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Krohn S, Holtrop T, Brandsma AM, Moerer P, Nederend M, Darzentas N, Brüggemann M, Klausz K, Leusen JHW, Peipp M. Combining Cellular Immunization and Phage Display Screening Results in Novel, FcγRI-Specific Antibodies. Viruses 2024; 16:596. [PMID: 38675937 PMCID: PMC11053525 DOI: 10.3390/v16040596] [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: 02/19/2024] [Revised: 04/04/2024] [Accepted: 04/09/2024] [Indexed: 04/28/2024] Open
Abstract
Antibodies that specifically bind to individual human fragment crystallizable γ receptors (FcγRs) are of interest as research tools in studying immune cell functions, as well as components in bispecific antibodies for immune cell engagement in cancer therapy. Monoclonal antibodies for human low-affinity FcγRs have been successfully generated by hybridoma technology and are widely used in pre-clinical research. However, the generation of monoclonal antibodies by hybridoma technology that specifically bind to the high-affinity receptor FcγRI is challenging. Monomeric mouse IgG2a, IgG2b, and IgG3 bind human FcγRI with high affinity via the Fc part, leading to an Fc-mediated rather than a fragment for antigen binding (Fab)-mediated selection of monoclonal antibodies. Blocking the Fc-binding site of FcγRI with an excess of human IgG or Fc during screening decreases the risk of Fc-mediated interactions but can also block the potential epitopes of new antibody candidates. Therefore, we replaced hybridoma technology with phage display of a single-chain fragment variable (scFv) antibody library that was generated from mice immunized with FcγRI-positive cells and screened it with a cellular panning approach assisted by next-generation sequencing (NGS). Seven new FcγRI-specific antibody sequences were selected with this methodology, which were produced as Fc-silent antibodies showing FcγRI-restricted specificity.
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Affiliation(s)
- Steffen Krohn
- Division of Antibody-Based Immunotherapy, Department of Internal Medicine II, University Medical Center Schleswig-Holstein and Christian-Albrechts-University Kiel, 24105 Kiel, Germany
| | - Tosca Holtrop
- Center for Translational Immunology, University Medical Center Utrecht, Heidelberglaan 100, 3584 CX Utrecht, The Netherlands (J.H.W.L.)
| | - Arianne M. Brandsma
- Center for Translational Immunology, University Medical Center Utrecht, Heidelberglaan 100, 3584 CX Utrecht, The Netherlands (J.H.W.L.)
| | - Petra Moerer
- Center for Translational Immunology, University Medical Center Utrecht, Heidelberglaan 100, 3584 CX Utrecht, The Netherlands (J.H.W.L.)
| | - Maaike Nederend
- Center for Translational Immunology, University Medical Center Utrecht, Heidelberglaan 100, 3584 CX Utrecht, The Netherlands (J.H.W.L.)
| | - Nikos Darzentas
- Unit for Hematological Diagnostics, Department of Internal Medicine II, University Medical Center Schleswig-Holstein and Christian-Albrechts-University Kiel, 24105 Kiel, Germany
| | - Monika Brüggemann
- Unit for Hematological Diagnostics, Department of Internal Medicine II, University Medical Center Schleswig-Holstein and Christian-Albrechts-University Kiel, 24105 Kiel, Germany
| | - Katja Klausz
- Division of Antibody-Based Immunotherapy, Department of Internal Medicine II, University Medical Center Schleswig-Holstein and Christian-Albrechts-University Kiel, 24105 Kiel, Germany
| | - Jeanette H. W. Leusen
- Center for Translational Immunology, University Medical Center Utrecht, Heidelberglaan 100, 3584 CX Utrecht, The Netherlands (J.H.W.L.)
| | - Matthias Peipp
- Division of Antibody-Based Immunotherapy, Department of Internal Medicine II, University Medical Center Schleswig-Holstein and Christian-Albrechts-University Kiel, 24105 Kiel, Germany
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2
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Aripov VS, Volkova NV, Ilyichev AA, Shcherbakov DN. Problems of creating antibody phage libraries and their solutions. Vavilovskii Zhurnal Genet Selektsii 2024; 28:249-257. [PMID: 38680186 PMCID: PMC11043502 DOI: 10.18699/vjgb-24-29] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2023] [Revised: 01/18/2024] [Accepted: 01/19/2023] [Indexed: 05/01/2024] Open
Abstract
Phage display has become an efficient, reliable and popular molecular technique for generating libraries encompassing millions or even billions of clones of divergent peptides or proteins. The method is based on the correspondence between phage genotype and phenotype, which ensures the presentation of recombinant proteins of known amino acid composition on the surface of phage particles. The use of affinity selection allows one to choose variants with affinity for different targets from phage libraries. The implementation of the antibody phage display technique has revolutionized the field of clinical immunology, both for developing tools to diagnose infectious diseases and for producing therapeutic agents. It has also become the basis for efficient and relatively inexpensive methods for studying protein-protein interactions, receptor binding sites, as well as epitope and mimotope identification. The antibody phage display technique involves a number of steps, and the final result depends on their successful implementation. The diversity, whether natural or obtained by combinatorial chemistry, is the basis of any library. The choice of molecular techniques is critical to ensure that this diversity is maintained during the phage library preparation step and during the transformation of E. coli cells. After a helper phage is added to the suspension of transformed E. coli cells, a bacteriophage library is formed, which is a working tool for performing the affinity selection procedure and searching for individual molecules. Despite the apparent simplicity of generating phage antibody libraries, a number of subtleties need to be taken into account. First, there are the features of phage vector preparation. Currently, a large number of phagemid vectors have been developed, and their selection is also of great importance. The key step is preparing competent E. coli cells and the technology of their transformation. The choice of a helper phage and the method used to generate it is also important. This article discusses the key challenges faced by researchers in constructing phage antibody libraries.
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Affiliation(s)
- V S Aripov
- State Research Center of Virology and Biotechnology "Vector", Koltsovo, Novosibirsk Region, Russia
| | - N V Volkova
- State Research Center of Virology and Biotechnology "Vector", Koltsovo, Novosibirsk Region, Russia
| | - A A Ilyichev
- State Research Center of Virology and Biotechnology "Vector", Koltsovo, Novosibirsk Region, Russia
| | - D N Shcherbakov
- State Research Center of Virology and Biotechnology "Vector", Koltsovo, Novosibirsk Region, Russia
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3
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Busato D, Capolla S, Durigutto P, Mossenta M, Bozzer S, Sblattero D, Macor P, Dal Bo M, Toffoli G. A novel complement-fixing IgM antibody targeting GPC1 as a useful immunotherapeutic strategy for the treatment of pancreatic ductal adenocarcinoma. J Transl Med 2023; 21:864. [PMID: 38017492 PMCID: PMC10685509 DOI: 10.1186/s12967-023-04745-9] [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: 10/06/2023] [Accepted: 11/20/2023] [Indexed: 11/30/2023] Open
Abstract
BACKGROUND Pancreatic ductal adenocarcinoma (PDAC) is one of the most aggressive cancers with a very low survival rate at 5 years. The use of chemotherapeutic agents results in only modest prolongation of survival and is generally associated with the occurrence of toxicity effects. Antibody-based immunotherapy has been proposed for the treatment of PDAC, but its efficacy has so far proved limited. The proteoglycan glypican-1 (GPC1) may be a useful immunotherapeutic target because it is highly expressed on the surface of PDAC cells, whereas it is not expressed or is expressed at very low levels in benign neoplastic lesions, chronic pancreatitis, and normal adult tissues. Here, we developed and characterized a specific mouse IgM antibody (AT101) targeting GPC1. METHODS We developed a mouse monoclonal antibody of the IgM class directed against an epitope of GPC1 in close proximity to the cell membrane. For this purpose, a 46 amino acid long peptide of the C-terminal region was used to immunize mice by an in-vivo electroporation protocol followed by serum titer and hybridoma formation. RESULTS The ability of AT101 to bind the GPC1 protein was demonstrated by ELISA, and by flow cytometry and immunofluorescence analysis in the GPC1-expressing "PDAC-like" BXPC3 cell line. In-vivo experiments in the BXPC3 xenograft model showed that AT101 was able to bind GPC1 on the cell surface and accumulate in the BXPC3 tumor masses. Ex-vivo analyses of BXPC3 tumor masses showed that AT101 was able to recruit immunological effectors (complement system components, NK cells, macrophages) to the tumor site and damage PDAC tumor tissue. In-vivo treatment with AT101 reduced tumor growth and prolonged survival of mice with BXPC3 tumor (p < 0.0001). CONCLUSIONS These results indicate that AT101, an IgM specific for an epitope of GPC1 close to PDAC cell surface, is a promising immunotherapeutic agent for GPC1-expressing PDAC, being able to selectively activate the complement system and recruit effector cells in the tumor microenvironment, thus allowing to reduce tumor mass growth and improve survival in treated mice.
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Affiliation(s)
- Davide Busato
- Experimental and Clinical Pharmacology, Centro Di Riferimento Oncologico (CRO) Di Aviano IRCCS, 33081, Aviano, Italy
- Department of Life Sciences, University of Trieste, 34127, Trieste, Italy
| | - Sara Capolla
- Experimental and Clinical Pharmacology, Centro Di Riferimento Oncologico (CRO) Di Aviano IRCCS, 33081, Aviano, Italy
| | - Paolo Durigutto
- Department of Life Sciences, University of Trieste, 34127, Trieste, Italy
| | - Monica Mossenta
- Experimental and Clinical Pharmacology, Centro Di Riferimento Oncologico (CRO) Di Aviano IRCCS, 33081, Aviano, Italy
- Department of Life Sciences, University of Trieste, 34127, Trieste, Italy
| | - Sara Bozzer
- Experimental and Clinical Pharmacology, Centro Di Riferimento Oncologico (CRO) Di Aviano IRCCS, 33081, Aviano, Italy
| | - Daniele Sblattero
- Department of Life Sciences, University of Trieste, 34127, Trieste, Italy
| | - Paolo Macor
- Department of Life Sciences, University of Trieste, 34127, Trieste, Italy
| | - Michele Dal Bo
- Experimental and Clinical Pharmacology, Centro Di Riferimento Oncologico (CRO) Di Aviano IRCCS, 33081, Aviano, Italy.
| | - Giuseppe Toffoli
- Experimental and Clinical Pharmacology, Centro Di Riferimento Oncologico (CRO) Di Aviano IRCCS, 33081, Aviano, Italy
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4
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Mitchell KG, Gong B, Hunter SS, Burkart-Waco D, Gavira-O'Neill CE, Templeton KM, Goethel ME, Bzymek M, MacNiven LM, Murray KD, Settles ML, Froenicke L, Trimmer JS. High-volume hybridoma sequencing on the NeuroMabSeq platform enables efficient generation of recombinant monoclonal antibodies and scFvs for neuroscience research. Sci Rep 2023; 13:16200. [PMID: 37758930 PMCID: PMC10533561 DOI: 10.1038/s41598-023-43233-4] [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: 06/28/2023] [Accepted: 09/21/2023] [Indexed: 09/29/2023] Open
Abstract
The Neuroscience Monoclonal Antibody Sequencing Initiative (NeuroMabSeq) is a concerted effort to determine and make publicly available hybridoma-derived sequences of monoclonal antibodies (mAbs) valuable to neuroscience research. Over 30 years of research and development efforts including those at the UC Davis/NIH NeuroMab Facility have resulted in the generation of a large collection of mouse mAbs validated for neuroscience research. To enhance dissemination and increase the utility of this valuable resource, we applied a high-throughput DNA sequencing approach to determine immunoglobulin heavy and light chain variable domain sequences from source hybridoma cells. The resultant set of sequences was made publicly available as a searchable DNA sequence database (neuromabseq.ucdavis.edu) for sharing, analysis and use in downstream applications. We enhanced the utility, transparency, and reproducibility of the existing mAb collection by using these sequences to develop recombinant mAbs. This enabled their subsequent engineering into alternate forms with distinct utility, including alternate modes of detection in multiplexed labeling, and as miniaturized single chain variable fragments or scFvs. The NeuroMabSeq website and database and the corresponding recombinant antibody collection together serve as a public DNA sequence repository of mouse mAb heavy and light chain variable domain sequences and as an open resource for enhancing dissemination and utility of this valuable collection of validated mAbs.
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Affiliation(s)
- Keith G Mitchell
- Department of Physiology and Membrane Biology, University of California Davis School of Medicine, Davis, Davis, CA, USA
- Bioinformatics Core, Genome Center, University of California Davis, Davis, CA, USA
| | - Belvin Gong
- Department of Physiology and Membrane Biology, University of California Davis School of Medicine, Davis, Davis, CA, USA
| | - Samuel S Hunter
- Bioinformatics Core, Genome Center, University of California Davis, Davis, CA, USA
| | - Diana Burkart-Waco
- DNA Technology Core, Genome Center, University of California Davis, Davis, CA, USA
| | - Clara E Gavira-O'Neill
- Department of Physiology and Membrane Biology, University of California Davis School of Medicine, Davis, Davis, CA, USA
| | - Kayla M Templeton
- Department of Physiology and Membrane Biology, University of California Davis School of Medicine, Davis, Davis, CA, USA
| | - Madeline E Goethel
- Department of Physiology and Membrane Biology, University of California Davis School of Medicine, Davis, Davis, CA, USA
| | - Malgorzata Bzymek
- Department of Physiology and Membrane Biology, University of California Davis School of Medicine, Davis, Davis, CA, USA
| | - Leah M MacNiven
- Department of Physiology and Membrane Biology, University of California Davis School of Medicine, Davis, Davis, CA, USA
| | - Karl D Murray
- Department of Physiology and Membrane Biology, University of California Davis School of Medicine, Davis, Davis, CA, USA
- Department of Psychiatry and Behavioral Sciences, University of California Davis School of Medicine, Davis, Davis, CA, USA
| | - Matthew L Settles
- Bioinformatics Core, Genome Center, University of California Davis, Davis, CA, USA
| | - Lutz Froenicke
- DNA Technology Core, Genome Center, University of California Davis, Davis, CA, USA
| | - James S Trimmer
- Department of Physiology and Membrane Biology, University of California Davis School of Medicine, Davis, Davis, CA, USA.
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5
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Quintero-Campos P, Gozalbo-Rovira R, Rodríguez-Díaz J, Maquieira Á, Morais S. Standardizing In Vitro β-Lactam Antibiotic Allergy Testing with Synthetic IgE. Anal Chem 2023; 95:12113-12121. [PMID: 37545056 PMCID: PMC10859892 DOI: 10.1021/acs.analchem.3c02284] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2023] [Accepted: 07/26/2023] [Indexed: 08/08/2023]
Abstract
The global prevalence of β-lactam allergy poses a major challenge in administering first-line antibiotics, such as penicillins, to a significant portion of the population. The lack of β-lactam IgE antibody pools with defined selectivity hampers the standardization and validation of in vitro assays for β-lactam allergy testing. To address this limitation, this study introduces a synthetic IgE specific to β-lactam antibiotics as a valuable tool for drug allergy research and diagnostic tests. Using phage display technology, we constructed a library of human single-chain antibody fragments (scFv) to target the primary determinant of amoxicillin, a widely used β-lactam antibiotic. Subsequently, we produced a complete human synthetic IgE molecule using the highly efficient baculovirus expression vector system. This synthetic IgE molecule served as a standard in an in vitro chemiluminescence immunoassay for β-lactam antibiotic allergy testing. Our results demonstrated a detection limit of 0.05 IU/mL (0.63 pM), excellent specificity (100%), and a four-fold higher clinical sensitivity (73%) compared to the in vitro reference assay when testing a cohort of 150 serum samples. These findings have significant implications for reliable interlaboratory comparison studies, accurate labeling of allergic patients, and combating the global public health threat of antimicrobial resistance. Furthermore, by serving as a valuable trueness control material, the synthetic IgE facilitates the standardization of diagnostic tests for β-lactam allergy and demonstrates the potential of utilizing this synthetic strategy as a promising approach for generating reference materials in drug allergy research and diagnostics.
