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Tenggara MK, Oh SH, Yang C, Nariya HK, Metz AM, Upadhyay AA, Gudipati DR, Guo L, McGhee EG, Gill K, Viox EG, Mason RD, Doria-Rose NA, Foulds KE, Mascola JR, Du Y, Fu H, Altman JD, Yan Q, Sheng Z, Bosinger SE, Kong R. Frequency-potency analysis of IgG+ memory B cells delineates neutralizing antibody responses at single-cell resolution. Cell Rep 2024; 43:113948. [PMID: 38483908 PMCID: PMC11003769 DOI: 10.1016/j.celrep.2024.113948] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2023] [Revised: 02/06/2024] [Accepted: 02/26/2024] [Indexed: 04/02/2024] Open
Abstract
Identifying individual functional B cell receptors (BCRs) is common, but two-dimensional analysis of B cell frequency versus BCR potency would delineate both quantity and quality of antigen-specific memory B cells. We efficiently determine quantitative BCR neutralizing activities using a single-cell-derived antibody supernatant analysis (SCAN) workflow and develop a frequency-potency algorithm to estimate B cell frequencies at various neutralizing activity or binding affinity cutoffs. In an HIV-1 fusion peptide (FP) immunization study, frequency-potency curves elucidate the quantity and quality of FP-specific immunoglobulin G (IgG)+ memory B cells for different animals, time points, and antibody lineages at single-cell resolution. The BCR neutralizing activities are mainly determined by their affinities to soluble envelope trimer. Frequency analysis definitively demonstrates dominant neutralizing antibody lineages. These findings establish SCAN and frequency-potency analyses as promising approaches for general B cell analysis and monoclonal antibody (mAb) discovery. They also provide specific rationales for HIV-1 FP-directed vaccine optimization.
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Affiliation(s)
- Michelle K Tenggara
- Emory Vaccine Center, Atlanta, GA 30329, USA; Emory National Primate Research Center, Atlanta, GA 30329, USA
| | - Seo-Ho Oh
- Emory Vaccine Center, Atlanta, GA 30329, USA; Emory National Primate Research Center, Atlanta, GA 30329, USA
| | - Catherine Yang
- Emory Vaccine Center, Atlanta, GA 30329, USA; Emory National Primate Research Center, Atlanta, GA 30329, USA
| | - Hardik K Nariya
- Emory Vaccine Center, Atlanta, GA 30329, USA; Emory National Primate Research Center, Atlanta, GA 30329, USA
| | - Amanda M Metz
- Emory National Primate Research Center, Atlanta, GA 30329, USA
| | - Amit A Upadhyay
- Emory National Primate Research Center, Atlanta, GA 30329, USA
| | - Dedeepya R Gudipati
- Emory Vaccine Center, Atlanta, GA 30329, USA; Emory National Primate Research Center, Atlanta, GA 30329, USA
| | - Lizheng Guo
- Emory Vaccine Center, Atlanta, GA 30329, USA; Emory National Primate Research Center, Atlanta, GA 30329, USA
| | - Emily G McGhee
- Emory Vaccine Center, Atlanta, GA 30329, USA; Emory National Primate Research Center, Atlanta, GA 30329, USA
| | - Kiran Gill
- Emory National Primate Research Center, Atlanta, GA 30329, USA
| | - Elise G Viox
- Vaccine Research Center, National Institutes of Health, Bethesda, MD 20892, USA
| | - Rosemarie D Mason
- Vaccine Research Center, National Institutes of Health, Bethesda, MD 20892, USA
| | - Nicole A Doria-Rose
- Vaccine Research Center, National Institutes of Health, Bethesda, MD 20892, USA
| | - Kathryn E Foulds
- Vaccine Research Center, National Institutes of Health, Bethesda, MD 20892, USA
| | - John R Mascola
- Vaccine Research Center, National Institutes of Health, Bethesda, MD 20892, USA
| | - Yuhong Du
- Department of Pharmacology and Chemical Biology, Emory University School of Medicine, Atlanta, GA 30322, USA; Emory Chemical Biology Discovery Center, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Haian Fu
- Department of Pharmacology and Chemical Biology, Emory University School of Medicine, Atlanta, GA 30322, USA; Emory Chemical Biology Discovery Center, Emory University School of Medicine, Atlanta, GA 30322, USA; Department of Hematology and Medical Oncology and Winship Cancer Institute, Emory University, Atlanta, GA 30322, USA
| | - John D Altman
- Emory Vaccine Center, Atlanta, GA 30329, USA; Emory National Primate Research Center, Atlanta, GA 30329, USA; Department of Microbiology and Immunology, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Qi Yan
- Department of Obstetrics and Gynecology, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Zizhang Sheng
- Aaron Diamond AIDS Research Center, Columbia University Vagelos College of Physicians and Surgeons, New York, NY 10032, USA
| | - Steven E Bosinger
- Emory Vaccine Center, Atlanta, GA 30329, USA; Emory National Primate Research Center, Atlanta, GA 30329, USA; Department of Pathology and Laboratory Medicine, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Rui Kong
- Emory Vaccine Center, Atlanta, GA 30329, USA; Emory National Primate Research Center, Atlanta, GA 30329, USA; Department of Pathology and Laboratory Medicine, Emory University School of Medicine, Atlanta, GA 30322, USA.
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Santos-López J, Gómez S, Fernández FJ, Vega MC. Protein-Protein Binding Kinetics by Biolayer Interferometry. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2024; 3234:73-88. [PMID: 38507201 DOI: 10.1007/978-3-031-52193-5_6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/22/2024]
Abstract
The specific kinetics and thermodynamics of protein-protein interactions underlie the molecular mechanisms of cellular functions; hence the characterization of these interaction parameters is central to the quantitative understanding of physiological and pathological processes. Many methods have been developed to study protein-protein interactions, which differ in various features including the interaction detection principle, the sensitivity, whether the method operates in vivo, in vitro, or in silico, the temperature control, the use of labels, immobilization, the amount of sample required, the number of measurements that can be accomplished simultaneously, or the cost. Bio-Layer Interferometry (BLI) is a label-free biophysical method to measure the kinetics of protein-protein interactions. Label-free interaction assays are a broad family of methods that do not require protein modifications (other than immobilization) or labels such as fusions with fluorescent proteins or transactivating domains or chemical modifications like biotinylation or reaction with radionuclides. Besides BLI, other label-free techniques that are widely used for determining protein-protein interactions include surface plasmon resonance (SPR), thermophoresis, and isothermal titration calorimetry (ITC), among others.
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Affiliation(s)
- Jorge Santos-López
- Centro de Investigaciones Biológicas Margarita Salas (CIB-CSIC), Madrid, Spain
| | - Sara Gómez
- Centro de Investigaciones Biológicas Margarita Salas (CIB-CSIC), Madrid, Spain
- Universidad Europea de Madrid, Madrid, Spain
| | | | - M Cristina Vega
- Centro de Investigaciones Biológicas Margarita Salas (CIB-CSIC), Madrid, Spain.
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3
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Sokal A, Barba-Spaeth G, Hunault L, Fernández I, Broketa M, Meola A, Fourati S, Azzaoui I, Vandenberghe A, Lagouge-Roussey P, Broutin M, Roeser A, Bouvier-Alias M, Crickx E, Languille L, Fournier M, Michel M, Godeau B, Gallien S, Melica G, Nguyen Y, Canoui-Poitrine F, Pirenne F, Megret J, Pawlotsky JM, Fillatreau S, Reynaud CA, Weill JC, Rey FA, Bruhns P, Mahévas M, Chappert P. SARS-CoV-2 Omicron BA.1 breakthrough infection drives late remodeling of the memory B cell repertoire in vaccinated individuals. Immunity 2023; 56:2137-2151.e7. [PMID: 37543032 DOI: 10.1016/j.immuni.2023.07.007] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2023] [Revised: 05/12/2023] [Accepted: 07/06/2023] [Indexed: 08/07/2023]
Abstract
How infection by a viral variant showing antigenic drift impacts a preformed mature human memory B cell (MBC) repertoire remains an open question. Here, we studied the MBC response up to 6 months after SARS-CoV-2 Omicron BA.1 breakthrough infection in individuals previously vaccinated with three doses of the COVID-19 mRNA vaccine. Longitudinal analysis, using single-cell multi-omics and functional analysis of monoclonal antibodies from RBD-specific MBCs, revealed that a BA.1 breakthrough infection mostly recruited pre-existing cross-reactive MBCs with limited de novo response against BA.1-restricted epitopes. Reorganization of clonal hierarchy and new rounds of germinal center reactions, however, combined to maintain diversity and induce progressive maturation of the MBC repertoire against common Hu-1 and BA.1, but not BA.5-restricted, SARS-CoV-2 Spike RBD epitopes. Such remodeling was further associated with a marked improvement in overall neutralizing breadth and potency. These findings have fundamental implications for the design of future vaccination booster strategies.
