151
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Böldicke T, Miethe S, Fühner V, Schirrmann T, Frenzel A, Hust M. Generation of Recombinant Antibodies Against Toxins and Viruses by Phage Display for Diagnostics and Therapy. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2016; 917:55-76. [PMID: 27236552 PMCID: PMC7121732 DOI: 10.1007/978-3-319-32805-8_4] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
Antibody phage display is an in vitro technology to generate recombinant antibodies. In particular for pathogens like viruses or toxins, antibody phage display is an alternative to hybridoma technology, since it circumvents the limitations of the immune system. Phage display allows the generation of human antibodies from naive antibody gene libraries when either immunized patients are not available or immunization is not ethically feasible. This technology also allows the construction of immune libraries to select in vivo affinity matured antibodies if immunized patients or animals are available.In this review, we describe the generation of human and human-like antibodies from naive antibody gene libraries and antibodies from immune antibody gene libraries. Furthermore, we give an overview about phage display derived recombinant antibodies against viruses and toxins for diagnostics and therapy.
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Affiliation(s)
- Thomas Böldicke
- grid.7490.aRecombinant protein exprsn/Intrabdy unit, Helmholtz-Centre for Infection Rese, Braunschweig, Germany
| | - Sebastian Miethe
- Abteilung Biotechnologie, Institut für Biochemie, Biotechnologie und Bioinformatik, Technische Universität Braunschweig, Spielmannstr. 7, 38106, Braunschweig, Germany
| | - Viola Fühner
- Abteilung Biotechnologie, Institut für Biochemie, Biotechnologie und Bioinformatik, Technische Universität Braunschweig, Spielmannstr. 7, 38106, Braunschweig, Germany
| | - Thomas Schirrmann
- Abteilung Biotechnologie, Institut für Biochemie, Biotechnologie und Bioinformatik, Technische Universität Braunschweig, Spielmannstr. 7, 38106, Braunschweig, Germany.,YUMAB GmbH, Rebenring 33, 38106, Braunschweig, Germany
| | - André Frenzel
- Abteilung Biotechnologie, Institut für Biochemie, Biotechnologie und Bioinformatik, Technische Universität Braunschweig, Spielmannstr. 7, 38106, Braunschweig, Germany.,YUMAB GmbH, Rebenring 33, 38106, Braunschweig, Germany
| | - Michael Hust
- Abteilung Biotechnologie, Institut für Biochemie, Biotechnologie und Bioinformatik, Technische Universität Braunschweig, Spielmannstr. 7, 38106, Braunschweig, Germany.
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152
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Na H, Laver JD, Jeon J, Singh F, Ancevicius K, Fan Y, Cao WX, Nie K, Yang Z, Luo H, Wang M, Rissland O, Westwood JT, Kim PM, Smibert CA, Lipshitz HD, Sidhu SS. A high-throughput pipeline for the production of synthetic antibodies for analysis of ribonucleoprotein complexes. RNA (NEW YORK, N.Y.) 2016; 22:636-655. [PMID: 26847261 PMCID: PMC4793217 DOI: 10.1261/rna.055186.115] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/06/2015] [Accepted: 12/12/2015] [Indexed: 06/05/2023]
Abstract
Post-transcriptional regulation of mRNAs plays an essential role in the control of gene expression. mRNAs are regulated in ribonucleoprotein (RNP) complexes by RNA-binding proteins (RBPs) along with associated protein and noncoding RNA (ncRNA) cofactors. A global understanding of post-transcriptional control in any cell type requires identification of the components of all of its RNP complexes. We have previously shown that these complexes can be purified by immunoprecipitation using anti-RBP synthetic antibodies produced by phage display. To develop the large number of synthetic antibodies required for a global analysis of RNP complex composition, we have established a pipeline that combines (i) a computationally aided strategy for design of antigens located outside of annotated domains, (ii) high-throughput antigen expression and purification in Escherichia coli, and (iii) high-throughput antibody selection and screening. Using this pipeline, we have produced 279 antibodies against 61 different protein components of Drosophila melanogaster RNPs. Together with those produced in our low-throughput efforts, we have a panel of 311 antibodies for 67 RNP complex proteins. Tests of a subset of our antibodies demonstrated that 89% immunoprecipitate their endogenous target from embryo lysate. This panel of antibodies will serve as a resource for global studies of RNP complexes in Drosophila. Furthermore, our high-throughput pipeline permits efficient production of synthetic antibodies against any large set of proteins.
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Affiliation(s)
- Hong Na
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, Ontario, Canada M5S 3E1
| | - John D Laver
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada M5S 1A8
| | - Jouhyun Jeon
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, Ontario, Canada M5S 3E1
| | - Fateh Singh
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, Ontario, Canada M5S 3E1
| | - Kristin Ancevicius
- Department of Biology, University of Toronto at Mississauga, Mississauga, Ontario, Canada L5L 1C6 Department of Cell and Systems Biology, University of Toronto at Mississauga, Mississauga, Ontario, Canada L5L 1C6
| | - Yujie Fan
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada M5S 1A8
| | - Wen Xi Cao
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada M5S 1A8
| | - Kun Nie
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, Ontario, Canada M5S 3E1 Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada M5S 1A8
| | - Zhenglin Yang
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada M5S 1A8
| | - Hua Luo
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada M5S 1A8
| | - Miranda Wang
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada M5S 1A8 Research Institute, Hospital for Sick Children, Toronto, Ontario, Canada M5G 0A4
| | - Olivia Rissland
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada M5S 1A8 Research Institute, Hospital for Sick Children, Toronto, Ontario, Canada M5G 0A4
| | - J Timothy Westwood
- Department of Biology, University of Toronto at Mississauga, Mississauga, Ontario, Canada L5L 1C6 Department of Cell and Systems Biology, University of Toronto at Mississauga, Mississauga, Ontario, Canada L5L 1C6
| | - Philip M Kim
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, Ontario, Canada M5S 3E1 Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada M5S 1A8 Department of Computer Science, University of Toronto, Toronto, Ontario, Canada M5S 1A8
| | - Craig A Smibert
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada M5S 1A8 Department of Biochemistry, University of Toronto, Toronto, Ontario, Canada M5S 1A8
| | - Howard D Lipshitz
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada M5S 1A8
| | - Sachdev S Sidhu
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, Ontario, Canada M5S 3E1 Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada M5S 1A8
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153
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Huang R, Fang P, Hao Z, Kay BK. Directed Evolution of a Highly Specific FN3 Monobody to the SH3 Domain of Human Lyn Tyrosine Kinase. PLoS One 2016; 11:e0145872. [PMID: 26731115 PMCID: PMC4701441 DOI: 10.1371/journal.pone.0145872] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2015] [Accepted: 12/09/2015] [Indexed: 11/26/2022] Open
Abstract
Affinity reagents of high affinity and specificity are very useful for studying the subcellular locations and quantities of individual proteins. To generate high-quality affinity reagents for human Lyn tyrosine kinase, a phage display library of fibronectin type III (FN3) monobodies was affinity selected with a recombinant form of the Lyn SH3 domain. While a highly specific monobody, TA8, was initially isolated, we chose to improve its affinity through directed evolution. A secondary library of 1.2 × 109 variants was constructed and screened by affinity selection, yielding three variants, two of which have affinities of ~ 40 nM, a 130-fold increase over the original TA8 monobody. One of the variants, 2H7, displayed high specificity to the Lyn SH3 domain, as shown by ELISA and probing arrays of 150 SH3 domains. Furthermore, the 2H7 monobody was able to pull down endogenous Lyn from a lysate of Burkitt's lymphoma cells, thereby demonstrating its utility as an affinity reagent for detecting Lyn in a complex biological mixture.
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Affiliation(s)
- Renhua Huang
- Department of Biological Sciences, University of Illinois at Chicago, Chicago, Illinois, United States of America
- * E-mail: (RH); (BK)
| | - Pete Fang
- Department of Biological Sciences, University of Illinois at Chicago, Chicago, Illinois, United States of America
| | - Zengping Hao
- Department of Biological Sciences, University of Illinois at Chicago, Chicago, Illinois, United States of America
| | - Brian K. Kay
- Department of Biological Sciences, University of Illinois at Chicago, Chicago, Illinois, United States of America
- * E-mail: (RH); (BK)
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154
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Recent Advances with ER Targeted Intrabodies. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2016; 917:77-93. [DOI: 10.1007/978-3-319-32805-8_5] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
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155
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Lum KK, Cristea IM. Proteomic approaches to uncovering virus-host protein interactions during the progression of viral infection. Expert Rev Proteomics 2016; 13:325-40. [PMID: 26817613 PMCID: PMC4919574 DOI: 10.1586/14789450.2016.1147353] [Citation(s) in RCA: 66] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2015] [Accepted: 01/25/2016] [Indexed: 01/10/2023]
Abstract
The integration of proteomic methods to virology has facilitated a significant breadth of biological insight into mechanisms of virus replication, antiviral host responses and viral subversion of host defenses. Throughout the course of infection, these cellular mechanisms rely heavily on the formation of temporally and spatially regulated virus-host protein-protein interactions. Reviewed here are proteomic-based approaches that have been used to characterize this dynamic virus-host interplay. Specifically discussed are the contribution of integrative mass spectrometry, antibody-based affinity purification of protein complexes, cross-linking and protein array techniques for elucidating complex networks of virus-host protein associations during infection with a diverse range of RNA and DNA viruses. The benefits and limitations of applying proteomic methods to virology are explored, and the contribution of these approaches to important biological discoveries and to inspiring new tractable avenues for the design of antiviral therapeutics is highlighted.
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Affiliation(s)
- Krystal K Lum
- Department of Molecular Biology, Princeton
University, Princeton, NJ, USA
| | - Ileana M Cristea
- Department of Molecular Biology, Princeton
University, Princeton, NJ, USA
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156
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Lei Y, Kong D, Hili R. A High-Fidelity Codon Set for the T4 DNA Ligase-Catalyzed Polymerization of Modified Oligonucleotides. ACS COMBINATORIAL SCIENCE 2015; 17:716-21. [PMID: 26513677 DOI: 10.1021/acscombsci.5b00119] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
In vitro selection of nucleic acid polymers can readily deliver highly specific receptors and catalysts for a variety of applications; however, it is suspected that the functional group deficit of nucleic acids has limited their potential with respect to proteinogenic polymers. This has stimulated research toward expanding their chemical diversity to bridge the functional gap between nucleic acids and proteins to develop a superior biopolymer. In this study, we investigate the effect of codon library size and composition on the sequence specificity of T4 DNA ligase in the DNA-templated polymerization of both unmodified and modified oligonucleotides. Using high-throughput DNA sequencing of duplex pairs, we have uncovered a 256-membered codon set that yields sequence-defined modified ssDNA polymers in high yield and with high fidelity.
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Affiliation(s)
- Yi Lei
- Department of Chemistry, University of Georgia, 140 Cedar Street, Athens, Georgia 30602, United States
| | - Dehui Kong
- Department of Chemistry, University of Georgia, 140 Cedar Street, Athens, Georgia 30602, United States
| | - Ryan Hili
- Department of Chemistry, University of Georgia, 140 Cedar Street, Athens, Georgia 30602, United States
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157
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Pleiner T, Bates M, Trakhanov S, Lee CT, Schliep JE, Chug H, Böhning M, Stark H, Urlaub H, Görlich D. Nanobodies: site-specific labeling for super-resolution imaging, rapid epitope-mapping and native protein complex isolation. eLife 2015; 4:e11349. [PMID: 26633879 PMCID: PMC4755751 DOI: 10.7554/elife.11349] [Citation(s) in RCA: 136] [Impact Index Per Article: 15.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2015] [Accepted: 12/02/2015] [Indexed: 12/23/2022] Open
Abstract
Nanobodies are single-domain antibodies of camelid origin. We generated nanobodies against the vertebrate nuclear pore complex (NPC) and used them in STORM imaging to locate individual NPC proteins with <2 nm epitope-label displacement. For this, we introduced cysteines at specific positions in the nanobody sequence and labeled the resulting proteins with fluorophore-maleimides. As nanobodies are normally stabilized by disulfide-bonded cysteines, this appears counterintuitive. Yet, our analysis showed that this caused no folding problems. Compared to traditional NHS ester-labeling of lysines, the cysteine-maleimide strategy resulted in far less background in fluorescence imaging, it better preserved epitope recognition and it is site-specific. We also devised a rapid epitope-mapping strategy, which relies on crosslinking mass spectrometry and the introduced ectopic cysteines. Finally, we used different anti-nucleoporin nanobodies to purify the major NPC building blocks – each in a single step, with native elution and, as demonstrated, in excellent quality for structural analysis by electron microscopy. The presented strategies are applicable to any nanobody and nanobody-target.
