1
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Ma J, Yakass MB, Jansen S, Malengier-Devlies B, Van Looveren D, Sanchez-Felipe L, Vercruysse T, Weynand B, Javarappa MPA, Quaye O, Matthys P, Roskams T, Neyts J, Thibaut HJ, Dallmeier K. Live-attenuated YF17D-vectored COVID-19 vaccine protects from lethal yellow fever virus infection in mouse and hamster models. EBioMedicine 2022; 83:104240. [PMID: 36041265 PMCID: PMC9419561 DOI: 10.1016/j.ebiom.2022.104240] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [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: 05/23/2022] [Revised: 07/29/2022] [Accepted: 08/10/2022] [Indexed: 01/09/2023] Open
Abstract
BACKGROUND The live-attenuated yellow fever vaccine YF17D holds great promise as alternative viral vector vaccine platform, showcased by our previously presented potent severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) vaccine candidate YF-S0. Besides protection from SARS-CoV-2, YF-S0 also induced strong yellow fever virus (YFV)-specific immunity, suggestive for full dual activity. A vaccine concomitantly protecting from SARS-CoV-2 and YFV would be of great benefit for those living in YFV-endemic areas with limited access to current SARS-CoV-2 vaccines. However, for broader applicability, pre-existing vector immunity should not impact the potency of such YF17D-vectored vaccines. METHODS The immunogenicity and efficacy of YF-S0 against YFV and SARS-CoV-2 in the presence of strong pre-existing YFV immunity were evaluated in mouse and hamster challenge models. FINDINGS Here, we show that a single dose of YF-S0 is sufficient to induce strong humoral and cellular immunity against YFV as well as SARS-CoV-2 in mice and hamsters; resulting in full protection from vigorous YFV challenge in either model; in mice against lethal intracranial YF17D challenge, and in hamsters against viscerotropic infection and liver disease following challenge with highly pathogenic hamster-adapted YFV-Asibi strain. Importantly, strong pre-existing immunity against the YF17D vector did not interfere with subsequent YF-S0 vaccination in mice or hamsters; nor with protection conferred against SARS-CoV-2 strain B1.1.7 (Alpha variant) infection in hamsters. INTERPRETATION Our findings warrant the development of YF-S0 as dual SARS-CoV-2 and YFV vaccine. Contrary to other viral vaccine platforms, use of YF17D does not suffer from pre-existing vector immunity. FUNDING Stated in the acknowledgments.
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Affiliation(s)
- Ji Ma
- KU Leuven Department of Microbiology, Immunology and Transplantation, Rega Institute, Laboratory of Virology, Molecular Vaccinology and Vaccine Discovery, Leuven, Belgium,Global Virus Network (GVN), Baltimore, MD, USA
| | - Michael Bright Yakass
- KU Leuven Department of Microbiology, Immunology and Transplantation, Rega Institute, Laboratory of Virology, Molecular Vaccinology and Vaccine Discovery, Leuven, Belgium,Global Virus Network (GVN), Baltimore, MD, USA,West African Centre for Cell Biology of Infectious Pathogens (WACCBIP), Department of Biochemistry, Cell and Molecular Biology, University of Ghana, Legon, Accra, Ghana
| | - Sander Jansen
- KU Leuven Department of Microbiology, Immunology and Transplantation, Rega Institute, Laboratory of Virology, Molecular Vaccinology and Vaccine Discovery, Leuven, Belgium,Global Virus Network (GVN), Baltimore, MD, USA
| | - Bert Malengier-Devlies
- KU Leuven Department of Microbiology, Immunology and Transplantation, Rega Institute, Immunity and Inflammation Research Group, Immunobiology Unit, KU Leuven, Leuven, Belgium
| | - Dominique Van Looveren
- KU Leuven Department of Microbiology, Immunology and Transplantation, Rega Institute, Laboratory of Virology, Molecular Vaccinology and Vaccine Discovery, Leuven, Belgium,Global Virus Network (GVN), Baltimore, MD, USA,KU Leuven Department of Microbiology, Immunology and Transplantation, Rega Institute, Laboratory of Virology and Chemotherapy, Translational Platform Virology and Chemotherapy, Leuven, Belgium
| | - Lorena Sanchez-Felipe
- KU Leuven Department of Microbiology, Immunology and Transplantation, Rega Institute, Laboratory of Virology, Molecular Vaccinology and Vaccine Discovery, Leuven, Belgium,Global Virus Network (GVN), Baltimore, MD, USA
| | - Thomas Vercruysse
