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Pan Y, Wang Z, Yan Z, Sun H, Zhang L, Zhang W. Novel Strategy for Screening Target Proteins by the Common Drugs─Sofosbuvir-Specific Profiling of HCV Patient Serum. Anal Chem 2024; 96:9535-9543. [PMID: 38804236 DOI: 10.1021/acs.analchem.4c00993] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/29/2024]
Abstract
It is the scientific basis of precision medicine to study all of the targets of drugs based on the interaction between drugs and proteins. It is worth paying attention to unknown proteins that interact with drugs to find new targets for the design of new drugs. Herein, we developed a protein profiling strategy based on drug-protein interactions and drug-modified magnetic nanoparticles and took hepatitis C virus (HCV) and its corresponding drug sofosbuvir (SOF) as an example. A SOF-modified magnetic separation medium (Fe3O4@POSS@SOF) was prepared, and a gradient elution strategy was employed and optimized to profile specific proteins interacted with SOF. A series of proteomic analyses were performed to profile proteins based on SOF-protein interactions (SPIs) in the serum of HCV patients to evaluate the specificity of the profiling strategy. As a result, five proteins were profiled with strong SPIs and exhibited high relevance with liver tissue, which were potentially new drug targets. Among them, HSP60 was used to confirm the highly specific interactions between the SOF and its binding proteins by Western blotting analysis. Besides, 124 and 29 differential proteins were profiled by SOF material from three HCV patient serum and pooled 20 HCV patient serum, respectively, by comparing with healthy human serum. In comparison with those profiled by the polyhedral oligomeric silsesquioxane (POSS) material, differential proteins profiled by the SOF material were highly associated with liver diseases through GO analysis and pathway analysis. Furthermore, four common differential proteins profiled by SOF material but not by POSS material were found to be identical and expressed consistently in both pooled serum samples and independent serum samples, which might potentially be biomarkers of HCV infection. Taken together, our study proposes a highly specific protein profiling strategy to display distinctive proteomic profiles, providing a novel idea for drug design and development.
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Affiliation(s)
- Yini Pan
- Shanghai Key Laboratory of Functional Materials Chemistry, School of Chemistry & Molecular Engineering, East China University of Science and Technology, Shanghai 200237, P. R. China
| | - Zhenxin Wang
- Department of Laboratory Medicine, Zhongshan Hospital, Fudan University, Shanghai 200032, P. R. China
| | - Zhichao Yan
- Shanghai Key Laboratory of Functional Materials Chemistry, School of Chemistry & Molecular Engineering, East China University of Science and Technology, Shanghai 200237, P. R. China
| | - Haofan Sun
- State Key Laboratory of Proteomics, National Center for Protein Sciences Beijing, Beijing Institute of Lifeomics, Beijing Proteome Research Center, Beijing 102413, P. R. China
| | - Lingyi Zhang
- Shanghai Key Laboratory of Functional Materials Chemistry, School of Chemistry & Molecular Engineering, East China University of Science and Technology, Shanghai 200237, P. R. China
| | - Weibing Zhang
- Shanghai Key Laboratory of Functional Materials Chemistry, School of Chemistry & Molecular Engineering, East China University of Science and Technology, Shanghai 200237, P. R. China
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Kanji JN, Bailey A, Fenton J, Robbin Lindsay L, Dibernardo A, Toledo NP, Waitt B, Lecocq N, Osiowy C, Giles E, Day J, Stokes W, MacDonald C, Turnbull L, Charlton C. Stability of SARS-CoV-2 IgG in multiple laboratory conditions and blood sample types. J Clin Virol 2021; 142:104933. [PMID: 34364133 PMCID: PMC8310571 DOI: 10.1016/j.jcv.2021.104933] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2021] [Revised: 06/24/2021] [Accepted: 06/27/2021] [Indexed: 11/28/2022]
Abstract
