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Laroche A, Orsini Delgado ML, Chalopin B, Cuniasse P, Dubois S, Sierocki R, Gallais F, Debroas S, Bellanger L, Simon S, Maillère B, Nozach H. Deep mutational engineering of broadly-neutralizing nanobodies accommodating SARS-CoV-1 and 2 antigenic drift. MAbs 2022; 14:2076775. [PMID: 35593235 PMCID: PMC9132424 DOI: 10.1080/19420862.2022.2076775] [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] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Here, we report the molecular engineering of nanobodies that bind with picomolar affinity to both SARS-CoV-1 and SARS-CoV-2 receptor-binding domains (RBD) and are highly neutralizing. We applied deep mutational engineering to VHH72, a nanobody initially specific for SARS-CoV-1 RBD with little cross-reactivity to SARS-CoV-2 antigen. We first identified all the individual VHH substitutions that increase binding to SARS-CoV-2 RBD and then screened highly focused combinatorial libraries to isolate engineered nanobodies with improved properties. The corresponding VHH-Fc molecules show high affinities for SARS-CoV-2 antigens from various emerging variants and SARS-CoV-1, block the interaction between ACE2 and RBD, and neutralize the virus with high efficiency. Its rare specificity across sarbecovirus relies on its peculiar epitope outside the immunodominant regions. The engineered nanobodies share a common motif of three amino acids, which contribute to the broad specificity of recognition. Our results show that deep mutational engineering is a very powerful method, especially to rapidly adapt existing antibodies to new variants of pathogens.
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Affiliation(s)
- Adrien Laroche
- CEA, INRAE, Medicines and Healthcare Technologies Department, SIMoS, Université Paris-Saclay, Gif-sur-Yvette, France
| | - Maria Lucia Orsini Delgado
- CEA, INRAE, Medicines and Healthcare Technologies Department, SPI, Université Paris-Saclay, Gif-sur-Yvette, France
| | - Benjamin Chalopin
- CEA, INRAE, Medicines and Healthcare Technologies Department, SIMoS, Université Paris-Saclay, Gif-sur-Yvette, France
| | - Philippe Cuniasse
- CNRS, CEA, Institute for Integrative Biology of the Cell (I2BC), Université Paris-Saclay, Gif-sur-Yvette, France
| | - Steven Dubois
- CEA, INRAE, Medicines and Healthcare Technologies Department, SIMoS, Université Paris-Saclay, Gif-sur-Yvette, France
| | - Raphaël Sierocki
- CEA, INRAE, Medicines and Healthcare Technologies Department, SIMoS, Université Paris-Saclay, Gif-sur-Yvette, France.,Deeptope SAS, Massy, France
| | - Fabrice Gallais
- CEA, INRAE, Département Médicaments et Technologies pour la Santé (DMTS), SPI, Université Paris Saclay, Bagnols-sur-Cèze, France
| | - Stéphanie Debroas
- CEA, INRAE, Département Médicaments et Technologies pour la Santé (DMTS), SPI, Université Paris Saclay, Bagnols-sur-Cèze, France
| | - Laurent Bellanger
- CEA, INRAE, Département Médicaments et Technologies pour la Santé (DMTS), SPI, Université Paris Saclay, Bagnols-sur-Cèze, France
| | - Stéphanie Simon
- CEA, INRAE, Medicines and Healthcare Technologies Department, SPI, Université Paris-Saclay, Gif-sur-Yvette, France
| | - Bernard Maillère
- CEA, INRAE, Medicines and Healthcare Technologies Department, SIMoS, Université Paris-Saclay, Gif-sur-Yvette, France
| | - Hervé Nozach
- CEA, INRAE, Medicines and Healthcare Technologies Department, SIMoS, Université Paris-Saclay, Gif-sur-Yvette, France
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Grenga L, Gallais F, Pible O, Gaillard JC, Gouveia D, Batina H, Bazaline N, Ruat S, Culotta K, Miotello G, Debroas S, Roncato MA, Steinmetz G, Foissard C, Desplan A, Alpha-Bazin B, Almunia C, Gas F, Bellanger L, Armengaud J. Shotgun proteomics analysis of SARS-CoV-2-infected cells and how it can optimize whole viral particle antigen production for vaccines. Emerg Microbes Infect 2020; 9:1712-1721. [PMID: 32619390 PMCID: PMC7473198 DOI: 10.1080/22221751.2020.1791737] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [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: 04/17/2020] [Accepted: 06/30/2020] [Indexed: 12/28/2022]
Abstract
Severe acute respiratory syndrome-related coronavirus 2 (SARS-CoV-2) has resulted in a pandemic and is continuing to spread rapidly around the globe. No effective vaccine is currently available to prevent COVID-19, and intense efforts are being invested worldwide into vaccine development. In this context, all technology platforms must overcome several challenges resulting from the use of an incompletely characterized new virus. These include finding the right conditions for virus amplification for the development of vaccines based on inactivated or attenuated whole viral particles. Here, we describe a shotgun tandem mass spectrometry workflow, the data produced can be used to guide optimization of the conditions for viral amplification. In parallel, we analysed the changes occurring in the host cell proteome following SARS-CoV-2 infection to glean information on the biological processes modulated by the virus that could be further explored as potential drug targets to deal with the pandemic.
