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Hanna R, Cardarelli L, Patel N, Blazer LL, Adams JJ, Sidhu SS. A phage-displayed single-chain Fab library optimized for rapid production of single-chain IgGs. Protein Sci 2020; 29:2075-2084. [PMID: 32803886 DOI: 10.1002/pro.3931] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2019] [Revised: 08/10/2020] [Accepted: 08/11/2020] [Indexed: 12/25/2022]
Abstract
Phage-displayed synthetic antibody (Ab) repertoires have become a major source of affinity reagents for basic and clinical research. Specific Abs identified from such libraries are often screened as fragments antigen binding (Fabs) produced in bacteria, and those with desired biochemical characteristics are reformatted for production as full-length immunoglobulin G (IgG) in mammalian cells. The conversion of Fabs to IgGs is a cumbersome and often rate-limiting step in the development of Abs. Moreover, biochemical properties required for lead IgG development are not always shared by the Fabs, and these issues are not uncovered until a significant effort has been spent on Abs that ultimately will not be useful. Thus, there is a need for simple and rapid techniques to convert phage-displayed Fabs to IgGs at an early stage of the Ab screening process. We report the generation of a highly diverse phage-displayed synthetic single-chain Fab (scFab) library, in which the light and heavy chains were tethered with an optimized linker. Following selection, pools of scFabs were converted to single-chain IgGs (scIgGs) en masse, enabling facile screening of hundreds of phage-derived scIgGs. We show that this approach can be used to rapidly screen for and select scIgGs that target cell-surface receptors, and scIgGs behave the same as conventional IgGs.
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Affiliation(s)
- Rachel Hanna
- Department of Molecular Genetics, Donnelly Centre, University of Toronto, Toronto, Ontario, Canada
| | - Lia Cardarelli
- Department of Molecular Genetics, Donnelly Centre, University of Toronto, Toronto, Ontario, Canada
| | - Nish Patel
- Department of Molecular Genetics, Donnelly Centre, University of Toronto, Toronto, Ontario, Canada
| | - Levi L Blazer
- Department of Molecular Genetics, Donnelly Centre, University of Toronto, Toronto, Ontario, Canada
| | - Jarrett J Adams
- Department of Molecular Genetics, Donnelly Centre, University of Toronto, Toronto, Ontario, Canada
| | - Sachdev S Sidhu
- Department of Molecular Genetics, Donnelly Centre, University of Toronto, Toronto, Ontario, Canada
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2
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Verma V, Joshi G, Gupta A, Chaudhary VK. An efficient ORF selection system for DNA fragment libraries based on split beta-lactamase complementation. PLoS One 2020; 15:e0235853. [PMID: 32701967 PMCID: PMC7377443 DOI: 10.1371/journal.pone.0235853] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2020] [Accepted: 06/23/2020] [Indexed: 11/29/2022] Open
Abstract
PCR-based amplification of annotated genes has allowed construction of expression clones at genome-scale using classical and recombination-based cloning technologies. However, genome-scale expression and purification of proteins for down-stream applications is often limited by challenges such as poor expression, low solubility, large size of multi-domain proteins, etc. Alternatively, DNA fragment libraries in expression vectors can serve as the source of protein fragments with each fragment encompassing a function of its whole protein counterpart. However, the random DNA fragmentation and cloning result in only 1 out of 18 clones being in the correct open-reading frame (ORF), thus, reducing the overall efficiency of the system. This necessitates the selection of correct ORF before expressing the protein fragments. This paper describes a highly efficient ORF selection system for DNA fragment libraries, which is based on split beta-lactamase protein fragment complementation. The system has been designed to allow seamless transfer of selected DNA fragment libraries into any downstream vector systems using a restriction enzyme-free cloning strategy. The strategy has been applied for the selection of ORF using model constructs to show near 100% selection of the clone encoding correct ORF. The system has been further validated by construction of an ORF-selected DNA fragment library of 30 genes of M. tuberculosis. Further, we have successfully demonstrated the cytosolic expression of ORF-selected protein fragments in E. coli.
