1
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Qin M, Hu J, Li X, Liu J, Jiang R, Shi Y, Wang Z, Zhang L, Zhao Y, Gao H, Zhang Q, Zhao H, Li M, Huang C. Exosomal membrane proteins analysis using a silicon nanowire field effect transistor biosensor. Talanta 2024; 278:126534. [PMID: 39002259 DOI: 10.1016/j.talanta.2024.126534] [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: 05/17/2024] [Revised: 07/03/2024] [Accepted: 07/08/2024] [Indexed: 07/15/2024]
Abstract
Exosomes are of great significance in clinical diagnosis, due to their high homology with parental generation, which can reflect the pathophysiological status. However, the quantitative and classification detection of exosomes is still faced with the challenges of low sensitivity and complex operation. In this study, we develop an electrical and label-free method to directly detect exosomes with high sensitivity based on a Silicon nanowire field effect transistor biosensor (Si-NW Bio-FET). First, the impact of Debye length on Si-NW Bio-FET detection was investigated through simulation. The simulation results demonstrated that as the Debye length increased, the electrical response to Si-NW produced by charged particle at a certain distance from the surface of Si-NW was greater. A Si-NW Bio-FET modified with specific antibody CD81 on the nanowire was fabricated then used for detection of cell line-derived exosomes, which achieved a low limit of detection (LOD) of 1078 particles/mL in 0.01 × PBS. Furthermore, the Si-NW Bio-FETs modified with specific antibody CD9, CD81 and CD63 respectively, were employed to distinguish exosomes derived from human promyelocytic leukemia (HL-60) cell line in three different states (control group, lipopolysaccharide (LPS) inflammation group, and LPS + Romidepsin (FK228) drug treatment group), which was consistent with nano-flow cytometry. This study provides a highly sensitive method of directly quantifying exosomes without labeling, indicating its potential as a tool for disease surveillance and medication instruction.
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Affiliation(s)
- Meiyan Qin
- Institute of Microelectronics of the Chinese Academy of Sciences, Beijing 100029, China; University of Chinese Academy of Sciences, Beijing 101408, China
| | - Jiawei Hu
- Institute of Microelectronics of the Chinese Academy of Sciences, Beijing 100029, China; North China University of Technology, Beijing 100144, China
| | - Xue Li
- Cerebrovascular Diseases Research Institute, Xuanwu Hospital of Capital Medical University, Beijing 100053, China
| | - Jinlong Liu
- Institute of Microelectronics of the Chinese Academy of Sciences, Beijing 100029, China; University of Chinese Academy of Sciences, Beijing 101408, China
| | - Rui Jiang
- Institute of Microelectronics of the Chinese Academy of Sciences, Beijing 100029, China; University of Chinese Academy of Sciences, Beijing 101408, China
| | - Yimin Shi
- Institute of Microelectronics of the Chinese Academy of Sciences, Beijing 100029, China; University of Chinese Academy of Sciences, Beijing 101408, China
| | - Zizhen Wang
- Institute of Microelectronics of the Chinese Academy of Sciences, Beijing 100029, China; University of Chinese Academy of Sciences, Beijing 101408, China
| | - Lingqian Zhang
- Institute of Microelectronics of the Chinese Academy of Sciences, Beijing 100029, China
| | - Yang Zhao
- Institute of Microelectronics of the Chinese Academy of Sciences, Beijing 100029, China
| | - Hang Gao
- Institute of Microelectronics of the Chinese Academy of Sciences, Beijing 100029, China
| | - Qingzhu Zhang
- Institute of Microelectronics of the Chinese Academy of Sciences, Beijing 100029, China
| | - Haiping Zhao
- Cerebrovascular Diseases Research Institute, Xuanwu Hospital of Capital Medical University, Beijing 100053, China
| | - Mingxiao Li
- Institute of Microelectronics of the Chinese Academy of Sciences, Beijing 100029, China.
| | - Chengjun Huang
- Institute of Microelectronics of the Chinese Academy of Sciences, Beijing 100029, China; University of Chinese Academy of Sciences, Beijing 101408, China
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2
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Lao T, Farnos O, Bueno A, Alvarez A, Rodríguez E, Palacios J, de la Luz KR, Kamen A, Carpio Y, Estrada MP. Transient Expression in HEK-293 Cells in Suspension Culture as a Rapid and Powerful Tool: SARS-CoV-2 N and Chimeric SARS-CoV-2N-CD154 Proteins as a Case Study. Biomedicines 2023; 11:3050. [PMID: 38002050 PMCID: PMC10669214 DOI: 10.3390/biomedicines11113050] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2023] [Revised: 11/03/2023] [Accepted: 11/08/2023] [Indexed: 11/26/2023] Open
Abstract
In a previous work, we proposed a vaccine chimeric antigen based on the fusion of the SARS-CoV-2 N protein to the extracellular domain of the human CD40 ligand (CD154). This vaccine antigen was named N-CD protein and its expression was carried out in HEK-293 stably transfected cells, grown in adherent conditions and serum-supplemented medium. The chimeric protein obtained in these conditions presented a consistent pattern of degradation. The immunization of mice and monkeys with this chimeric protein was able to induce a high N-specific IgG response with only two doses in pre-clinical experiments. In order to explore ways to diminish protein degradation, in the present work, the N and N-CD proteins were produced in suspension cultures and serum-free media following transient transfection of the HEK-293 clone 3F6, at different scales, including stirred-tank controlled bioreactors. The results showed negligible or no degradation of the target proteins. Further, clones stably expressing N-CD were obtained and adapted to suspension culture, obtaining similar results to those observed in the transient expression experiments in HEK-293-3F6. The evidence supports transient protein expression in suspension cultures and serum-free media as a powerful tool to produce in a short period of time high levels of complex proteins susceptible to degradation, such as the SARS-CoV-2 N protein.