- KU Leuven Department of Microbiology, Immunology and Transplantation, Rega Institute, Laboratory of Virology, Molecular Vaccinology and Vaccine Discovery, Leuven, Belgium,Global Virus Network (GVN), Baltimore, MD, USA,KU Leuven Department of Microbiology, Immunology and Transplantation, Rega Institute, Laboratory of Virology and Chemotherapy, Translational Platform Virology and Chemotherapy, Leuven, Belgium
| | - Birgit Weynand
- KU Leuven Department of Imaging and Pathology, Translational Cell and Tissue Research, Leuven, Belgium
| | - Mahadesh Prasad Arkalagud Javarappa
- KU Leuven Department of Microbiology, Immunology and Transplantation, Rega Institute, Laboratory of Virology, Molecular Vaccinology and Vaccine Discovery, Leuven, Belgium,Global Virus Network (GVN), Baltimore, MD, USA
| | - Osbourne Quaye
- KU Leuven Department of Microbiology, Immunology and Transplantation, Rega Institute, Laboratory of Virology, Molecular Vaccinology and Vaccine Discovery, Leuven, Belgium,Global Virus Network (GVN), Baltimore, MD, USA,West African Centre for Cell Biology of Infectious Pathogens (WACCBIP), Department of Biochemistry, Cell and Molecular Biology, University of Ghana, Legon, Accra, Ghana
| | - Patrick Matthys
- KU Leuven Department of Microbiology, Immunology and Transplantation, Rega Institute, Immunity and Inflammation Research Group, Immunobiology Unit, KU Leuven, Leuven, Belgium
| | - Tania Roskams
- KU Leuven Department of Imaging and Pathology, Translational Cell and Tissue Research, Leuven, Belgium
| | - Johan Neyts
- KU Leuven Department of Microbiology, Immunology and Transplantation, Rega Institute, Laboratory of Virology, Molecular Vaccinology and Vaccine Discovery, Leuven, Belgium,Global Virus Network (GVN), Baltimore, MD, USA
| | - Hendrik Jan Thibaut
- KU Leuven Department of Microbiology, Immunology and Transplantation, Rega Institute, Laboratory of Virology, Molecular Vaccinology and Vaccine Discovery, Leuven, Belgium,Global Virus Network (GVN), Baltimore, MD, USA,KU Leuven Department of Microbiology, Immunology and Transplantation, Rega Institute, Laboratory of Virology and Chemotherapy, Translational Platform Virology and Chemotherapy, Leuven, Belgium
| | - Kai Dallmeier
- KU Leuven Department of Microbiology, Immunology and Transplantation, Rega Institute, Laboratory of Virology, Molecular Vaccinology and Vaccine Discovery, Leuven, Belgium,Global Virus Network (GVN), Baltimore, MD, USA,Corresponding author.
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2
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Imbrechts M, Maes W, Ampofo L, Van den Berghe N, Calcoen B, Van Looveren D, Kerstens W, Rasulova M, Vercruysse T, Noppen S, Abdelnabi R, Foo C, Hollevoet K, Maes P, Zhang X, Jochmans D, Ven K, Lammertyn J, Vanhoorelbeke K, Callewaert N, De Munter P, Schols D, Thibaut HJ, Neyts J, Declerck P, Geukens N. Potent neutralizing anti-SARS-CoV-2 human antibodies cure infection with SARS-CoV-2 variants in hamster model. iScience 2022; 25:104705. [PMID: 35813873 PMCID: PMC9250818 DOI: 10.1016/j.isci.2022.104705] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [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: 12/10/2021] [Revised: 03/15/2022] [Accepted: 06/28/2022] [Indexed: 12/01/2022] Open
Abstract
Treatment with neutralizing monoclonal antibodies (mAbs) against severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) contributes to COVID-19 management. Unfortunately, SARS-CoV-2 variants escape several of these recently approved mAbs, highlighting the need for additional discovery and development. In a convalescent patient with COVID-19, we identified six mAbs, classified in four epitope groups, that potently neutralized SARS-CoV-2 D614G, beta, gamma, and delta infection in vitro, with three mAbs neutralizing omicron as well. In hamsters, mAbs 3E6 and 3B8 potently cured infection with SARS-CoV-2 Wuhan, beta, and delta when administered post-viral infection at 5 mg/kg. Even at 0.2 mg/kg, 3B8 still reduced viral titers. Intramuscular delivery of DNA-encoded 3B8 resulted in in vivo mAb production of median serum levels up to 90 μg/mL, and protected hamsters against delta infection. Overall, our data mark 3B8 as a promising candidate against COVID-19, and highlight advances in both the identification and gene-based delivery of potent human mAbs.
