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Madsen AV, Mejias-Gomez O, Pedersen LE, Preben Morth J, Kristensen P, Jenkins TP, Goletz S. Structural trends in antibody-antigen binding interfaces: a computational analysis of 1833 experimentally determined 3D structures. Comput Struct Biotechnol J 2024; 23:199-211. [PMID: 38161735 PMCID: PMC10755492 DOI: 10.1016/j.csbj.2023.11.056] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2023] [Revised: 11/27/2023] [Accepted: 11/28/2023] [Indexed: 01/03/2024] Open
Abstract
Antibodies are attractive therapeutic candidates due to their ability to bind cognate antigens with high affinity and specificity. Still, the underlying molecular rules governing the antibody-antigen interface remain poorly understood, making in silico antibody design inherently difficult and keeping the discovery and design of novel antibodies a costly and laborious process. This study investigates the characteristics of antibody-antigen binding interfaces through a computational analysis of more than 850,000 atom-atom contacts from the largest reported set of antibody-antigen complexes with 1833 nonredundant, experimentally determined structures. The analysis compares binding characteristics of conventional antibodies and single-domain antibodies (sdAbs) targeting both protein- and peptide antigens. We find clear patterns in the number antibody-antigen contacts and amino acid frequencies in the paratope. The direct comparison of sdAbs and conventional antibodies helps elucidate the mechanisms employed by sdAbs to compensate for their smaller size and the fact that they harbor only half the number of complementarity-determining regions compared to conventional antibodies. Furthermore, we pinpoint antibody interface hotspot residues that are often found at the binding interface and the amino acid frequencies at these positions. These findings have direct potential applications in antibody engineering and the design of improved antibody libraries.
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Affiliation(s)
- Andreas V. Madsen
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Kgs. Lyngby, Denmark
| | - Oscar Mejias-Gomez
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Kgs. Lyngby, Denmark
| | - Lasse E. Pedersen
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Kgs. Lyngby, Denmark
| | - J. Preben Morth
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Kgs. Lyngby, Denmark
| | - Peter Kristensen
- Department of Chemistry and Bioscience, Aalborg University, Aalborg, Denmark
| | - Timothy P. Jenkins
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Kgs. Lyngby, Denmark
| | - Steffen Goletz
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Kgs. Lyngby, Denmark
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Heremans J, Maximilian Awad R, Bridoux J, Ertveldt T, Caveliers V, Madder A, Hoogenboom R, Devoogdt N, Ballet S, Hernot S, Breckpot K, Martin C. Sustained release of a human PD-L1 single-domain antibody using peptide-based hydrogels. Eur J Pharm Biopharm 2024; 196:114183. [PMID: 38246566 DOI: 10.1016/j.ejpb.2024.114183] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2024] [Accepted: 01/14/2024] [Indexed: 01/23/2024]
Abstract
Monoclonal antibodies (mAbs) targeting the immune checkpoint axis, which contains the programmed cell death protein-1 (PD-1) and its ligand PD-L1, revolutionized the field of oncology. Unfortunately, the large size of mAbs and the presence of an Fc fraction limit their tumor penetrative capacities and support off-target effects, potentially resulting in unresponsive patients and immune-related adverse events (irAEs) respectively. Single-domain antibodies (sdAbs) are ten times smaller than conventional mAbs and represent an emerging antibody subclass that has been proposed as next generation immune checkpoint inhibitor (ICI) therapeutics. They demonstrate favorable characteristics, such as an excellent stability, high antigen-binding affinity and an enhanced tumor penetration. Because sdAbs have a short half-life, methods to prolong their presence in the circulation and at the target site might be necessary in some cases to unfold their full therapeutic potential. In this study, we investigated a peptide-based hydrogel as an injectable biomaterial depot formulation for the sustained release of the human PD-L1 sdAb K2. We showed that a hydrogel composed of the amphipathic hexapeptide hydrogelator H-FQFQFK-NH2 prolonged the in vivo release of K2 after subcutaneous (s.c.) injection, up to at least 72 h, as monitored by SPECT/CT and fluorescence imaging. Additionally, after encapsulation in the hydrogel and s.c. administration, a significantly extended systemic presence and tumor uptake of K2 was observed in mice bearing a melanoma tumor expressing human PD-L1. Altogether, this study describes how peptide hydrogels can be exploited to provide the sustained release of sdAbs, thereby potentially enhancing its clinical and therapeutic effects.
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Affiliation(s)
- Julie Heremans
- Research Group of Organic Chemistry, Vrije Universiteit Brussel, B-1050 Brussels, Belgium
| | - Robin Maximilian Awad
- Laboratory for Molecular and Cellular Therapy, Department of Biomedical Sciences, Vrije Universiteit Brussel, 1090 Brussels, Belgium
| | - Jessica Bridoux
- In Vivo Cellular and Molecular Imaging Laboratory, Vrije Universiteit Brussel, 1090 Brussels, Belgium
| | - Thomas Ertveldt
- Laboratory for Molecular and Cellular Therapy, Department of Biomedical Sciences, Vrije Universiteit Brussel, 1090 Brussels, Belgium
| | - Vicky Caveliers
- In Vivo Cellular and Molecular Imaging Laboratory, Vrije Universiteit Brussel, 1090 Brussels, Belgium
| | - Annemieke Madder
- Organic and Biomimetic Chemistry Research Group, Ghent University, 9000 Ghent, Belgium
| | - Richard Hoogenboom
- Supramolecular Chemistry Group, Centre of Macromolecular Chemistry (CMaC), Department of Organic and Macromolecular Chemistry, Ghent University, 9000 Ghent, Belgium
| | - Nick Devoogdt
- In Vivo Cellular and Molecular Imaging Laboratory, Vrije Universiteit Brussel, 1090 Brussels, Belgium
| | - Steven Ballet
- Research Group of Organic Chemistry, Vrije Universiteit Brussel, B-1050 Brussels, Belgium
| | - Sophie Hernot
- In Vivo Cellular and Molecular Imaging Laboratory, Vrije Universiteit Brussel, 1090 Brussels, Belgium
| | - Karine Breckpot
- Laboratory for Molecular and Cellular Therapy, Department of Biomedical Sciences, Vrije Universiteit Brussel, 1090 Brussels, Belgium
| | - Charlotte Martin
- Research Group of Organic Chemistry, Vrije Universiteit Brussel, B-1050 Brussels, Belgium
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Chen F, Liu Z, Kang W, Jiang F, Yang X, Yin F, Zhou Z, Li Z. Single-domain antibodies against SARS-CoV-2 RBD from a two-stage phage screening of universal and focused synthetic libraries. BMC Infect Dis 2024; 24:199. [PMID: 38350843 PMCID: PMC10865538 DOI: 10.1186/s12879-024-09022-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2023] [Accepted: 01/16/2024] [Indexed: 02/15/2024] Open
Abstract
BACKGROUND Coronavirus disease 2019 (COVID-19) is an evolving global pandemic, and nanobodies, as well as other single-domain antibodies (sdAbs), have been recognized as a potential diagnostic and therapeutic tool for infectious diseases. High-throughput screening techniques such as phage display have been developed as an alternative to in vivo immunization for the discovery of antibody-like target-specific binders. METHODS We designed and constructed a highly diverse synthetic phage library sdAb-U (single-domain Antibody - Universal library ) based on a human framework. The SARS-CoV-2 receptor-binding domain (RBD) was expressed and purified. The universal library sdAb-U was panned against the RBD protein target for two rounds, followed by monoclonal phage ELISA (enzyme-linked immunosorbent assay) to identify RBD-specific binders (the first stage). High-affinity binders were sequenced and the obtained CDR1 and CDR2 sequences were combined with fully randomized CDR3 to construct a targeted (focused) phage library sdAb-RBD, for subsequent second-stage phage panning (also two rounds) and screening. Then, sequences with high single-to-background ratios in phage ELISA were selected for expression. The binding affinities of sdAbs to RBD were measured by an ELISA-based method. In addition, we conducted competition ELISA (using ACE2 ectodomain S19-D615) and SARS-CoV-2 pseudovirus neutralization assays for the high-affinity RBD-binding sdAb39. RESULTS Significant enrichments were observed in both the first-stage (universal library) and the second-stage (focused library) phage panning. Five RBD-specific binders were identified in the first stage with high ELISA signal-to-background ratios. In the second stage, we observed a much higher possibility of finding RBD-specific clones in phage ELISA. Among 45 selected RBD-positive sequences, we found eight sdAbs can be well expressed, and five of them show high-affinity to RBD (EC50 < 100nM). We finally found that sdAb39 (EC50 ~ 4nM) can compete with ACE2 for binding to RBD. CONCLUSION Overall, this two-stage strategy of synthetic phage display libraries enables rapid selection of SARS-CoV-2 RBD sdAb with potential therapeutic activity, and this two-stage strategy can potentially be used for rapid discovery of sdAbs against other targets.
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Affiliation(s)
- Fangfang Chen
- Department of Pharmacy, Shenzhen Hospital, Southern Medical University, Shenzhen, China
| | - Zhihong Liu
- Pingshan Translational Medicine Center, Shenzhen Bay Laboratory, Shenzhen, China
| | - Wei Kang
- NanoAI Biotech Co., Ltd, Pingshan District, Shenzhen, China
| | - Fan Jiang
- NanoAI Biotech Co., Ltd, Pingshan District, Shenzhen, China.
| | - Xixiao Yang
- Department of Pharmacy, Shenzhen Hospital, Southern Medical University, Shenzhen, China
| | - Feng Yin
- Pingshan Translational Medicine Center, Shenzhen Bay Laboratory, Shenzhen, China
- State Key Laboratory of Chemical Oncogenomics, School of Chemical Biology and Biotechnology, Peking University Shenzhen Graduate School, Shenzhen, China
| | - Ziyuan Zhou
- National Cancer Center, National Clinical Research Center for Cancer/Cancer Hospital & Shenzhen Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Shenzhen, China
| | - Zigang Li
- Pingshan Translational Medicine Center, Shenzhen Bay Laboratory, Shenzhen, China.
- State Key Laboratory of Chemical Oncogenomics, School of Chemical Biology and Biotechnology, Peking University Shenzhen Graduate School, Shenzhen, China.
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Nikkhoi SK, Heydarzadeh H, Vandavasi VG, Yang G, Louro P, Polunas M, Owji H, Hatefi A. A high affinity and specificity anti-HER2 single-domain antibody (VHH) that targets trastuzumab's epitope with versatile biochemical, biological, and medical applications. Immunol Res 2024; 72:103-118. [PMID: 37632647 PMCID: PMC10842867 DOI: 10.1007/s12026-023-09418-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2023] [Accepted: 08/19/2023] [Indexed: 08/28/2023]
Abstract
In the past decade, various single-domain antibodies from llamas, also known as VHH or nanobody, have been discovered with applications in tumor imaging and cancer therapy. However, the potential application of anti-HER2 VHHs as a diagnostic tool suitable for ELISA, flow cytometry, cell imaging, bispecific antibody engineering, and immunohistochemistry has not been fully elucidated. To investigate this potential, HER2 antigen was expressed in HEK293 F cells, purified, and used to immunize llama. Using phage display, anti-HER2 VHHs with high affinity and specificity were isolated, sequenced, and constructed with a Histag and c-Myc tag. The constructed anti-HER2 VHHs were then expressed in E. coli, purified, and evaluated for their use in ELISA, flow cytometry, cell imaging, and immunohistochemistry. The affinities of the anti-HER2 VHHs toward the HER2 antigen were determined using biolayer interferometry. Furthermore, the binding sites of the anti-HER2 VHHs were evaluated by epitope mapping and in silico modeling and docking. Here, we report the sequence of an anti-HER2 VHH with high affinity (sub-nanomolar), specificity, and selectivity. This VHH binds to the same epitope as trastuzumab and can be utilized to generate bispecific antibodies or used as a diagnostic tool to differentiate HER2+ from HER2- antigens on plates, cells, and tissues. This discovery has broad applications in biochemical, biological, and medical sciences.
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Affiliation(s)
- Shahryar Khoshtinat Nikkhoi
- Department of Pharmaceutics, Rutgers University, Room 222, 160 Frelinghuysen Road, Piscataway, NJ, 08854, USA
| | - Hediyeh Heydarzadeh
- Department of Pharmaceutics, Rutgers University, Room 222, 160 Frelinghuysen Road, Piscataway, NJ, 08854, USA
| | - Venu Gopal Vandavasi
- Department of Chemistry, Biophysics Core Facility, Princeton University, Princeton, NJ, 08544, USA
| | - Ge Yang
- Department of Pharmaceutics, Rutgers University, Room 222, 160 Frelinghuysen Road, Piscataway, NJ, 08854, USA
| | - Pedro Louro
- Rutgers Research Pathology Services, Rutgers University, Piscataway, NJ, 08854, USA
| | - Marianne Polunas
- Rutgers Research Pathology Services, Rutgers University, Piscataway, NJ, 08854, USA
| | - Hajar Owji
- Department of Pharmaceutics, Rutgers University, Room 222, 160 Frelinghuysen Road, Piscataway, NJ, 08854, USA
| | - Arash Hatefi
- Department of Pharmaceutics, Rutgers University, Room 222, 160 Frelinghuysen Road, Piscataway, NJ, 08854, USA.
- Cancer Pharmacology Program, Rutgers Cancer Institute of New Jersey, New Brunswick, NJ, 08901, USA.
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Matthys A, Saelens X. Promises and challenges of single-domain antibodies to control influenza. Antiviral Res 2024; 222:105807. [PMID: 38219914 DOI: 10.1016/j.antiviral.2024.105807] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2023] [Revised: 01/05/2024] [Accepted: 01/09/2024] [Indexed: 01/16/2024]
Abstract
The World Health Organization advices the use of a quadrivalent vaccine as prophylaxis against influenza, to prevent severe influenza-associated disease and -mortality, and to keep up with influenza antigenic diversity. Different small molecule antivirals to treat influenza have become available. However, emergence of drug resistant influenza viruses has been observed upon use of these antivirals. An appealing alternative approach to prevent or treat influenza is the use of antibody-based antivirals, such as conventional monoclonal antibodies and single-domain antibodies (sdAbs). The surface of the influenza A and B virion is decorated with hemagglutinin molecules, which act as receptor-binding and membrane fusion proteins and represent the main target of neutralizing antibodies. SdAbs that target influenza A and B hemagglutinin have been described. In addition, sdAbs directed against the influenza A virus neuraminidase have been reported, whereas no sdAbs targeting influenza B neuraminidase have been described to date. SdAbs directed against influenza A matrix protein 2 or its ectodomain have been reported, while no sdAbs have been described targeting the influenza B matrix protein 2. Known for their high specificity, ease of production and formatting, sdAb-based antivirals could be a major leap forward in influenza control.
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Affiliation(s)
- Arne Matthys
- VIB Center for Medical Biotechnology, VIB, Ghent, Belgium; Department of Biochemistry and Microbiology, Ghent University, Ghent, Belgium
| | - Xavier Saelens
- VIB Center for Medical Biotechnology, VIB, Ghent, Belgium; Department of Biochemistry and Microbiology, Ghent University, Ghent, Belgium.