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Affiliation(s)
- Vaishali Verma
- Centre for Innovation in Infectious Disease Research, Education and Training (CIIDRET), University of Delhi South Campus, New Delhi, India
| | - Gopal Joshi
- Centre for Innovation in Infectious Disease Research, Education and Training (CIIDRET), University of Delhi South Campus, New Delhi, India
| | - Amita Gupta
- Centre for Innovation in Infectious Disease Research, Education and Training (CIIDRET), University of Delhi South Campus, New Delhi, India
- Department of Biochemistry, University of Delhi South Campus, New Delhi, India
| | - Vijay K. Chaudhary
- Centre for Innovation in Infectious Disease Research, Education and Training (CIIDRET), University of Delhi South Campus, New Delhi, India
- Department of Biochemistry, University of Delhi South Campus, New Delhi, India
- * E-mail:
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3
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Wang Z, Li Y, Hou B, Pronobis MI, Wang M, Wang Y, Cheng G, Weng W, Wang Y, Tang Y, Xu X, Pan R, Lin F, Wang N, Chen Z, Wang S, Ma LZ, Li Y, Huang D, Jiang L, Wang Z, Zeng W, Zhang Y, Du X, Lin Y, Li Z, Xia Q, Geng J, Dai H, Yu Y, Zhao XD, Yuan Z, Yan J, Nie Q, Zhang X, Wang K, Chen F, Zhang Q, Zhu Y, Zheng S, Poss KD, Tao SC, Meng X. An array of 60,000 antibodies for proteome-scale antibody generation and target discovery. SCIENCE ADVANCES 2020; 6:eaax2271. [PMID: 32195335 PMCID: PMC7065887 DOI: 10.1126/sciadv.aax2271] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/05/2019] [Accepted: 12/13/2019] [Indexed: 05/28/2023]
Abstract
Antibodies are essential for elucidating gene function. However, affordable technology for proteome-scale antibody generation does not exist. To address this, we developed Proteome Epitope Tag Antibody Library (PETAL) and its array. PETAL consists of 62,208 monoclonal antibodies (mAbs) against 15,199 peptides from diverse proteomes. PETAL harbors binders for a great multitude of proteins in nature due to antibody multispecificity, an intrinsic antibody feature. Distinctive combinations of 10,000 to 20,000 mAbs were found to target specific proteomes by array screening. Phenotype-specific mAb-protein pairs were found for maize and zebrafish samples. Immunofluorescence and flow cytometry mAbs for membrane proteins and chromatin immunoprecipitation-sequencing mAbs for transcription factors were identified from respective proteome-binding PETAL mAbs. Differential screening of cell surface proteomes of tumor and normal tissues identified internalizing tumor antigens for antibody-drug conjugates. By finding high-affinity mAbs at a fraction of current time and cost, PETAL enables proteome-scale antibody generation and target discovery.
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Affiliation(s)
- Zhaohui Wang
- School of Life Sciences, Northwest University, Xi’an, Shanxi 710069, China
- Abmart, 333 Guiping Road, Shanghai 200033, China
| | - Yang Li
- Shanghai Center for Systems Biomedicine, Key Laboratory of Systems Biomedicine (Ministry of Education), Shanghai Jiao Tong University, Shanghai 200240, China
| | - Bing Hou
- School of Life Sciences, Northwest University, Xi’an, Shanxi 710069, China
- Abmart, 333 Guiping Road, Shanghai 200033, China
| | - Mira I. Pronobis
- Department of Cell Biology, Duke University Medical Center, Durham, NC 27710, USA
| | | | - Yuemeng Wang
- Abmart, 333 Guiping Road, Shanghai 200033, China
| | | | - Weining Weng
- Abmart, 333 Guiping Road, Shanghai 200033, China
| | - Yiqiang Wang
- Abmart, 333 Guiping Road, Shanghai 200033, China
| | - Yanfang Tang
- Abmart, 333 Guiping Road, Shanghai 200033, China
| | - Xuefan Xu
- Abmart, 333 Guiping Road, Shanghai 200033, China
| | - Rong Pan
- Abmart, 333 Guiping Road, Shanghai 200033, China
| | - Fei Lin
- Abmart, 333 Guiping Road, Shanghai 200033, China
| | - Nan Wang
- Shanghai Center for Systems Biomedicine, Key Laboratory of Systems Biomedicine (Ministry of Education), Shanghai Jiao Tong University, Shanghai 200240, China
| | - Ziqing Chen
- Shanghai Center for Systems Biomedicine, Key Laboratory of Systems Biomedicine (Ministry of Education), Shanghai Jiao Tong University, Shanghai 200240, China
| | - Shiwei Wang
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
| | - Luyan zulie Ma
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
| | - Yangrui Li
- Guangxi Key Laboratory of Sugarcane Genetic Improvement/Key Laboratory of Sugarcane Biotechnology and Genetic Improvement (Guangxi), Ministry of Agriculture, Nanning, Guangxi 530007, China
| | - Dongliang Huang
- Guangxi Key Laboratory of Sugarcane Genetic Improvement/Key Laboratory of Sugarcane Biotechnology and Genetic Improvement (Guangxi), Ministry of Agriculture, Nanning, Guangxi 530007, China
| | - Li Jiang
- Key Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture and National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China
| | - Zhiqiang Wang
- Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou, Henan 450009, China
| | - Wenfang Zeng
- Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou, Henan 450009, China
| | - Ying Zhang
- Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou, Henan 450009, China
| | - Xuemei Du
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100083, China
| | - Ying Lin
- State Key Laboratory of Silkworm Genome Biology, Southwest University, Chongqing 400716, China
| | - Zhiqing Li
- State Key Laboratory of Silkworm Genome Biology, Southwest University, Chongqing 400716, China
| | - Qingyou Xia
- State Key Laboratory of Silkworm Genome Biology, Southwest University, Chongqing 400716, China
| | - Jing Geng
- Department of Pulmonary and Critical Care Medicine, Center of Respiratory Medicine, China-Japan Friendship Hospital, National Clinical Research Center for Respiratory Diseases, Beijing 100029, China
| | - Huaping Dai
- Department of Pulmonary and Critical Care Medicine, Center of Respiratory Medicine, China-Japan Friendship Hospital, National Clinical Research Center for Respiratory Diseases, Beijing 100029, China
| | - Yuan Yu
- School of Life Sciences, Northwest University, Xi’an, Shanxi 710069, China
| | - Xiao-dong Zhao
- School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Zheng Yuan
- School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Jian Yan
- Ludwig Institute for Cancer Research, 9500 Gilman Dr., La Jolla, CA 92093, USA
- Department of Medical Biochemistry and Biophysics, Division of Functional Genomics and Systems Biology, Karolinska Institutet, 171 65 Stockholm, Sweden
| | - Qinghua Nie
- College of Animal Science, South China Agricultural University, Guangzhou, Guangdong 510642, China
- Guangdong Provincial Key Laboratory of Agro-Animal Genomics and Molecular Breeding, and Key Laboratory of Chicken Genetics, Breeding and Reproduction, Ministry of Agriculture, South China Agricultural University, Guangzhou, Guangdong 510642, China
| | - Xiquan Zhang
- College of Animal Science, South China Agricultural University, Guangzhou, Guangdong 510642, China
- Guangdong Provincial Key Laboratory of Agro-Animal Genomics and Molecular Breeding, and Key Laboratory of Chicken Genetics, Breeding and Reproduction, Ministry of Agriculture, South China Agricultural University, Guangzhou, Guangdong 510642, China
| | - Kun Wang
- Institute for Advanced Studies and College of Life Sciences, Wuhan University, Wuhan, China
| | - Fulin Chen
- School of Life Sciences, Northwest University, Xi’an, Shanxi 710069, China
| | - Qin Zhang
- Key Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture and National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China
| | - Yuxian Zhu
- Institute for Advanced Studies and College of Life Sciences, Wuhan University, Wuhan, China
| | - Susan Zheng
- Department of Cell Biology, Duke University Medical Center, Durham, NC 27710, USA
| | - Kenneth D. Poss
- Department of Cell Biology, Duke University Medical Center, Durham, NC 27710, USA
| | - Sheng-ce Tao
- Shanghai Center for Systems Biomedicine, Key Laboratory of Systems Biomedicine (Ministry of Education), Shanghai Jiao Tong University, Shanghai 200240, China
- School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai 200240, China
- State Key Laboratory of Oncogenes and Related Genes, Shanghai 200240, China
| | - Xun Meng
- School of Life Sciences, Northwest University, Xi’an, Shanxi 710069, China
- Abmart, 333 Guiping Road, Shanghai 200033, China
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4
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Russo G, Theisen U, Fahr W, Helmsing S, Hust M, Köster RW, Dübel S. Sequence defined antibodies improve the detection of cadherin 2 (N-cadherin) during zebrafish development. N Biotechnol 2018; 45:98-112. [DOI: 10.1016/j.nbt.2017.12.008] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2017] [Revised: 12/26/2017] [Accepted: 12/27/2017] [Indexed: 12/18/2022]
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5
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Frenzel A, Kügler J, Helmsing S, Meier D, Schirrmann T, Hust M, Dübel S. Designing Human Antibodies by Phage Display. Transfus Med Hemother 2017; 44:312-318. [PMID: 29070976 DOI: 10.1159/000479633] [Citation(s) in RCA: 60] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2017] [Accepted: 07/18/2017] [Indexed: 12/13/2022] Open
Abstract
With six approved products and more than 60 candidates in clinical testing, human monoclonal antibody discovery by phage display is well established as a robust and reliable source for the generation of therapeutic antibodies. While a vast diversity of library generation philosophies and selection strategies have been conceived, the power of molecular design offered by controlling the in vitro selection step is still to be recognized by a broader audience outside of the antibody engineering community. Here, we summarize some opportunities and achievements, e.g., the generation of antibodies which could not be generated otherwise, and the design of antibody properties by different panning strategies, including the adjustment of kinetic parameters.