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Affiliation(s)
- Aurélien Sokal
- Institut Necker Enfants Malades, INSERM U1151/CNRS UMR 8253, Action thématique incitative sur programme-Avenir Team, Auto-Immune and Immune B cells, Université Paris Cité, Université Paris Est-Créteil, Créteil, France; Service de Médecine interne, Hôpital Beaujon, Assistance Publique-Hôpitaux de Paris (AP-HP), Université de Paris Cité, Clichy, France; Service de Médecine Interne, Centre Hospitalier Universitaire Henri-Mondor, Assistance Publique-Hôpitaux de Paris (AP-HP), Université Paris-Est Créteil (UPEC), Créteil, France
| | - Giovanna Barba-Spaeth
- Institut Pasteur, Université de Paris Cité, CNRS UMR 3569, Unité de Virologie Structurale, Paris, France
| | - Lise Hunault
- Institut Pasteur, Université de Paris Cité, INSERM UMR1222, Unit of Antibodies in Therapy and Pathology, Paris, France; Sorbonne University, ED394, Paris, France; Sorbonne Université, INSERM, CNRS, Centre d'Immunologie et des Maladies Infectieuses (CIMI-Paris), 75013 Paris, France
| | - Ignacio Fernández
- Institut Pasteur, Université de Paris Cité, CNRS UMR 3569, Unité de Virologie Structurale, Paris, France
| | - Matteo Broketa
- Institut Pasteur, Université de Paris Cité, INSERM UMR1222, Unit of Antibodies in Therapy and Pathology, Paris, France; Sorbonne University, ED394, Paris, France
| | - Annalisa Meola
- Institut Pasteur, Université de Paris Cité, CNRS UMR 3569, Unité de Virologie Structurale, Paris, France
| | - Slim Fourati
- Département de Virologie, Bactériologie, Hygiène et Mycologie-Parasitologie, Centre Hospitalier Universitaire Henri Mondor, Assistance Publique-Hôpitaux de Paris (AP-HP), Créteil, France; INSERM U955, équipe 18. Institut Mondor de Recherche Biomédicale (IMRB), Université Paris-Est Créteil (UPEC), Créteil, France
| | - Imane Azzaoui
- Service de Médecine Interne, Centre Hospitalier Universitaire Henri-Mondor, Assistance Publique-Hôpitaux de Paris (AP-HP), Université Paris-Est Créteil (UPEC), Créteil, France; INSERM U955, équipe 2. Institut Mondor de Recherche Biomédicale (IMRB), Université Paris-Est Créteil (UPEC), Créteil, France
| | - Alexis Vandenberghe
- Institut Necker Enfants Malades, INSERM U1151/CNRS UMR 8253, Action thématique incitative sur programme-Avenir Team, Auto-Immune and Immune B cells, Université Paris Cité, Université Paris Est-Créteil, Créteil, France; Service de Médecine Interne, Centre Hospitalier Universitaire Henri-Mondor, Assistance Publique-Hôpitaux de Paris (AP-HP), Université Paris-Est Créteil (UPEC), Créteil, France; INSERM U955, équipe 2. Institut Mondor de Recherche Biomédicale (IMRB), Université Paris-Est Créteil (UPEC), Créteil, France
| | - Pauline Lagouge-Roussey
- Institut Necker Enfants Malades, INSERM U1151/CNRS UMR 8253, Action thématique incitative sur programme-Avenir Team, Auto-Immune and Immune B cells, Université Paris Cité, Université Paris Est-Créteil, Créteil, France; Service de Médecine Interne, Centre Hospitalier Universitaire Henri-Mondor, Assistance Publique-Hôpitaux de Paris (AP-HP), Université Paris-Est Créteil (UPEC), Créteil, France; INSERM U955, équipe 2. Institut Mondor de Recherche Biomédicale (IMRB), Université Paris-Est Créteil (UPEC), Créteil, France
| | - Manon Broutin
- Institut Necker Enfants Malades, INSERM U1151/CNRS UMR 8253, Action thématique incitative sur programme-Avenir Team, Auto-Immune and Immune B cells, Université Paris Cité, Université Paris Est-Créteil, Créteil, France; INSERM U955, équipe 2. Institut Mondor de Recherche Biomédicale (IMRB), Université Paris-Est Créteil (UPEC), Créteil, France
| | - Anais Roeser
- Institut Necker Enfants Malades, INSERM U1151/CNRS UMR 8253, Action thématique incitative sur programme-Avenir Team, Auto-Immune and Immune B cells, Université Paris Cité, Université Paris Est-Créteil, Créteil, France; Service de Médecine Interne, Centre Hospitalier Universitaire Henri-Mondor, Assistance Publique-Hôpitaux de Paris (AP-HP), Université Paris-Est Créteil (UPEC), Créteil, France
| | - Magali Bouvier-Alias
- Département de Virologie, Bactériologie, Hygiène et Mycologie-Parasitologie, Centre Hospitalier Universitaire Henri Mondor, Assistance Publique-Hôpitaux de Paris (AP-HP), Créteil, France; INSERM U955, équipe 18. Institut Mondor de Recherche Biomédicale (IMRB), Université Paris-Est Créteil (UPEC), Créteil, France
| | - Etienne Crickx
- Institut Necker Enfants Malades, INSERM U1151/CNRS UMR 8253, Action thématique incitative sur programme-Avenir Team, Auto-Immune and Immune B cells, Université Paris Cité, Université Paris Est-Créteil, Créteil, France; Service de Médecine Interne, Centre Hospitalier Universitaire Henri-Mondor, Assistance Publique-Hôpitaux de Paris (AP-HP), Université Paris-Est Créteil (UPEC), Créteil, France; INSERM U955, équipe 2. Institut Mondor de Recherche Biomédicale (IMRB), Université Paris-Est Créteil (UPEC), Créteil, France
| | - Laetitia Languille
- Service de Médecine Interne, Centre Hospitalier Universitaire Henri-Mondor, Assistance Publique-Hôpitaux de Paris (AP-HP), Université Paris-Est Créteil (UPEC), Créteil, France
| | - Morgane Fournier
- Institut Necker Enfants Malades, INSERM U1151/CNRS UMR 8253, Action thématique incitative sur programme-Avenir Team, Auto-Immune and Immune B cells, Université Paris Cité, Université Paris Est-Créteil, Créteil, France; Service de Médecine Interne, Centre Hospitalier Universitaire Henri-Mondor, Assistance Publique-Hôpitaux de Paris (AP-HP), Université Paris-Est Créteil (UPEC), Créteil, France
| | - Marc Michel
- Service de Médecine Interne, Centre Hospitalier Universitaire Henri-Mondor, Assistance Publique-Hôpitaux de Paris (AP-HP), Université Paris-Est Créteil (UPEC), Créteil, France
| | - Bertrand Godeau
- Service de Médecine Interne, Centre Hospitalier Universitaire Henri-Mondor, Assistance Publique-Hôpitaux de Paris (AP-HP), Université Paris-Est Créteil (UPEC), Créteil, France
| | - Sébastien Gallien
- Service de Maladies Infectieuses, Centre Hospitalier Universitaire Henri Mondor, Assistance Publique-Hôpitaux de Paris (AP-HP), Université Paris-Est Créteil (UPEC), Créteil, France
| | - Giovanna Melica
- Service de Maladies Infectieuses, Centre Hospitalier Universitaire Henri Mondor, Assistance Publique-Hôpitaux de Paris (AP-HP), Université Paris-Est Créteil (UPEC), Créteil, France
| | - Yann Nguyen
- Service de Médecine Interne, Centre Hospitalier Universitaire Cochin, Assistance Publique-Hôpitaux de Paris (AP-HP), Paris, France
| | - Florence Canoui-Poitrine
- Département de Santé Publique, Unité de Recherche Clinique (URC), CEpiA (Clinical Epidemiology and Ageing), EA 7376- Institut Mondor de Recherche Biomédicale (IMRB), Centre Hospitalier Universitaire Henri-Mondor, Assistance Publique-Hôpitaux de Paris (AP-HP), Université Paris-Est Créteil (UPEC), Créteil, France
| | - France Pirenne
- INSERM U955, équipe 18. Institut Mondor de Recherche Biomédicale (IMRB), Université Paris-Est Créteil (UPEC), Créteil, France; Etablissement Français du Sang (EFS) Ile de France, Créteil, France
| | - Jérôme Megret
- Plateforme de Cytométrie en Flux, Structure Fédérative de Recherche Necker, INSERM US24-CNRS UMS3633, Paris, France
| | - Jean-Michel Pawlotsky
- Département de Virologie, Bactériologie, Hygiène et Mycologie-Parasitologie, Centre Hospitalier Universitaire Henri Mondor, Assistance Publique-Hôpitaux de Paris (AP-HP), Créteil, France; INSERM U955, équipe 18. Institut Mondor de Recherche Biomédicale (IMRB), Université Paris-Est Créteil (UPEC), Créteil, France
| | - Simon Fillatreau
- Institut Necker Enfants Malades (INEM), INSERM U1151/CNRS UMR 8253, Université de Paris, Paris, France
| | - Claude-Agnès Reynaud
- Institut Necker Enfants Malades, INSERM U1151/CNRS UMR 8253, Action thématique incitative sur programme-Avenir Team, Auto-Immune and Immune B cells, Université Paris Cité, Université Paris Est-Créteil, Créteil, France
| | - Jean-Claude Weill
- Institut Necker Enfants Malades, INSERM U1151/CNRS UMR 8253, Action thématique incitative sur programme-Avenir Team, Auto-Immune and Immune B cells, Université Paris Cité, Université Paris Est-Créteil, Créteil, France
| | - Félix A Rey
- Institut Pasteur, Université de Paris Cité, CNRS UMR 3569, Unité de Virologie Structurale, Paris, France
| | - Pierre Bruhns
- Institut Pasteur, Université de Paris Cité, INSERM UMR1222, Unit of Antibodies in Therapy and Pathology, Paris, France
| | - Matthieu Mahévas
- Institut Necker Enfants Malades, INSERM U1151/CNRS UMR 8253, Action thématique incitative sur programme-Avenir Team, Auto-Immune and Immune B cells, Université Paris Cité, Université Paris Est-Créteil, Créteil, France; Service de Médecine Interne, Centre Hospitalier Universitaire Henri-Mondor, Assistance Publique-Hôpitaux de Paris (AP-HP), Université Paris-Est Créteil (UPEC), Créteil, France; INSERM U955, équipe 2. Institut Mondor de Recherche Biomédicale (IMRB), Université Paris-Est Créteil (UPEC), Créteil, France.
| | - Pascal Chappert
- Institut Necker Enfants Malades, INSERM U1151/CNRS UMR 8253, Action thématique incitative sur programme-Avenir Team, Auto-Immune and Immune B cells, Université Paris Cité, Université Paris Est-Créteil, Créteil, France; INSERM U955, équipe 2. Institut Mondor de Recherche Biomédicale (IMRB), Université Paris-Est Créteil (UPEC), Créteil, France.
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Alhassan AM, Shirure VS, Luo J, Nguyen BB, Rollins ZA, Shergill BS, Zhu X, Baumgarth N, George SC. A microfluidic strategy to capture antigen-specific high affinity B cells. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.07.12.548739. [PMID: 37503139 PMCID: PMC10369944 DOI: 10.1101/2023.07.12.548739] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/29/2023]
Abstract
Assessing B cell affinity to pathogen-specific antigens prior to or following exposure could facilitate the assessment of immune status. Current standard tools to assess antigen-specific B cell responses focus on equilibrium binding of the secreted antibody in serum. These methods are costly, time-consuming, and assess antibody affinity under zero-force. Recent findings indicate that force may influence BCR-antigen binding interactions and thus immune status. Here, we designed a simple laminar flow microfluidic chamber in which the antigen (hemagglutinin of influenza A) is bound to the chamber surface to assess antigen-specific BCR binding affinity of five hemagglutinin-specific hybridomas under 65- to 650-pN force range. Our results demonstrate that both increasing shear force and bound lifetime can be used to enrich antigen-specific high affinity B cells. The affinity of the membrane-bound BCR in the flow chamber correlates well with the affinity of the matched antibodies measured in solution. These findings demonstrate that a microfluidic strategy can rapidly assess BCR-antigen binding properties and identify antigen-specific high affinity B cells. This strategy has the potential to both assess functional immune status from peripheral B cells and be a cost-effective way of identifying individual B cells as antibody sources for a range of clinical applications.
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Affiliation(s)
- Ahmed M. Alhassan
- Department of Biomedical Engineering, University of California, Davis
| | | | - Jean Luo
- Department of Pathology, Microbiology, and Immunology, University of California, Davis
| | - Bryan B. Nguyen
- Department of Biomedical Engineering, University of California, Davis
| | | | | | - Xiangdong Zhu
- Department of Physics and Astronomy, University of California, Davis
| | - Nicole Baumgarth
- Department of Pathology, Microbiology, and Immunology, University of California, Davis
- Department of Molecular Microbiology and Immunology, Bloomberg School of Public Health and Department of Molecular and Comparative Pathobiology, School of Medicine, Johns Hopkins University, Baltimore, MD
| | - Steven C. George
- Department of Biomedical Engineering, University of California, Davis
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5
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Abstract
In the computational design of antibodies, the interaction analysis between target antigen and antibody is an essential process to obtain feedback for validation and optimization of the design. Kinetic and thermodynamic parameters as well as binding affinity (KD) allow for a more detailed evaluation and understanding of the molecular recognition. In this chapter, we summarize the conventional experimental methods which can calculate KD value (ELISA, FP), analyze a binding activity to actual cells (FCM), and evaluate the kinetic and thermodynamic parameters (ITC, SPR, BLI), including high-throughput analysis and a recently developed experimental technique.