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Affiliation(s)
- Maya Imbrechts
- KU Leuven, PharmAbs: the KU Leuven Antibody Center, Herestraat 49 box 820, 3000 Leuven, Belgium
- KU Leuven, Department Pharmaceutical and Pharmacological Sciences, Laboratory for Therapeutic and Diagnostic Antibodies, 3000 Leuven, Belgium
- KU Leuven, MabMine: KU Leuven Single B Cell Mining Platform, Herestraat 49 box 820, 3000 Leuven, Belgium
| | - Wim Maes
- KU Leuven, PharmAbs: the KU Leuven Antibody Center, Herestraat 49 box 820, 3000 Leuven, Belgium
- KU Leuven, MabMine: KU Leuven Single B Cell Mining Platform, Herestraat 49 box 820, 3000 Leuven, Belgium
- KU Leuven Campus Kortrijk, IRF Life Sciences, Laboratory for Thrombosis Research, 3000 Leuven, Belgium
| | - Louanne Ampofo
- KU Leuven, PharmAbs: the KU Leuven Antibody Center, Herestraat 49 box 820, 3000 Leuven, Belgium
- KU Leuven, MabMine: KU Leuven Single B Cell Mining Platform, Herestraat 49 box 820, 3000 Leuven, Belgium
| | - Nathalie Van den Berghe
- KU Leuven, Department Pharmaceutical and Pharmacological Sciences, Laboratory for Therapeutic and Diagnostic Antibodies, 3000 Leuven, Belgium
| | - Bas Calcoen
- KU Leuven Campus Kortrijk, IRF Life Sciences, Laboratory for Thrombosis Research, 3000 Leuven, Belgium
| | - Dominique Van Looveren
- KU Leuven Department of Microbiology, Immunology and Transplantation, Rega Institute, Translational Platform Virology and Chemotherapy (TPVC), KU Leuven, Leuven, Belgium
| | - Winnie Kerstens
- KU Leuven Department of Microbiology, Immunology and Transplantation, Rega Institute, Translational Platform Virology and Chemotherapy (TPVC), KU Leuven, Leuven, Belgium
| | - Madina Rasulova
- KU Leuven Department of Microbiology, Immunology and Transplantation, Rega Institute, Translational Platform Virology and Chemotherapy (TPVC), KU Leuven, Leuven, Belgium
| | - Thomas Vercruysse
- KU Leuven Department of Microbiology, Immunology and Transplantation, Rega Institute, Translational Platform Virology and Chemotherapy (TPVC), KU Leuven, Leuven, Belgium
| | - Sam Noppen
- KU Leuven, Department of Microbiology, Immunology and Transplantation, Rega Institute for Medical Research, Laboratory of Virology and Chemotherapy, 3000 Leuven, Belgium
| | - Rana Abdelnabi
- KU Leuven, Department of Microbiology, Immunology and Transplantation, Rega Institute for Medical Research, Laboratory of Virology and Chemotherapy, 3000 Leuven, Belgium
- GVN, Global Virus Network
| | - Caroline Foo
- KU Leuven, Department of Microbiology, Immunology and Transplantation, Rega Institute for Medical Research, Laboratory of Virology and Chemotherapy, 3000 Leuven, Belgium
- GVN, Global Virus Network
| | - Kevin Hollevoet
- KU Leuven, PharmAbs: the KU Leuven Antibody Center, Herestraat 49 box 820, 3000 Leuven, Belgium
- KU Leuven, Department Pharmaceutical and Pharmacological Sciences, Laboratory for Therapeutic and Diagnostic Antibodies, 3000 Leuven, Belgium
| | - Piet Maes
- KU Leuven, Department of Microbiology, Immunology and Transplantation, Rega Institute for Medical Research, Laboratory of Virology and Chemotherapy, 3000 Leuven, Belgium
- GVN, Global Virus Network
| | - Xin Zhang
- KU Leuven, Department of Microbiology, Immunology and Transplantation, Rega Institute for Medical Research, Laboratory of Virology and Chemotherapy, 3000 Leuven, Belgium
- GVN, Global Virus Network
| | - Dirk Jochmans
- KU Leuven, Department of Microbiology, Immunology and Transplantation, Rega Institute for Medical Research, Laboratory of Virology and Chemotherapy, 3000 Leuven, Belgium
- GVN, Global Virus Network
| | - Karen Ven
- KU Leuven, MabMine: KU Leuven Single B Cell Mining Platform, Herestraat 49 box 820, 3000 Leuven, Belgium
- KU Leuven, Department of Biosystems, Biosensors Group, 3000 Leuven, Belgium
| | - Jeroen Lammertyn