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Affiliation(s)
- André Frenzel
- Institute of Biochemistry, Biotechnology and Bioinformatics, Department of Biotechnology, Technische Universität Braunschweig, Braunschweig, Germany.,Yumab GmbH, Braunschweig, Germany
| | | | - Saskia Helmsing
- Institute of Biochemistry, Biotechnology and Bioinformatics, Department of Biotechnology, Technische Universität Braunschweig, Braunschweig, Germany
| | - Doris Meier
- Institute of Biochemistry, Biotechnology and Bioinformatics, Department of Biotechnology, Technische Universität Braunschweig, Braunschweig, Germany
| | | | - Michael Hust
- Institute of Biochemistry, Biotechnology and Bioinformatics, Department of Biotechnology, Technische Universität Braunschweig, Braunschweig, Germany
| | - Stefan Dübel
- Institute of Biochemistry, Biotechnology and Bioinformatics, Department of Biotechnology, Technische Universität Braunschweig, Braunschweig, Germany
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6
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Säll A, Walle M, Wingren C, Müller S, Nyman T, Vala A, Ohlin M, Borrebaeck CAK, Persson H. Generation and analyses of human synthetic antibody libraries and their application for protein microarrays. Protein Eng Des Sel 2016; 29:427-437. [DOI: 10.1093/protein/gzw042] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2016] [Accepted: 07/21/2016] [Indexed: 11/12/2022] Open
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7
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Antibodies inside of a cell can change its outside: Can intrabodies provide a new therapeutic paradigm? Comput Struct Biotechnol J 2016; 14:304-8. [PMID: 27570612 PMCID: PMC4990636 DOI: 10.1016/j.csbj.2016.07.003] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2016] [Revised: 07/25/2016] [Accepted: 07/26/2016] [Indexed: 11/21/2022] Open
Abstract
Challenges posed by complex diseases such as cancer, chronic viral infections, neurodegenerative disorders and many others have forced researchers to think beyond classic small molecule drugs, exploring new therapeutic strategies such as therapy with RNAi, CRISPR/Cas9 or antibody therapies as single or as combination therapies with existing drugs. While classic antibody therapies based on parenteral application can only reach extracellular targets, intracellular application of antibodies could provide specific advantages but is so far little recognized in translational research. Intrabodies allow high specificity and targeting of splice variants or post translational modifications. At the same time off target effects can be minimized by thorough biochemical characterization. Knockdown of cellular proteins by intrabodies has been reported for a significant number of disease-relevant targets, including ErbB-2, EGFR, VEGFR-2, Metalloproteinase MMP2 and MMP9, β-amyloid protein, α-synuclein, HIV gp120, HCV core and many others. This review outlines the recent advances in ER intrabody technology and their potential use in therapy.
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8
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Jeon J, Arnold R, Singh F, Teyra J, Braun T, Kim PM. PAT: predictor for structured units and its application for the optimization of target molecules for the generation of synthetic antibodies. BMC Bioinformatics 2016; 17:150. [PMID: 27039071 PMCID: PMC4818438 DOI: 10.1186/s12859-016-1001-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2016] [Accepted: 03/23/2016] [Indexed: 11/22/2022] Open
Abstract
Background The identification of structured units in a protein sequence is an important first step for most biochemical studies. Importantly for this study, the identification of stable structured region is a crucial first step to generate novel synthetic antibodies. While many approaches to find domains or predict structured regions exist, important limitations remain, such as the optimization of domain boundaries and the lack of identification of non-domain structured units. Moreover, no integrated tool exists to find and optimize structural domains within protein sequences. Results Here, we describe a new tool, PAT (http://www.kimlab.org/software/pat) that can efficiently identify both domains (with optimized boundaries) and non-domain putative structured units. PAT automatically analyzes various structural properties, evaluates the folding stability, and reports possible structural domains in a given protein sequence. For reliability evaluation of PAT, we applied PAT to identify antibody target molecules based on the notion that soluble and well-defined protein secondary and tertiary structures are appropriate target molecules for synthetic antibodies. Conclusion PAT is an efficient and sensitive tool to identify structured units. A performance analysis shows that PAT can characterize structurally well-defined regions in a given sequence and outperforms other efforts to define reliable boundaries of domains. Specially, PAT successfully identifies experimentally confirmed target molecules for antibody generation. PAT also offers the pre-calculated results of 20,210 human proteins to accelerate common queries. PAT can therefore help to investigate large-scale structured domains and improve the success rate for synthetic antibody generation. Electronic supplementary material The online version of this article (doi:10.1186/s12859-016-1001-1) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Jouhyun Jeon
- Terrence Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, M5S 3E1, ON, Canada
| | - Roland Arnold
- Terrence Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, M5S 3E1, ON, Canada
| | - Fateh Singh
- Terrence Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, M5S 3E1, ON, Canada
| | - Joan Teyra
- Terrence Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, M5S 3E1, ON, Canada
| | - Tatjana Braun
- Terrence Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, M5S 3E1, ON, Canada
| | - Philip M Kim
- Terrence Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, M5S 3E1, ON, Canada. .,Department of Molecular Genetics, University of Toronto, Toronto, M5S 3E1, ON, Canada. .,Department of Computer Science, University of Toronto, Toronto, M5S 3E1, ON, Canada.
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9
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Groff K, Brown J, Clippinger AJ. Modern affinity reagents: Recombinant antibodies and aptamers. Biotechnol Adv 2015; 33:1787-98. [PMID: 26482034 DOI: 10.1016/j.biotechadv.2015.10.004] [Citation(s) in RCA: 80] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2015] [Revised: 10/09/2015] [Accepted: 10/12/2015] [Indexed: 12/13/2022]
Abstract
Affinity reagents are essential tools in both basic and applied research; however, there is a growing concern about the reproducibility of animal-derived monoclonal antibodies. The need for higher quality affinity reagents has prompted the development of methods that provide scientific, economic, and time-saving advantages and do not require the use of animals. This review describes two types of affinity reagents, recombinant antibodies and aptamers, which are non-animal technologies that can replace the use of animal-derived monoclonal antibodies. Recombinant antibodies are protein-based reagents, while aptamers are nucleic-acid-based. In light of the scientific advantages of these technologies, this review also discusses ways to gain momentum in the use of modern affinity reagents, including an update to the 1999 National Academy of Sciences monoclonal antibody production report and federal incentives for recombinant antibody and aptamer efforts. In the long-term, these efforts have the potential to improve the overall quality and decrease the cost of scientific research.