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Affiliation(s)
- Pedro Quintero-Campos
- Instituto
Interuniversitario de Investigación de Reconocimiento Molecular
y Desarrollo Tecnológico (IDM), Universitat Politècnica
de València-Universitat de València, 46022 Valencia, Spain
| | - Roberto Gozalbo-Rovira
- Departamento
de Microbiología, Facultad de Medicina, Universidad de València, Av. Blasco Ibáñez 17, 46010 València, Spain
- Hospital
Clínico Universitario de Valencia, Instituto de Investigación INCLIVA, 46010 Valencia, Spain
| | - Jesús Rodríguez-Díaz
- Departamento
de Microbiología, Facultad de Medicina, Universidad de València, Av. Blasco Ibáñez 17, 46010 València, Spain
- Hospital
Clínico Universitario de Valencia, Instituto de Investigación INCLIVA, 46010 Valencia, Spain
| | - Ángel Maquieira
- Instituto
Interuniversitario de Investigación de Reconocimiento Molecular
y Desarrollo Tecnológico (IDM), Universitat Politècnica
de València-Universitat de València, 46022 Valencia, Spain
- Unidad
Mixta UPV-La Fe, Nanomedicine and Sensors, IIS La Fe, Av. de Fernando Abril Martorell,
106, 46026 València, Spain
- Departamento
de Química, Universitat Politècnica
de València, Camino
de Vera s/n, 46022 Valencia, Spain
| | - Sergi Morais
- Instituto
Interuniversitario de Investigación de Reconocimiento Molecular
y Desarrollo Tecnológico (IDM), Universitat Politècnica
de València-Universitat de València, 46022 Valencia, Spain
- Unidad
Mixta UPV-La Fe, Nanomedicine and Sensors, IIS La Fe, Av. de Fernando Abril Martorell,
106, 46026 València, Spain
- Departamento
de Química, Universitat Politècnica
de València, Camino
de Vera s/n, 46022 Valencia, Spain
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6
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Oksanen S, Saarinen R, Korkiakoski A, Lamminmäki U, Huovinen T. Genotyped functional screening of soluble Fab clones enables in-depth analysis of mutation effects. Sci Rep 2023; 13:13107. [PMID: 37567990 PMCID: PMC10421887 DOI: 10.1038/s41598-023-40241-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2023] [Accepted: 08/07/2023] [Indexed: 08/13/2023] Open
Abstract
Monoclonal antibodies (mAbs) and their fragments are widely used in therapeutics, diagnostics and basic research. Although display methods such as phage display offer high-throughput, affinities of individual antibodies need to be accurately measured in soluble format. We have developed a screening platform capable of providing genotyped functional data from a total of 9216 soluble, individual antigen binding fragment (Fab) clones by employing next-generation sequencing (NGS) with hierarchical indexing. Full-length, paired variable domain sequences (VL-VH) are linked to functional screening data, enabling in-depth analysis of mutation effects. The platform was applied to four phage display-selected scFv/Fab screening projects and one site-saturation VH affinity maturation project. Genotyped functional screening simultaneously enabled the identification of affinity improving mutations in the VH domain of Fab 49A3 recognizing Dengue virus non-structural protein 1 (NS1) serotype 2 and informed on VH residue positions which cannot be changed from wild-type without decreasing the affinity. Genotype-based identification revealed to us the extent of intraclonal signal variance inherent to single point screening data, a phenomenon often overlooked in the field. Moreover, genotyped screening eliminated the redundant selection of identical genotypes for further study and provided a new analysis tool to evaluate the success of phage display selections and remaining clonal diversity in the screened repertoires.
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Affiliation(s)
- Sami Oksanen
- Department of Life Sciences, University of Turku, 20520, Turku, Finland.
| | - Roope Saarinen
- Department of Life Sciences, University of Turku, 20520, Turku, Finland
| | | | - Urpo Lamminmäki
- Department of Life Sciences, University of Turku, 20520, Turku, Finland
| | - Tuomas Huovinen
- Department of Life Sciences, University of Turku, 20520, Turku, Finland.
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7
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Mitchell KG, Gong B, Hunter SS, Burkart-Waco D, Gavira-O’Neill CE, Templeton KM, Goethel ME, Bzymek M, MacNiven LM, Murray KD, Settles ML, Froenicke L, Trimmer JS. NeuroMabSeq: high volume acquisition, processing, and curation of hybridoma sequences and their use in generating recombinant monoclonal antibodies and scFvs for neuroscience research. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.06.28.546392. [PMID: 37425915 PMCID: PMC10327083 DOI: 10.1101/2023.06.28.546392] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/11/2023]
Abstract
The Neuroscience Monoclonal Antibody Sequencing Initiative (NeuroMabSeq) is a concerted effort to determine and make publicly available hybridoma-derived sequences of monoclonal antibodies (mAbs) valuable to neuroscience research. Over 30 years of research and development efforts including those at the UC Davis/NIH NeuroMab Facility have resulted in the generation of a large collection of mouse mAbs validated for neuroscience research. To enhance dissemination and increase the utility of this valuable resource, we applied a high-throughput DNA sequencing approach to determine immunoglobulin heavy and light chain variable domain sequences from source hybridoma cells. The resultant set of sequences was made publicly available as searchable DNA sequence database ( neuromabseq.ucdavis.edu ) for sharing, analysis and use in downstream applications. We enhanced the utility, transparency, and reproducibility of the existing mAb collection by using these sequences to develop recombinant mAbs. This enabled their subsequent engineering into alternate forms with distinct utility, including alternate modes of detection in multiplexed labeling, and as miniaturized single chain variable fragments or scFvs. The NeuroMabSeq website and database and the corresponding recombinant antibody collection together serve as a public DNA sequence repository of mouse mAb heavy and light chain variable domain sequences and as an open resource for enhancing dissemination and utility of this valuable collection of validated mAbs.
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Affiliation(s)
- Keith G. Mitchell
- Department of Physiology and Membrane Biology, University of California Davis School of Medicine, Davis, CA
- Bioinformatics Core, Genome Center, University of California Davis, CA
| | - Belvin Gong
- Department of Physiology and Membrane Biology, University of California Davis School of Medicine, Davis, CA
| | - Samuel S. Hunter
- Bioinformatics Core, Genome Center, University of California Davis, CA
| | | | - Clara E. Gavira-O’Neill
- Department of Physiology and Membrane Biology, University of California Davis School of Medicine, Davis, CA
| | - Kayla M. Templeton
- Department of Physiology and Membrane Biology, University of California Davis School of Medicine, Davis, CA
| | - Madeline E. Goethel
- Department of Physiology and Membrane Biology, University of California Davis School of Medicine, Davis, CA
| | - Malgorzata Bzymek
- Department of Physiology and Membrane Biology, University of California Davis School of Medicine, Davis, CA
| | - Leah M. MacNiven
- Department of Physiology and Membrane Biology, University of California Davis School of Medicine, Davis, CA
| | - Karl D. Murray
- Department of Physiology and Membrane Biology, University of California Davis School of Medicine, Davis, CA
- Department of Psychiatry and Behavioral Sciences, University of California Davis School of Medicine, Davis, CA
| | | | - Lutz Froenicke
- DNA Technology Core, Genome Center, University of California Davis, CA
| | - James S. Trimmer
- Department of Physiology and Membrane Biology, University of California Davis School of Medicine, Davis, CA
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8
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Moeller T, Shah SB, Lai K, Lopez-Barbosa N, Desai P, Wang W, Zhong Z, Redmond D, Singh A, DeLisa MP. Profiling Germinal Center-like B Cell Responses to Conjugate Vaccines Using Synthetic Immune Organoids. ACS CENTRAL SCIENCE 2023; 9:787-804. [PMID: 37122450 PMCID: PMC10141597 DOI: 10.1021/acscentsci.2c01473] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/11/2022] [Indexed: 05/03/2023]
Abstract
Glycoengineered bacteria have emerged as a cost-effective platform for rapid and controllable biosynthesis of designer conjugate vaccines. However, little is known about the engagement of such conjugates with naïve B cells to induce the formation of germinal centers (GC), a subanatomical microenvironment that converts naïve B cells into antibody-secreting plasma cells. Using a three-dimensional biomaterials-based B-cell follicular organoid system, we demonstrate that conjugates triggered robust expression of hallmark GC markers, B cell receptor clustering, intracellular signaling, and somatic hypermutation. These responses depended on the relative immunogenicity of the conjugate and correlated with the humoral response in vivo. The occurrence of these mechanisms was exploited for the discovery of high-affinity antibodies against components of the conjugate on a time scale that was significantly shorter than for typical animal immunization-based workflows. Collectively, these findings highlight the potential of synthetic organoids for rapidly predicting conjugate vaccine efficacy as well as expediting antigen-specific antibody discovery.
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Affiliation(s)
- Tyler
D. Moeller
- Robert
F. Smith School of Chemical and Biomolecular Engineering, Cornell University, Ithaca, New York 14853, United States
| | - Shivem B. Shah
- Nancy
E. and Peter C. Meinig School of Biomedical Engineering, Cornell University, Ithaca, New York 14853, United States
| | - Kristine Lai
- George
W. Woodruff School of Mechanical Engineering, Georgia Institute of Technology, Atlanta, Georgia 30332, United States
| | - Natalia Lopez-Barbosa
- Robert
F. Smith School of Chemical and Biomolecular Engineering, Cornell University, Ithaca, New York 14853, United States
| | - Primit Desai
- Biochemistry,
Molecular and Cell Biology, Cornell University, Ithaca, New York 14853, United States
| | - Weiyao Wang
- Robert
F. Smith School of Chemical and Biomolecular Engineering, Cornell University, Ithaca, New York 14853, United States
| | - Zhe Zhong
- George
W. Woodruff School of Mechanical Engineering, Georgia Institute of Technology, Atlanta, Georgia 30332, United States
| | - David Redmond
- Institute
for Computational Biomedicine, Weill Cornell Medicine, Cornell University, New York, New York 10021, United States
- Department
of Physiology and Biophysics, Weill Cornell Medicine, Cornell University, New York, New York 10021, United States
| | - Ankur Singh
- George
W. Woodruff School of Mechanical Engineering, Georgia Institute of Technology, Atlanta, Georgia 30332, United States
- Wallace
H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology, Atlanta, Georgia 30332, United States
| | - Matthew P. DeLisa
- Robert
F. Smith School of Chemical and Biomolecular Engineering, Cornell University, Ithaca, New York 14853, United States
- Nancy
E. and Peter C. Meinig School of Biomedical Engineering, Cornell University, Ithaca, New York 14853, United States
- Biochemistry,
Molecular and Cell Biology, Cornell University, Ithaca, New York 14853, United States
- Cornell
Institute of Biotechnology, Cornell University, Ithaca, New York 14853, United States
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9
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Sae-Foo W, Yusakul G, Kitisripanya T, Nuntawong P, Sakamoto S, Putalun W. Comparative stability and analytical performance of anti-miroestrol recombinant antibody in different cassettes. Appl Microbiol Biotechnol 2023; 107:2887-2896. [PMID: 36995382 DOI: 10.1007/s00253-023-12492-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2022] [Revised: 03/13/2023] [Accepted: 03/18/2023] [Indexed: 03/31/2023]
Abstract
Immunoassays are efficient for the phytochemical analysis of various matrices. However, producing an appropriate recombinant antibody for small molecules is challenging, resulting in costly analyses. In this study, we aimed to develop recombinant fragment antigen-binding (Fab) antibodies against miroestrol, a potent phytoestrogen marker of Pueraria candollei. Two expression cassettes of Fab were established for the production of active Fab antibodies using SHuffle® T7 Escherichia coli cells. The orientation of variable fragment heavy chain (VH) and variable fragment light chain (VL) in the expression vector constructs influences the reactivity, stability, and binding specificity of the resultant Fab. Stability testing of antibodies demonstrated that Fab is a more stable form of recombinant antibody than a single-chain variable fragment (ScFv) antibody in all conditions. Based on the obtained Fab, the ELISA specifically detected miroestrol in the range of 39.06-625.00 ng/mL. The intra- and inter-assay precisions were 0.74-2.98% and 6.57-9.76%, respectively. The recovery of authentic miroestrol spiked into samples was 106.70-110.14%, and the limit of detection was 11.07 ng/mL. The results for P. candollei roots and products determined using our developed ELISA with Fab antibody and an ELISA with anti-miroestrol monoclonal antibody (mAb) were consistent (R2 = 0.9758). The developed ELISA can be applied for the quality control of miroestrol derived from P. candollei. Therefore, the appropriate expression platform of Fab resulted in the stable binding specificity of the recombinant antibody and was applicable for immunoassays.Key points• ELISAs with Fab has higher sensitivity than that with ScFv.• Fab is more stable than ScFv.• Fab-based ELISA can be used for miroestrol determination of Pueraria candollei.
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10
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Silva RP, Huang Y, Nguyen AW, Hsieh CL, Olaluwoye OS, Kaoud TS, Wilen RE, Qerqez AN, Park JG, Khalil AM, Azouz LR, Le KC, Bohanon AL, DiVenere AM, Liu Y, Lee AG, Amengor DA, Shoemaker SR, Costello SM, Padlan EA, Marqusee S, Martinez-Sobrido L, Dalby KN, D'Arcy S, McLellan JS, Maynard JA. Identification of a conserved S2 epitope present on spike proteins from all highly pathogenic coronaviruses. eLife 2023; 12:e83710. [PMID: 36942851 PMCID: PMC10030117 DOI: 10.7554/elife.83710] [Citation(s) in RCA: 25] [Impact Index Per Article: 25.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2022] [Accepted: 03/04/2023] [Indexed: 03/23/2023] Open
Abstract
To address the ongoing SARS-CoV-2 pandemic and prepare for future coronavirus outbreaks, understanding the protective potential of epitopes conserved across SARS-CoV-2 variants and coronavirus lineages is essential. We describe a highly conserved, conformational S2 domain epitope present only in the prefusion core of β-coronaviruses: SARS-CoV-2 S2 apex residues 980-1006 in the flexible hinge. Antibody RAY53 binds the native hinge in MERS-CoV and SARS-CoV-2 spikes on the surface of mammalian cells and mediates antibody-dependent cellular phagocytosis and cytotoxicity against SARS-CoV-2 spike in vitro. Hinge epitope mutations that ablate antibody binding compromise pseudovirus infectivity, but changes elsewhere that affect spike opening dynamics, including those found in Omicron BA.1, occlude the epitope and may evade pre-existing serum antibodies targeting the S2 core. This work defines a third class of S2 antibody while providing insights into the potency and limitations of S2 core epitope targeting.
