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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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2
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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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3
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Tajima N, Simorowski N, Yovanno RA, Regan MC, Michalski K, Gómez R, Lau AY, Furukawa H. Development and characterization of functional antibodies targeting NMDA receptors. Nat Commun 2022; 13:923. [PMID: 35177668 PMCID: PMC8854693 DOI: 10.1038/s41467-022-28559-3] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2021] [Accepted: 01/27/2022] [Indexed: 12/13/2022] Open
Abstract
N-methyl-D-aspartate receptors (NMDARs) are critically involved in basic brain functions and neurodegeneration as well as tumor invasiveness. Targeting specific subtypes of NMDARs with distinct activities has been considered an effective therapeutic strategy for neurological disorders and diseases. However, complete elimination of off-target effects of small chemical compounds has been challenging and thus, there is a need to explore alternative strategies for targeting NMDAR subtypes. Here we report identification of a functional antibody that specifically targets the GluN1-GluN2B NMDAR subtype and allosterically down-regulates ion channel activity as assessed by electrophysiology. Through biochemical analysis, x-ray crystallography, single-particle electron cryomicroscopy, and molecular dynamics simulations, we show that this inhibitory antibody recognizes the amino terminal domain of the GluN2B subunit and increases the population of the non-active conformational state. The current study demonstrates that antibodies may serve as specific reagents to regulate NMDAR functions for basic research and therapeutic objectives. Selective targeting individual subtypes of N-methyl-D-aspartate receptors (NMDARs) is a desirable therapeutic strategy for neurological disorders. Here, the authors report identification of a functional antibody that specifically targets and allosterically down-regulates ion channel activity of the GluN1—GluN2B NMDAR subtype.
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Affiliation(s)
- Nami Tajima
- W.M. Keck Structural Biology Laboratory, Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, NY, 11724, USA
| | - Noriko Simorowski
- W.M. Keck Structural Biology Laboratory, Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, NY, 11724, USA
| | - Remy A Yovanno
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins University School of Medicine, 725 N. Wolfe Street, WBSB 706, Baltimore, MD, 21205, USA
| | - Michael C Regan
- W.M. Keck Structural Biology Laboratory, Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, NY, 11724, USA
| | - Kevin Michalski
- W.M. Keck Structural Biology Laboratory, Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, NY, 11724, USA
| | - Ricardo Gómez
- W.M. Keck Structural Biology Laboratory, Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, NY, 11724, USA
| | - Albert Y Lau
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins University School of Medicine, 725 N. Wolfe Street, WBSB 706, Baltimore, MD, 21205, USA.
| | - Hiro Furukawa
- W.M. Keck Structural Biology Laboratory, Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, NY, 11724, USA.
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4
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Single-Dose P2 X4R Single-Chain Fragment Variable Antibody Permanently Reverses Chronic Pain in Male Mice. Int J Mol Sci 2021; 22:ijms222413612. [PMID: 34948407 PMCID: PMC8706307 DOI: 10.3390/ijms222413612] [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: 10/26/2021] [Revised: 12/02/2021] [Accepted: 12/16/2021] [Indexed: 11/22/2022] Open
Abstract
Non-opioid single-chain variable fragment (scFv) small antibodies were generated as pain-reducing block of P2X4R receptor (P2X4R). A panel of scFvs targeting an extracellular peptide sequence of P2X4R was generated followed by cell-free ribosome display for recombinant antibody selection. After three rounds of bio-panning, a panel of recombinant antibodies was isolated and characterized by ELISA, cross-reactivity analysis, and immunoblotting/immunostaining. Generated scFv antibodies feature binding activity similar to monoclonal antibodies but with stronger affinity and increased tissue penetrability due to their ~30% smaller size. Two anti-P2X4R scFv clones (95, 12) with high specificity and affinity binding were selected for in vivo testing in male and female mice with trigeminal nerve chronic neuropathic pain (FRICT-ION model) persisting for several months in untreated BALBc mice. A single dose of P2X4R scFv (4 mg/kg, i.p.) successfully, completely, and permanently reversed chronic neuropathic pain-like measures in male mice only, providing retention of baseline behaviors indefinitely. Untreated mice retained hypersensitivity, and developed anxiety- and depression-like behaviors within 5 weeks. In vitro P2X4R scFv 95 treatment significantly increased the rheobase of larger-diameter (>25 µm) trigeminal ganglia (TG) neurons from FRICT-ION mice compared to controls. The data support use of engineered scFv antibodies as non-opioid biotherapeutic interventions for chronic pain.