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Affiliation(s)
- Thailin Lao
- Center for Genetic Engineering and Biotechnology, Animal Biotechnology Department, Havana 10600, Cuba; (T.L.)
| | - Omar Farnos
- Department of Bioengineering, McGill University, Montreal, QC H3A 0E9, Canada; (O.F.); (A.K.)
| | - Alexi Bueno
- Process Development Department, Center of Molecular Immunology, Havana 11600, Cuba (J.P.); (K.R.d.l.L.)
| | - Anays Alvarez
- Center for Genetic Engineering and Biotechnology, Animal Biotechnology Department, Havana 10600, Cuba; (T.L.)
| | - Elsa Rodríguez
- Center for Genetic Engineering and Biotechnology, Animal Biotechnology Department, Havana 10600, Cuba; (T.L.)
| | - Julio Palacios
- Process Development Department, Center of Molecular Immunology, Havana 11600, Cuba (J.P.); (K.R.d.l.L.)
| | - Kathya Rashida de la Luz
- Process Development Department, Center of Molecular Immunology, Havana 11600, Cuba (J.P.); (K.R.d.l.L.)
| | - Amine Kamen
- Department of Bioengineering, McGill University, Montreal, QC H3A 0E9, Canada; (O.F.); (A.K.)
| | - Yamila Carpio
- Center for Genetic Engineering and Biotechnology, Animal Biotechnology Department, Havana 10600, Cuba; (T.L.)
| | - Mario Pablo Estrada
- Center for Genetic Engineering and Biotechnology, Animal Biotechnology Department, Havana 10600, Cuba; (T.L.)
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3
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Stocks BB, Thibeault MP, L’Abbé D, Stuible M, Durocher Y, Melanson JE. Production and Characterization of a SARS-CoV-2 Nucleocapsid Protein Reference Material. ACS MEASUREMENT SCIENCE AU 2022; 2:620-628. [PMID: 36785774 PMCID: PMC9662649 DOI: 10.1021/acsmeasuresciau.2c00050] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/19/2022] [Revised: 08/22/2022] [Accepted: 08/23/2022] [Indexed: 05/02/2023]
Abstract
Rapid antigen tests have become a widely used COVID-19 diagnostic tool with demand accelerating in response to the highly contagious SARS-CoV-2 Omicron variant. Hundreds of such test kits are approved for use worldwide, predominantly reporting on the presence of the viral nucleocapsid (N) protein, yet the comparability among manufacturers remains unclear and the need for reference standards is recognized. To address this lack of standardization, the National Research Council Canada has developed a SARS-CoV-2 nucleocapsid protein reference material solution, NCAP-1. Reference value determination for N protein content was realized by amino acid analysis (AAA) via double isotope dilution liquid chromatography-tandem mass spectrometry (LC-ID-MS/MS) following acid hydrolysis of the protein, in conjunction with UV spectrophotometry based on tryptophan and tyrosine absorbance at 280 nm. The homogeneity of the material was established through spectrophotometric absorbance readings at 280 nm. The molar concentration of the N protein in NCAP-1 was 10.0 ± 1.9 μmol L-1 (k = 2, 95% confidence interval). Reference mass concentration and mass fraction values were subsequently calculated using the protein molecular weight and density of the NCAP-1 solution. Changes to protein higher-order structure, probed by size-exclusion liquid chromatography (LC-SEC) with UV detection, were used to evaluate transportation and storage stabilities. LC-SEC revealed nearly 90% of the N protein in the material is present as a mixture of hexamers and tetramers. The remaining low molecular weight species (<30 kDa) were interrogated by top-down mass spectrometry and determined to be autolysis products homologous to those previously documented for N protein of the original SARS-CoV [Biochem. Biophys. Res. Commun.2008t, 377, 429-433].
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Affiliation(s)
- Bradley B. Stocks
- Metrology, National Research Council Canada, 1200 Montreal Road, Ottawa, ON K1A
0R6, Canada
| | - Marie-Pier Thibeault
- Metrology, National Research Council Canada, 1200 Montreal Road, Ottawa, ON K1A
0R6, Canada
| | - Denis L’Abbé
- Human
Health Therapeutics, National Research Council
Canada, 6100 Royalmount
Avenue, Montreal, QC H4P 2R2, Canada
| | - Matthew Stuible
- Human
Health Therapeutics, National Research Council
Canada, 6100 Royalmount
Avenue, Montreal, QC H4P 2R2, Canada
| | - Yves Durocher
- Human
Health Therapeutics, National Research Council
Canada, 6100 Royalmount
Avenue, Montreal, QC H4P 2R2, Canada
| | - Jeremy E. Melanson
- Metrology, National Research Council Canada, 1200 Montreal Road, Ottawa, ON K1A
0R6, Canada
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4
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Boehme KW, Kennedy JL, Snowden J, Owens SM, Kouassi M, Mann RL, Paredes A, Putt C, James L, Jin J, Du R, Kirkpatrick C, Modi Z, Caid K, Young S, Zohoori N, Kothari A, Boyanton BL, Craig Forrest J. Pediatric SARS-CoV-2 Seroprevalence in Arkansas Over the First Year of the COVID-19 Pandemic. J Pediatric Infect Dis Soc 2022; 11:248-256. [PMID: 35294550 PMCID: PMC8992271 DOI: 10.1093/jpids/piac010] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/23/2021] [Accepted: 02/04/2022] [Indexed: 11/29/2022]
Abstract
BACKGROUND Severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) seroprevalence studies largely focus on adults, but little is known about spread in children. We determined SARS-CoV-2 seroprevalence in children and adolescents from Arkansas over the first year of the coronavirus disease of 2019 (COVID-19) pandemic. METHODS We tested remnant serum samples from children ages 1-18 years who visited Arkansas hospitals or clinics for non-COVID-19-related reasons from April 2020 through April 2021 for SARS-CoV-2 antibodies. We used univariable and multivariable regression models to determine the association between seropositivity and participant characteristics. RESULTS Among 2357 participants, seroprevalence rose from 7.9% in April/May 2020 (95% CI, 4.9-10.9) to 25.0% in April 2021 (95% CI, 21.5-28.5). Hispanic and black children had a higher association with antibody positivity than non-Hispanic and white children, respectively, in multiple sampling periods. CONCLUSIONS By spring 2021, most children in Arkansas were not infected with SARS-CoV-2. With the emergence of SARS-CoV-2 variants, recognition of long-term effects of COVID-19, and the lack of an authorized pediatric SARS-CoV-2 vaccine at the time, these results highlight the importance of including children in SARS-CoV-2 public health, clinical care, and research strategies.