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Affiliation(s)
- Aki Tanabe
- Department of Bioengineering, School of Engineering, The University of Tokyo, Tokyo, Japan
- AIDS Research Center, National Institute of Infectious Diseases, Tokyo, Japan
| | - Kouhei Tsumoto
- Department of Bioengineering, School of Engineering, The University of Tokyo, Tokyo, Japan.
- Department of Chemistry and Biotechnology, School of Engineering, The University of Tokyo, Tokyo, Japan.
- The Institute of Medical Science, The University of Tokyo, Tokyo, Japan.
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6
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Houy C, Ming M, Ettorre L, Jin R, Thangavadivel N, Chen T, Su J, Gajewska B. Epitope Profiling of Diphtheria Toxoid Provides Enhanced Monitoring for Consistency Testing during Manufacturing Process Changes. Vaccines (Basel) 2022; 10:vaccines10050775. [PMID: 35632531 PMCID: PMC9147534 DOI: 10.3390/vaccines10050775] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2022] [Revised: 04/30/2022] [Accepted: 05/10/2022] [Indexed: 11/16/2022] Open
Abstract
In the vaccine industry, multiple physicochemical, immunological, in vitro and in vivo analytical methods are applied throughout the manufacturing process to characterize and monitor the quality of vaccines. Presented here is the Single Epitope Antigenicity Test (SEAT), an innovative, quantitative epitope profiling method which provides an extended immunochemical analysis for diphtheria toxoid (DTxd) to be used for consistency testing during manufacturing process changes. The method uses BioLayer Interferometry (BLI) and a panel of monoclonal antibodies (mAbs) to independently assess nine individual antigenic sites of DTxd. The panel includes mAbs which are functional, bind distinct sites on DTxd and are able to distinguish intact DTxd from that which has been exposed to heat treatment. The SEAT method was qualified for precision, accuracy, and linearity, and was used to define a preliminary comparability range for DTxd made using the current manufacturing process. DTxd lots manufactured using alternate processes were assessed in the context of this range to determine the impact on DTxd antigenicity. Epitope profiling by SEAT provides quantitative information on the integrity of multiple important antigenic regions of DTxd, and therefore represents a valuable tool in a comprehensive analytical test package which can be used to support manufacturing process changes for vaccines.
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Affiliation(s)
- Camille Houy
- Correspondence: ; Tel.: +1-476-667-2700 (ext. 7629)
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7
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Sun H, Hu N, Wang J. Application of Microfluidic Technology in Antibody Screening. Biotechnol J 2022; 17:e2100623. [PMID: 35481726 DOI: 10.1002/biot.202100623] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2021] [Revised: 04/13/2022] [Accepted: 04/23/2022] [Indexed: 11/07/2022]
Abstract
Specific antibodies are widely used in the biomedical field. Current screening methods for specific antibodies mainly involve hybridoma technology and antibody engineering techniques. However, these technologies suffer from tedious screening processes, long preparation periods, high costs, low efficiency, and a degree of automation, which have become a bottleneck for the screening of specific antibodies. To overcome these difficulties, microfluidics has been developed as a promising technology for high-throughput screening and high purity of antibody. In this review, we provide an overview of the recent advances in microfluidic applications for specific antibody screening. In particular, hybridoma technology and four antibody engineering techniques (including phage display, single B cell antibody screening, antibody expression, and cell-free protein synthesis) based on microfluidics have been introduced, challenges, and the future outlook of these technologies are also discussed. This article is protected by copyright. All rights reserved.
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Affiliation(s)
- Heng Sun
- Key Laboratory of Biorheological Science and Technology, Ministry of Education, College of Bioengineering, Chongqing University, Chongqing, 400044, China
| | - Ning Hu
- Key Laboratory of Biorheological Science and Technology, Ministry of Education, College of Bioengineering, Chongqing University, Chongqing, 400044, China
| | - Jianhua Wang
- Key Laboratory of Biorheological Science and Technology, Ministry of Education, College of Bioengineering, Chongqing University, Chongqing, 400044, China
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8
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Sokal A, Broketa M, Barba-Spaeth G, Meola A, Fernández I, Fourati S, Azzaoui I, de La Selle A, Vandenberghe A, Roeser A, Bouvier-Alias M, Crickx E, Languille L, Michel M, Godeau B, Gallien S, Melica G, Nguyen Y, Zarrouk V, Canoui-Poitrine F, Noizat-Pirenne F, Megret J, Pawlotsky JM, Fillatreau S, Simon-Lorière E, Weill JC, Reynaud CA, Rey FA, Bruhns P, Chappert P, Mahévas M. Analysis of mRNA vaccination-elicited RBD-specific memory B cells reveals strong but incomplete immune escape of the SARS-CoV-2 Omicron variant. Immunity 2022; 55:1096-1104.e4. [PMID: 35483354 PMCID: PMC8986479 DOI: 10.1016/j.immuni.2022.04.002] [Citation(s) in RCA: 32] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2021] [Revised: 02/16/2022] [Accepted: 04/04/2022] [Indexed: 11/05/2022]
Abstract
The SARS-CoV-2 Omicron variant can escape neutralization by vaccine-elicited and convalescent antibodies. Memory B cells (MBCs) represent another layer of protection against SARS-CoV-2, as they persist after infection and vaccination and improve their affinity. Whether MBCs elicited by mRNA vaccines can recognize the Omicron variant remains unclear. We assessed the affinity and neutralization potency against the Omicron variant of several hundred naturally expressed MBC-derived monoclonal IgG antibodies from vaccinated COVID-19-recovered and -naive individuals. Compared with other variants of concern, Omicron evaded recognition by a larger proportion of MBC-derived antibodies, with only 30% retaining high affinity against the Omicron RBD, and the reduction in neutralization potency was even more pronounced. Nonetheless, neutralizing MBC clones could be found in all the analyzed individuals. Therefore, despite the strong immune escape potential of the Omicron variant, these results suggest that the MBC repertoire generated by mRNA vaccines still provides some protection against the Omicron variant in vaccinated individuals.
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9
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Vander Mause ER, Atanackovic D, Lim CS, Luetkens T. Roadmap to affinity-tuned antibodies for enhanced chimeric antigen receptor T cell function and selectivity. Trends Biotechnol 2022; 40:875-890. [DOI: 10.1016/j.tibtech.2021.12.009] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2021] [Revised: 12/16/2021] [Accepted: 12/17/2021] [Indexed: 12/29/2022]
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10
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Miyoshi T, Friedman TB, Watanabe N. Fast-dissociating but highly specific antibodies are novel tools in biology, especially useful for multiplex super-resolution microscopy. STAR Protoc 2021; 2:100967. [PMID: 34841279 PMCID: PMC8605432 DOI: 10.1016/j.xpro.2021.100967] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Fast-dissociating, highly specific monoclonal antibodies (FDSAs) are single-molecule imaging probes useful for many biological assays including consecutive, multiplexable super-resolution microscopy. We developed a screening assay to characterize the kinetics of antibody-antigen interactions using single-molecule microscopy and established a pipeline to identify FDSAs from thousands of monoclonal candidates. Provided here are detailed protocols to prepare multi-well glass-bottom plates necessary for our assay to identify hybridoma clones secreting FDSAs. Synthesis of fluorescently labeled Fab fragments (Fab probes) from FDSAs is also described. For complete details on the use and execution of this protocol, please refer to Miyoshi et al. (2021).
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Affiliation(s)
- Takushi Miyoshi
- Laboratory of Single-Molecule Cell Biology, Graduate School of Biostudies, Kyoto University, Kyoto 606-8501, Japan
- Department of Pharmacology, Graduate School of Medicine, Kyoto University, Kyoto 606-8501, Japan
- Laboratory of Molecular Genetics, National Institute on Deafness and Other Communication Disorders, National Institutes of Health, Porter Neuroscience Research Center, Room 1F-143A, Bethesda, MD 20892, USA
- Department of Otolaryngology - Head and Neck Surgery, Graduate School of Medicine, Kyoto University, Kyoto 606-8507, Japan
| | - Thomas B. Friedman
- Laboratory of Molecular Genetics, National Institute on Deafness and Other Communication Disorders, National Institutes of Health, Porter Neuroscience Research Center, Room 1F-143A, Bethesda, MD 20892, USA
| | - Naoki Watanabe
- Laboratory of Single-Molecule Cell Biology, Graduate School of Biostudies, Kyoto University, Kyoto 606-8501, Japan
- Department of Pharmacology, Graduate School of Medicine, Kyoto University, Kyoto 606-8501, Japan
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11
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Li A, Harris RJ, Fry BG, Barnes AC. A single-step, high throughput, and highly reproducible method for measuring IgM quantity and avidity directly from fish serum via biolayer interferometry (BLI). FISH & SHELLFISH IMMUNOLOGY 2021; 119:231-237. [PMID: 34626789 DOI: 10.1016/j.fsi.2021.10.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/31/2021] [Revised: 09/29/2021] [Accepted: 10/05/2021] [Indexed: 06/13/2023]
Abstract
Quantification of specific antibody responses is critical in determining activation of MHCII-dependent immune memory and is generally performed by enzyme-linked immunosorbent assay (ELISA). Antibody avidity for a particular antigen is also informative of the quality of the adaptive immune response following vaccination. Avidity can be determined by chaotropic elution ELISA, pre-absorption ELISA, or surface plasmon resonance (SPR), although multimeric antibodies such as IgM are problematic for SPR. ELISA-based assays are very time consuming, require secondary antibody reagents, and are poorly repeatable. Here we demonstrate that biolayer interferometry (BLI) using an Octet HTX instrument can robustly and reproducibly quantify and determine avidity of specific IgM for an antigen directly from fish serum in a single step. We collected sera from giant grouper (Epinephelus lanceolatus) that had been vaccinated with the hapten 2,4-dinitrophenol conjugated to keyhole limpet hemocyanin (DNP-KLH) and from control fish injected with phosphate buffered saline. The specific IgM in the serum and its avidity for DNP were quantified via ELISA and BLI. BLI was precise and highly repeatable for determination of the quantity and avidity of antibody in the serum compared to ELISA. The wet-lab preparation and machine running time for BLI was 3-5 times faster than ELISA to generate the same amount of data. The ELISA inter-plate variation significantly affected reproducibility while BLI was consistent and repeatable between samples and plates. Indeed, the consistency of BLI data indicated that technical triplicates were redundant. Biological replication alone was sufficient to elucidate the effect of treatments. However, BLI required a lower serum dilution than ELISA for similar sensitivity, and thus more serum was required to produce high resolution data. BLI is an extremely high-throughput assay, providing teleost serum IgM quantification and avidity data as a single-step, agile alternative to ELISA.
