Selection and characterization of human scFvs targeting the SARS-CoV-2 nucleocapsid protein isolated from antibody libraries of COVID-19 patients.


Journal

Scientific reports
ISSN: 2045-2322
Titre abrégé: Sci Rep
Pays: England
ID NLM: 101563288

Informations de publication

Date de publication:
09 Jul 2024
Historique:
received: 18 01 2024
accepted: 02 07 2024
medline: 10 7 2024
pubmed: 10 7 2024
entrez: 9 7 2024
Statut: epublish

Résumé

In 2019, the novel SARS-CoV-2 coronavirus emerged in China, causing the pneumonia named COVID-19. At the beginning, all research efforts were focused on the spike (S) glycoprotein. However, it became evident that the nucleocapsid (N) protein is pivotal in viral replication, genome packaging and evasion of the immune system, is highly immunogenic, which makes it another compelling target for antibody development alongside the spike protein. This study focused on the construction of single chain fragments variable (scFvs) libraries from SARS-CoV-2-infected patients to establish a valuable, immortalized and extensive antibodies source. We used the Intracellular Antibody Capture Technology to select a panel of scFvs against the SARS-CoV-2 N protein. The whole panel of scFv was expressed and characterized both as intrabodies and recombinant proteins. ScFvs were then divided into 2 subgroups: those that exhibited high binding activity to N protein when expressed in yeast or in mammalian cells as intrabodies, and those purified as recombinant proteins, displaying affinity for recombinant N protein in the nanomolar range. This panel of scFvs against the N protein represents a novel platform for research and potential diagnostic applications.

Identifiants

pubmed: 38982108
doi: 10.1038/s41598-024-66558-0
pii: 10.1038/s41598-024-66558-0
doi:

Substances chimiques

Single-Chain Antibodies 0
Antibodies, Viral 0
Coronavirus Nucleocapsid Proteins 0
nucleocapsid phosphoprotein, SARS-CoV-2 0
Phosphoproteins 0
Recombinant Proteins 0
Peptide Library 0

Types de publication

Journal Article

Langues

eng

Sous-ensembles de citation

IM

Pagination

15864

Subventions

Organisme : Regione Lombardia
ID : 2014IT16RFOP012 - POR FESR REGIONE LOMBARDIA 2014 - 2020 - ASSE 1: AZIONEI.1. B.1.3
Organisme : Regione Lombardia
ID : 2014IT16RFOP012 - POR FESR REGIONE LOMBARDIA 2014 - 2020 - ASSE 1: AZIONEI.1. B.1.3
Organisme : Regione Toscana
ID : Ricerca Salute 2018 "Tuscany Antiviral Research Network (TUSCAVIR.NET)"

Informations de copyright

© 2024. The Author(s).