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6
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Lei EK, Ryan S, van Faassen H, Foss M, Robotham A, Baltat I, Fulton K, Henry KA, Chen W, Hussack G. Isolation and characterization of a VHH targeting the Acinetobacter baumannii cell surface protein CsuA/B. Appl Microbiol Biotechnol 2023:10.1007/s00253-023-12594-1. [PMID: 37284893 DOI: 10.1007/s00253-023-12594-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2023] [Revised: 04/18/2023] [Accepted: 05/15/2023] [Indexed: 06/08/2023]
Abstract
Acinetobacter baumannii is a Gram-negative bacterial pathogen that exhibits high intrinsic resistance to antimicrobials, with treatment often requiring the use of last-resort antibiotics. Antibiotic-resistant strains have become increasingly prevalent, underscoring a need for new therapeutic interventions. The aim of this study was to use A. baumannii outer membrane vesicles as immunogens to generate single-domain antibodies (VHHs) against bacterial cell surface targets. Llama immunization with the outer membrane vesicle preparations from four A. baumannii strains (ATCC 19606, ATCC 17961, ATCC 17975, and LAC-4) elicited a strong heavy-chain IgG response, and VHHs were selected against cell surface and/or extracellular targets. For one VHH, OMV81, the target antigen was identified using a combination of gel electrophoresis, mass spectrometry, and binding studies. Using these techniques, OMV81 was shown to specifically recognize CsuA/B, a protein subunit of the Csu pilus, with an equilibrium dissociation constant of 17 nM. OMV81 specifically bound to intact A. baumannii cells, highlighting its potential use as a targeting agent. We anticipate the ability to generate antigen-specific antibodies against cell surface A. baumannii targets could provide tools for further study and treatment of this pathogen. KEY POINTS: •Llama immunization with bacterial OMV preparations for VHH generation •A. baumannii CsuA/B, a pilus subunit, identified by mass spectrometry as VHH target •High-affinity and specific VHH binding to CsuA/B and A. baumannii cells.
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Affiliation(s)
- Eric K Lei
- Human Health Therapeutics Research Centre, National Research Council Canada, Ottawa, Ontario, Canada
| | - Shannon Ryan
- Human Health Therapeutics Research Centre, National Research Council Canada, Ottawa, Ontario, Canada
| | - Henk van Faassen
- Human Health Therapeutics Research Centre, National Research Council Canada, Ottawa, Ontario, Canada
| | - Mary Foss
- Human Health Therapeutics Research Centre, National Research Council Canada, Ottawa, Ontario, Canada
| | - Anna Robotham
- Human Health Therapeutics Research Centre, National Research Council Canada, Ottawa, Ontario, Canada
| | - Isabel Baltat
- Human Health Therapeutics Research Centre, National Research Council Canada, Ottawa, Ontario, Canada
| | - Kelly Fulton
- Human Health Therapeutics Research Centre, National Research Council Canada, Ottawa, Ontario, Canada
| | - Kevin A Henry
- Human Health Therapeutics Research Centre, National Research Council Canada, Ottawa, Ontario, Canada
- Department of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa, Ontario, Canada
| | - Wangxue Chen
- Human Health Therapeutics Research Centre, National Research Council Canada, Ottawa, Ontario, Canada
- Department of Biology, Brock University, St. Catharines, Ontario, Canada
| | - Greg Hussack
- Human Health Therapeutics Research Centre, National Research Council Canada, Ottawa, Ontario, Canada.
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Hirao A, Nagatoishi S, Ikeuchi E, Yamawaki T, Mori C, Nakakido M, Tsumoto K. Design of single-domain VHH antibodies to increase the binding activity in SPR amine coupling. Biochem Biophys Res Commun 2023; 663:54-60. [PMID: 37119766 DOI: 10.1016/j.bbrc.2023.04.048] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2023] [Accepted: 04/17/2023] [Indexed: 05/01/2023]
Abstract
Single-domain antibodies, or VHH, nanobodies, are attractive tools in biotechnology and pharmaceuticals due to their favorable biophysical properties. Single-domain antibodies have potential for use in sensing materials to detect antigens, and in this paper, we propose a generic design strategy of single-domain antibodies for the highly efficient use of immobilized antibodies on a sensing substrate. Amine coupling was used to immobilize the single-domain antibodies on the substrate through a robust covalent bond. First, for two model single-domain antibodies with lysines at four highly conserved positions (K48, K72, K84, and K95), we mutated the lysines to alanine and measured the binding activity of the mutants (the percentage of immobilized antibodies that can bind antigen) using surface plasmon resonance. The two model single-domain antibodies tended to have higher binding activities when K72, which is close to the antigen binding site, was mutated. Adding a Lys-tag to the C-terminus of single-domain antibodies also increased the binding activity. We also mutated the lysine for another model single-domain antibodies with the lysine in a different position than the four residues mentioned above and measured the binding activity. Thus, single-domain antibodies immobilized in an orientation accessible to the antigen tended to have a high binding activity, provided that the physical properties of the single-domain antibodies themselves (affinity and structural stability) were not significantly reduced. Specifically, the design strategy of single-domain antibodies with high binding activity included mutating the lysine at or near the antigen binding site, adding a Lys-tag to the C-terminus, and mutating a residue away from the antigen binding site to lysine. It is noteworthy that mutating K72 close to the antigen binding site was more effective in increasing the binding activity than Lys-tag addition, and immobilization at the N-terminus close to the antigen binding site did not have such a negative effect on the binding activity compared to immobilization at the K72.
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Affiliation(s)
- Atsunori Hirao
- Department of Chemistry and Biotechnology, School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-8656, Japan
| | - Satoru Nagatoishi
- The Institute of Medical Science, The University of Tokyo, 4-6-1 Shirokanedai, Minato-ku, Tokyo, 108-8639, Japan.
| | - Emina Ikeuchi
- Department of Bioengineering, School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-8656, Japan
| | - Tsukushi Yamawaki
- Department of Chemistry and Biotechnology, School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-8656, Japan
| | - Chinatsu Mori
- Department of Chemistry and Biotechnology, School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-8656, Japan
| | - Makoto Nakakido
- Department of Chemistry and Biotechnology, School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-8656, Japan; Department of Bioengineering, School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-8656, Japan
| | - Kouhei Tsumoto
- Department of Chemistry and Biotechnology, School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-8656, Japan; The Institute of Medical Science, The University of Tokyo, 4-6-1 Shirokanedai, Minato-ku, Tokyo, 108-8639, Japan; Department of Bioengineering, School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-8656, Japan.
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Rossotti MA, Trempe F, van Faassen H, Hussack G, Arbabi-Ghahroudi M. Isolation and Characterization of Single-Domain Antibodies from Immune Phage Display Libraries. Methods Mol Biol 2023; 2702:107-147. [PMID: 37679618 DOI: 10.1007/978-1-0716-3381-6_7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/09/2023]
Abstract
Naturally occurring heavy chain antibodies (HCAbs) in Camelidae species were a surprise discovery in 1993 by Hamers et al. Since that time, antibody fragments derived from HCAbs have garnered considerable attention by researchers and biotechnology companies. Due to their biophysico-chemical advantages over conventional antibody fragments, camelid single-domain antibodies (sdAbs, VHHs, nanobodies) are being increasingly utilized as viable immunotherapeutic modalities. Currently there are multiple VHH-based therapeutic agents in different phases of clinical trials in various formats such as bi- and multivalent, bi- and multi-specific, CAR-T, and antibody-drug conjugates. The first approved VHH, a bivalent humanized VHH (caplacizumab), was approved for treating rare blood clotting disorders in 2018 by the EMA and the FDA in 2019. This was followed by the approval of an anti-BCMA VHH-based CAR-T cell product in 2022 (ciltacabtagene autoleucel; CARVYKTI™) and more recently a trivalent antitumor necrosis factor alpha-based VHH drug (ozoralizumab; Nanozora®) in Japan for the treatment of rheumatoid arthritis. In this chapter we provide protocols describing the latest developments in isolating antigen-specific VHHs including llama immunization, construction of phage-displayed libraries, phage panning and screening of the soluble VHHs by ELISA, affinity measurements by surface plasmon resonance, functional cell binding by flow cytometry, and additional validation by immunoprecipitation. We present and discuss comprehensive, step-by-step methods for isolating and characterization of antigen-specific VHHs. This includes protocols for expression, biotinylation, purification, and characterization of the isolated VHHs. To demonstrate the feasibility of the entire strategy, we present examples of VHHs previously isolated and characterized in our laboratory.
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Affiliation(s)
- Martin A Rossotti
- Human Health Therapeutics Research Centre, National Research Council Canada, Ottawa, ON, Canada
| | - Frederic Trempe
- Human Health Therapeutics Research Centre, National Research Council Canada, Ottawa, ON, Canada
| | - Henk van Faassen
- Human Health Therapeutics Research Centre, National Research Council Canada, Ottawa, ON, Canada
| | - Greg Hussack
- Human Health Therapeutics Research Centre, National Research Council Canada, Ottawa, ON, Canada
| | - Mehdi Arbabi-Ghahroudi
- Human Health Therapeutics Research Centre, National Research Council Canada, Ottawa, ON, Canada.
- Department of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa, ON, Canada.
- Department of Biology, Carleton University, Ottawa, ON, Canada.
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9
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Lowden MJ, Lei EK, Hussack G, Henry KA. Applications of High-Throughput DNA Sequencing to Single-Domain Antibody Discovery and Engineering. Methods Mol Biol 2023; 2702:489-540. [PMID: 37679637 DOI: 10.1007/978-1-0716-3381-6_26] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/09/2023]
Abstract
Next-generation DNA sequencing (NGS) technologies have made it possible to interrogate antibody repertoires to unprecedented depths, typically via sequencing of cDNAs encoding immunoglobulin variable domains. In the absence of heavy-light chain pairing, the variable domains of heavy chain-only antibodies (HCAbs), referred to as single-domain antibodies (sdAbs), are uniquely amenable to NGS analyses. In this chapter, we provide simple and rapid protocols for producing and sequencing multiplexed immunoglobulin variable domain (VHH, VH, or VL) amplicons derived from a variety of sources using the Illumina MiSeq platform. Generation of such amplicon libraries is relatively inexpensive, requiring no specialized equipment and only a limited set of PCR primers. We also present several applications of NGS to sdAb discovery and engineering, including: (1) evaluation of phage-displayed sdAb library sequence diversity and monitoring of panning experiments; (2) identification of sdAbs of predetermined epitope specificity following competitive elution of phage-displayed sdAb libraries; (3) direct selection of B cells expressing antigen-specific, membrane-bound HCAb using antigen-coupled magnetic beads and identification of antigen-specific sdAbs, and (4) affinity maturation of lead sdAbs using tandem phage display selection and NGS. These methods can easily be adapted to other types of proteins and libraries and expand the utility of in vitro display technology.
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Affiliation(s)
- Michael J Lowden
- Human Health Therapeutics Research Centre, National Research Council Canada, Ottawa, ON, Canada
| | - Eric K Lei
- Human Health Therapeutics Research Centre, National Research Council Canada, Ottawa, ON, Canada
| | - Greg Hussack
- Human Health Therapeutics Research Centre, National Research Council Canada, Ottawa, ON, Canada
| | - Kevin A Henry
- Human Health Therapeutics Research Centre, National Research Council Canada, Ottawa, ON, Canada.
- Department of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa, ON, Canada.
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Miyakawa Y, Imada K, Ichikawa S, Uchiyama H, Ueda Y, Yonezawa A, Fujitani S, Ogawa Y, Matsushita T, Asakura H, Nishio K, Suzuki K, Hashimoto Y, Murakami H, Tahara S, Tanaka T, Matsumoto M. The efficacy and safety of caplacizumab in Japanese patients with immune-mediated thrombotic thrombocytopenic purpura: an open-label phase 2/3 study. Int J Hematol 2023; 117:366-377. [PMID: 36427162 PMCID: PMC9970947 DOI: 10.1007/s12185-022-03495-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2022] [Revised: 11/09/2022] [Accepted: 11/09/2022] [Indexed: 11/27/2022]
Abstract
Caplacizumab is an anti-von Willebrand factor humanized single-variable-domain immunoglobulin fragment whose efficacy and safety in immune-mediated thrombotic thrombocytopenia purpura (iTTP) have been demonstrated in international studies. This prospective, open-label phase 2/3 study evaluated caplacizumab 10 mg administered daily during plasma exchange and for 30 days afterward, in combination with immunosuppressive treatment, in Japanese adults with a clinical diagnosis of iTTP (new or recurrent). The primary endpoint was prevention of iTTP recurrence; key secondary endpoints included time to platelet count response, time to organ damage normalization, and safety. Among 21 treated patients, 1 of 15 (6.7%) evaluable patients developed iTTP recurrence. Median time to normalization was 2.79 days for platelet count and 2.65 days for organ damage markers (n = 15). Treatment-emergent adverse events (TEAEs) were mostly mild to moderate in severity; the most frequently reported caplacizumab-related TEAEs were increased alanine aminotransferase, epistaxis, and gastrointestinal hemorrhage (all in 9.5% of patients). At least one bleeding event was reported in 7 of 21 patients (33%). Caplacizumab was effective in Japanese patients with iTTP, with a low rate of iTTP recurrence, rapid normalization of platelet counts and organ damage markers, and no unexpected TEAEs. Trial registration: ClinicalTrials.gov identifier, NCT04074187.
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Affiliation(s)
- Yoshitaka Miyakawa
- Department of Hematology, Saitama Medical University Hospital, Saitama, Japan
| | - Kazunori Imada
- Department of Hematology, Japanese Red Cross Osaka Hospital, Osaka, Japan
| | - Satoshi Ichikawa
- Department of Hematology, Tohoku University Hospital, Sendai, Japan
| | - Hitoji Uchiyama
- Department of Hematology, Japanese Red Cross Kyoto Daiichi Hospital, Kyoto, Japan
| | - Yasunori Ueda
- Department of Hematology/Oncology, Kurashiki Central Hospital, Kurashiki, Japan
| | - Akihito Yonezawa
- Department of Hematology, Kokura Memorial Hospital, Kitakyushu, Japan
| | - Shigeki Fujitani
- Department of Emergency and Critical Care Medicine, St. Marianna University School of Medicine Hospital, Kawasaki, Japan
| | - Yoshiyuki Ogawa
- Department of Hematology, Gunma University Hospital, Maebashi, Japan
| | - Tadashi Matsushita
- Department of Transfusion Medicine, Nagoya University Hospital, Nagoya, Japan
| | - Hidesaku Asakura
- Department of Hematology, Kanazawa University Hospital, Kanazawa, Japan
| | - Kenji Nishio
- Department of General Medicine, Nara Medical University Hospital, Kashihara, Japan
| | - Kodai Suzuki
- Department of Hematology, Saitama Medical University Hospital, Saitama, Japan
| | | | | | | | | | - Masanori Matsumoto
- Department of Blood Transfusion Medicine, Nara Medical University, 840 Shijyo-Cho, Kashihara, Nara, 634-8522, Japan.
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11
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Guilbaud A, Pecorari F. Construction of Synthetic VHH Libraries in Ribosome Display Format. Methods Mol Biol 2023; 2681:19-31. [PMID: 37405640 DOI: 10.1007/978-1-0716-3279-6_2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/06/2023]
Abstract
Single-domain antibodies, or VHH, represent an attractive molecular basis to design affinity proteins with favorable properties. Beyond high affinity and specificity for their cognate target, they usually show high stability and high production yields in bacteria, yeast, or mammalian cells. In addition to these favorable properties, their ease of engineering makes them useful for many applications. Until the past few years, the generation of VHH involved the immunization of a Camelidae with the target antigen, followed by a phage display selection using phage libraries encoding the VHH repertoire of the animal blood sample. However, this approach is constrained by the accessibility to the animals, and the output relies on the animal's immune system.Recently, synthetic VHH libraries have been designed to avoid the use of animals. Here, we describe the construction of VHH combinatorial libraries and their use for the selection of binders by ribosome display, a fully in vitro selection technique.
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Affiliation(s)
- Audrey Guilbaud
- Nantes Université, Univ Angers, INSERM, CNRS, Immunology and New Concepts in ImmunoTherapy, INCIT, UMR 1302/EMR6001, Nantes, France
| | - Frédéric Pecorari
- Nantes Université, Univ Angers, INSERM, CNRS, Immunology and New Concepts in ImmunoTherapy, INCIT, UMR 1302/EMR6001, Nantes, France.