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Pornnoppadol G, Zhang B, Desai AA, Berardi A, Remmer HA, Tessier PM, Greineder CF. A hybridoma-derived monoclonal antibody with high homology to the aberrant myeloma light chain. PLoS One 2021; 16:e0252558. [PMID: 34634047 PMCID: PMC8504763 DOI: 10.1371/journal.pone.0252558] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2021] [Accepted: 09/20/2021] [Indexed: 11/23/2022] Open
Abstract
The identification of antibody variable regions in the heavy (VH) and light (VL) chains from hybridomas is necessary for the production of recombinant, sequence-defined monoclonal antibodies (mAbs) and antibody derivatives. This process has received renewed attention in light of recent reports of hybridomas having unintended specificities due to the production of non-antigen specific heavy and/or light chains for the intended antigen. Here we report a surprising finding and potential pitfall in variable domain sequencing of an anti-human CD63 hybridoma. We amplified multiple VL genes from the hybridoma cDNA, including the well-known aberrant Sp2/0 myeloma VK and a unique, full-length VL. After finding that the unique VL failed to yield a functional antibody, we discovered an additional full-length sequence with surprising similarity (~95% sequence identify) to the non-translated myeloma kappa chain but with a correction of its key frameshift mutation. Expression of the recombinant mAb confirmed that this highly homologous sequence is the antigen-specific light chain. Our results highlight the complexity of PCR-based cloning of antibody genes and strategies useful for identification of correct sequences.
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Affiliation(s)
- Ghasidit Pornnoppadol
- Department of Pharmaceutical Sciences, University of Michigan, Ann Arbor, Michigan, United States of America
- BioInterfaces Institute, University of Michigan, Ann Arbor, Michigan, United States of America
| | - Boya Zhang
- BioInterfaces Institute, University of Michigan, Ann Arbor, Michigan, United States of America
- Department of Pharmacology, University of Michigan, Ann Arbor, Michigan, United States of America
| | - Alec A. Desai
- BioInterfaces Institute, University of Michigan, Ann Arbor, Michigan, United States of America
- Department of Chemical Engineering, University of Michigan, Ann Arbor, Michigan, United States of America
| | - Anthony Berardi
- BioInterfaces Institute, University of Michigan, Ann Arbor, Michigan, United States of America
- Department of Macromolecular Science & Engineering, University of Michigan, Ann Arbor, Michigan, United States of America
| | - Henriette A. Remmer
- Proteomics & Peptide Synthesis Core, University of Michigan, Ann Arbor, Michigan, United States of America
| | - Peter M. Tessier
- Department of Pharmaceutical Sciences, University of Michigan, Ann Arbor, Michigan, United States of America
- BioInterfaces Institute, University of Michigan, Ann Arbor, Michigan, United States of America
- Department of Chemical Engineering, University of Michigan, Ann Arbor, Michigan, United States of America
- Department of Biomedical Engineering, University of Michigan, Ann Arbor, Michigan, United States of America
| | - Colin F. Greineder
- BioInterfaces Institute, University of Michigan, Ann Arbor, Michigan, United States of America
- Department of Pharmacology, University of Michigan, Ann Arbor, Michigan, United States of America
- Department of Emergency Medicine, University of Michigan, Ann Arbor, Michigan, United States of America
- * E-mail:
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Newton ND, Hardy JM, Modhiran N, Hugo LE, Amarilla AA, Bibby S, Venugopal H, Harrison JJ, Traves RJ, Hall RA, Hobson-Peters J, Coulibaly F, Watterson D. The structure of an infectious immature flavivirus redefines viral architecture and maturation. SCIENCE ADVANCES 2021; 7:eabe4507. [PMID: 33990320 PMCID: PMC8121421 DOI: 10.1126/sciadv.abe4507] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/24/2020] [Accepted: 03/24/2021] [Indexed: 06/12/2023]
Abstract
Flaviviruses are the cause of severe human diseases transmitted by mosquitoes and ticks. These viruses use a potent fusion machinery to enter target cells that needs to be restrained during viral assembly and egress. A molecular chaperone, premembrane (prM) maintains the virus particles in an immature, fusion-incompetent state until they exit the cell. Taking advantage of an insect virus that produces particles that are both immature and infectious, we determined the structure of the first immature flavivirus with a complete spike by cryo-electron microscopy. Unexpectedly, the prM chaperone forms a supporting pillar that maintains the immature spike in an asymmetric and upright state, primed for large rearrangements upon acidification. The collapse of the spike along a path defined by the prM chaperone is required, and its inhibition by a multivalent immunoglobulin M blocks infection. The revised architecture and collapse model are likely to be conserved across flaviviruses.