Références

Zhu, N. et al. Brief report: A novel coronavirus from patients with pneumonia in China, 2019. N. Engl. J. Med. 382, 727 (2020).
doi: 10.1056/NEJMoa2001017
Wu, F. et al. A new coronavirus associated with human respiratory disease in China. Nature 579, 265 (2020).
doi: 10.1038/s41586-020-2008-3
Yang, H. & Rao, Z. Structural biology of SARS-CoV-2 and implications for therapeutic development. Nat. Rev. Microbiol. 19, 685 (2021).
doi: 10.1038/s41579-021-00630-8
Lu, R. et al. Genomic characterisation and epidemiology of 2019 novel coronavirus: implications for virus origins and receptor binding. Lancet (London, England) 395, 565 (2020).
Kim, D. et al. The Architecture of SARS-CoV-2 Transcriptome. Cell 181, 914 (2020).
doi: 10.1016/j.cell.2020.04.011
Finkel, Y. et al. The coding capacity of SARS-CoV-2. Nat. 2020 5897840 589, 125–130 (2020).
Li, W. et al. Angiotensin-converting enzyme 2 is a functional receptor for the SARS coronavirus. Nature 426, 450 (2003).
doi: 10.1038/nature02145
Arruda, H. R. S. et al. Conformational stability of SARS-CoV-2 glycoprotein spike variants. iScience 26, (2023).
Shroff, A. & Nazarko, T. Y. The Molecular Interplay between Human Coronaviruses and Autophagy. Cells 10, (2021).
Bai, Z., Cao, Y., Liu, W. & Li, J. The sars-cov-2 nucleocapsid protein and its role in viral structure, biological functions, and a potential target for drug or vaccine mitigation. Viruses. 13. https://doi.org/10.3390/v13061115 (2021).
Wu, W., Cheng, Y., Zhou, H., Sun, C. & Zhang, S. The SARS-CoV-2 nucleocapsid protein: its role in the viral life cycle, structure and functions, and use as a potential target in the development of vaccines and diagnostics. Virol. J. 20, 1–16 (2023).
doi: 10.1186/s12985-023-01968-6
Li, J. Y. et al. The ORF6, ORF8 and nucleocapsid proteins of SARS-CoV-2 inhibit type I interferon signaling pathway. Virus Res. 286, 198074 (2020).
doi: 10.1016/j.virusres.2020.198074
Ribeiro-Filho, H. V. et al. Structural dynamics of SARS-CoV-2 nucleocapsid protein induced by RNA binding. PLOS Comput. Biol. 18, e1010121 (2022).
doi: 10.1371/journal.pcbi.1010121
Qu, J. et al. Profile of IgG and IgM antibodies against severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Clin. Infect. Dis. An Off. Publ. Infect. Dis. Soc. Am. 71, 2255–2258 (2020).
Zhao, J. et al. Antibody responses to SARS-CoV-2 in patients of novel coronavirus disease 2019. Clin. Infect. Dis. An Off. Publ. Infect. Dis. Soc. Am. 71, 2027–2034 (2020).
Mittal, A., Khattri, A. & Verma, V. Structural and antigenic variations in the spike protein of emerging SARS-CoV-2 variants. PLoS Pathog. 18, (2022).
Greaney, A. J. et al. Complete mapping of mutations to the SARS-CoV-2 spike receptor-binding domain that escape antibody recognition. Cell Host. Microbe. 29, 44 (2021).
doi: 10.1016/j.chom.2020.11.007
Grifoni, A. et al. A sequence homology and bioinformatic approach can predict candidate targets for immune responses to SARS-CoV-2. Cell Host. Microbe. 27, 671 (2020).
doi: 10.1016/j.chom.2020.03.002
Khetran, S. R. & Mustafa, R. Mutations of SARS-CoV-2 Structural Proteins in the Alpha, Beta, Gamma, and Delta Variants: Bioinformatics Analysis. Jmir Bioinforma. Biotechnol. 4, (2023).
Visintin, M., Tse, E., Axelson, H., Rabbitts, T. H. & Cattaneo, A. Selection of antibodies for intracellular function using a two-hybrid in vivo system. Proc. Natl. Acad. Sci. U S A 96, 11723–11728 (1999).
doi: 10.1073/pnas.96.21.11723
Visintin, M. et al. The intracellular antibody capture technology (IACT): Towards a consensus sequence for intracellular antibodies. J. Mol. Biol. 317, 73–83 (2002).
doi: 10.1006/jmbi.2002.5392
Biocca, S. & Cattaneo, A. Intracellular immunization: Antibody targeting to subcellular compartments. Trends Cell Biol. 5, 248–252 (1995).
doi: 10.1016/S0962-8924(00)89019-4
Cattaneo, A. & Chirichella, M. Targeting the post-translational proteome with intrabodies. Trends Biotechnol. 37, 578–591 (2019).
doi: 10.1016/j.tibtech.2018.11.009
Visintin, M., Meli, G. A., Cannistraci, I. & Cattaneo, A. Intracellular antibodies for proteomics. J. Immunol. Methods 290, 135–153 (2004).
doi: 10.1016/j.jim.2004.04.014
Hanahan, D. Studies on transformation of Escherichia coli with plasmids. J. Mol. Biol. 166, 557–580 (1983).
doi: 10.1016/S0022-2836(83)80284-8
Velappan, N., Sblattero, D., Chasteen, L., Pavlik, P. & Bradbury, A. R. M. Plasmid incompatibility: More compatible than previously thought?. Protein Eng. Des. Sel. 20, 309–313 (2007).
doi: 10.1093/protein/gzm005
Tomoiaga, D., Bubnell, J., Herndon, L. & Feinstein, P. High rates of plasmid cotransformation in E. coli overturn the clonality myth and reveal colony development. Sci. Rep. 12, (2022).
Goldsmith, M., Kiss, C., Bradbury, A. R. M. & Tawfik, D. S. Avoiding and controlling double transformation artifacts. Protein Eng. Des. Sel. 20, 315–318 (2007).
doi: 10.1093/protein/gzm026
Fantini, M. et al. Assessment of antibody library diversity through next generation sequencing and technical error compensation. PLoS One 12, (2017).
Smits, V. A. J. et al. The Nucleocapsid protein triggers the main humoral immune response in COVID-19 patients. Biochem. Biophys. Res. Commun. 543, 45 (2021).
doi: 10.1016/j.bbrc.2021.01.073