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Affiliation(s)
- Lucia Grenga
- Département Médicaments et Technologies pour la Santé (DMTS), Université Paris Saclay, CEA, INRAE, SPIBagnols-sur-Cèze, France
| | - Fabrice Gallais
- Département Médicaments et Technologies pour la Santé (DMTS), Université Paris Saclay, CEA, INRAE, SPIBagnols-sur-Cèze, France
| | - Olivier Pible
- Département Médicaments et Technologies pour la Santé (DMTS), Université Paris Saclay, CEA, INRAE, SPIBagnols-sur-Cèze, France
| | - Jean-Charles Gaillard
- Département Médicaments et Technologies pour la Santé (DMTS), Université Paris Saclay, CEA, INRAE, SPIBagnols-sur-Cèze, France
| | - Duarte Gouveia
- Département Médicaments et Technologies pour la Santé (DMTS), Université Paris Saclay, CEA, INRAE, SPIBagnols-sur-Cèze, France
| | - Hélène Batina
- Département Médicaments et Technologies pour la Santé (DMTS), Université Paris Saclay, CEA, INRAE, SPIBagnols-sur-Cèze, France
| | - Niza Bazaline
- Département Médicaments et Technologies pour la Santé (DMTS), Université Paris Saclay, CEA, INRAE, SPIBagnols-sur-Cèze, France
| | - Sylvie Ruat
- Département Médicaments et Technologies pour la Santé (DMTS), Université Paris Saclay, CEA, INRAE, SPIBagnols-sur-Cèze, France
| | - Karen Culotta
- Département Médicaments et Technologies pour la Santé (DMTS), Université Paris Saclay, CEA, INRAE, SPIBagnols-sur-Cèze, France
| | - Guylaine Miotello
- Département Médicaments et Technologies pour la Santé (DMTS), Université Paris Saclay, CEA, INRAE, SPIBagnols-sur-Cèze, France
| | - Stéphanie Debroas
- Département Médicaments et Technologies pour la Santé (DMTS), Université Paris Saclay, CEA, INRAE, SPIBagnols-sur-Cèze, France
| | - Marie-Anne Roncato
- Département Médicaments et Technologies pour la Santé (DMTS), Université Paris Saclay, CEA, INRAE, SPIBagnols-sur-Cèze, France
| | - Gérard Steinmetz
- Département Médicaments et Technologies pour la Santé (DMTS), Université Paris Saclay, CEA, INRAE, SPIBagnols-sur-Cèze, France
| | - Charlotte Foissard
- Département Médicaments et Technologies pour la Santé (DMTS), Université Paris Saclay, CEA, INRAE, SPIBagnols-sur-Cèze, France
| | - Anne Desplan
- Département Médicaments et Technologies pour la Santé (DMTS), Université Paris Saclay, CEA, INRAE, SPIBagnols-sur-Cèze, France
| | - Béatrice Alpha-Bazin
- Département Médicaments et Technologies pour la Santé (DMTS), Université Paris Saclay, CEA, INRAE, SPIBagnols-sur-Cèze, France
| | - Christine Almunia
- Département Médicaments et Technologies pour la Santé (DMTS), Université Paris Saclay, CEA, INRAE, SPIBagnols-sur-Cèze, France
| | - Fabienne Gas
- Département Médicaments et Technologies pour la Santé (DMTS), Université Paris Saclay, CEA, INRAE, SPIBagnols-sur-Cèze, France
| | - Laurent Bellanger
- Département Médicaments et Technologies pour la Santé (DMTS), Université Paris Saclay, CEA, INRAE, SPIBagnols-sur-Cèze, France
| | - Jean Armengaud
- Département Médicaments et Technologies pour la Santé (DMTS), Université Paris Saclay, CEA, INRAE, SPIBagnols-sur-Cèze, France
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Gouveia D, Miotello G, Gallais F, Gaillard JC, Debroas S, Bellanger L, Lavigne JP, Sotto A, Grenga L, Pible O, Armengaud J. Proteotyping SARS-CoV-2 Virus from Nasopharyngeal Swabs: A Proof-of-Concept Focused on a 3 Min Mass Spectrometry Window. J Proteome Res 2020; 19:4407-4416. [PMID: 32697082 PMCID: PMC7640971 DOI: 10.1021/acs.jproteome.0c00535] [Citation(s) in RCA: 78] [Impact Index Per Article: 19.5] [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: 07/13/2020] [Indexed: 12/13/2022]