- KU Leuven, MabMine: KU Leuven Single B Cell Mining Platform, Herestraat 49 box 820, 3000 Leuven, Belgium
- KU Leuven, Department of Biosystems, Biosensors Group, 3000 Leuven, Belgium
| | - Karen Vanhoorelbeke
- KU Leuven, PharmAbs: the KU Leuven Antibody Center, Herestraat 49 box 820, 3000 Leuven, Belgium
- KU Leuven, MabMine: KU Leuven Single B Cell Mining Platform, Herestraat 49 box 820, 3000 Leuven, Belgium
- KU Leuven Campus Kortrijk, IRF Life Sciences, Laboratory for Thrombosis Research, 3000 Leuven, Belgium
| | - Nico Callewaert
- AZ Groeninge Hospital Clinical Laboratory, 8500 Kortrijk, Belgium
| | - Paul De Munter
- Department of Internal Medicine, University Hospitals Leuven, 3000 Leuven, Belgium
- KU Leuven, Department of Microbiology, Immunology and Transplantation, Laboratory for Clinical Infectious and Inflammatory Disorders, 3000 Leuven, Belgium
| | - Dominique Schols
- KU Leuven, Department of Microbiology, Immunology and Transplantation, Rega Institute for Medical Research, Laboratory of Virology and Chemotherapy, 3000 Leuven, Belgium
| | - Hendrik Jan Thibaut
- KU Leuven Department of Microbiology, Immunology and Transplantation, Rega Institute, Translational Platform Virology and Chemotherapy (TPVC), KU Leuven, Leuven, Belgium
| | - Johan Neyts
- KU Leuven, Department of Microbiology, Immunology and Transplantation, Rega Institute for Medical Research, Laboratory of Virology and Chemotherapy, 3000 Leuven, Belgium
- Molecular Vaccinology and Vaccine Discovery, 3000 Leuven, Belgium
- GVN, Global Virus Network
| | - Paul Declerck
- KU Leuven, PharmAbs: the KU Leuven Antibody Center, Herestraat 49 box 820, 3000 Leuven, Belgium
- KU Leuven, Department Pharmaceutical and Pharmacological Sciences, Laboratory for Therapeutic and Diagnostic Antibodies, 3000 Leuven, Belgium
- KU Leuven, MabMine: KU Leuven Single B Cell Mining Platform, Herestraat 49 box 820, 3000 Leuven, Belgium
| | - Nick Geukens
- KU Leuven, PharmAbs: the KU Leuven Antibody Center, Herestraat 49 box 820, 3000 Leuven, Belgium
- KU Leuven, MabMine: KU Leuven Single B Cell Mining Platform, Herestraat 49 box 820, 3000 Leuven, Belgium
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3
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Boudewijns R, Pérez P, Lázaro-Frías A, Van Looveren D, Vercruysse T, Thibaut HJ, Weynand B, Coelmont L, Neyts J, Astorgano D, Montenegro D, Puentes E, Rodríguez E, Dallmeier K, Esteban M, García-Arriaza J. MVA-CoV2-S Vaccine Candidate Neutralizes Distinct Variants of Concern and Protects Against SARS-CoV-2 Infection in Hamsters. Front Immunol 2022; 13:845969. [PMID: 35371064 PMCID: PMC8966703 DOI: 10.3389/fimmu.2022.845969] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [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: 12/30/2021] [Accepted: 02/17/2022] [Indexed: 12/31/2022] Open
Abstract
To control the coronavirus disease 2019 (COVID-19) pandemic and the emergence of different variants of concern (VoCs), novel vaccines against severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) are needed. In this study, we report the potent immunogenicity and efficacy induced in hamsters by a vaccine candidate based on a modified vaccinia virus Ankara (MVA) vector expressing a human codon optimized full-length SARS-CoV-2 spike (S) protein (MVA-S). Immunization with one or two doses of MVA-S elicited high titers of S- and receptor-binding domain (RBD)-binding IgG antibodies and neutralizing antibodies against parental SARS-CoV-2 and VoC alpha, beta, gamma, delta, and omicron. After SARS-CoV-2 challenge, MVA-S-vaccinated hamsters showed a significantly strong reduction of viral RNA and infectious virus in the lungs compared to the MVA-WT control group. Moreover, a marked reduction in lung histopathology was also observed in MVA-S-vaccinated hamsters. These results favor the use of MVA-S as a potential vaccine candidate for SARS-CoV-2 in clinical trials.