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Affiliation(s)
- Karl W Boehme
- Department of Microbiology & Immunology, College of Medicine, University of Arkansas for Medical Sciences, Little Rock, Arkansas, USA
- Center for Microbial Pathogenesis and Host Inflammatory Responses, University of Arkansas for Medical Sciences, Little Rock, Arkansas, USA
- Winthrop P. Rockefeller Cancer Institute, University of Arkansas for Medical Sciences, Little Rock, Arkansas, USA
| | - Joshua L Kennedy
- Department of Pediatrics, College of Medicine, University of Arkansas for Medical Sciences, Little Rock, Arkansas, USA
- Department of Internal Medicine, College of Medicine, University of Arkansas for Medical Sciences, Little Rock, Arkansas, USA
- Arkansas Children’s Research Institute, Little Rock, Arkansas, USA
| | - Jessica Snowden
- Department of Pediatrics, College of Medicine, University of Arkansas for Medical Sciences, Little Rock, Arkansas, USA
- Department of Environmental and Occupational Health, Fay W. Boozman College of Public Health, University of Arkansas for Medical Sciences, Little Rock, Arkansas, USA
| | - Shana M Owens
- Department of Microbiology & Immunology, College of Medicine, University of Arkansas for Medical Sciences, Little Rock, Arkansas, USA
| | - Marianne Kouassi
- Department of Microbiology & Immunology, College of Medicine, University of Arkansas for Medical Sciences, Little Rock, Arkansas, USA
| | - Ryan L Mann
- Department of Microbiology & Immunology, College of Medicine, University of Arkansas for Medical Sciences, Little Rock, Arkansas, USA
| | - Amairani Paredes
- Department of Microbiology & Immunology, College of Medicine, University of Arkansas for Medical Sciences, Little Rock, Arkansas, USA
| | - Claire Putt
- Department of Pediatrics, College of Medicine, University of Arkansas for Medical Sciences, Little Rock, Arkansas, USA
| | - Laura James
- Department of Pediatrics, College of Medicine, University of Arkansas for Medical Sciences, Little Rock, Arkansas, USA
| | - Jing Jin
- Department of Environmental and Occupational Health, Fay W. Boozman College of Public Health, University of Arkansas for Medical Sciences, Little Rock, Arkansas, USA
| | - Ruofei Du
- Department of Environmental and Occupational Health, Fay W. Boozman College of Public Health, University of Arkansas for Medical Sciences, Little Rock, Arkansas, USA
| | | | - Zeel Modi
- Department of Internal Medicine, College of Medicine, University of Arkansas for Medical Sciences, Little Rock, Arkansas, USA
| | - Katherine Caid
- Arkansas Children’s Research Institute, Little Rock, Arkansas, USA
| | - Sean Young
- Department of Biostatistics, College of Public Health, University of Arkansas for Medical Sciences, Little Rock, AR, USA
| | - Namvar Zohoori
- Department of Epidemiology, College of Public Health, University of Arkansas for Medical Sciences, Little Rock, Arkansas, USA
- Arkansas Department of Health, Little Rock, Arkansas, USA
| | - Atul Kothari
- Department of Internal Medicine, College of Medicine, University of Arkansas for Medical Sciences, Little Rock, Arkansas, USA
- Arkansas Department of Health, Little Rock, Arkansas, USA
- Department of Bioinformatics, College of Medicine, University of Arkansas for Medical Sciences, Little Rock, Arkansas, USA
| | - Bobby L Boyanton
- Department of Pathology, Arkansas Children’s Hospital and University of Arkansas for Medical Sciences, Little Rock, Arkansas, USA
| | - J Craig Forrest
- Department of Microbiology & Immunology, College of Medicine, University of Arkansas for Medical Sciences, Little Rock, Arkansas, USA
- Center for Microbial Pathogenesis and Host Inflammatory Responses, University of Arkansas for Medical Sciences, Little Rock, Arkansas, USA
- Winthrop P. Rockefeller Cancer Institute, University of Arkansas for Medical Sciences, Little Rock, Arkansas, USA
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5
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De Vos J, Pereira Aguilar P, Köppl C, Fischer A, Grünwald-Gruber C, Dürkop M, Klausberger M, Mairhofer J, Striedner G, Cserjan-Puschmann M, Jungbauer A, Lingg N. Production of full-length SARS-CoV-2 nucleocapsid protein from Escherichia coli optimized by native hydrophobic interaction chromatography hyphenated to multi-angle light scattering detection. Talanta 2021; 235:122691. [PMID: 34517577 PMCID: PMC8284068 DOI: 10.1016/j.talanta.2021.122691] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2021] [Revised: 07/02/2021] [Accepted: 07/03/2021] [Indexed: 11/22/2022]
Abstract
The nucleocapsid protein (NP) of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is critical for several steps of the viral life cycle, and is abundantly expressed during infection, making it an ideal diagnostic target protein. This protein has a strong tendency for dimerization and interaction with nucleic acids. For the first time, high titers of NP were expressed in E. coli with a CASPON tag, using a growth-decoupled protein expression system. Purification was accomplished by nuclease treatment of the cell homogenate and a sequence of downstream processing (DSP) steps. An analytical method consisting of native hydrophobic interaction chromatography hyphenated to multi-angle light scattering detection (HIC-MALS) was established for in-process control, in particular, to monitor product fragmentation and multimerization throughout the purification process. 730 mg purified NP per liter of fermentation could be produced by the optimized process, corresponding to a yield of 77% after cell lysis. The HIC-MALS method was used to demonstrate that the NP product can be produced with a purity of 95%. The molecular mass of the main NP fraction is consistent with dimerized protein as was verified by a complementary native size-exclusion separation (SEC)-MALS analysis. Peptide mapping mass spectrometry and host cell specific enzyme-linked immunosorbent assay confirmed the high product purity, and the presence of a minor endogenous chaperone explained the residual impurities. The optimized HIC-MALS method enables monitoring of the product purity, and simultaneously access its molecular mass, providing orthogonal information complementary to established SEC-MALS methods. Enhanced resolving power can be achieved over SEC, attributed to the extended variables to tune selectivity in HIC mode.
