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Guliy OI, Evstigneeva SS, Khanadeev VA, Dykman LA. Antibody Phage Display Technology for Sensor-Based Virus Detection: Current Status and Future Prospects. BIOSENSORS 2023; 13:640. [PMID: 37367005 DOI: 10.3390/bios13060640] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/26/2023] [Revised: 05/31/2023] [Accepted: 06/08/2023] [Indexed: 06/28/2023]
Abstract
Viruses are widespread in the environment, and many of them are major pathogens of serious plant, animal, and human diseases. The risk of pathogenicity, together with the capacity for constant mutation, emphasizes the need for measures to rapidly detect viruses. The need for highly sensitive bioanalytical methods to diagnose and monitor socially significant viral diseases has increased in the past few years. This is due, on the one hand, to the increased incidence of viral diseases in general (including the unprecedented spread of a new coronavirus infection, SARS-CoV-2), and, on the other hand, to the need to overcome the limitations of modern biomedical diagnostic methods. Phage display technology antibodies as nano-bio-engineered macromolecules can be used for sensor-based virus detection. This review analyzes the commonly used virus detection methods and approaches and shows the prospects for the use of antibodies prepared by phage display technology as sensing elements for sensor-based virus detection.
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Affiliation(s)
- Olga I Guliy
- Institute of Biochemistry and Physiology of Plants and Microorganisms, Subdivision of the Federal State Budgetary Research Institution Saratov Federal Scientific Centre of the Russian Academy of Sciences (IBPPM RAS), 13 Prospect Entuziastov, Saratov 410049, Russia
| | - Stella S Evstigneeva
- Institute of Biochemistry and Physiology of Plants and Microorganisms, Subdivision of the Federal State Budgetary Research Institution Saratov Federal Scientific Centre of the Russian Academy of Sciences (IBPPM RAS), 13 Prospect Entuziastov, Saratov 410049, Russia
| | - Vitaly A Khanadeev
- Institute of Biochemistry and Physiology of Plants and Microorganisms, Subdivision of the Federal State Budgetary Research Institution Saratov Federal Scientific Centre of the Russian Academy of Sciences (IBPPM RAS), 13 Prospect Entuziastov, Saratov 410049, Russia
| | - Lev A Dykman
- Institute of Biochemistry and Physiology of Plants and Microorganisms, Subdivision of the Federal State Budgetary Research Institution Saratov Federal Scientific Centre of the Russian Academy of Sciences (IBPPM RAS), 13 Prospect Entuziastov, Saratov 410049, Russia
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Welles HC, King HAD, Nettey L, Cavett N, Gorman J, Zhou T, Tsybovsky Y, Du R, Song K, Nguyen R, Ambrozak D, Ransier A, Schramm CA, Doria-Rose NA, Swanstrom AE, Hoxie JA, LaBranche C, Montefiori DC, Douek DC, Kwong PD, Mascola JR, Roederer M, Mason RD. Broad coverage of neutralization-resistant SIV strains by second-generation SIV-specific antibodies targeting the region involved in binding CD4. PLoS Pathog 2022; 18:e1010574. [PMID: 35709309 PMCID: PMC9242510 DOI: 10.1371/journal.ppat.1010574] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2021] [Revised: 06/29/2022] [Accepted: 05/06/2022] [Indexed: 11/19/2022] Open
Abstract
Both SIV and SHIV are powerful tools for evaluating antibody-mediated prevention and treatment of HIV-1. However, owing to a lack of rhesus-derived SIV broadly neutralizing antibodies (bnAbs), testing of bnAbs for HIV-1 prevention or treatment has thus far been performed exclusively in the SHIV NHP model using bnAbs from HIV-1-infected individuals. Here we describe the isolation and characterization of multiple rhesus-derived SIV bnAbs capable of neutralizing most isolates of SIV. Eight antibodies belonging to two clonal families, ITS102 and ITS103, which target unique epitopes in the CD4 binding site (CD4bs) region, were found to be broadly neutralizing and together neutralized all SIV strains tested. A rare feature of these bnAbs and two additional antibody families, ITS92 and ITS101, which mediate strain-specific neutralizing activity against SIV from sooty mangabeys (SIVsm), was their ability to achieve near complete (i.e. 100%) neutralization of moderately and highly neutralization-resistant SIV. Overall, these newly identified SIV bnAbs highlight the potential for evaluating HIV-1 prophylactic and therapeutic interventions using fully simian, rhesus-derived bnAbs in the SIV NHP model, thereby circumventing issues related to rapid antibody clearance of human-derived antibodies, Fc mismatch and limited genetic diversity of SHIV compared to SIV.
