike protein S1/S2 subunits upstream of the metalloprotease TMPRSS2 common proteolytic site. Here, we describe a new approach based on specific epitopes selection from the region involved in proteolytic activation and infectivity for the engineering of precision candidate vaccinating antigens. This approach was developed through its application to the design of SARS-CoV-2 cross-variant candidates vaccinating antigens. It includes an in silico structural analysis of the viral region involved in infectivity, the identification of conserved immunogenic epitopes and the selection of those eliciting specific immune responses in infected people. The following step consists of engineering vaccinating antigens that carry the selected epitopes and mimic their 3D native structure. Using this approach, we demonstrated through a Covid-19 patient-centered study of a 500 patients' cohort, that the epitopes selected from SARS-CoV-2 protein S1/S2 junction elicited a neutralizing antibody response significantly associated with mild and asymptomatic COVID-19 (p<0.001), which strongly suggests protective immunity. Engineered antigens containing the SARS-CoV-2 selected epitopes and mimicking the native epitopes 3D structure generated neutralizing antibody response in mice. Our data show the potential of this combined computational and experimental approach for designing precision vaccines against viruses whose pathogenicity is contingent upon proteolytic activation.
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Affiliation(s)
- Khaled Trabelsi
- Health Biotechnology Program, King Fahad Chair for Health Biotechnology, Department of Life Sciences College of Graduate Studies, Arabian Gulf University, Manama, Bahrain
| | - Noureddin Ben Khalaf
- Health Biotechnology Program, King Fahad Chair for Health Biotechnology, Department of Life Sciences College of Graduate Studies, Arabian Gulf University, Manama, Bahrain
| | - Ahmed R. Ramadan
- Health Biotechnology Program, King Fahad Chair for Health Biotechnology, Department of Life Sciences College of Graduate Studies, Arabian Gulf University, Manama, Bahrain
| | - Amany Elsharkawy
- Department of Biology, College of Arts and Sciences, Georgia State University, Atlanta, GA, United States
| | - Dana Ashoor
- Health Biotechnology Program, King Fahad Chair for Health Biotechnology, Department of Life Sciences College of Graduate Studies, Arabian Gulf University, Manama, Bahrain
| | - Sadok Chlif
- Department of Family and Community Medicine, College of Medicine and Medical Sciences, Arabian Gulf University, Manama, Bahrain
| | - Thouraya Boussoffara
- Transmission, Control and Immunobiology of Infections Laboratory, Institute Pasteur of Tunis, Tunis, Tunisia
| | - Melika Ben-Ahmed
- Transmission, Control and Immunobiology of Infections Laboratory, Institute Pasteur of Tunis, Tunis, Tunisia
| | - Mukesh Kumar
- Department of Biology, College of Arts and Sciences, Georgia State University, Atlanta, GA, United States
| | - M-Dahmani Fathallah
- Health Biotechnology Program, King Fahad Chair for Health Biotechnology, Department of Life Sciences College of Graduate Studies, Arabian Gulf University, Manama, Bahrain
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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. Corrigendum: Experimental validation of immunogenic SARS-CoV-2 T cell epitopes identified by artificial intelligence. Front Immunol 2024; 15:1377041. [PMID: 38449865 PMCID: PMC10916508 DOI: 10.3389/fimmu.2024.1377041] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2024] [Accepted: 02/05/2024] [Indexed: 03/08/2024] Open
Abstract
[This corrects the article DOI: 10.3389/fimmu.2023.1265044.].