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Affiliation(s)
- Tino Pleiner
- Department of Cellular Logistics, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany
| | - Mark Bates
- Department of NanoBiophotonics, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany
| | - Sergei Trakhanov
- Department of Cellular Logistics, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany
| | - Chung-Tien Lee
- Bioanalytical Mass Spectrometry, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany.,Bioanalytics, Institute for Clinical Chemistry, University Medical Center Göttingen, Göttingen, Germany
| | - Jan Erik Schliep
- 3D Electron Cryo-Microscopy Group, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany
| | - Hema Chug
- Department of Cellular Logistics, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany
| | - Marc Böhning
- Department of Cellular Logistics, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany
| | - Holger Stark
- 3D Electron Cryo-Microscopy Group, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany
| | - Henning Urlaub
- Bioanalytical Mass Spectrometry, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany.,Bioanalytics, Institute for Clinical Chemistry, University Medical Center Göttingen, Göttingen, Germany
| | - Dirk Görlich
- Department of Cellular Logistics, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany
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158
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On-bead antibody-small molecule conjugation using high-capacity magnetic beads. J Immunol Methods 2015; 426:95-103. [DOI: 10.1016/j.jim.2015.08.008] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2015] [Revised: 08/19/2015] [Accepted: 08/20/2015] [Indexed: 01/26/2023]
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159
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Zhong N, Loppnau P, Seitova A, Ravichandran M, Fenner M, Jain H, Bhattacharya A, Hutchinson A, Paduch M, Lu V, Olszewski M, Kossiakoff AA, Dowdell E, Koide A, Koide S, Huang H, Nadeem V, Sidhu SS, Greenblatt JF, Marcon E, Arrowsmith CH, Edwards AM, Gräslund S. Optimizing Production of Antigens and Fabs in the Context of Generating Recombinant Antibodies to Human Proteins. PLoS One 2015; 10:e0139695. [PMID: 26437229 PMCID: PMC4593582 DOI: 10.1371/journal.pone.0139695] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2015] [Accepted: 09/16/2015] [Indexed: 01/18/2023] Open
Abstract
We developed and optimized a high-throughput project workflow to generate renewable recombinant antibodies to human proteins involved in epigenetic signalling. Three different strategies to produce phage display compatible protein antigens in bacterial systems were compared, and we found that in vivo biotinylation through the use of an Avi tag was the most productive method. Phage display selections were performed on 265 in vivo biotinylated antigen domains. High-affinity Fabs (<20nM) were obtained for 196. We constructed and optimized a new expression vector to produce in vivo biotinylated Fabs in E. coli. This increased average yields up to 10-fold, with an average yield of 4 mg/L. For 118 antigens, we identified Fabs that could immunoprecipitate their full-length endogenous targets from mammalian cell lysates. One Fab for each antigen was converted to a recombinant IgG and produced in mammalian cells, with an average yield of 15 mg/L. In summary, we have optimized each step of the pipeline to produce recombinant antibodies, significantly increasing both efficiency and yield, and also showed that these Fabs and IgGs can be generally useful for chromatin immunoprecipitation (ChIP) protocols.
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Affiliation(s)
- Nan Zhong
- Structural Genomics Consortium, University of Toronto, MaRS South tower, 101 College street, Toronto, ON M5G 1L7, Canada
| | - Peter Loppnau
- Structural Genomics Consortium, University of Toronto, MaRS South tower, 101 College street, Toronto, ON M5G 1L7, Canada
| | - Alma Seitova
- Structural Genomics Consortium, University of Toronto, MaRS South tower, 101 College street, Toronto, ON M5G 1L7, Canada
| | - Mani Ravichandran
- Structural Genomics Consortium, University of Toronto, MaRS South tower, 101 College street, Toronto, ON M5G 1L7, Canada
| | - Maria Fenner
- Structural Genomics Consortium, University of Toronto, MaRS South tower, 101 College street, Toronto, ON M5G 1L7, Canada
| | - Harshika Jain
- Structural Genomics Consortium, University of Toronto, MaRS South tower, 101 College street, Toronto, ON M5G 1L7, Canada
| | - Anandi Bhattacharya
- Structural Genomics Consortium, University of Toronto, MaRS South tower, 101 College street, Toronto, ON M5G 1L7, Canada
| | - Ashley Hutchinson
- Structural Genomics Consortium, University of Toronto, MaRS South tower, 101 College street, Toronto, ON M5G 1L7, Canada
| | - Marcin Paduch
- Department of Biochemistry and Molecular Biology, Knapp Center for Biomedical Discovery, University of Chicago, 900 East 57th St., Chicago, IL 60637, United States of America
| | - Vincent Lu
- Department of Biochemistry and Molecular Biology, Knapp Center for Biomedical Discovery, University of Chicago, 900 East 57th St., Chicago, IL 60637, United States of America
| | - Michal Olszewski
- Department of Biochemistry and Molecular Biology, Knapp Center for Biomedical Discovery, University of Chicago, 900 East 57th St., Chicago, IL 60637, United States of America
| | - Anthony A. Kossiakoff
- Department of Biochemistry and Molecular Biology, Knapp Center for Biomedical Discovery, University of Chicago, 900 East 57th St., Chicago, IL 60637, United States of America
| | - Evan Dowdell
- Department of Biochemistry and Molecular Biology, Knapp Center for Biomedical Discovery, University of Chicago, 900 East 57th St., Chicago, IL 60637, United States of America
| | - Akiko Koide
- Department of Biochemistry and Molecular Biology, Knapp Center for Biomedical Discovery, University of Chicago, 900 East 57th St., Chicago, IL 60637, United States of America
| | - Shohei Koide
- Department of Biochemistry and Molecular Biology, Knapp Center for Biomedical Discovery, University of Chicago, 900 East 57th St., Chicago, IL 60637, United States of America
| | - Haiming Huang
- Terrence Donnelly Center for Cellular & Biomolecular Research, University of Toronto, 160 College Street, Toronto, ON M5S 3E1, Canada
| | - Vincent Nadeem
- Terrence Donnelly Center for Cellular & Biomolecular Research, University of Toronto, 160 College Street, Toronto, ON M5S 3E1, Canada
| | - Sachdev S. Sidhu
- Terrence Donnelly Center for Cellular & Biomolecular Research, University of Toronto, 160 College Street, Toronto, ON M5S 3E1, Canada
| | - Jack F. Greenblatt
- Terrence Donnelly Center for Cellular & Biomolecular Research, University of Toronto, 160 College Street, Toronto, ON M5S 3E1, Canada
- Department of Molecular Genetics, University of Toronto, 1 Kings College Circle, MSB-4180, Toronto, ON M5S 1A8, Canada
| | - Edyta Marcon
- Terrence Donnelly Center for Cellular & Biomolecular Research, University of Toronto, 160 College Street, Toronto, ON M5S 3E1, Canada
| | - Cheryl H. Arrowsmith
- Structural Genomics Consortium, University of Toronto, MaRS South tower, 101 College street, Toronto, ON M5G 1L7, Canada
| | - Aled M. Edwards
- Structural Genomics Consortium, University of Toronto, MaRS South tower, 101 College street, Toronto, ON M5G 1L7, Canada
| | - Susanne Gräslund
- Structural Genomics Consortium, University of Toronto, MaRS South tower, 101 College street, Toronto, ON M5G 1L7, Canada
- * E-mail:
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160
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Liu S, Zhang H, Dai J, Hu S, Pino I, Eichinger DJ, Lyu H, Zhu H. Characterization of monoclonal antibody's binding kinetics using oblique-incidence reflectivity difference approach. MAbs 2015; 7:110-9. [PMID: 25530170 PMCID: PMC4622085 DOI: 10.4161/19420862.2014.985919] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Monoclonal antibodies (mAbs) against human proteins are the primary protein capture reagents for basic research, diagnosis, and molecular therapeutics. The 2 most important attributes of mAbs used in all of these applications are their specificity and avidity. While specificity of a mAb raised against a human protein can be readily defined based on its binding profile on a human proteome microarray, it has been a challenge to determine avidity values for mAbs in a high-throughput and cost-effective fashion. To undertake this challenge, we employed the oblique-incidence reflectivity difference (OIRD) platform to characterize mAbs in a protein microarray format. We first systematically determined the Kon and Koff values of 50 mAbs measured with the OIRD method and deduced the avidity values. Second, we established a multiplexed approach that simultaneously measured avidity values of a mixture of 9 mono-specific mAbs that do not cross-react to the antigens. Third, we demonstrated that avidity values of a group of mAbs could be sequentially determined using a flow-cell device. Finally, we implemented a sequential competition assay that allowed us to bin multiple mAbs that recognize the same antigens. Our study demonstrated that OIRD offers a high-throughput and cost-effective platform for characterization of the binding kinetics of mAbs.
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Affiliation(s)
- Shuang Liu
- a Institute of Physics; Chinese Academy of Sciences ; Beijing , China
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161
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Ferrara F, Kim CY, Naranjo LA, Bradbury ARM. Large scale production of phage antibody libraries using a bioreactor. MAbs 2015; 7:26-31. [PMID: 25524379 DOI: 10.4161/19420862.2015.989034] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
One of the limitations of the use of phage antibody libraries in high throughput selections is the production of sufficient phage antibody library at the appropriate quality. Here, we successfully adapt a bioreactor-based protocol for the production of phage peptide libraries to the production of phage antibody libraries. The titers obtained in the stirred-tank bioreactor are 4 to 5 times higher than in a standard shake flask procedure, and the quality of the phage antibody library produced is indistinguishable to that produced using standard procedures as assessed by Western blotting and functional selections. Availability of this protocol will facilitate the use of phage antibody libraries in high-throughput scale selections.
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162
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DREADD-Induced Silencing of the Medial Olfactory Tubercle Disrupts the Preference of Female Mice for Opposite-Sex Chemosignals(1,2,3). eNeuro 2015; 2:eN-NWR-0078-15. [PMID: 26478911 PMCID: PMC4603255 DOI: 10.1523/eneuro.0078-15.2015] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2015] [Revised: 08/21/2015] [Accepted: 08/29/2015] [Indexed: 12/15/2022] Open
Abstract
Attraction to opposite-sex pheromones during rodent courtship involves a pathway that includes inputs to the medial amygdala (Me) from the main and accessory olfactory bulbs, and projections from the Me to nuclei in the medial hypothalamus that control reproduction. However, the consideration of circuitry that attributes hedonic properties to opposite-sex odors has been lacking. The medial olfactory tubercle (mOT) has been implicated in the reinforcing effects of natural stimuli and drugs of abuse. We performed a tract-tracing study wherein estrous female mice that had received injections of the retrograde tracer, cholera toxin B, into the mOT were exposed to volatile odors from soiled bedding. Both the anterior Me and ventral tegmental area sent direct projections to the mOT, of which a significant subset was selectively activated (expressed Fos protein) by testes-intact male (but not female) volatile odors from soiled bedding. Next, the inhibitory DREADD (designer receptors exclusively activated by designer drugs) receptor hM4Di was bilaterally expressed in the mOT of female mice. Urinary preferences were then assessed after intraperitoneal injection of either saline or clozapine-N-oxide (CNO), which binds to the hM4Di receptor to hyperpolarize infected neurons. After receiving CNO, estrous females lost their preference for male over female urinary odors, whereas the ability to discriminate these odors remained intact. Male odor preference returned after vehicle treatment in counterbalanced tests. There were no deficits in locomotor activity or preference for food odors when subject mice received CNO injections prior to testing. The mOT appears to be a critical segment in the pheromone–reward pathway of female mice.
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163
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Houlihan G, Gatti-Lafranconi P, Lowe D, Hollfelder F. Directed evolution of anti-HER2 DARPins by SNAP display reveals stability/function trade-offs in the selection process. Protein Eng Des Sel 2015; 28:269-79. [PMID: 26134501 PMCID: PMC4550541 DOI: 10.1093/protein/gzv029] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2014] [Revised: 05/05/2015] [Accepted: 05/07/2015] [Indexed: 01/08/2023] Open
Abstract
In vitro display technologies have proved to be powerful tools for obtaining high-affinity protein binders. We recently described SNAP display, an entirely in vitro DNA display system that uses the SNAP-tag to link protein with its encoding DNA in water-in-oil emulsions. Here, we apply SNAP display for the affinity maturation of a designed ankyrin repeat proteins (DARPin) that binds to the extracellular domain of HER2 previously isolated by ribosome display. After four SNAP display selection cycles, proteins that bound specifically to HER2 in vitro, with dissociation constants in the low- to sub-nanomolar range, were isolated. In vitro affinities of the panel of evolved DARPins directly correlated with the fluorescence intensities of evolved DARPins bound to HER2 on a breast cancer cell line. A stability trade-off is observed as the most improved DARPins have decreased thermostability, when compared with the parent DARPin used as a starting point for affinity maturation. Dissection of the framework mutations of the highest affinity variant, DARPin F1, shows that functionally destabilising and compensatory mutations accumulated throughout the four rounds of evolution.