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Affiliation(s)
- Jelle De Vos
- Vrije Universiteit Brussel, Department of Chemical Engineering, 1050, Brussels, Belgium; Department of Biotechnology, University of Natural Resources and Life Sciences, Vienna (BOKU), 1190 Vienna, Austria
| | - Patricia Pereira Aguilar
- Department of Biotechnology, University of Natural Resources and Life Sciences, Vienna (BOKU), 1190 Vienna, Austria; acib - Austrian Centre of Industrial Biotechnology, 1190, Vienna, Austria.
| | - Christoph Köppl
- acib - Austrian Centre of Industrial Biotechnology, 1190, Vienna, Austria
| | - Andreas Fischer
- acib - Austrian Centre of Industrial Biotechnology, 1190, Vienna, Austria
| | - Clemens Grünwald-Gruber
- BOKU Core Facility Mass Spectrometry, University of Natural Resources and Life Sciences, Vienna (BOKU), 1190, Vienna, Austria
| | - Mark Dürkop
- Department of Biotechnology, University of Natural Resources and Life Sciences, Vienna (BOKU), 1190 Vienna, Austria; Novasign GmbH, 1190, Vienna, Austria
| | - Miriam Klausberger
- Department of Biotechnology, University of Natural Resources and Life Sciences, Vienna (BOKU), 1190 Vienna, Austria
| | | | - Gerald Striedner
- Department of Biotechnology, University of Natural Resources and Life Sciences, Vienna (BOKU), 1190 Vienna, Austria; acib - Austrian Centre of Industrial Biotechnology, 1190, Vienna, Austria; enGenes Biotech GmbH, 1190, Vienna, Austria
| | - Monika Cserjan-Puschmann
- Department of Biotechnology, University of Natural Resources and Life Sciences, Vienna (BOKU), 1190 Vienna, Austria; acib - Austrian Centre of Industrial Biotechnology, 1190, Vienna, Austria
| | - Alois Jungbauer
- Department of Biotechnology, University of Natural Resources and Life Sciences, Vienna (BOKU), 1190 Vienna, Austria; acib - Austrian Centre of Industrial Biotechnology, 1190, Vienna, Austria
| | - Nico Lingg
- Department of Biotechnology, University of Natural Resources and Life Sciences, Vienna (BOKU), 1190 Vienna, Austria; acib - Austrian Centre of Industrial Biotechnology, 1190, Vienna, Austria
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6
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Meyer B, Chiaravalli J, Gellenoncourt S, Brownridge P, Bryne DP, Daly LA, Grauslys A, Walter M, Agou F, Chakrabarti LA, Craik CS, Eyers CE, Eyers PA, Gambin Y, Jones AR, Sierecki E, Verdin E, Vignuzzi M, Emmott E. Characterising proteolysis during SARS-CoV-2 infection identifies viral cleavage sites and cellular targets with therapeutic potential. Nat Commun 2021; 12:5553. [PMID: 34548480 PMCID: PMC8455558 DOI: 10.1038/s41467-021-25796-w] [Citation(s) in RCA: 60] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2021] [Accepted: 08/24/2021] [Indexed: 02/08/2023] Open
Abstract
SARS-CoV-2 is the causative agent behind the COVID-19 pandemic, responsible for over 170 million infections, and over 3.7 million deaths worldwide. Efforts to test, treat and vaccinate against this pathogen all benefit from an improved understanding of the basic biology of SARS-CoV-2. Both viral and cellular proteases play a crucial role in SARS-CoV-2 replication. Here, we study proteolytic cleavage of viral and cellular proteins in two cell line models of SARS-CoV-2 replication using mass spectrometry to identify protein neo-N-termini generated through protease activity. We identify previously unknown cleavage sites in multiple viral proteins, including major antigens S and N: the main targets for vaccine and antibody testing efforts. We discover significant increases in cellular cleavage events consistent with cleavage by SARS-CoV-2 main protease, and identify 14 potential high-confidence substrates of the main and papain-like proteases. We show that siRNA depletion of these cellular proteins inhibits SARS-CoV-2 replication, and that drugs targeting two of these proteins: the tyrosine kinase SRC and Ser/Thr kinase MYLK, show a dose-dependent reduction in SARS-CoV-2 titres. Overall, our study provides a powerful resource to understand proteolysis in the context of viral infection, and to inform the development of targeted strategies to inhibit SARS-CoV-2 and treat COVID-19.