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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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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: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [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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Alvarez I, Antón LC, James EA. Editorial: alternative antigen processing and presentation in immune disorders. Front Immunol 2022; 13:993393. [PMID: 36159790 PMCID: PMC9493697 DOI: 10.3389/fimmu.2022.993393] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2022] [Accepted: 07/18/2022] [Indexed: 11/22/2022] Open
Affiliation(s)
- Iñaki Alvarez
- Immunology Unit, Department of Cell Biology, Physiology and Immunology, Autonomous University of Barcelona, Bellaterra, Spain.,Institute of Biotechnology and Biomedicine, Autonomous University of Barcelona, Bellaterra, Spain
| | - Luis C Antón
- Centro de Biología Molecular Severo Ochoa, CSIC/UAM, C/Nicolás Cabrera, Madrid, Spain
| | - Eddie A James
- Center for Translational Immunology, Benaroya Research Institute, Seattle, WA, United States
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Abstract
Systemic lupus erythematosus (SLE) is a chronic complex systemic autoimmune disease characterized by multiple autoantibodies and clinical manifestations, with the potential to affect nearly every organ. SLE treatments, including corticosteroids and immunosuppressive drugs, have greatly increased survival rates, but there is no curative therapy and SLE management is limited by drug complications and toxicities. There is an obvious clinical need for safe, effective SLE treatments. A promising treatment avenue is to restore immunological tolerance to reduce inflammatory clinical manifestations of SLE. Indeed, recent clinical trials of low-dose IL-2 supplementation in SLE patients showed that in vivo expansion of regulatory T cells (Treg cells) is associated with dramatic but transient improvement in SLE disease markers and clinical manifestations. However, the Treg cells that expanded were short-lived and unstable. Alternatively, antigen-specific tolerance (ASIT) approaches that establish long-lived immunological tolerance could be deployed in the context of SLE. In this review, we discuss the potential benefits and challenges of nanoparticle ASIT approaches to induce prolonged immunological tolerance in SLE.
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Affiliation(s)
- Sean Robinson
- School of Medicine, Faculty of Medicine and Biomedical Sciences, University of Queensland, St Lucia, QLD, Australia
| | - Ranjeny Thomas
- University of Queensland Diamantina Institute, The University of Queensland, Princess Alexandra Hospital, Woolloongabba, QLD, Australia
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Chiu NC, Lin YJ, Tzang RF, Li YS, Lin HJ, Das S, Chen CG, Chen CC, Hsu K. Optimization of an Anti-NMDA Receptor Autoantibody Diagnostic Bioassay. Front Neurol 2018; 9:661. [PMID: 30186218 PMCID: PMC6113861 DOI: 10.3389/fneur.2018.00661] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2018] [Accepted: 07/24/2018] [Indexed: 12/21/2022] Open
Abstract
Anti-N-methyl-D-aspartate receptor (anti-NMDAR) encephalitis is one of the most frequently encountered autoimmune encephalitis. The pathogenesis of both anti-NMDAR encephalitis and schizophrenia involve down-regulation of NMDA receptors. Whether autoantibody-mediated destruction of neuronal NMDA receptors is associated with schizophrenia or first-episode psychosis (FEP) remains unclear, as the current findings from different groups are inconsistent. The main culprits are likely due to heterogeneity of autoantibodies (autoAbs) in a patient's blood or cerebrospinal fluid (CSF), as well as due to limitation of the current detection methods for anti-NMDAR autoAbs. Here, we optimized the current diagnostic method based on the only commercially-available anti-NMDAR test kit. We first increased detection sensitivity by replacing reporter fluorophore fluorescein isothiocyanate (FITC) in the kit with Alexa Fluor 488, which is superior in resisting photobleaching. We also found that using an advanced imaging system could increase the detection limit, compared to using a simple fluorescence microscope. To improve test accuracy, we implemented secondary labeling with a well-characterized mouse anti-NR1 monoclonal antibody (mAb) after immunostaining with a patient's sample. The degree of colocalization between mouse and human antisera in NMDAR-expressing cells served to validate test results to be truly anti-NMDAR positive or false-positive. We also incorporated DNA-specific DAPI to simultaneously differentiate autoAbs targeting the plasma membrane from those targeting cell nuclei or perinuclear compartments. All the technical implementation could be integrated in a general hospital laboratory setting, without the need of specialized expertise or equipment. By sharing our experience, we hope this may help improve sensitivity and accuracy of the mainstream method for anti-NMDAR detection.