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Affiliation(s)
- Angus Li
- The University of Queensland, School of Biological Sciences, Brisbane, QLD, 4072, Australia
| | - Richard J Harris
- The University of Queensland, School of Biological Sciences, Brisbane, QLD, 4072, Australia
| | - Bryan G Fry
- The University of Queensland, School of Biological Sciences, Brisbane, QLD, 4072, Australia
| | - Andrew C Barnes
- The University of Queensland, School of Biological Sciences, Brisbane, QLD, 4072, Australia.
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12
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Sokal A, Barba-Spaeth G, Fernández I, Broketa M, Azzaoui I, de La Selle A, Vandenberghe A, Fourati S, Roeser A, Meola A, Bouvier-Alias M, Crickx E, Languille L, Michel M, Godeau B, Gallien S, Melica G, Nguyen Y, Zarrouk V, Canoui-Poitrine F, Pirenne F, Mégret J, Pawlotsky JM, Fillatreau S, Bruhns P, Rey FA, Weill JC, Reynaud CA, Chappert P, Mahévas M. mRNA vaccination of naive and COVID-19-recovered individuals elicits potent memory B cells that recognize SARS-CoV-2 variants. Immunity 2021; 54:2893-2907.e5. [PMID: 34614412 PMCID: PMC8452492 DOI: 10.1016/j.immuni.2021.09.011] [Citation(s) in RCA: 87] [Impact Index Per Article: 29.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2021] [Revised: 08/05/2021] [Accepted: 09/14/2021] [Indexed: 01/04/2023]
Abstract
In addition to serum immunoglobulins, memory B cell (MBC) generation against severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is another layer of immune protection, but the quality of MBC responses in naive and coronavirus disease 2019 (COVID-19)-recovered individuals after vaccination remains ill defined. We studied longitudinal cohorts of naive and disease-recovered individuals for up to 2 months after SARS-CoV-2 mRNA vaccination. We assessed the quality of the memory response by analysis of antibody repertoires, affinity, and neutralization against variants of concern (VOCs) using unbiased cultures of 2,452 MBCs. Upon boosting, the MBC pool of recovered individuals expanded selectively, matured further, and harbored potent neutralizers against VOCs. Although naive individuals had weaker neutralizing serum responses, half of their RBD-specific MBCs displayed high affinity toward multiple VOCs, including delta (B.1.617.2), and one-third retained neutralizing potency against beta (B.1.351). Our data suggest that an additional challenge in naive vaccinees could recall such affinity-matured MBCs and allow them to respond efficiently to VOCs.
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Affiliation(s)
- Aurélien Sokal
- Institut Necker Enfants Malades (INEM), INSERM U1151/CNRS UMS 8253, Université de Paris, Paris, France; Service de Médecine Interne, Centre Hospitalier Universitaire Henri-Mondor, Assistance Publique-Hôpitaux de Paris (AP-HP), Université Paris-Est Créteil (UPEC), Créteil, France
| | - Giovanna Barba-Spaeth
- Institut Pasteur, Université de Paris, Unité de Virologie Structurale, CNRS UMR 3569, Paris 75015, France
| | - Ignacio Fernández
- Institut Pasteur, Université de Paris, Unité de Virologie Structurale, CNRS UMR 3569, Paris 75015, France
| | - Matteo Broketa
- Institut Pasteur, Université de Paris, INSERM UMR 1222, Unit of Antibodies in Therapy and Pathology, Paris 75015, France; Sorbonne Université, Collège doctoral, Paris 75005, France
| | - Imane Azzaoui
- Service de Médecine Interne, Centre Hospitalier Universitaire Henri-Mondor, Assistance Publique-Hôpitaux de Paris (AP-HP), Université Paris-Est Créteil (UPEC), Créteil, France; INSERM U955, Équipe 2, Institut Mondor de Recherche Biomédicale (IMRB), Université Paris-Est Créteil (UPEC), Créteil, France
| | - Andréa de La Selle
- Institut Necker Enfants Malades (INEM), INSERM U1151/CNRS UMS 8253, Université de Paris, Paris, France; Service de Médecine Interne, Centre Hospitalier Universitaire Henri-Mondor, Assistance Publique-Hôpitaux de Paris (AP-HP), Université Paris-Est Créteil (UPEC), Créteil, France
| | - Alexis Vandenberghe
- Service de Médecine Interne, Centre Hospitalier Universitaire Henri-Mondor, Assistance Publique-Hôpitaux de Paris (AP-HP), Université Paris-Est Créteil (UPEC), Créteil, France; INSERM U955, Équipe 2, Institut Mondor de Recherche Biomédicale (IMRB), Université Paris-Est Créteil (UPEC), Créteil, France
| | - Slim Fourati
- Département de Virologie, Bactériologie, Hygiène et Mycologie-Parasitologie, Centre Hospitalier Universitaire Henri-Mondor, Assistance Publique-Hôpitaux de Paris (AP-HP), Créteil, France; INSERM U955, Équipe 18, Institut Mondor de Recherche Biomédicale (IMRB), Université Paris-Est Créteil (UPEC), Créteil, France
| | - Anais Roeser
- Institut Necker Enfants Malades (INEM), INSERM U1151/CNRS UMS 8253, Université de Paris, Paris, France; Service de Médecine Interne, Centre Hospitalier Universitaire Henri-Mondor, Assistance Publique-Hôpitaux de Paris (AP-HP), Université Paris-Est Créteil (UPEC), Créteil, France
| | - Annalisa Meola
- Institut Pasteur, Université de Paris, Unité de Virologie Structurale, CNRS UMR 3569, Paris 75015, France
| | - Magali Bouvier-Alias
- Département de Virologie, Bactériologie, Hygiène et Mycologie-Parasitologie, Centre Hospitalier Universitaire Henri-Mondor, Assistance Publique-Hôpitaux de Paris (AP-HP), Créteil, France; INSERM U955, Équipe 18, Institut Mondor de Recherche Biomédicale (IMRB), Université Paris-Est Créteil (UPEC), Créteil, France
| | - Etienne Crickx
- Institut Necker Enfants Malades (INEM), INSERM U1151/CNRS UMS 8253, Université de Paris, Paris, France; Service de Médecine Interne, Centre Hospitalier Universitaire Henri-Mondor, Assistance Publique-Hôpitaux de Paris (AP-HP), Université Paris-Est Créteil (UPEC), Créteil, France
| | - Laetitia Languille
- Service de Médecine Interne, Centre Hospitalier Universitaire Henri-Mondor, Assistance Publique-Hôpitaux de Paris (AP-HP), Université Paris-Est Créteil (UPEC), Créteil, France
| | - Marc Michel
- Service de Médecine Interne, Centre Hospitalier Universitaire Henri-Mondor, Assistance Publique-Hôpitaux de Paris (AP-HP), Université Paris-Est Créteil (UPEC), Créteil, France
| | - Bertrand Godeau
- Service de Médecine Interne, Centre Hospitalier Universitaire Henri-Mondor, Assistance Publique-Hôpitaux de Paris (AP-HP), Université Paris-Est Créteil (UPEC), Créteil, France
| | - Sébastien Gallien
- Service de Maladies Infectieuses, Centre Hospitalier Universitaire Henri-Mondor, Assistance Publique-Hôpitaux de Paris (AP-HP), Université Paris-Est Créteil (UPEC), Créteil, France
| | - Giovanna Melica
- Service de Maladies Infectieuses, Centre Hospitalier Universitaire Henri-Mondor, Assistance Publique-Hôpitaux de Paris (AP-HP), Université Paris-Est Créteil (UPEC), Créteil, France
| | - Yann Nguyen
- Service de Médecine Interne, Hôpital Beaujon, Assistance Publique-Hôpitaux de Paris, Université de Paris, Clichy, France
| | - Virginie Zarrouk
- Service de Médecine Interne, Hôpital Beaujon, Assistance Publique-Hôpitaux de Paris, Université de Paris, Clichy, France
| | - Florence Canoui-Poitrine
- Département de Santé Publique, Unité de Recherche Clinique (URC), CEpiA (Clinical Epidemiology and Ageing), EA 7376, Institut Mondor de Recherche Biomédicale (IMRB), Centre Hospitalier Universitaire Henri-Mondor, Assistance Publique-Hôpitaux de Paris (AP-HP), Université Paris-Est Créteil (UPEC), Créteil, France
| | - France Pirenne
- INSERM U955, Équipe 2, Institut Mondor de Recherche Biomédicale (IMRB), Université Paris-Est Créteil (UPEC), Créteil, France; Etablissement Français du Sang (EFS) Ile de France, Créteil, France
| | - Jérôme Mégret
- Plateforme de Cytométrie en Flux, Structure Fédérative de Recherche Necker, INSERM US24-CNRS UMS3633, Paris, France
| | - Jean-Michel Pawlotsky
- Département de Virologie, Bactériologie, Hygiène et Mycologie-Parasitologie, Centre Hospitalier Universitaire Henri-Mondor, Assistance Publique-Hôpitaux de Paris (AP-HP), Créteil, France; INSERM U955, Équipe 18, Institut Mondor de Recherche Biomédicale (IMRB), Université Paris-Est Créteil (UPEC), Créteil, France
| | - Simon Fillatreau
- Institut Necker Enfants Malades (INEM), INSERM U1151/CNRS UMS 8253, Université de Paris, Paris, France
| | - Pierre Bruhns
- Institut Pasteur, Université de Paris, INSERM UMR 1222, Unit of Antibodies in Therapy and Pathology, Paris 75015, France
| | - Felix A Rey
- Institut Pasteur, Université de Paris, Unité de Virologie Structurale, CNRS UMR 3569, Paris 75015, France
| | - Jean-Claude Weill
- Institut Necker Enfants Malades (INEM), INSERM U1151/CNRS UMS 8253, Université de Paris, Paris, France.
| | - Claude-Agnès Reynaud
- Institut Necker Enfants Malades (INEM), INSERM U1151/CNRS UMS 8253, Université de Paris, Paris, France.
| | - Pascal Chappert
- Institut Necker Enfants Malades (INEM), INSERM U1151/CNRS UMS 8253, Université de Paris, Paris, France; Inovarion, Paris, France.
| | - Matthieu Mahévas
- Institut Necker Enfants Malades (INEM), INSERM U1151/CNRS UMS 8253, Université de Paris, Paris, France; Service de Médecine Interne, Centre Hospitalier Universitaire Henri-Mondor, Assistance Publique-Hôpitaux de Paris (AP-HP), Université Paris-Est Créteil (UPEC), Créteil, France; INSERM U955, Équipe 2, Institut Mondor de Recherche Biomédicale (IMRB), Université Paris-Est Créteil (UPEC), Créteil, France.