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Affiliation(s)
- Rui P Silva
- Department of Molecular Biosciences, The University of Texas at AustinAustinUnited States
| | - Yimin Huang
- Department of Molecular Biosciences, The University of Texas at AustinAustinUnited States
| | - Annalee W Nguyen
- Department of Chemical Engineering, The University of Texas at AustinAustinUnited States
| | - Ching-Lin Hsieh
- Department of Molecular Biosciences, The University of Texas at AustinAustinUnited States
| | - Oladimeji S Olaluwoye
- Department of Chemistry and Biochemistry, The University of Texas at DallasDallasUnited States
| | - Tamer S Kaoud
- Division of Chemical Biology and Medicinal Chemistry, The University of Texas at AustinAustinUnited States
| | - Rebecca E Wilen
- Department of Chemical Engineering, The University of Texas at AustinAustinUnited States
| | - Ahlam N Qerqez
- Department of Chemical Engineering, The University of Texas at AustinAustinUnited States
| | - Jun-Gyu Park
- Texas Biomedical Research InstituteSan AntonioUnited States
- Laboratory of Veterinary Zoonosis, College of Veterinary Medicine, Chonnam National UniversityGwangjuRepublic of Korea
| | - Ahmed M Khalil
- Texas Biomedical Research InstituteSan AntonioUnited States
| | - Laura R Azouz
- Department of Chemical Engineering, The University of Texas at AustinAustinUnited States
| | - Kevin C Le
- Department of Chemical Engineering, The University of Texas at AustinAustinUnited States
| | - Amanda L Bohanon
- Department of Molecular Biosciences, The University of Texas at AustinAustinUnited States
| | - Andrea M DiVenere
- Department of Chemical Engineering, The University of Texas at AustinAustinUnited States
| | - Yutong Liu
- Department of Chemical Engineering, The University of Texas at AustinAustinUnited States
| | - Alison G Lee
- Department of Molecular Biosciences, The University of Texas at AustinAustinUnited States
| | - Dzifa A Amengor
- Department of Molecular Biosciences, The University of Texas at AustinAustinUnited States
| | - Sophie R Shoemaker
- Department of Molecular and Cell Biology, University of California, BerkeleyBerkeleyUnited States
| | - Shawn M Costello
- Biophysics Graduate Program, University of California, BerkeleyBerkeleyUnited States
| | | | - Susan Marqusee
- Department of Molecular and Cell Biology, University of California, BerkeleyBerkeleyUnited States
- Department of Chemistry, University of California, BerkeleyBerkeleyUnited States
| | | | - Kevin N Dalby
- Division of Chemical Biology and Medicinal Chemistry, The University of Texas at AustinAustinUnited States
| | - Sheena D'Arcy
- Department of Chemistry and Biochemistry, The University of Texas at DallasDallasUnited States
| | - Jason S McLellan
- Department of Molecular Biosciences, The University of Texas at AustinAustinUnited States
- LaMontagne Center for Infectious Diseases, The University of Texas at AustinAustinUnited States
| | - Jennifer A Maynard
- Department of Chemical Engineering, The University of Texas at AustinAustinUnited States
- LaMontagne Center for Infectious Diseases, The University of Texas at AustinAustinUnited States
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11
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Chen L, Lu J, Yue J, Wang R, Du P, Yu Y, Guo J, Wang X, Jiang Y, Cheng K, Yang Z, Zheng T. A humanized anti-human adenovirus 55 monoclonal antibody with good neutralization ability. Front Immunol 2023; 14:1132822. [PMID: 37006289 PMCID: PMC10060833 DOI: 10.3389/fimmu.2023.1132822] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2022] [Accepted: 03/06/2023] [Indexed: 03/18/2023] Open
Abstract
BackgroundHuman adenovirus type 55 (HAdV55) has a re-emerged as pathogen causing an acute respiratory disease presenting as a severe lower respiratory illness that can cause death. To date, there is no HAdV55 vaccine or treatment available for general use.MethodsHerein, a monoclonal antibody specific for HAdV55, mAb 9-8, was isolated from an scFv-phage display library derived from mice immunized with the purified inactived-HAdV55 virions. By using ELISA and a virus micro-neutralization assay, we evaluated the binding and neutralizing activity of mAb 9-8 following humanization. Western blotting analysis and antigen-antibody molecular docking analysis were used to identify the antigenic epitopes that the humanized monoclonal antibody 9-8-h2 recognized. After that, their thermal stability was determined.ResultsMAb 9-8 showed potent neutralization activity against HAdV55. After humanization, the humanized neutralizing monoclonal antibody (9-8-h2) was identified to neutralize HAdV55 infection with an IC50 of 0.6050 nM. The mAb 9-8-h2 recognized HAdV55 and HAdV7 virus particles, but not HAdV4 particles. Although mAb 9-8-h2 could recognize HAdV7, it could not neutralize HAdV7. Furthermore, mAb 9-8-h2 recognized a conformational neutralization epitope of the fiber protein and the crucial amino acid residues (Arg 288, Asp 157, and Asn 200) were identified. MAb 9-8-h2 also showed favorable general physicochemical properties, including good thermostability and pH stability.ConclusionsOverall, mAb 9-8-h2 might be a promising molecule for the prevention and treatment of HAdV55.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | | | - Tao Zheng
- *Correspondence: Tao Zheng, ; Zhixin Yang,
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12
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Guliy OI, Evstigneeva SS, Dykman LA. The Use of Phage Antibodies for Microbial Cell Detection. APPL BIOCHEM MICRO+ 2022. [DOI: 10.1134/s0003683822100076] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/01/2023]
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13
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Structural basis of interleukin-17B receptor in complex with a neutralizing antibody for guiding humanization and affinity maturation. Cell Rep 2022; 41:111555. [DOI: 10.1016/j.celrep.2022.111555] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2022] [Revised: 08/22/2022] [Accepted: 10/02/2022] [Indexed: 11/20/2022] Open
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14
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Hietanen E, Tripathi L, Brockmann EC, Merilahti P, Lamminmäki U, Susi P. Isolation and characterization of phage display-derived scFv antibodies against human parechovirus 1 VP0 protein. Sci Rep 2022; 12:13453. [PMID: 35927325 PMCID: PMC9352675 DOI: 10.1038/s41598-022-17678-y] [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: 05/07/2022] [Accepted: 07/29/2022] [Indexed: 11/25/2022] Open
Abstract
Human parechoviruses (PeVs) are common viruses that are associated with a variety of diseases from mild gastrointestinal and respiratory symptoms to severe central nervous system infections. Until now there has not been antibodies for visualizing parechovirus infection. We used E. coli recombinant PeV-A1-VP0 protein as a target in phage display single chain variable fragment (scFv) antibody library panning. Three rounds of panning allowed identification and isolation of several candidate scFv clones, which tested positive in enzyme-linked immunosorbent assay (ELISA) against VP0. Three scFv clones (scFv-55, -59 and -71) with different CDR-3 sequences were further purified and tested in ELISA, Western blot and immunofluorescence microscopy (IFA) against a set of PeV-A1 isolates and a few isolates representing PeV types 2–6. In IFA, all three scFv binders recognized twenty PeV-A1 isolates. ScFv-55 and -71 also recognized clinical representatives of PeV types 1–6 both in IFA and in capture ELISA, while scFv-59 only recognized PeV-A1, -A2 and -A6. PeV-A1-VP0 (Harris strain) sequence was used to generate a peptide library, which allowed identification of a putative unique conformational antibody epitope with fully conserved flanking regions and a more variable core VVTYDSKL, shared between the scFv antibodies. Sequencing of the VP0 region of virus samples and sequence comparisons against parechoviral sequences in GenBank revealed 107 PeV-A1, -A3, -A8, -A17, -A (untyped) sequences with this exact epitope core sequence, which was most dominant among PeV-A1 isolates. These data suggest the first-time isolation of broad range phage display antibodies against human parechoviruses that may be used in diagnostic antibody development.
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Affiliation(s)
- Eero Hietanen
- Institute of Biomedicine, University of Turku, Turku, Finland
| | - Lav Tripathi
- Institute of Biomedicine, University of Turku, Turku, Finland
| | | | - Pirjo Merilahti
- Institute of Biomedicine, University of Turku, Turku, Finland.,Biovian Ltd, Turku, Finland
| | - Urpo Lamminmäki
- Department of Biotechnology, University of Turku, Turku, Finland
| | - Petri Susi
- Institute of Biomedicine, University of Turku, Turku, Finland.
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15
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Juengsanguanpornsuk W, Kitisripanya T, Boonsnongcheep P, Yusakul G, Srisongkram T, Sakamoto S, Putalun W. Improvement in the binding specificity of anti-isomiroestrol antibodies by expression as fragments under oxidizing conditions inside the SHuffle T7 E. coli cytoplasm. Biosci Biotechnol Biochem 2022; 86:1368-1377. [PMID: 35876636 DOI: 10.1093/bbb/zbac126] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2022] [Accepted: 07/18/2022] [Indexed: 11/14/2022]
Abstract
Sensitive and specific analysis of isomiroestrol (Iso) is required for the quality control of Pueraria candollei, an herb used to treat menopausal disorders. The anti-isomiroestrol monoclonal antibody (Iso-mAb) exhibits cross-reactivity with miroestrol and deoxymiroestrol, which impacts the analytical results. Here, the active and soluble forms of the single-chain variable fragment (Iso-scFv) and fragment antigen-binding (Iso-Fab) against Iso were expressed using Escherichia coli SHuffle® T7 to alter the binding specificity. The Iso-scFv format exhibited a higher binding activity than the Iso-Fab format. The reactivity of Iso-scFv towards Iso was comparable to that of the parental Iso-mAb. Remarkably, the binding specificity of the scFv structure was improved and cross-reactivity against analogs was reduced from 13.3-21.0% to less than 1%. The structure of recombinant antibodies affects the binding characteristics. Therefore, the immunoassays should improve specificity; these findings can be useful in agricultural processes and for quality monitoring of P. candollei-related materials.
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Affiliation(s)
| | - Tharita Kitisripanya
- Department of Pharmacognosy, Faculty of Pharmacy, Mahidol University, Bangkok 10400, Thailand
| | | | - Gorawit Yusakul
- School of Pharmacy, Walailak University, Nakhon Si Thammarat 80160, Thailand
| | - Tarapong Srisongkram
- Faculty of Pharmaceutical Sciences, Khon Kaen University, Khon Kaen 40002, Thailand
| | - Seiichi Sakamoto
- Graduate School of Pharmaceutical Sciences, Kyushu University, Fukuoka 812-8582, Japan
| | - Waraporn Putalun
- Faculty of Pharmaceutical Sciences, Khon Kaen University, Khon Kaen 40002, Thailand
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16
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Li Y, Yu Q, Yu W, Zhang S, Wen K, Shen J, Wang Z, Yu X. Development of Fluorescence Polarization Immunoassay With scFv to Detect Fumonisin Bs in Maize and Simultaneous Study of Their Molecular Recognition Mechanism. Front Chem 2022; 10:829038. [PMID: 35265585 PMCID: PMC8900220 DOI: 10.3389/fchem.2022.829038] [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: 12/04/2021] [Accepted: 01/12/2022] [Indexed: 11/13/2022] Open
Abstract
In this study, a fluorescence polarization immunoassay (FPIA) was developed based on the single-chain variable fragments (scFvs) for fumonisin Bs (FBs). The scFvs were prepared from FBs-specific monoclonal antibody secreting hybridomas (4F5 and 4B9). The established FPIA could determine the sum of fumonisin B1 (FB1) and fumonisin B2 (FB2) within a short time. The IC50 of FPIA for the detection of FB1 and FB2 were 29.36 ng/ml and 1,477.82 ng/ml with 4F5 scFv, and 125.16 ng/ml and 30.44 ng/ml with 4B9 scFv, so the 4B9 scFv was selected for detection of FB1 and FB2 in maize samples with a limit of detection of 441.54 μg/kg and 344.933 μg/kg. The recoveries ranged from 84.7 to 104.1% with a coefficient of variation less than 14.1% in spiked samples, and the result of the FPIA method was in good consistency with that of HPLC-MS/MS. To supply a better understanding of the immunoassay results, the interactions mechanism of scFvs-FBs was further revealed by the homology modelling, molecular docking, and molecular dynamic simulation. It was indicated that six complementarity-determining regions (CDRs) were involved in 4B9 scFv recognition, forming a narrow binding cavity, and FB1/FB2 could be inserted into this binding cavity stably through strong hydrogen bonds and other interactions. While in 4F5 scFv, only the FB1 stably inserted in the binding pocket formed by four CDRs through strong hydrogen bonds, and FB2 did not fit the binding cavity due to the lack of hydroxyl at C10, which is the key recognition site of 4F5 scFv. Also, the binding energy of FB2-4B9 scFv complex is higher than the FB2-4F5 scFv complex. This study established a FPIA method with scFv for the detection of FB1 and FB1 in maize, and systematically predicted recognition mechanism of FBs and scFvs, which provided a reference for the better understanding of the immunoassay mechanism.
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17
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Silva RP, DiVenere AM, Amengor D, Maynard JA. Antibodies binding diverse pertactin epitopes protect mice from B. pertussis infection. J Biol Chem 2022; 298:101715. [PMID: 35151691 PMCID: PMC8931430 DOI: 10.1016/j.jbc.2022.101715] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2021] [Revised: 02/03/2022] [Accepted: 02/08/2022] [Indexed: 11/27/2022] Open
Abstract
Infection by the bacterium Bordetella pertussis continues to cause considerable morbidity and mortality worldwide. Many current acellular pertussis vaccines include the antigen pertactin, which has presumptive adhesive and immunomodulatory activities, but is rapidly lost from clinical isolates after the introduction of these vaccines. To better understand the contributions of pertactin antibodies to protection and pertactin's role in pathogenesis, we isolated and characterized recombinant antibodies binding four distinct epitopes on pertactin. We demonstrate that four of these antibodies bind epitopes that are conserved across all three classical Bordetella strains, and competition assays further showed that antibodies binding these epitopes are also elicited by B. pertussis infection of baboons. Surprisingly, we found that representative antibodies binding each epitope protected mice against experimental B. pertussis infection. A cocktail of antibodies from each epitope group protected mice against a subsequent lethal dose of B. pertussis and greatly reduced lung colonization levels after sublethal challenge. Each antibody reduced B. pertussis lung colonization levels up to 100-fold when administered individually, which was significantly reduced when antibody effector functions were impaired, with no antibody mediating antibody-dependent complement-induced lysis. These data suggest that antibodies binding multiple pertactin epitopes protect primarily by the same bactericidal mechanism, which overshadows contributions from blockade of other pertactin functions. These antibodies expand the available tools to further dissect pertactin's role in infection and understand the impact of antipertactin antibodies on bacterial fitness.
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18
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Issafras H, Fan S, Tseng CL, Cheng Y, Lin P, Xiao L, Huang YJ, Tu CH, Hsiao YC, Li M, Chen YH, Ho CH, Li O, Wang Y, Chen S, Ji Z, Zhang E, Mao YT, Liu E, Yang S, Jiang W. Structural basis of HLX10 PD-1 receptor recognition, a promising anti-PD-1 antibody clinical candidate for cancer immunotherapy. PLoS One 2021; 16:e0257972. [PMID: 34972111 PMCID: PMC8719770 DOI: 10.1371/journal.pone.0257972] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2021] [Accepted: 09/14/2021] [Indexed: 12/30/2022] Open
Abstract
Cancer immunotherapies, such as checkpoint blockade of programmed cell death protein-1 (PD-1), represents a breakthrough in cancer treatment, resulting in unprecedented results in terms of overall and progression-free survival. Discovery and development of novel anti PD-1 inhibitors remains a field of intense investigation, where novel monoclonal antibodies (mAbs) and novel antibody formats (e.g., novel isotype, bispecific mAb and low-molecular-weight compounds) are major source of future therapeutic candidates. HLX10, a fully humanized IgG4 monoclonal antibody against PD-1 receptor, increased functional activities of human T-cells and showed in vitro, and anti-tumor activity in several tumor models. The combined inhibition of PD-1/PDL-1 and angiogenesis pathways using anti-VEGF antibody may enhance a sustained suppression of cancer-related angiogenesis and tumor elimination. To elucidate HLX10's mode of action, we solved the structure of HLX10 in complex with PD-1 receptor. Detailed epitope analysis showed that HLX10 has a unique mode of recognition compared to the clinically approved PD1 antibodies Pembrolizumab and Nivolumab. Notably, HLX10's epitope was closer to Pembrolizumab's epitope than Nivolumab's epitope. However, HLX10 and Pembrolizumab showed an opposite heavy chain (HC) and light chain (LC) usage, which recognizes several overlapping amino acid residues on PD-1. We compared HLX10 to Nivolumab and Pembrolizumab and it showed similar or better bioactivity in vitro and in vivo, providing a rationale for clinical evaluation in cancer immunotherapy.