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Affiliation(s)
- Natalee D Newton
- Australian Infectious Diseases Research Centre, School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD, Australia
| | - Joshua M Hardy
- Infection and Immunity Program, Biomedicine Discovery Institute, and Department of Biochemistry and Molecular Biology, Monash University, Clayton, VIC, Australia
| | - Naphak Modhiran
- Australian Infectious Diseases Research Centre, School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD, Australia
| | - Leon E Hugo
- Mosquito Control Laboratory, QIMR Berghofer Medical Research Institute, Brisbane, QLD, Australia
| | - Alberto A Amarilla
- Australian Infectious Diseases Research Centre, School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD, Australia
| | - Summa Bibby
- Australian Infectious Diseases Research Centre, School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD, Australia
| | - Hariprasad Venugopal
- Ramaciotti Centre for Cryo-Electron Microscopy, Monash University, Clayton, VIC, Australia
| | - Jessica J Harrison
- Australian Infectious Diseases Research Centre, School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD, Australia
| | - Renee J Traves
- Australian Infectious Diseases Research Centre, School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD, Australia
| | - Roy A Hall
- Australian Infectious Diseases Research Centre, School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD, Australia
| | - Jody Hobson-Peters
- Australian Infectious Diseases Research Centre, School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD, Australia.
| | - Fasséli Coulibaly
- Infection and Immunity Program, Biomedicine Discovery Institute, and Department of Biochemistry and Molecular Biology, Monash University, Clayton, VIC, Australia.
| | - Daniel Watterson
- Australian Infectious Diseases Research Centre, School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD, Australia.
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Trimmer JS. Recombinant Antibodies in Basic Neuroscience Research. CURRENT PROTOCOLS IN NEUROSCIENCE 2020; 94:e106. [PMID: 33151027 PMCID: PMC7665837 DOI: 10.1002/cpns.106] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
Basic neuroscience research employs antibodies as key reagents to label, capture, and modulate the function of proteins of interest. Antibodies are immunoglobulin proteins. Recombinant antibodies are immunoglobulin proteins whose nucleic acid coding regions, or fragments thereof, have been cloned into expression plasmids that allow for unlimited production. Recombinant antibodies offer many advantages over conventional antibodies including their unambiguous identification and digital archiving via DNA sequencing, reliable expression, ease and reliable distribution as DNA sequences and as plasmids, and the opportunity for numerous forms of engineering to enhance their utility. Recombinant antibodies exist in many different forms, each of which offers potential advantages and disadvantages for neuroscience research applications. I provide an overview of recombinant antibodies and their development. Examples of their emerging use as valuable reagents in basic neuroscience research are also discussed. Many of these examples employ recombinant antibodies in innovative experimental approaches that cannot be pursued with conventional antibodies. © 2020 Wiley Periodicals LLC.
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Affiliation(s)
- James S Trimmer
- Department of Physiology and Membrane Biology, University of California Davis School of Medicine, Davis, California
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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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9
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Wang JP, Dong J, Duan CF, Zhang HC, He X, Wang GN, Zhao GX, Liu J. Production and Directional Evolution of Antisarafloxacin ScFv Antibody for Immunoassay of Fluoroquinolones in Milk. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2016; 64:7957-7965. [PMID: 27718569 DOI: 10.1021/acs.jafc.6b03356] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
A recombinant antisarafloxacin ScFv antibody was produced by direct transformation of its gene into Rosetta-gami(DE3) for expression, and then its recognition mechanisms for 12 fluoroquinolones were studied using the molecular docking method. On the basis of the results of virtual mutation, the ScFv antibody was evolved by directional mutagenesis of contact amino acid residue Tyr99 to His. The ScFv mutant showed highly increased affinity for the 12 drugs with up to sevenfold improved sensitivity. Finally, the mutant was used to develop an indirect competitive enzyme linked immunosorbent assay for determination of the 12 drugs in milk. The limits of detection were in the range of 0.3-8.0 ng/mL; the ties were in the range of 5-106%, and the recoveries from the standard fortified blank milk were in the range of 62.0-89.3%. This is the first study reporting the evolution of an ScFv antibody using a directional mutagenesis strategy based on virtual mutation.