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Affiliation(s)
- Gillian Houlihan
- Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, Cambridge CB2 1GA, UK MedImmune Ltd, Milstein Building, Granta Park, Cambridge CB1 6GH, UK
| | - Pietro Gatti-Lafranconi
- Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, Cambridge CB2 1GA, UK
| | - David Lowe
- MedImmune Ltd, Milstein Building, Granta Park, Cambridge CB1 6GH, UK
| | - Florian Hollfelder
- Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, Cambridge CB2 1GA, UK
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164
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Helma J, Cardoso MC, Muyldermans S, Leonhardt H. Nanobodies and recombinant binders in cell biology. J Cell Biol 2015; 209:633-44. [PMID: 26056137 PMCID: PMC4460151 DOI: 10.1083/jcb.201409074] [Citation(s) in RCA: 158] [Impact Index Per Article: 17.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Antibodies are key reagents to investigate cellular processes. The development of recombinant antibodies and binders derived from natural protein scaffolds has expanded traditional applications, such as immunofluorescence, binding arrays, and immunoprecipitation. In addition, their small size and high stability in ectopic environments have enabled their use in all areas of cell research, including structural biology, advanced microscopy, and intracellular expression. Understanding these novel reagents as genetic modules that can be integrated into cellular pathways opens up a broad experimental spectrum to monitor and manipulate cellular processes.
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Affiliation(s)
- Jonas Helma
- Department of Biology II, Ludwig Maximilians University Munich and Center for Integrated Protein Science Munich, 82152 Planegg-Martinsried, Germany
| | - M Cristina Cardoso
- Department of Biology, Technical University of Darmstadt, 64287 Darmstadt, Germany
| | - Serge Muyldermans
- Laboratory of Cellular and Molecular Immunology, Vrije Universiteit Brussel, 1050 Brussels, Belgium
| | - Heinrich Leonhardt
- Department of Biology II, Ludwig Maximilians University Munich and Center for Integrated Protein Science Munich, 82152 Planegg-Martinsried, Germany
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165
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Hornsby M, Paduch M, Miersch S, Sääf A, Matsuguchi T, Lee B, Wypisniak K, Doak A, King D, Usatyuk S, Perry K, Lu V, Thomas W, Luke J, Goodman J, Hoey RJ, Lai D, Griffin C, Li Z, Vizeacoumar FJ, Dong D, Campbell E, Anderson S, Zhong N, Gräslund S, Koide S, Moffat J, Sidhu S, Kossiakoff A, Wells J. A High Through-put Platform for Recombinant Antibodies to Folded Proteins. Mol Cell Proteomics 2015; 14:2833-47. [PMID: 26290498 PMCID: PMC4597156 DOI: 10.1074/mcp.o115.052209] [Citation(s) in RCA: 87] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2015] [Indexed: 01/09/2023] Open
Abstract
Antibodies are key reagents in biology and medicine, but commercial sources are rarely recombinant and thus do not provide a permanent and renewable resource. Here, we describe an industrialized platform to generate antigens and validated recombinant antibodies for 346 transcription factors (TFs) and 211 epigenetic antigens. We describe an optimized automated phage display and antigen expression pipeline that in aggregate produced about 3000 sequenced Fragment antigen-binding domain that had high affinity (typically EC50<20 nm), high stability (Tm∼80 °C), good expression in E. coli (∼5 mg/L), and ability to bind antigen in complex cell lysates. We evaluated a subset of Fabs generated to homologous SCAN domains for binding specificities. These Fragment antigen-binding domains were monospecific to their target SCAN antigen except in rare cases where they cross-reacted with a few highly related antigens. Remarkably, immunofluorescence experiments in six cell lines for 270 of the TF antigens, each having multiple antibodies, show that ∼70% stain predominantly in the cytosol and ∼20% stain in the nucleus which reinforces the dominant role that translocation plays in TF biology. These cloned antibody reagents are being made available to the academic community through our web site recombinant-antibodies.org to allow a more system-wide analysis of TF and chromatin biology. We believe these platforms, infrastructure, and automated approaches will facilitate the next generation of renewable antibody reagents to the human proteome in the coming decade.
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Affiliation(s)
- Michael Hornsby
- From the ‡Department of Pharmaceutical Chemistry University of California, San Francisco, California 94158
| | - Marcin Paduch
- §Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, Illinois 60637
| | - Shane Miersch
- ¶Donnelly Center for Cellular and Biomolecular Research, Department of Molecular Genetics, University of Toronto, Toronto, MG5 1L6, Canada
| | - Annika Sääf
- §Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, Illinois 60637
| | - Tet Matsuguchi
- From the ‡Department of Pharmaceutical Chemistry University of California, San Francisco, California 94158
| | - Brian Lee
- From the ‡Department of Pharmaceutical Chemistry University of California, San Francisco, California 94158
| | - Karolina Wypisniak
- From the ‡Department of Pharmaceutical Chemistry University of California, San Francisco, California 94158
| | - Allison Doak
- From the ‡Department of Pharmaceutical Chemistry University of California, San Francisco, California 94158
| | - Daniel King
- §Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, Illinois 60637
| | - Svitlana Usatyuk
- §Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, Illinois 60637
| | - Kimberly Perry
- §Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, Illinois 60637
| | - Vince Lu
- §Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, Illinois 60637
| | - William Thomas
- §Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, Illinois 60637
| | - Judy Luke
- §Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, Illinois 60637
| | - Jay Goodman
- §Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, Illinois 60637
| | - Robert J Hoey
- §Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, Illinois 60637
| | - Darson Lai
- §Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, Illinois 60637
| | - Carly Griffin
- ¶Donnelly Center for Cellular and Biomolecular Research, Department of Molecular Genetics, University of Toronto, Toronto, MG5 1L6, Canada
| | - Zhijian Li
- ¶Donnelly Center for Cellular and Biomolecular Research, Department of Molecular Genetics, University of Toronto, Toronto, MG5 1L6, Canada
| | - Franco J Vizeacoumar
- **Saskatchewan Cancer Agency, University of Saskatchewan, Saskatoon, S7N 4H4, Canada
| | - Debbie Dong
- ¶Donnelly Center for Cellular and Biomolecular Research, Department of Molecular Genetics, University of Toronto, Toronto, MG5 1L6, Canada
| | - Elliot Campbell
- ‖Center for Advanced Biotechnology and Medicine, Department of Molecular Biology and Biochemistry, Rutgers University, Piscataway, New Jersey 08854
| | - Stephen Anderson
- ‖Center for Advanced Biotechnology and Medicine, Department of Molecular Biology and Biochemistry, Rutgers University, Piscataway, New Jersey 08854
| | - Nan Zhong
- ‡‡Structural Genomics Consortium, Toronto, M5G Il7, Canada
| | | | - Shohei Koide
- §Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, Illinois 60637
| | - Jason Moffat
- ¶Donnelly Center for Cellular and Biomolecular Research, Department of Molecular Genetics, University of Toronto, Toronto, MG5 1L6, Canada
| | - Sachdev Sidhu
- ¶Donnelly Center for Cellular and Biomolecular Research, Department of Molecular Genetics, University of Toronto, Toronto, MG5 1L6, Canada;
| | - Anthony Kossiakoff
- §Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, Illinois 60637;
| | - James Wells
- From the ‡Department of Pharmaceutical Chemistry University of California, San Francisco, California 94158;
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166
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Marschall ALJ, Dübel S, Böldicke T. Specific in vivo knockdown of protein function by intrabodies. MAbs 2015; 7:1010-35. [PMID: 26252565 PMCID: PMC4966517 DOI: 10.1080/19420862.2015.1076601] [Citation(s) in RCA: 78] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2015] [Revised: 07/19/2015] [Accepted: 07/20/2015] [Indexed: 01/02/2023] Open
Abstract
Intracellular antibodies (intrabodies) are recombinant antibody fragments that bind to target proteins expressed inside of the same living cell producing the antibodies. The molecules are commonly used to study the function of the target proteins (i.e., their antigens). The intrabody technology is an attractive alternative to the generation of gene-targeted knockout animals, and complements knockdown techniques such as RNAi, miRNA and small molecule inhibitors, by-passing various limitations and disadvantages of these methods. The advantages of intrabodies include very high specificity for the target, the possibility to knock down several protein isoforms by one intrabody and targeting of specific splice variants or even post-translational modifications. Different types of intrabodies must be designed to target proteins at different locations, typically either in the cytoplasm, in the nucleus or in the endoplasmic reticulum (ER). Most straightforward is the use of intrabodies retained in the ER (ER intrabodies) to knock down the function of proteins passing the ER, which disturbs the function of members of the membrane or plasma proteomes. More effort is needed to functionally knock down cytoplasmic or nuclear proteins because in this case antibodies need to provide an inhibitory effect and must be able to fold in the reducing milieu of the cytoplasm. In this review, we present a broad overview of intrabody technology, as well as applications both of ER and cytoplasmic intrabodies, which have yielded valuable insights in the biology of many targets relevant for drug development, including α-synuclein, TAU, BCR-ABL, ErbB-2, EGFR, HIV gp120, CCR5, IL-2, IL-6, β-amyloid protein and p75NTR. Strategies for the generation of intrabodies and various designs of their applications are also reviewed.
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Affiliation(s)
- Andrea LJ Marschall
- Technische Universität Braunschweig, Institute of Biochemistry, Biotechnology and Bioinformatics; Braunschweig, Germany
| | - Stefan Dübel
- Technische Universität Braunschweig, Institute of Biochemistry, Biotechnology and Bioinformatics; Braunschweig, Germany
| | - Thomas Böldicke
- Helmholtz Centre for Infection Research, Recombinant Protein Expression/Intrabody Unit, Helmholtz Centre for Infection Research; Braunschweig, Germany
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167
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Horvatovich P, Lundberg EK, Chen YJ, Sung TY, He F, Nice EC, Goode RJ, Yu S, Ranganathan S, Baker MS, Domont GB, Velasquez E, Li D, Liu S, Wang Q, He QY, Menon R, Guan Y, Corrales FJ, Segura V, Casal JI, Pascual-Montano A, Albar JP, Fuentes M, Gonzalez-Gonzalez M, Diez P, Ibarrola N, Degano RM, Mohammed Y, Borchers CH, Urbani A, Soggiu A, Yamamoto T, Salekdeh GH, Archakov A, Ponomarenko E, Lisitsa A, Lichti CF, Mostovenko E, Kroes RA, Rezeli M, Végvári Á, Fehniger TE, Bischoff R, Vizcaíno JA, Deutsch EW, Lane L, Nilsson CL, Marko-Varga G, Omenn GS, Jeong SK, Lim JS, Paik YK, Hancock WS. Quest for Missing Proteins: Update 2015 on Chromosome-Centric Human Proteome Project. J Proteome Res 2015; 14:3415-31. [DOI: 10.1021/pr5013009] [Citation(s) in RCA: 52] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Affiliation(s)
- Péter Horvatovich
- Analytical
Biochemistry, Department of Pharmacy, University of Groningen, A. Deusinglaan
1, 9713 AV Groningen, The Netherlands
| | - Emma K. Lundberg
- Science
for Life Laboratory, KTH - Royal Institute of Technology, SE-171 21 Stockholm, Sweden
| | - Yu-Ju Chen
- Institute
of Chemistry, Academia Sinica, 128 Academia Road Sec. 2, Taipei 115, Taiwan
| | - Ting-Yi Sung
- Institute
of Information Science, Academia Sinica, 128 Academia Road Sec. 2, Taipei 115, Taiwan
| | - Fuchu He
- The State Key Laboratory of Proteomics, Beijing Proteome Research Center, Beijing Institute of Radiation Medicine, No. 27 Taiping Road, Haidian District, Beijing 100850, China
| | - Edouard C. Nice
- Department
of Biochemistry and Molecular Biology, Monash University, Clayton, Victoria 3800, Australia
| | - Robert J. Goode
- Department
of Biochemistry and Molecular Biology, Monash University, Clayton, Victoria 3800, Australia
| | - Simon Yu
- Department
of Biochemistry and Molecular Biology, Monash University, Clayton, Victoria 3800, Australia
| | - Shoba Ranganathan
- Department
of Chemistry and Biomolecular Sciences and ARC Centre of Excellence
in Bioinformatics, Macquarie University, Sydney, New South Wales 2109, Australia
| | - Mark S. Baker
- Australian
School of Advanced Medicine, Macquarie University, Sydney, NSW 2109, Australia
| | - Gilberto B. Domont
- Proteomics Unit, Institute of Chemistry, Federal University of Rio de Janeiro, Cidade Universitária, Av Athos da Silveira Ramos 149, CT-A542, 21941-909 Rio de Janeriro, Rj, Brazil
| | - Erika Velasquez
- Proteomics Unit, Institute of Chemistry, Federal University of Rio de Janeiro, Cidade Universitária, Av Athos da Silveira Ramos 149, CT-A542, 21941-909 Rio de Janeriro, Rj, Brazil
| | - Dong Li
- The State Key Laboratory of Proteomics, Beijing Proteome Research Center, Beijing Institute of Radiation Medicine, No. 27 Taiping Road, Haidian District, Beijing 100850, China
| | - Siqi Liu
- Beijing Institute of Genomics and BGI Shenzhen, No. 1 Beichen West Road, Chaoyang District, Beijing 100101, China
- BGI Shenzhen, Beishan Road, Yantian District, Shenzhen, 518083, China