Background : COVID-19 seroprevalence studies use serum/plasma samples to detect SARS-CoV-2 IgG. Data supporting alternate specimen types and freeze-thaw antibody stability is lacking. The stability of IgG and other immunoglobulins in multiple blood sample types stored in differing conditions and multiple freeze-thaw cycles (FTCs) was evaluated. Materials and methods : Serum, plasma, and heparinized-plasma samples were collected from COVID-19 recovered individuals. Samples underwent testing for SARS-CoV-2 antibodies upon collection, after each of 10–12 FTCs, and storage at -70°C, -20°C, 4°C, and room-temperature for 10–12 days using four high-throughput commercial assays, two rapid-test cassettes, a manual ELISA, and a surrogate neutralization assay. Results : All three specimen types were collected from 34 COVID-19 recovered seropositive individuals (≥21 days post-symptoms). Using the Architect and Liaison assays, a positive qualitative SARS-CoV-2 IgG result was detected daily up to 12 FTCs and up to 10 days of storage at different temperatures. An additional 25 plasma samples consistently demonstrated detection of SARS-CoV-2 antibodies daily after 12 FTCs and storage at -20°C using two rapid test cassette assays (SD Biosensor and Hangzhou All Test), manual (Beijing Wantai) and surrogate neutralization (GenScript) ELISAs, and two high-throughput assays (Roche Elecsys nucleocapsid and spike). IgM antibodies were less frequently detected by one of the rapid test cassette assays. Conclusions : Serum, plasma, and heparinized-plasma constitute reliable samples for SARS-CoV-2 antibody detection. In particular, the IgG response was stable and reliably detected after multiple FTCs and storage at common laboratory conditions. IgM detection was variable due to the labile nature of this antibody class.
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Affiliation(s)
- Jamil N Kanji
- Division of Infectious Diseases, Department of Medicine, University of Alberta, 8440 - 112 Street NW, Edmonton, AB, T6G 2B7, Canada; Public Health Laboratory, Alberta Precision Laboratories, University of Alberta Hospital, 8440 - 112 Street NW, Edmonton, AB, T6G 2B7, Canada; Department of Laboratory Medicine & Pathology, Faculty of Medicine & Dentistry, University of Alberta, 8440 - 112 Street NW, Edmonton, AB, T6G 2B7, Canada.
| | - Ashley Bailey
- Public Health Laboratory, Alberta Precision Laboratories, University of Alberta Hospital, 8440 - 112 Street NW, Edmonton, AB, T6G 2B7, Canada
| | - Jayne Fenton
- Public Health Laboratory, Alberta Precision Laboratories, University of Alberta Hospital, 8440 - 112 Street NW, Edmonton, AB, T6G 2B7, Canada
| | - L Robbin Lindsay
- National Microbiology Laboratory, Public Health Agency of Canada, 1015 Arlington Street Winnipeg, MB, R3E 3M4
| | - Antonia Dibernardo
- National Microbiology Laboratory, Public Health Agency of Canada, 1015 Arlington Street Winnipeg, MB, R3E 3M4
| | - Nikki Pl Toledo
- National Microbiology Laboratory, Public Health Agency of Canada, 1015 Arlington Street Winnipeg, MB, R3E 3M4
| | - Brooks Waitt
- National Microbiology Laboratory, Public Health Agency of Canada, 1015 Arlington Street Winnipeg, MB, R3E 3M4
| | - Nadine Lecocq
- National Microbiology Laboratory, Public Health Agency of Canada, 1015 Arlington Street Winnipeg, MB, R3E 3M4
| | - Carla Osiowy
- National Microbiology Laboratory, Public Health Agency of Canada, 1015 Arlington Street Winnipeg, MB, R3E 3M4
| | - Elizabeth Giles
- National Microbiology Laboratory, Public Health Agency of Canada, 1015 Arlington Street Winnipeg, MB, R3E 3M4
| | - Jacqueline Day
- National Microbiology Laboratory, Public Health Agency of Canada, 1015 Arlington Street Winnipeg, MB, R3E 3M4
| | - William Stokes
- Division of Infectious Diseases, Department of Medicine, University of Alberta, 8440 - 112 Street NW, Edmonton, AB, T6G 2B7, Canada; Public Health Laboratory, Alberta Precision Laboratories, University of Alberta Hospital, 8440 - 112 Street NW, Edmonton, AB, T6G 2B7, Canada; Department of Laboratory Medicine & Pathology, Faculty of Medicine & Dentistry, University of Alberta, 8440 - 112 Street NW, Edmonton, AB, T6G 2B7, Canada