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Affiliation(s)
- Jian Ping Wang
- College of Veterinary Medicine, Agricultural University of Hebei , Baoding Hebei, China 071000
| | - Jun Dong
- College of Veterinary Medicine, Agricultural University of Hebei , Baoding Hebei, China 071000
| | - Chang Fei Duan
- College of Veterinary Medicine, Agricultural University of Hebei , Baoding Hebei, China 071000
| | - Hui Cai Zhang
- College of Animal Science and Technology, Agricultural University of Hebei , Baoding Hebei, China 071000
| | - Xin He
- College of Veterinary Medicine, Agricultural University of Hebei , Baoding Hebei, China 071000
| | - Geng Nan Wang
- College of Veterinary Medicine, Agricultural University of Hebei , Baoding Hebei, China 071000
| | - Guo Xian Zhao
- College of Animal Science and Technology, Agricultural University of Hebei , Baoding Hebei, China 071000
| | - Jing Liu
- College of Veterinary Medicine, Agricultural University of Hebei , Baoding Hebei, China 071000
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10
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Greineder CF, Hood ED, Yao A, Khoshnejad M, Brenner JS, Johnston IH, Poncz M, Gottstein C, Muzykantov VR. Molecular engineering of high affinity single-chain antibody fragment for endothelial targeting of proteins and nanocarriers in rodents and humans. J Control Release 2016; 226:229-37. [PMID: 26855052 DOI: 10.1016/j.jconrel.2016.02.006] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2015] [Accepted: 02/03/2016] [Indexed: 11/30/2022]
Abstract
Endothelial cells (EC) represent an important target for pharmacologic intervention, given their central role in a wide variety of human pathophysiologic processes. Studies in lab animal species have established that conjugation of drugs and carriers with antibodies directed to surface targets like the Platelet Endothelial Cell Adhesion Molecule-1 (PECAM-1, a highly expressed endothelial transmembrane protein) help to achieve specific therapeutic interventions in ECs. To translate such "vascular immunotargeting" to clinical practice, it is necessary to replace antibodies by advanced ligands that are more amenable to use in humans. We report the molecular design of a single chain variable antibody fragment (scFv) that binds with high affinity to human PECAM-1 and cross-reacts with its counterpart in rats and other animal species, allowing parallel testing in vivo and in human endothelial cells in microfluidic model. Site-specific modification of the scFv allows conjugation of protein cargo and liposomes, enabling their endothelial targeting in these models. This study provides a template for molecular engineering of ligands, enabling studies of drug targeting in animal species and subsequent use in humans.
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Affiliation(s)
- Colin F Greineder
- Department of Pharmacology, Institute for Translational Medicine and Therapeutics, 3400 Civic Center Blvd, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, United States; Center for Targeted Therapeutics and Translational Nanomedicine, Institute for Translational Medicine and Therapeutics, 3400 Civic Center Blvd, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, United States.
| | - Elizabeth D Hood
- Department of Pharmacology, Institute for Translational Medicine and Therapeutics, 3400 Civic Center Blvd, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, United States; Center for Targeted Therapeutics and Translational Nanomedicine, Institute for Translational Medicine and Therapeutics, 3400 Civic Center Blvd, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, United States
| | - Anning Yao
- Department of Pharmacology, Institute for Translational Medicine and Therapeutics, 3400 Civic Center Blvd, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, United States; Center for Targeted Therapeutics and Translational Nanomedicine, Institute for Translational Medicine and Therapeutics, 3400 Civic Center Blvd, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, United States
| | - Makan Khoshnejad
- Department of Pharmacology, Institute for Translational Medicine and Therapeutics, 3400 Civic Center Blvd, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, United States; Center for Targeted Therapeutics and Translational Nanomedicine, Institute for Translational Medicine and Therapeutics, 3400 Civic Center Blvd, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, United States
| | - Jake S Brenner
- Department of Pharmacology, Institute for Translational Medicine and Therapeutics, 3400 Civic Center Blvd, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, United States; Center for Targeted Therapeutics and Translational Nanomedicine, Institute for Translational Medicine and Therapeutics, 3400 Civic Center Blvd, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, United States
| | - Ian H Johnston