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Affiliation(s)
- Katherine Groff
- PETA International Science Consortium Ltd., Society Building, 8 All Saints Street, London N1 9RL, England.
| | - Jeffrey Brown
- PETA International Science Consortium Ltd., Society Building, 8 All Saints Street, London N1 9RL, England.
| | - Amy J Clippinger
- PETA International Science Consortium Ltd., Society Building, 8 All Saints Street, London N1 9RL, England.
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10
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Roncador G, Engel P, Maestre L, Anderson AP, Cordell JL, Cragg MS, Šerbec VČ, Jones M, Lisnic VJ, Kremer L, Li D, Koch-Nolte F, Pascual N, Rodríguez-Barbosa JI, Torensma R, Turley H, Pulford K, Banham AH. The European antibody network's practical guide to finding and validating suitable antibodies for research. MAbs 2015; 8:27-36. [PMID: 26418356 PMCID: PMC4966524 DOI: 10.1080/19420862.2015.1100787] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Antibodies are widely exploited as research/diagnostic tools and therapeutics. Despite providing exciting research opportunities, the multitude of available antibodies also offers a bewildering array of choice. Importantly, not all companies comply with the highest standards, and thus many reagents fail basic validation tests. The responsibility for antibodies being fit for purpose rests, surprisingly, with their user. This paper condenses the extensive experience of the European Monoclonal Antibody Network to help researchers identify antibodies specific for their target antigen. A stepwise strategy is provided for prioritising antibodies and making informed decisions regarding further essential validation requirements. Web-based antibody validation guides provide practical approaches for testing antibody activity and specificity. We aim to enable researchers with little or no prior experience of antibody characterization to understand how to determine the suitability of their antibody for its intended purpose, enabling both time and cost effective generation of high quality antibody-based data fit for publication.
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Affiliation(s)
- Giovanna Roncador
- a Monoclonal Antibody Unit; Spanish National Cancer Research Center ; Madrid , Spain
| | - Pablo Engel
- b Immunology Unit, Department of Cell Biology; Immunology and Neurosciences ; Medical School, University of Barcelona ; Spain
| | - Lorena Maestre
- a Monoclonal Antibody Unit; Spanish National Cancer Research Center ; Madrid , Spain
| | - Amanda P Anderson
- c NDCLS, Radcliffe Department of Medicine ; University of Oxford ; Oxford , UK
| | | | - Mark S Cragg
- e Antibody and Vaccine Group; Cancer Sciences Unit; University of Southampton; Faculty of Medicine; General Hospital , Southampton , UK
| | - Vladka Č Šerbec
- f Center for the Production of Diagnostic Reagents and for Research; Blood Transfusion Center of Slovenia ; Ljubljana , Slovenia
| | - Margaret Jones
- c NDCLS, Radcliffe Department of Medicine ; University of Oxford ; Oxford , UK
| | - Vanda J Lisnic
- g Center for Proteomics; Faculty of Medicine; University of Rijeka ; Rijeka , Croatia
| | - Leonor Kremer
- h Department of Immunology and Oncology ; Spanish National Center for Biotechnology; Consejo Superior de Investigaciones Científicas (CNB/CSIC) ; Madrid , Spain
| | - Demin Li
- c NDCLS, Radcliffe Department of Medicine ; University of Oxford ; Oxford , UK
| | | | - Núria Pascual
- j Custom Antibody Service (CAbS); IQAC-CSIC/CIBER-BBN ; Barcelona , Spain
| | | | - Ruurd Torensma
- l Department of Tumorimmunology ; Radboud University Medical Center ; Nijmegen , The Netherlands
| | - Helen Turley
- c NDCLS, Radcliffe Department of Medicine ; University of Oxford ; Oxford , UK
| | - Karen Pulford
- c NDCLS, Radcliffe Department of Medicine ; University of Oxford ; Oxford , UK
| | - Alison H Banham
- c NDCLS, Radcliffe Department of Medicine ; University of Oxford ; Oxford , UK
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11
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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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12
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Huang H, Economopoulos NO, Liu BA, Uetrecht A, Gu J, Jarvik N, Nadeem V, Pawson T, Moffat J, Miersch S, Sidhu SS. Selection of recombinant anti-SH3 domain antibodies by high-throughput phage display. Protein Sci 2015; 24:1890-900. [PMID: 26332758 DOI: 10.1002/pro.2799] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2015] [Accepted: 08/26/2015] [Indexed: 01/01/2023]
Abstract
Antibodies are indispensable tools in biochemical research and play an expanding role as therapeutics. While hybridoma technology is the dominant method for antibody production, phage display is an emerging technology. Here, we developed and employed a high-throughput pipeline that enables selection of antibodies against hundreds of antigens in parallel. Binding selections using a phage-displayed synthetic antigen-binding fragment (Fab) library against 110 human SH3 domains yielded hundreds of Fabs targeting 58 antigens. Affinity assays demonstrated that representative Fabs bind tightly and specifically to their targets. Furthermore, we developed an efficient affinity maturation strategy adaptable to high-throughput, which increased affinity dramatically but did not compromise specificity. Finally, we tested Fabs in common cell biology applications and confirmed recognition of the full-length antigen in immunoprecipitation, immunoblotting and immunofluorescence assays. In summary, we have established a rapid and robust high-throughput methodology that can be applied to generate highly functional and renewable antibodies targeting protein domains on a proteome-wide scale.