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Affiliation(s)
- Hugh C. Welles
- Vaccine Research Center, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Hannah A. D. King
- Vaccine Research Center, National Institutes of Health, Bethesda, Maryland, United States of America
- U.S. Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, Maryland, United States of America
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, Maryland, United States of America
| | - Leonard Nettey
- Vaccine Research Center, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Nicole Cavett
- Vaccine Research Center, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Jason Gorman
- Vaccine Research Center, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Tongqing Zhou
- Vaccine Research Center, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Yaroslav Tsybovsky
- Vaccine Research Center Electron Microscopy Unit, Cancer Research Technology Program, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, Frederick, Maryland, United States of America
| | - Renguang Du
- Vaccine Research Center, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Kaimei Song
- Vaccine Research Center, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Richard Nguyen
- Vaccine Research Center, National Institutes of Health, Bethesda, Maryland, United States of America
| | - David Ambrozak
- Vaccine Research Center, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Amy Ransier
- Vaccine Research Center, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Chaim A. Schramm
- Vaccine Research Center, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Nicole A. Doria-Rose
- Vaccine Research Center, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Adrienne E. Swanstrom
- AIDS and Cancer Virus Program, Frederick National Laboratory for Cancer Research, Frederick, Maryland, United States of America
| | - James A. Hoxie
- Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Celia LaBranche
- Department of Surgery, Duke University Medical Center, Durham, North Carolina, United States of America
| | - David C. Montefiori
- Department of Surgery, Duke University Medical Center, Durham, North Carolina, United States of America
| | - Daniel C. Douek
- Vaccine Research Center, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Peter D. Kwong
- Vaccine Research Center, National Institutes of Health, Bethesda, Maryland, United States of America
| | - John R. Mascola
- Vaccine Research Center, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Mario Roederer
- Vaccine Research Center, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Rosemarie D. Mason
- Vaccine Research Center, National Institutes of Health, Bethesda, Maryland, United States of America
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Roth KDR, Wenzel EV, Ruschig M, Steinke S, Langreder N, Heine PA, Schneider KT, Ballmann R, Fühner V, Kuhn P, Schirrmann T, Frenzel A, Dübel S, Schubert M, Moreira GMSG, Bertoglio F, Russo G, Hust M. Developing Recombinant Antibodies by Phage Display Against Infectious Diseases and Toxins for Diagnostics and Therapy. Front Cell Infect Microbiol 2021; 11:697876. [PMID: 34307196 PMCID: PMC8294040 DOI: 10.3389/fcimb.2021.697876] [Citation(s) in RCA: 35] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2021] [Accepted: 06/21/2021] [Indexed: 12/30/2022] Open
Abstract
Antibodies are essential molecules for diagnosis and treatment of diseases caused by pathogens and their toxins. Antibodies were integrated in our medical repertoire against infectious diseases more than hundred years ago by using animal sera to treat tetanus and diphtheria. In these days, most developed therapeutic antibodies target cancer or autoimmune diseases. The COVID-19 pandemic was a reminder about the importance of antibodies for therapy against infectious diseases. While monoclonal antibodies could be generated by hybridoma technology since the 70ies of the former century, nowadays antibody phage display, among other display technologies, is robustly established to discover new human monoclonal antibodies. Phage display is an in vitro technology which confers the potential for generating antibodies from universal libraries against any conceivable molecule of sufficient size and omits the limitations of the immune systems. If convalescent patients or immunized/infected animals are available, it is possible to construct immune phage display libraries to select in vivo affinity-matured antibodies. A further advantage is the availability of the DNA sequence encoding the phage displayed antibody fragment, which is packaged in the phage particles. Therefore, the selected antibody fragments can be rapidly further engineered in any needed antibody format according to the requirements of the final application. In this review, we present an overview of phage display derived recombinant antibodies against bacterial, viral and eukaryotic pathogens, as well as microbial toxins, intended for diagnostic and therapeutic applications.