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Affiliation(s)
- Bjoern Meyer
- Viral Populations and Pathogenesis Unit, CNRS, UMR 3569, Institut Pasteur, CEDEX 15, Paris, France
| | - Jeanne Chiaravalli
- Chemogenomic and Biological Screening Core Facility, C2RT, Departments of Cell Biology & Infection and of Structural Biology & Chemistry, Institut Pasteur, CEDEX 15, Paris, France
| | - Stacy Gellenoncourt
- CIVIC Group, Virus & Immunity Unit, Institut Pasteur and CNRS, UMR 3569, Paris, France
| | - Philip Brownridge
- Centre for Proteome Research, Department of Biochemistry & Systems Biology, Institute of Systems, Molecular & Integrative Biology, Biosciences Building, Crown Street, University of Liverpool, Liverpool, L69 7ZB, UK
| | - Dominic P Bryne
- Department of Biochemistry & Systems Biology, Institute of Systems, Molecular & Integrative Biology, Biosciences Building, Crown Street, University of Liverpool, Liverpool, L69 7ZB, UK
| | - Leonard A Daly
- Centre for Proteome Research, Department of Biochemistry & Systems Biology, Institute of Systems, Molecular & Integrative Biology, Biosciences Building, Crown Street, University of Liverpool, Liverpool, L69 7ZB, UK
| | - Arturas Grauslys
- Computational Biology Facility, LIV-SRF, Institute of Systems, Molecular & Integrative Biology, Biosciences Building, Crown Street, University of Liverpool, Liverpool, L69 7ZB, UK
| | - Marius Walter
- Buck Institute for Research on Aging, Novato, CA, 94945, USA
| | - Fabrice Agou
- Chemogenomic and Biological Screening Core Facility, C2RT, Departments of Cell Biology & Infection and of Structural Biology & Chemistry, Institut Pasteur, CEDEX 15, Paris, France
| | - Lisa A Chakrabarti
- CIVIC Group, Virus & Immunity Unit, Institut Pasteur and CNRS, UMR 3569, Paris, France
| | - Charles S Craik
- Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, CA, USA
| | - Claire E Eyers
- Centre for Proteome Research, Department of Biochemistry & Systems Biology, Institute of Systems, Molecular & Integrative Biology, Biosciences Building, Crown Street, University of Liverpool, Liverpool, L69 7ZB, UK
| | - Patrick A Eyers
- Department of Biochemistry & Systems Biology, Institute of Systems, Molecular & Integrative Biology, Biosciences Building, Crown Street, University of Liverpool, Liverpool, L69 7ZB, UK
| | - Yann Gambin
- EMBL Australia Node for Single Molecule Sciences, and School of Medical Sciences, Botany Road, The University of New South Wales, Sydney, NSW, 2052, Australia
| | - Andrew R Jones
- Department of Biochemistry & Systems Biology, Institute of Systems, Molecular & Integrative Biology, Biosciences Building, Crown Street, University of Liverpool, Liverpool, L69 7ZB, UK
| | - Emma Sierecki
- EMBL Australia Node for Single Molecule Sciences, and School of Medical Sciences, Botany Road, The University of New South Wales, Sydney, NSW, 2052, Australia
| | - Eric Verdin
- Buck Institute for Research on Aging, Novato, CA, 94945, USA
| | - Marco Vignuzzi
- Viral Populations and Pathogenesis Unit, CNRS, UMR 3569, Institut Pasteur, CEDEX 15, Paris, France
| | - Edward Emmott
- Centre for Proteome Research, Department of Biochemistry & Systems Biology, Institute of Systems, Molecular & Integrative Biology, Biosciences Building, Crown Street, University of Liverpool, Liverpool, L69 7ZB, UK.
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7
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Lutomski C, El-Baba TJ, Bolla JR, Robinson CV. Multiple Roles of SARS-CoV-2 N Protein Facilitated by Proteoform-Specific Interactions with RNA, Host Proteins, and Convalescent Antibodies. JACS AU 2021; 1:1147-1157. [PMID: 34462738 PMCID: PMC8231660 DOI: 10.1021/jacsau.1c00139] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/26/2021] [Indexed: 05/12/2023]
Abstract
The SARS-CoV-2 nucleocapsid (N) protein is a highly immunogenic viral protein that plays essential roles in replication and virion assembly. Here, using native mass spectrometry, we show that dimers are the functional unit of ribonucleoprotein assembly and that N protein binds RNA with a preference for GGG motifs, a common motif in coronavirus packaging signals. Unexpectedly, proteolytic processing of N protein resulted in the formation of additional proteoforms. The N-terminal proteoforms bind RNA, with the same preference for GGG motifs, and bind to cyclophilin A, an interaction which can be abolished by approved immunosuppressant cyclosporin A. Furthermore, N proteoforms showed significantly different interactions with IgM, IgG, and IgA antibodies from convalescent plasma. Notably, the C-terminal proteoform exhibited a heightened interaction with convalescent antibodies, suggesting the antigenic epitope is localized to the C-terminus. Overall, the different interactions of N proteoforms highlight potential avenues for therapeutic intervention and identify a stable and immunogenic proteoform as a possible candidate for immune-directed therapies.
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Affiliation(s)
- Corinne
A. Lutomski
- Physical
and Theoretical Chemistry Laboratory, University
of Oxford, South Parks Road, OX13QZ Oxford, U.K.
| | - Tarick J. El-Baba
- Physical
and Theoretical Chemistry Laboratory, University
of Oxford, South Parks Road, OX13QZ Oxford, U.K.
| | - Jani R. Bolla
- Physical
and Theoretical Chemistry Laboratory, University
of Oxford, South Parks Road, OX13QZ Oxford, U.K.
| | - Carol V. Robinson
- Physical
and Theoretical Chemistry Laboratory, University
of Oxford, South Parks Road, OX13QZ Oxford, U.K.