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Affiliation(s)
- Haiming Huang
- The Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, Ontario, Canada, M5S 3E1.,Banting and Best Department of Medical Research, University of Toronto, Toronto, Ontario, Canada, M5S 3E1
| | - Nicolas O Economopoulos
- The Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, Ontario, Canada, M5S 3E1.,Banting and Best Department of Medical Research, University of Toronto, Toronto, Ontario, Canada, M5S 3E1
| | - Bernard A Liu
- Samuel Lunenfeld Research Institute, Mount Sinai Hospital, University of Toronto, Toronto, Ontario, Canada, M5S 3E1.,Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada, M5S 3E1
| | - Andrea Uetrecht
- The 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 3E1
| | - Jun Gu
- The Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, Ontario, Canada, M5S 3E1.,Banting and Best Department of Medical Research, University of Toronto, Toronto, Ontario, Canada, M5S 3E1
| | - Nick Jarvik
- The Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, Ontario, Canada, M5S 3E1
| | - Vincent Nadeem
- The Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, Ontario, Canada, M5S 3E1.,Banting and Best Department of Medical Research, University of Toronto, Toronto, Ontario, Canada, M5S 3E1
| | - Tony Pawson
- Samuel Lunenfeld Research Institute, Mount Sinai Hospital, University of Toronto, Toronto, Ontario, Canada, M5S 3E1.,Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada, M5S 3E1
| | - Jason Moffat
- The 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 3E1
| | - Shane Miersch
- The Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, Ontario, Canada, M5S 3E1.,Banting and Best Department of Medical Research, University of Toronto, Toronto, Ontario, Canada, M5S 3E1
| | - Sachdev S Sidhu
- The Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, Ontario, Canada, M5S 3E1.,Banting and Best Department of Medical Research, University of Toronto, Toronto, Ontario, Canada, M5S 3E1.,Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada, M5S 3E1
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13
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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: 86] [Impact Index Per Article: 9.6] [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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14
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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: 77] [Impact Index Per Article: 8.6] [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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15
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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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16
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Parker SJ, Raedschelders K, Van Eyk JE. Emerging proteomic technologies for elucidating context-dependent cellular signaling events: A big challenge of tiny proportions. Proteomics 2015; 15:1486-502. [PMID: 25545106 DOI: 10.1002/pmic.201400448] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2014] [Revised: 10/31/2014] [Accepted: 12/23/2014] [Indexed: 12/11/2022]
Abstract
Aberrant cell signaling events either drive or compensate for nearly all pathologies. A thorough description and quantification of maladaptive signaling flux in disease is a critical step in drug development, and complex proteomic approaches can provide valuable mechanistic insights. Traditional proteomics-based signaling analyses rely heavily on in vitro cellular monoculture. The characterization of these simplified systems generates a rich understanding of the basic components and complex interactions of many signaling networks, but they cannot capture the full complexity of the microenvironments in which pathologies are ultimately made manifest. Unfortunately, techniques that can directly interrogate signaling in situ often yield mass-limited starting materials that are incompatible with traditional proteomics workflows. This review provides an overview of established and emerging techniques that are applicable to context-dependent proteomics. Analytical approaches are illustrated through recent proteomics-based studies in which selective sample acquisition strategies preserve context-dependent information, and where the challenge of minimal starting material is met by optimized sensitivity and coverage. This review is organized into three major technological themes: (i) LC methods in line with MS; (ii) antibody-based approaches; (iii) MS imaging with a discussion of data integration and systems modeling. Finally, we conclude with future perspectives and implications of context-dependent proteomics.
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Affiliation(s)
- Sarah J Parker
- Department of Medicine, McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University, Baltimore, MD, USA; Advanced Clinical Biosystems Research Institute, Los Angeles, CA, USA; Heart Institute, Cedars-Sinai Medical Center, Los Angeles, CA, USA; Department of Medicine, Cedars-Sinai Medical Center, Los Angeles, CA, USA
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17
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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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18
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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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19
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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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20
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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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21
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Gadermaier E, Levin M, Flicker S, Ohlin M. The human IgE repertoire. Int Arch Allergy Immunol 2013; 163:77-91. [PMID: 24296690 DOI: 10.1159/000355947] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
IgE is a key mediator in allergic diseases. However, in strong contrast to other antibody isotypes, many details of the composition of the human IgE repertoire are poorly defined. The low levels of human IgE in the circulation and the rarity of IgE-producing B cells are important reasons for this lack of knowledge. In this review, we summarize the current knowledge on these repertoires both in terms of their complexity and activity, i.e. knowledge which despite the difficulties encountered when studying the molecular details of human IgE has been acquired in recent years. We also take a look at likely future developments, for instance through improvements in sequencing technology and methodology that allow the isolation of additional allergen-specific human antibodies mimicking IgE, as this certainly will support our understanding of human IgE in the context of human disease in the years to come.