Abstract
Rapid but yet sensitive, specific, and high-throughput detection of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in clinical samples is key to diagnose infected people and to better control the spread of the virus. Alternative methodologies to PCR and immunodiagnostics that would not require specific reagents are worthy to investigate not only for fighting the COVID-19 pandemic but also to detect other emergent pathogenic threats. Here, we propose the use of tandem mass spectrometry to detect SARS-CoV-2 marker peptides in nasopharyngeal swabs. We documented that the signal from the microbiota present in such samples is low and can be overlooked when interpreting shotgun proteomic data acquired on a restricted window of the peptidome landscape. In this proof-of-concept study, simili nasopharyngeal swabs spiked with different quantities of purified SARS-CoV-2 viral material were used to develop a nanoLC-MS/MS acquisition method, which was then successfully applied on COVID-19 clinical samples. We argue that peptides ADETQALPQR and GFYAQGSR from the nucleocapsid protein are of utmost interest as their signal is intense and their elution can be obtained within a 3 min window in the tested conditions. These results pave the way for the development of time-efficient viral diagnostic tests based on mass spectrometry.
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Affiliation(s)
- Duarte Gouveia
- INRAE,
Département Médicaments et Technologies pour la Santé
(DMTS), SPI, Université Paris Saclay,
CEA, 30200 Bagnols-sur-Cèze, France
| | - Guylaine Miotello
- INRAE,
Département Médicaments et Technologies pour la Santé
(DMTS), SPI, Université Paris Saclay,
CEA, 30200 Bagnols-sur-Cèze, France
| | - Fabrice Gallais
- INRAE,
Département Médicaments et Technologies pour la Santé
(DMTS), SPI, Université Paris Saclay,
CEA, 30200 Bagnols-sur-Cèze, France
| | - Jean-Charles Gaillard
- INRAE,
Département Médicaments et Technologies pour la Santé
(DMTS), SPI, Université Paris Saclay,
CEA, 30200 Bagnols-sur-Cèze, France
| | - Stéphanie Debroas
- INRAE,
Département Médicaments et Technologies pour la Santé
(DMTS), SPI, Université Paris Saclay,
CEA, 30200 Bagnols-sur-Cèze, France
| | - Laurent Bellanger
- INRAE,
Département Médicaments et Technologies pour la Santé
(DMTS), SPI, Université Paris Saclay,
CEA, 30200 Bagnols-sur-Cèze, France
| | - Jean-Philippe Lavigne
- U1047,
Institut National de la Santé et de la Recherche Médicale, Université Montpellier, Montpellier, France
- VBMI,
INSERM U1047, Université de Montpellier, Service de Microbiologie
et Hygiène Hospitalière, CHU
Nîmes, Nîmes, France
| | - Albert Sotto
- VBMI,
INSERM U1047, Université de Montpellier, Service des Maladies
Infectieuses et Tropicales, CHU Nîmes, Nîmes, France
| | - Lucia Grenga
- INRAE,
Département Médicaments et Technologies pour la Santé
(DMTS), SPI, Université Paris Saclay,
CEA, 30200 Bagnols-sur-Cèze, France
| | - Olivier Pible
- INRAE,
Département Médicaments et Technologies pour la Santé
(DMTS), SPI, Université Paris Saclay,
CEA, 30200 Bagnols-sur-Cèze, France
| | - Jean Armengaud
- INRAE,
Département Médicaments et Technologies pour la Santé
(DMTS), SPI, Université Paris Saclay,
CEA, 30200 Bagnols-sur-Cèze, France
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