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8
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Frumence E, Lebeau G, Viranaicken W, Dobi A, Vagner D, Lalarizo Rakoto M, Sandenon Seteyen AL, Giry C, Septembre-Malaterre A, Raffray L, Gasque P. Robust and low-cost ELISA based on IgG-Fc tagged recombinant proteins to screen for anti-SARS-CoV-2 antibodies. J Immunol Methods 2021; 495:113082. [PMID: 34051226 PMCID: PMC8152238 DOI: 10.1016/j.jim.2021.113082] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2020] [Revised: 05/22/2021] [Accepted: 05/24/2021] [Indexed: 11/06/2022]
Abstract
The development of new diagnostic assays become a priority for managing COVID-19. To this aim, we presented here an in-house ELISA based on the production of two major recombinant and high-quality antigens from SARS-CoV-2. Full-length N and S-RBD fragment proteins fused to mouse IgG2a-Fc were produced in the CHO cell line. Secreted recombinant proteins were easily purified with standard Protein A chromatography and were used in an in-house ELISA to detect anti-N and anti-RBD IgGs in the plasma of COVID-19 RTPCR-positive patients. High reactivity against recombinant antigens was readily detected in all positive plasma samples, whereas no recognition was observed with control healthy subject's plasmas. Remarkably, unpurified recombinant N protein obtained from cell culture supernatant was also suitable for the monitoring by ELISA of IgG levels in positive patients. This work provides an early prospection for low price but high-quality serological kit development.
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Affiliation(s)
- Etienne Frumence
- Unité de recherche en Pharmaco-Immunologie (UR-EPI), Université et CHU de La Réunion, Saint-Denis 97400, France; Laboratoire d'immunologie Clinique et expérimentale de la ZOI (LICE-OI), Pôle de Biologie, CHU de La Réunion, Saint-Denis 97400, France.
| | - Grégorie Lebeau
- Unité de recherche en Pharmaco-Immunologie (UR-EPI), Université et CHU de La Réunion, Saint-Denis 97400, France; Laboratoire d'immunologie Clinique et expérimentale de la ZOI (LICE-OI), Pôle de Biologie, CHU de La Réunion, Saint-Denis 97400, France
| | - Wildriss Viranaicken
- UMR PIMIT 'Processus Infectieux en Milieu Insulaire Tropical' CNRS 9192, INSERM1187, IRD 249, Université de La Réunion, Saint-Denis 97400, France
| | - Anthony Dobi
- Unité de recherche en Pharmaco-Immunologie (UR-EPI), Université et CHU de La Réunion, Saint-Denis 97400, France; Laboratoire d'immunologie Clinique et expérimentale de la ZOI (LICE-OI), Pôle de Biologie, CHU de La Réunion, Saint-Denis 97400, France
| | - Damien Vagner
- Laboratoire d'immunologie Clinique et expérimentale de la ZOI (LICE-OI), Pôle de Biologie, CHU de La Réunion, Saint-Denis 97400, France; UMR PIMIT 'Processus Infectieux en Milieu Insulaire Tropical' CNRS 9192, INSERM1187, IRD 249, Université de La Réunion, Saint-Denis 97400, France
| | - Mahary Lalarizo Rakoto
- Unité de recherche en Pharmaco-Immunologie (UR-EPI), Université et CHU de La Réunion, Saint-Denis 97400, France; Laboratoire d'immunologie Clinique et expérimentale de la ZOI (LICE-OI), Pôle de Biologie, CHU de La Réunion, Saint-Denis 97400, France; Faculté de Médecine, Campus universitaire Ambohitsaina, BP375, Université d'Antananarivo, Madagascar
| | - Anne-Laure Sandenon Seteyen
- Unité de recherche en Pharmaco-Immunologie (UR-EPI), Université et CHU de La Réunion, Saint-Denis 97400, France; Laboratoire d'immunologie Clinique et expérimentale de la ZOI (LICE-OI), Pôle de Biologie, CHU de La Réunion, Saint-Denis 97400, France
| | - Claude Giry
- CNR associé arbovirus, Laboratoire de Microbiologie, Pôle de Biologie, CHU de La Réunion, Saint-Denis 97440, France
| | - Axelle Septembre-Malaterre
- Unité de recherche en Pharmaco-Immunologie (UR-EPI), Université et CHU de La Réunion, Saint-Denis 97400, France; Laboratoire d'immunologie Clinique et expérimentale de la ZOI (LICE-OI), Pôle de Biologie, CHU de La Réunion, Saint-Denis 97400, France
| | - Loïc Raffray
- UMR PIMIT 'Processus Infectieux en Milieu Insulaire Tropical' CNRS 9192, INSERM1187, IRD 249, Université de La Réunion, Saint-Denis 97400, France; Service de Médecine Interne, Centre Hospitalier Universitaire La Réunion Site Félix Guyon, CS11021, 97400 Saint Denis de La Réunion, France
| | - Philippe Gasque
- Unité de recherche en Pharmaco-Immunologie (UR-EPI), Université et CHU de La Réunion, Saint-Denis 97400, France; Laboratoire d'immunologie Clinique et expérimentale de la ZOI (LICE-OI), Pôle de Biologie, CHU de La Réunion, Saint-Denis 97400, France
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9
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Serological antibody testing in the COVID-19 pandemic: their molecular basis and applications. Biochem Soc Trans 2021; 48:2851-2863. [PMID: 33170924 DOI: 10.1042/bst20200744] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2020] [Revised: 10/26/2020] [Accepted: 10/30/2020] [Indexed: 12/23/2022]
Abstract
The ongoing COVID-19 pandemic has placed an overwhelming burden on the healthcare system, and caused major disruption to the world economy. COVID-19 is caused by SARS-CoV-2, a novel coronavirus that leads to a variety of symptoms in humans, including cough, fever and respiratory failure. SARS-CoV-2 infection can trigger extensive immune responses, including the production of antibodies. The detection of antibody response by serological testing provides a supplementary diagnostic tool to molecular tests. We hereby present a succinct yet comprehensive review on the antibody response to SARS-CoV-2 infection, as well as molecular mechanisms behind the strengths and limitations of serological antibody tests. The presence of antibodies can be detected in patient sera within days post symptom onset. Serological tests demonstrate superior sensitivity to molecular tests in some periods of time during disease development. Compared with the molecular tests, serological tests can be used for point-of-care testing, providing faster results at a lower cost. Commercially available serological tests show variable sensitivity and specificity, and the molecular basis of these variabilities are analysed. We discuss assays of different complexities that are used to specifically quantitate neutralising antibodies against SARS-CoV-2, which has important implications for vaccine development and herd immunity. Furthermore, we discuss examples of successful applications of serological tests to contact tracing and community-level sero-surveying, which provide invaluable information for pandemic management and assessment.