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MESH Headings
- Angiogenesis Inhibitors/therapeutic use
- Animals
- Antibodies, Monoclonal/chemistry
- Antibodies, Monoclonal/pharmacokinetics
- Antibodies, Monoclonal, Humanized/chemistry
- Antibodies, Monoclonal, Humanized/therapeutic use
- Bevacizumab/therapeutic use
- CD4-Positive T-Lymphocytes/immunology
- Cell Line, Tumor
- Cell Proliferation
- Epithelial-Mesenchymal Transition/drug effects
- Epitopes/immunology
- Humans
- Immunoglobulin Fab Fragments/metabolism
- Immunotherapy
- Interferon-gamma/metabolism
- Interleukin-2/metabolism
- Ligands
- Macaca fascicularis
- Mice, Inbred NOD
- Mice, SCID
- Models, Molecular
- Neoplasms/drug therapy
- Neoplasms/immunology
- Neoplasms/therapy
- Nivolumab/chemistry
- Nivolumab/therapeutic use
- Programmed Cell Death 1 Receptor/chemistry
- Programmed Cell Death 1 Receptor/immunology
- Protein Binding
- Rats
- Vascular Endothelial Growth Factor A/antagonists & inhibitors
- Vascular Endothelial Growth Factor A/metabolism
- Xenograft Model Antitumor Assays
- Mice
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Affiliation(s)
| | - Shilong Fan
- National Protein Science Facility, Tsinghua University, Beijing, China
| | | | | | - Peihua Lin
- Hengenix Inc., Fremont, CA, United States of America
| | - Lisa Xiao
- Shanghai Henlius Biotech, Inc., Shanghai, P. R. China
| | | | | | | | - Min Li
- National Protein Science Facility, Tsinghua University, Beijing, China
| | | | | | - Ou Li
- Hengenix Inc., Fremont, CA, United States of America
| | - Yanling Wang
- Hengenix Inc., Fremont, CA, United States of America
| | - Sandra Chen
- Anwita Biosciences, San Carlos, CA, United States of America
| | - Zhenyu Ji
- Shanghai Henlius Biotech, Inc., Shanghai, P. R. China
| | - Eric Zhang
- Shanghai Henlius Biotech, Inc., Shanghai, P. R. China
| | - Yi-Ting Mao
- Hengenix Inc., Fremont, CA, United States of America
| | - Eugene Liu
- Taipei Medical University, Taipei, Taiwan
| | - Shumin Yang
- Shanghai Henlius Biotech, Inc., Shanghai, P. R. China
| | - Weidong Jiang
- Hengenix Inc., Fremont, CA, United States of America
- Shanghai Henlius Biotech, Inc., Shanghai, P. R. China
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19
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Patterson-Orazem AC, Qerqez AN, Azouz LR, Ma MT, Hill SE, Ku Y, Schildmeyer LA, Maynard JA, Lieberman RL. Recombinant antibodies recognize conformation-dependent epitopes of the leucine zipper of misfolding-prone myocilin. J Biol Chem 2021; 297:101067. [PMID: 34384785 PMCID: PMC8408531 DOI: 10.1016/j.jbc.2021.101067] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2021] [Revised: 08/02/2021] [Accepted: 08/06/2021] [Indexed: 11/11/2022] Open
Abstract
Recombinant antibodies with well-characterized epitopes and known conformational specificities are critical reagents to support robust interpretation and reproducibility of immunoassays across biomedical research. For myocilin, a protein prone to misfolding that is associated with glaucoma and an emerging player in other human diseases, currently available antibodies are unable to differentiate among the numerous disease-associated protein states. This fundamentally constrains efforts to understand the connection between myocilin structure, function, and disease. To address this concern, we used protein engineering methods to develop new recombinant antibodies that detect the N-terminal leucine zipper structural domain of myocilin and that are cross-reactive for human and mouse myocilin. After harvesting spleens from immunized mice and in vitro library panning, we identified two antibodies, 2A4 and 1G12. 2A4 specifically recognizes a folded epitope while 1G12 recognizes a range of conformations. We matured antibody 2A4 for improved biophysical properties, resulting in variant 2H2. In a human IgG1 format, 2A4, 1G12, and 2H2 immunoprecipitate full-length folded myocilin present in the spent media of human trabecular meshwork (TM) cells, and 2H2 can visualize myocilin in fixed human TM cells using fluorescence microscopy. These new antibodies should find broad application in glaucoma and other research across multiple species platforms.
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Affiliation(s)
| | - Ahlam N Qerqez
- Department of Chemical Engineering, University of Texas at Austin, Austin, Texas, USA
| | - Laura R Azouz
- Department of Chemical Engineering, University of Texas at Austin, Austin, Texas, USA
| | - Minh Thu Ma
- School of Chemistry & Biochemistry, Georgia Institute of Technology, Atlanta, Georgia, USA
| | - Shannon E Hill
- School of Chemistry & Biochemistry, Georgia Institute of Technology, Atlanta, Georgia, USA
| | - Yemo Ku
- School of Chemistry & Biochemistry, Georgia Institute of Technology, Atlanta, Georgia, USA
| | - Lisa A Schildmeyer
- School of Chemistry & Biochemistry, Georgia Institute of Technology, Atlanta, Georgia, USA
| | - Jennifer A Maynard
- Department of Chemical Engineering, University of Texas at Austin, Austin, Texas, USA; Department of Molecular Biosciences, University of Texas at Austin, Austin, Texas, USA.
| | - Raquel L Lieberman
- School of Chemistry & Biochemistry, Georgia Institute of Technology, Atlanta, Georgia, USA.
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20
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Chen X, Du H, Hong Y, Wang Y, Shu M, Wang D, Dai P, Deng W, Xiong J, Yang W. Development of a single-chain variable fragment-alkaline phosphatase fusion protein-based direct competitive enzyme-linked immunosorbent assay for furaltadone metabolite in ctenopharyngodon idellus. FOOD AGR IMMUNOL 2021. [DOI: 10.1080/09540105.2021.1957781] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022] Open
Affiliation(s)
- Xinzhu Chen
- Key Laboratory of Agricultural Products Processing and Quality Control of Nanchang City/College of Food Science and Engineering, Jiangxi Agricultural University, Nanchang, People’s Republic of China
| | - Huaying Du
- Key Laboratory of Agricultural Products Processing and Quality Control of Nanchang City/College of Food Science and Engineering, Jiangxi Agricultural University, Nanchang, People’s Republic of China
| | - Yanping Hong
- Key Laboratory of Agricultural Products Processing and Quality Control of Nanchang City/College of Food Science and Engineering, Jiangxi Agricultural University, Nanchang, People’s Republic of China
| | - Yubo Wang
- Key Laboratory of Agricultural Products Processing and Quality Control of Nanchang City/College of Food Science and Engineering, Jiangxi Agricultural University, Nanchang, People’s Republic of China
| | - Mei Shu
- Key Laboratory of Agricultural Products Processing and Quality Control of Nanchang City/College of Food Science and Engineering, Jiangxi Agricultural University, Nanchang, People’s Republic of China
| | - Dan Wang
- Key Laboratory of Agricultural Products Processing and Quality Control of Nanchang City/College of Food Science and Engineering, Jiangxi Agricultural University, Nanchang, People’s Republic of China
| | - Peng Dai
- Key Laboratory of Agricultural Products Processing and Quality Control of Nanchang City/College of Food Science and Engineering, Jiangxi Agricultural University, Nanchang, People’s Republic of China
| | - Weijie Deng
- Key Laboratory of Agricultural Products Processing and Quality Control of Nanchang City/College of Food Science and Engineering, Jiangxi Agricultural University, Nanchang, People’s Republic of China
| | - Jianhua Xiong
- Key Laboratory of Agricultural Products Processing and Quality Control of Nanchang City/College of Food Science and Engineering, Jiangxi Agricultural University, Nanchang, People’s Republic of China
| | - Wuying Yang
- Key Laboratory of Agricultural Products Processing and Quality Control of Nanchang City/College of Food Science and Engineering, Jiangxi Agricultural University, Nanchang, People’s Republic of China
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21
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Fontes CM, Lipes BD, Liu J, Agans KN, Yan A, Shi P, Cruz DF, Kelly G, Luginbuhl KM, Joh DY, Foster SL, Heggestad J, Hucknall A, Mikkelsen MH, Pieper CF, Horstmeyer RW, Geisbert TW, Gunn MD, Chilkoti A. Ultrasensitive point-of-care immunoassay for secreted glycoprotein detects Ebola infection earlier than PCR. Sci Transl Med 2021; 13:13/588/eabd9696. [PMID: 33827978 DOI: 10.1126/scitranslmed.abd9696] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2020] [Accepted: 03/12/2021] [Indexed: 12/23/2022]
Abstract
Ebola virus (EBOV) hemorrhagic fever outbreaks have been challenging to deter due to the lack of health care infrastructure in disease-endemic countries and a corresponding inability to diagnose and contain the disease at an early stage. EBOV vaccines and therapies have improved disease outcomes, but the advent of an affordable, easily accessed, mass-produced rapid diagnostic test (RDT) that matches the performance of more resource-intensive polymerase chain reaction (PCR) assays would be invaluable in containing future outbreaks. Here, we developed and demonstrated the performance of a new ultrasensitive point-of-care immunoassay, the EBOV D4 assay, which targets the secreted glycoprotein of EBOV. The EBOV D4 assay is 1000-fold more sensitive than the U.S. Food and Drug Administration-approved RDTs and detected EBOV infection earlier than PCR in a standard nonhuman primate model. The EBOV D4 assay is suitable for low-resource settings and may facilitate earlier detection, containment, and treatment during outbreaks of the disease.
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Affiliation(s)
- Cassio M Fontes
- Department of Biomedical Engineering, Duke University, Durham, NC 27708, USA
| | - Barbara D Lipes
- Department of Medicine, Duke University Medical Center, Durham, NC 27710, USA
| | - Jason Liu
- Department of Biomedical Engineering, Duke University, Durham, NC 27708, USA
| | - Krystle N Agans
- Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, TX 77555, USA.,Galveston National Laboratory, University of Texas Medical Branch at Galveston, Galveston, TX 77550, USA
| | - Aiwei Yan
- Department of Medicine, Duke University Medical Center, Durham, NC 27710, USA
| | - Patricia Shi
- Department of Medicine, Duke University Medical Center, Durham, NC 27710, USA
| | - Daniela F Cruz
- Department of Biomedical Engineering, Duke University, Durham, NC 27708, USA
| | - Garrett Kelly
- Department of Biomedical Engineering, Duke University, Durham, NC 27708, USA
| | - Kelli M Luginbuhl
- Department of Biomedical Engineering, Duke University, Durham, NC 27708, USA
| | - Daniel Y Joh
- Department of Biomedical Engineering, Duke University, Durham, NC 27708, USA
| | - Stephanie L Foster
- Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, TX 77555, USA.,Galveston National Laboratory, University of Texas Medical Branch at Galveston, Galveston, TX 77550, USA
| | - Jacob Heggestad
- Department of Biomedical Engineering, Duke University, Durham, NC 27708, USA
| | - Angus Hucknall
- Department of Biomedical Engineering, Duke University, Durham, NC 27708, USA
| | - Maiken H Mikkelsen
- Department of Electrical and Computer Engineering, Duke University, Durham, NC 27708, USA
| | - Carl F Pieper
- Departments of Biostatistics and Bioinformatics, Duke University Medical Center, Durham, NC 27710, USA
| | - Roarke W Horstmeyer
- Department of Biomedical Engineering, Duke University, Durham, NC 27708, USA
| | - Thomas W Geisbert
- Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, TX 77555, USA.,Galveston National Laboratory, University of Texas Medical Branch at Galveston, Galveston, TX 77550, USA
| | - Michael D Gunn
- Department of Medicine, Duke University Medical Center, Durham, NC 27710, USA.
| | - Ashutosh Chilkoti
- Department of Biomedical Engineering, Duke University, Durham, NC 27708, USA.
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22
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Bogen JP, Grzeschik J, Jakobsen J, Bähre A, Hock B, Kolmar H. Treating Bladder Cancer: Engineering of Current and Next Generation Antibody-, Fusion Protein-, mRNA-, Cell- and Viral-Based Therapeutics. Front Oncol 2021; 11:672262. [PMID: 34123841 PMCID: PMC8191463 DOI: 10.3389/fonc.2021.672262] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2021] [Accepted: 05/11/2021] [Indexed: 01/02/2023] Open
Abstract
Bladder cancer is a frequent malignancy and has a clinical need for new therapeutic approaches. Antibody and protein technologies came a long way in recent years and new engineering approaches were applied to generate innovative therapeutic entities with novel mechanisms of action. Furthermore, mRNA-based pharmaceuticals recently reached the market and CAR-T cells and viral-based gene therapy remain a major focus of biomedical research. This review focuses on the engineering of biologics, particularly therapeutic antibodies and their application in preclinical development and clinical trials, as well as approved monoclonal antibodies for the treatment of bladder cancer. Besides, newly emerging entities in the realm of bladder cancer like mRNA, gene therapy or cell-based therapeutics are discussed and evaluated. As many discussed molecules exhibit unique mechanisms of action based on innovative protein engineering, they reflect the next generation of cancer drugs. This review will shed light on the engineering strategies applied to develop these next generation treatments and provides deeper insights into their preclinical profiles, clinical stages, and ongoing trials. Furthermore, the distribution and expression of the targeted antigens and the intended mechanisms of action are elucidated.
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Affiliation(s)
- Jan P Bogen
- Institute for Organic Chemistry and Biochemistry, Technical University of Darmstadt, Darmstadt, Germany.,Ferring Darmstadt Laboratory, Biologics Technology and Development, Darmstadt, Germany
| | - Julius Grzeschik
- Ferring Darmstadt Laboratory, Biologics Technology and Development, Darmstadt, Germany
| | - Joern Jakobsen
- Ferring Pharmaceuticals, International PharmaScience Center, Copenhagen, Denmark
| | - Alexandra Bähre
- Ferring Pharmaceuticals, International PharmaScience Center, Copenhagen, Denmark
| | - Björn Hock
- Global Pharmaceutical Research and Development, Ferring International Center S.A., Saint-Prex, Switzerland
| | - Harald Kolmar
- Institute for Organic Chemistry and Biochemistry, Technical University of Darmstadt, Darmstadt, Germany
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23
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Zhou BR, Bai Y. Preparation of scFv stabilized chromatosomes for single-particle cryo-EM structure determination. STAR Protoc 2021; 2:100396. [PMID: 33786462 PMCID: PMC7994535 DOI: 10.1016/j.xpro.2021.100396] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Abstract
The chromatosome, a nucleosome bound to a histone H1, is the structural unit of metazoan chromatin. Determination of the high-resolution structure of the chromatosome is challenging due to the dynamic nature of H1 binding. Here, we present a protocol for purifying an optimized single-chain antibody variable fragment (scFv) that can be used to stabilize the chromatosome for single-particle cryo-EM studies. This protocol facilitates high-resolution cryo-EM structure determination of nucleosomes with a natural DNA sequence, chromatosomes, and other protein nucleosome complexes. For complete details on the use and execution of this protocol, please refer to Zhou et al. (2021). Optimization of nucleosome antibody fragment (scFv) construct to increase its stability Strategy for refolding and purification of the scFv from the inclusion body Use of scFv to facilitate single-particle cryo-EM of the protein nucleosome complex
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Affiliation(s)
- Bing-Rui Zhou
- Laboratory of Biochemistry and Molecular Biology, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Yawen Bai
- Laboratory of Biochemistry and Molecular Biology, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
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24
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Nannini F, Senicar L, Parekh F, Kong KJ, Kinna A, Bughda R, Sillibourne J, Hu X, Ma B, Bai Y, Ferrari M, Pule MA, Onuoha SC. Combining phage display with SMRTbell next-generation sequencing for the rapid discovery of functional scFv fragments. MAbs 2021; 13:1864084. [PMID: 33382949 PMCID: PMC7781620 DOI: 10.1080/19420862.2020.1864084] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2020] [Revised: 12/06/2020] [Accepted: 12/10/2020] [Indexed: 12/18/2022] Open
Abstract
Phage display technology in combination with next-generation sequencing (NGS) currently is a state-of-the-art method for the enrichment and isolation of monoclonal antibodies from diverse libraries. However, the current NGS methods employed for sequencing phage display libraries are limited by the short contiguous read lengths associated with second-generation sequencing platforms. Consequently, the identification of antibody sequences has conventionally been restricted to individual antibody domains or to the analysis of single domain binding moieties such as camelid VHH or cartilaginous fish IgNAR antibodies. In this study, we report the application of third-generation sequencing to address this limitation. We used single molecule real time (SMRT) sequencing coupled with hairpin adaptor loop ligation to facilitate the accurate interrogation of full-length single-chain Fv (scFv) libraries. Our method facilitated the rapid isolation and testing of scFv antibodies enriched from phage display libraries within days following panning. Two libraries against CD160 and CD123 were panned and monitored by NGS. Analysis of NGS antibody data sets led to the isolation of several functional scFv antibodies that were not identified by conventional panning and screening strategies. Our approach, which combines phage display selection of immune libraries with the full-length interrogation of scFv fragments, is an easy method to discover functional antibodies, with a range of affinities and biophysical characteristics.