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13
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Shmool TA, Martin LK, Bui-Le L, Moya-Ramirez I, Kotidis P, Matthews RP, Venter GA, Kontoravdi C, Polizzi KM, Hallett JP. An experimental approach probing the conformational transitions and energy landscape of antibodies: a glimmer of hope for reviving lost therapeutic candidates using ionic liquid. Chem Sci 2021; 12:9528-9545. [PMID: 34349928 PMCID: PMC8278930 DOI: 10.1039/d1sc02520a] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2021] [Accepted: 05/26/2021] [Indexed: 12/26/2022] Open
Abstract
Understanding protein folding in different environmental conditions is fundamentally important for predicting protein structures and developing innovative antibody formulations. While the thermodynamics and kinetics of folding and unfolding have been extensively studied by computational methods, experimental methods for determining antibody conformational transition pathways are lacking. Motivated to fill this gap, we prepared a series of unique formulations containing a high concentration of a chimeric immunoglobin G4 (IgG4) antibody with different excipients in the presence and absence of the ionic liquid (IL) choline dihydrogen phosphate. We determined the effects of different excipients and IL on protein thermal and structural stability by performing variable temperature circular dichroism and bio-layer interferometry analyses. To further rationalise the observations of conformational changes with temperature, we carried out molecular dynamics simulations on a single antibody binding fragment from IgG4 in the different formulations, at low and high temperatures. We developed a methodology to study the conformational transitions and associated thermodynamics of biomolecules, and we showed IL-induced conformational transitions. We showed that the increased propensity for conformational change was driven by preferential binding of the dihydrogen phosphate anion to the antibody fragment. Finally, we found that a formulation containing IL with sugar, amino acids and surfactant is a promising candidate for stabilising proteins against conformational destabilisation and aggregation. We hope that ultimately, we can help in the quest to understand the molecular basis of the stability of antibodies and protein misfolding phenomena and offer new candidate formulations with the potential to revive lost therapeutic candidates.
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Affiliation(s)
- Talia A Shmool
- Department of Chemical Engineering, Imperial College London South Kensington Campus London SW7 2AZ UK +44 (0)20 7594 5388
| | - Laura K Martin
- Department of Engineering Science, University of Oxford Parks Road Oxford OX1 3PJ UK
| | - Liem Bui-Le
- Department of Chemical Engineering, Imperial College London South Kensington Campus London SW7 2AZ UK +44 (0)20 7594 5388
| | - Ignacio Moya-Ramirez
- Department of Chemical Engineering, Imperial College London South Kensington Campus London SW7 2AZ UK +44 (0)20 7594 5388
| | - Pavlos Kotidis
- Department of Chemical Engineering, Imperial College London South Kensington Campus London SW7 2AZ UK +44 (0)20 7594 5388
| | - Richard P Matthews
- Department of Chemical Engineering, Imperial College London South Kensington Campus London SW7 2AZ UK +44 (0)20 7594 5388
| | - Gerhard A Venter
- Scientific Computing Research Unit, Department of Chemistry, University of Cape Town Rondebosch Cape Town 7701 South Africa
| | - Cleo Kontoravdi
- Department of Chemical Engineering, Imperial College London South Kensington Campus London SW7 2AZ UK +44 (0)20 7594 5388
| | - Karen M Polizzi
- Department of Chemical Engineering, Imperial College London South Kensington Campus London SW7 2AZ UK +44 (0)20 7594 5388
| | - Jason P Hallett
- Department of Chemical Engineering, Imperial College London South Kensington Campus London SW7 2AZ UK +44 (0)20 7594 5388
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14
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Trkulja CL, Jungholm O, Davidson M, Jardemark K, Marcus MM, Hägglund J, Karlsson A, Karlsson R, Bruton J, Ivarsson N, Srinivasa SP, Cavallin A, Svensson P, Jeffries GDM, Christakopoulou MN, Reymer A, Ashok A, Willman G, Papadia D, Johnsson E, Orwar O. Rational antibody design for undruggable targets using kinetically controlled biomolecular probes. SCIENCE ADVANCES 2021; 7:7/16/eabe6397. [PMID: 33863724 PMCID: PMC8051879 DOI: 10.1126/sciadv.abe6397] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/03/2020] [Accepted: 02/26/2021] [Indexed: 05/07/2023]
Abstract
Several important drug targets, e.g., ion channels and G protein-coupled receptors, are extremely difficult to approach with current antibody technologies. To address these targets classes, we explored kinetically controlled proteases as structural dynamics-sensitive druggability probes in native-state and disease-relevant proteins. By using low-Reynolds number flows, such that a single or a few protease incisions are made, we could identify antibody binding sites (epitopes) that were translated into short-sequence antigens for antibody production. We obtained molecular-level information of the epitope-paratope region and could produce high-affinity antibodies with programmed pharmacological function against difficult-to-drug targets. We demonstrate the first stimulus-selective monoclonal antibodies targeting the transient receptor potential vanilloid 1 (TRPV1) channel, a clinically validated pain target widely considered undruggable with antibodies, and apoptosis-inducing antibodies selectively mediating cytotoxicity in KRAS-mutated cells. It is our hope that this platform will widen the scope of antibody therapeutics for the benefit of patients.
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Affiliation(s)
| | - Oscar Jungholm
- Department of Physiology and Pharmacology, Karolinska Institutet, SE-171 77 Stockholm, Sweden
| | - Max Davidson
- Oblique Therapeutics AB, SE-41346 Gothenburg, Sweden
| | - Kent Jardemark
- Department of Physiology and Pharmacology, Karolinska Institutet, SE-171 77 Stockholm, Sweden
| | - Monica M Marcus
- Department of Physiology and Pharmacology, Karolinska Institutet, SE-171 77 Stockholm, Sweden
| | - Jessica Hägglund
- Oblique Therapeutics AB, SE-41346 Gothenburg, Sweden
- Department of Physiology and Pharmacology, Karolinska Institutet, SE-171 77 Stockholm, Sweden
| | - Anders Karlsson
- Oblique Therapeutics AB, SE-41346 Gothenburg, Sweden
- Nanoxis Consulting AB, SE-40016 Gothenburg, Sweden
| | - Roger Karlsson
- Oblique Therapeutics AB, SE-41346 Gothenburg, Sweden
- Nanoxis Consulting AB, SE-40016 Gothenburg, Sweden
| | - Joseph Bruton
- Department of Physiology and Pharmacology, Karolinska Institutet, SE-171 77 Stockholm, Sweden
| | - Niklas Ivarsson
- Department of Physiology and Pharmacology, Karolinska Institutet, SE-171 77 Stockholm, Sweden
| | | | - Alexandra Cavallin
- Department of Physiology and Pharmacology, Karolinska Institutet, SE-171 77 Stockholm, Sweden
| | - Peder Svensson
- Integrative Research Laboratories, SE-41346, Gothenburg, Sweden
| | | | | | - Anna Reymer
- Oblique Therapeutics AB, SE-41346 Gothenburg, Sweden
- Department of Chemistry and Molecular Biology, University of Gothenburg, SE-405 30 Gothenburg, Sweden
| | | | | | | | - Emma Johnsson
- Oblique Therapeutics AB, SE-41346 Gothenburg, Sweden
| | - Owe Orwar
- Oblique Therapeutics AB, SE-41346 Gothenburg, Sweden.
- Department of Physiology and Pharmacology, Karolinska Institutet, SE-171 77 Stockholm, Sweden
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15
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Epitope Binning of Novel Monoclonal Anti F1 and Anti LcrV Antibodies and Their Application in a Simple, Short, HTRF Test for Clinical Plague Detection. Pathogens 2021; 10:pathogens10030285. [PMID: 33801490 PMCID: PMC8001648 DOI: 10.3390/pathogens10030285] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2021] [Revised: 02/24/2021] [Accepted: 02/25/2021] [Indexed: 11/18/2022] Open
Abstract
Mouse monoclonal antibodies were raised against plague disease biomarkers: the bacterial capsular protein fraction 1 (F1) and the low-calcium response—LcrV virulence factor (Vag). A novel tandem assay, employing BioLayer Interferometry (BLI), enabled the isolation of antibodies against four different epitopes on Vag. The tandem assay was carried out with hybridoma supernatants, circumventing the need for antibody purification. The BioLayer assay was further adopted for characterization of epitope-repetitive antigens, enabling the discovery of two unique epitopes on F1. The selected antibodies were purified and applied as “oligo-clonal” reagents for the immuno-detection of both biomarkers. The developed Homogenous Time Resolved Fluorescence (HTRF) tests were short (10 min) and simple (no washing steps), allowing for detection of 10 ng/mL F1 and 2.5 ng/mL Vag. The tests were successfully applied for detection of disease biomarkers produced by various Y. pestis strains during growth in blood culture vials.
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16
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Kisovec M, Anderluh G, Podobnik M, Caserman S. In-line detection of monoclonal antibodies in the effluent of protein A chromatography with QCM sensor. Anal Biochem 2020; 608:113899. [PMID: 32763307 DOI: 10.1016/j.ab.2020.113899] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2020] [Revised: 07/27/2020] [Accepted: 07/29/2020] [Indexed: 10/23/2022]
Abstract
A major drawback of the IgG capture step is the high cost of the protein A resin. For a better utilization of the resin, a continuous multi-column operation was recently proposed. In this method, accurate detection of leaking IgG is crucial to divert the breakthrough fluid from the waste to the next column and prolong the loading step without product loss. The detection of a breakthrough point as a change in UV absorption is based on a relatively small signal addition of IgGs to the bulk signal of host cell proteins. To achieve specificity, we used a quartz crystal microbalance and immobilized protein A as specific ligand on the sensor surface. We integrated the quartz crystal microbalance sensor in-line after the protein A column for real-time detection of IgGs in the breakthrough fluid. We show that this specific IgG detection in the breakthrough fluid can be more sensitive than with the UV detector. The use of the same product-specific ligand in the affinity column and in the sensor allows simultaneous in-line regeneration of column and sensor in a single step. Such a sensor could support cost-efficient load control during the entire continuous multi-column capture step in downstream processing.
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Affiliation(s)
- Matic Kisovec
- Department of Molecular Biology and Nanobiotechnology, National Institute of Chemistry, Hajdrihova Ulica 19, SI-1000, Ljubljana, Slovenia
| | - Gregor Anderluh
- Department of Molecular Biology and Nanobiotechnology, National Institute of Chemistry, Hajdrihova Ulica 19, SI-1000, Ljubljana, Slovenia
| | - Marjetka Podobnik
- Department of Molecular Biology and Nanobiotechnology, National Institute of Chemistry, Hajdrihova Ulica 19, SI-1000, Ljubljana, Slovenia
| | - Simon Caserman
- Department of Molecular Biology and Nanobiotechnology, National Institute of Chemistry, Hajdrihova Ulica 19, SI-1000, Ljubljana, Slovenia.
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Choi JR, Kim MJ, Tae N, Wi TM, Kim SH, Lee ES, Kim DH. BLI-Based Functional Assay in Phage Display Benefits the Development of a PD-L1-Targeting Therapeutic Antibody. Viruses 2020; 12:v12060684. [PMID: 32630442 PMCID: PMC7354572 DOI: 10.3390/v12060684] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2020] [Revised: 06/09/2020] [Accepted: 06/24/2020] [Indexed: 12/21/2022] Open
Abstract
The therapeutic functionality of the antibodies from phage display is verified after an initial screening. Several immunological assays such as ELISA, flow cytometry, the western blot, and surface plasmon resonance (SPR) assay are commonly used; the IgG-format antibody is usually preferred to verify the functionality of antibodies, which need elaborative mammalian expression and purification work. Here, we describe a biolayer interferometry (BLI)-based assay that can evaluate the inhibitory functions of antibodies at an earlier stage of screening. To develop a PD-L1-targeting antibody from phage display, we applied the BLI assay to the initial scFv antibody screening, in addition to common ELISA and fluorescence-activated cell sorting (FACS) assays, which showed high advantages and relevance with the in vitro cell-based PD-1/PD-L1 inhibition assay. The same assays for IgG-format antibodies showed high efficiency of the BLI assay in the functional characterization of antibodies, and one candidate selected from the BLI assay resulted in highly efficacious antitumor activity in an in vivo syngeneic mouse study. The BLI assay was also beneficial when searching for antibodies with diverse epitopes. These results demonstrated that the BLI-based inhibition assay is an excellent technique for high-throughput scFv antibody screening in earlier stages and can make phage-display antibody screening more efficient to develop therapeutic candidates.