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10
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Demurtas OC, Massa S, Illiano E, De Martinis D, Chan PKS, Di Bonito P, Franconi R. Antigen Production in Plant to Tackle Infectious Diseases Flare Up: The Case of SARS. FRONTIERS IN PLANT SCIENCE 2016; 7:54. [PMID: 26904039 PMCID: PMC4742786 DOI: 10.3389/fpls.2016.00054] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/04/2015] [Accepted: 01/13/2016] [Indexed: 05/09/2023]
Abstract
Severe acute respiratory syndrome (SARS) is a dangerous infection with pandemic potential. It emerged in 2002 and its aetiological agent, the SARS Coronavirus (SARS-CoV), crossed the species barrier to infect humans, showing high morbidity and mortality rates. No vaccines are currently licensed for SARS-CoV and important efforts have been performed during the first outbreak to develop diagnostic tools. Here we demonstrate the transient expression in Nicotiana benthamiana of two important antigenic determinants of the SARS-CoV, the nucleocapsid protein (N) and the membrane protein (M) using a virus-derived vector or agro-infiltration, respectively. For the M protein, this is the first description of production in plants, while for plant-derived N protein we demonstrate that it is recognized by sera of patients from the SARS outbreak in Hong Kong in 2003. The availability of recombinant N and M proteins from plants opens the way to further evaluation of their potential utility for the development of diagnostic and protection/therapy tools to be quickly manufactured, at low cost and with minimal risk, to face potential new highly infectious SARS-CoV outbreaks.
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Affiliation(s)
- Olivia C. Demurtas
- Department of Sustainability, Biotechnology Laboratory, Italian National Agency for New Technologies, Energy and Sustainable Economic DevelopmentRome, Italy
| | - Silvia Massa
- Department of Sustainability, Biotechnology Laboratory, Italian National Agency for New Technologies, Energy and Sustainable Economic DevelopmentRome, Italy
| | - Elena Illiano
- Department of Sustainability, Biomedical Technology Laboratory, Italian National Agency for New Technologies, Energy and Sustainable Economic DevelopmentRome, Italy
- Department of Pharmacological and Biomolecular Sciences, Università degli Studi di MilanoMilan, Italy
| | - Domenico De Martinis
- International Relations Office, Italian National Agency for New Technologies, Energy and Sustainable Economic DevelopmentRome, Italy
| | - Paul K. S. Chan
- Department of Microbiology, Faculty of Medicine, The Chinese University of Hong Kong, Prince of Wales HospitalHong Kong, China
- Centre for Emerging Infectious Diseases, Faculty of Medicine, The Chinese University of Hong Kong, Prince of Wales HospitalHong Kong, China
| | - Paola Di Bonito
- Istituto Superiore di Sanità, Department of Infectious, Parasitic and Immune-Mediated DiseasesRome, Italy
- *Correspondence: Rosella Franconi, ; Paola Di Bonito,
| | - Rosella Franconi
- Department of Sustainability, Biomedical Technology Laboratory, Italian National Agency for New Technologies, Energy and Sustainable Economic DevelopmentRome, Italy
- *Correspondence: Rosella Franconi, ; Paola Di Bonito,
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11
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Chang CK, Hou MH, Chang CF, Hsiao CD, Huang TH. The SARS coronavirus nucleocapsid protein--forms and functions. Antiviral Res 2014; 103:39-50. [PMID: 24418573 PMCID: PMC7113676 DOI: 10.1016/j.antiviral.2013.12.009] [Citation(s) in RCA: 339] [Impact Index Per Article: 33.9] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2013] [Revised: 12/08/2013] [Accepted: 12/20/2013] [Indexed: 12/14/2022]
Abstract
Coronavirus N proteins share the same modular organization. Structures of SARS-CoV N protein provide insight into nucleocapsid formation. N protein binds to nucleic acid at multiple sites in a coupled-allostery manner. A RNP packaging model highlighting the importance of disorder and modularity is proposed.
The nucleocapsid phosphoprotein of the severe acute respiratory syndrome coronavirus (SARS-CoV N protein) packages the viral genome into a helical ribonucleocapsid (RNP) and plays a fundamental role during viral self-assembly. It is a protein with multifarious activities. In this article we will review our current understanding of the N protein structure and its interaction with nucleic acid. Highlights of the progresses include uncovering the modular organization, determining the structures of the structural domains, realizing the roles of protein disorder in protein–protein and protein–nucleic acid interactions, and visualizing the ribonucleoprotein (RNP) structure inside the virions. It was also demonstrated that N-protein binds to nucleic acid at multiple sites with a coupled-allostery manner. We propose a SARS-CoV RNP model that conforms to existing data and bears resemblance to the existing RNP structures of RNA viruses. The model highlights the critical role of modular organization and intrinsic disorder of the N protein in the formation and functions of the dynamic RNP capsid in RNA viruses. This paper forms part of a symposium in Antiviral Research on “From SARS to MERS: 10 years of research on highly pathogenic human coronaviruses.”
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Affiliation(s)
- Chung-ke Chang
- Institute of Biomedical Sciences, Academia Sinica, Taipei 11529, Taiwan, ROC
| | - Ming-Hon Hou
- Department of Life Science, National Chung Hsing University, Taichung 40254, Taiwan, ROC
| | - Chi-Fon Chang
- The Genomics Research Center, Academia Sinica, Taipei 11529, Taiwan, ROC
| | - Chwan-Deng Hsiao
- Institute of Molecular Biology, Academia Sinica, Taipei 11529, Taiwan, ROC
| | - Tai-huang Huang
- Institute of Biomedical Sciences, Academia Sinica, Taipei 11529, Taiwan, ROC; The Genomics Research Center, Academia Sinica, Taipei 11529, Taiwan, ROC; Department of Physics, National Taiwan Normal University, Taipei 11677, Taiwan, ROC.