| | - Quanhui Wang
- Beijing Institute of Genomics and BGI Shenzhen, No. 1 Beichen West Road, Chaoyang District, Beijing 100101, China
| | - Qing-Yu He
- Key Laboratory of Functional Protein
Research of Guangdong
Higher Education Institutes, College of Life Science and Technology, Jinan University, Guangzhou 510632, China
| | - Rajasree Menon
- Department of Computational Medicine & Bioinformatics, University of Michigan, 100 Washtenaw Avenue, Ann Arbor, Michigan 48109-2218, United States
| | - Yuanfang Guan
- Departments of Computational Medicine & Bioinformatics and Computer Sciences, University of Michigan, 100 Washtenaw Avenue, Ann Arbor, Michigan 48109-2218, United States
| | - Fernando J. Corrales
- ProteoRed-ISCIII,
Biomolecular and Bioinformatics Resources Platform (PRB2), Spanish
Consortium of C-HPP (Chr-16), CIMA, University of Navarra, 31008 Pamplona, Spain
- Chr16 SpHPP Consortium, CIMA, University of Navarra, 31008 Pamplona, Spain
| | - Victor Segura
- ProteoRed-ISCIII,
Biomolecular and Bioinformatics Resources Platform (PRB2), Spanish
Consortium of C-HPP (Chr-16), CIMA, University of Navarra, 31008 Pamplona, Spain
- Chr16 SpHPP Consortium, CIMA, University of Navarra, 31008 Pamplona, Spain
| | - J. Ignacio Casal
- Department
of Cellular and Molecular Medicine, Centro de Investigaciones Biológicas (CIB-CSIC), 28040 Madrid, Spain
| | | | - Juan P. Albar
- Centro Nacional de Biotecnologia (CNB-CSIC), Cantoblanco, 28049 Madrid, Spain
| | - Manuel Fuentes
- Cancer
Research Center. Proteomics Unit and General Service of Cytometry,
Department of Medicine, University of Salmanca-CSIC, IBSAL, Campus Miguel de Unamuno
s/n, 37007 Salamanca, Spain
| | - Maria Gonzalez-Gonzalez
- Cancer
Research Center. Proteomics Unit and General Service of Cytometry,
Department of Medicine, University of Salmanca-CSIC, IBSAL, Campus Miguel de Unamuno
s/n, 37007 Salamanca, Spain
| | - Paula Diez
- Cancer
Research Center. Proteomics Unit and General Service of Cytometry,
Department of Medicine, University of Salmanca-CSIC, IBSAL, Campus Miguel de Unamuno
s/n, 37007 Salamanca, Spain
| | - Nieves Ibarrola
- Cancer
Research Center. Proteomics Unit and General Service of Cytometry,
Department of Medicine, University of Salmanca-CSIC, IBSAL, Campus Miguel de Unamuno
s/n, 37007 Salamanca, Spain
| | - Rosa M. Degano
- Cancer
Research Center. Proteomics Unit and General Service of Cytometry,
Department of Medicine, University of Salmanca-CSIC, IBSAL, Campus Miguel de Unamuno
s/n, 37007 Salamanca, Spain
| | - Yassene Mohammed
- University of Victoria-Genome British Columbia Proteomics
Centre, Vancouver Island
Technology Park, #3101−4464 Markham Street, Victoria, British Columbia V8Z 7X8, Canada
- Center
for Proteomics and Metabolomics, Leiden University Medical Center, 2333 ZA Leiden, The Netherlands
| | - Christoph H. Borchers
- University of Victoria-Genome British Columbia Proteomics
Centre, Vancouver Island
Technology Park, #3101−4464 Markham Street, Victoria, British Columbia V8Z 7X8, Canada
| | - Andrea Urbani
- Proteomics
and Metabonomic, Laboratory, Fondazione Santa Lucia, Rome, Italy
- Department
of Experimental Medicine and Surgery, University of Rome “Tor Vergata”, Rome, Italy
| | - Alessio Soggiu
- Department
of Veterinary Science and Public Health (DIVET), University of Milano, via Celoria 10, 20133 Milano, Italy
| | - Tadashi Yamamoto
- Institute
of Nephrology, Graduate School of Medical and Dental Sciences, Niigata University, Niigata, Japan
| | - Ghasem Hosseini Salekdeh
- Department of Molecular Systems Biology at Cell Science Research Center, Royan Institute for Stem Cell Biology and Technology, ACECR, Tehran, Iran
- Department of Systems Biology, Agricultural Biotechnology Research Institute of Iran, Karaj, Iran
| | | | | | - Andrey Lisitsa
- Orechovich Institute of Biomedical Chemistry, Moscow, Russia
| | - Cheryl F. Lichti
- Department
of Pharmacology and Toxicology, The University of Texas Medical Branch, Galveston, Texas 77555-0617, United States
| | - Ekaterina Mostovenko
- Department
of Pharmacology and Toxicology, The University of Texas Medical Branch, Galveston, Texas 77555-0617, United States
| | - Roger A. Kroes
- Falk Center for Molecular Therapeutics, Department of Biomedical Engineering, Northwestern University, 1801 Maple Ave., Suite 4300, Evanston, Illinois 60201, United States
| | - Melinda Rezeli
- Clinical Protein Science & Imaging, Department of Biomedical Engineering, Lund University, BMC D13, 221 84 Lund, Sweden
| | - Ákos Végvári
- Clinical Protein Science & Imaging, Department of Biomedical Engineering, Lund University, BMC D13, 221 84 Lund, Sweden
| | - Thomas E. Fehniger
- Clinical Protein Science & Imaging, Department of Biomedical Engineering, Lund University, BMC D13, 221 84 Lund, Sweden
| | - Rainer Bischoff
- Analytical
Biochemistry, Department of Pharmacy, University of Groningen, A. Deusinglaan
1, 9713 AV Groningen, The Netherlands
| | - Juan Antonio Vizcaíno
- European Molecular
Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, CB10 1SD, Hinxton, Cambridge, United Kingdom
| | - Eric W. Deutsch
- Institute for Systems Biology, 401 Terry Avenue North, Seattle, Washington 98109, United States
| | - Lydie Lane
- SIB Swiss Institute of Bioinformatics, Geneva, Switzerland
- Department
of Human Protein Science, Faculty of Medicine, University of Geneva, Geneva, Switzerland
| | - Carol L. Nilsson
- Department
of Pharmacology and Toxicology, The University of Texas Medical Branch, Galveston, Texas 77555-0617, United States
| | - György Marko-Varga
- Clinical Protein Science & Imaging, Department of Biomedical Engineering, Lund University, BMC D13, 221 84 Lund, Sweden
| | - Gilbert S. Omenn
- Departments of Computational Medicine & Bioinformatics, Internal Medicine, Human Genetics and School of Public Health, University of Michigan, 100 Washtenaw Avenue, Ann Arbor, Michigan 48109-2218, United States
| | - Seul-Ki Jeong
- Departments of Integrated Omics for Biomedical Science & Biochemistry, College of Life Science and Technology, Yonsei Proteome Research Center, Yonsei University, Seoul, 120-749, Korea
| | - Jong-Sun Lim
- Departments of Integrated Omics for Biomedical Science & Biochemistry, College of Life Science and Technology, Yonsei Proteome Research Center, Yonsei University, Seoul, 120-749, Korea
| | - Young-Ki Paik
- Departments of Integrated Omics for Biomedical Science & Biochemistry, College of Life Science and Technology, Yonsei Proteome Research Center, Yonsei University, Seoul, 120-749, Korea
| | - William S. Hancock
- The
Barnett Institute of Chemical and Biological Analysis, Northeastern University, 140 The Fenway, Boston, Massachusetts 02115, United States
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168
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Identification of optimal protein binders through the use of large genetically encoded display libraries. Curr Opin Chem Biol 2015; 26:16-24. [DOI: 10.1016/j.cbpa.2015.01.003] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2014] [Accepted: 01/08/2015] [Indexed: 01/05/2023]
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169
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Kügler J, Wilke S, Meier D, Tomszak F, Frenzel A, Schirrmann T, Dübel S, Garritsen H, Hock B, Toleikis L, Schütte M, Hust M. Generation and analysis of the improved human HAL9/10 antibody phage display libraries. BMC Biotechnol 2015; 15:10. [PMID: 25888378 PMCID: PMC4352240 DOI: 10.1186/s12896-015-0125-0] [Citation(s) in RCA: 96] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2014] [Accepted: 02/09/2015] [Indexed: 12/29/2022] Open
Abstract
BACKGROUND Antibody phage display is a proven key technology that allows the generation of human antibodies for diagnostics and therapy. From naive antibody gene libraries - in theory - antibodies against any target can be selected. Here we describe the design, construction and characterization of an optimized antibody phage display library. RESULTS The naive antibody gene libraries HAL9 and HAL10, with a combined theoretical diversity of 1.5×10(10) independent clones, were constructed from 98 healthy donors using improved phage display vectors. In detail, most common phagemids employed for antibody phage display are using a combined His/Myc tag for detection and purification. We show that changing the tag order to Myc/His improved the production of soluble antibodies, but did not affect antibody phage display. For several published antibody libraries, the selected number of kappa scFvs were lower compared to lambda scFvs, probably due to a lower kappa scFv or Fab expression rate. Deletion of a phenylalanine at the end of the CL linker sequence in our new phagemid design increased scFv production rate and frequency of selected kappa antibodies significantly. The HAL libraries and 834 antibodies selected against 121 targets were analyzed regarding the used germline V-genes, used V-gene combinations and CDR-H3/-L3 length and composition. The amino acid diversity and distribution in the CDR-H3 of the initial library was retrieved in the CDR-H3 of selected antibodies showing that all CDR-H3 amino acids occurring in the human antibody repertoire can be functionally used and is not biased by E. coli expression or phage selection. Further, the data underline the importance of CDR length variations. CONCLUSION The highly diverse universal antibody gene libraries HAL9/10 were constructed using an optimized scFv phagemid vector design. Analysis of selected antibodies revealed that the complete amino acid diversity in the CDR-H3 was also found in selected scFvs showing the functionality of the naive CDR-H3 diversity.
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Affiliation(s)
- Jonas Kügler
- Technische Universität Braunschweig, Institut für Biochemie, Biotechnologie und Bioinformatik, Spielmannstr. 7, 38106, Braunschweig, Germany. .,mAb-factory GmbH, Gelsenkirchenstr. 5, 38108, Braunschweig, Germany.
| | - Sonja Wilke
- mAb-factory GmbH, Gelsenkirchenstr. 5, 38108, Braunschweig, Germany.
| | - Doris Meier
- Technische Universität Braunschweig, Institut für Biochemie, Biotechnologie und Bioinformatik, Spielmannstr. 7, 38106, Braunschweig, Germany.
| | - Florian Tomszak
- Technische Universität Braunschweig, Institut für Biochemie, Biotechnologie und Bioinformatik, Spielmannstr. 7, 38106, Braunschweig, Germany.
| | - André Frenzel
- Technische Universität Braunschweig, Institut für Biochemie, Biotechnologie und Bioinformatik, Spielmannstr. 7, 38106, Braunschweig, Germany. .,YUMAB GmbH, Rebenring 33, 38106, Braunschweig, Germany.
| | - Thomas Schirrmann
- Technische Universität Braunschweig, Institut für Biochemie, Biotechnologie und Bioinformatik, Spielmannstr. 7, 38106, Braunschweig, Germany. .,YUMAB GmbH, Rebenring 33, 38106, Braunschweig, Germany.
| | - Stefan Dübel
- Technische Universität Braunschweig, Institut für Biochemie, Biotechnologie und Bioinformatik, Spielmannstr. 7, 38106, Braunschweig, Germany.
| | - Henk Garritsen
- Klinikum Braunschweig g GmbH, Institut für Klinische Transfusionsmedizin, Celler Str. 38, 38114, Braunschweig, Germany. .,Department Vaccinology, Helmholtz-Zentrum für Infektionsforschung, Inhoffenstraße 7, 38124, Braunschweig, Germany.
| | | | | | | | - Michael Hust
- Technische Universität Braunschweig, Institut für Biochemie, Biotechnologie und Bioinformatik, Spielmannstr. 7, 38106, Braunschweig, Germany.
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170
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Miersch S, Li Z, Hanna R, McLaughlin ME, Hornsby M, Matsuguchi T, Paduch M, Sääf A, Wells J, Koide S, Kossiakoff A, Sidhu SS. Scalable high throughput selection from phage-displayed synthetic antibody libraries. J Vis Exp 2015:51492. [PMID: 25651360 DOI: 10.3791/51492] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/31/2022] Open
Abstract
The demand for antibodies that fulfill the needs of both basic and clinical research applications is high and will dramatically increase in the future. However, it is apparent that traditional monoclonal technologies are not alone up to this task. This has led to the development of alternate methods to satisfy the demand for high quality and renewable affinity reagents to all accessible elements of the proteome. Toward this end, high throughput methods for conducting selections from phage-displayed synthetic antibody libraries have been devised for applications involving diverse antigens and optimized for rapid throughput and success. Herein, a protocol is described in detail that illustrates with video demonstration the parallel selection of Fab-phage clones from high diversity libraries against hundreds of targets using either a manual 96 channel liquid handler or automated robotics system. Using this protocol, a single user can generate hundreds of antigens, select antibodies to them in parallel and validate antibody binding within 6-8 weeks. Highlighted are: i) a viable antigen format, ii) pre-selection antigen characterization, iii) critical steps that influence the selection of specific and high affinity clones, and iv) ways of monitoring selection effectiveness and early stage antibody clone characterization. With this approach, we have obtained synthetic antibody fragments (Fabs) to many target classes including single-pass membrane receptors, secreted protein hormones, and multi-domain intracellular proteins. These fragments are readily converted to full-length antibodies and have been validated to exhibit high affinity and specificity. Further, they have been demonstrated to be functional in a variety of standard immunoassays including Western blotting, ELISA, cellular immunofluorescence, immunoprecipitation and related assays. This methodology will accelerate antibody discovery and ultimately bring us closer to realizing the goal of generating renewable, high quality antibodies to the proteome.