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Affiliation(s)
| | | | | | - Khai J. Kong
- Cancer Institute, University College London, London, UK
| | | | | | | | - Xihao Hu
- GV20 Therapeutics LLC, Cambridge, MA, USA
| | - Biao Ma
- Autolus Therapeutics, London, UK
| | | | | | - Martin A. Pule
- Cancer Institute, University College London, London, UK
- Autolus Therapeutics, London, UK
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25
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Stravinskiene D, Sliziene A, Baranauskiene L, Petrikaite V, Zvirbliene A. Inhibitory Monoclonal Antibodies and Their Recombinant Derivatives Targeting Surface-Exposed Carbonic Anhydrase XII on Cancer Cells. Int J Mol Sci 2020; 21:ijms21249411. [PMID: 33321910 PMCID: PMC7763246 DOI: 10.3390/ijms21249411] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2020] [Accepted: 12/08/2020] [Indexed: 01/17/2023] Open
Abstract
Monoclonal and recombinant antibodies are widely used for the diagnostics and therapy of cancer. They are generated to interact with cell surface proteins which are usually involved in the development and progression of cancer. Carbonic anhydrase XII (CA XII) contributes to the survival of tumors under hypoxic conditions thus is considered a candidate target for antibody-based therapy. In this study, we have generated a novel collection of monoclonal antibodies (MAbs) against the recombinant extracellular domain of CA XII produced in HEK-293 cells. Eighteen out of 24 MAbs were reactive with cellular CA XII on the surface of live kidney and lung cancer cells as determined by flow cytometry. One MAb 14D6 also inhibited the enzymatic activity of recombinant CA XII as measured by the stopped-flow assay. MAb 14D6 showed the migrastatic effect on human lung carcinoma A549 and renal carcinoma A498 cell lines in a ‘wound healing’ assay. It did not reduce the growth of multicellular lung and renal cancer spheroids but reduced the cell viability by the ATP Bioluminescence assay. Epitope mapping revealed the surface-exposed amino acid sequence (35-FGPDGENS-42) close to the catalytic center of CA XII recognized by the MAb 14D6. The variable regions of the heavy and light chains of MAb 14D6 were sequenced and their complementarity-determining regions were defined. The obtained variable sequences were used to generate recombinant antibodies in two formats: single-chain fragment variable (scFv) expressed in E. coli and scFv fused to human IgG1 Fc fragment (scFv-Fc) expressed in Chinese Hamster Ovary (CHO) cells. Both recombinant antibodies maintained the same specificity for CA XII as the parental MAb 14D6. The novel antibodies may represent promising tools for CA XII-related cancer research and immunotherapy.
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Affiliation(s)
- Dovile Stravinskiene
- Department of Immunology and Cell Biology, Institute of Biotechnology, Life Sciences Center, Vilnius University, Sauletekio al. 7, LT-10257 Vilnius, Lithuania; (A.S.); (A.Z.)
- Correspondence:
| | - Aiste Sliziene
- Department of Immunology and Cell Biology, Institute of Biotechnology, Life Sciences Center, Vilnius University, Sauletekio al. 7, LT-10257 Vilnius, Lithuania; (A.S.); (A.Z.)
| | - Lina Baranauskiene
- Department of Biothermodynamics and Drug Design, Institute of Biotechnology, Life Sciences Center, Vilnius University, Sauletekio al. 7, LT-10257 Vilnius, Lithuania; (L.B.); (V.P.)
| | - Vilma Petrikaite
- Department of Biothermodynamics and Drug Design, Institute of Biotechnology, Life Sciences Center, Vilnius University, Sauletekio al. 7, LT-10257 Vilnius, Lithuania; (L.B.); (V.P.)
- Laboratory of Drug Targets Histopathology, Institute of Cardiology, Lithuanian University of Health Sciences, Sukileliu pr. 13, LT-50162 Kaunas, Lithuania
| | - Aurelija Zvirbliene
- Department of Immunology and Cell Biology, Institute of Biotechnology, Life Sciences Center, Vilnius University, Sauletekio al. 7, LT-10257 Vilnius, Lithuania; (A.S.); (A.Z.)
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26
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Nannini F, Parekh F, Wawrzyniecka P, Mekkaoui L, Righi M, Dastjerdi FV, Yeung J, Roddie C, Bai Y, Ma B, Ferrari M, Onuoha S, Chester K, Pule M. A primer set for the rapid isolation of scFv fragments against cell surface antigens from immunised rats. Sci Rep 2020; 10:19168. [PMID: 33154441 PMCID: PMC7644676 DOI: 10.1038/s41598-020-76069-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2020] [Accepted: 10/21/2020] [Indexed: 12/20/2022] Open
Abstract
Antibody phage display is a powerful platform for discovery of clinically applicable high affinity monoclonal antibodies against a broad range of targets. Libraries generated from immunized animals offer the advantage of in vivo affinity-maturation of V regions prior to library generation. Despite advantages, few studies have described isolation of antibodies from rats using immune phage display. In our study, we describe a novel primer set, covering the full rat heavy chain variable and kappa light chain variable regions repertoire for the generation of an unbiased immune libraries. Since the immune repertoire of rats is poorly understood, we first performed a deep sequencing analysis of the V(D)J regions of VH and VLK genes, demonstrating the high abundance of IGVH2 and IGVH5 families for VH and IGVLK12 and IGVLK22 for VLK. The comparison of gene's family usage in naïve rats have been used to validate the frequency's distribution of the primer set, confirming the absence of PCR-based biases. The primers were used to generate and assemble a phage display library from human CD160-vaccinated rats. CD160 represents a valid therapeutic target as it has been shown to be expressed on chronic lymphocytic leukaemia cells and on the surface of newly formed vessels. We utilised a novel phage display panning strategy to isolate a high affinity pool (KD range: 0.399-233 nM) of CD160 targeting monoclonal antibodies. Subsequently, identified binders were tested for function as third generation Chimeric Antigen Receptors (CAR) T cells demonstrating specific cytolytic activity. Our novel primer set coupled with a streamlined strategy for phage display panning enable the rapid isolation and identification of high affinity antibodies from immunised rats. The therapeutic utility of these antibodies was demonstrated in CAR format.
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Affiliation(s)
- Francesco Nannini
- Research Department of Haematology, UCL Cancer Institute, 72 Huntley Street, London, WC1E 6DD, UK
| | - Farhaan Parekh
- Research Department of Haematology, UCL Cancer Institute, 72 Huntley Street, London, WC1E 6DD, UK
| | - Patrycja Wawrzyniecka
- Research Department of Haematology, UCL Cancer Institute, 72 Huntley Street, London, WC1E 6DD, UK
| | - Leila Mekkaoui
- Research Department of Haematology, UCL Cancer Institute, 72 Huntley Street, London, WC1E 6DD, UK
| | - Matteo Righi
- Research Department of Haematology, UCL Cancer Institute, 72 Huntley Street, London, WC1E 6DD, UK
| | | | - Jenny Yeung
- Research Department of Oncology, UCL Cancer Institute, London, UK
| | - Claire Roddie
- Research Department of Haematology, UCL Cancer Institute, 72 Huntley Street, London, WC1E 6DD, UK
| | | | - Biao Ma
- Autolus Therapeutics, London, UK
| | | | | | - Kerry Chester
- Research Department of Oncology, UCL Cancer Institute, London, UK
| | - Martin Pule
- Research Department of Haematology, UCL Cancer Institute, 72 Huntley Street, London, WC1E 6DD, UK.
- Autolus Therapeutics, London, UK.
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27
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Brockmann EC, Pyykkö M, Hannula H, Khan K, Lamminmäki U, Huovinen T. Combinatorial mutagenesis with alternative CDR-L1 and -H2 loop lengths contributes to affinity maturation of antibodies. N Biotechnol 2020; 60:173-182. [PMID: 33039698 DOI: 10.1016/j.nbt.2020.09.002] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2020] [Revised: 09/17/2020] [Accepted: 09/26/2020] [Indexed: 10/23/2022]
Abstract
Loop length variation in the complementary determining regions (CDRs) 1 and 2 encoded in germline variable antibody genes provides structural diversity in naïve antibody libraries. In synthetic single framework libraries the parental CDR-1 and CDR-2 length is typically unchanged and alternative lengths are provided only at CDR-3 sites. Based on an analysis of the germline repertoire and structure-solved anti-hapten and anti-peptide antibodies, we introduced combinatorial diversity with alternative loop lengths into the CDR-L1, CDR-L3 and CDR-H2 loops of anti-digoxigenin and anti-microcystin-LR single chain Fv fragments (scFvs) sharing human IGKV3-20/IGHV3-23 frameworks. The libraries were phage display selected for folding and affinity, and analysed by single clone screening and deep sequencing. Among microcystin-LR binders the most frequently encountered alternative loop lengths were one amino acid shorter (6 aa) and four amino acids longer (11 aa) CDR-L1 loops leading up to 17- and 28-fold improved affinity, respectively. Among digoxigenin binders, 2 amino acids longer (10 aa) CDR-H2 loops were strongly enriched, but affinity improved anti-digoxigenin scFvs were also encountered with 7 aa CDR-H2 and 11 aa CDR-L1 loops. Despite the fact that CDR-L3 loop length variants were not specifically enriched in selections, one clone with 22-fold improved digoxigenin binding affinity was identified containing a 2 residues longer (10 aa) CDR-L3 loop. Based on our results the IGKV3-20/IGHV3-23 scaffold tolerates loop length variation, particularly in CDR-L1 and CDR-H2 loops, without compromising antibody stability, laying the foundation for developing novel synthetic antibody libraries with loop length combinations not existing in the natural human Ig gene repertoire.
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Affiliation(s)
| | - Mikko Pyykkö
- University of Turku, Department of Biochemistry/Biotechnology, Turku, Finland
| | - Heidi Hannula
- University of Turku, Department of Biochemistry/Biotechnology, Turku, Finland; Current Affiliation: Microelectronics Research Unit, Faculty of Information Technology and Electrical Engineering, University of Oulu, Finland
| | - Kamran Khan
- University of Turku, Department of Biochemistry/Biotechnology, Turku, Finland
| | - Urpo Lamminmäki
- University of Turku, Department of Biochemistry/Biotechnology, Turku, Finland
| | - Tuomas Huovinen
- University of Turku, Department of Biochemistry/Biotechnology, Turku, Finland.
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28
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Mucosal or systemic microbiota exposures shape the B cell repertoire. Nature 2020; 584:274-278. [PMID: 32760003 DOI: 10.1038/s41586-020-2564-6] [Citation(s) in RCA: 115] [Impact Index Per Article: 28.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2019] [Accepted: 05/18/2020] [Indexed: 01/20/2023]
Abstract
Colonization by the microbiota causes a marked stimulation of B cells and induction of immunoglobulin, but mammals colonized with many taxa have highly complex and individualized immunoglobulin repertoires1,2. Here we use a simplified model of defined transient exposures to different microbial taxa in germ-free mice3 to deconstruct how the microbiota shapes the B cell pool and its functional responsiveness. We followed the development of the immunoglobulin repertoire in B cell populations, as well as single cells by deep sequencing. Microbial exposures at the intestinal mucosa generated oligoclonal responses that differed from those of germ-free mice, and from the diverse repertoire that was generated after intravenous systemic exposure to microbiota. The IgA repertoire-predominantly to cell-surface antigens-did not expand after dose escalation, whereas increased systemic exposure broadened the IgG repertoire to both microbial cytoplasmic and cell-surface antigens. These microbial exposures induced characteristic immunoglobulin heavy-chain repertoires in B cells, mainly at memory and plasma cell stages. Whereas sequential systemic exposure to different microbial taxa diversified the IgG repertoire and facilitated alternative specific responses, sequential mucosal exposure produced limited overlapping repertoires and the attrition of initial IgA binding specificities. This shows a contrast between a flexible response to systemic exposure with the need to avoid fatal sepsis, and a restricted response to mucosal exposure that reflects the generic nature of host-microbial mutualism in the mucosa.
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29
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Dong J, Li Z, Wang Y, Jin M, Shen Y, Xu Z, Abd El-Aty AM, Gee SJ, Hammock BD, Sun Y, Wang H. Generation of functional single-chain fragment variable from hybridoma and development of chemiluminescence enzyme immunoassay for determination of total malachite green in tilapia fish. Food Chem 2020; 337:127780. [PMID: 32799164 DOI: 10.1016/j.foodchem.2020.127780] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2020] [Revised: 08/01/2020] [Accepted: 08/03/2020] [Indexed: 11/15/2022]
Abstract
To determine malachite green (MG) and its major metabolite, leucomalachite green (LMG) residual levels in tilapia fish, chemiluminescent enzyme immunoassay (CLEIA) was developed based on a single-chain variable fragment (scFv)-alkaline phosphatase (AP) fusion protein. At first, VH and VL gene sequences were cloned from hybridoma cell lines secreting monoclonal antibody against LMG, and then thoroughly by database-assisted sequence analysis. Finally, the productive VH and VL were assembled to an intact scFv sequence and engineered to produce scFv-AP fusion protein. The fusion protein was further identified as a bifunctional reagent for immunoassay, then a sensitive one-step CLEIA against LMG was developed with a half-maximal inhibitory concentration (IC50) and limit of detection (LOD) of 1.3 and 0.04 ng/mL, respectively. The validation results of this novel competitive CLEIA was in line with those obtained by classical HPLC method for determination of total MG in spiked and field incurred samples.
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Affiliation(s)
- Jiexian Dong
- Guangdong Provincial Key Laboratory of Food Quality and Safety, South China Agricultural University, Guangzhou 510642, China; Department of Entomology and UCD Comprehensive Cancer Center, University of California, Davis, CA 95616, United States
| | - Zhenfeng Li
- Department of Entomology and UCD Comprehensive Cancer Center, University of California, Davis, CA 95616, United States; Guangzhou Nabo Antibody Technology Co. Ltd, Guangzhou 510530, China
| | - Yu Wang
- Guangdong Provincial Key Laboratory of Food Quality and Safety, South China Agricultural University, Guangzhou 510642, China; Guangzhou Institute for Food Control, Guangzhou 510410, China
| | - Maojun Jin
- Institute of Quality Standard &Testing Technology for Agro-Products, Chinese Academy of Agricultural Science, Beijing 100081, China
| | - Yudong Shen
- Guangdong Provincial Key Laboratory of Food Quality and Safety, South China Agricultural University, Guangzhou 510642, China
| | - Zhenlin Xu
- Guangdong Provincial Key Laboratory of Food Quality and Safety, South China Agricultural University, Guangzhou 510642, China
| | - A M Abd El-Aty
- Department of Pharmacology, Faculty of Veterinary Medicine, Cairo University, Giza 12211, Egypt; State Key Laboratory of Biobased Material and Green Papermaking, Qilu University of Technology, Shandong Academy of Sciences, Jinan 250353, China; Department of Medical Pharmacology, Medical Faculty, Ataturk University, Erzurum, Turkey
| | - Shirley J Gee
- Department of Entomology and UCD Comprehensive Cancer Center, University of California, Davis, CA 95616, United States
| | - Bruce D Hammock
- Department of Entomology and UCD Comprehensive Cancer Center, University of California, Davis, CA 95616, United States
| | - Yuanming Sun
- Guangdong Provincial Key Laboratory of Food Quality and Safety, South China Agricultural University, Guangzhou 510642, China
| | - Hong Wang
- Guangdong Provincial Key Laboratory of Food Quality and Safety, South China Agricultural University, Guangzhou 510642, China.
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30
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Sehnert B, Burkhardt H, Dübel S, Voll RE. Cell-Type Targeted NF-kappaB Inhibition for the Treatment of Inflammatory Diseases. Cells 2020; 9:E1627. [PMID: 32640727 PMCID: PMC7407293 DOI: 10.3390/cells9071627] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2020] [Revised: 06/30/2020] [Accepted: 07/02/2020] [Indexed: 12/29/2022] Open
Abstract
Deregulated NF-k activation is not only involved in cancer but also contributes to the pathogenesis of chronic inflammatory diseases like rheumatoid arthritis (RA) and multiple sclerosis (MS). Ideally, therapeutic NF-KappaB inhibition should only take place in those cell types that are involved in disease pathogenesis to maintain physiological cell functions in all other cells. In contrast, unselective NF-kappaB inhibition in all cells results in multiple adverse effects, a major hindrance in drug development. Hitherto, various substances exist to inhibit different steps of NF-kappaB signaling. However, powerful tools for cell-type specific NF-kappaB inhibition are not yet established. Here, we review the role of NF-kappaB in inflammatory diseases, current strategies for drug delivery and NF-kappaB inhibition and point out the "sneaking ligand" approach. Sneaking ligand fusion proteins (SLFPs) are recombinant proteins with modular architecture consisting of three domains. The prototype SLC1 binds specifically to the activated endothelium and blocks canonical NF-kappaB activation. In vivo, SLC1 attenuated clinical and histological signs of experimental arthritides. The SLFP architecture allows an easy exchange of binding and effector domains and represents an attractive approach to study disease-relevant biological targets in a broad range of diseases. In vivo, SLFP treatment might increase therapeutic efficacy while minimizing adverse effects.