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12
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Chen Y, Zhu S, Fu J, Lin J, Sun Y, Lv G, Xie M, Xu T, Qiu L. Development of a radiolabeled site-specific single-domain antibody positron emission tomography probe for monitoring PD-L1 expression in cancer. J Pharm Anal 2022; 12:869-78. [PMID: 36605578 DOI: 10.1016/j.jpha.2022.09.001] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2022] [Revised: 09/06/2022] [Accepted: 09/13/2022] [Indexed: 01/07/2023] Open
Abstract
Despite advances in immunotherapy for the treatment of cancers, not all patients can benefit from programmed cell death ligand 1 (PD-L1) immune checkpoint blockade therapy. Anti-PD-L1 therapeutic effects reportedly correlate with the PD-L1 expression level; hence, accurate detection of PD-L1 expression can guide immunotherapy to achieve better therapeutic effects. Therefore, based on the high affinity antibody Nb109, a new site-specifically radiolabeled tracer, 68Ga-NODA-cysteine, aspartic acid, and valine (CDV)-Nb109, was designed and synthesized to accurately monitor PD-L1 expression. The tracer 68Ga-NODA-CDV-Nb109 was obtained using a site-specific conjugation strategy with a radiochemical yield of about 95% and radiochemical purity of 97%. It showed high affinity for PD-L1 with a dissociation constant of 12.34 ± 1.65 nM. Both the cell uptake assay and positron emission tomography (PET) imaging revealed higher tracer uptake in PD-L1-positive A375-hPD-L1 and U87 tumor cells than in PD-L1-negative A375 tumor cells. Meanwhile, dynamic PET imaging of a NCI-H1299 xenograft indicated that doxorubicin could upregulate PD-L1 expression, allowing timely interventional immunotherapy. In conclusion, this tracer could sensitively and dynamically monitor changes in PD-L1 expression levels in different cancers and help screen patients who can benefit from anti-PD-L1 immunotherapy.
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13
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Wang M, Wei L, Xiang H, Ren B, Liu X, Jiang L, Yang N, Shi J. A megadiverse naïve library derived from numerous camelids for efficient and rapid development of VHH antibodies. Anal Biochem 2022; 657:114871. [PMID: 36108795 DOI: 10.1016/j.ab.2022.114871] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2021] [Revised: 07/20/2022] [Accepted: 08/17/2022] [Indexed: 11/01/2022]
Abstract
The field of antibody development is under pressure to meet rising demands for speed, cost-effectiveness, efficacy, reliability, and large-scale production. It is costly and time-consuming to immunize animals and build a single-domain antibody (sdAb) library for each target. Using the variable domain (VHH) of heavy-chain only antibodies (HcAbs) derived from blood samples of 75 non-immunized camelid animals (51 alpacas, 13 llamas, 11 Bactrian camels), and spleens from two Bactrian camels, a naïve sdAb library with extensive megadiversity and reusability was constructed. The library was evaluated using next-generation DNA sequencing (NGS) and was found to contain hundreds of billions of unique clones. To confirm the availability of target-specific VHHs, a naive library was screened for a variety of targets. At least two VHH candidates were extracted for each target using a 20-day selection pipeline. Some binders had ultrahigh potencies, with binding affinities in the nanomolar range. This naïve library, in particular, offers the possibility of acquiring unique antibodies targeting antigens of interest with low feasible dissociation constant (kD) without the time, effort, and price associated in producing antibodies in animals via antigen injection. Overall, the study shows that the megadiverse naïve library provides a rapid, adaptable, and easy platform for antibody creation, emphasizing its therapeutic and diagnostic implications.
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Affiliation(s)
- Meiniang Wang
- BGI-Shenzhen, Shenzhen, 518103, China; China National GeneBank, BGI-Shenzhen, Shenzhen, 518120, China
| | - Likun Wei
- Department of Biomedical Sciences, City University of Hong Kong, Hong Kong SAR, China; Biotechnology and Health Centre, City University of Hong Kong, Shenzhen Research Institute, Shenzhen, China
| | - Haitao Xiang
- BGI-Shenzhen, Shenzhen, 518103, China; China National GeneBank, BGI-Shenzhen, Shenzhen, 518120, China; BGI Education Center, University of Chinese Academy of Sciences, Shenzhen, 518083, China
| | - Bingzhao Ren
- BGI-Shenzhen, Shenzhen, 518103, China; China National GeneBank, BGI-Shenzhen, Shenzhen, 518120, China
| | - Xiaopan Liu
- BGI-Shenzhen, Shenzhen, 518103, China; China National GeneBank, BGI-Shenzhen, Shenzhen, 518120, China; BGI Education Center, University of Chinese Academy of Sciences, Shenzhen, 518083, China
| | - Lin Jiang
- BGI-Shenzhen, Shenzhen, 518103, China
| | - Naibo Yang
- BGI-Shenzhen, Shenzhen, 518103, China; China National GeneBank, BGI-Shenzhen, Shenzhen, 518120, China; Complete Genomics, Inc., 2904 Orchard Parkway, San Jose, CA, 95134, USA.
| | - Jiahai Shi
- Synthetic Biology Translational Research Programmes, Yong Loo Lin School of Medicine, National University of Singapore, Singapore; Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore.
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14
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Abstract
VHHs are antigen-binding domains cloned from heavy-chain antibodies found in camelids. These proteins have generated considerable interest in a variety of applications as research reagents, crystallization chaperones, and therapeutics. The evolutionary adaptations of VHHs have resulted in biophysical properties and antigen-binding modalities which are distinct from those of conventional antibodies. A detailed molecular analysis of VHH interactions with their cognate protein antigens is valuable for understanding structure-function relationships and for protein engineering. The majority of VHHs bind to folded proteins and thus recognize discontinuous three-dimensional epitopes. While multiple approaches exist for dissecting the interaction between a protein antigen and a VHH, X-ray crystallography remains the highest resolution method available. Here, we provide an updated procedure for determining and analyzing the X-ray structure of a VHH in complex with a protein antigen. We describe the recombinant expression and purification of VHHs and protein antigens, purification and analysis of protein complexes, crystallization, and optimization, X-ray structure determination by molecular replacement, and analysis of the complex.
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15
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Trempe F, Rossotti MA, Maqbool T, MacKenzie CR, Arbabi-Ghahroudi M. Llama DNA Immunization and Isolation of Functional Single-Domain Antibody Binders. Methods Mol Biol 2022; 2446:37-70. [PMID: 35157268 DOI: 10.1007/978-1-0716-2075-5_3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Genetic immunization is a simple, cost-effective, and powerful tool for inducing innate and adaptive immune responses to combat infectious diseases and difficult-to-treat illnesses. DNA immunization is increasingly used in the generation of monoclonal antibodies against targets for which pure proteins are unavailable or are difficult to express and purify (e.g., ion channels and receptors, transmembrane proteins, and emerging infectious pathogens). Genetic immunization has been successfully utilized in small inbred laboratory animals (mostly rodents); however, low immunogenicity of DNA/RNA injected into large mammals, including humans, is still a major challenge. Here, we provide a method for the genetic immunization of llamas, using a combination of biolistic transfection with a gene gun and intradermal injection with a DERMOJET® device, to elicit heavy-chain IgG responses against epidermal growth factor receptor (EGFR). We show the technique can be used to generate single-domain antibodies (VHHs) with nanomolar affinities to EGFR. We provide methods for gene gun bullet preparation, llama immunization, serology, phage-display library construction and panning, and VHH characterization.
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Affiliation(s)
- Frédéric Trempe
- Human Health Therapeutics Research Centre, National Research Council Canada, Ottawa, ON, Canada
| | - Martin A Rossotti
- Human Health Therapeutics Research Centre, National Research Council Canada, Ottawa, ON, Canada
| | | | - C Roger MacKenzie
- Human Health Therapeutics Research Centre, National Research Council Canada, Ottawa, ON, Canada
| | - Mehdi Arbabi-Ghahroudi
- Human Health Therapeutics Research Centre, National Research Council Canada, Ottawa, ON, Canada. .,Department of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa, ON, Canada. .,Department of Biology, Carleton University, Ottawa, ON, Canada.
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16
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Pang Q, Chen Y, Mukhtar H, Xiong J, Wang X, Xu T, Hammock BD, Wang J. Camelization of a murine single-domain antibody against aflatoxin B 1 and its antigen-binding analysis. Mycotoxin Res 2022; 38:51-60. [PMID: 35023020 PMCID: PMC8754551 DOI: 10.1007/s12550-021-00433-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2021] [Revised: 05/15/2021] [Accepted: 05/27/2021] [Indexed: 11/25/2022]
Abstract
Aflatoxin B1 (AFB1), a highly toxic mycotoxin, always contaminated in a variety of agricultural products. Camelid variable domain of heavy chain antibody (VHH) is a noteworthy reagent in immunoassay, owing to its excellent characteristics. Immunization of camelid animals is a straightforward strategy to produce VHHs. In this study, to avoid the dependence on the large animals, the camelized, murine antibody (cVHs) against AFB1 was prepared in vitro based on the identities between murine VH and camelid VHH and then to develop an immunoassay for AFB1. A murine anti-AFB1 VH fragment (VH-2E6) was selected for camelization through replacement of conserved hydrophobic residues in framework region 2 (FR2) (cVH-FR2), point mutation at position 103 in the FR4 region (cVH-103), and CDR3-grafted with a high AFB1-affinity VHH (cVH-Nb26). The cVH-Nb26 had a yield of 5 mg/L as refolded protein expressed from Escherichia coli and 10 mg/L expressed from Pichia pastoris. Compared with anti-AFB1 single-chain fragment variable (scFv) 2E6, cVH-Nb26 performed more than 20-fold enhancement of AFB1-binding interactions. Although the AFB1-affinity of cVH-Nb26 cannot meet the application requirement in the present form, our study provides effective strategies for preparation of camelized antibody in vitro, which could be a promising immunoreagent for AFB1 detection.
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Affiliation(s)
- Qian Pang
- College of Food Science and Technology, Huazhong Agricultural University, Wuhan, 430070, Hubei, China
| | - Yanhong Chen
- College of Food Science and Technology, Huazhong Agricultural University, Wuhan, 430070, Hubei, China
| | - Hina Mukhtar
- College of Food Science and Technology, Huazhong Agricultural University, Wuhan, 430070, Hubei, China
| | - Jing Xiong
- College of Food Science and Technology, Huazhong Agricultural University, Wuhan, 430070, Hubei, China
| | - Xiaohong Wang
- College of Food Science and Technology, Huazhong Agricultural University, Wuhan, 430070, Hubei, China
- Key Laboratory of Environment Correlative Dietology, Ministry of Education, Huazhong Agricultural University, Wuhan, China
| | - Ting Xu
- College of Resources and Environmental Sciences, China Agricultural University, Beijing, 100193, China
| | - Bruce D Hammock
- Department of Entomology and UCD Comprehensive Cancer Center, University of California, Davis, CA, 95616, USA
| | - Jia Wang
- College of Food Science and Technology, Huazhong Agricultural University, Wuhan, 430070, Hubei, China.
- Key Laboratory of Environment Correlative Dietology, Ministry of Education, Huazhong Agricultural University, Wuhan, China.
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17
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Abstract
Humanization of therapeutic antibodies derived from animal immunizations is often required to minimize immunogenicity risks in humans, which can cause potentially harmful and serious side effects and reduce antibody efficacy. Humanization is typically applied to conventional monoclonal antibodies derived in rodents as well as single-domain antibodies isolated from camelids and sharks (VHHs and VNARs). A streamlined protocol is described here for sequence humanization of camelid VHHs, which represent a promising biotherapeutic format with many desirable attributes. From human framework selection and complementarity-determining region grafting strategies to empirical scoring for prioritization of back-mutations, step-by-step instructions, and templates are provided along with bioinformatics resources to assist each step of the humanization process. Alternative approaches, warnings, and caveats are also presented.
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Affiliation(s)
- Traian Sulea
- Human Health Therapeutics Research Centre, National Research Council Canada, Montreal, QC, Canada.
- Institute of Parasitology, McGill University, Sainte-Anne-de-Bellevue, QC, Canada.
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18
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Abstract
Single-domain antibodies (sdAbs) are binders that consist of a single immunoglobulin domain. SdAbs have gained importance as therapeutics, diagnostic reagents, and research tools. Functional sdAbs are commonly produced in Escherichia coli, which is a simple and widely used host for production of recombinant proteins. However, there are drawbacks of the E. coli expression system, including the potential for misfolded recombinant proteins and pyrogenic contamination with toxic lipopolysaccharides. Pichia pastoris is an alternative host for the production of heterologous proteins because of its high recombinant protein yields and the ability to produce soluble, properly folded proteins without lipopolysaccharide contamination. Here, we describe a method to produce sdAbs in P. pastoris. We present methods for the cloning of sdAb-encoding genes into a P. pastoris expression vector, production and purification of sdAbs, and measurement of sdAb-binding kinetics. Functional sdAbs are easily and routinely obtained using these methods.
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Affiliation(s)
- Yusei Matsuzaki
- Division of Applied Life Sciences, Graduate School of Agriculture, Kyoto University, Kyoto, Japan
| | - Kaho Kajiwara
- Division of Applied Life Sciences, Graduate School of Agriculture, Kyoto University, Kyoto, Japan
| | - Wataru Aoki
- Division of Applied Life Sciences, Graduate School of Agriculture, Kyoto University, Kyoto, Japan
- Core Research for Evolutionary Science and Technology (CREST), Japan Science and Technology Agency (JST), Tokyo, Japan
| | - Mitsuyoshi Ueda
- Division of Applied Life Sciences, Graduate School of Agriculture, Kyoto University, Kyoto, Japan.
- Core Research for Evolutionary Science and Technology (CREST), Japan Science and Technology Agency (JST), Tokyo, Japan.
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19
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Abstract
Multimerization of single-domain antibodies (sdAbs) is instrumental for construction of antibody molecules with high avidity, extended in vivo half-life, and tailor-made biological activity. Two-component superglues, based on bacterium-derived peptides (Tags) and small protein domains (Catchers) that form isopeptide bonds when in close proximity, enable the creation of multimers by simply mixing of the individual components. Here, we provide detailed methods for the construction of sdAbs and scaffolds bearing genetically fused superglue components and their assembly into multimeric complexes.
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Affiliation(s)
- Paul J Wichgers Schreur
- Department of Virology and Molecular Biology, Wageningen Bioveterinary Research, Lelystad, The Netherlands.
| | - Sandra van de Water
- Department of Virology and Molecular Biology, Wageningen Bioveterinary Research, Lelystad, The Netherlands
| | - Jeroen Kortekaas
- Department of Virology and Molecular Biology, Wageningen Bioveterinary Research, Lelystad, The Netherlands
- Laboratory of Virology, Wageningen University, Lelystad, The Netherlands
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20
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Lowden MJ, van Faassen H, Raphael S, Ryan S, Hussack G, Henry KA. Facile Affinity Maturation of Single-Domain Antibodies Using Next-Generation DNA Sequencing. Methods Mol Biol 2022; 2446:245-268. [PMID: 35157277 DOI: 10.1007/978-1-0716-2075-5_12] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Binding affinity is one of the primary determinants of antibody function. Here, we provide a protocol for simple and rapid affinity maturation of single-domain antibodies (sdAbs) using tandem phage display selection and next-generation DNA sequencing. The sequence of a model camelid sdAb directed against Clostridioides difficile toxin A (A26.8) was diversified using either random or site-saturation mutagenesis and cloned into a phagemid vector upstream of gene 3. The resulting phage-displayed sdAb libraries were panned against C. difficile toxin A and the panning outputs interrogated using Illumina MiSeq sequencing. Through bioinformatic analyses, we were able to identify individual affinity-enhancing amino acid substitutions in the sdAb complementarity-determining regions that, when combined, resulted in affinity improvements of approximately 10-fold. The advantages of this method are that it does not require extensive screening and characterization of individual clones, nor structural information on the mechanism of the sdAb:antigen interaction.
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Affiliation(s)
- Michael J Lowden
- Human Health Therapeutics Research Centre, Life Sciences Division, National Research Council Canada, Ottawa, ON, Canada
| | - Henk van Faassen
- Human Health Therapeutics Research Centre, Life Sciences Division, National Research Council Canada, Ottawa, ON, Canada
| | - Shalini Raphael
- Human Health Therapeutics Research Centre, Life Sciences Division, National Research Council Canada, Ottawa, ON, Canada
| | - Shannon Ryan
- Human Health Therapeutics Research Centre, Life Sciences Division, National Research Council Canada, Ottawa, ON, Canada
| | - Greg Hussack
- Human Health Therapeutics Research Centre, Life Sciences Division, National Research Council Canada, Ottawa, ON, Canada
| | - Kevin A Henry
- Human Health Therapeutics Research Centre, Life Sciences Division, National Research Council Canada, Ottawa, ON, Canada.