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Affiliation(s)
- Jong Rip Choi
- Scripps Korea Antibody Institute, KNU Chuncheon Campus, Chuncheon, Gangwon 200-701, Korea; (J.R.C.); (M.J.K.); (N.T.); (T.M.W.)
- Department of Systems Immunology, College of Biomedical Science, Kangwon National University, Chuncheon, Gangwon 200-701, Korea;
| | - Min Jung Kim
- Scripps Korea Antibody Institute, KNU Chuncheon Campus, Chuncheon, Gangwon 200-701, Korea; (J.R.C.); (M.J.K.); (N.T.); (T.M.W.)
- Department of Systems Immunology, College of Biomedical Science, Kangwon National University, Chuncheon, Gangwon 200-701, Korea;
| | - Nara Tae
- Scripps Korea Antibody Institute, KNU Chuncheon Campus, Chuncheon, Gangwon 200-701, Korea; (J.R.C.); (M.J.K.); (N.T.); (T.M.W.)
| | - Tae Min Wi
- Scripps Korea Antibody Institute, KNU Chuncheon Campus, Chuncheon, Gangwon 200-701, Korea; (J.R.C.); (M.J.K.); (N.T.); (T.M.W.)
| | - Se-Ho Kim
- Department of Systems Immunology, College of Biomedical Science, Kangwon National University, Chuncheon, Gangwon 200-701, Korea;
| | - Eung Suk Lee
- Scripps Korea Antibody Institute, KNU Chuncheon Campus, Chuncheon, Gangwon 200-701, Korea; (J.R.C.); (M.J.K.); (N.T.); (T.M.W.)
- Correspondence: (E.S.L.); (D.H.K.); Tel.: +82-33-250-8097 (E.S.L.); +82-33-250-8089 (D.H.K.)
| | - Dae Hee Kim
- Scripps Korea Antibody Institute, KNU Chuncheon Campus, Chuncheon, Gangwon 200-701, Korea; (J.R.C.); (M.J.K.); (N.T.); (T.M.W.)
- Correspondence: (E.S.L.); (D.H.K.); Tel.: +82-33-250-8097 (E.S.L.); +82-33-250-8089 (D.H.K.)
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18
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Lowegard AU, Frenkel MS, Holt GT, Jou JD, Ojewole AA, Donald BR. Novel, provable algorithms for efficient ensemble-based computational protein design and their application to the redesign of the c-Raf-RBD:KRas protein-protein interface. PLoS Comput Biol 2020; 16:e1007447. [PMID: 32511232 PMCID: PMC7329130 DOI: 10.1371/journal.pcbi.1007447] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2019] [Revised: 07/01/2020] [Accepted: 05/13/2020] [Indexed: 11/25/2022] Open
Abstract
The K* algorithm provably approximates partition functions for a set of states (e.g., protein, ligand, and protein-ligand complex) to a user-specified accuracy ε. Often, reaching an ε-approximation for a particular set of partition functions takes a prohibitive amount of time and space. To alleviate some of this cost, we introduce two new algorithms into the osprey suite for protein design: fries, a Fast Removal of Inadequately Energied Sequences, and EWAK*, an Energy Window Approximation to K*. fries pre-processes the sequence space to limit a design to only the most stable, energetically favorable sequence possibilities. EWAK* then takes this pruned sequence space as input and, using a user-specified energy window, calculates K* scores using the lowest energy conformations. We expect fries/EWAK* to be most useful in cases where there are many unstable sequences in the design sequence space and when users are satisfied with enumerating the low-energy ensemble of conformations. In combination, these algorithms provably retain calculational accuracy while limiting the input sequence space and the conformations included in each partition function calculation to only the most energetically favorable, effectively reducing runtime while still enriching for desirable sequences. This combined approach led to significant speed-ups compared to the previous state-of-the-art multi-sequence algorithm, BBK*, while maintaining its efficiency and accuracy, which we show across 40 different protein systems and a total of 2,826 protein design problems. Additionally, as a proof of concept, we used these new algorithms to redesign the protein-protein interface (PPI) of the c-Raf-RBD:KRas complex. The Ras-binding domain of the protein kinase c-Raf (c-Raf-RBD) is the tightest known binder of KRas, a protein implicated in difficult-to-treat cancers. fries/EWAK* accurately retrospectively predicted the effect of 41 different sets of mutations in the PPI of the c-Raf-RBD:KRas complex. Notably, these mutations include mutations whose effect had previously been incorrectly predicted using other computational methods. Next, we used fries/EWAK* for prospective design and discovered a novel point mutation that improves binding of c-Raf-RBD to KRas in its active, GTP-bound state (KRasGTP). We combined this new mutation with two previously reported mutations (which were highly-ranked by osprey) to create a new variant of c-Raf-RBD, c-Raf-RBD(RKY). fries/EWAK* in osprey computationally predicted that this new variant binds even more tightly than the previous best-binding variant, c-Raf-RBD(RK). We measured the binding affinity of c-Raf-RBD(RKY) using a bio-layer interferometry (BLI) assay, and found that this new variant exhibits single-digit nanomolar affinity for KRasGTP, confirming the computational predictions made with fries/EWAK*. This new variant binds roughly five times more tightly than the previous best known binder and roughly 36 times more tightly than the design starting point (wild-type c-Raf-RBD). This study steps through the advancement and development of computational protein design by presenting theory, new algorithms, accurate retrospective designs, new prospective designs, and biochemical validation. Computational structure-based protein design is an innovative tool for redesigning proteins to introduce a particular or novel function. One such function is improving the binding of one protein to another, which can increase our understanding of important protein systems. Herein we introduce two novel, provable algorithms, fries and EWAK*, for more efficient computational structure-based protein design as well as their application to the redesign of the c-Raf-RBD:KRas protein-protein interface. These new algorithms speed-up computational structure-based protein design while maintaining accurate calculations, allowing for larger, previously infeasible protein designs. Additionally, using fries and EWAK* within the osprey suite, we designed the tightest known binder of KRas, a heavily studied cancer target that interacts with a number of different proteins. This previously undiscovered variant of a KRas-binding domain, c-Raf-RBD, has potential to serve as a tool to further probe the protein-protein interface of KRas with its effectors and its discovery alone emphasizes the potential for more successful applications of computational structure-based protein design.
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Affiliation(s)
- Anna U. Lowegard
- Program in Computational Biology and Bioinformatics, Duke University Medical Center, Durham, North Carolina, United States of America
- Department of Computer Science, Duke University, Durham, North Carolina, United States of America
| | - Marcel S. Frenkel
- Department of Biochemistry, Duke University Medical Center, Durham, North Carolina, United States of America
| | - Graham T. Holt
- Program in Computational Biology and Bioinformatics, Duke University Medical Center, Durham, North Carolina, United States of America
- Department of Computer Science, Duke University, Durham, North Carolina, United States of America
| | - Jonathan D. Jou
- Department of Computer Science, Duke University, Durham, North Carolina, United States of America
| | - Adegoke A. Ojewole
- Program in Computational Biology and Bioinformatics, Duke University Medical Center, Durham, North Carolina, United States of America
- Department of Computer Science, Duke University, Durham, North Carolina, United States of America
| | - Bruce R. Donald
- Department of Computer Science, Duke University, Durham, North Carolina, United States of America
- Department of Biochemistry, Duke University Medical Center, Durham, North Carolina, United States of America
- * E-mail:
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19
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Parray HA, Shukla S, Samal S, Shrivastava T, Ahmed S, Sharma C, Kumar R. Hybridoma technology a versatile method for isolation of monoclonal antibodies, its applicability across species, limitations, advancement and future perspectives. Int Immunopharmacol 2020; 85:106639. [PMID: 32473573 PMCID: PMC7255167 DOI: 10.1016/j.intimp.2020.106639] [Citation(s) in RCA: 92] [Impact Index Per Article: 23.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2020] [Revised: 05/06/2020] [Accepted: 05/22/2020] [Indexed: 02/06/2023]
Abstract
The advancements in technology and manufacturing processes have allowed the development of new derivatives, biosimilar or advanced improved versions for approved antibodies each year for treatment regimen. There are more than 700 antibody-based molecules that are in different stages of phase I/II/ III clinical trials targeting new unique targets. To date, approximately more than 80 monoclonal antibodies (mAbs) have been approved. A total of 7 novel antibody therapeutics had been granted the first approval either in the United States or European Union in the year 2019, representing approximately 20% of the total number of approved drugs. Most of these licenced mAbs or their derivatives are either of hybridoma origin or their improvised engineered versions. Even with the recent development of high throughput mAb generation technologies, hybridoma is the most favoured method due to its indigenous nature to preserve natural cognate antibody pairing information and preserves innate functions of immune cells. The recent advent of antibody engineering technology has superseded the species level barriers and has shown success in isolation of hybridoma across phylogenetically distinct species. This has led to the isolation of monoclonal antibodies against human targets that are conserved and non-immunogenic in the rodent. In this review, we have discussed in detail about hybridoma technology, its expansion towards different animal species, the importance of antibodies isolated from different animal sources that are useful in biological applications, advantages, and limitations. This review also summarizes the challenges and recent progress associated with hybridoma development, and how it has been overcome in these years to provide new insights for the isolation of mAbs.
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Affiliation(s)
- Hilal Ahmed Parray
- Translational Health Science & Technology Institute, NCR Biotech Science Cluster, Faridabad, Haryana 121001, India
| | - Shivangi Shukla
- Translational Health Science & Technology Institute, NCR Biotech Science Cluster, Faridabad, Haryana 121001, India
| | - Sweety Samal
- Translational Health Science & Technology Institute, NCR Biotech Science Cluster, Faridabad, Haryana 121001, India
| | - Tripti Shrivastava
- Translational Health Science & Technology Institute, NCR Biotech Science Cluster, Faridabad, Haryana 121001, India
| | - Shubbir Ahmed
- Translational Health Science & Technology Institute, NCR Biotech Science Cluster, Faridabad, Haryana 121001, India
| | - Chandresh Sharma
- Translational Health Science & Technology Institute, NCR Biotech Science Cluster, Faridabad, Haryana 121001, India.
| | - Rajesh Kumar
- Translational Health Science & Technology Institute, NCR Biotech Science Cluster, Faridabad, Haryana 121001, India.