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Affiliation(s)
- Shane Miersch
- The Recombinant Antibody Network; The Banting and Best Department of Medical Research, University of Toronto;
| | - Zhijian Li
- The Recombinant Antibody Network; The Banting and Best Department of Medical Research, University of Toronto
| | - Rachel Hanna
- The Recombinant Antibody Network; The Banting and Best Department of Medical Research, University of Toronto
| | - Megan E McLaughlin
- The Recombinant Antibody Network; The Banting and Best Department of Medical Research, University of Toronto
| | - Michael Hornsby
- The Recombinant Antibody Network; Antibiome Center, University of California, San Francisco at Mission Bay
| | - Tet Matsuguchi
- The Recombinant Antibody Network; Antibiome Center, University of California, San Francisco at Mission Bay
| | - Marcin Paduch
- The Recombinant Antibody Network; Department of Biochemistry and Molecular Biology, The University of Chicago
| | - Annika Sääf
- The Recombinant Antibody Network; Department of Biochemistry and Molecular Biology, The University of Chicago
| | - Jim Wells
- The Recombinant Antibody Network; Antibiome Center, University of California, San Francisco at Mission Bay
| | - Shohei Koide
- The Recombinant Antibody Network; Department of Biochemistry and Molecular Biology, The University of Chicago
| | - Anthony Kossiakoff
- The Recombinant Antibody Network; Department of Biochemistry and Molecular Biology, The University of Chicago
| | - Sachdev S Sidhu
- The Recombinant Antibody Network; The Banting and Best Department of Medical Research, University of Toronto
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171
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Wang K, Huang C, Nice E. Recent advances in proteomics: towards the human proteome. Biomed Chromatogr 2015; 28:848-57. [PMID: 24861753 DOI: 10.1002/bmc.3157] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
After the successful completion of the Human Genome project in 2003, the next major challenge was to understand when and where the encoded proteins were expressed, and to generate a map of the complex, interconnected pathways, networks and molecular systems (the human proteome) that, taken together, control the workings of all cells, tissues, organs and organisms. Proteomics will be fundamental for such studies. This review summarizes the key discoveries that laid down the foundations for proteomics as we now know it, and describes key recent technological advances that will undoubtedly contribute to achieving the initial goal of the Human Proteome Organization of identifying and characterizing at least one protein product and representative post-translational modifications, single amino acid polymorphisms and splice variant isoforms from the 20,300 human protein-coding genes within the next 10 years. Successful unraveling of the human proteome will undoubtedly improve our understanding of human biology at the cellular level and lay the foundations for improved diagnostic, prognostic, therapeutic and preventive medical outcomes as we enter the era of personalized medicine.
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Affiliation(s)
- Kui Wang
- The State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, 610041, People's Republic of China; Department of Biochemistry and Molecular Biology, Monash University, Clayton, Victoria, 3800, Australia
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172
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Koerber JT, Hornsby MJ, Wells JA. An improved single-chain Fab platform for efficient display and recombinant expression. J Mol Biol 2014; 427:576-86. [PMID: 25481745 DOI: 10.1016/j.jmb.2014.11.017] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2014] [Revised: 11/17/2014] [Accepted: 11/25/2014] [Indexed: 12/13/2022]
Abstract
Antibody phage display libraries combined with high-throughput selections have recently demonstrated tremendous promise to create the next generation of renewable, recombinant antibodies to study proteins and their many post-translational modification states; however, many challenges still remain, such as optimized antibody scaffolds. Recently, a single-chain fragment antigen binding (Fab) (scFab) format, in which the carboxy-terminus of the light chain is linked to the amino-terminus of the heavy chain, was described to potentially combine the high display levels of a single-chain fragment variable with the high stability of purified Fabs. However, this format required removal of the interchain disulfide bond to achieve modest display levels and subsequent bacterial expression resulted in high levels of aggregated scFab, hindering further use of scFabs. Here, we developed an improved scFab format that retains the interchain disulfide bond by increasing the linker length between the light and heavy chains to improve display and bacterial expression levels to 1-3 mg/L. Furthermore, rerouting of the scFab to the co-translational signal recognition particle pathway combined with reengineering of the signal peptide sequence results in display levels 24-fold above the original scFab format and 3-fold above parent Fab levels. This optimized scFab scaffold can be easily reformatted in a single step for expression in a bacterial or mammalian host to produce stable (Tm of 81 °C), predominantly monomeric (>90%) antibodies at a high yield. Ultimately, this new scFab format will advance high-throughput antibody generation platforms to discover the next generation of research and therapeutic antibodies.
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Affiliation(s)
- James T Koerber
- Department of Pharmaceutical Chemistry, University of California, San Francisco, CA, 94158, USA; Department of Cellular and Molecular Pharmacology, University of California, San Francisco, CA, 94158, USA; Recombinant Antibody Network, University of California, San Francisco, CA, 94158, USA
| | - Michael J Hornsby
- Department of Pharmaceutical Chemistry, University of California, San Francisco, CA, 94158, USA; Department of Cellular and Molecular Pharmacology, University of California, San Francisco, CA, 94158, USA; Recombinant Antibody Network, University of California, San Francisco, CA, 94158, USA
| | - James A Wells
- Department of Pharmaceutical Chemistry, University of California, San Francisco, CA, 94158, USA; Department of Cellular and Molecular Pharmacology, University of California, San Francisco, CA, 94158, USA; Recombinant Antibody Network, University of California, San Francisco, CA, 94158, USA.
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173
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Genetic methods of antibody generation and their use in immunohistochemistry. Methods 2014; 70:20-7. [DOI: 10.1016/j.ymeth.2014.02.031] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2013] [Revised: 01/22/2014] [Accepted: 02/21/2014] [Indexed: 12/18/2022] Open
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174
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Bailey LJ, Sheehy KM, Hoey RJ, Schaefer ZP, Ura M, Kossiakoff AA. Applications for an engineered Protein-G variant with a pH controllable affinity to antibody fragments. J Immunol Methods 2014; 415:24-30. [PMID: 25450256 DOI: 10.1016/j.jim.2014.10.003] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2014] [Revised: 10/09/2014] [Accepted: 10/13/2014] [Indexed: 01/28/2023]
Abstract
Immunoglobulin binding proteins (IBPs) are broadly used as reagents for the purification and detection of antibodies. Among the IBPs, the most widely used are Protein-A and Protein-G. The C2 domain of Protein-G from Streptococcus is a multi-specific protein domain; it possesses a high affinity (K(D) ~10 nM) for the Fc region of the IgG, but a much lower affinity (KD~low μM) for the constant domain of the antibody fragment (Fab), which limits some of its applications. Here, we describe the engineering of the Protein-G interface using phage display to create Protein-G-A1, a variant with 8 point mutations and an approximately 100-fold improved affinity over the parent domain for the 4D5 Fab scaffold. Protein-G-A1 is capable of robust binding to Fab fragments for numerous applications. Furthermore, we isolated a variant with pH-dependent affinity, demonstrating a 1,000-fold change in affinity from pH7 to 4. Additional rational mutagenesis endowed Protein-G with significantly enhanced stability in basic conditions relative to the parent domain while maintaining high affinity to the Fab. This property is particularly useful to regenerate Protein-G affinity columns. Lastly, the affinity-matured Protein-G-A1 variant was tethered together to produce dimers capable of providing multivalent affinity enhancement to a low affinity antibody fragment-antigen interaction. Engineered Protein-G variants should find widespread application in the use of Fab-based affinity reagents.
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Affiliation(s)
- Lucas J Bailey
- Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, IL, 60637, USA
| | - Kimberly M Sheehy
- Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, IL, 60637, USA
| | - Robert J Hoey
- Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, IL, 60637, USA
| | - Zachary P Schaefer
- Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, IL, 60637, USA
| | - Marcin Ura
- Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, IL, 60637, USA
| | - Anthony A Kossiakoff
- Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, IL, 60637, USA.
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175
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D'Angelo S, Glanville J, Ferrara F, Naranjo L, Gleasner CD, Shen X, Bradbury ARM, Kiss C. The antibody mining toolbox: an open source tool for the rapid analysis of antibody repertoires. MAbs 2014; 6:160-72. [PMID: 24423623 PMCID: PMC3929439 DOI: 10.4161/mabs.27105] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
Abstract
In vitro selection has been an essential tool in the development of recombinant antibodies against various antigen targets. Deep sequencing has recently been gaining ground as an alternative and valuable method to analyze such antibody selections. The analysis provides a novel and extremely detailed view of selected antibody populations, and allows the identification of specific antibodies using only sequencing data, potentially eliminating the need for expensive and laborious low-throughput screening methods such as enzyme-linked immunosorbant assay. The high cost and the need for bioinformatics experts and powerful computer clusters, however, have limited the general use of deep sequencing in antibody selections. Here, we describe the AbMining ToolBox, an open source software package for the straightforward analysis of antibody libraries sequenced by the three main next generation sequencing platforms (454, Ion Torrent, MiSeq). The ToolBox is able to identify heavy chain CDR3s as effectively as more computationally intense software, and can be easily adapted to analyze other portions of antibody variable genes, as well as the selection outputs of libraries based on different scaffolds. The software runs on all common operating systems (Microsoft Windows, Mac OS X, Linux), on standard personal computers, and sequence analysis of 1–2 million reads can be accomplished in 10–15 min, a fraction of the time of competing software. Use of the ToolBox will allow the average researcher to incorporate deep sequence analysis into routine selections from antibody display libraries.
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Affiliation(s)
| | | | | | - Leslie Naranjo
- B Division; Los Alamos National Laboratory; Los Alamos, NM USA
| | | | - Xiaohong Shen
- B Division; Los Alamos National Laboratory; Los Alamos, NM USA
| | | | - Csaba Kiss
- B Division; Los Alamos National Laboratory; Los Alamos, NM USA
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176
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Barker SL, Pastor J, Carranza D, Quiñones H, Griffith C, Goetz R, Mohammadi M, Ye J, Zhang J, Hu MC, Kuro-o M, Moe OW, Sidhu SS. The demonstration of αKlotho deficiency in human chronic kidney disease with a novel synthetic antibody. Nephrol Dial Transplant 2014; 30:223-33. [PMID: 25324355 DOI: 10.1093/ndt/gfu291] [Citation(s) in RCA: 115] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023] Open
Abstract
BACKGROUND αKlotho is the prototypic member of the Klotho family and is most highly expressed in the kidney. αKlotho has pleiotropic biologic effects, and in the kidney, its actions include regulation of ion transport, cytoprotection, anti-oxidation and anti-fibrosis. In rodent models of chronic kidney disease (CKD), αKlotho deficiency has been shown to be an early biomarker as well as a pathogenic factor. The database for αKlotho in human CKD remains controversial even after years of study. METHODS We used a synthetic antibody library to identify a high-affinity human antigen-binding fragment that recognizes human, rat and mouse αKlotho primarily in its native, rather than denatured, form. RESULTS Using an immunoprecipitation-immunoblot (IP-IB) assay, we measured both serum and urinary levels of full-length soluble αKlotho in humans and established that human CKD is associated with αKlotho deficiency in serum and urine. αKlotho levels were detectably lower in early CKD preceding disturbances in other parameters of mineral metabolism and progressively declined with CKD stages. We also found that exogenously added αKlotho is inherently unstable in the CKD milieu suggesting that decreased production may not be the sole reason for αKlotho deficiency. CONCLUSION Synthetic antibody libraries harbor tremendous potential for a variety of biomedical and clinical applications. Using such a reagent, we furnish data in support of αKlotho deficiency in human CKD, and we set the foundation for the development of diagnostic and therapeutic applications of anti-αKlotho antibodies.