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Affiliation(s)
- Bettina Sehnert
- Department of Rheumatology and Clinical Immunology, Medical Center—University of Freiburg, Faculty of Medicine, University of Freiburg, 79098 Freiburg, Germany
| | - Harald Burkhardt
- Division of Rheumatology, University Hospital Frankfurt, Goethe University, and Branch for Translational Medicine and Pharmacology TMP, Fraunhofer Institute for Molecular Biology and Applied Ecology IME, 60590 Frankfurt am Main, Germany;
| | - Stefan Dübel
- Institute of Biochemistry and Biotechnology, Technical University Braunschweig, 38106 Braunschweig, Germany;
| | - Reinhard E. Voll
- Department of Rheumatology and Clinical Immunology, Medical Center—University of Freiburg, Faculty of Medicine, University of Freiburg, 79098 Freiburg, Germany
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31
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Expression of actively soluble antigen-binding fragment (Fab) antibody and GFP fused Fab in the cytoplasm of the engineered Escherichia coli. Mol Biol Rep 2020; 47:4519-4529. [PMID: 32394307 DOI: 10.1007/s11033-020-05502-7] [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: 10/24/2019] [Accepted: 05/06/2020] [Indexed: 01/11/2023]
Abstract
The expression of recombinant antibody fragments in the cytoplasmic space of Escherichia coli and the refolding process for restoring the structure and activity of such antibodies are not efficient. Herein, fragment antigen-binding (Fab) antibodies against miroestrol and deoxymiroestrol (MD-Fab) and their fusions with a green fluorescent protein (GFP) were expressed. The reactive MD-Fabs were successfully expressed as soluble and active forms in the cytoplasm of the SHuffle® T7 E. coli strain. Regarding the construct of MD-Fab alone, VH-CH1 could associate VL-CL into Fab in the oxidizing cytoplasm of the E. coli strain, and no additional in vitro refolding was needed. In the case of the fusions with GFP, when the C-terminus of VH-CH1 was linked with the N-terminus of GFP, the MD-Fab binding reactivity was retained, but the fluorescent activity of GFP interfered. When the C-terminus of GFP was linked to the N-terminus of VL-CL, the binding activity of MD-Fab was not observed. The constructed MD-Fabs had higher specificity toward deoxymiroestrol than the parental monoclonal antibody clone 12G11. In conclusion, MD-Fabs could be expressed using SHuffle® T7 E. coli cells. This process could be considered an economical, productive, and effective method to produce antibody fragments for immunoassay techniques.
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32
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Pongkitwitoon B, Boonsnongcheep P, Kitisripanya T, Yusakul G, Sakamoto S, Tanaka H, Morimoto S, Putalun W. Preparation of a highly specific single chain variable fragment antibody targeting miroestrol and its application in quality control of Pueraria candollei by enzyme-linked immunosorbent assay. PHYTOCHEMICAL ANALYSIS : PCA 2019; 30:600-608. [PMID: 31025473 DOI: 10.1002/pca.2832] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/16/2019] [Revised: 03/11/2019] [Accepted: 03/12/2019] [Indexed: 06/09/2023]
Abstract
INTRODUCTION Miroestrol is the potent phytoestrogen isolated from White Kwao Krua (Pueraria candollei var. mirifica (Airy Shaw & Suvat.) Niyomdham, a Thai traditional medicinal plant. Nowadays, various health supplementary products featuring White Kwao Krua are available worldwide. A sensitive and rapid analytical method for quantification of miroestrol is necessary for quality control of these products. OBJECTIVES To prepare a single-chain variable fragment (scFv) antibody specific to miroestrol and develop a scFv-based enzyme-linked immunosorbent assay (ELISA) for quantitative analysis of miroestrol in plant materials and health supplementary products. METHODS A gene encoding anti-miroestrol scFv antibody was constructed and expressed in Escherichia coli SHuffle T7 strain. Anti-miroestrol scFv antibody was characterised and applied to ELISA. The developed scFv-based ELISA method was validated for its sensitivity, specificity, accuracy and precision. RESULTS Anti-miroestrol scFv antibody was highly specific to miroestrol. The scFv-based ELISA was applied to determine miroestrol in the range 0.06-7.81 μg/mL, with the limit of quantification of 0.06 μg/mL miroestrol. The accuracy of the assay was validated by its 95.08-103.99% recovery from the spiked miroestrol recovery experiment and in good correlation with the results from the monoclonal antibody-based ELISA. The relative standard deviation of the intra- and inter-assay were less than 6.0%. CONCLUSION The developed scFv-based ELISA was sensitive, specific, accurate, and precise for determination of miroestrol and useful for quality control of P. candollei plant raw materials and supplementary products.
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Affiliation(s)
- Benyakan Pongkitwitoon
- Department of Pharmaceutical Botany, Faculty of Pharmacy, Mahidol University, Bangkok, Thailand
| | - Panitch Boonsnongcheep
- Faculty of Pharmaceutical Sciences, Khon Kaen University, Khon Kaen, Thailand
- Research Group for Pharmaceutical Activities of Natural Products using Pharmaceutical Biotechnology (PANPB), National Research University Khon Kaen University, Khon Kaen, Thailand
| | - Tharita Kitisripanya
- Department of Pharmacognosy, Faculty of Pharmacy, Mahidol University, Bangkok, Thailand
| | - Gorawit Yusakul
- School of Pharmacy, Walailak University, Nakhon Si Thammarat, Thailand
| | - Seiichi Sakamoto
- Department of Pharmacognosy, Graduate School of Pharmaceutical Sciences, Kyushu University, Fukuoka, Japan
| | - Hiroyuki Tanaka
- Department of Pharmacognosy, Graduate School of Pharmaceutical Sciences, Kyushu University, Fukuoka, Japan
| | - Satoshi Morimoto
- Department of Pharmacognosy, Graduate School of Pharmaceutical Sciences, Kyushu University, Fukuoka, Japan
| | - Waraporn Putalun
- Faculty of Pharmaceutical Sciences, Khon Kaen University, Khon Kaen, Thailand
- Research Group for Pharmaceutical Activities of Natural Products using Pharmaceutical Biotechnology (PANPB), National Research University Khon Kaen University, Khon Kaen, Thailand
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Optimal combination of beneficial mutations for improved ADCC effector function of aglycosylated antibodies. Mol Immunol 2019; 114:62-71. [PMID: 31336250 DOI: 10.1016/j.molimm.2019.07.007] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2019] [Revised: 07/10/2019] [Accepted: 07/10/2019] [Indexed: 01/07/2023]
Abstract
The Fc region of IgG antibodies is crucial for binding to Fc receptors expressed on the surfaces of various immune leukocytes and eliciting therapeutic effector functions such as clearance of antibody-opsonized tumor cells. Despite abrogated Fc gamma receptor (FcγR) binding and therapeutic effector function in the absence of N-linked glycosylation at Asn297, the aglycosylated Fc region of IgG antibodies has bioprocessing advantages such as the absence of glycan heterogeneity and simple bacterial antibody production. Therefore, these antibodies have been comprehensively engineered as effector functional units for human therapy. In this work, we constructed a huge library of Fc variants with combinations of 25 beneficial mutations that were previously identified to improve binding of glycosylated or aglycosylated Fc regions to human FcγRs in previous studies. High-throughput screening of the resulting library led to the identification of an aglycosylated Fc variant that exhibited almost double the antibody-dependent cell-mediated cytotoxicity than wild-type glycosylated Fc. All mutations in this aglycosylated Fc variant were derived from previously identified beneficial mutations for engineered aglycosylated Fc variants as opposed to glycosylated variants, suggesting that significantly different sets of beneficial mutations are necessary to improve the effector function of aglycosylated Fc.
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Meyer L, López T, Espinosa R, Arias CF, Vollmers C, DuBois RM. A simplified workflow for monoclonal antibody sequencing. PLoS One 2019; 14:e0218717. [PMID: 31233538 PMCID: PMC6590890 DOI: 10.1371/journal.pone.0218717] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2019] [Accepted: 06/07/2019] [Indexed: 11/19/2022] Open
Abstract
The diversity of antibody variable regions makes cDNA sequencing challenging, and conventional monoclonal antibody cDNA amplification requires the use of degenerate primers. Here, we describe a simplified workflow for amplification of IgG antibody variable regions from hybridoma RNA by a specialized RT-PCR followed by Sanger sequencing. We perform three separate reactions for each hybridoma: one each for kappa, lambda, and heavy chain transcripts. We prime reverse transcription with a primer specific to the respective constant region and use a template-switch oligonucleotide, which creates a custom sequence at the 5’ end of the antibody cDNA. This template-switching circumvents the issue of low sequence homology and the need for degenerate primers. Instead, subsequent PCR amplification of the antibody cDNA molecules requires only two primers: one primer specific for the template-switch oligonucleotide sequence and a nested primer to the respective constant region. We successfully sequenced the variable regions of five mouse monoclonal IgG antibodies using this method, which enabled us to design chimeric mouse/human antibody expression plasmids for recombinant antibody production in mammalian cell culture expression systems. All five recombinant antibodies bind their respective antigens with high affinity, confirming that the amino acid sequences determined by our method are correct and demonstrating the high success rate of our method. Furthermore, we also designed RT-PCR primers and amplified the variable regions from RNA of cells transfected with chimeric mouse/human antibody expression plasmids, showing that our approach is also applicable to IgG antibodies of human origin. Our monoclonal antibody sequencing method is highly accurate, user-friendly, and very cost-effective.
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Affiliation(s)
- Lena Meyer
- Department of Biomolecular Engineering, University of California Santa Cruz, Santa Cruz, California, United States of America
| | - Tomás López
- Departamento de Genética del Desarrollo y Fisiología Molecular, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, México
| | - Rafaela Espinosa
- Departamento de Genética del Desarrollo y Fisiología Molecular, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, México
| | - Carlos F. Arias
- Departamento de Genética del Desarrollo y Fisiología Molecular, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, México
| | - Christopher Vollmers
- Department of Biomolecular Engineering, University of California Santa Cruz, Santa Cruz, California, United States of America
- * E-mail: (RMD); (CV)
| | - Rebecca M. DuBois
- Department of Biomolecular Engineering, University of California Santa Cruz, Santa Cruz, California, United States of America
- * E-mail: (RMD); (CV)
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Abstract
Ribosome display has proven to be a powerful in vitro selection and evolution method for generating high-affinity binders from libraries of folded proteins. It works entirely in vitro, and this has two important consequences. First, since no transformation of any cells is required, libraries with much greater diversity can be handled than with most other techniques. Second, since a library does not have to be cloned and transformed, it is very convenient to introduce random errors in the library by PCR-based methods and select improved binders. Thus, a true directed evolution, an iteration between randomization and selection over several generations, can be conveniently carried out, e.g., for affinity maturation, either on a given clone or on the whole library. Ribosome display has been successfully applied to antibody single-chain Fv fragments (scFv), which can be selected not only for specificity but also for stability and catalytic activity. High-affinity binders with new target specificity can be obtained from highly diverse libraries in only a few selection rounds. In this protocol, the selection from the library and the process of affinity maturation and off-rate selection are explained in detail.
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Andrews NP, Boeckman JX, Manning CF, Nguyen JT, Bechtold H, Dumitras C, Gong B, Nguyen K, van der List D, Murray KD, Engebrecht J, Trimmer JS. A toolbox of IgG subclass-switched recombinant monoclonal antibodies for enhanced multiplex immunolabeling of brain. eLife 2019; 8:43322. [PMID: 30667360 PMCID: PMC6377228 DOI: 10.7554/elife.43322] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2018] [Accepted: 01/21/2019] [Indexed: 11/17/2022] Open
Abstract
Generating recombinant monoclonal antibodies (R-mAbs) from mAb-producing hybridomas offers numerous advantages that increase the effectiveness, reproducibility, and transparent reporting of research. We report here the generation of a novel resource in the form of a library of recombinant R-mAbs validated for neuroscience research. We cloned immunoglobulin G (IgG) variable domains from cryopreserved hybridoma cells and input them into an integrated pipeline for expression and validation of functional R-mAbs. To improve efficiency over standard protocols, we eliminated aberrant Sp2/0-Ag14 hybridoma-derived variable light transcripts using restriction enzyme treatment. Further, we engineered a plasmid backbone that allows for switching of the IgG subclasses without altering target binding specificity to generate R-mAbs useful in simultaneous multiplex labeling experiments not previously possible. The method was also employed to rescue IgG variable sequences and generate functional R-mAbs from a non-viable cryopreserved hybridoma. All R-mAb sequences and plasmids will be archived and disseminated from open source suppliers. The immune system fights off disease-causing microbes using antibodies: Y-shaped proteins that each bind to a specific foreign molecule. Indeed, these proteins bind so tightly and so specifically that they can pick out a single target in a complex mixture of different molecules. This property also makes them useful in research. For example, neurobiologists can use antibodies to mark target proteins in thin sections of brain tissue. This reveals their position inside brain cells, helping to link the structure of the brain to the roles the different parts of this structure perform. To use antibodies in this way, scientists need to be able to produce them in large quantities without losing their target specificity. The most common way to do this is with cells called hybridomas. A hybridoma is a hybrid of an antibody-producing immune cell and a cancer cell, and it has properties of both. From the immune cell, it inherits the genes to make a specific type of antibody. From the cancer cell, it inherits the ability to go on dividing forever. In theory, hybridomas should be immortal antibody factories, but they have some limitations. They are expensive to keep alive, hard to transport between labs, and their genes can be unstable. Problems can creep into their genetic code, halting their growth or changing the targets their antibodies recognize. When this happens, scientists can lose vital research tools. Instead of keeping the immune cells alive, an alternative approach is to make recombinant antibodies. Rather than store the whole cell, this approach just stores the parts of the genes that encode antibody target-specificity. Andrews et al. set out to convert a valuable toolbox of neuroscience antibodies into recombinant form. This involved copying the antibody genes from a large library of preserved hybridoma cells. However, many hybridomas also carry genes that produce non-functional antibodies. A step in the process removed these DNA sequences, ensuring that only working antibodies made it into the final library. Using frozen cells made it possible to recover antibody genes from hybridoma cells that could no longer grow. The recombinant DNA sequences provide a permanent record of useful antibodies. Not only does this prevent the loss of research tools, it is also much more shareable than living cells. Modifications to the DNA sequences in the library allow for the use of many antibodies at once. This could help when studying the interactions between different molecules in the brain. Toolkits like these could also make it easier to collaborate, and to reproduce data gathered by different researchers around the world.