Lineburg, K. E. et al. CD8+ T cells specific for an immunodominant SARS-CoV-2 nucleocapsid epitope cross-react with selective seasonal coronaviruses. Immunity 54, 1055 (2021).
doi: 10.1016/j.immuni.2021.04.006
Le Bert, N. et al. SARS-CoV-2-specific T cell immunity in cases of COVID-19 and SARS, and uninfected controls. Nat. 2020 5847821 584, 457–462 (2020).
Gil, D. & Schrum, A. G. Strategies to stabilize compact folding and minimize aggregation of antibody-based fragments. Adv. Biosci. Biotechnol. 4, 73 (2013).
doi: 10.4236/abb.2013.44A011
Sun, W. et al. A combined strategy improves the solubility of aggregation-prone single-chain variable fragment antibodies. Protein Expr. Purif. 83, 21–29 (2012).
doi: 10.1016/j.pep.2012.02.006
Martin, N. et al. Refolding of aggregation-prone ScFv antibody fragments assisted by hydrophobically modified poly(sodium acrylate) derivatives. Macromol. Biosci. 17, 1600213 (2017).
doi: 10.1002/mabi.201600213
Dangi, T. et al. Improved control of SARS-CoV-2 by treatment with a nucleocapsid-specific monoclonal antibody. J. Clin. Invest. 132, (2022).
Focosi, D., Franchini, M. & Casadevall, A. On the need to determine the contribution of anti-nucleocapsid antibodies as potential contributors to COVID-19 convalescent plasma efficacy. Viruses 14, (2022).
Statement on the fifteenth meeting of the IHR (2005) Emergency Committee on the COVID-19 pandemic. https://www.who.int/news/item/05-05-2023-statement-on-the-fifteenth-meeting-of-the-international-health-regulations-(2005)-emergency-committee-regarding-the-coronavirus-disease-(covid-19)-pandemic .
WHO chief declares end to COVID-19 as a global health emergency | UN News. https://news.un.org/en/story/2023/05/1136367 .
Sharma, A. et al. COVID-19 diagnosis: Current and future techniques. Int. J. Biol. Macromol. 193, 1835 (2021).
doi: 10.1016/j.ijbiomac.2021.11.016
Song, W. et al. The role of SARS-CoV-2 N protein in diagnosis and vaccination in the context of emerging variants: Present status and prospects. Front. Microbiol. 14, 1217567 (2023).
doi: 10.3389/fmicb.2023.1217567
Royster, A. et al. SARS-CoV-2 nucleocapsid protein is a potential therapeutic target for anticoronavirus drug discovery. Microbiol. Spectr. 11, (2023).
Fan, S. et al. The highly conserved RNA-binding specificity of nucleocapsid protein facilitates the identification of drugs with broad anti-coronavirus activity. Comput. Struct. Biotechnol. J. 20, 5040 (2022).
doi: 10.1016/j.csbj.2022.09.007
Feng, W. et al. Nucleocapsid protein of SARS‐CoV‐2 is a potential target for developing new generation of vaccine. J. Clin. Lab. Anal. 36, (2022).
Sariol, A. & Perlman, S. Lessons for COVID-19 immunity from other coronavirus infections. Immunity 53, 248–263 (2020).
doi: 10.1016/j.immuni.2020.07.005
Lopez-Munoz, A. D., Kosik, I., Holly, J. & Yewdell, J. W. Cell surface SARS-CoV-2 nucleocapsid protein modulates innate and adaptive immunity. Sci. Adv. 8, 9770 (2022).
doi: 10.1126/sciadv.abp9770
Sblattero, D. & Bradbury, A. Exploiting recombination in single bacteria to make large phage antibody libraries. Nat. Biotechnol. 18, 75–80 (2000).
doi: 10.1038/71958
Melchionna, T. & Cattaneo, A. A protein silencing switch by ligand-induced proteasome-targeting intrabodies. J. Mol. Biol. 374, 641–654 (2007).
doi: 10.1016/j.jmb.2007.09.053
Cattaneo, A. & Chirichella, M. Targeting the post-translational proteome with intrabodies. Trends Biotechnol. 37, 578–591 (2019).
doi: 10.1016/j.tibtech.2018.11.009
Fabiani, L. et al. Magnetic beads combined with carbon black-based screen-printed electrodes for COVID-19: A reliable and miniaturized electrochemical immunosensor for SARS-CoV-2 detection in saliva. Biosens. Bioelectron. 171, 112686 (2021).
doi: 10.1016/j.bios.2020.112686
Marks, J. D. & Bradbury, A. PCR cloning of human immunoglobulin genes. Methods Mol. Biol. 248, 117–134 (2004).
Elsaesser, R. & Paysan, J. Liquid gel amplification of complex plasmid libraries. Biotechniques 37, 200–202 (2004).
López-Santibáñez-Jácome, L., Avendaño-Vázquez, S. E. & Flores-Jasso, C. F. The pipeline repertoire for Ig-Seq analysis. Front. Immunol. 10, 899 (2019).
doi: 10.3389/fimmu.2019.00899
Shugay, M. et al. Towards error-free profiling of immune repertoires. Nat. Methods 11, 653–655 (2014).
doi: 10.1038/nmeth.2960
Bolotin, D. A. et al. MiXCR: software for comprehensive adaptive immunity profiling. Nat. Methods 12, 380–381 (2015).
doi: 10.1038/nmeth.3364
Shugay, M. et al. VDJtools: Unifying post-analysis of T cell receptor repertoires. PLoS Comput. Biol. 11, 1004503 (2015).
doi: 10.1371/journal.pcbi.1004503
Möckli, N. & Auerbach, D. Quantitative β-galactosidase assay suitable for high-throughput applications in the yeast two-hybrid system. Biotechniques 36, 872–876 (2004).
doi: 10.2144/04365PT03
Meli, G., Visintin, M., Cannistraci, I. & Cattaneo, A. Direct in vivo intracellular selection of conformation-sensitive antibody domains targeting Alzheimer’s amyloid-β oligomers. J. Mol. Biol. 387, 584–606 (2009).
doi: 10.1016/j.jmb.2009.01.061
Rudolph R., BoÈhm G., Lilie H. & Jaenicke R. Folding proteins. In Protein Function, a Practical Approach. (IRL-Press. Oxford University Press, Oxford, UK, 1997).
Chirichella, M. et al. Post-translational selective intracellular silencing of acetylated proteins with de novo selected intrabodies. Nat. Methods 14, 279–282 (2017).
doi: 10.1038/nmeth.4144