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Affiliation(s)
- Robbert Boudewijns
- KU Leuven Department of Microbiology, Immunology and Transplantation, Rega Institute, Laboratory of Virology and Chemotherapy, Leuven, Belgium
| | - Patricia Pérez
- Department of Molecular and Cellular Biology, Centro Nacional de Biotecnología (CNB), Consejo Superior de Investigaciones Científicas (CSIC), Madrid, Spain.,Centro de Investigación Biomédica en Red de Enfermedades Infecciosas (CIBERINFEC), Madrid, Spain
| | - Adrián Lázaro-Frías
- Department of Molecular and Cellular Biology, Centro Nacional de Biotecnología (CNB), Consejo Superior de Investigaciones Científicas (CSIC), Madrid, Spain.,Centro de Investigación Biomédica en Red de Enfermedades Infecciosas (CIBERINFEC), Madrid, Spain
| | - Dominique Van Looveren
- KU Leuven Department of Microbiology, Immunology and Transplantation, Rega Institute, Translational Platform Virology and Chemotherapy (TPVC), Leuven, Belgium
| | - Thomas Vercruysse
- KU Leuven Department of Microbiology, Immunology and Transplantation, Rega Institute, Translational Platform Virology and Chemotherapy (TPVC), Leuven, Belgium
| | - Hendrik Jan Thibaut
- KU Leuven Department of Microbiology, Immunology and Transplantation, Rega Institute, Translational Platform Virology and Chemotherapy (TPVC), Leuven, Belgium
| | - Birgit Weynand
- KU Leuven Department of Imaging and Pathology, Translational Cell and Tissue Research, Leuven, Belgium
| | - Lotte Coelmont
- KU Leuven Department of Microbiology, Immunology and Transplantation, Rega Institute, Laboratory of Virology and Chemotherapy, Leuven, Belgium
| | - Johan Neyts
- KU Leuven Department of Microbiology, Immunology and Transplantation, Rega Institute, Laboratory of Virology and Chemotherapy, Leuven, Belgium
| | - David Astorgano
- Department of Molecular and Cellular Biology, Centro Nacional de Biotecnología (CNB), Consejo Superior de Investigaciones Científicas (CSIC), Madrid, Spain
| | | | | | | | - Kai Dallmeier
- KU Leuven Department of Microbiology, Immunology and Transplantation, Rega Institute, Laboratory of Virology and Chemotherapy, Leuven, Belgium
| | - Mariano Esteban
- Department of Molecular and Cellular Biology, Centro Nacional de Biotecnología (CNB), Consejo Superior de Investigaciones Científicas (CSIC), Madrid, Spain
| | - Juan García-Arriaza
- Department of Molecular and Cellular Biology, Centro Nacional de Biotecnología (CNB), Consejo Superior de Investigaciones Científicas (CSIC), Madrid, Spain.,Centro de Investigación Biomédica en Red de Enfermedades Infecciosas (CIBERINFEC), Madrid, Spain
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4
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Van Looveren D, Giacomazzi G, Thiry I, Sampaolesi M, Gijsbers R. Improved functionality and potency of next generation BinMLV viral vectors toward safer gene therapy. Mol Ther Methods Clin Dev 2021; 23:51-67. [PMID: 34553002 PMCID: PMC8433069 DOI: 10.1016/j.omtm.2021.07.003] [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] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/23/2021] [Accepted: 07/16/2021] [Indexed: 10/27/2022]
Abstract
To develop safer retroviral murine leukemia virus (MLV)-based vectors, we previously mutated and re-engineered the MLV integrase: the W390A mutation abolished the interaction with its cellular tethering factors, BET proteins, and a retargeting peptide (the chromodomain of the CBX1 protein) was fused C-terminally. The resulting BET-independent MLVW390A-CBX was shown to integrate efficiently and more randomly, away from typical retroviral markers. In this study, we assessed the functionality and stability of expression of the redistributed MLVW390A-CBX vector in more depth, and evaluated safety using a clinically more relevant vector design encompassing a self-inactivated (SIN) LTR and a weak internal elongation factor 1α short (EFS) promoter. MLVW390A-CBX-EFS produced like MLVWT and efficiently transduced laboratory cells and primary human CD34+ hematopoetic stem cells (HSC) without transgene silencing over time, while displaying a more preferred, redistributed, and safer integration pattern. In a human mesoangioblast (MAB) stem cell model, the myogenic fusion capacity was hindered following MLVWT transduction, while this remained unaffected when applying MLVW390A-CBX. Likewise, smooth muscle cell differentiation of MABs was unaltered by MLVW390A-CBX-EFS. Taken together, our results underscore the potential of MLVW390A-CBX-EFS as a clinically relevant viral vector for ex-vivo gene therapy, combining efficient production with a preferable integration site distribution profile and stable expression over time.