- Department of Pediatrics, Division of Hematology, The Children's Hospital of Philadelphia, Philadelphia, PA 19104, United States
| | - Mortimer Poncz
- Department of Pediatrics, Division of Hematology, The Children's Hospital of Philadelphia, Philadelphia, PA 19104, United States
| | - Claudia Gottstein
- Department of Molecular, Cellular and Developmental Biology, University of California Santa Barbara, Santa Barbara, CA 93106, United States
| | - Vladimir R Muzykantov
- Department of Pharmacology, Institute for Translational Medicine and Therapeutics, 3400 Civic Center Blvd, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, United States; Center for Targeted Therapeutics and Translational Nanomedicine, Institute for Translational Medicine and Therapeutics, 3400 Civic Center Blvd, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, United States
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Kim JW, Young JS, Solomaha E, Kanojia D, Lesniak MS, Balyasnikova IV. A novel single-chain antibody redirects adenovirus to IL13Rα2-expressing brain tumors. Sci Rep 2015; 5:18133. [PMID: 26656559 PMCID: PMC4677343 DOI: 10.1038/srep18133] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2015] [Accepted: 11/13/2015] [Indexed: 11/10/2022] Open
Abstract
The generation of a targeting agent that strictly binds to IL13Rα2 will significantly expand the therapeutic potential for the treatment of IL13Rα2-expressing cancers. In order to fulfill this goal, we generated a single-chain antibody (scFv47) from our parental IL13Rα2 monoclonal antibody and tested its binding properties. Furthermore, to demonstrate the potential therapeutic applicability of scFv47, we engineered an adenovirus by incorporating scFv47 as the targeting moiety in the viral fiber and characterized its properties in vitro and in vivo. The scFv47 binds to human recombinant IL13Rα2, but not to IL13Rα1 with a high affinity of 0.9 · 10−9 M, similar to that of the parental antibody. Moreover, the scFv47 successfully redirects adenovirus to IL13Rα2 expressing glioma cells both in vitro and in vivo. Our data validate scFv47 as a highly selective IL13Rα2 targeting agent and justify further development of scFv47-modified oncolytic adenovirus and other therapeutics for the treatment of IL13Rα2-expressing glioma and other malignancies.
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Affiliation(s)
- Julius W Kim
- The Brain Tumor Center, The University of Chicago, Chicago, IL 60637, USA
| | - Jacob S Young
- The Brain Tumor Center, The University of Chicago, Chicago, IL 60637, USA
| | - Elena Solomaha
- Biophysics Core Facility, The University of Chicago, Chicago, IL 60637, USA
| | - Deepak Kanojia
- The Brain Tumor Center, The University of Chicago, Chicago, IL 60637, USA
| | - Maciej S Lesniak
- The Brain Tumor Center, The University of Chicago, Chicago, IL 60637, USA
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Expression, purification, crystallization, and preliminary X-ray crystallographic studies of the human adiponectin receptors, AdipoR1 and AdipoR2. ACTA ACUST UNITED AC 2015; 16:11-23. [PMID: 25575462 PMCID: PMC4329188 DOI: 10.1007/s10969-014-9192-z] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2014] [Accepted: 11/19/2014] [Indexed: 01/21/2023]
Abstract
The adiponectin receptors (AdipoR1 and AdipoR2) are membrane proteins with seven transmembrane helices. These receptors regulate glucose and fatty acid metabolism, thereby ameliorating type 2 diabetes. The full-length human AdipoR1 and a series of N-terminally truncated mutants of human AdipoR1 and AdipoR2 were expressed in insect cells. In small-scale size exclusion chromatography, the truncated mutants AdipoR1Δ88 (residues 89–375) and AdipoR2Δ99 (residues 100–386) eluted mostly in the intact monodisperse state, while the others eluted primarily as aggregates. However, gel filtration chromatography of the large-scale preparation of the tag-affinity-purified AdipoR1Δ88 revealed the presence of an excessive amount of the aggregated state over the intact state. Since aggregation due to contaminating nucleic acids may have occurred during the sample concentration step, anion-exchange column chromatography was performed immediately after affinity chromatography, to separate the intact AdipoR1Δ88 from the aggregating species. The separated intact AdipoR1Δ88 did not undergo further aggregation, and was successfully purified to homogeneity by gel filtration chromatography. The purified AdipoR1Δ88 and AdipoR2Δ99 proteins were characterized by thermostability assays with 7-diethylamino-3-(4-maleimidophenyl)-4-methyl coumarin, thin layer chromatography of bound lipids, and surface plasmon resonance analysis of ligand binding, demonstrating their structural integrities. The AdipoR1Δ88 and AdipoR2Δ99 proteins were crystallized with the anti-AdipoR1 monoclonal antibody Fv fragment, by the lipidic mesophase method. X-ray diffraction data sets were obtained at resolutions of 2.8 and 2.4 Å, respectively.