- Department of Biochemistry, Microbiology and Immunology, Faculty of Medicine, University of Ottawa, Ottawa, ON, Canada.
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21
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Abstract
Chimeric antigen receptors (CARs) are engineered fusion proteins constructed from antigen-recognition, signaling, and costimulatory domains. CARs can be expressed in T cells with the purpose of reprogramming the T cells to specifically target tumor cells. This strategy thereby avoids the requirement for antigen processing and presentation by the target cell. Glypican-2 (GPC2) is a cell surface heparan sulfate proteoglycan with highly tumor-specific expression in neuroblastoma compared with nonmalignant cells. Therefore, GPC2 is an attractive target candidate for CAR T-cell therapy. Single-domain antibodies (sdAbs) can access epitopes different from those targeted by single-chain variable fragments and, because of their stability and modularity, could serve as ideal antigen-recognition domains in CAR T cells. Here, we describe a protocol for generating GPC2-targeted sdAb CAR T cells. We also present a methodology for assessing the efficiency of CAR expression on human T cells and their ability to kill GPC2-positive neuroblastoma cells in vitro and in vivo. The method described here is applicable to the production of CAR T cells derived from all types of sdAbs including VHHs and VNARs.
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Affiliation(s)
- Nan Li
- Laboratory of Molecular Biology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Mitchell Ho
- Laboratory of Molecular Biology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA.
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22
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Li D, Peng Q, Huang C, Zang B, Ren J, Ji F, Muyldermans S, Jia L. Cytoplasmic Expression of Nanobodies with Formylglycine Generating Enzyme Tag and Conversion to a Bio-Orthogonal Aldehyde Group. Methods Mol Biol 2022; 2446:357-371. [PMID: 35157283 DOI: 10.1007/978-1-0716-2075-5_18] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Nanobodies (Nbs) can be successfully retrieved following phage, bacterial, yeast, or ribosome display of immune, synthetic, or naïve libraries. However, after panning, multiple individual Nb clones need to be screened and assessed for solubility, antigen specificity, affinity, and potential biological function. Therefore, it is highly desirable to have a convenient expression strategy to obtain sufficient protein for in-depth characterization of the Nbs. The presence of a purification and detection tag, as well as a chemically reactive group to enable simple generation of Nb derivatives, would be of great help in this regard. Here, we provide a general protocol for high yield cytoplasmic expression and purification of formylglycine generating enzyme (FGE)-tagged Nbs. The cysteine within the FGE tag is easily converted to formylglycine by passing the FGE-tag containing Nb over a continuous-flow bio-catalysis system. The aldehyde group within the formylglycine side chain at the C-terminal end of the Nb is suitably located for subsequent bio-orthogonal reactions to fluorescent dyes, biotin, polyethylene glycol, or chromatography resins. We also include methods for production of high yield recombinant FGE, as well as conditions for its immobilization on Sepharose to produce the continuous-flow bio-catalysis system.
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Affiliation(s)
- Da Li
- Liaoning Key Laboratory of Molecular Recognition and Imaging, School of Bioengineering, Dalian University of Technology, Dalian, Liaoning, China
| | - Qiang Peng
- Liaoning Key Laboratory of Molecular Recognition and Imaging, School of Bioengineering, Dalian University of Technology, Dalian, Liaoning, China
| | - Chungdong Huang
- Liaoning Key Laboratory of Molecular Recognition and Imaging, School of Bioengineering, Dalian University of Technology, Dalian, Liaoning, China
| | - Berlin Zang
- Liaoning Key Laboratory of Molecular Recognition and Imaging, School of Bioengineering, Dalian University of Technology, Dalian, Liaoning, China
| | - Jun Ren
- Liaoning Key Laboratory of Molecular Recognition and Imaging, School of Bioengineering, Dalian University of Technology, Dalian, Liaoning, China
| | - Fangling Ji
- Liaoning Key Laboratory of Molecular Recognition and Imaging, School of Bioengineering, Dalian University of Technology, Dalian, Liaoning, China
| | - Serge Muyldermans
- Liaoning Key Laboratory of Molecular Recognition and Imaging, School of Bioengineering, Dalian University of Technology, Dalian, Liaoning, China.
- Cellular and Molecular Immunology, Vrije Universiteit Brussel, Brussels, Belgium.
| | - Lingyun Jia
- Liaoning Key Laboratory of Molecular Recognition and Imaging, School of Bioengineering, Dalian University of Technology, Dalian, Liaoning, China
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23
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Abstract
The discovery of single-domain antibodies has opened new avenues for drug development. Single-domain antibodies, also known as nanobodies, can access buried epitopes that are inaccessible to conventional antibodies. These antigen-binding domains have a high level of solubility and stability, which makes them well suited for therapeutic development. This chapter will discuss the design, production, and testing of single-domain antibody-based recombinant immunotoxins. Recombinant immunotoxins are chimeric proteins that combine the specificity of an antibody with the ribosomal-inhibitory domain of a bacterial toxin. Immunotoxins using the Pseudomonas exotoxin domain have been well studied in clinical trials. Recently, an anti-CD22 immunotoxin was granted marketing approval for use in patients with relapsed or refractory hairy cell leukemia. This supports the idea that treatment with recombinant immunotoxins can be explored for cancers that have not responded to standard therapies.
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Affiliation(s)
- Bryan D Fleming
- Laboratory of Molecular Biology, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Mitchell Ho
- Laboratory of Molecular Biology, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA.
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24
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Gettemans J. Site-Specific Fluorescent Labeling, Single-Step Immunocytochemistry, and Delivery of Nanobodies into Living Cells. Methods Mol Biol 2022; 2446:373-393. [PMID: 35157284 DOI: 10.1007/978-1-0716-2075-5_19] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
The smallest natural antibody fragments currently available are single-domain antibodies obtained from camelid species and sharks (variable new antigen receptors). These molecules consist of a single amino acid chain of ~120 amino acids that adopts a typical immunoglobulin fold. Single-domain antibodies (nanobodies) are monovalent and can be isolated from immunized animals, from naïve libraries, or from synthetic libraries. Importantly, their complete DNA sequences are readily obtained by default, which greatly facilitates their rapid manipulation for various applications. Here, a PCR-based protocol for inserting a sortase A recognition sequence at the carboxy-terminus of a nanobody is described. Subsequently, a sortase A-catalyzed biochemical reaction results in tagging of the nanobody with a short carboxy-terminal amino acid sequence that carries a non-canonical residue (propargyl glycine). This allows click chemistry to be performed with an azido-derivatized fluorophore, with the ensuing fluorescent nanobody being covalently and site-specifically labeled. The labeled nanobody can be used directly for immunocytochemistry, omitting the classical secondary antibody step. Also described are methods for delivery of fluorescent nanobodies into the cytoplasm of mammalian cells by photoporation, a very low-toxicity approach involving laser light and graphene quantum dots. The combined protocol embodies a novel route for studying protein function in living cells at high resolution.
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Affiliation(s)
- Jan Gettemans
- Department of Biomolecular Medicine, Faculty of Medicine and Health Sciences, Ghent University, Ghent, Belgium.
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Abstract
Ricin is a plant-derived toxin with a history as a biothreat agent. The toxin's enzymatic subunit, ricin toxin A chain (RTA), is a ribosome-inactivating protein that, when delivered into the cytoplasm of mammalian cells, arrests protein synthesis with extraordinary efficiency. Once within the cytoplasm, RTA is shielded from circulating toxin-neutralizing antibodies. Here, we describe methods we developed to neutralize RTA within the cytoplasm of Vero cells using DNA-based delivery of alpaca-derived single-domain antibodies (VHHs) targeting RTA's active site. We describe the design of the VHH expression vectors, assessment of transient expression of VHHs in Vero cells by enzyme-linked immunosorbent assay and western blotting, and cytotoxicity studies. While the protocols here are specific to ricin, they are easily modified for other toxins or even intracellular pathogens such as viruses.
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Affiliation(s)
- Timothy F Czajka
- Department of Biomedical Sciences, University at Albany School of Public Health, Albany, NY, USA
| | - Nicholas J Mantis
- Department of Biomedical Sciences, University at Albany School of Public Health, Albany, NY, USA.
- Division of Infectious Diseases, New York State Department of Health, Wadsworth Center, Albany, NY, USA.
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26
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Malaquias ADM, Marques LEC, Pereira SS, de Freitas Fernandes C, Maranhão AQ, Stabeli RG, Florean EOPT, Guedes MIF, Fernandes CFC. A review of plant-based expression systems as a platform for single-domain recombinant antibody production. Int J Biol Macromol 2021; 193:1130-1137. [PMID: 34699899 DOI: 10.1016/j.ijbiomac.2021.10.126] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2021] [Revised: 10/15/2021] [Accepted: 10/18/2021] [Indexed: 12/17/2022]
Abstract
Monoclonal antibodies have contributed to improving the treatment of several diseases. However, limitations related to pharmacokinetic parameters and production costs have instigated the search for alternative products. Camelids produce functional immunoglobulins G devoid of light chains and CH1 domains, in which the antigenic recognition site is formed by a single domain called VHH or nanobody. VHHs' small size and similarity to the human VH domain contribute to high tissue penetration and low immunogenicity. In addition, VHHs provide superior antigen recognition compared to human antibodies, better solubility and stability. Due to these characteristics and the possibility of obtaining gene-encoding VHHs, applications of this biological tool, whether as a monomer or in related recombinant constructs, have been reported. To ensure antibody efficacy and cost-effectiveness, strategies for their expression, either using prokaryotic or eukaryotic systems, have been utilized. Plant-based expression systems are useful for VHH related constructs that require post-translational modifications. This system has exhibited versatility, low-cost upstream production, and safety. This article presents the main advances associated to the heterologous expression of VHHs in plant systems. Besides, we show insights related to the use of VHHs as a strategy for plant pathogen control and a tool for genomic manipulation in plant systems.
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Affiliation(s)
| | | | - Soraya S Pereira
- Fundação Oswaldo Cruz, Fiocruz Rondônia, Porto Velho, Rondônia, Brazil
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27
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Lecocq Q, Debie P, Puttemans J, Awad RM, De Beck L, Ertveldt T, De Vlaeminck Y, Goyvaerts C, Raes G, Keyaerts M, Breckpot K, Devoogdt N. Evaluation of single domain antibodies as nuclear tracers for imaging of the immune checkpoint receptor human lymphocyte activation gene-3 in cancer. EJNMMI Res 2021; 11:115. [PMID: 34727262 PMCID: PMC8563901 DOI: 10.1186/s13550-021-00857-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2021] [Accepted: 10/22/2021] [Indexed: 12/29/2022] Open
Abstract
Recent advancements in the field of immune-oncology have led to a significant increase in life expectancy of patients with diverse forms of cancer, such as hematologic malignancies, melanoma and lung cancer. Unfortunately, these encouraging results are not observed in the majority of patients, who remain unresponsive and/or encounter adverse events. Currently, researchers are collecting more insight into the cellular and molecular mechanisms that underlie these variable responses. As an example, the human lymphocyte activation gene-3 (huLAG-3), an inhibitory immune checkpoint receptor, is increasingly studied as a therapeutic target in immune-oncology. Noninvasive molecular imaging of the immune checkpoint programmed death protein-1 (PD-1) or its ligand PD-L1 has shown its value as a strategy to guide and monitor PD-1/PD-L1-targeted immune checkpoint therapy. Yet, radiotracers that allow dynamic, whole body imaging of huLAG-3 expression are not yet described. We here developed single-domain antibodies (sdAbs) that bind huLAG-3 and showed that these sdAbs can image huLAG-3 in tumors, therefore representing promising tools for further development into clinically applicable radiotracers.
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Affiliation(s)
- Q Lecocq
- Laboratory for Molecular and Cellular Therapy, Department of Biomedical Sciences, Vrije Universiteit Brussel, Laarbeeklaan 103/E, 1090, Brussels, Belgium
| | - P Debie
- In Vivo Cellular and Molecular Imaging Laboratory, Department of Medical Imaging, Vrije Universiteit Brussel, Laarbeeklaan 103/K, 1090, Brussels, Belgium
| | - J Puttemans
- In Vivo Cellular and Molecular Imaging Laboratory, Department of Medical Imaging, Vrije Universiteit Brussel, Laarbeeklaan 103/K, 1090, Brussels, Belgium
| | - R M Awad
- Laboratory for Molecular and Cellular Therapy, Department of Biomedical Sciences, Vrije Universiteit Brussel, Laarbeeklaan 103/E, 1090, Brussels, Belgium
| | - L De Beck
- Laboratory for Molecular and Cellular Therapy, Department of Biomedical Sciences, Vrije Universiteit Brussel, Laarbeeklaan 103/E, 1090, Brussels, Belgium
| | - T Ertveldt
- Laboratory for Molecular and Cellular Therapy, Department of Biomedical Sciences, Vrije Universiteit Brussel, Laarbeeklaan 103/E, 1090, Brussels, Belgium
| | - Y De Vlaeminck
- Laboratory for Molecular and Cellular Therapy, Department of Biomedical Sciences, Vrije Universiteit Brussel, Laarbeeklaan 103/E, 1090, Brussels, Belgium
| | - C Goyvaerts
- Laboratory for Molecular and Cellular Therapy, Department of Biomedical Sciences, Vrije Universiteit Brussel, Laarbeeklaan 103/E, 1090, Brussels, Belgium
| | - G Raes
- Myeloid Cell Immunology Laboratory, VIB Center for Inflammation Research, Brussels, Belgium.,Cellular and Molecular Immunology Laboratory, Vrije Universiteit Brussel, Brussels, Belgium
| | - M Keyaerts
- In Vivo Cellular and Molecular Imaging Laboratory, Department of Medical Imaging, Vrije Universiteit Brussel, Laarbeeklaan 103/K, 1090, Brussels, Belgium.,Nuclear Medicine Department, UZ Brussel, Brussels, Belgium
| | - K Breckpot
- Laboratory for Molecular and Cellular Therapy, Department of Biomedical Sciences, Vrije Universiteit Brussel, Laarbeeklaan 103/E, 1090, Brussels, Belgium.
| | - N Devoogdt
- In Vivo Cellular and Molecular Imaging Laboratory, Department of Medical Imaging, Vrije Universiteit Brussel, Laarbeeklaan 103/K, 1090, Brussels, Belgium.
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28
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Duray E, Lejeune M, Baron F, Beguin Y, Devoogdt N, Krasniqi A, Lauwers Y, Zhao YJ, D'Huyvetter M, Dumoulin M, Caers J. A non-internalised CD38-binding radiolabelled single-domain antibody fragment to monitor and treat multiple myeloma. J Hematol Oncol 2021; 14:183. [PMID: 34727950 PMCID: PMC8561907 DOI: 10.1186/s13045-021-01171-6] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2021] [Accepted: 09/22/2021] [Indexed: 12/21/2022] Open
Abstract
Background Antibody-based therapies targeting CD38 are currently used as single agents as well as in combination regimens for multiple myeloma, a malignant plasma cell disorder. In this study, we aimed to develop anti-CD38 single-domain antibodies (sdAbs) that can be used to trace CD38+ tumour cells and subsequently used for targeted radionuclide therapy. SdAbs are derived from Camelidae heavy-chain antibodies and have emerged as promising theranostic agents due to their favourable pharmacological properties. Methods Four different anti-CD38 sdAbs were produced, and their binding affinities and potential competition with the monoclonal antibody daratumumab were tested using biolayer interferometry. Their binding kinetics and potential cell internalisation were further studied after radiolabelling with the diagnostic radioisotope Indium-111. The resulting radiotracers were evaluated in vivo for their tumour-targeting potential and biodistribution through single-photon emission computed tomography (SPECT/CT) imaging and serial dissections. Finally, therapeutic efficacy of a lead anti-CD38 sdAb, radiolabelled with the therapeutic radioisotope Lutetium-177, was evaluated in a CD38+ MM xenograft model. Results We retained anti-CD38 sdAb #2F8 as lead based on its excellent affinity and superior stability, the absence of competition with daratumumab and the lack of receptor-mediated internalisation. When intravenously administered to tumour-xenografted mice, radiolabelled sdAb #2F8 revealed specific and sustained tumour retention with low accumulation in other tissues, except kidneys, resulting in high tumour-to-normal tissue ratios. In a therapeutic setting, myeloma-bearing mice received three consecutive intravenous administrations of a high (18.5 MBq) or a low radioactive dose (9.3 MBq) of 177Lu-DTPA-2F8 or an equal volume of vehicle solution. A dose-dependent tumour regression was observed, which translated into a prolonged median survival from 43 days for vehicle-treated mice, to 62 days (p = 0.027) in mice receiving the low and 65 days in mice receiving the high (p = 0.0007) radioactive dose regimen, respectively. Conclusions These results highlight the theranostic potential of radiolabelled anti-CD38 sdAbs for the monitoring and treatment of multiple myeloma. Supplementary Information The online version contains supplementary material available at 10.1186/s13045-021-01171-6.