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Affiliation(s)
- Dominique Van Looveren
- Laboratory for Viral Vector Technology and Gene Therapy, Department of Pharmacological and Pharmaceutical Sciences, KU Leuven, 3000 Leuven, Belgium
| | - Giorgia Giacomazzi
- Laboratory of Translational Cardiomyology, Department of Development and Regeneration, Stem Cell Research Institute, KU Leuven, 3000 Leuven, Belgium
| | - Irina Thiry
- Laboratory for Viral Vector Technology and Gene Therapy, Department of Pharmacological and Pharmaceutical Sciences, KU Leuven, 3000 Leuven, Belgium
| | - Maurilio Sampaolesi
- Laboratory of Translational Cardiomyology, Department of Development and Regeneration, Stem Cell Research Institute, KU Leuven, 3000 Leuven, Belgium
| | - Rik Gijsbers
- Laboratory for Viral Vector Technology and Gene Therapy, Department of Pharmacological and Pharmaceutical Sciences, KU Leuven, 3000 Leuven, Belgium
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5
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Baggen J, Persoons L, Vanstreels E, Jansen S, Van Looveren D, Boeckx B, Geudens V, De Man J, Jochmans D, Wauters J, Wauters E, Vanaudenaerde BM, Lambrechts D, Neyts J, Dallmeier K, Thibaut HJ, Jacquemyn M, Maes P, Daelemans D. Genome-wide CRISPR screening identifies TMEM106B as a proviral host factor for SARS-CoV-2. Nat Genet 2021; 53:435-444. [PMID: 33686287 DOI: 10.1038/s41588-021-00805-2] [Citation(s) in RCA: 131] [Impact Index Per Article: 43.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2020] [Accepted: 01/27/2021] [Indexed: 01/31/2023]
Abstract
The ongoing COVID-19 pandemic has caused a global economic and health crisis. To identify host factors essential for coronavirus infection, we performed genome-wide functional genetic screens with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and human coronavirus 229E. These screens uncovered virus-specific as well as shared host factors, including TMEM41B and PI3K type 3. We discovered that SARS-CoV-2 requires the lysosomal protein TMEM106B to infect human cell lines and primary lung cells. TMEM106B overexpression enhanced SARS-CoV-2 infection as well as pseudovirus infection, suggesting a role in viral entry. Furthermore, single-cell RNA-sequencing of airway cells from patients with COVID-19 demonstrated that TMEM106B expression correlates with SARS-CoV-2 infection. The present study uncovered a collection of coronavirus host factors that may be exploited to develop drugs against SARS-CoV-2 infection or future zoonotic coronavirus outbreaks.
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Affiliation(s)
- Jim Baggen
- KU Leuven Department of Microbiology, Immunology and Transplantation, Laboratory of Virology and Chemotherapy, Rega Institute, Leuven, Belgium.
| | - Leentje Persoons
- KU Leuven Department of Microbiology, Immunology and Transplantation, Laboratory of Virology and Chemotherapy, Rega Institute, Leuven, Belgium
| | - Els Vanstreels
- KU Leuven Department of Microbiology, Immunology and Transplantation, Laboratory of Virology and Chemotherapy, Rega Institute, Leuven, Belgium
| | - Sander Jansen
- KU Leuven Department of Microbiology, Immunology and Transplantation, Laboratory of Virology and Chemotherapy, Rega Institute, Leuven, Belgium
| | - Dominique Van Looveren
- KU Leuven Department of Microbiology, Immunology and Transplantation, Laboratory of Virology and Chemotherapy, Rega Institute, Leuven, Belgium.,KU Leuven Department of Microbiology, Immunology and Transplantation, Laboratory of Virology and Chemotherapy, Translational Platform Virology and Chemotherapy, Rega Institute, Leuven, Belgium
| | - Bram Boeckx
- KU Leuven Department of Human Genetics, Laboratory for Translational Genetics, Leuven, Belgium.,VIB Center for Cancer Biology, VIB, Leuven, Belgium
| | - Vincent Geudens
- KU Leuven Department of Chronic Diseases and Metabolism, Laboratory of Respiratory Diseases and Thoracic Surgery (BREATHE), Leuven, Belgium
| | - Julie De Man
- KU Leuven Department of Microbiology, Immunology and Transplantation, Laboratory of Virology and Chemotherapy, Rega Institute, Leuven, Belgium
| | - Dirk Jochmans
- KU Leuven Department of Microbiology, Immunology and Transplantation, Laboratory of Virology and Chemotherapy, Rega Institute, Leuven, Belgium
| | - Joost Wauters
- KU Leuven Department of Microbiology, Immunology and Transplantation, Laboratory of Clinical Infectious and Inflammatory Disorders, Leuven, Belgium
| | - Els Wauters
- KU Leuven Department of Chronic Diseases and Metabolism, Laboratory of Respiratory Diseases and Thoracic Surgery (BREATHE), Leuven, Belgium
| | - Bart M Vanaudenaerde
- KU Leuven Department of Chronic Diseases and Metabolism, Laboratory of Respiratory Diseases and Thoracic Surgery (BREATHE), Leuven, Belgium
| | - Diether Lambrechts
- KU Leuven Department of Human Genetics, Laboratory for Translational Genetics, Leuven, Belgium.,VIB Center for Cancer Biology, VIB, Leuven, Belgium
| | - Johan Neyts
- KU Leuven Department of Microbiology, Immunology and Transplantation, Laboratory of Virology and Chemotherapy, Rega Institute, Leuven, Belgium
| | - Kai Dallmeier