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12
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Ahn I, Jeong BJ, Son HS. Comparative study of synonymous codon usage variations between the nucleocapsid and spike genes of coronavirus, and C-type lectin domain genes of human and mouse. Exp Mol Med 2010; 41:746-56. [PMID: 19561398 PMCID: PMC2772977 DOI: 10.3858/emm.2009.41.10.081] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022] Open
Abstract
Coronaviruses (CoVs) are single-stranded RNA viruses which contain the largest RNA genomes, and severe acute respiratory syndrome coronavirus (SARS-CoV), a newly found group 2 CoV, emerged as infectious disease with high mortality rate. In this study, we compared the synonymous codon usage patterns between the nucleocapsid and spike genes of CoVs, and C-type lectin domain (CTLD) genes of human and mouse on the codon basis. Findings indicate that the nucleocapsid genes of CoVs were affected from the synonymous codon usage bias than spike genes, and the CTLDs of human and mouse partially overlapped with the nucleocapsid genes of CoVs. In addition, we observed that CTLDs which showed the similar relative synonymous codon usage (RSCU) patterns with CoVs were commonly derived from the human chromosome 12, and mouse chromosome 6 and 12, suggesting that there might be a specific genomic region or chromosomes which show a more similar synonymous codon usage pattern with viral genes. Our findings contribute to developing the codon-optimization method in DNA vaccines, and further study is needed to determine a specific correlation between the codon usage patterns and the chromosomal locations in higher organisms.
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Affiliation(s)
- Insung Ahn
- Supercomputing Center, Korea Institute of Science and Technology Information, Daejon 305-806, Korea
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13
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Coronavirus nucleocapsid protein facilitates template switching and is required for efficient transcription. J Virol 2009; 84:2169-75. [PMID: 19955314 DOI: 10.1128/jvi.02011-09] [Citation(s) in RCA: 154] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
Purified nucleocapsid protein (N protein) from transmissible gastroenteritis virus (TGEV) enhanced hammerhead ribozyme self-cleavage and favored nucleic acid annealing, properties that define RNA chaperones, as previously reported. Several TGEV N-protein deletion mutants were expressed in Escherichia coli and purified, and their RNA binding ability and RNA chaperone activity were evaluated. The smallest N-protein domain analyzed with RNA chaperone activity, facilitating DNA and RNA annealing, contained the central unstructured region (amino acids 117 to 268). Interestingly, N protein and its deletion mutants with RNA chaperone activity enhanced template switching in a retrovirus-derived heterologous system, reinforcing the concept that TGEV N protein is an RNA chaperone that could be involved in template switching. This result is in agreement with the observation that in vivo, N protein is not necessary for TGEV replication, but it is required for efficient transcription.
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14
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Green fluorescent protein – Tagged HCV non-enveloped capsid like particles: Development of a new tool for tracking HCV core uptake. Biochimie 2009; 91:903-15. [DOI: 10.1016/j.biochi.2009.04.016] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2009] [Accepted: 04/15/2009] [Indexed: 12/30/2022]
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15
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Ishikawa FN, Chang HK, Curreli M, Liao HI, Olson AC, Chen PC, Zhang R, Roberts RW, Sun R, Cote RJ, Thompson ME, Zhou C. Label-free, electrical detection of the SARS virus N-protein with nanowire biosensors utilizing antibody mimics as capture probes. ACS NANO 2009; 3:1219-24. [PMID: 19422193 PMCID: PMC2765574 DOI: 10.1021/nn900086c] [Citation(s) in RCA: 138] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
Antibody mimic proteins (AMPs) are polypeptides that bind to their target analytes with high affinity and specificity, just like conventional antibodies, but are much smaller in size (2-5 nm, less than 10 kDa). In this report, we describe the first application of AMP in the field of nanobiosensors. In(2)O(3) nanowire based biosensors have been configured with an AMP (Fibronectin, Fn) to detect nucleocapsid (N) protein, a biomarker for severe acute respiratory syndrome (SARS). Using these devices, N protein was detected at subnanomolar concentration in the presence of 44 microM bovine serum albumin as a background. Furthermore, the binding constant of the AMP to Fn was determined from the concentration dependence of the response of our biosensors.
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Affiliation(s)
- Fumiaki N. Ishikawa
- Department of Electrical Engineering, University of Southern California, Los Angeles, CA 90089
| | - Hsiao-Kang Chang
- Department of Electrical Engineering, University of Southern California, Los Angeles, CA 90089
| | - Marco Curreli
- Department of Chemistry, University of Southern California, Los Angeles, CA 90089
| | - Hsiang-I Liao
- Department of Molecular and Medical Pharmacology, University of California Los Angeles, Los Angels, CA 90095
| | - Anders C. Olson
- Department of Chemistry, University of Southern California, Los Angeles, CA 90089
| | - Po-Chiang Chen
- Department of Electrical Engineering, University of Southern California, Los Angeles, CA 90089
| | - Rui Zhang
- Department of Chemistry, University of Southern California, Los Angeles, CA 90089
| | - Richard W. Roberts
- Department of Chemistry, University of Southern California, Los Angeles, CA 90089
| | - Ren Sun
- Department of Molecular and Medical Pharmacology, University of California Los Angeles, Los Angels, CA 90095
| | - Richard J. Cote
- Department of Pathology, University of Southern California, Los Angeles, CA 90089
| | - Mark E. Thompson
- Department of Chemistry, University of Southern California, Los Angeles, CA 90089
| | - Chongwu Zhou
- Department of Electrical Engineering, University of Southern California, Los Angeles, CA 90089
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