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Affiliation(s)
- Elodie Duray
- Laboratory of Haematology, GIGA-I3, University of Liège, Liège, Belgium.,NEPTUNS, Nanobodies To Explore Protein Structure and Functions, Centre for Protein Engineering (CIP), University of Liège, Liège, Belgium
| | - Margaux Lejeune
- Laboratory of Haematology, GIGA-I3, University of Liège, Liège, Belgium
| | - Frederic Baron
- Laboratory of Haematology, GIGA-I3, University of Liège, Liège, Belgium.,Division of Haematology, Department of Medicine, University and CHU of Liège, Liège, Belgium
| | - Yves Beguin
- Laboratory of Haematology, GIGA-I3, University of Liège, Liège, Belgium.,Division of Haematology, Department of Medicine, University and CHU of Liège, Liège, Belgium
| | - Nick Devoogdt
- Department of Medical Imaging, Laboratory for In Vivo Cellular and Molecular Imaging, Vrije Universiteit Brussel, Brussels, Belgium
| | - Ahmet Krasniqi
- Department of Medical Imaging, Laboratory for In Vivo Cellular and Molecular Imaging, Vrije Universiteit Brussel, Brussels, Belgium
| | - Yoline Lauwers
- Department of Medical Imaging, Laboratory for In Vivo Cellular and Molecular Imaging, Vrije Universiteit Brussel, Brussels, Belgium
| | - Yong Juan Zhao
- School of Chemical Biology and Biotechnology, University Shenzhen Graduate School, Peking, China
| | - Matthias D'Huyvetter
- Department of Medical Imaging, Laboratory for In Vivo Cellular and Molecular Imaging, Vrije Universiteit Brussel, Brussels, Belgium
| | - Mireille Dumoulin
- NEPTUNS, Nanobodies To Explore Protein Structure and Functions, Centre for Protein Engineering (CIP), University of Liège, Liège, Belgium
| | - Jo Caers
- Laboratory of Haematology, GIGA-I3, University of Liège, Liège, Belgium. .,Division of Haematology, Department of Medicine, University and CHU of Liège, Liège, Belgium.
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de Smit H, Ackerschott B, Tierney R, Stickings P, Harmsen MM. A novel single-domain antibody multimer that potently neutralizes tetanus neurotoxin. Vaccine X 2021; 8:100099. [PMID: 34169269 PMCID: PMC8207222 DOI: 10.1016/j.jvacx.2021.100099] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2020] [Revised: 04/17/2021] [Accepted: 05/27/2021] [Indexed: 11/30/2022] Open
Abstract
Tetanus antitoxin, produced in animals, has been used for the prevention and treatment of tetanus for more than 100 years. The availability of antitoxins, ethical issues around production, and risks involved in the use of animal derived serum products are a concern. We therefore developed a llama derived single-domain antibody (VHH) multimer to potentially replace the conventional veterinary product. In total, 28 different tetanus neurotoxin (TeNT) binding VHHs were isolated, 14 of which were expressed in yeast for further characterization. Four VHH monomers (T2, T6, T15 and T16) binding TeNT with high affinity (KD < 1 nM), covering different antigenic domains as revealed by epitope binning, and including 3 monomers (T6, T15 and T16) that inhibited TeNT binding to neuron gangliosides, were chosen as building blocks to generate 11 VHH multimers. These multimers contained either 1 or 2 different TeNT binding VHHs fused to 1 VHH binding to either albumin (A12) or immunoglobulin (G13) to extend serum half-life in animals. Multimers consisting of 2 TeNT binding VHHs showed more than a 10-fold increase in affinity (KD of 4-23 pM) when compared to multimers containing only one TeNT binding VHH. The T6 and T16 VHHs showed synergistic in vivo TeNT neutralization and, when incorporated into a single VHH trimer (T6T16A12), they showed a very high TeNT neutralizing capacity (1,510 IU/mg).
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Affiliation(s)
- Hans de Smit
- R&D, Smivet B.V., Diemewei 4110, 6605XC Wijchen, the Netherlands
| | - Bart Ackerschott
- R&D, Smivet B.V., Diemewei 4110, 6605XC Wijchen, the Netherlands
| | - Robert Tierney
- Division of Bacteriology, National Institute for Biological Standards and Control (NIBSC), MHRA, Potters Bar, Hertfordshire EN6 3QG, UK
| | - Paul Stickings
- Division of Bacteriology, National Institute for Biological Standards and Control (NIBSC), MHRA, Potters Bar, Hertfordshire EN6 3QG, UK
| | - Michiel M. Harmsen
- Wageningen Bioveterinary Research, P.O. Box 65, 8200 AB Lelystad, the Netherlands
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30
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Liu J, Hong H, Shi J, Xie Y, Lu Z, Liu Z, Zhou Z, Bian Z, Huang Z, Wu Z. Dinitrophenol-mediated modulation of an anti-PD-L1 VHH for Fc-dependent effector functions and prolonged serum half-life. Eur J Pharm Sci 2021; 165:105941. [PMID: 34256102 DOI: 10.1016/j.ejps.2021.105941] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2020] [Revised: 04/25/2021] [Accepted: 06/20/2021] [Indexed: 01/11/2023]
Abstract
Single-domain antibodies, VHHs or nanobodies, represent a promising set of alternatives to conventional therapeutic antibodies, gaining substantial attention in the field of cancer immunotherapy. However, inherent drawbacks of nanobodies such as fast clearance from blood circulation and lack of immune effector functions often led to unsatisfactory therapeutic efficacy. We previously reported that dinitrophenyl modification of an anti-EGFR VHH conferred Fc-dependent immune effector functions and elongated serum half-life on it through recruiting of hapten antibodies, resulting in improved immunotherapy efficacy in vivo. In the present work, we further tested the versatility of this approach in the case of an anti-PD-L1 blockade VHH (KN035). Site-specific dinitrophenyl conjugation did not impair the binding capacity of KN035 portion to PD-L1, but indirectly restored its immune effector functions, manifested by the observed antibody dependent cell-mediated cytotoxicity, antibody-dependent cellular phagocytosis and complement-dependent cytotoxicity against PD-L1 positive tumor cells. Significant delay of blood clearance of dinitrophenylated KN035 was evidenced by the prolonged half-life of ca. 22 h. This approach, using small hapten molecule conjugation, loaded additional antibody-mediated tumor killing mechanisms to PD-L1 blockade VHH and therefore improved efficacy is anticipated in the future in vivo therapeutic studies. Thus, our results underscore the power of this versatile approach for achieving desirable properties of VHH-based or similar therapeutics.
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Affiliation(s)
- Jinlong Liu
- Key Laboratory of Carbohydrate Chemistry & Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, China
| | - Haofei Hong
- Key Laboratory of Carbohydrate Chemistry & Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, China
| | - Jie Shi
- Key Laboratory of Carbohydrate Chemistry & Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, China.
| | - Yuntian Xie
- Key Laboratory of Carbohydrate Chemistry & Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, China
| | - Zhongkai Lu
- Key Laboratory of Carbohydrate Chemistry & Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, China
| | - Zhicheng Liu
- Key Laboratory of Carbohydrate Chemistry & Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, China
| | - Zhifang Zhou
- Key Laboratory of Carbohydrate Chemistry & Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, China
| | - Zehua Bian
- Wuxi Cancer Institute, Affiliated Hospital of Jiangnan University, Wuxi, Jiangsu 214122, China
| | - Zhaohui Huang
- Wuxi Cancer Institute, Affiliated Hospital of Jiangnan University, Wuxi, Jiangsu 214122, China.
| | - Zhimeng Wu
- Key Laboratory of Carbohydrate Chemistry & Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, China.
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Lee HT, Park UB, Jeong TJ, Gu N, Lee SH, Kim Y, Heo YS. High-resolution structure of the vWF A1 domain in complex with caplacizumab, the first nanobody-based medicine for treating acquired TTP. Biochem Biophys Res Commun 2021; 567:49-55. [PMID: 34144500 DOI: 10.1016/j.bbrc.2021.06.030] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2021] [Accepted: 06/08/2021] [Indexed: 11/19/2022]
Abstract
von Willebrand factor (vWF) is a huge oligomeric glycoprotein involved in blood homeostasis. However, this protein is also implicated in acquired thrombotic thrombocytopenic purpura (TTP). The blocking of its binding with platelets has been recognized as an attractive therapeutic strategy for treating acquired TTP. Caplacizumab, a bivalent single-domain antibody (VHH), is the first FDA-approved nanobody drug against vWF for the treatment of acquired TTP. Here, we describe the crystal structure of the A1 domain of vWF in complex with the caplacizumab nanobody at the resolution of 1.60 Å. This structure elucidates the precise epitope and binding mode of caplacizumab. Unexpectedly, caplacizumab binds to the bottom face of the vWF A1 domain and does not create any steric clash with platelet-receptor glycoprotein Ib (GPIb) bound to vWF. However, its binding can stabilize the different conformation within the N-terminus and α1β2 loop from the GPIb bound structure, suggesting that the mechanisms of caplacizumab would not be the direct competition of GPIb binding to vWF A1 domain but the conformational arrestment of vWF in an inappropriate state to platelet adhesion. This high-resolution structure would provide helpful information for the design of improved anti-vWF therapeutics for the treatment of acquired TTP.
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Affiliation(s)
- Hyun Tae Lee
- Department of Chemistry, Konkuk University, 120 Neungdong-ro, Gwangjin-gu, Seoul, 05029. Republic of Korea
| | - Ui Beom Park
- Department of Chemistry, Konkuk University, 120 Neungdong-ro, Gwangjin-gu, Seoul, 05029. Republic of Korea
| | - Tae Jun Jeong
- Department of Chemistry, Konkuk University, 120 Neungdong-ro, Gwangjin-gu, Seoul, 05029. Republic of Korea
| | - Nahyeon Gu
- Department of Chemistry, Konkuk University, 120 Neungdong-ro, Gwangjin-gu, Seoul, 05029. Republic of Korea
| | - Sang Hyung Lee
- Department of Chemistry, Konkuk University, 120 Neungdong-ro, Gwangjin-gu, Seoul, 05029. Republic of Korea
| | - Yujin Kim
- Department of Chemistry, Konkuk University, 120 Neungdong-ro, Gwangjin-gu, Seoul, 05029. Republic of Korea
| | - Yong-Seok Heo
- Department of Chemistry, Konkuk University, 120 Neungdong-ro, Gwangjin-gu, Seoul, 05029. Republic of Korea.
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Fernandes CFC, Pereira SS, Luiz MB, Silva NKRL, Silva MCS, Marinho ACM, Fonseca MHG, Furtado GP, Trevizani R, Nicolete R, Soares AM, Zuliani JP, Stabeli RG. Engineering of single-domain antibodies for next-generation snakebite antivenoms. Int J Biol Macromol 2021; 185:240-250. [PMID: 34118288 DOI: 10.1016/j.ijbiomac.2021.06.043] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2021] [Revised: 06/04/2021] [Accepted: 06/06/2021] [Indexed: 12/29/2022]
Abstract
Given the magnitude of the global snakebite crisis, strategies to ensure the quality of antivenom, as well as the availability and sustainability of its supply are under development by several research groups. Recombinant DNA technology has allowed the engineering of monoclonal antibodies and recombinant fragments as alternatives to conventional antivenoms. Besides having higher therapeutic efficacy, with broad neutralization capacity against local and systemic toxicity, novel antivenoms need to be safe and cost-effective. Due to the biological and physical chemical properties of camelid single-domain antibodies, with high volume of distribution to distal tissue, their modular format, and their versatility, their biotechnological application has grown considerably in recent decades. This article presents the most up-to-date developments concerning camelid single-domain-based antibodies against major toxins from snake venoms, the main venomous animals responsible for reported envenoming cases and related human deaths. A brief discussion on the composition, challenges, and perspectives of antivenoms is presented, as well as the road ahead for next-generation antivenoms based on single-domain antibodies.
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Affiliation(s)
| | - Soraya S Pereira
- Fundação Oswaldo Cruz, Fiocruz Rondônia, and Instituto Nacional de Ciência e Tecnologia em Epidemiologia da Amazônia Ocidental, INCT-EpiAmO, Porto Velho, Rondônia, Brazil
| | - Marcos B Luiz
- Fundação Oswaldo Cruz, Fiocruz Rondônia, and Instituto Nacional de Ciência e Tecnologia em Epidemiologia da Amazônia Ocidental, INCT-EpiAmO, Porto Velho, Rondônia, Brazil
| | - Nauanny K R L Silva
- Fundação Oswaldo Cruz, Fiocruz Rondônia, and Instituto Nacional de Ciência e Tecnologia em Epidemiologia da Amazônia Ocidental, INCT-EpiAmO, Porto Velho, Rondônia, Brazil
| | - Marcela Cristina S Silva
- Fundação Oswaldo Cruz, Fiocruz Rondônia, and Instituto Nacional de Ciência e Tecnologia em Epidemiologia da Amazônia Ocidental, INCT-EpiAmO, Porto Velho, Rondônia, Brazil
| | | | | | | | | | | | - Andreimar M Soares
- Fundação Oswaldo Cruz, Fiocruz Rondônia, and Instituto Nacional de Ciência e Tecnologia em Epidemiologia da Amazônia Ocidental, INCT-EpiAmO, Porto Velho, Rondônia, Brazil
| | - Juliana P Zuliani
- Fundação Oswaldo Cruz, Fiocruz Rondônia, and Instituto Nacional de Ciência e Tecnologia em Epidemiologia da Amazônia Ocidental, INCT-EpiAmO, Porto Velho, Rondônia, Brazil; Universidade Federal de Rondônia, UNIR, Porto Velho, Rondônia, Brazil
| | - Rodrigo G Stabeli
- Plataforma Bi-Institucional de Medicina Translacional (Fiocruz-USP), Ribeirão Preto, São Paulo, Brazil
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Henry KA, Nguyen TD, Baral TN, Hussack G, Raphael S, Arbabi-Ghahroudi M, Robert A, Durocher Y, Wu C, Jaramillo ML, MacKenzie CR. Biparatopic single-domain antibodies against Axl achieve ultra-high affinity through intramolecular engagement. Biochem Biophys Res Commun 2021; 562:154-161. [PMID: 34058562 DOI: 10.1016/j.bbrc.2021.05.030] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2021] [Accepted: 05/10/2021] [Indexed: 10/21/2022]
Abstract
Overexpression of Axl, a TAM-family receptor tyrosine kinase, plays key roles in the formation, growth, and spread of tumors as well as resistance to targeted therapies and chemotherapies. We identified novel llama VHHs against human Axl using multiple complementary phage display selection strategies and characterized a subset of high-affinity VHHs. The VHHs targeted multiple sites in Ig-like domains 1 and 2 of the Axl extracellular domain, including an immunodominant epitope overlapping the site of Gas6 interaction and two additional non-Gas6 competitive epitopes recognized by murine monoclonal antibodies. Only a subset of VHHs cross-reacted with cynomolgus monkey Axl and none recognized mouse Axl. As fusions to human IgG1 Fc, VHH-Fcs bound Axl+ tumor cell lines and mertansine-loaded VHH-Fcs were cytotoxic in vitro against Axl+ cells in proportion to their binding affinities. Engineered biparatopic VHH-VHH heterodimers bound Axl avidly, and a subset of molecules showed dramatically enhanced association rates indicative of intramolecular binding. These VHHs may have applications as modular elements of biologic drugs such as antibody-drug conjugates.