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Affiliation(s)
- Nicolas P Andrews
- Department of Neurobiology, Physiology and Behavior, University of California, Davis, United States
| | - Justin X Boeckman
- Department of Neurobiology, Physiology and Behavior, University of California, Davis, United States
| | - Colleen F Manning
- Department of Neurobiology, Physiology and Behavior, University of California, Davis, United States
| | - Joe T Nguyen
- Department of Molecular and Cellular Biology, University of California, Davis, United States
| | - Hannah Bechtold
- Department of Molecular and Cellular Biology, University of California, Davis, United States
| | - Camelia Dumitras
- Department of Neurobiology, Physiology and Behavior, University of California, Davis, United States
| | - Belvin Gong
- Department of Neurobiology, Physiology and Behavior, University of California, Davis, United States
| | - Kimberly Nguyen
- Department of Neurobiology, Physiology and Behavior, University of California, Davis, United States
| | - Deborah van der List
- Department of Neurobiology, Physiology and Behavior, University of California, Davis, United States
| | - Karl D Murray
- Department of Neurobiology, Physiology and Behavior, University of California, Davis, United States
| | - JoAnne Engebrecht
- Department of Molecular and Cellular Biology, University of California, Davis, United States
| | - James S Trimmer
- Department of Neurobiology, Physiology and Behavior, University of California, Davis, United States.,Department of Physiology and Membrane Biology, University of California, Davis, United States
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Dal Ferro M, Rizzo S, Rizzo E, Marano F, Luisi I, Tarasiuk O, Sblattero D. Phage Display Technology for Human Monoclonal Antibodies. Methods Mol Biol 2019; 1904:319-338. [PMID: 30539478 DOI: 10.1007/978-1-4939-8958-4_15] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
During the last 20 years in vitro technologies opened powerful routes to combine the generation of large libraries together with fast selection and screening procedures to identify lead candidates. One of the most successful methods is based on the use of filamentous phages. Functional Antibodies (Abs) fragments can be displayed on the surface of phages by fusing the coding sequence of the antibody variable (V) regions to the phage minor coat protein pIII. By creating large libraries, antibodies with affinities comparable to those obtained using traditional hybridoma technology can be isolated by a series of cycles of selection on the antigen of interest. In this system, antibody genes can be recovered simultaneously with selection and can be easily further engineered, for example by increasing their affinity to levels unobtainable in the immune system, or by modulating their specificity and their effector functions (by recloning into a full-length immunoglobulin scaffold). This chapter describes the basic protocols for antibody library construction and selection of binder with desired specificity.
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Affiliation(s)
- Marco Dal Ferro
- Department of Life Sciences, University of Trieste, Trieste, Italy
| | - Serena Rizzo
- Department of Life Sciences, University of Trieste, Trieste, Italy
| | - Emanuela Rizzo
- Department of Life Sciences, University of Trieste, Trieste, Italy
| | - Francesca Marano
- Department of Life Sciences, University of Trieste, Trieste, Italy
| | - Immacolata Luisi
- Department of Life Sciences, University of Trieste, Trieste, Italy
| | - Olga Tarasiuk
- Department of Health Sciences and IRCAD, University of Eastern Piedmont, Novara, Italy
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A novel approach for rapid high-throughput selection of recombinant functional rat monoclonal antibodies. BMC Immunol 2018; 19:35. [PMID: 30514214 PMCID: PMC6280491 DOI: 10.1186/s12865-018-0274-8] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2018] [Accepted: 11/26/2018] [Indexed: 11/10/2022] Open
Abstract
Background Most monoclonal antibodies against mouse antigens have been derived from rat spleen-mouse myeloma fusions, which are valuable tools for purposes ranging from general laboratory reagents to therapeutic drugs, and yet selecting and expressing them remains a time-consuming and inefficient process. Here, we report a novel approach for the rapid high-throughput selection and expression of recombinant functional rat monoclonal antibodies with different isotypes. Results We have developed a robust system for generating rat monoclonal antibodies through several processes involving simultaneously immunizing rats with three different antigens expressing in a mixed cell pools, preparing hybridoma cell pools, in vitro screening and subsequent cloning of the rearranged light and heavy chains into a single expression plasmid using a highly efficient assembly method, which can decrease the time and effort required by multiple immunizations and fusions, traditional clonal selection and expression methods. Using this system, we successfully selected several rat monoclonal antibodies with different IgG isotypes specifically targeting the mouse PD-1, LAG-3 or AFP protein from a single fusion. We applied these recombinant anti-PD-1 monoclonal antibodies (32D6) in immunotherapy for therapeutic purposes that produced the expected results. Conclusions This method can be used to facilitate an increased throughput of the entire process from multiplex immunization to acquisition of functional rat monoclonal antibodies and facilitate their expression and feasibility using a single plasmid. Electronic supplementary material The online version of this article (10.1186/s12865-018-0274-8) contains supplementary material, which is available to authorized users.
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Bifunctional PD-1 × αCD3 × αCD33 fusion protein reverses adaptive immune escape in acute myeloid leukemia. Blood 2018; 132:2484-2494. [PMID: 30275109 DOI: 10.1182/blood-2018-05-849802] [Citation(s) in RCA: 50] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2018] [Accepted: 09/19/2018] [Indexed: 12/12/2022] Open
Abstract
The CD33-targeting bispecific T-cell engager (BiTE) AMG 330 proved to be highly efficient in mediating cytolysis of acute myeloid leukemia (AML) cells in vitro and in mouse models. Yet, T-cell activation is correlated with upregulation of programmed cell death-ligand 1 (PD-L1) and other inhibitory checkpoints on AML cells that confer adaptive immune resistance. PD-1 and PD-L1 blocking agents may counteract T-cell dysfunction, however, at the expense of broadly distributed immune-related adverse events (irAEs). We developed a bifunctional checkpoint inhibitory T cell-engaging (CiTE) antibody that combines T-cell redirection to CD33 on AML cells with locally restricted immune checkpoint blockade. This is accomplished by fusing the extracellular domain of PD-1 (PD-1ex), which naturally holds a low affinity to PD-L1, to an αCD3.αCD33 BiTE-like scaffold. By a synergistic effect of checkpoint blockade and avidity-dependent binding, the PD-1ex attachment increases T-cell activation (3.3-fold elevation of interferon-γ) and leads to efficient and highly selective cytotoxicity against CD33+PD-L1+ cell lines (50% effective concentration = 2.3-26.9 pM) as well as patient-derived AML cells (n = 8). In a murine xenograft model, the CiTE induces complete AML eradication without initial signs of irAEs as measured by body weight loss. We conclude that our molecule preferentially targets AML cells, whereas high-affinity blockers, such as clinically approved anticancer agents, also address PD-L1+ non-AML cells. By combining the high efficacy of T-cell engagers with immune checkpoint blockade in a single molecule, we expect to minimize irAEs associated with the systemic application of immune checkpoint inhibitors and suggest high therapeutic potential, particularly for patients with relapsed/ refractory AML.
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Jo M, Hwang B, Yoon HW, Jung ST. Escherichia coli inner membrane display system for high-throughput screening of dimeric proteins. Biotechnol Bioeng 2018; 115:2849-2858. [PMID: 30171695 DOI: 10.1002/bit.26826] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2018] [Revised: 08/23/2018] [Accepted: 08/30/2018] [Indexed: 11/10/2022]
Abstract
Multimer formation is indispensable to the intrinsicbiologicalfunctions of many natural proteins. For example, the human immunoglobulin G (IgG) antibody has two variable regions (heavy chain variable domain [VH] and light chain variable domain [VL]) that must be assembled for specific antigen binding, and homodimerization of the antibody's Fc domain is essential for eliciting therapeutic effector functions. For the more efficient high-throughput directed evolution of multimeric proteins with ease of cultivation and handling, here we report a membrane protein drift and assembly (MPDA) system, in which a multimeric protein is displayed on a bacterial inner membrane by drifting and auto-assembling membrane-anchored subunit polypeptides. This system enabled the auto-assembly of membrane-tethered Fv domains (VH and VL) or the monomeric Fc domain into a functional hetero- or homodimeric protein complex on the bacterial inner membrane. This system could also be used to enrich a desired engineered Fc variant from a mixture containing a million-fold excess of wild-type Fc domain, indicating the applicability of the MPDA system for the high-throughput directed evolution of a variety of multimeric proteins, such as cytokines, enzymes, or structural proteins.
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Affiliation(s)
- Migyeong Jo
- Department of Applied Chemistry, Kookmin University, Seoul, Korea
| | - Bora Hwang
- Department of Applied Chemistry, Kookmin University, Seoul, Korea
| | - Hyun Woung Yoon
- Department of Applied Chemistry, Kookmin University, Seoul, Korea
| | - Sang Taek Jung
- Department of Applied Chemistry, Kookmin University, Seoul, Korea
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Yermanos A, Greiff V, Krautler NJ, Menzel U, Dounas A, Miho E, Oxenius A, Stadler T, Reddy ST. Comparison of methods for phylogenetic B-cell lineage inference using time-resolved antibody repertoire simulations (AbSim). Bioinformatics 2018; 33:3938-3946. [PMID: 28968873 DOI: 10.1093/bioinformatics/btx533] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2016] [Accepted: 08/30/2017] [Indexed: 01/13/2023] Open
Abstract
Motivation The evolution of antibody repertoires represents a hallmark feature of adaptive B-cell immunity. Recent advancements in high-throughput sequencing have dramatically increased the resolution to which we can measure the molecular diversity of antibody repertoires, thereby offering for the first time the possibility to capture the antigen-driven evolution of B cells. However, there does not exist a repertoire simulation framework yet that enables the comparison of commonly utilized phylogenetic methods with regard to their accuracy in inferring antibody evolution. Results Here, we developed AbSim, a time-resolved antibody repertoire simulation framework, which we exploited for testing the accuracy of methods for the phylogenetic reconstruction of B-cell lineages and antibody molecular evolution. AbSim enables the (i) simulation of intermediate stages of antibody sequence evolution and (ii) the modeling of immunologically relevant parameters such as duration of repertoire evolution, and the method and frequency of mutations. First, we validated that our repertoire simulation framework recreates replicates topological similarities observed in experimental sequencing data. Second, we leveraged Absim to show that current methods fail to a certain extent to predict the true phylogenetic tree correctly. Finally, we formulated simulation-validated guidelines for antibody evolution, which in the future will enable the development of accurate phylogenetic methods. Availability and implementation https://cran.r-project.org/web/packages/AbSim/index.html. Contact sai.reddy@ethz.ch. Supplementary information Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Alexander Yermanos
- Department of Biosystems Science and Engineering, ETH Zürich, 4058 Basel, Switzerland
| | - Victor Greiff
- Department of Biosystems Science and Engineering, ETH Zürich, 4058 Basel, Switzerland
| | | | - Ulrike Menzel
- Department of Biosystems Science and Engineering, ETH Zürich, 4058 Basel, Switzerland
| | - Andreas Dounas
- Department of Chemistry and Applied Biosciences, ETH Zürich, 8093 Zürich, Switzerland
| | - Enkelejda Miho
- Department of Biosystems Science and Engineering, ETH Zürich, 4058 Basel, Switzerland
| | | | - Tanja Stadler
- Department of Biosystems Science and Engineering, ETH Zürich, 4058 Basel, Switzerland
| | - Sai T Reddy
- Department of Biosystems Science and Engineering, ETH Zürich, 4058 Basel, Switzerland
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Ongey EL, Giessmann RT, Fons M, Rappsilber J, Adrian L, Neubauer P. Heterologous Biosynthesis, Modifications and Structural Characterization of Ruminococcin-A, a Lanthipeptide From the Gut Bacterium Ruminococcus gnavus E1, in Escherichia coli. Front Microbiol 2018; 9:1688. [PMID: 30093894 PMCID: PMC6071512 DOI: 10.3389/fmicb.2018.01688] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2018] [Accepted: 07/06/2018] [Indexed: 11/13/2022] Open
Abstract
Ruminococcin A (RumA) is a lanthipeptide with high activity against pathogenic clostridia and is naturally produced by the strict anaerobic bacterium Ruminococcus gnavus E1, isolated from human intestine. Cultivating R. gnavus E1 is challenging, limiting high-quality production, further biotechnological development and therapeutic exploitation of RumA. To supply an alternative production system, the gene encoding RumA-modifying enzyme (RumM) and the gene encoding the unmodified precursor peptide (preRumA) were amplified from the chromosome of R. gnavus E1 and coexpressed in Escherichia coli. Our results show that the ruminococcin-A lanthionine synthetase RumM catalyzed dehydration of threonine and serine residues and subsequently installed thioether bridges into the core structure of a mutant version of preRumA (preRumA∗). These modifications were achieved when the peptide was expressed as a fusion protein together with green fluorescence protein (GFP), demonstrating that a larger attachment to the N-terminus of the leader peptide does not obstruct in vivo processivity of RumM in modifying the core peptide. The leader peptide serves as a docking sequence which the modifying enzyme recognizes and interacts with, enabling its catalytic role. We further investigated RumM catalysis in conjunction with the formation of complexes observed between RumM and the chimeric GFP fusion protein. Results obtained suggested some insights into the catalytic mechanisms of class II lanthipeptide synthetases. Our data further indicated the presence of three thioether bridges, contradicting a previous report whose findings ruled out the possibility of forming a third ring in RumA. Modified preRumA∗ was activated in vitro by removing the leader peptide using trypsin and biological activity was achieved against Bacillus subtilis ATCC 6633. A production yield of 6 mg of pure modified preRumA∗ per liter of E. coli culture was attained and considering the size ratio of the leader-to-core segments of preRumA∗, this amount would generate a final yield of approximately 1-2 mg of active RumA when the leader peptide is removed. The yield of our system exceeds that attainable in the natural producer by several 1000-fold. The system developed herein supplies useful tools for product optimization and for performing in vivo peptide engineering to generate new analogs with superior anti-infective properties.
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Affiliation(s)
- Elvis L Ongey
- Chair of Bioprocess Engineering, Institute of Biotechnology, Technische Universität Berlin, Berlin, Germany
| | - Robert T Giessmann
- Chair of Bioprocess Engineering, Institute of Biotechnology, Technische Universität Berlin, Berlin, Germany
| | - Michel Fons
- Aix Marseille Univ, CNRS, BIP UMR 7281, Marseille, France
| | - Juri Rappsilber
- Institute of Biotechnology, Technische Universität Berlin, Berlin, Germany
| | - Lorenz Adrian
- Department of Isotope Biogeochemistry, Helmholtz Centre for Environmental Research - UFZ, Leipzig, Germany.,Chair of Geobiotechnology, Institute of Biotechnology, Technische Universität Berlin, Berlin, Germany
| | - Peter Neubauer
- Chair of Bioprocess Engineering, Institute of Biotechnology, Technische Universität Berlin, Berlin, Germany
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Bradbury ARM, Trinklein ND, Thie H, Wilkinson IC, Tandon AK, Anderson S, Bladen CL, Jones B, Aldred SF, Bestagno M, Burrone O, Maynard J, Ferrara F, Trimmer JS, Görnemann J, Glanville J, Wolf P, Frenzel A, Wong J, Koh XY, Eng HY, Lane D, Lefranc MP, Clark M, Dübel S. When monoclonal antibodies are not monospecific: Hybridomas frequently express additional functional variable regions. MAbs 2018; 10:539-546. [PMID: 29485921 PMCID: PMC5973764 DOI: 10.1080/19420862.2018.1445456] [Citation(s) in RCA: 63] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
Monoclonal antibodies are commonly assumed to be monospecific, but anecdotal studies have reported genetic diversity in antibody heavy chain and light chain genes found within individual hybridomas. As the prevalence of such diversity has never been explored, we analyzed 185 random hybridomas, in a large multicenter dataset. The hybridomas analyzed were not biased towards those with cloning difficulties or known to have additional chains. Of the hybridomas we evaluated, 126 (68.1%) contained no additional productive chains, while the remaining 59 (31.9%) contained one or more additional productive heavy or light chains. The expression of additional chains degraded properties of the antibodies, including specificity, binding signal and/or signal-to-noise ratio, as determined by enzyme-linked immunosorbent assay and immunohistochemistry. The most abundant mRNA transcripts found in a hybridoma cell line did not necessarily encode the antibody chains providing the correct specificity. Consequently, when cloning antibody genes, functional validation of all possible VH and VL combinations is required to identify those with the highest affinity and lowest cross-reactivity. These findings, reflecting the current state of hybridomas used in research, reiterate the importance of using sequence-defined recombinant antibodies for research or diagnostic use.