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Affiliation(s)
- Elisabeth Gadermaier
- Division of Immunopathology, Department of Pathophysiology, Center for Pathophysiology, Infectiology and Immunology, Medical University of Vienna, Vienna, Austria
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22
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Ding X, Yang KL. Antibody-free Detection of Human Chorionic Gonadotropin by Use of Liquid Crystals. Anal Chem 2013; 85:10710-6. [DOI: 10.1021/ac400732n] [Citation(s) in RCA: 50] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Xiaokang Ding
- Department of Chemical and
Biomolecular Engineering, National University of Singapore, 4 Engineering
Drive 4, Singapore 117585
| | - Kun-Lin Yang
- Department of Chemical and
Biomolecular Engineering, National University of Singapore, 4 Engineering
Drive 4, Singapore 117585
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23
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Koerber JT, Thomsen ND, Hannigan BT, Degrado WF, Wells JA. Nature-inspired design of motif-specific antibody scaffolds. Nat Biotechnol 2013; 31:916-21. [PMID: 23955275 PMCID: PMC3795957 DOI: 10.1038/nbt.2672] [Citation(s) in RCA: 56] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2013] [Accepted: 07/17/2013] [Indexed: 12/26/2022]
Abstract
Aberrant changes in post-translational modifications (PTMs) such as phosphorylation underlie a majority of human diseases. However, detection and quantification of PTMs for diagnostic or biomarker applications often requires monoclonal PTM-specific antibodies, which are challenging to generate using traditional antibody-generation platforms. Here we outline a general strategy for producing synthetic PTM-specific antibodies by engineering a motif-specific ‘hot spot’ into an antibody scaffold. Inspired by a natural phosphate-binding motif, we designed antibody scaffolds with hot spots specific for phosphoserine, phosphothreonine, or phosphotyrosine. Crystal structures of the phospho-specific antibodies revealed two distinct modes of phosphoresidue recognition. Our data suggest that each hot spot functions independently of the surrounding scaffold, as phage display antibody libraries using these scaffolds yielded >50 phospho- and target-specific antibodies against 70% of target peptides. Ultimately, our motif-specific scaffold strategy may provide a general solution for the rapid, robust development of monoclonal anti-PTM antibodies for signaling, diagnostic and therapeutic applications.
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Affiliation(s)
- James T Koerber
- Department of Pharmaceutical Chemistry, University of California, San Francisco, California, USA
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24
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Frenzel A, Hust M, Schirrmann T. Expression of recombinant antibodies. Front Immunol 2013; 4:217. [PMID: 23908655 PMCID: PMC3725456 DOI: 10.3389/fimmu.2013.00217] [Citation(s) in RCA: 219] [Impact Index Per Article: 19.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2013] [Accepted: 07/15/2013] [Indexed: 12/15/2022] Open
Abstract
Recombinant antibodies are highly specific detection probes in research, diagnostics, and have emerged over the last two decades as the fastest growing class of therapeutic proteins. Antibody generation has been dramatically accelerated by in vitro selection systems, particularly phage display. An increasing variety of recombinant production systems have been developed, ranging from Gram-negative and positive bacteria, yeasts and filamentous fungi, insect cell lines, mammalian cells to transgenic plants and animals. Currently, almost all therapeutic antibodies are still produced in mammalian cell lines in order to reduce the risk of immunogenicity due to altered, non-human glycosylation patterns. However, recent developments of glycosylation-engineered yeast, insect cell lines, and transgenic plants are promising to obtain antibodies with "human-like" post-translational modifications. Furthermore, smaller antibody fragments including bispecific antibodies without any glycosylation are successfully produced in bacteria and have advanced to clinical testing. The first therapeutic antibody products from a non-mammalian source can be expected in coming next years. In this review, we focus on current antibody production systems including their usability for different applications.
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Affiliation(s)
- André Frenzel
- Abteilung Biotechnologie, Institut für Biochemie, Biotechnologie und Bioinformatik, Technische Universität Braunschweig, Braunschweig, Germany
| | - Michael Hust
- Abteilung Biotechnologie, Institut für Biochemie, Biotechnologie und Bioinformatik, Technische Universität Braunschweig, Braunschweig, Germany
| | - Thomas Schirrmann
- Abteilung Biotechnologie, Institut für Biochemie, Biotechnologie und Bioinformatik, Technische Universität Braunschweig, Braunschweig, Germany
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25
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Stoevesandt O, Taussig MJ. European and international collaboration in affinity proteomics. N Biotechnol 2012; 29:511-4. [PMID: 22682155 DOI: 10.1016/j.nbt.2012.05.003] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
In affinity proteomics, specific protein-binding molecules (a.k.a. binders), principally antibodies, are applied as reagents in proteome analysis. In recent years, advances in binder technologies have created the potential for an unprecedented view on protein expression and distribution patterns in plasma, cells and tissues and increasingly on protein function. Particular strengths of affinity proteomics methods include detecting proteins in their natural environments of cell or tissue, high sensitivity and selectivity for detection of low abundance proteins and exploiting binding actions such as functional interference in living cells. To maximise the use and impact of affinity reagents, it will be essential to create comprehensive, standardised binder collections. With this in mind, the EU FP7 programme AFFINOMICS (http://www.affinomics.org), together with the preceding EU programmes ProteomeBinders and AffinityProteome, aims to extend affinity proteomics research by generating a large-scale resource of validated protein-binding molecules for characterisation of the human proteome. Activity is directed at producing binders to about 1000 protein targets, primarily in signal transduction and cancer, by establishing a high throughput, coordinated production pipeline. An important aspect of AFFINOMICS is the development of highly efficient recombinant selection methods, based on phage, cell and ribosome display, capable of producing high quality binders at greater throughput and lower cost than hitherto. The programme also involves development of innovative and sensitive technologies for specific detection of target proteins and their interactions, and deployment of binders in proteomics studies of clinical relevance. The need for such binder generation programmes is now recognised internationally, with parallel initiatives in the USA for cancer (NCI) and transcription factors (NIH) and within the Human Proteome Organisation (HUPO). The papers in this volume of New Biotechnology are all contributed by participants at the 5th ESF Workshop on Affinity Proteomics organised by the AFFINOMICS consortium and held in Alpbach, Austria, in March 2011.