| | - Clayton MacDonald
- Public Health Laboratory, Alberta Precision Laboratories, University of Alberta Hospital, 8440 - 112 Street NW, Edmonton, AB, T6G 2B7, Canada
| | - LeeAnn Turnbull
- Public Health Laboratory, Alberta Precision Laboratories, University of Alberta Hospital, 8440 - 112 Street NW, Edmonton, AB, T6G 2B7, Canada
| | - Carmen Charlton
- Public Health Laboratory, Alberta Precision Laboratories, University of Alberta Hospital, 8440 - 112 Street NW, Edmonton, AB, T6G 2B7, Canada; Department of Laboratory Medicine & Pathology, Faculty of Medicine & Dentistry, University of Alberta, 8440 - 112 Street NW, Edmonton, AB, T6G 2B7, Canada; Li Ka Shing Institute of Virology, University of Alberta, 6-010 Katz Group Centre for Pharmacy and Health Research, Edmonton, Alberta T6G 2E1, Canada
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Chigbu DI, Loonawat R, Sehgal M, Patel D, Jain P. Hepatitis C Virus Infection: Host⁻Virus Interaction and Mechanisms of Viral Persistence. Cells 2019; 8:cells8040376. [PMID: 31027278 PMCID: PMC6523734 DOI: 10.3390/cells8040376] [Citation(s) in RCA: 80] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2018] [Revised: 03/25/2019] [Accepted: 04/17/2019] [Indexed: 12/11/2022] Open
Abstract
Hepatitis C (HCV) is a major cause of liver disease, in which a third of individuals with chronic HCV infections may develop liver cirrhosis. In a chronic HCV infection, host immune factors along with the actions of HCV proteins that promote viral persistence and dysregulation of the immune system have an impact on immunopathogenesis of HCV-induced hepatitis. The genome of HCV encodes a single polyprotein, which is translated and processed into structural and nonstructural proteins. These HCV proteins are the target of the innate and adaptive immune system of the host. Retinoic acid-inducible gene-I (RIG-I)-like receptors and Toll-like receptors are the main pattern recognition receptors that recognize HCV pathogen-associated molecular patterns. This interaction results in a downstream cascade that generates antiviral cytokines including interferons. The cytolysis of HCV-infected hepatocytes is mediated by perforin and granzyme B secreted by cytotoxic T lymphocyte (CTL) and natural killer (NK) cells, whereas noncytolytic HCV clearance is mediated by interferon gamma (IFN-γ) secreted by CTL and NK cells. A host-HCV interaction determines whether the acute phase of an HCV infection will undergo complete resolution or progress to the development of viral persistence with a consequential progression to chronic HCV infection. Furthermore, these host-HCV interactions could pose a challenge to developing an HCV vaccine. This review will focus on the role of the innate and adaptive immunity in HCV infection, the failure of the immune response to clear an HCV infection, and the factors that promote viral persistence.
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Affiliation(s)
- DeGaulle I Chigbu
- Department of Microbiology and Immunology, and the Institute for Molecular Medicine and Infectious Disease, Drexel University College of Medicine, 2900 West Queen Lane, Philadelphia, PA 19129, USA.
- Pennsylvania College of Optometry at Salus University, Elkins Park, PA 19027, USA.
| | - Ronak Loonawat
- Department of Microbiology and Immunology, and the Institute for Molecular Medicine and Infectious Disease, Drexel University College of Medicine, 2900 West Queen Lane, Philadelphia, PA 19129, USA.
| | - Mohit Sehgal
- Immunology, Microenvironment & Metastasis Program, The Wistar Institute, Philadelphia, PA 19104, USA.
| | - Dip Patel
- Department of Microbiology and Immunology, and the Institute for Molecular Medicine and Infectious Disease, Drexel University College of Medicine, 2900 West Queen Lane, Philadelphia, PA 19129, USA.
| | - Pooja Jain
- Department of Microbiology and Immunology, and the Institute for Molecular Medicine and Infectious Disease, Drexel University College of Medicine, 2900 West Queen Lane, Philadelphia, PA 19129, USA.
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