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Affiliation(s)
- Kevin A Henry
- Human Health Therapeutics Research Centre, National Research Council Canada, 100 Sussex Drive, Ottawa, Ontario, K1A 0R6, Canada; Department of Biochemistry, Microbiology and Immunology, University of Ottawa, 451 Smyth Road, Ottawa, Ontario, K1H 8M5, Canada
| | - Thanh-Dung Nguyen
- Human Health Therapeutics Research Centre, National Research Council Canada, 100 Sussex Drive, Ottawa, Ontario, K1A 0R6, Canada
| | - Toya Nath Baral
- Human Health Therapeutics Research Centre, National Research Council Canada, 100 Sussex Drive, Ottawa, Ontario, K1A 0R6, Canada
| | - Greg Hussack
- Human Health Therapeutics Research Centre, National Research Council Canada, 100 Sussex Drive, Ottawa, Ontario, K1A 0R6, Canada
| | - Shalini Raphael
- Human Health Therapeutics Research Centre, National Research Council Canada, 100 Sussex Drive, Ottawa, Ontario, K1A 0R6, Canada
| | - Mehdi Arbabi-Ghahroudi
- Human Health Therapeutics Research Centre, National Research Council Canada, 100 Sussex Drive, Ottawa, Ontario, K1A 0R6, Canada; Department of Biochemistry, Microbiology and Immunology, University of Ottawa, 451 Smyth Road, Ottawa, Ontario, K1H 8M5, Canada
| | - Alma Robert
- Human Health Therapeutics Research Centre, National Research Council Canada, 6100 Royalmount Ave, Montréal, Québec, H4P 2R2, Canada
| | - Yves Durocher
- Human Health Therapeutics Research Centre, National Research Council Canada, 6100 Royalmount Ave, Montréal, Québec, H4P 2R2, Canada
| | - Cunle Wu
- Human Health Therapeutics Research Centre, National Research Council Canada, 6100 Royalmount Ave, Montréal, Québec, H4P 2R2, Canada
| | - Maria L Jaramillo
- Human Health Therapeutics Research Centre, National Research Council Canada, 6100 Royalmount Ave, Montréal, Québec, H4P 2R2, Canada
| | - C Roger MacKenzie
- Human Health Therapeutics Research Centre, National Research Council Canada, 100 Sussex Drive, Ottawa, Ontario, K1A 0R6, Canada.
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Bessalah S, Jebahi S, Mejri N, Salhi I, Khorchani T, Hammadi M. Perspective on therapeutic and diagnostic potential of camel nanobodies for coronavirus disease-19 (COVID-19). 3 Biotech 2021; 11:89. [PMID: 33500874 PMCID: PMC7820838 DOI: 10.1007/s13205-021-02647-5] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2020] [Accepted: 01/06/2021] [Indexed: 12/11/2022] Open
Abstract
In this paper, we focus on the camelid nanobodies as a revolutionary therapy that can guide efforts to discover new drugs for Coronavirus disease (COVID-19). The small size property makes nanobodies capable of penetrating efficiently into tissues and recognizing cryptic antigens. Strong antigen affinity and stability in the gastrointestinal tract allow them to be used via oral administration. In fact, the use of nanobodies as inhalant can be directly delivered to the target organ, conferring high pulmonary drug concentrations and low systemic drug concentrations and minimal systemic side effects. For that, nanobodies are referred as a class of next-generation antibodies. Nanobodies permit the construction of multivalent formats that may achieve ultra-high neutralization potency and then may prevent mutational escape and can neutralize a wide range of SARS-CoV-2 variants. Due to their distinctive characteristics, nanobodies can be of great use in the development of promising treatment or preventive strategies against SARS-CoV-2 infection. In this review, the state-of-the-art of camel nanobodies design strategies against the virus including SARS-CoV-2 are critically summarized. The application of general nanotechnology was also discussed to mitigate and control emerging SARS-CoV-2 infection.
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Affiliation(s)
- Salma Bessalah
- Livestock and Wildlife Laboratory, Arid Lands Institute (I.R.A), University of Gabès, 4119 Médenine, Tunisia
| | - Samira Jebahi
- Laboratory on Energy and Matter for Nuclear Sciences Development (LR16CNSTN02), National Centre for Nuclear Sciences and Technologies, Sidi Thabet Technopark, 2020 Sidi Thabet, Tunisia, Pole technologique, BP 72, 2020 Sidi Thabet, Tunisia
| | - Naceur Mejri
- Laboratory on Energy and Matter for Nuclear Sciences Development (LR16CNSTN02), National Centre for Nuclear Sciences and Technologies, Sidi Thabet Technopark, 2020 Sidi Thabet, Tunisia, Pole technologique, BP 72, 2020 Sidi Thabet, Tunisia
| | - Imed Salhi
- Livestock and Wildlife Laboratory, Arid Lands Institute (I.R.A), University of Gabès, 4119 Médenine, Tunisia
| | - Touhami Khorchani
- Livestock and Wildlife Laboratory, Arid Lands Institute (I.R.A), University of Gabès, 4119 Médenine, Tunisia
| | - Mohamed Hammadi
- Livestock and Wildlife Laboratory, Arid Lands Institute (I.R.A), University of Gabès, 4119 Médenine, Tunisia
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Abstract
Present review summarizes the current applications of nanobodies in plant science and biotechnology, including plant expression of nanobodies, plant biotechnological applications, nanobody-based immunodetection, and nanobody-mediated resistance against plant pathogens. Nanobodies (Nbs) are variable domains of heavy chain-only antibodies (HCAbs) isolated from camelids. In spite of their single domain structure, nanobodies display many unique features, such as small size, high stability, and cryptic epitopes accessibility, which make them ideal for sophisticated applications in plants and animals. In this review, we summarize the current applications of nanobodies in plant science and biotechnology, focusing on nanobody expression in plants, plant biotechnological applications, determination of plant toxins and pathogens, and nanobody-mediated resistance against plant pathogens. Prospects and challenges of nanobody applications in plants are also discussed.
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Affiliation(s)
- Wenyi Wang
- Institute for Medical Biology and Hubei Provincial Key Laboratory for Protection and Application of Special Plants in Wuling Area of China, College of Life Sciences, South-Central University for Nationalities, Wuhan, Hubei, China.
- Precision Medicine R&D Center, Zhuhai Institute of Advanced Technology, Chinese Academy of Sciences, Zhuhai, Guangdong Province, China.
- Institute of Biomedicine and Biotechnology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, Guangdong Province, China.
| | - Jumao Yuan
- Precision Medicine R&D Center, Zhuhai Institute of Advanced Technology, Chinese Academy of Sciences, Zhuhai, Guangdong Province, China
- Institute of Biomedicine and Biotechnology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, Guangdong Province, China
| | - Changan Jiang
- Precision Medicine R&D Center, Zhuhai Institute of Advanced Technology, Chinese Academy of Sciences, Zhuhai, Guangdong Province, China
- Institute of Biomedicine and Biotechnology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, Guangdong Province, China
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Wang HC, Hung HC, Huang PN, Kung YA, Tseng SN, Wang YM, Shih SR, Tsu-An Hsu J. Engineering a novel IgG-like bispecific antibody against enterovirus A71. Biochem Biophys Rep 2020; 24:100860. [PMID: 34095549 PMCID: PMC8164134 DOI: 10.1016/j.bbrep.2020.100860] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2020] [Revised: 10/02/2020] [Accepted: 11/05/2020] [Indexed: 11/12/2022] Open
Abstract
Frequent outbreaks of enterovirus A71 (EVA71) occur in the Asia-Pacific area, and these are closely associated with severe neurological symptoms in young children. No effective antiviral therapy is currently available for the treatment of EVA71 infection. The development of monoclonal antibodies (mAbs) has demonstrated promise as a novel therapy for the prevention and treatment of infectious diseases. Several medical conditions have been treated using bispecific or multi-specific antibodies that recognize two or more distinct epitopes simultaneously. However, bispecific or multi-specific antibodies often encounter protein expression and product stability problems. In this study, we developed an IgG-like bispecific antibody (E18-F1) comprising two anti-EVA71 antibodies: E18 mAb and llama-derived F1 single-domain antibody. E18-F1 was demonstrated to exhibit superior binding affinity and antiviral activity compared with E18 or F1. Additionally, E18-F1 not only improved survival rate, but also reduced clinical signs in human SCARB2 receptor (hSCARB2) transgenic mice challenged with a lethal dose of EVA71. Altogether, our results reveal that E18-F1 is a simple format bispecific antibody with promising antiviral activity for EVA71.
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Affiliation(s)
- Hsiang-Ching Wang
- Department of Biological Science and Technology, National Chiao Tung University, Hsinchu, Taiwan
- Biomedical Technology and Device Research Laboratories, Industrial Technology Research Institute, Hsinchu, Taiwan
| | - Hui-Chen Hung
- Institute of Biotechnology and Pharmaceutical Research, National Health Research Institutes, Miaoli, Taiwan
| | - Peng-Nien Huang
- Research Center for Emerging Viral Infections, Chang Gung University, Taoyuan, Taiwan
- Division of Infectious Diseases, Department of Pediatrics, Linkou Chang Gung Memorial Hospital, Taoyuan, Taiwan
| | - Yu-An Kung
- Research Center for Emerging Viral Infections, Chang Gung University, Taoyuan, Taiwan
| | - Sung-Nien Tseng
- Research Center for Emerging Viral Infections, Chang Gung University, Taoyuan, Taiwan
| | - Yun-Ming Wang
- Department of Biological Science and Technology, Institute of Molecular Medicine and Bioengineering, Center For Intelligent Drug Systems and Smart Bio-devices (IDS2B), National Chiao Tung University, Hsinchu, Taiwan
| | - Shin-Ru Shih
- Research Center for Emerging Viral Infections, Chang Gung University, Taoyuan, Taiwan
- Department of Laboratory Medicine, Linkou Chang Gung Memorial Hospital, Taoyuan, Taiwan
| | - John Tsu-An Hsu
- Department of Biological Science and Technology, National Chiao Tung University, Hsinchu, Taiwan
- Institute of Biotechnology and Pharmaceutical Research, National Health Research Institutes, Miaoli, Taiwan
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Chen T, Liu X, Hong H, Wei H. Novel single-domain antibodies against the EGFR domain III epitope exhibit the anti-tumor effect. J Transl Med 2020; 18:376. [PMID: 33023595 PMCID: PMC7541222 DOI: 10.1186/s12967-020-02538-y] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2020] [Accepted: 09/21/2020] [Indexed: 01/11/2023] Open
Abstract
Background Monoclonal antibodies (mAbs) have been used for cancer therapy. They are large and have some disadvantages limiting their use. Smaller antibody fragments are needed as their alternatives. A fully human single-domain antibody (sdAb) has a small size of only 15 kDa and consists of only the variable domain of the human antibody heavy chain (VH). It has no immunogenicity. It can easily penetrate into tumor tissues, target an epitope inaccessible to mAb and be manufactured in bacteria for a low cost. Epidermal growth factor receptor (EGFR) is over-expressed in many cancer cells and is a good target for cancer therapy. Methods The EGFR protein fragment located on the EGFR extracellular domain III was chosen to screen a human sdAb library. Five human anti-EGFR sdAbs were identified. Their specific binding to EGFR was confirmed by ELISA, Western blotting and flow cytometry. Their anti-tumor effects were tested. Results Five novel fully human anti-EGFR sdAbs were isolated. They specifically bound to EGFR, not to the seven unrelated proteins as negative controls. They also bound to the three different human cancer cell lines, but not to the two cell lines as negative controls. They inhibited cell proliferation, migration and invasion and increased apoptosis of these three cancer cell lines. Two of them were tested for their anti-tumor effect in vivo and showed the anti-tumor activity in a mouse xenograft model for human lung cancer. Immunohistochemical staining of xenograft tumors also showed that their anti-tumor effects were associated with the inhibition of cancer cell proliferation and the promotion of cancer cell apoptosis. Conclusions This study clearly demonstrated that the anti-EGFR sdAbs could inhibit cancer cell growth in vitro and tumor growth in vivo. They could be potential therapeutics for the treatment of different human cancers.
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Affiliation(s)
- Tao Chen
- Department of Cell Biology and Institute of Biomedicine, National Engineering Research Center of Genetic Medicine, Guangdong Provincial Key Laboratory of Bioengineering Medicine, College of Life Science and Technology, Jinan University, Guangzhou, 510632, Guangdong, China
| | - Xue Liu
- Department of Cell Biology and Institute of Biomedicine, National Engineering Research Center of Genetic Medicine, Guangdong Provincial Key Laboratory of Bioengineering Medicine, College of Life Science and Technology, Jinan University, Guangzhou, 510632, Guangdong, China
| | - Haifeng Hong
- Department of Cell Biology and Institute of Biomedicine, National Engineering Research Center of Genetic Medicine, Guangdong Provincial Key Laboratory of Bioengineering Medicine, College of Life Science and Technology, Jinan University, Guangzhou, 510632, Guangdong, China
| | - Henry Wei
- Department of Cell Biology and Institute of Biomedicine, National Engineering Research Center of Genetic Medicine, Guangdong Provincial Key Laboratory of Bioengineering Medicine, College of Life Science and Technology, Jinan University, Guangzhou, 510632, Guangdong, China.
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Rezaei ZS, Shahangian SS, Hasannia S, Sajedi RH. Development of a phage display-mediated immunoassay for the detection of vascular endothelial growth factor. Anal Bioanal Chem 2020; 412:7639-7648. [PMID: 32876721 DOI: 10.1007/s00216-020-02901-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2020] [Revised: 08/15/2020] [Accepted: 08/19/2020] [Indexed: 01/08/2023]
Abstract
Because of the critical role of vascular endothelial growth factor (VEGF) in angiogenesis and its significantly increased serum levels in early stages of cancer, VEGF is considered an important prognostic biomarker in different cancers. Herein, the amplification power of PCR combined with phage displaying anti-VEGF VHH, a sensitive real-time immunoassay, was precisely designed based on phage display-mediated immuno-PCR (PD-IPCR) for the detection of VEGF. This system benefits from strong and specific binding of antigen and antibody in a sandwich immunosorbent assay platform using avastin (anti-VEGF monoclonal antibody) as the capture antibody. The anti-VEGF phage particles were used as both anti-VEGF agent and DNA template in the PD-IPCR. Anti-VEGF phage ELISA showed a linear range of 3-250 ng/ml and a limit of detection (LOD) of 1.1 ng/ml. Using the PD-IPCR method, the linear range of VEGF detection was found to be 0.06-700 ng/ml, with a detection limit of 3 pg/ml. The recovery rate in serum ranged from 83% to 99%, with a relative standard deviation of 1.2-4.9%. These values indicate that the method has good sensitivity for use in clinical analysis. The proposed method was successfully applied to the clinical determination of VEGF in human serum samples, and the results showed excellent correlation with conventional ELISA (R2 = 0.995). The novel immunoassay provides a specific and sensitive immunoassay protocol for VEGF detection at very low levels. Graphical abstract.
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Affiliation(s)
- Zahra S Rezaei
- Department of Biochemistry, Faculty of Biological Sciences, Tarbiat Modares University, Jalal Ale Ahmad Highway, Tehran, 14115-154, Iran
| | - S Shirin Shahangian
- Department of Biology, Faculty of Sciences, University of Guilan, Rasht, Guilan, 4199613776, Iran
| | - Sadegh Hasannia
- Department of Biochemistry, Faculty of Biological Sciences, Tarbiat Modares University, Jalal Ale Ahmad Highway, Tehran, 14115-154, Iran
| | - Reza H Sajedi
- Department of Biochemistry, Faculty of Biological Sciences, Tarbiat Modares University, Jalal Ale Ahmad Highway, Tehran, 14115-154, Iran.