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Affiliation(s)
- Kristian Daniel Ralph Roth
- Institut für Biochemie, Biotechnologie und Bioinformatik, Abteilung Biotechnologie, Technische Universität Braunschweig, Braunschweig, Germany
| | - Esther Veronika Wenzel
- Institut für Biochemie, Biotechnologie und Bioinformatik, Abteilung Biotechnologie, Technische Universität Braunschweig, Braunschweig, Germany.,Abcalis GmbH, Braunschweig, Germany
| | - Maximilian Ruschig
- Institut für Biochemie, Biotechnologie und Bioinformatik, Abteilung Biotechnologie, Technische Universität Braunschweig, Braunschweig, Germany
| | - Stephan Steinke
- Institut für Biochemie, Biotechnologie und Bioinformatik, Abteilung Biotechnologie, Technische Universität Braunschweig, Braunschweig, Germany
| | - Nora Langreder
- Institut für Biochemie, Biotechnologie und Bioinformatik, Abteilung Biotechnologie, Technische Universität Braunschweig, Braunschweig, Germany
| | - Philip Alexander Heine
- Institut für Biochemie, Biotechnologie und Bioinformatik, Abteilung Biotechnologie, Technische Universität Braunschweig, Braunschweig, Germany
| | - Kai-Thomas Schneider
- Institut für Biochemie, Biotechnologie und Bioinformatik, Abteilung Biotechnologie, Technische Universität Braunschweig, Braunschweig, Germany
| | - Rico Ballmann
- Institut für Biochemie, Biotechnologie und Bioinformatik, Abteilung Biotechnologie, Technische Universität Braunschweig, Braunschweig, Germany
| | - Viola Fühner
- Institut für Biochemie, Biotechnologie und Bioinformatik, Abteilung Biotechnologie, Technische Universität Braunschweig, Braunschweig, Germany
| | | | | | | | - Stefan Dübel
- Institut für Biochemie, Biotechnologie und Bioinformatik, Abteilung Biotechnologie, Technische Universität Braunschweig, Braunschweig, Germany.,Abcalis GmbH, Braunschweig, Germany.,YUMAB GmbH, Braunschweig, Germany
| | - Maren Schubert
- Institut für Biochemie, Biotechnologie und Bioinformatik, Abteilung Biotechnologie, Technische Universität Braunschweig, Braunschweig, Germany
| | | | - Federico Bertoglio
- Institut für Biochemie, Biotechnologie und Bioinformatik, Abteilung Biotechnologie, Technische Universität Braunschweig, Braunschweig, Germany
| | - Giulio Russo
- Institut für Biochemie, Biotechnologie und Bioinformatik, Abteilung Biotechnologie, Technische Universität Braunschweig, Braunschweig, Germany.,Abcalis GmbH, Braunschweig, Germany
| | - Michael Hust
- Institut für Biochemie, Biotechnologie und Bioinformatik, Abteilung Biotechnologie, Technische Universität Braunschweig, Braunschweig, Germany.,YUMAB GmbH, Braunschweig, Germany
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Han SY, Antoine A, Howard D, Chang B, Chang WS, Slein M, Deikus G, Kossida S, Duroux P, Lefranc MP, Sebra RP, Smith ML, Fofana IBF. Coupling of Single Molecule, Long Read Sequencing with IMGT/HighV-QUEST Analysis Expedites Identification of SIV gp140-Specific Antibodies from scFv Phage Display Libraries. Front Immunol 2018; 9:329. [PMID: 29545792 PMCID: PMC5837965 DOI: 10.3389/fimmu.2018.00329] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2017] [Accepted: 02/06/2018] [Indexed: 12/20/2022] Open
Abstract
The simian immunodeficiency virus (SIV)/macaque model of human immunodeficiency virus (HIV)/acquired immunodeficiency syndrome pathogenesis is critical for furthering our understanding of the role of antibody responses in the prevention of HIV infection, and will only increase in importance as macaque immunoglobulin (IG) gene databases are expanded. We have previously reported the construction of a phage display library from a SIV-infected rhesus macaque (Macaca mulatta) using oligonucleotide primers based on human IG gene sequences. Our previous screening relied on