- KU Leuven Department of Microbiology, Immunology and Transplantation, Laboratory of Virology and Chemotherapy, Rega Institute, Leuven, Belgium
| | - Hendrik Jan Thibaut
- KU Leuven Department of Microbiology, Immunology and Transplantation, Laboratory of Virology and Chemotherapy, Rega Institute, Leuven, Belgium.,KU Leuven Department of Microbiology, Immunology and Transplantation, Laboratory of Virology and Chemotherapy, Translational Platform Virology and Chemotherapy, Rega Institute, Leuven, Belgium
| | - Maarten Jacquemyn
- KU Leuven Department of Microbiology, Immunology and Transplantation, Laboratory of Virology and Chemotherapy, Rega Institute, Leuven, Belgium
| | - Piet Maes
- KU Leuven Department of Microbiology, Immunology and Transplantation, Laboratory of Clinical and Epidemiological Virology, Rega Institute, Leuven, Belgium
| | - Dirk Daelemans
- KU Leuven Department of Microbiology, Immunology and Transplantation, Laboratory of Virology and Chemotherapy, Rega Institute, Leuven, Belgium.
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6
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Vansant G, Vranckx LS, Zurnic I, Van Looveren D, Van de Velde P, Nobles C, Gijsbers R, Christ F, Debyser Z. Impact of LEDGIN treatment during virus production on residual HIV-1 transcription. Retrovirology 2019; 16:8. [PMID: 30940165 PMCID: PMC6444612 DOI: 10.1186/s12977-019-0472-3] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [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: 02/20/2019] [Accepted: 03/23/2019] [Indexed: 11/24/2022] Open
Abstract
Background Persistence of latent, replication-competent provirus is the main impediment towards the cure of HIV infection. One of the critical questions concerning HIV latency is the role of integration site selection in HIV expression. Inhibition of the interaction between HIV integrase and its chromatin tethering cofactor LEDGF/p75 is known to reduce integration and to retarget residual provirus to regions resistant to reactivation. LEDGINs, small molecule inhibitors of the interaction between HIV integrase and LEDGF/p75, provide an interesting tool to study the underlying mechanisms. During early infection, LEDGINs block the interaction with LEDGF/p75 and allosterically inhibit the catalytic activity of IN (i.e. the early effect). When present during virus production, LEDGINs interfere with proper maturation due to enhanced IN oligomerization in the progeny virions (i.e. the late effect). Results We studied the effect of LEDGINs present during virus production on the transcriptional state of the residual virus. Infection of cells with viruses produced in the presence of LEDGINs resulted in a residual reservoir that was refractory to activation. Integration of residual provirus was less favored near epigenetic markers associated with active transcription. However, integration near H3K36me3 and active genes, both targeted by LEDGF/p75, was not affected. Also in primary cells, LEDGIN treatment induced a reservoir resistant to activation due to a combined early and late effect. Conclusion LEDGINs present a research tool to study the link between integration and transcription, an essential question in retrovirology. LEDGIN treatment during virus production altered integration of residual provirus in a LEDGF/p75-independent manner, resulting in a reservoir that is refractory to activation. Electronic supplementary material The online version of this article (10.1186/s12977-019-0472-3) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Gerlinde Vansant
- Laboratory for Molecular Virology and Gene Therapy, Department of Pharmaceutical and Pharmacological Sciences, KU Leuven, Herestraat 49, Box 1023, 3000, Leuven, Flanders, Belgium
| | - Lenard S Vranckx
- Laboratory for Molecular Virology and Gene Therapy, Department of Pharmaceutical and Pharmacological Sciences, KU Leuven, Herestraat 49, Box 1023, 3000, Leuven, Flanders, Belgium
| | - Irena Zurnic
- Laboratory for Molecular Virology and Gene Therapy, Department of Pharmaceutical and Pharmacological Sciences, KU Leuven, Herestraat 49, Box 1023, 3000, Leuven, Flanders, Belgium
| | - Dominique Van Looveren
- Laboratory for Viral Vector Technology and Gene Therapy, Department of Pharmaceutical and Pharmacological Sciences, KU Leuven, Herestraat 49, Box 1023, 3000, Leuven, Belgium
| | - Paulien Van de Velde
- Laboratory for Molecular Virology and Gene Therapy, Department of Pharmaceutical and Pharmacological Sciences, KU Leuven, Herestraat 49, Box 1023, 3000, Leuven, Flanders, Belgium
| | - Christopher Nobles
- Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, USA
| | - Rik Gijsbers
- Laboratory for Viral Vector Technology and Gene Therapy, Department of Pharmaceutical and Pharmacological Sciences, KU Leuven, Herestraat 49, Box 1023, 3000, Leuven, Belgium
| | - Frauke Christ
- Laboratory for Molecular Virology and Gene Therapy, Department of Pharmaceutical and Pharmacological Sciences, KU Leuven, Herestraat 49, Box 1023, 3000, Leuven, Flanders, Belgium
| | - Zeger Debyser
- Laboratory for Molecular Virology and Gene Therapy, Department of Pharmaceutical and Pharmacological Sciences, KU Leuven, Herestraat 49, Box 1023, 3000, Leuven, Flanders, Belgium.