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Abstract
The antibody repertoire of cartilaginous fish comprises an additional heavy-chain-only antibody isotype that is referred to as IgNAR (immunoglobulin novel antigen receptor). Its antigen-binding site consists of one single domain (vNAR) that is reportedly able to engage a respective antigen with affinities similar to those achieved by conventional antibodies. While vNAR domains offer a reduced size, which is often favorable for applications in a therapeutic as well as a biotechnological setup, they also exhibit a high physicochemical stability. Together with their ability to target difficult-to-address antigens such as virus particles or toxins, these shark-derived antibody domains seem to be predestined as tools for biotechnological and diagnostic applications. In the following chapter, we will describe the isolation of anti-idiotypic vNAR domains targeting monoclonal antibody paratopes from semi-synthetic, yeast-displayed libraries. Anti-idiotypic vNAR variants could be employed for the characterization of antibody-based therapeutics (such as antibody-drug conjugates) or as positive controls in immunogenicity assays. Peculiarly, when using semi-synthetic vNAR libraries, we found that it is not necessary to deplete the libraries using unrelated antibody targets, which enables a fast and facile screening procedure that exclusively delivers anti-idiotypic binders.
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Affiliation(s)
- Doreen Könning
- Antibody-Drug Conjugates and Targeted NBE Therapeutics, Merck KGaA, Darmstadt, Germany
| | - Stefan Zielonka
- Protein Engineering and Antibody Technologies (PEAT), Merck KGaA, Darmstadt, Germany
| | - Anna Kaempffe
- Antibody-Drug Conjugates and Targeted NBE Therapeutics, Merck KGaA, Darmstadt, Germany.,Institute for Organic Chemistry and Biochemistry, Technische Universität Darmstadt, Darmstadt, Germany
| | - Sebastian Jäger
- Antibody-Drug Conjugates and Targeted NBE Therapeutics, Merck KGaA, Darmstadt, Germany.,Institute for Organic Chemistry and Biochemistry, Technische Universität Darmstadt, Darmstadt, Germany
| | - Harald Kolmar
- Institute for Organic Chemistry and Biochemistry, Technische Universität Darmstadt, Darmstadt, Germany
| | - Christian Schröter
- Antibody-Drug Conjugates and Targeted NBE Therapeutics, Merck KGaA, Darmstadt, Germany.
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40
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Jayathilake C, Kumachi S, Arai H, Motohashi M, Terai T, Murakami A, Nemoto N. In vitro selection of anti-gliadin single-domain antibodies from a naïve library for cDNA-display mediated immuno-PCR. Anal Biochem 2019; 589:113490. [PMID: 31678363 DOI: 10.1016/j.ab.2019.113490] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2019] [Revised: 10/13/2019] [Accepted: 10/23/2019] [Indexed: 02/06/2023]
Abstract
Gluten intolerance, or adverse intestinal reactions to gluten, is a fairly common problem among certain groups of people. Celiac disease is the most severe form of gluten intolerance, which can lead to permanent damage in the digestive system. Since lifelong avoidance of gluten is the only available treatment, development of reliable techniques to identify gluten contamination in food is important. Gliadin, a component of gluten, is known to play a major role in gluten toxicity. In this study, cDNA display method was used to select specific single-domain antibodies against toxic gliadin from an alpaca-derived naïve VHH library. The cDNA display method is a promising in vitro display technique, which uniquely converts an unstable mRNA-protein fusion molecule to a stable mRNA/cDNA-protein fusion molecule using a well-designed puromycin linker. Three candidate VHHs were selected and the affinities of the VHHs were observed by pulldown assay and indirect ELISA method. In addition, a novel cDNA display mediated immuno-PCR method (cD-IPCR) was successfully applied to detect gliadin in food. We believe this work demonstrates the potential application of the cDNA display method in selecting binders against toxic and heterogeneous targets such as gliadin with an immunization-free preparation manner.
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Affiliation(s)
- Chathuni Jayathilake
- Graduate School of Science and Engineering, Saitama University, Saitama, 338-8570, Japan
| | | | - Hidenao Arai
- Epsilon Molecular Engineering, Inc, Saitama, 338-8570, Japan
| | - Maiko Motohashi
- Epsilon Molecular Engineering, Inc, Saitama, 338-8570, Japan
| | - Takuya Terai
- Graduate School of Science and Engineering, Saitama University, Saitama, 338-8570, Japan
| | - Akikazu Murakami
- Graduate School of Medicine, University of the Ryukyus, Okinawa, 903-0215, Japan
| | - Naoto Nemoto
- Graduate School of Science and Engineering, Saitama University, Saitama, 338-8570, Japan; Epsilon Molecular Engineering, Inc, Saitama, 338-8570, Japan.
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Ling J, Cheloha RW, McCaul N, Sun ZYJ, Wagner G, Ploegh HL. A nanobody that recognizes a 14-residue peptide epitope in the E2 ubiquitin-conjugating enzyme UBC6e modulates its activity. Mol Immunol 2019; 114:513-523. [PMID: 31518855 DOI: 10.1016/j.molimm.2019.08.008] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2019] [Revised: 08/06/2019] [Accepted: 08/12/2019] [Indexed: 12/28/2022]
Abstract
A substantial fraction of eukaryotic proteins is folded and modified in the endoplasmic reticulum (ER) prior to export and secretion. Proteins that enter the ER but fail to fold correctly must be degraded, mostly in a process termed ER-associated degradation (ERAD). Both protein folding in the ER and ERAD are essential for proper immune function. Several E2 and E3 enzymes localize to the ER and are essential for various aspects of ERAD, but their functions and regulation are incompletely understood. Here we identify and characterize single domain antibody fragments derived from the variable domain of alpaca heavy chain-only antibodies (VHHs or nanobodies) that bind to the ER-localized E2 UBC6e, an enzyme implicated in ERAD. One such VHH, VHH05 recognizes a 14 residue stretch and enhances the rate of E1-catalyzed ubiquitin E2 loading in vitroand interferes with phosphorylation of UBC6e in response to cell stress. Identification of the peptide epitope recognized by VHH05 places it outside the E2 catalytic core, close to the position of activation-induced phosphorylation on Ser184. Our data thus suggests a site involved in allosteric regulation of UBC6e's activity. This VHH should be useful not only to dissect the participation of UBC6e in ERAD and in response to cell stress, but also as a high affinity epitope tag-specific reagent of more general utility.
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Affiliation(s)
- Jingjing Ling
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
| | - Ross W Cheloha
- Program in Cellular and Molecular Medicine, Boston Children's Hospital and Harvard Medical School, Boston, MA, 02115, USA
| | - Nicholas McCaul
- Program in Cellular and Molecular Medicine, Boston Children's Hospital and Harvard Medical School, Boston, MA, 02115, USA
| | - Zhen-Yu J Sun
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, 02115, USA
| | - Gerhard Wagner
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, 02115, USA
| | - Hidde L Ploegh
- Program in Cellular and Molecular Medicine, Boston Children's Hospital and Harvard Medical School, Boston, MA, 02115, USA.
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Bao F, Wang L, Zhao X, Lu T, Na AM, Wang X, Cao J, Du Y. Preparation and characterization of a single-domain antibody specific for the porcine epidemic diarrhea virus spike protein. AMB Express 2019; 9:104. [PMID: 31300902 PMCID: PMC6626092 DOI: 10.1186/s13568-019-0834-1] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2019] [Accepted: 07/05/2019] [Indexed: 11/10/2022] Open
Abstract
Porcine epidemic diarrhea (PED) is a diarrheal disease of swine caused by porcine epidemic diarrhea virus (PEDV). It is characterized by acute watery diarrhea, dehydration and vomiting in swine of all ages and is especially fatal for neonatal and postweaning piglets. The spike protein of PEDV plays an important role in mediating virus attachment and fusion to target cells, and recent studies also reported that the neutralizing epitopes of the spike protein were mainly located in the S1 subunit, which makes it a candidate for vaccine development and clinical diagnosis. In this study, we successfully constructed an immune phage display single-domain antibody library with a library size of 3.4 × 106. A single-domain antibody, named S7, specific for the spike protein of PEDV was identified from the phage display single-domain antibody library. S7 could be expressed in a soluble form in E. coli, bound to the spike protein of PEDV in ELISA and stained the PEDV virus in Vero cells, but it showed no neutralization activity on PEDV. These results indicated the potent application of the S7 antibody as an imaging probe or as a candidate for the development of a diagnostic assay.
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Henry KA, van Faassen H, Harcus D, Marcil A, Hill JJ, Muyldermans S, MacKenzie CR. Llama peripheral B-cell populations producing conventional and heavy chain-only IgG subtypes are phenotypically indistinguishable but immunogenetically distinct. Immunogenetics 2019; 71:307-320. [PMID: 30656359 DOI: 10.1007/s00251-018-01102-9] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2018] [Accepted: 12/11/2018] [Indexed: 12/24/2022]
Abstract
Camelid ungulates produce homodimeric heavy chain-only antibodies (HCAbs) in addition to conventional antibodies consisting of paired heavy and light chains. In the llama, HCAbs are made up by at least two subclasses (long-hinge IgG2b and short-hinge IgG2c HCAbs vs. conventional heterotetrameric IgG1s). Here, we generated murine monoclonal antibodies (mAbs) specific for the hinge-CH2 boundary of llama IgG2b (mAb 1C10) and the Fc of llama IgG2c HCAbs (mAb 5E4). Flow cytometric analysis of llama peripheral blood lymphocytes revealed that IgG1+, IgG2b+ and IgG2c+ B cells could be distinguished using mAbs 1C10/5E4 but had equivalent expression of three other cell-surface markers. MiSeq sequencing of the peripheral B cell repertoires of three llamas showed that (i) IgG2b and IgG2c HCAbs were present in similar proportions in the repertoire, (ii) a subset of IgG2b and IgG2c HCAbs, but not IgG1s, entirely lacked a hinge exon and showed direct VHH-CH2 splicing; these "hingeless" HCAbs were clonally expanded, somatically mutated and derived from hinged HCAb precursors, (iii) substantial repertoire overlap existed between IgG subclasses, especially between IgG2b and IgG2c HCAbs, (iv) the complementarity-determining region (CDR)-H3 length distributions of IgG2b and IgG2c HCAbs were broader and biased towards longer lengths compared with IgG1s due to increased N-nucleotide addition, (v) IgG2b and IgG2c HCAbs used a more restricted set of IGHV genes compared with IgG1s, and (vi) IgG2b and IgG2c HCAbs had elevated somatic mutations rates of both CDRs and framework regions (FRs) compared with IgG1s, especially of CDR-H1 and FR3. The distinct molecular features of llama IgG1, IgG2b and IgG2c antibodies imply that these subclasses may have divergent immunological functions and suggest that specific mechanisms operate to diversify HCAb repertoires in the absence of a light chain.
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Affiliation(s)
- Kevin A Henry
- Human Health Therapeutics Research Centre, National Research Council Canada, 100 Sussex Drive, Ottawa, ON, K1A 0R6, Canada.
| | - Henk van Faassen
- Human Health Therapeutics Research Centre, National Research Council Canada, 100 Sussex Drive, Ottawa, ON, K1A 0R6, Canada
| | - Doreen Harcus
- Human Health Therapeutics Research Centre, National Research Council Canada, 6100 Royalmount Avenue, Montréal, QC, H4P 2R2, Canada
| | - Anne Marcil
- Human Health Therapeutics Research Centre, National Research Council Canada, 6100 Royalmount Avenue, Montréal, QC, H4P 2R2, Canada
| | - Jennifer J Hill
- Human Health Therapeutics Research Centre, National Research Council Canada, 100 Sussex Drive, Ottawa, ON, K1A 0R6, Canada
| | - Serge Muyldermans
- Laboratory of Cellular and Molecular Immunology, Vrije Universiteit Brussel, Brussels, Belgium
| | - C Roger MacKenzie
- Human Health Therapeutics Research Centre, National Research Council Canada, 100 Sussex Drive, Ottawa, ON, K1A 0R6, Canada.,School of Environmental Sciences, University of Guelph, 50 Stone Road East, Guelph, ON, N1G 2W1, Canada
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De Vlaeminck Y, Lecocq Q, Giron P, Heirman C, Geeraerts X, Bolli E, Movahedi K, Massa S, Schoonooghe S, Thielemans K, Goyvaerts C, Van Ginderachter JA, Breckpot K. Single-domain antibody fusion proteins can target and shuttle functional proteins into macrophage mannose receptor expressing macrophages. J Control Release 2019; 299:107-120. [PMID: 30797866 DOI: 10.1016/j.jconrel.2019.02.023] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2018] [Revised: 01/20/2019] [Accepted: 02/18/2019] [Indexed: 12/14/2022]
Abstract
The tumor microenvironment of numerous prevalent cancer types is abundantly infiltrated with tumor-associated macrophages (TAMs). Macrophage mannose receptor (MMR or CD206) expressing TAMs have been shown to be key promoters of tumor progression and major opponents of successful cancer therapy. Therefore, depleting MMR+ TAMs is an interesting approach to synergize with current antitumor therapies. We studied the potential of single-domain antibodies (sdAbs) specific for MMR to target proteins to MMR+ TAMs. Anti-MMR sdAbs were genetically coupled to a reporter protein, mWasabi (wasabi green, WG), generating sdAb "drug" fusion proteins (SFPs), referred to as WG-SFPs. The resulting WG-SFPs were highly efficient in targeting MMR+ macrophages both in vitro and in vivo. As we showed that second mitochondria-derived activator of caspase (SMAC) mimetics modulate MMR+ macrophages, we further coupled the anti-MMR sdAb to an active form of SMAC, referred to as tSMAC. The resulting tSMAC-SFPs were able to bind and upregulate caspase3/7 activity in MMR+ macrophages in vitro. In conclusion, we report the proof-of-concept of an elegant approach to conjugate anti-MMR sdAbs to proteins, which opens new avenues for targeted manipulation of MMR+ tumor-promoting TAMs.
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Affiliation(s)
- Yannick De Vlaeminck
- Laboratory of Molecular and Cellular Therapy, Department of Biomedical Sciences, Vrije Universiteit Brussel, Brussels, Belgium
| | - Quentin Lecocq
- Laboratory of Molecular and Cellular Therapy, Department of Biomedical Sciences, Vrije Universiteit Brussel, Brussels, Belgium
| | - Philippe Giron
- Laboratory of Medical and Molecular Oncology, Oncologic Research Centre, Vrije Universiteit Brussel, Brussels, Belgium
| | - Carlo Heirman
- Laboratory of Molecular and Cellular Therapy, Department of Biomedical Sciences, Vrije Universiteit Brussel, Brussels, Belgium
| | - Xenia Geeraerts
- Myeloid Cell Immunology Lab, VIB Center for Inflammation Research, Brussels, Belgium; Lab of Cellular and Molecular Immunology, Vrije Universiteit Brussel, Brussels, Belgium
| | - Evangelia Bolli
- Myeloid Cell Immunology Lab, VIB Center for Inflammation Research, Brussels, Belgium; Lab of Cellular and Molecular Immunology, Vrije Universiteit Brussel, Brussels, Belgium
| | - Kiavash Movahedi
- Myeloid Cell Immunology Lab, VIB Center for Inflammation Research, Brussels, Belgium; Lab of Cellular and Molecular Immunology, Vrije Universiteit Brussel, Brussels, Belgium
| | - Sam Massa
- Myeloid Cell Immunology Lab, VIB Center for Inflammation Research, Brussels, Belgium
| | - Steve Schoonooghe
- Myeloid Cell Immunology Lab, VIB Center for Inflammation Research, Brussels, Belgium; Lab of Cellular and Molecular Immunology, Vrije Universiteit Brussel, Brussels, Belgium
| | - Kris Thielemans
- Laboratory of Molecular and Cellular Therapy, Department of Biomedical Sciences, Vrije Universiteit Brussel, Brussels, Belgium
| | - Cleo Goyvaerts
- Laboratory of Molecular and Cellular Therapy, Department of Biomedical Sciences, Vrije Universiteit Brussel, Brussels, Belgium
| | - Jo A Van Ginderachter
- Myeloid Cell Immunology Lab, VIB Center for Inflammation Research, Brussels, Belgium; Lab of Cellular and Molecular Immunology, Vrije Universiteit Brussel, Brussels, Belgium
| | - Karine Breckpot
- Laboratory of Molecular and Cellular Therapy, Department of Biomedical Sciences, Vrije Universiteit Brussel, Brussels, Belgium.