Auteurs

Simonetta Lisi (S)

Bio@SNS Laboratory, Scuola Normale Superiore, 56126, Pisa, Italy.

Francesca Malerba (F)

Fondazione EBRI (European Brain Research Institute) Rita Levi-Montalcini, 00161, Rome, Italy.

Paola Quaranta (P)

Retrovirus Centre, Department of Translational Research, University of Pisa, 56126, Pisa, Italy.
Virology Operative Unit, Pisa University Hospital, 56124, Pisa, Italy.

Rita Florio (R)

Fondazione EBRI (European Brain Research Institute) Rita Levi-Montalcini, 00161, Rome, Italy.

Ottavia Vitaloni (O)

Bio@SNS Laboratory, Scuola Normale Superiore, 56126, Pisa, Italy.

Elisa Monaca (E)

Structural Biology and Biophysics Unit, Fondazione Ri.MED, 90133, Palermo, Italy.

Bruno Bruni Ercole (B)

Fondazione EBRI (European Brain Research Institute) Rita Levi-Montalcini, 00161, Rome, Italy.

Angela Rachel Bitonti (AR)

Bio@SNS Laboratory, Scuola Normale Superiore, 56126, Pisa, Italy.

Olga Del Perugia (O)

Bio@SNS Laboratory, Scuola Normale Superiore, 56126, Pisa, Italy.

Marianna Mignanelli (M)

Bio@SNS Laboratory, Scuola Normale Superiore, 56126, Pisa, Italy.

Paola Perrera (P)

Retrovirus Centre, Department of Translational Research, University of Pisa, 56126, Pisa, Italy.

Raffaele Sabbatella (R)

Structural Biology and Biophysics Unit, Fondazione Ri.MED, 90133, Palermo, Italy.

Francesco Raimondi (F)

Bio@SNS Laboratory, Scuola Normale Superiore, 56126, Pisa, Italy.

Carmen Rita Piazza (CR)

Retrovirus Centre, Department of Translational Research, University of Pisa, 56126, Pisa, Italy.
Department of Medical Biotechnologies, University of Siena, 53100, Siena, Italy.

Anna Moles (A)

Genomnia Srl, 20091, Bresso, MI, Italy.
Institute of Biochemistry and Cell Biology, CNR, 80131, Napoli, Italy.

Caterina Alfano (C)

Structural Biology and Biophysics Unit, Fondazione Ri.MED, 90133, Palermo, Italy.

Mauro Pistello (M)

Retrovirus Centre, Department of Translational Research, University of Pisa, 56126, Pisa, Italy.
Virology Operative Unit, Pisa University Hospital, 56124, Pisa, Italy.

Antonino Cattaneo (A)

Bio@SNS Laboratory, Scuola Normale Superiore, 56126, Pisa, Italy. antonino.cattaneo@sns.it.
Fondazione EBRI (European Brain Research Institute) Rita Levi-Montalcini, 00161, Rome, Italy. antonino.cattaneo@sns.it.

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