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Affiliation(s)
- Sarah L Barker
- Banting and Best Department of Medical Research and Department of Molecular Genetics, The Donnelly Centre, University of Toronto, Toronto, ON, Canada
| | - Johanne Pastor
- Department of Pathology, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Danielle Carranza
- Banting and Best Department of Medical Research and Department of Molecular Genetics, The Donnelly Centre, University of Toronto, Toronto, ON, Canada
| | - Henry Quiñones
- Department of Internal Medicine, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Carolyn Griffith
- Charles and Jane Pak Center for Mineral Metabolism and Clinical Research, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Regina Goetz
- Department of Biochemistry and Molecular Pharmacology, New York University School of Medicine, New York, NY, USA
| | - Moosa Mohammadi
- Department of Biochemistry and Molecular Pharmacology, New York University School of Medicine, New York, NY, USA
| | - Jianfeng Ye
- Charles and Jane Pak Center for Mineral Metabolism and Clinical Research, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Jianning Zhang
- Department of Internal Medicine, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Ming Chang Hu
- Department of Internal Medicine, University of Texas Southwestern Medical Center, Dallas, TX, USA Charles and Jane Pak Center for Mineral Metabolism and Clinical Research, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Makoto Kuro-o
- Department of Pathology, University of Texas Southwestern Medical Center, Dallas, TX, USA Charles and Jane Pak Center for Mineral Metabolism and Clinical Research, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Orson W Moe
- Department of Internal Medicine, University of Texas Southwestern Medical Center, Dallas, TX, USA Charles and Jane Pak Center for Mineral Metabolism and Clinical Research, University of Texas Southwestern Medical Center, Dallas, TX, USA Department of Physiology, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Sachdev S Sidhu
- Banting and Best Department of Medical Research and Department of Molecular Genetics, The Donnelly Centre, University of Toronto, Toronto, ON, Canada
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177
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Stech M, Hust M, Schulze C, Dübel S, Kubick S. Cell-free eukaryotic systems for the production, engineering, and modification of scFv antibody fragments. Eng Life Sci 2014; 14:387-398. [PMID: 25821419 PMCID: PMC4374706 DOI: 10.1002/elsc.201400036] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2014] [Revised: 05/06/2014] [Accepted: 05/08/2014] [Indexed: 01/27/2023] Open
Abstract
Open cell-free translation systems based on Escherichia coli cell lysates have successfully been used to produce antibodies and antibody fragments. In this study, we demonstrate the cell-free expression of functional single-chain antibody variable fragments (scFvs) in a eukaryotic and endotoxin-free in vitro translation system based on Spodoptera frugiperda (Sf21) insect cell extracts. Three scFv candidates with different specificities were chosen as models. The first scFv candidate SH527-IIA4 specifically discriminates between its phosphorylated (SMAD2-P) and nonphosphorylated antigens (SMAD2) (where SMAD is mothers against decapentaplegic homolog 2), whereas the second scFv candidate SH527-IIC10 recognizes both, SMAD2-P and SMAD2. The third scFv candidate SH855-C11 binds specifically to a linear epitope of the CXC chemokine receptor type 5. The translocation of antibody fragments into the lumen of endogenous microsomal vesicles, which are contained in the lysate, was facilitated by fusion of scFv genes to the insect cell specific signal sequence of honeybee melittin. We compared the binding capabilities of scFv fragments with and without melittin signal peptide and detected that translocated scFv fragments were highly functional, whereas scFvs synthesized in the cytosol of the cell extract showed strongly decreased binding capabilities. Additionally, we describe a cell-free protein synthesis method for the incorporation of noncanonical amino acids into scFv molecules in eukaryotic cell lysates. We demonstrate the successful cotranslational labeling of de novo synthesized scFv molecules with fluorescent amino acids, using residue-specific as well as site-specific labeling.
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Affiliation(s)
- Marlitt Stech
- Fraunhofer Institute for Cell Therapy and Immunology (IZI), Branch Bioanalytics and Bioprocesses Potsdam-Golm Potsdam, Germany
| | - Michael Hust
- Department of Biotechnology, Institute for Biochemistry, Biotechnology and Bioinformatics, Technische Universität Braunschweig Braunschweig, Germany
| | - Corina Schulze
- Department of Life Sciences and Technology, Beuth Hochschule für Technik Berlin, University of Applied Sciences Berlin, Germany
| | - Stefan Dübel
- Department of Biotechnology, Institute for Biochemistry, Biotechnology and Bioinformatics, Technische Universität Braunschweig Braunschweig, Germany
| | - Stefan Kubick
- Fraunhofer Institute for Cell Therapy and Immunology (IZI), Branch Bioanalytics and Bioprocesses Potsdam-Golm Potsdam, Germany
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178
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Larsen AC, Gillig A, Shah P, Sau SP, Fenton KE, Chaput JC. General approach for characterizing in vitro selected peptides with protein binding affinity. Anal Chem 2014; 86:7219-23. [PMID: 24970615 PMCID: PMC4215864 DOI: 10.1021/ac501614d] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
![]()
In
vitro selection technologies are important tools for identifying
high affinity peptides to proteins of broad medical and biological
interest. However, the technological advances that have made it possible
to generate long lists of candidate peptides have far outpaced our
ability to characterize the binding properties of individual peptides.
Here, we describe a low cost strategy to rapidly synthesize, purify,
screen, and characterize peptides for high binding affinity. Peptides
are assayed in a 96-well dot blot apparatus using membranes that enable
partitioning of bound and unbound peptide–protein complexes.
We have validated the binding affinity constants produced by this
method using known peptide ligands and applied this process to discover
five new peptides with nanomolar affinity to human α-thrombin.
Given the need for new analytical tools that can accelerate peptide
discovery and characterization, we feel that this approach would be
useful to a wide range of technologies that utilize high affinity
peptides.
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Affiliation(s)
- Andrew C Larsen
- Department of Chemistry and Biochemistry and ‡The Biodesign Institute, Arizona State University , Tempe, Arizona 85287, United States
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179
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Cha B, Chen T, Sarker R, Yang J, Raben D, Tse CM, Kovbasnjuk O, Donowitz M. Lysophosphatidic acid stimulation of NHE3 exocytosis in polarized epithelial cells occurs with release from NHERF2 via ERK-PLC-PKCδ signaling. Am J Physiol Cell Physiol 2014; 307:C55-65. [PMID: 24760985 PMCID: PMC4080180 DOI: 10.1152/ajpcell.00045.2014] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2014] [Accepted: 04/03/2014] [Indexed: 01/19/2023]
Abstract
The Na(+)/H(+) exchanger 3 (NHE3) is a brush border (BB) Na(+)/H(+) antiporter that accounts for the majority of physiologic small intestinal and renal Na(+) absorption. It is regulated physiologically and in disease via changes in endocytosis/exocytosis. Paradoxically, NHE3 is fixed to the microvillar (MV) actin cytoskeleton and has little basal mobility. This fixation requires NHE3 binding to the multi-PDZ domain scaffold proteins Na(+)/H(+) exchanger regulatory factor (NHERF)1 and NHERF2 and to ezrin. Coordinated release of NHE3 from the MV cytoskeleton has been demonstrated during both stimulation and inhibition of NHE3. However, the signaling molecules involved in coordinating NHE3 trafficking and cytoskeletal association have not been identified. This question was addressed by studying lysophosphatidic acid (LPA) stimulation of NHE3 in polarized renal proximal tubule opossum kidney (OK) cells that occurs via apical LPA5 receptors and is NHERF2 dependent and mediated by epidermal growth factor receptor (EGFR), Rho/Rho-associated kinase (ROCK), and ERK. NHE3 activity was determined by BCECF/fluorometry and NHE3 microvillar mobility by FRAP/confocal microscopy using NHE3-EGFP. Apical LPA (3 μM)/LPA5R stimulated NHE3 activity, increased NHE3 mobility, and decreased the NHE3/NHERF2 association. The LPA stimulation of NHE3 was also PKCδ dependent. PKCδ was necessary for LPA stimulation of NHE3 mobility and NHE3/NHERF2 association. Moreover, the LPA-induced translocation to the membrane of PKCδ was both ERK and phospholipase C dependent with ERK acting upstream of PLC. We conclude that LPA stimulation of NHE3 exocytosis includes a signaling pathway that regulates fixation of NHE3 to the MV cytoskeleton. This involves a signaling module consisting of ERK-PLC-PKCδ, which dynamically and reversibly releases NHE3 from NHERF2 to contribute to the changes in NHE3 MV mobility.
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Affiliation(s)
- Boyoung Cha
- Departments of Physiology and Medicine, Gastrointestinal Division, The Johns Hopkins University School of Medicine, Baltimore, Maryland; and
| | - Tiane Chen
- Departments of Physiology and Medicine, Gastrointestinal Division, The Johns Hopkins University School of Medicine, Baltimore, Maryland; and
| | - Rafiquel Sarker
- Departments of Physiology and Medicine, Gastrointestinal Division, The Johns Hopkins University School of Medicine, Baltimore, Maryland; and
| | - Jianbo Yang
- Departments of Physiology and Medicine, Gastrointestinal Division, The Johns Hopkins University School of Medicine, Baltimore, Maryland; and
| | - Daniel Raben
- Department of Biological Chemistry, The Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - C Ming Tse
- Departments of Physiology and Medicine, Gastrointestinal Division, The Johns Hopkins University School of Medicine, Baltimore, Maryland; and
| | - Olga Kovbasnjuk
- Departments of Physiology and Medicine, Gastrointestinal Division, The Johns Hopkins University School of Medicine, Baltimore, Maryland; and
| | - Mark Donowitz
- Departments of Physiology and Medicine, Gastrointestinal Division, The Johns Hopkins University School of Medicine, Baltimore, Maryland; and
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180
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Marschall ALJ, Zhang C, Frenzel A, Schirrmann T, Hust M, Perez F, Dübel S. Delivery of antibodies to the cytosol: debunking the myths. MAbs 2014; 6:943-56. [PMID: 24848507 DOI: 10.4161/mabs.29268] [Citation(s) in RCA: 58] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
The use of antibodies to target their antigens in living cells is a powerful analytical tool for cell biology research. Not only can molecules be localized and visualized in living cells, but interference with cellular processes by antibodies may allow functional analysis down to the level of individual post-translational modifications and splice variants, which is not possible with genetic or RNA-based methods. To utilize the vast resource of available antibodies, an efficient system to deliver them into the cytosol from the outside is needed. Numerous strategies have been proposed, but the most robust and widely applicable procedure still remains to be identified, since a quantitative ranking of the efficiencies has not yet been done. To achieve this, we developed a novel efficiency evaluation method for antibody delivery based on a fusion protein consisting of a human IgG 1 Fc and the recombination enzyme Cre (Fc-Cre). Applied to suitable GFP reporter cells, it allows the important distinction between proteins trapped in endosomes and those delivered to the cytosol. Further, it ensures viability of positive cells and is unsusceptible to fixation artifacts and misinterpretation of cellular localization in microscopy and flow cytometry. Very low cytoplasmic delivery efficiencies were found for various profection reagents and membrane penetrating peptides, leaving electroporation as the only practically useful delivery method for antibodies. This was further verified by the successful application of this method to bind antibodies to cytosolic components in living cells.
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Affiliation(s)
- Andrea L J Marschall
- Technische Universität Braunschweig; Institute of Biochemistry, Biotechnology and Bioinformatics; Braunschweig, Germany
| | - Congcong Zhang
- Georg-Speyer-Haus; Institute for Tumor Biology und experimental Therapy; Frankfurt, Germany
| | - André Frenzel
- Technische Universität Braunschweig; Institute of Biochemistry, Biotechnology and Bioinformatics; Braunschweig, Germany
| | | | - Michael Hust
- Technische Universität Braunschweig; Institute of Biochemistry, Biotechnology and Bioinformatics; Braunschweig, Germany
| | - Franck Perez
- Institut Curie; Centre de Recherche; Paris, France; CNRS UMR144; Paris, France
| | - Stefan Dübel
- Technische Universität Braunschweig; Institute of Biochemistry, Biotechnology and Bioinformatics; Braunschweig, Germany
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181
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Taussig MJ, Schmidt R, Cook EA, Stoevesandt O. Development of proteome-wide binding reagents for research and diagnostics. Proteomics Clin Appl 2014; 7:756-66. [PMID: 24178846 DOI: 10.1002/prca.201300060] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2013] [Revised: 09/09/2013] [Accepted: 09/10/2013] [Indexed: 01/11/2023]
Abstract
Alongside MS, antibodies and other specific protein-binding molecules have a special place in proteomics as affinity reagents in a toolbox of applications for determining protein location, quantitative distribution and function (affinity proteomics). The realisation that the range of research antibodies available, while apparently vast is nevertheless still very incomplete and frequently of uncertain quality, has stimulated projects with an objective of raising comprehensive, proteome-wide sets of protein binders. With progress in automation and throughput, a remarkable number of recent publications refer to the practical possibility of selecting binders to every protein encoded in the genome. Here we review the requirements of a pipeline of production of protein binders for the human proteome, including target prioritisation, antigen design, 'next generation' methods, databases and the approaches taken by ongoing projects in Europe and the USA. While the task of generating affinity reagents for all human proteins is complex and demanding, the benefits of well-characterised and quality-controlled pan-proteome binder resources for biomedical research, industry and life sciences in general would be enormous and justify the effort. Given the technical, personnel and financial resources needed to fulfil this aim, expansion of current efforts may best be addressed through large-scale international collaboration.