Sanger sequencing, which was inefficient and generated only a few dozen sequences. Here, we re-analyzed this library using single molecule, real-time (SMRT) sequencing on the Pacific Biosciences (PacBio) platform to generate thousands of highly accurate circular consensus sequencing (CCS) reads corresponding to full length single chain fragment variable. CCS data were then analyzed through the international ImMunoGeneTics information system® (IMGT®)/HighV-QUEST (www.imgt.org) to identify variable genes and perform statistical analyses. Overall the library was very diverse, with 2,569 different IMGT clonotypes called for the 5,238 IGHV sequences assigned to an IMGT clonotype. Within the library, SIV-specific antibodies represented a relatively limited number of clones, with only 135 different IMGT clonotypes called from 4,594 IGHV-assigned sequences. Our data did confirm that the IGHV4 and IGHV3 gene usage was the most abundant within the rhesus antibodies screened, and that these genes were even more enriched among SIV gp140-specific antibodies. Although a broad range of VH CDR3 amino acid (AA) lengths was observed in the unpanned library, the vast majority of SIV gp140-specific antibodies demonstrated a more uniform VH CDR3 length (20 AA). This uniformity was far less apparent when VH CDR3 were classified according to their clonotype (range: 9–25 AA), which we believe is more relevant for specific antibody identification. Only 174 IGKV and 588 IGLV clonotypes were identified within the VL sequences associated with SIV gp140-specific VH. Together, these data strongly suggest that the combination of SMRT sequencing with the IMGT/HighV-QUEST querying tool will facilitate and expedite our understanding of polyclonal antibody responses during SIV infection and may serve to rapidly expand the known scope of macaque V genes utilized during these responses.
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Affiliation(s)
- Seung Yub Han
- Biology Department, Boston College, Chestnut Hill, MA, United States
| | - Alesia Antoine
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, Icahn Institute of Genomics and Multiscale Biology, New York, NY, United States
| | - David Howard
- Biology Department, Boston College, Chestnut Hill, MA, United States
| | - Bryant Chang
- Biology Department, Boston College, Chestnut Hill, MA, United States
| | - Woo Sung Chang
- Biology Department, Boston College, Chestnut Hill, MA, United States
| | - Matthew Slein
- Biology Department, Boston College, Chestnut Hill, MA, United States
| | - Gintaras Deikus
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, Icahn Institute of Genomics and Multiscale Biology, New York, NY, United States
| | - Sofia Kossida
- The international ImMunoGeneTics information system® (IMGT®), Laboratoire d'ImmunoGénétique Moléculaire (LIGM), Institut de Génétique Humaine (IGH), UMR CNRS, Montpellier University, Montpellier, France
| | - Patrice Duroux
- The international ImMunoGeneTics information system® (IMGT®), Laboratoire d'ImmunoGénétique Moléculaire (LIGM), Institut de Génétique Humaine (IGH), UMR CNRS, Montpellier University, Montpellier, France
| | - Marie-Paule Lefranc
- The international ImMunoGeneTics information system® (IMGT®), Laboratoire d'ImmunoGénétique Moléculaire (LIGM), Institut de Génétique Humaine (IGH), UMR CNRS, Montpellier University, Montpellier, France
| | - Robert P Sebra
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, Icahn Institute of Genomics and Multiscale Biology, New York, NY, United States
| | - Melissa L Smith
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, Icahn Institute of Genomics and Multiscale Biology, New York, NY, United States
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