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El Ashkar S, Van Looveren D, Schenk F, Vranckx LS, Demeulemeester J, De Rijck J, Debyser Z, Modlich U, Gijsbers R. Engineering Next-Generation BET-Independent MLV Vectors for Safer Gene Therapy. Mol Ther Nucleic Acids 2017. [PMID: 28624199 PMCID: PMC5415309 DOI: 10.1016/j.omtn.2017.04.002] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Retroviral vectors have shown their curative potential in clinical trials correcting monogenetic disorders. However, therapeutic benefits were compromised due to vector-induced dysregulation of cellular genes and leukemia development in a subset of patients. Bromodomain and extraterminal domain (BET) proteins act as cellular cofactors that tether the murine leukemia virus (MLV) pre-integration complex to host chromatin via interaction with the MLV integrase (IN) and thereby define the typical gammaretroviral integration distribution. We engineered next-generation BET-independent (Bin) MLV vectors to retarget their integration to regions where they are less likely to dysregulate nearby genes. We mutated MLV IN to uncouple BET protein interaction and fused it with chromatin-binding peptides. The addition of the CBX1 chromodomain to MLV INW390A efficiently targeted integration away from gene regulatory elements. The retargeted vector produced at high titers and efficiently transduced CD34+ hematopoietic stem cells, while fewer colonies were detected in a serial colony-forming assay, a surrogate test for genotoxicity. Our findings underscore the potential of the engineered vectors to reduce the risk of insertional mutagenesis without compromising transduction efficiency. Ultimately, combined with other safety features in vector design, next-generation BinMLV vectors can improve the safety of gammaretroviral vectors for gene therapy.
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Affiliation(s)
- Sara El Ashkar
- Laboratory for Molecular Virology and Drug Discovery, Department of Pharmaceutical and Pharmacological Sciences, 3000 Leuven, KU Leuven, Belgium
| | - Dominique Van Looveren
- Laboratory for Viral Vector Technology and Gene Therapy, Department of Pharmaceutical and Pharmacological Sciences, KU Leuven, 3000 Leuven, Belgium
| | - Franziska Schenk
- RG Gene Modification in Stem Cells, LOEWE Center for Cell and Gene Therapy Frankfurt, Paul-Ehrlich-Institute, 63225 Langen, Germany
| | - Lenard S Vranckx
- Laboratory for Molecular Virology and Drug Discovery, Department of Pharmaceutical and Pharmacological Sciences, 3000 Leuven, KU Leuven, Belgium
| | - Jonas Demeulemeester
- Laboratory for Molecular Virology and Drug Discovery, Department of Pharmaceutical and Pharmacological Sciences, 3000 Leuven, KU Leuven, Belgium
| | - Jan De Rijck
- Laboratory for Molecular Virology and Drug Discovery, Department of Pharmaceutical and Pharmacological Sciences, 3000 Leuven, KU Leuven, Belgium
| | - Zeger Debyser
- Laboratory for Molecular Virology and Drug Discovery, Department of Pharmaceutical and Pharmacological Sciences, 3000 Leuven, KU Leuven, Belgium
| | - Ute Modlich
- RG Gene Modification in Stem Cells, LOEWE Center for Cell and Gene Therapy Frankfurt, Paul-Ehrlich-Institute, 63225 Langen, Germany
| | - Rik Gijsbers
- Laboratory for Viral Vector Technology and Gene Therapy, Department of Pharmaceutical and Pharmacological Sciences, KU Leuven, 3000 Leuven, Belgium; Leuven Viral Vector Core, KU Leuven, 3000 Leuven, Belgium.
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