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13
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Mohseni Nodehi S, Repp R, Kellner C, Bräutigam J, Staudinger M, Schub N, Peipp M, Gramatzki M, Humpe A. Enhanced ADCC activity of affinity maturated and Fc-engineered mini-antibodies directed against the AML stem cell antigen CD96. PLoS One 2012; 7:e42426. [PMID: 22879978 PMCID: PMC3411760 DOI: 10.1371/journal.pone.0042426] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2011] [Accepted: 07/09/2012] [Indexed: 12/23/2022] Open
Abstract
CD96, a cell surface antigen recently described to be preferentially expressed on acute myeloid leukemia (AML) leukemic stem cells (LSC) may represent an interesting target structure for the development of antibody-based therapeutic approaches. The v-regions from the CD96-specific hybridoma TH-111 were isolated and used to generate a CD96-specific single chain fragment of the variable regions (scFv). An affinity maturated variant resulting in 4-fold enhanced CD96-binding was generated by random mutagenesis and stringent selection using phage display. The affinity maturated scFv CD96-S32F was used to generate bivalent mini-antibodies by genetically fusing an IgG1 wild type Fc region or a variant with enhanced CD16a binding. Antibody dependent cell-mediated cytotoxicity (ADCC) experiments revealed that Fc engineering was essential to trigger significant effector cell-mediated lysis when the wild type scFv was used. The mini-antibody variant generated by fusing the affinity-maturated scFv with the optimized Fc variant demonstrated the highest ADCC activity (2.3-fold enhancement in efficacy). In conclusion, our data provide proof of concept that CD96 could serve as a target structure for effector cell-mediated lysis and demonstrate that both enhancing affinity for CD96 and for CD16a resulted in mini-antibodies with the highest cytolytic potential.
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MESH Headings
- Amino Acid Sequence
- Antibody Affinity/immunology
- Antibody Specificity/immunology
- Antibody-Dependent Cell Cytotoxicity/immunology
- Antigens, CD/chemistry
- Antigens, CD/immunology
- Antigens, Neoplasm/immunology
- Cell Line, Tumor
- Dose-Response Relationship, Immunologic
- Humans
- Hybridomas
- Immunoglobulin G/immunology
- Leukemia, Myeloid, Acute/immunology
- Leukemia, Myeloid, Acute/pathology
- Models, Molecular
- Molecular Sequence Data
- Mutant Proteins/chemistry
- Mutant Proteins/metabolism
- Mutation/genetics
- Neoplastic Stem Cells/immunology
- Protein Binding
- Protein Engineering
- Protein Structure, Tertiary
- Receptors, Fc/immunology
- Sequence Alignment
- Single-Chain Antibodies/immunology
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Affiliation(s)
- Sahar Mohseni Nodehi
- Division of Stem Cell Transplantation and Immunotherapy, Department of Medicine II, Zoological Institute, Christian-Albrechts-University, Kiel, Germany
| | - Roland Repp
- Division of Stem Cell Transplantation and Immunotherapy, Department of Medicine II, Zoological Institute, Christian-Albrechts-University, Kiel, Germany
| | - Christian Kellner
- Division of Stem Cell Transplantation and Immunotherapy, Department of Medicine II, Zoological Institute, Christian-Albrechts-University, Kiel, Germany
| | - Joachim Bräutigam
- Department of Structural Biology, Zoological Institute, Christian-Albrechts-University, Kiel, Germany
| | - Matthias Staudinger
- Division of Stem Cell Transplantation and Immunotherapy, Department of Medicine II, Zoological Institute, Christian-Albrechts-University, Kiel, Germany
| | - Natalie Schub
- Division of Stem Cell Transplantation and Immunotherapy, Department of Medicine II, Zoological Institute, Christian-Albrechts-University, Kiel, Germany
| | - Matthias Peipp
- Division of Stem Cell Transplantation and Immunotherapy, Department of Medicine II, Zoological Institute, Christian-Albrechts-University, Kiel, Germany
| | - Martin Gramatzki
- Division of Stem Cell Transplantation and Immunotherapy, Department of Medicine II, Zoological Institute, Christian-Albrechts-University, Kiel, Germany
| | - Andreas Humpe
- Division of Stem Cell Transplantation and Immunotherapy, Department of Medicine II, Zoological Institute, Christian-Albrechts-University, Kiel, Germany
- * E-mail:
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Characterisation of monoclonal antibody against aflatoxin B1 produced in hybridoma 2C12 and its single-chain variable fragment expressed in recombinant Escherichia coli. Food Chem 2011. [DOI: 10.1016/j.foodchem.2010.11.088] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
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