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Affiliation(s)
- Nan-Chang Chiu
- Division of Pediatric Neurology, Department of Pediatrics, MacKay Children's Hospital, Taipei, Taiwan.,MacKay Junior College of Medicine, Nursing and Management, New Taipei City, Taiwan.,MacKay Medical College, New Taipei City, Taiwan
| | - Yi-Jie Lin
- Division of Pediatric Neurology, Department of Pediatrics, MacKay Children's Hospital, Taipei, Taiwan
| | - Ruu-Fen Tzang
- MacKay Junior College of Medicine, Nursing and Management, New Taipei City, Taiwan.,MacKay Medical College, New Taipei City, Taiwan.,Department of Psychiatry, MacKay Memorial Hospital, Taipei, Taiwan
| | - Ying-Syuan Li
- MacKay Memorial Hospital Transfusion Medicine & Immunogenetics Laboratories, Tamsui, Taiwan
| | - Hui-Ju Lin
- MacKay Memorial Hospital Transfusion Medicine & Immunogenetics Laboratories, Tamsui, Taiwan
| | - Subir Das
- Institute of Biophotonics, National Yang-Ming University, Taipei, Taiwan
| | - Caleb G Chen
- MacKay Medical College, New Taipei City, Taiwan.,Department of Internal Medicine, MacKay Memorial Hospital, Taipei, Taiwan
| | - Chiao-Chicy Chen
- MacKay Medical College, New Taipei City, Taiwan.,Department of Psychiatry, MacKay Memorial Hospital, Taipei, Taiwan
| | - Kate Hsu
- MacKay Memorial Hospital Transfusion Medicine & Immunogenetics Laboratories, Tamsui, Taiwan
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Ndeboko B, Lemamy GJ, Nielsen PE, Cova L. Therapeutic Potential of Cell Penetrating Peptides (CPPs) and Cationic Polymers for Chronic Hepatitis B. Int J Mol Sci 2015; 16:28230-41. [PMID: 26633356 PMCID: PMC4691041 DOI: 10.3390/ijms161226094] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2015] [Revised: 11/17/2015] [Accepted: 11/20/2015] [Indexed: 02/06/2023] Open
Abstract
Chronic hepatitis B virus (HBV) infection remains a major health problem worldwide. Because current anti-HBV treatments are only virostatic, there is an urgent need for development of alternative antiviral approaches. In this context, cell-penetrating peptides (CPPs) and cationic polymers, such as chitosan (CS), appear of particular interest as nonviral vectors due to their capacity to facilitate cellular delivery of bioactive cargoes including peptide nucleic acids (PNAs) or DNA vaccines. We have investigated the ability of a PNA conjugated to different CPPs to inhibit the replication of duck hepatitis B virus (DHBV), a reference model for human HBV infection. The in vivo administration of PNA-CPP conjugates to neonatal ducklings showed that they reached the liver and inhibited DHBV replication. Interestingly, our results indicated also that a modified CPP (CatLip) alone, in the absence of its PNA cargo, was able to drastically inhibit late stages of DHBV replication. In the mouse model, conjugation of HBV DNA vaccine to modified CS (Man-CS-Phe) improved cellular and humoral responses to plasmid-encoded antigen. Moreover, other systems for gene delivery were investigated including CPP-modified CS and cationic nanoparticles. The results showed that these nonviral vectors considerably increased plasmid DNA uptake and expression. Collectively promising results obtained in preclinical studies suggest the usefulness of these safe delivery systems for the development of novel therapeutics against chronic hepatitis B.
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Affiliation(s)
- Bénédicte Ndeboko
- Institut National de la Sante et Recherche Medicale (INSERM) U1052, Cancer Research Center of Lyon (CRCL), Lyon 69003, France.
- Département de Biologie Cellulaire and Moléculaire-Génétique, Faculté de Médecine, Université des Sciences de la Santé, Libreville 241, Gabon.
| | - Guy Joseph Lemamy
- Département de Biologie Cellulaire and Moléculaire-Génétique, Faculté de Médecine, Université des Sciences de la Santé, Libreville 241, Gabon.
| | - Peter E Nielsen
- Department of Cellular and Molecular Medicine, Departement of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, the Panum Institute, University of Copenhagen, Copenhagen DK 2200N, Denmark.
| | - Lucyna Cova
- Institut National de la Sante et Recherche Medicale (INSERM) U1052, Cancer Research Center of Lyon (CRCL), Lyon 69003, France.
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