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Affiliation(s)
- Michael J Taussig
- Protein Technology Group, The Babraham Institute, Cambridge, UK; Cambridge Protein Arrays Ltd, Babraham Research Campus, Cambridge, UK
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182
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Jalali-Yazdi F, Corbin JM, Takahashi TT, Roberts RW. Robust, quantitative analysis of proteins using peptide immunoreagents, in vitro translation, and an ultrasensitive acoustic resonant sensor. Anal Chem 2014; 86:4715-22. [PMID: 24749546 PMCID: PMC4030805 DOI: 10.1021/ac500084d] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/04/2022]
Abstract
![]()
A major benefit of
proteomic and genomic data is the potential
for developing thousands of novel diagnostic and analytical tests
of cells, tissues, and clinical samples. Monoclonal antibody technologies,
phage display and mRNA display, are methods that could be used to
generate affinity ligands against each member of the proteome. Increasingly,
the challenge is not ligand generation, rather the analysis and affinity
rank-ordering of the many ligands generated by these methods. Here,
we developed a quantitative method to analyze protein interactions
using in vitro translated ligands. In this assay, in vitro translated
ligands generate a signal by simultaneously binding to a target immobilized
on a magnetic bead and to a sensor surface in a commercial acoustic
sensing device. We then normalize the binding of each ligand with
its relative translation efficiency in order to rank-order the different
ligands. We demonstrate the method with peptides directed against
the cancer marker Bcl-xL. Our method has 4- to 10-fold
higher sensitivity, using 100-fold less protein and 5-fold less antibody
per sample, as compared directly with ELISA. Additionally, all analysis
can be conducted in complex mixtures at physiological ionic strength.
Lastly, we demonstrate the ability to use peptides as ultrahigh affinity
reagents that function in complex matrices, as would be needed in
diagnostic applications.
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Affiliation(s)
- Farzad Jalali-Yazdi
- 3710 McClintock Avenue, RTH 507, Los Angeles, California 90089-2905, United States
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183
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Akbani R, Becker KF, Carragher N, Goldstein T, de Koning L, Korf U, Liotta L, Mills GB, Nishizuka SS, Pawlak M, Petricoin EF, Pollard HB, Serrels B, Zhu J. Realizing the promise of reverse phase protein arrays for clinical, translational, and basic research: a workshop report: the RPPA (Reverse Phase Protein Array) society. Mol Cell Proteomics 2014; 13:1625-43. [PMID: 24777629 DOI: 10.1074/mcp.o113.034918] [Citation(s) in RCA: 134] [Impact Index Per Article: 13.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
Reverse phase protein array (RPPA) technology introduced a miniaturized "antigen-down" or "dot-blot" immunoassay suitable for quantifying the relative, semi-quantitative or quantitative (if a well-accepted reference standard exists) abundance of total protein levels and post-translational modifications across a variety of biological samples including cultured cells, tissues, and body fluids. The recent evolution of RPPA combined with more sophisticated sample handling, optical detection, quality control, and better quality affinity reagents provides exquisite sensitivity and high sample throughput at a reasonable cost per sample. This facilitates large-scale multiplex analysis of multiple post-translational markers across samples from in vitro, preclinical, or clinical samples. The technical power of RPPA is stimulating the application and widespread adoption of RPPA methods within academic, clinical, and industrial research laboratories. Advances in RPPA technology now offer scientists the opportunity to quantify protein analytes with high precision, sensitivity, throughput, and robustness. As a result, adopters of RPPA technology have recognized critical success factors for useful and maximum exploitation of RPPA technologies, including the following: preservation and optimization of pre-analytical sample quality, application of validated high-affinity and specific antibody (or other protein affinity) detection reagents, dedicated informatics solutions to ensure accurate and robust quantification of protein analytes, and quality-assured procedures and data analysis workflows compatible with application within regulated clinical environments. In 2011, 2012, and 2013, the first three Global RPPA workshops were held in the United States, Europe, and Japan, respectively. These workshops provided an opportunity for RPPA laboratories, vendors, and users to share and discuss results, the latest technology platforms, best practices, and future challenges and opportunities. The outcomes of the workshops included a number of key opportunities to advance the RPPA field and provide added benefit to existing and future participants in the RPPA research community. The purpose of this report is to share and disseminate, as a community, current knowledge and future directions of the RPPA technology.
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Affiliation(s)
- Rehan Akbani
- From the *University of Texas M.D. Anderson Cancer Center, Houston, Texas
| | | | - Neil Carragher
- §Edinburgh Cancer Research UK Centre, MRC Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, Scotland, UK
| | - Ted Goldstein
- ¶Center for Biomolecular Science and Engineering, University of California, Santa Cruz, California
| | | | - Ulrike Korf
- **German Cancer Research Center (DKFZ), Heidelberg, Germany
| | | | - Gordon B Mills
- From the *University of Texas M.D. Anderson Cancer Center, Houston, Texas
| | | | - Michael Pawlak
- §§§The Natural and Medical Sciences Institute, Reutlingen, Germany
| | | | - Harvey B Pollard
- ¶¶Uniformed Services University of the Health Sciences, Bethesda, Maryland
| | - Bryan Serrels
- §Edinburgh Cancer Research UK Centre, MRC Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, Scotland, UK
| | - Jingchun Zhu
- ¶Center for Biomolecular Science and Engineering, University of California, Santa Cruz, California
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184
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Conroy PJ, Law RHP, Gilgunn S, Hearty S, Caradoc-Davies TT, Lloyd G, O'Kennedy RJ, Whisstock JC. Reconciling the structural attributes of avian antibodies. J Biol Chem 2014; 289:15384-92. [PMID: 24737329 DOI: 10.1074/jbc.m114.562470] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Antibodies are high value therapeutic, diagnostic, biotechnological, and research tools. Combinatorial approaches to antibody discovery have facilitated access to unique antibodies by surpassing the diversity limitations of the natural repertoire, exploitation of immune repertoires from multiple species, and tailoring selections to isolate antibodies with desirable biophysical attributes. The V-gene repertoire of the chicken does not utilize highly diverse sequence and structures, which is in stark contrast to the mechanism employed by humans, mice, and primates. Recent exploitation of the avian immune system has generated high quality, high affinity antibodies to a wide range of antigens for a number of therapeutic, diagnostic and biotechnological applications. Furthermore, extensive examination of the amino acid characteristics of the chicken repertoire has provided significant insight into mechanisms employed by the avian immune system. A paucity of avian antibody crystal structures has limited our understanding of the structural consequences of these uniquely chicken features. This paper presents the crystal structure of two chicken single chain fragment variable (scFv) antibodies generated from large libraries by phage display against important human antigen targets, which capture two unique CDRL1 canonical classes in the presence and absence of a non-canonical disulfide constrained CDRH3. These structures cast light on the unique structural features of chicken antibodies and contribute further to our collective understanding of the unique mechanisms of diversity and biochemical attributes that render the chicken repertoire of particular value for antibody generation.
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Affiliation(s)
- Paul J Conroy
- From the Department of Biochemistry and Molecular Biology, Faculty of Medicine, Nursing and Health Science, Monash University, Melbourne, Victoria 3800, Australia
| | - Ruby H P Law
- From the Department of Biochemistry and Molecular Biology, Faculty of Medicine, Nursing and Health Science, Monash University, Melbourne, Victoria 3800, Australia
| | - Sarah Gilgunn
- School of Biotechnology, Dublin City University, Dublin 9, Ireland
| | - Stephen Hearty
- Biomedical Diagnostics Institute, National Centre for Sensor Research, Dublin City University, Dublin 9, Ireland, and
| | - Tom T Caradoc-Davies
- Australian Synchrotron, 800 Blackburn Road, Clayton, Melbourne, Victoria 3168, Australia
| | - Gordon Lloyd
- From the Department of Biochemistry and Molecular Biology, Faculty of Medicine, Nursing and Health Science, Monash University, Melbourne, Victoria 3800, Australia
| | - Richard J O'Kennedy
- School of Biotechnology, Dublin City University, Dublin 9, Ireland, Biomedical Diagnostics Institute, National Centre for Sensor Research, Dublin City University, Dublin 9, Ireland, and
| | - James C Whisstock
- From the Department of Biochemistry and Molecular Biology, Faculty of Medicine, Nursing and Health Science, Monash University, Melbourne, Victoria 3800, Australia,
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185
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Tiede C, Tang AAS, Deacon SE, Mandal U, Nettleship JE, Owen RL, George SE, Harrison DJ, Owens RJ, Tomlinson DC, McPherson MJ. Adhiron: a stable and versatile peptide display scaffold for molecular recognition applications. Protein Eng Des Sel 2014; 27:145-55. [PMID: 24668773 PMCID: PMC4000234 DOI: 10.1093/protein/gzu007] [Citation(s) in RCA: 109] [Impact Index Per Article: 10.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
We have designed a novel non-antibody scaffold protein, termed Adhiron, based on a phytocystatin consensus sequence. The Adhiron scaffold shows high thermal stability (Tm ca. 101°C), and is expressed well in Escherichia coli. We have determined the X-ray crystal structure of the Adhiron scaffold to 1.75 Å resolution revealing a compact cystatin-like fold. We have constructed a phage-display library in this scaffold by insertion of two variable peptide regions. The library is of high quality and complexity comprising 1.3 × 1010 clones. To demonstrate library efficacy, we screened against the yeast Small Ubiquitin-like Modifier (SUMO). In selected clones, variable region 1 often contained sequences homologous to the known SUMO interactive motif (V/I-X-V/I-V/I). Four Adhirons were further characterised and displayed low nanomolar affinities and high specificity for yeast SUMO with essentially no cross-reactivity to human SUMO protein isoforms. We have identified binders against >100 target molecules to date including as examples, a fibroblast growth factor (FGF1), platelet endothelial cell adhesion molecule (PECAM-1; CD31), the SH2 domain Grb2 and a 12-aa peptide. Adhirons are highly stable and well expressed allowing highly specific binding reagents to be selected for use in molecular recognition applications.
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Affiliation(s)
- Christian Tiede
- Biomedical Health Research Centre, BioScreening Technology Group, University of Leeds, Leeds LS2 9JT, UK
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186
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Pisitkun T, Dummer P, Somparn P, Hirankarn N, Kopp JB, Knepper MA. Integrated Design of Antibodies for Systems Biology Using Ab Designer.. JOURNAL OF PROTEOMICS & BIOINFORMATICS 2014; 7:088-94. [PMID: 25328345 PMCID: PMC4201049 DOI: 10.4172/jpb.1000307] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
In the current era of large-scale biology, systems biology has evolved as a powerful approach to identify complex interactions within biological systems. In addition to high throughput identification and quantification techniques, methods based on high-quality mono-specific antibodies remain an essential element of the approach. To assist the large-scale design and production of peptide-directed antibodies for systems biology studies, we developed a fully integrated online application, AbDesigner (http://helixweb.nih.gov/AbDesigner/), to help researchers select optimal peptide immunogens for antibody generation against relatively disordered regions of target proteins. Here we describe AbDesigner in terms of its features, comparing it to other software tools, and use it to design three antibodies against kidney disease-related proteins in human, viz. nephrin, podocin, and apolipoprotein L1.
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Affiliation(s)
- Trairak Pisitkun
- Epithelial Systems Biology Laboratory, National Heart, Lung and Blood Institute, NIH, Bethesda, MD, USA ; Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand
| | - Patrick Dummer
- Kidney Disease Section, National Institute of Diabetes and Digestive and Kidney Diseases, NIH, Bethesda, MD, USA
| | | | | | - Jeffrey B Kopp
- Kidney Disease Section, National Institute of Diabetes and Digestive and Kidney Diseases, NIH, Bethesda, MD, USA
| | - Mark A Knepper
- Epithelial Systems Biology Laboratory, National Heart, Lung and Blood Institute, NIH, Bethesda, MD, USA
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187
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Iizuka A, Komiyama M, Oshita C, Kume A, Ashizawa T, Mitsuya K, Hayashi N, Nakasu Y, Yamaguchi K, Akiyama Y. Anti-vascular endothelial growth factor receptor (VEGFR) 2 autoantibody identification in glioblastoma patient using single B cell-based antibody gene cloning. Immunol Lett 2014; 159:15-22. [PMID: 24534640 DOI: 10.1016/j.imlet.2014.02.004] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2013] [Revised: 02/04/2014] [Accepted: 02/05/2014] [Indexed: 01/05/2023]
Abstract
Antibody direct cloning from single B cells is simple and efficient and has been successful in antibody identification of infectious diseases. However, although a recent whole-exome sequencing revealed abundant heterogeneic mutation accumulation in cancers, identification and synthesis of autoantibodies against specific cancer-associated antigens is still difficult in cancer patients owing to the very small number of B cells producing autoantibodies. In the present study, to identify autoantibodies targeting tumor antigens, we measured the titer of autoantibodies in high-grade glioma patients' plasma and identified two patients with elevated autoantibodies to a few transmembrane proteins. Specific B cells producing autoantibody against vascular endothelial growth factor receptor (VEGFR) 2 were immunostained with labeled protein and anti-human IgG antibody, and then collected by a single cell sorter. Finally, 22 antibody genes were successfully identified using direct IgG cloning from single B cell mRNA, and two antibody clones were found to have significant VEGFR2-specific binding affinity. The current direct human IgG gene cloning technique for identifying human antibodies derived from IgG-memory B cells avoids time-consuming procedures such as phage display-based antibody-library screening, and therefore may be applicable to identifying human autoantibodies in a variety of disorders including cancers even when antibody elevation is not detected because of a very small number of memory B cells.