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Affiliation(s)
| | | | - Holger Thie
- c Miltenyi Biotec GmbH , Friedrich-Ebert-Str. 68, Bergisch Gladbach , Germany
| | - Ian C Wilkinson
- d Absolute Antibody, Wilton Centre , Redcar , Cleveland TS10 4RF , United Kingdom
| | - Atul K Tandon
- e NeoBiotechnologies , 2 Union Square, Union City , CA , USA
| | - Stephen Anderson
- d Absolute Antibody, Wilton Centre , Redcar , Cleveland TS10 4RF , United Kingdom
| | - Catherine L Bladen
- d Absolute Antibody, Wilton Centre , Redcar , Cleveland TS10 4RF , United Kingdom
| | - Brittany Jones
- e NeoBiotechnologies , 2 Union Square, Union City , CA , USA
| | | | - Marco Bestagno
- f International Centre for Genetic Engineering and Biotechnology (ICGEB) , Padriciano 99, Trieste , Italy
| | - Oscar Burrone
- f International Centre for Genetic Engineering and Biotechnology (ICGEB) , Padriciano 99, Trieste , Italy
| | - Jennifer Maynard
- g The University of Texas at Austin, Cockrell School of Engineering , McKetta Department of Chemical Engineering , 200 E Dean Keeton St. Stop C0400, Austin , Texas , USA
| | | | - James S Trimmer
- h Department of Physiology and Membrane Biology , University of California , Davis, One Shields Avenue, Davis , CA , USA
| | - Janina Görnemann
- i Institute for Molecular Genetics , University of Heidelberg , Im Neuenheimer Field 260, Heidelberg , Germany
| | - Jacob Glanville
- j Stanford University, School of Medicine , Stanford , California , USA
| | - Philipp Wolf
- k Department of Urology , Medical Center, University of Freiburg , Breisacher Str. 66, Freiburg , Germany
| | - Andre Frenzel
- l Yumab GmbH , Inhoffenstr. 7, Braunschweig , Germany.,p Technische Universität Braunschweig, Institute of Biochemistry, Biotechnology and Bioinformatics , Spielmannstr. 7, Braunschweig , Germany
| | - Julin Wong
- m A*Star p53 laboratory , 06-06 Immunos, Singapore , Singapore
| | - Xin Yu Koh
- m A*Star p53 laboratory , 06-06 Immunos, Singapore , Singapore
| | - Hui-Yan Eng
- m A*Star p53 laboratory , 06-06 Immunos, Singapore , Singapore
| | - David Lane
- m A*Star p53 laboratory , 06-06 Immunos, Singapore , Singapore
| | - Marie-Paule Lefranc
- n IMGT®, the international ImMunoGeneTics information system®, Laboratoire d'ImmunoGénétique Moléculaire LIGM, Institut de Génétique Humaine IGH, UPR CNRS 1142, Montpellier University , Montpellier cedex 5 , France
| | - Mike Clark
- o Clark Antibodies Ltd , 10 Wellington Street, Cambridge , CB1 1HW , United Kingdom
| | - Stefan Dübel
- p Technische Universität Braunschweig, Institute of Biochemistry, Biotechnology and Bioinformatics , Spielmannstr. 7, Braunschweig , Germany
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Chen Y, Chaudhary N, Yang N, Granato A, Turner JA, Howard SL, Devereaux C, Zuo T, Shrestha A, Goel RR, Neuberg D, Wesemann DR. Microbial symbionts regulate the primary Ig repertoire. J Exp Med 2018; 215:1397-1415. [PMID: 29588346 PMCID: PMC5940265 DOI: 10.1084/jem.20171761] [Citation(s) in RCA: 40] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2017] [Revised: 01/23/2018] [Accepted: 03/09/2018] [Indexed: 01/26/2023] Open
Abstract
Symbiotic relationships help shape immune fitness. Chen et al. demonstrate that microbial symbionts influence host immunity by enriching frequencies of antibacterial specificities within the naive B cell receptor repertoire and that this may have consequences for mucosal and systemic immunity. The ability of immunoglobulin (Ig) to recognize pathogens is critical for optimal immune fitness. Early events that shape preimmune Ig repertoires, expressed on IgM+ IgD+ B cells as B cell receptors (BCRs), are poorly defined. Here, we studied germ-free mice and conventionalized littermates to explore the hypothesis that symbiotic microbes help shape the preimmune Ig repertoire. Ig-binding assays showed that exposure to conventional microbial symbionts enriched frequencies of antibacterial IgM+ IgD+ B cells in intestine and spleen. This enrichment affected follicular B cells, involving a diverse set of Ig-variable region gene segments, and was T cell–independent. Functionally, enrichment of microbe reactivity primed basal levels of small intestinal T cell–independent, symbiont-reactive IgA and enhanced systemic IgG responses to bacterial immunization. These results demonstrate that microbial symbionts influence host immunity by enriching frequencies of antibacterial specificities within preimmune B cell repertoires and that this may have consequences for mucosal and systemic immunity.
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Affiliation(s)
- Yuezhou Chen
- Department of Medicine, Division of Rheumatology, Immunology, and Allergy, Brigham and Women's Hospital and Harvard Medical School, Boston, MA
| | - Neha Chaudhary
- Department of Medicine, Division of Rheumatology, Immunology, and Allergy, Brigham and Women's Hospital and Harvard Medical School, Boston, MA
| | - Nicole Yang
- Department of Medicine, Division of Rheumatology, Immunology, and Allergy, Brigham and Women's Hospital and Harvard Medical School, Boston, MA
| | - Alessandra Granato
- Department of Medicine, Division of Rheumatology, Immunology, and Allergy, Brigham and Women's Hospital and Harvard Medical School, Boston, MA
| | - Jacob A Turner
- Department of Medicine, Division of Rheumatology, Immunology, and Allergy, Brigham and Women's Hospital and Harvard Medical School, Boston, MA
| | - Shannon L Howard
- Department of Medicine, Division of Rheumatology, Immunology, and Allergy, Brigham and Women's Hospital and Harvard Medical School, Boston, MA
| | - Colby Devereaux
- Department of Medicine, Division of Rheumatology, Immunology, and Allergy, Brigham and Women's Hospital and Harvard Medical School, Boston, MA
| | - Teng Zuo
- Department of Medicine, Division of Rheumatology, Immunology, and Allergy, Brigham and Women's Hospital and Harvard Medical School, Boston, MA
| | - Akritee Shrestha
- Department of Medicine, Division of Rheumatology, Immunology, and Allergy, Brigham and Women's Hospital and Harvard Medical School, Boston, MA
| | - Rishi R Goel
- Department of Medicine, Division of Rheumatology, Immunology, and Allergy, Brigham and Women's Hospital and Harvard Medical School, Boston, MA
| | - Donna Neuberg
- Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute, Boston, MA
| | - Duane R Wesemann
- Department of Medicine, Division of Rheumatology, Immunology, and Allergy, Brigham and Women's Hospital and Harvard Medical School, Boston, MA
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46
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Wendel U, Persson N, Risinger C, Bengtsson E, Nodin B, Danielsson L, Welinder C, Nordin Fredrikson G, Jansson B, Blixt O. A novel monoclonal antibody targeting carboxymethyllysine, an advanced glycation end product in atherosclerosis and pancreatic cancer. PLoS One 2018; 13:e0191872. [PMID: 29420566 PMCID: PMC5805250 DOI: 10.1371/journal.pone.0191872] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2017] [Accepted: 01/13/2018] [Indexed: 12/12/2022] Open
Abstract
Advanced glycation end products are formed by non-enzymatic reactions between proteins and carbohydrates, causing irreversible lysine and arginine alterations that severely affect protein structure and function. The resulting modifications induce inflammation by binding to scavenger receptors. An increase in advanced glycation end products is observed in a number of diseases e.g. atherosclerosis and cancer. Since advanced glycation end products also are present in healthy individuals, their detection and quantification are of great importance for usage as potential biomarkers. Current methods for advanced glycation end product detection are though limited and solely measure total glycation. This study describes a new epitope-mapped single chain variable fragment, D1-B2, against carboxymethyllysine, produced from a phage library that was constructed from mouse immunizations. The phage library was selected against advanced glycation end product targets using a phage display platform. Characterization of its binding pattern was performed using large synthetic glycated peptide and protein libraries displayed on microarray slides. D1-B2 showed a preference for an aspartic acid, three positions N-terminally from a carboxymethyllysine residue and also bound to a broad collection of glycated proteins. Positive immunohistochemical staining of mouse atherosclerotic plaques and of a tissue microarray of human pancreatic tumors confirmed the usability of the new scFv for advanced glycation end product detection in tissues. This study demonstrates a promising methodology for high-throughput generation of epitope-mapped monoclonal antibodies against AGE.
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Affiliation(s)
- Ulrika Wendel
- Chemical Glyco-Biology Laboratory, Department of Chemistry, Faculty of Science, University of Copenhagen, Copenhagen, Denmark
| | - Nina Persson
- Chemical Glyco-Biology Laboratory, Department of Chemistry, Faculty of Science, University of Copenhagen, Copenhagen, Denmark
| | - Christian Risinger
- Chemical Glyco-Biology Laboratory, Department of Chemistry, Faculty of Science, University of Copenhagen, Copenhagen, Denmark
| | - Eva Bengtsson
- Department of Clinical Sciences Malmö, Scania University Hospital, Malmö Lund University, Malmö, Sweden
| | - Björn Nodin
- Division of Oncology and Pathology, Department of Clinical Sciences Lund, Lund University, Lund, Sweden
| | - Lena Danielsson
- Clinical Chemistry and Pharmacology, Department of Laboratory Medicine, Lund University, Lund, Sweden
| | - Charlotte Welinder
- Division of Oncology and Pathology, Department of Clinical Sciences Lund, Lund University, Lund, Sweden
- Centre of Excellence in Biological and Medical Mass Spectrometry “CEBMMS”, Biomedical Centre D13, Lund University, Lund, Sweden
| | - Gunilla Nordin Fredrikson
- Department of Clinical Sciences Malmö, Scania University Hospital, Malmö Lund University, Malmö, Sweden
| | - Bo Jansson
- Division of Oncology and Pathology, Department of Clinical Sciences Lund, Lund University, Lund, Sweden
| | - Ola Blixt
- Chemical Glyco-Biology Laboratory, Department of Chemistry, Faculty of Science, University of Copenhagen, Copenhagen, Denmark
- * E-mail:
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47
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Microfluidic single-cell technology in immunology and antibody screening. Mol Aspects Med 2018; 59:47-61. [DOI: 10.1016/j.mam.2017.09.004] [Citation(s) in RCA: 56] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2017] [Revised: 09/06/2017] [Accepted: 09/13/2017] [Indexed: 11/20/2022]
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48
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Optimized Generation of High-Affinity, High-Specificity Single-Chain Fv Antibodies from Multi-Antigen Immunized Chickens. Methods Mol Biol 2018. [PMID: 27730560 DOI: 10.1007/978-1-4939-6412-3_16] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/09/2023]
Abstract
High-affinity, highly specific binding proteins are a key class of molecules used in the development of new affinity chromatography methods. Traditionally, antibody-based methods have relied on the use of immunoglobulins purified from immune animal sera, from egg yolks, or from murine monoclonal hybridoma supernatants. To accelerate and refine the reagent antibody generation process, we have developed optimized methods that allow the rapid assembly of scFv libraries from chickens immunized with pools of immunogens. These methods allow the simplified generation of a single, moderately sized library of single chain Fv (scFv) and the subsequent isolation of diverse, high affinity, and high specificity monoclonals for each individual immunogen, via phage display. Using these methods, antibodies can be derived that exhibit the desired selectivity, including exquisite specificity or cross-reactivity to multiple orthologues of the same protein.
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49
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Melnik S, Neumann AC, Karongo R, Dirndorfer S, Stübler M, Ibl V, Niessner R, Knopp D, Stoger E. Cloning and plant-based production of antibody MC10E7 for a lateral flow immunoassay to detect [4-arginine]microcystin in freshwater. PLANT BIOTECHNOLOGY JOURNAL 2018; 16:27-38. [PMID: 28421663 PMCID: PMC5785354 DOI: 10.1111/pbi.12746] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/06/2016] [Revised: 03/14/2017] [Accepted: 04/12/2017] [Indexed: 06/07/2023]
Abstract
Antibody MC10E7 is one of a small number of monoclonal antibodies that bind specifically to [Arg4]-microcystins, and it can be used to survey natural water sources and food samples for algal toxin contamination. However, the development of sensitive immunoassays in different test formats, particularly user-friendly tests for on-site analysis, requires a sensitive but also cost-effective antibody. The original version of MC10E7 was derived from a murine hybridoma, but we determined the sequence of the variable regions using the peptide mass-assisted cloning strategy and expressed a scFv (single-chain variable fragment) format of this antibody in yeast and a chimeric full-size version in leaves of Nicotiana tabacum and Nicotiana benthamiana to facilitate inexpensive and scalable production. The specific antigen-binding activity of the purified antibody was verified by surface plasmon resonance spectroscopy and ELISA, confirming the same binding specificity as its hybridoma-derived counterpart. The plant-derived antibody was used to design a lateral flow immunoassay (dipstick) for the sensitive detection of [Arg4]-microcystins at concentrations of 100-300 ng/L in freshwater samples collected at different sites. Plant-based production will likely reduce the cost of the antibody, currently the most expensive component of the dipstick immunoassay, and will allow the development of further antibody-based analytical devices and water purification adsorbents for the efficient removal of toxic contaminants.
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Affiliation(s)
- Stanislav Melnik
- Department of Applied Genetics and Cell Biology, University of Natural Resources and Life Sciences, Vienna, Austria
| | - Anna-Cathrine Neumann
- Institute of Hydrochemistry and Chair for Analytical Chemistry, Technical University Munich, Munich, Germany
| | - Ryan Karongo
- Institute of Hydrochemistry and Chair for Analytical Chemistry, Technical University Munich, Munich, Germany
| | - Sebastian Dirndorfer
- Institute of Hydrochemistry and Chair for Analytical Chemistry, Technical University Munich, Munich, Germany
| | - Martin Stübler
- Department of Applied Genetics and Cell Biology, University of Natural Resources and Life Sciences, Vienna, Austria
| | - Verena Ibl
- Department of Applied Genetics and Cell Biology, University of Natural Resources and Life Sciences, Vienna, Austria
| | - Reinhard Niessner
- Institute of Hydrochemistry and Chair for Analytical Chemistry, Technical University Munich, Munich, Germany
| | - Dietmar Knopp
- Institute of Hydrochemistry and Chair for Analytical Chemistry, Technical University Munich, Munich, Germany
| | - Eva Stoger
- Department of Applied Genetics and Cell Biology, University of Natural Resources and Life Sciences, Vienna, Austria
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50
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Gandhi S, Banga I, Maurya PK, Eremin SA. A gold nanoparticle-single-chain fragment variable antibody as an immunoprobe for rapid detection of morphine by dipstick. RSC Adv 2018; 8:1511-1518. [PMID: 35540925 PMCID: PMC9077121 DOI: 10.1039/c7ra12810j] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2017] [Accepted: 12/15/2017] [Indexed: 11/21/2022] Open
Abstract
Gold nanoparticle (AuNP)-based optical assays are of significant interest since the molecular phenomenon can be examined easily with change in the color of AuNPs. Herein, we report the development of a dipstick using a AuNP-labeled single-chain fragment variable (scFv) antibody for the detection of morphine. The scFv antibodies for morphine were developed using phage display-based antibody library. Immunoglobulin variable regions of heavy (VH)- and light (VL)-chain genes were connected via a glycine–serine linker isolated from murine immune repertoire and cloned into the expression vector pIT2. The scFv was produced in Escherichia coli HB2151, yielding a functional protein with a molecular weight of approximately 32 kDa. The morphine scFv was labeled with gold nanoparticles and used as an optical immunoprobe in a dipstick. The competitive dipstick assay characterized the ability of the scFv antibody to recognize free morphine. The detection range was 1–1000 ng mL−1 with a limit of detection (LOD) of 5 ng mL−1 under optimal conditions, and the IC50 value was 14 ng mL−1 for morphine. The developed optical dipstick kit of scFv antibody was capable of specifically binding to free morphine and its analogs in a solution in less than 5 min and could be useful for on-site screening of a real sample in blood, urine, and saliva. Dipstick device developed on the principle of lateral flow using gold nanoparticles for analysis of morphine in urine by morphine/scFv/immunoprobe.![]()
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Affiliation(s)
- Sonu Gandhi
- Institute of Biotechnology
- Amity University
- Noida-201313
- India
| | - Ivneet Banga
- Institute of Biotechnology
- Amity University
- Noida-201313
- India
| | - Pawan Kumar Maurya
- Institute of Biotechnology
- Amity University
- Noida-201313
- India
- Universidade Federal de Sao Paulo
| | - Sergei A. Eremin
- Faculty of Chemistry
- M.V.Lomonosov Moscow State University
- 119991 Moscow
- Russia
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