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Salvador JP, Vilaplana L, Marco MP. Nanobody: outstanding features for diagnostic and therapeutic applications. Anal Bioanal Chem 2019; 411:1703-1713. [PMID: 30734854 DOI: 10.1007/s00216-019-01633-4] [Citation(s) in RCA: 143] [Impact Index Per Article: 28.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2018] [Revised: 01/16/2019] [Accepted: 01/21/2019] [Indexed: 11/28/2022]
Abstract
Nanobodies (Nbs) have arisen as an alternative to conventional antibodies (Abs) and show great potential when used as tools in different biotechnology fields such as diagnostics and therapy. Different approaches have been described for the production of Nbs and these methods face new challenges focused on improving yield, affinity, and reducing production costs. This review summarizes these challenges, and also the latest advances in the detection of different kinds of molecules, such as proteins and small molecules, and describes their potential use for noninvasive in vivo imaging and for in vitro assays. Moreover, the unique properties of Nbs are outlined like internalization, size, thermal and chemical stability, affinity, blood clearance, and labeling procedures. Concerning therapeutic applications, we highlight some already reported examples about Nbs being used for the treatment of several diseases such as cancer, neurodegenerative or infectious diseases among others. Finally, future trends, opportunities, and disadvantages are also discussed.
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Affiliation(s)
- J-Pablo Salvador
- Nanobiotechnology for Diagnostics Group (Nb4D), Department of Chemical and Biomolecular Nanotechnology, Institute for Advanced Chemistry of Catalonia (IQAC) of the Spanish Council for Scientific Research (CSIC), Jordi Girona 18-26, 08034, Barcelona, Spain.
- CIBER de Bioingeniería, Biomateriales y Nanomedicina (CIBER-BBN), Jordi Girona 18-26, 08034, Barcelona, Spain.
| | - Lluïsa Vilaplana
- Nanobiotechnology for Diagnostics Group (Nb4D), Department of Chemical and Biomolecular Nanotechnology, Institute for Advanced Chemistry of Catalonia (IQAC) of the Spanish Council for Scientific Research (CSIC), Jordi Girona 18-26, 08034, Barcelona, Spain
- CIBER de Bioingeniería, Biomateriales y Nanomedicina (CIBER-BBN), Jordi Girona 18-26, 08034, Barcelona, Spain
| | - M-Pilar Marco
- Nanobiotechnology for Diagnostics Group (Nb4D), Department of Chemical and Biomolecular Nanotechnology, Institute for Advanced Chemistry of Catalonia (IQAC) of the Spanish Council for Scientific Research (CSIC), Jordi Girona 18-26, 08034, Barcelona, Spain
- CIBER de Bioingeniería, Biomateriales y Nanomedicina (CIBER-BBN), Jordi Girona 18-26, 08034, Barcelona, Spain
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Hussack G, Raphael S, Lowden MJ, Henry KA. Isolation and characterization of camelid single-domain antibodies against HER2. BMC Res Notes 2018; 11:866. [PMID: 30518413 PMCID: PMC6282393 DOI: 10.1186/s13104-018-3955-8] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2018] [Accepted: 11/26/2018] [Indexed: 01/01/2023] Open
Abstract
OBJECTIVE To isolate and characterize novel high-affinity llama single-domain antibodies against human HER2. RESULTS We immunized a llama with human HER2, constructed a phage-displayed VHH library from the lymphocytes of the animal, and isolated six unique HER2-specific VHHs by panning. All six VHHs were unique at the amino acid level and were clonally unrelated, as reflected by their distinct CDR3 lengths. All six VHHs recognized recombinant human HER2 ectodomain with monovalent affinities ranging from 1 to 51 nM, had comparable affinities for cynomolgus monkey HER2, and bound HER2+ SKOV3 cells by flow cytometry. Three of the VHHs recognized recombinant murine HER2 with no loss of affinity compared with human and cynomolgus monkey HER2. The VHHs recognized three major epitopes on HER2 (including one conserved across the human, simian and murine orthologues), all of which were distinct from that of trastuzumab. These VHHs may be useful in the design of modular cancer immunotherapeutics.
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Affiliation(s)
- Greg Hussack
- Human Health Therapeutics Research Centre, National Research Council Canada, 100 Sussex Drive, Ottawa, ON K1A 0R6 Canada
| | - Shalini Raphael
- Human Health Therapeutics Research Centre, National Research Council Canada, 100 Sussex Drive, Ottawa, ON K1A 0R6 Canada
| | - Michael J. Lowden
- Human Health Therapeutics Research Centre, National Research Council Canada, 100 Sussex Drive, Ottawa, ON K1A 0R6 Canada
| | - Kevin A. Henry
- Human Health Therapeutics Research Centre, National Research Council Canada, 100 Sussex Drive, Ottawa, ON K1A 0R6 Canada
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Noor A, Walser G, Wesseling M, Giron P, Laffra AM, Haddouchi F, De Grève J, Kronenberger P. Production of a mono-biotinylated EGFR nanobody in the E. coli periplasm using the pET22b vector. BMC Res Notes 2018; 11:751. [PMID: 30348204 PMCID: PMC6196415 DOI: 10.1186/s13104-018-3852-1] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2018] [Accepted: 10/12/2018] [Indexed: 01/19/2023] Open
Abstract
OBJECTIVE Our aim was to produce a mono-biotinylated single domain antibody ('nanobody') specific for the epidermal growth factor receptor (EGFR), which is overexpressed in many cancer cells. The binding of the nanobody and its function are tested in cancer cells. The construct could be used to carry variable therapeutic or diagnostic load using biotin-streptavidin bridging. RESULTS The EGFR-specific 7D12 nanobody was genetically fused to an IgA hinge linker and to a C-terminal biotin ligase acceptor sequence, allowing mono-biotinylation in E. coli. Expression was in strain BL21-DE3 from a T7 RNA polymerase driven pET22b vector. The biotinylated nanobody, isolated from the periplasm, was purified using streptavidin-mutein affinity chromatography. Final yields were up to 5 mg/l of cell culture. We showed that the construct could bind to EGFR expressing A431 epidermoid carcinoma cells, and to transiently transformed EGFR overexpressing HEK293T cells and not to EGFR negative control cells. The specificity for the EGFR was further demonstrated by immunoprecipitation. To test the functionality, PC9 non-small cell lung cancer cells were treated with mono-biotinylated nanobody or with streptavidin-coupled tetravalent nanobodies. Both were able to block mutant EGFR phosphorylation and slow down growth of PC9 cells. Tetravalent nanobodies were able to downregulate AKT phosphorylation.
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Affiliation(s)
- Alfiah Noor
- Laboratory of Medical and Molecular Oncology, Vrije Universiteit Brussel, Laarbeeklaan 109, 1090, Brussels, Belgium.
| | - Gudrun Walser
- Laboratory of Biotechnology, Erasmushogeschool Brussel, Laarbeeklaan 121, 1090, Brussels, Belgium
| | - Matthijs Wesseling
- Laboratory of Biotechnology, Erasmushogeschool Brussel, Laarbeeklaan 121, 1090, Brussels, Belgium
| | - Philippe Giron
- Laboratory of Medical and Molecular Oncology, Vrije Universiteit Brussel, Laarbeeklaan 109, 1090, Brussels, Belgium
| | - Albert-Menno Laffra
- Laboratory of Biotechnology, Erasmushogeschool Brussel, Laarbeeklaan 121, 1090, Brussels, Belgium
| | - Fatima Haddouchi
- Laboratory of Biotechnology, Erasmushogeschool Brussel, Laarbeeklaan 121, 1090, Brussels, Belgium
| | - Jacques De Grève
- Laboratory of Medical and Molecular Oncology, Vrije Universiteit Brussel, Laarbeeklaan 109, 1090, Brussels, Belgium
| | - Peter Kronenberger
- Laboratory of Medical and Molecular Oncology, Vrije Universiteit Brussel, Laarbeeklaan 109, 1090, Brussels, Belgium. .,Laboratory of Biotechnology, Erasmushogeschool Brussel, Laarbeeklaan 121, 1090, Brussels, Belgium.
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Zhou Z, Vaidyanathan G, McDougald D, Kang CM, Balyasnikova I, Devoogdt N, Ta AN, McNaughton BR, Zalutsky MR. Fluorine-18 Labeling of the HER2-Targeting Single-Domain Antibody 2Rs15d Using a Residualizing Label and Preclinical Evaluation. Mol Imaging Biol 2017; 19:867-77. [PMID: 28409338 DOI: 10.1007/s11307-017-1082-x] [Citation(s) in RCA: 40] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Abstract
PURPOSE Our previous studies with F-18-labeled anti-HER2 single-domain antibodies (sdAbs) utilized 5F7, which binds to the same epitope on HER2 as trastuzumab, complicating its use for positron emission tomography (PET) imaging of patients undergoing trastuzumab therapy. On the other hand, sdAb 2Rs15d binds to a different epitope on HER2 and thus might be a preferable vector for imaging in these patients. The aim of this study was to evaluate the tumor targeting of F-18 -labeled 2Rs15d in HER2-expressing breast carcinoma cells and xenografts. PROCEDURES sdAb 2Rs15d was labeled with the residualizing labels N-succinimidyl 3-((4-(4-[18F]fluorobutyl)-1H-1,2,3-triazol-1-yl)methyl)-5-(guanidinomethyl)benzoate ([18F]RL-I) and N-succinimidyl 4-guanidinomethyl-3-[125I]iodobenzoate ([125I]SGMIB), and the purity and HER2-specific binding affinity and immunoreactivity were assessed after labeling. The biodistribution of I-125- and F-18-labeled 2Rs15d was determined in SCID mice bearing subcutaneous BT474M1 xenografts. MicroPET/x-ray computed tomograph (CT) imaging of [18F]RL-I-2Rs15d was performed in this model and compared to that of nonspecific sdAb [18F]RL-I-R3B23. MicroPET/CT imaging was also done in an intracranial HER2-positive breast cancer brain metastasis model after administration of 2Rs15d-, 5F7-, and R3B23-[18F]RL-I conjugates. RESULTS [18F]RL-I was conjugated to 2Rs15d in 40.8 ± 9.1 % yield and with a radiochemical purity of 97-100 %. Its immunoreactive fraction (IRF) and affinity for HER2-specific binding were 79.2 ± 5.4 % and 7.1 ± 0.4 nM, respectively. [125I]SGMIB was conjugated to 2Rs15d in 58.4 ± 8.2 % yield and with a radiochemical purity of 95-99 %; its IRF and affinity for HER2-specific binding were 79.0 ± 12.9 % and 4.5 ± 0.8 nM, respectively. Internalized radioactivity in BT474M1 cells in vitro for [18F]RL-I-2Rs15d was 43.7 ± 3.6, 36.5 ± 2.6, and 21.7 ± 1.2 % of initially bound radioactivity at 1, 2, and 4 h, respectively, and was similar to that seen for [125I]SGMIB-2Rs15d. Uptake of [18F]RL-I-2Rs15d in subcutaneous xenografts was 16-20 %ID/g over 1-3 h. Subcutaneous tumor could be clearly delineated by microPET/CT imaging with [18F]RL-I-2Rs15d but not with [18F]RL-I-R3B23. Intracranial breast cancer brain metastases could be visualized after intravenous administration of both [18F]RL-I-2Rs15d and [18F]RL-I-5F7. CONCLUSIONS Although radiolabeled 2Rs15d conjugates exhibited lower tumor cell retention both in vitro and in vivo than that observed previously for 5F7, given that it binds to a different epitope on HER2 from those targeted by the clinically utilized HER2-targeted therapeutic antibodies trastuzumab and pertuzumab, F-18-labeled 2Rs15d has potential for assessing HER2 status by PET imaging after trastuzumab and/or pertuzumab therapy.
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Zanganeh S, Rouhani Nejad H, Mehrabadi JF, Hosseini R, Shahi B, Tavassoli Z, Aramvash A. Rapid and Sensitive Detection of Staphylococcal Enterotoxin B by Recombinant Nanobody Using Phage Display Technology. Appl Biochem Biotechnol 2019; 187:493-505. [PMID: 29984392 DOI: 10.1007/s12010-018-2762-y] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2018] [Accepted: 04/12/2018] [Indexed: 02/06/2023]
Abstract
Staphylococcal enterotoxin B, from Staphylococcus aureus (S. aureus), is one of the most potent bacterial superantigens with profound toxic effects on the immune system. It is associated with food poisoning, toxic shock, atopic dermatitis, asthma, and nasal polyps in humans. The current diagnostic methods for staphylococcal enterotoxin are mainly based on traditional monoclonal antibodies which hardly meet the requirements for clinical applications, and hybridoma clones lose their ability to secrete antibodies during time. The present study investigates the development of a novel, highly specific, low-cost, and sensitive nanobody capable of being used in immunoassays for Staphylococcal enterotoxin B (SEB) detection in suspicious foods. For this purpose, Camelus dromedarius was immunized against SEB toxin. After obtaining acceptable titration, a high-quality phage display nanobody library (4 × 1010 PFU/ml) was constructed. High-affinity SEB-specific nanobodies were retrieved from constructed libraries. After phage rescue and five round of biopanning, clone screening was performed by phage ELISA. Recombinant nanobodies which were expressed from C7 and C21 clone showed the highest affinity for SEB. The presence of high quality and pure nanobody band at ~ 15 kDa was confirmed by SDS-PAGE and western blotting. The affinity constant which was measured by ELISA was calculated to be around 10-9 M. The results suggest that the proposed detection method by nanobodies is an alternative diagnostic tool enabling a rapid, inexpensive, and specific detection of the SEB.
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Henry KA, Tanha J. Performance evaluation of phage-displayed synthetic human single-domain antibody libraries: A retrospective analysis. J Immunol Methods 2018; 456:81-86. [PMID: 29462605 DOI: 10.1016/j.jim.2018.02.009] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2017] [Revised: 01/25/2018] [Accepted: 02/15/2018] [Indexed: 02/06/2023]
Abstract
Fully human synthetic single-domain antibodies (sdAbs) are desirable therapeutic molecules but their development is a considerable challenge. Here, using a retrospective analysis of in-house historical data, we examined the parameters that impact the outcome of screening phage-displayed synthetic human sdAb libraries to discover antigen-specific binders. We found no evidence for a differential effect of domain type (VH or VL), library randomization strategy, incorporation of a stabilizing disulfide linkage or sdAb display format (monovalent vs. multivalent) on the probability of obtaining any antigen-binding human sdAbs, instead finding that the success of library screens was primarily related to properties of target antigens, especially molecular mass. The solubility and binding affinity of sdAbs isolated from successful screens depended both on properties of the sdAb libraries (primarily domain type) and the target antigens. Taking attrition of sdAbs with major manufacturability concerns (aggregation; low expression) and sdAbs that do not recognize native cell-surface antigens as independent probabilities, we calculate the overall likelihood of obtaining ≥1 antigen-binding human sdAb from a single library-target screen as ~24%. Successful library-target screens should be expected to yield ~1.3 human sdAbs on average, each with average binding affinity of ~2 μM.
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Affiliation(s)
- Kevin A Henry
- Human Health Therapeutics Research Centre, National Research Council Canada, 100 Sussex Drive, Ottawa, Ontario K1A 0R6, Canada
| | - Jamshid Tanha
- Human Health Therapeutics Research Centre, National Research Council Canada, 100 Sussex Drive, Ottawa, Ontario K1A 0R6, Canada; School of Environmental Sciences, University of Guelph, 50 Stone Road East, Guelph, Ontario N1G 2W1, Canada; Department of Biochemistry, Microbiology and Immunology, University of Ottawa, 451 Smyth Road, Ottawa, Ontario K1H 8M5, Canada.
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