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20
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Li J, Zhai X, Ding C, Liu Y, Dong Q, Xu D, Wang X, Qiu J, Zhang Q, Pan J, Liu Q. Development of a Bacterial Macroarray for the Rapid Screening of Targeted Antibody-Secreted Hybridomas. SLAS DISCOVERY 2018; 24:190-198. [PMID: 30304643 DOI: 10.1177/2472555218804990] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Hybridoma screening is a key step for the successful generation of high-affinity analyte-specific monoclonal antibodies (MAbs). This work presents an innovative screening method, known as a bacterial macroarray, generated by contact printing of hybridoma cell supernatant samples on a nitrocellulose (NC) membrane initially coated with fluorescein isothiocyanate (FITC)-labeled bacteria. Given that bacterial fixation will be influenced by complex bacterial surface structures, we selected both gram-positive bacteria ( Staphylococcus aureus and Listeria monocytogenes) and gram-negative bacteria ( Escherichia coli O157:H7 and Cronobacter sakazakii) to optimize the fixation conditions for binding to the NC membrane, such as the aperture of the NC membrane, the concentration of bacteria, the dosage of glycerin in the spotting buffer, and the fixation time and temperature. As a result, we found that a better bacterial macroarray could be developed when the spotting buffer, containing 1011 CFU mL-1 of FITC-labeled bacteria and 15% (V/V) glycerol, was spotted onto a 0.45 µm NC membrane with an incubation of 2 h at 37 °C. Finally, we verified the stability and specificity of the prepared bacterial macroarray by detecting cell cultures with the addition of two MAbs ( Escherichia coli O157:H7 MAb E7 and Cronobacter sakazakii MAb 1E9) to simulate the screening experiments. Here, we describe a bacterial macroarray to efficiently screen the targeted antibody-secreted hybridomas.
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Affiliation(s)
- Jie Li
- 1 School of Medical Instrument and Food Engineering, University of Shanghai for Science and Technology, Shanghai, PR China
| | - XuZhao Zhai
- 1 School of Medical Instrument and Food Engineering, University of Shanghai for Science and Technology, Shanghai, PR China
| | - Chengchao Ding
- 1 School of Medical Instrument and Food Engineering, University of Shanghai for Science and Technology, Shanghai, PR China
| | - Yali Liu
- 2 Lanzhou University Second Hospital, Lanzhou, China
| | - Qingli Dong
- 1 School of Medical Instrument and Food Engineering, University of Shanghai for Science and Technology, Shanghai, PR China
| | - Dongpo Xu
- 1 School of Medical Instrument and Food Engineering, University of Shanghai for Science and Technology, Shanghai, PR China
| | - Xiang Wang
- 1 School of Medical Instrument and Food Engineering, University of Shanghai for Science and Technology, Shanghai, PR China
| | - Jingxuan Qiu
- 1 School of Medical Instrument and Food Engineering, University of Shanghai for Science and Technology, Shanghai, PR China
| | - Qi Zhang
- 1 School of Medical Instrument and Food Engineering, University of Shanghai for Science and Technology, Shanghai, PR China
| | - Jing Pan
- 1 School of Medical Instrument and Food Engineering, University of Shanghai for Science and Technology, Shanghai, PR China
| | - Qing Liu
- 1 School of Medical Instrument and Food Engineering, University of Shanghai for Science and Technology, Shanghai, PR China.,3 Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao, PR China
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21
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Petersen RL. Strategies Using Bio-Layer Interferometry Biosensor Technology for Vaccine Research and Development. BIOSENSORS-BASEL 2017; 7:bios7040049. [PMID: 29088096 PMCID: PMC5746772 DOI: 10.3390/bios7040049] [Citation(s) in RCA: 74] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/14/2017] [Revised: 10/26/2017] [Accepted: 10/28/2017] [Indexed: 12/13/2022]
Abstract
Bio-layer interferometry (BLI) real-time, label-free technology has greatly contributed to advances in vaccine research and development. BLI Octet platforms offer high-throughput, ease of use, reliability, and high precision analysis when compared with common labeling techniques. Many different strategies have been used to immobilize the pathogen or host molecules on BLI biosensors for real-time kinetics and affinity analysis, quantification, or high-throughput titer. These strategies can be used in multiple applications and shed light onto the structural and functional aspects molecules play during pathogen-host interactions. They also provide crucial information on how to achieve protection. This review summarizes some key BLI strategies used in human vaccine research and development.
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22
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Kamat V, Rafique A. Designing binding kinetic assay on the bio-layer interferometry (BLI) biosensor to characterize antibody-antigen interactions. Anal Biochem 2017; 536:16-31. [PMID: 28802648 DOI: 10.1016/j.ab.2017.08.002] [Citation(s) in RCA: 68] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2017] [Revised: 08/03/2017] [Accepted: 08/07/2017] [Indexed: 01/24/2023]
Abstract
The Octet biosensors provide a high-throughput alternative to the well-established surface plasmon resonance (SPR) and SPR imaging (SPRi) biosensors to characterize antibody-antigen interactions. However, the utility of the Octet biosensors for accurate and reproducible measurement of binding rate constants of monoclonal antibodies (mAbs) is limited due to challenges such as analyte rebinding, and mass transport limitation (MTL). This study focuses on addressing these challenges and provides experimental conditions to reliably measure kinetics of mAb-antigen interactions. The mAb capture density of less than 0.6 nm was found to be optimal to measure a wide range of binding affinities on Octet HTX biosensor. The titration kinetic and single cycle kinetic assays performed on Octet HTX generated reproducible binding kinetic parameters and correlated with the values measured on Biacore 4000 and MASS-1. Kinetic assays performed on 0.1 nm density mAb surfaces significantly reduced MTL and enabled characterization of picomolar affinity mAbs. Finally, kinetic analysis performed on 150 antibodies to 10 antigens with molecular weights ranging from 21kD to 105kD showed concordance between Octet HTX, Biacore 4000 and MASS-1 (R2 > 0.90). The data presented in this study suggest that under optimal experimental conditions, Octet biosensor is capable of generating kinetic values comparable to SPR/SPRi biosensors.
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Affiliation(s)
- Vishal Kamat
- Biomolecular HTS Center, Therapeutic Proteins, Regeneron Pharmaceuticals, 777 Old Saw Mill River Road, Tarrytown, NY 10591, USA.
| | - Ashique Rafique
- Biomolecular HTS Center, Therapeutic Proteins, Regeneron Pharmaceuticals, 777 Old Saw Mill River Road, Tarrytown, NY 10591, USA
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23
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Tao Z, Yang H, Shi Q, Fan Q, Wan L, Lu X. Targeted Delivery to Tumor-associated Pericytes via an Affibody with High Affinity for PDGFRβ Enhances the in vivo Antitumor Effects of Human TRAIL. Theranostics 2017; 7:2261-2276. [PMID: 28740549 PMCID: PMC5505058 DOI: 10.7150/thno.19091] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2017] [Accepted: 04/06/2017] [Indexed: 02/05/2023] Open
Abstract
Human tumor necrosis factor-related apoptosis-inducing ligand (hTRAIL) has exhibited superior in vitro cytotoxicity in a variety of tumor cells. However, hTRAIL showed a disappointing anticancer effect in clinical trials, although hTRAIL-based regimens were well tolerated. One important reason might be that hTRAIL was largely trapped by its decoy receptors, which are ubiquitously expressed on normal cells. Tumor-targeted delivery might improve the tumor uptake and thus enhance the antitumor effect of hTRAIL. Platelet-derived growth factor receptor β (PDGFRβ)-expressing pericytes are enriched in tumor tissues derived both from patients with colon cancer and from mice bearing colorectal tumor xenografts. A ZPDGFRβ affibody showed high affinity (nM) for PDGFRβ and was predominantly distributed on tumor-associated PDGFRβ-positive pericytes. Co-administration with the ZPDGFRβ affibody did not significantly enhance the antitumor effect of hTRAIL in mice bearing tumor xenografts. Fusion to the ZPDGFRβ affibody endows hTRAIL with PDGFRβ-binding ability but does not interfere with its death receptor binding and activation. The fused ZPDGFRβ affibody mediated PDGFRβ-dependent binding of hTRAIL to pericytes. In addition, hTRAIL bound on pericytes could kill tumor cells through juxtatropic activity or exhibit cytotoxicity in tumor cells after being released from pericytes. Intravenously injected hTRAIL fused to ZPDGFRβ affibody initially accumulated on tumor-associated pericytes and then diffused to the tumor parenchyma over time. Fusion to the ZPDGFRβ affibody increased the tumor uptake of hTRAIL, thus enhancing the antitumor effect of hTRAIL in mice bearing tumor xenografts. These results demonstrate that pericyte-targeted delivery mediated by a ZPDGFRβ affibody is an alternative strategy for tumor-targeted delivery of anticancer agents.
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Affiliation(s)
- Ze Tao
- Key Lab of Transplant Engineering and Immunology, MOH, West China Hospital, Sichuan University, Chengdu, 610041, China
- Regenerative Medical Research Center, West China Hospital, Sichuan University, Chengdu, 610041, China
| | - Hao Yang
- Key Lab of Transplant Engineering and Immunology, MOH, West China Hospital, Sichuan University, Chengdu, 610041, China
| | - Qiuxiao Shi
- Key Lab of Transplant Engineering and Immunology, MOH, West China Hospital, Sichuan University, Chengdu, 610041, China
- Regenerative Medical Research Center, West China Hospital, Sichuan University, Chengdu, 610041, China
| | - Qing Fan
- Key Lab of Transplant Engineering and Immunology, MOH, West China Hospital, Sichuan University, Chengdu, 610041, China
- Regenerative Medical Research Center, West China Hospital, Sichuan University, Chengdu, 610041, China
| | - Lin Wan
- Key Lab of Transplant Engineering and Immunology, MOH, West China Hospital, Sichuan University, Chengdu, 610041, China
| | - Xiaofeng Lu
- Key Lab of Transplant Engineering and Immunology, MOH, West China Hospital, Sichuan University, Chengdu, 610041, China
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24
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Yang D, Singh A, Wu H, Kroe-Barrett R. Determination of High-affinity Antibody-antigen Binding Kinetics Using Four Biosensor Platforms. J Vis Exp 2017. [PMID: 28448040 PMCID: PMC5564993 DOI: 10.3791/55659] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/05/2022] Open
Abstract
Label-free optical biosensors are powerful tools in drug discovery for the characterization of biomolecular interactions. In this study, we describe the use of four routinely used biosensor platforms in our laboratory to evaluate the binding affinity and kinetics of ten high-affinity monoclonal antibodies (mAbs) against human proprotein convertase subtilisin kexin type 9 (PCSK9). While both Biacore T100 and ProteOn XPR36 are derived from the well-established Surface Plasmon Resonance (SPR) technology, the former has four flow cells connected by serial flow configuration, whereas the latter presents 36 reaction spots in parallel through an improvised 6 x 6 crisscross microfluidic channel configuration. The IBIS MX96 also operates based on the SPR sensor technology, with an additional imaging feature that provides detection in spatial orientation. This detection technique coupled with the Continuous Flow Microspotter (CFM) expands the throughput significantly by enabling multiplex array printing and detection of 96 reaction sports simultaneously. In contrast, the Octet RED384 is based on the BioLayer Interferometry (BLI) optical principle, with fiber-optic probes acting as the biosensor to detect interference pattern changes upon binding interactions at the tip surface. Unlike the SPR-based platforms, the BLI system does not rely on continuous flow fluidics; instead, the sensor tips collect readings while they are immersed in analyte solutions of a 384-well microplate during orbital agitation. Each of these biosensor platforms has its own advantages and disadvantages. To provide a direct comparison of these instruments' ability to provide quality kinetic data, the described protocols illustrate experiments that use the same assay format and the same high-quality reagents to characterize antibody-antigen kinetics that fit the simple 1:1 molecular interaction model.