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Affiliation(s)
- Akira Iizuka
- Immunotherapy Division, Shizuoka Cancer Center Research Institute, Japan
| | - Masaru Komiyama
- Immunotherapy Division, Shizuoka Cancer Center Research Institute, Japan
| | - Chie Oshita
- Immunotherapy Division, Shizuoka Cancer Center Research Institute, Japan
| | - Akiko Kume
- Immunotherapy Division, Shizuoka Cancer Center Research Institute, Japan
| | - Tadashi Ashizawa
- Immunotherapy Division, Shizuoka Cancer Center Research Institute, Japan
| | - Koichi Mitsuya
- Department of Neurosurgery, Shizuoka Cancer Center Hospital, 1007 Shimonagakubo, Nagaizumi-cho, Sunto-gun, Shizuoka 411-8777, Japan
| | - Nakamasa Hayashi
- Department of Neurosurgery, Shizuoka Cancer Center Hospital, 1007 Shimonagakubo, Nagaizumi-cho, Sunto-gun, Shizuoka 411-8777, Japan
| | - Yoko Nakasu
- Department of Neurosurgery, Shizuoka Cancer Center Hospital, 1007 Shimonagakubo, Nagaizumi-cho, Sunto-gun, Shizuoka 411-8777, Japan
| | - Ken Yamaguchi
- Immunotherapy Division, Shizuoka Cancer Center Research Institute, Japan
| | - Yasuto Akiyama
- Immunotherapy Division, Shizuoka Cancer Center Research Institute, Japan.
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188
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Liu P, Cai Z, Kang JW, Boyle AJ, Adams J, Lu Y, Ngo Ndjock Mbong G, Sidhu S, Reilly RM, Winnik MA. Intracellular routing in breast cancer cells of streptavidin-conjugated trastuzumab Fab fragments linked to biotinylated doxorubicin-functionalized metal chelating polymers. Biomacromolecules 2014; 15:715-25. [PMID: 24506198 DOI: 10.1021/bm401483a] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
We describe the synthesis of a heterotelechelic metal-chelating polymer (Bi-MCP-Dox), a polyacrylamide with a number average degree of polymerization DPn = 50 (PDI = 1.2), with biotin (Bi) and doxorubicin (Dox) as functional chain ends and diethylenetriaminepentaacetic acid (DTPA) pendant groups as the binding sites for metal ions. We compared its behavior in cell-uptake experiments with a similar polymer (Bi-MCP) without Dox. These MCPs were complexed with trastuzumab Fab (tmFab) fragments covalently linked to streptavidin (SAv) to form tmFab-SAv-Bi-MCP-Dox and tmFab-SAv-Bi-MCP via the strong affinity between Bi and SAv. tmFab targets human epidermal growth factor receptor-2 (HER2), which is overexpressed on certain human breast cancer cells. Surface plasmon resonance (SPR) experiments with the extracellular domain (ECD) of HER2 showed that incorporation of the MCPs in these complexes had no significant effect on the association or dissociation rate with the HER2 ECD and the dissociation constants. The tmFab-complexed MCPs were subsequently labeled with (111)In (an Auger electron emitting radionuclide). Auger electrons can cause lethal DNA double strand breaks (DSBs) but only if they are emitted intracellularly and especially, in close proximity to the nucleus. To evaluate the cellular and nuclear uptake of tmFab-SAv-Bi-MCP-Dox, we incubated HER2+ SK-BR-3 human breast cancer cells with the complexes saturated with stable In(3+) and visualized their distribution by confocal fluorescence microscopy, monitoring the fluorescence of Dox. In parallel, we carried out cell fractionation studies on tmFab-SAv-Bi-MCP-Dox and on tmFab-SAv-Bi-MCP labeled with (111)In. Both radiolabeled complexes showed cell internalization and nuclear localization. We conclude that metal-chelating polymers with this composition appear to encourage internalization, nuclear uptake, and chromatin (DNA) binding of trastuzumab fragments modified with streptavidin in human breast cancer cells expressing HER2. Further study is needed to understand the impact of polymer charge on cellular uptake and distribution to intracellular compartments.
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Affiliation(s)
- Peng Liu
- Department of Chemistry, University of Toronto , 80 St. George Street, Toronto, Ontario, Canada , M5S 3H6
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189
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190
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Fung KYC, Nice E, Priebe I, Belobrajdic D, Phatak A, Purins L, Tabor B, Pompeia C, Lockett T, Adams TE, Burgess A, Cosgrove L. Colorectal cancer biomarkers: To be or not to be? Cautionary tales from a road well travelled. World J Gastroenterol 2014; 20:888-898. [PMID: 24574763 PMCID: PMC3921542 DOI: 10.3748/wjg.v20.i4.888] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/26/2013] [Revised: 11/26/2013] [Accepted: 01/06/2014] [Indexed: 02/06/2023] Open
Abstract
Colorectal cancer (CRC) is the second most common cause of cancer-related death worldwide and places a major economic burden on the global health care system. The time frame for development from premalignant to malignant disease typically spans 10-15 years, and this latent period provides an ideal opportunity for early detection and intervention to improve patient outcomes. Currently, early diagnosis of CRC is hampered by a lack of suitable non-invasive biomarkers that are clinically or economically acceptable for population-based screening. New blood-based protein biomarkers for early detection of CRC are therefore urgently required. The success of clinical biomarker discovery and validation studies is critically dependent on understanding and adjusting for potential experimental, analytical, and biological factors that can interfere with the robust interpretation of results. In this review we outline some important considerations for research groups undertaking biomarker research with exemplars from our studies. Implementation of experimental strategies to minimise the potential effects of these problems will facilitate the identification of panels of biomarkers with the sensitivity and specificity required for the development of successful tests for the early detection and surveillance of CRC.
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191
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Hu FJ, Uhlen M, Rockberg J. Generation of HER2 monoclonal antibodies using epitopes of a rabbit polyclonal antibody. N Biotechnol 2014; 31:35-43. [PMID: 24120493 DOI: 10.1016/j.nbt.2013.10.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2013] [Revised: 09/25/2013] [Accepted: 10/01/2013] [Indexed: 10/26/2022]
Abstract
One of the issues in using polyclonal antibodies is the limited amount of reagent available from an immunisation, leading to batch-to-batch variation and difficulties in obtaining the same antibody performance when the same antigen is re-immunised into several separate animals. This led to the development of hybridoma technology allowing, at least theoretically, for an unlimited production of a specific binder. Nevertheless, polyclonal antibodies are widely used in research and diagnostics and there exists a need for robust methods to convert a polyclonal antibody with good binding performance into a renewable monoclonal with identical or similar binding specificity. Here we have used precise information regarding the functional recognition sequence (epitope) of a rabbit polyclonal antibody with attractive binding characteristics as the basis for generation of a renewable mouse monoclonal antibody. First, the original protein fragment antigen was used for immunisation and generation of mouse hybridoma, without obtaining binders to the same epitope region. Instead a peptide designed using the functional epitope and structural information was synthesised and used for hybridoma production. Several of the monoclonal antibodies generated were found to have similar binding characteristics to those of the original polyclonal antibody. These monoclonal antibodies detected native HER2 on cell lines and were also able to stain HER2 in immunohistochemistry using xenografted mice, as well as human normal and cancer tissues.
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Affiliation(s)
- Francis Jingxin Hu
- School of Biotechnology, KTH Royal Institute of Technology, SE-106 91 Stockholm, Sweden
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192
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Stoevesandt O, Taussig MJ. Affinity proteomics: the role of specific binding reagents in human proteome analysis. Expert Rev Proteomics 2014; 9:401-14. [DOI: 10.1586/epr.12.34] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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193
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194
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Hust M, Frenzel A, Schirrmann T, Dübel S. Selection of recombinant antibodies from antibody gene libraries. Methods Mol Biol 2014; 1101:305-20. [PMID: 24233787 DOI: 10.1007/978-1-62703-721-1_14] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Antibodies are indispensable detection reagents for research and diagnostics and represent the biggest class of biological therapeutics on the market. In vitro antibody selection systems offer many advantages over animal-based technologies because the whole selection process is independent of the in vivo immune response. In the last two decades antibody phage display has evolved to the most robust and widely used method and has already yielded thousands of antibodies. The selection of binders by phage display is also referred to as "panning" and based on the specific molecular interaction of antibody phage with an immobilized antigen thus allowing the enrichment and isolation of antigen-specific monoclonal binders from very large antibody gene libraries. Here, we give detailed protocols for the selection of recombinant antibody fragments from antibody gene libraries in microtiter plates.
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Affiliation(s)
- Michael Hust
- Abteilung Biotechnologie, Institut für Biochemie, Biotechnologie und Bioinformatik, Technische Universität Braunschweig, Braunschweig, Germany
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195
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Frenzel A, Kügler J, Wilke S, Schirrmann T, Hust M. Construction of human antibody gene libraries and selection of antibodies by phage display. Methods Mol Biol 2014; 1060:215-243. [PMID: 24037844 DOI: 10.1007/978-1-62703-586-6_12] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
Antibody phage display is the most commonly used in vitro selection technology and has yielded thousands of useful antibodies for research, diagnostics, and therapy.The prerequisite for successful generation and development of human recombinant antibodies using phage display is the construction of a high-quality antibody gene library. Here, we describe the methods for the construction of human immune and naive scFv gene libraries.The success also depends on the panning strategy for the selection of binders from these libraries. In this article, we describe a panning strategy that is high-throughput compatible and allows parallel selection in microtiter plates.
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Affiliation(s)
- André Frenzel
- Abteilung Biotechnologie Technische Universität Braunschweig, Institut für Biochemie, Biotechnologie und Bioinformatik, Braunschweig, Germany
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196
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Abstract
Proteins naturally expressed in eukaryotic organisms often require host chaperones, binding partners, and posttranslational modifications for correct folding. Ideally the heterologous expression system chosen should be as similar to the natural host as possible. For example, mammalian proteins should be expressed in mammalian expression systems. However this does not guarantee a protein will be expressed in a sufficient high yield for structural or biochemical studies or antibody generation. Often a screening process is undertaken in which many variants including truncations, point mutations, investigation of orthologues, fusion to peptide or protein tags at the N- or C-terminus, the co-expression of binding partners, and even culture conditions are varied to identify the optimal expression conditions. This requires multi-parallel expression screening in mammalian cells similar to that already described for E. coli expression. Here we describe in detail a multi-parallel method to express proteins in mammalian suspension cells by transient transfection in 24-well blocks.
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197
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Abstract
Highly functional synthetic antibody libraries can be used to generate antibodies against a multitude of antigens with affinities and specificities that rival or exceed those of natural antibodies. Current design and generation of synthetic antibody libraries are dependent on our insights from previous studies of simplified synthetic antibody libraries, in addition to our knowledge of antibody structure and function and sequence diversity of natural antibody repertoires. We describe a detailed protocol for the design and generation of phage-displayed synthetic antibody libraries built on a single framework with diversity restricted to four complementarity-determining regions by using precisely designed degenerate oligonucleotides. This general methodology could be applied to generation of large, functional synthetic antibody libraries using standard supplies, equipment, and molecular biology techniques.
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Affiliation(s)
- Gang Chen
- University of Toronto, Toronto, ON, Canada
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198
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Engineering protein thermostability using a generic activity-independent biophysical screen inside the cell. Nat Commun 2013; 4:2901. [DOI: 10.1038/ncomms3901] [Citation(s) in RCA: 67] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2013] [Accepted: 11/08/2013] [Indexed: 11/08/2022] Open
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199
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Oligopeptide m13 phage display in pathogen research. Viruses 2013; 5:2531-45. [PMID: 24136040 PMCID: PMC3814601 DOI: 10.3390/v5102531] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2013] [Revised: 10/08/2013] [Accepted: 10/09/2013] [Indexed: 12/19/2022] Open
Abstract
Phage display has become an established, widely used method for selection of peptides, antibodies or alternative scaffolds. The use of phage display for the selection of antigens from genomic or cDNA libraries of pathogens which is an alternative to the classical way of identifying immunogenic proteins is not well-known. In recent years several new applications for oligopeptide phage display in disease related fields have been developed which has led to the identification of various new antigens. These novel identified immunogenic proteins provide new insights into host pathogen interactions and can be used for the development of new diagnostic tests and vaccines. In this review we focus on the M13 oligopeptide phage display system for pathogen research but will also give examples for lambda phage display and for applications in other disease related fields. In addition, a detailed technical work flow for the identification of immunogenic oligopeptides using the pHORF system is given. The described identification of immunogenic proteins of pathogens using oligopeptide phage display can be linked to antibody phage display resulting in a vaccine pipeline.
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200
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