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Affiliation(s)
- Danlin Yang
- Department of Biotherapeutics Discovery, Immune Modulation and Biotherapeutics Discovery, Boehringer Ingelheim Pharmaceuticals, Inc
| | - Ajit Singh
- The Fu Foundation School of Engineering and Applied Science, Columbia University
| | - Helen Wu
- Department of Biotherapeutics Discovery, Immune Modulation and Biotherapeutics Discovery, Boehringer Ingelheim Pharmaceuticals, Inc
| | - Rachel Kroe-Barrett
- Department of Biotherapeutics Discovery, Immune Modulation and Biotherapeutics Discovery, Boehringer Ingelheim Pharmaceuticals, Inc.;
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25
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Dippong M, Carl P, Lenz C, Schenk JA, Hoffmann K, Schwaar T, Schneider RJ, Kuhne M. Hapten-Specific Single-Cell Selection of Hybridoma Clones by Fluorescence-Activated Cell Sorting for the Generation of Monoclonal Antibodies. Anal Chem 2017; 89:4007-4012. [DOI: 10.1021/acs.analchem.6b04569] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Affiliation(s)
- Martin Dippong
- Bundesanstalt für Materialforschung und -prüfung (BAM), Richard-Willstätter-Str.
11, 12489 Berlin, Germany
- University of Potsdam, Institute for Biochemistry and
Biology, Karl-Liebknecht-Str.
24-25, 14476 Potsdam, Germany
- Fraunhofer Institute for Cell Therapy and Immunology (IZI), Branch Bioanalytics and Bioprocesses Potsdam-Golm, Am Mühlenberg 13, 14476 Potsdam, Germany
| | - Peter Carl
- Bundesanstalt für Materialforschung und -prüfung (BAM), Richard-Willstätter-Str.
11, 12489 Berlin, Germany
- Humboldt-Universität zu Berlin, Department of Chemistry, Brook-Taylor-Str. 2, 12489 Berlin, Germany
| | - Christine Lenz
- UP Transfer GmbH, Am Neuen
Palais 10, 14469 Potsdam, Germany
- Hybrotec GmbH, Am Mühlenberg
11, 14476 Potsdam-Golm, Germany
| | - Jörg A. Schenk
- UP Transfer GmbH, Am Neuen
Palais 10, 14469 Potsdam, Germany
- Hybrotec GmbH, Am Mühlenberg
11, 14476 Potsdam-Golm, Germany
| | - Katrin Hoffmann
- Bundesanstalt für Materialforschung und -prüfung (BAM), Richard-Willstätter-Str.
11, 12489 Berlin, Germany
| | - Timm Schwaar
- Bundesanstalt für Materialforschung und -prüfung (BAM), Richard-Willstätter-Str.
11, 12489 Berlin, Germany
- Humboldt-Universität zu Berlin, Department of Chemistry, Brook-Taylor-Str. 2, 12489 Berlin, Germany
| | - Rudolf J. Schneider
- Bundesanstalt für Materialforschung und -prüfung (BAM), Richard-Willstätter-Str.
11, 12489 Berlin, Germany
| | - Maren Kuhne
- Bundesanstalt für Materialforschung und -prüfung (BAM), Richard-Willstätter-Str.
11, 12489 Berlin, Germany
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26
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Hsiao YH, Huang CY, Hu CY, Wu YY, Wu CH, Hsu CH, Chen C. Continuous microfluidic assortment of interactive ligands (CMAIL). Sci Rep 2016; 6:32454. [PMID: 27578501 PMCID: PMC5006012 DOI: 10.1038/srep32454] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2016] [Accepted: 08/09/2016] [Indexed: 01/15/2023] Open
Abstract
Finding an interactive ligand-receptor pair is crucial to many applications, including the development of monoclonal antibodies. Biopanning, a commonly used technique for affinity screening, involves a series of washing steps and is lengthy and tedious. Here we present an approach termed continuous microfluidic assortment of interactive ligands, or CMAIL, for the screening and sorting of antigen-binding single-chain variable antibody fragments (scFv) displayed on bacteriophages (phages). Phages carrying native negative charges on their coat proteins were electrophoresed through a hydrogel matrix functionalized with target antigens under two alternating orthogonal electric fields. During the weak horizontal electric field phase, phages were differentially swept laterally depending on their affinity for the antigen, and all phages were electrophoresed down to be collected during the strong vertical electric field phase. Phages of different affinity were spatially separated, allowing the continuous operation. More than 105 CFU (colony forming unit) antigen-interacting phages were isolated with ~100% specificity from a phage library containing 3 × 109 individual members within 40 minutes of sorting using CMAIL. CMAIL is rapid, sensitive, specific, and does not employ washing, elution or magnetic beads. In conclusion, we have developed an efficient and cost-effective method for isolating and sorting affinity reagents involving phage display.
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Affiliation(s)
- Yi-Hsing Hsiao
- Institute of Nanoengineering and Microsystems, National Tsing Hua University, Hsinchu 30013, Taiwan.,Institute of Biomedical Engineering and Nanomedicine, National Health Research Institutes, Miaoli 35053, Taiwan
| | - Chao-Yang Huang
- Development Center for Biotechnology, New Taipei City 22180, Taiwan
| | - Chih-Yung Hu
- Development Center for Biotechnology, New Taipei City 22180, Taiwan
| | - Yen-Yu Wu
- Development Center for Biotechnology, New Taipei City 22180, Taiwan
| | - Chung-Hsiun Wu
- Development Center for Biotechnology, New Taipei City 22180, Taiwan
| | - Chia-Hsien Hsu
- Institute of Nanoengineering and Microsystems, National Tsing Hua University, Hsinchu 30013, Taiwan.,Institute of Biomedical Engineering and Nanomedicine, National Health Research Institutes, Miaoli 35053, Taiwan
| | - Chihchen Chen
- Institute of Nanoengineering and Microsystems, National Tsing Hua University, Hsinchu 30013, Taiwan.,Department of Power Mechanical Engineering, National Tsing Hua University, Hsinchu 30013, Taiwan
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McGivern JG, Howes R. JBS special issue on therapeutic antibody discovery and development: biologics come of age. ACTA ACUST UNITED AC 2016; 20:433-6. [PMID: 25805607 DOI: 10.1177/1087057115572999] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
In this special issue of the Journal of biomolecular screening, we have assembled a series of articles that exemplify and discuss various aspects and challenges associated with the discovery, development, and manufacture of biologics with an emphasis on those topics that we feel will appeal to readers of this journal. We hope you enjoy them!
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Yu Y, Mitchell S, Lynaugh H, Brown M, Nobrega RP, Zhi X, Sun T, Caffry I, Cao Y, Yang R, Burnina I, Xu Y, Estep P. Understanding ForteBio's Sensors for High-Throughput Kinetic and Epitope Screening for Purified Antibodies and Yeast Culture Supernatant. ACTA ACUST UNITED AC 2015; 21:88-95. [PMID: 26442912 PMCID: PMC4708621 DOI: 10.1177/1087057115609564] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2015] [Accepted: 09/09/2015] [Indexed: 01/26/2023]
Abstract
Real-time and label-free antibody screening systems are becoming more popular because of the increasing output of purified antibodies and antibody supernatant from many antibody discovery platforms. However, the properties of the biosensor can greatly affect the kinetic and epitope binning results generated by these label-free screening systems. ForteBio human-specific ProA, anti-human IgG quantitation (AHQ), anti-human Fc capture (AHC) sensors, and custom biotinylated-anti-human Fc capture (b-AHFc) sensors were evaluated in terms of loading ability, regeneration, kinetic characterization, and epitope binning with both purified IgG and IgG supernatant. AHC sensors proved unreliable for kinetic or binning assays at times, whereas AHQ sensors showed poor loading and regeneration abilities. ProA sensors worked well with both purified IgG and IgG supernatant. However, the interaction between ProA sensors and the Fab region of the IgG with VH3 germline limited the application of ProA sensors, especially in the epitope binning experiment. In an attempt to generate a biosensor type that would be compatible with a variety of germlines and sample types, we found that the custom b-AHFc sensors appeared to be robust working with both purified IgG and IgG supernatant, with little evidence of sensor-related artifacts.
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Affiliation(s)
- Yao Yu
- Protein Analytics, Adimab, LLC, Lebanon, NH, USA
| | - Scott Mitchell
- Thayer School of Engineering, Dartmouth College, Hanover, NH, USA
| | | | | | | | - Xiaoyong Zhi
- Protein Analytics, Adimab, LLC, Lebanon, NH, USA
| | - Tingwan Sun
- Protein Analytics, Adimab, LLC, Lebanon, NH, USA
| | | | - Yuan Cao
- Protein Analytics, Adimab, LLC, Lebanon, NH, USA
| | - Rong Yang
- Protein Analytics, Adimab, LLC, Lebanon, NH, USA
| | | | - Yingda Xu
- Protein Analytics, Adimab, LLC, Lebanon, NH, USA
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29
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Current advances in the development of high-throughput purification strategies for the generation of therapeutic antibodies. ACTA ACUST UNITED AC 2015. [DOI: 10.4155/pbp.15.23] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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30
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Solution Equilibrium Titration for High-Throughput Affinity Estimation of Unpurified Antibodies and Antibody Fragments. ACTA ACUST UNITED AC 2015; 20:1256-67. [DOI: 10.1177/1087057115595002] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2015] [Accepted: 06/14/2015] [Indexed: 01/14/2023]
Abstract
The generation of therapeutic antibodies with extremely high affinities down to the low picomolar range is today feasible with state-of-the art recombinant technologies. However, reliable and efficient identification of lead candidates with the desired affinity from a pool of thousands of antibody clones remains a challenge. Here, we describe a high-throughput procedure that allows reliable affinity screening of unpurified immunoglobulin G or antibody fragments. The method is based on the principle of solution equilibrium titration (SET) using highly sensitive electrochemiluminescence as a readout system. Because the binding partners are not labeled, the resulting KD represents a sound approximation of the real affinity. For screening, diluted bacterial lysates or cell culture supernatants are equilibrated with four different concentrations of a soluble target molecule, and unbound antibodies are subsequently quantified on 384-well Meso Scale Discovery (MSD) plates coated with the respective antigen. For determination of KD values from the resulting titration curves, fit models deduced from the law of mass action for 1:1 and 2:1 binding modes are applied to assess hundreds of interactions simultaneously. The accuracy of the method is demonstrated by comparing results from different screening campaigns from affinity optimization projects with results from detailed affinity characterization.
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