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Luna Coronell JA, Syed P, Sergelen K, Gyurján I, Weinhäusel A. The current status of cancer biomarker research using tumour-associated antigens for minimal invasive and early cancer diagnostics. J Proteomics 2012; 76 Spec No.:102-15. [PMID: 22842156 DOI: 10.1016/j.jprot.2012.07.022] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2012] [Revised: 06/22/2012] [Accepted: 07/16/2012] [Indexed: 11/30/2022]
Abstract
Tumour-associated antigens (TAA) can be detected prior to clinical diagnosis and thus would be ideal biomarkers for early detection of cancer using only a few microliters of a patient's serum. In this article we provide a summary of TAA screening and serum-profiling conducted for breast, prostate, lung and colon cancers. Different methodological approaches, including SEREX, SERPA, and phage display for TAA identification and TAA panels are summarised, and a revision of array based techniques is provided. The most promising studies performed on these cancers (performed with 80-400 serum samples, including controls) obtained sensitivities in a range of 44-95% and specificities of 80-100%. From the various studies reviewed, only one performed cross validation (AUC=0.71) in a prostate cancer study. Thus, albeit receiver operation characteristics are very promising, cross validation of most studies is still missing. Additionally, the concerted action of research groups for standardization of serum-TAA testing and cross validation is required. Along with today's technological options, the chances of establishing TAA biomarkers are now higher than ever before. This may also be true for confirmation and validation of already existing data, which is a prerequisite for implementation of TAA biomarkers into clinical diagnostics. This article is part of a Special Issue entitled: Integrated omics.
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Affiliation(s)
- Johana A Luna Coronell
- Molecular Diagnostics, AIT Austrian Institute of Technology GmbH, Muthgasse 11, 1190 Vienna, Austria.
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27
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Zhang C, Helmsing S, Zagrebelsky M, Schirrmann T, Marschall ALJ, Schüngel M, Korte M, Hust M, Dübel S. Suppression of p75 neurotrophin receptor surface expression with intrabodies influences Bcl-xL mRNA expression and neurite outgrowth in PC12 cells. PLoS One 2012; 7:e30684. [PMID: 22292018 PMCID: PMC3265506 DOI: 10.1371/journal.pone.0030684] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2011] [Accepted: 12/20/2011] [Indexed: 11/19/2022] Open
Abstract
BACKGROUND Although p75 neurotrophin receptor (p75NTR) is the first neurotrophin receptor isolated, its diverse physiological functions and signaling have remained elusive for many years. Loss-of-function phenotypic analyses for p75NTR were mainly focused at the genetic level; however these approaches were impacted by off-target effect, insufficient stability, unspecific stress response or alternative active splicing products. In this study, p75NTR surface expression was suppressed for the first time at the protein level by endoplasmic reticulum (ER) retained intrabodies. RESULTS Three monoclonal recombinant antibody fragments (scFv) with affinities in the low nanomolar range to murine p75NTR were isolated by antibody phage display. To suppress p75NTR cell surface expression, the encoding genes of these scFvs extended by the ER retention peptide KDEL were transiently transfected into the neuron-like rat pheochromocytoma cell line PC12 and the mouse neuroblastoma x mouse spinal cord hybrid cell line NSC19. The ER retained intrabody construct, SH325-G7-KDEL, mediated a downregulation of p75NTR cell surface expression as shown by flow cytometry. This effect was maintained over a period of at least eight days without activating an unfolded protein response (UPR). Moreover, the ER retention of p75NTR resulted in downregulation of mRNA levels of the anti-apoptotic protein Bcl-xL as well as in strong inhibition of NGF-induced neurite outgrowth in PC12 cells. CONCLUSION The ER retained intrabody SH325-G7-KDEL not only induces phenotypic knockdown of this p75NTR but also p75NTR-associated cellular responses in PC12 cells.
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MESH Headings
- Animals
- Antibodies, Monoclonal/pharmacology
- Antigens, Surface/genetics
- Antigens, Surface/metabolism
- Cells, Cultured
- Down-Regulation/drug effects
- Down-Regulation/genetics
- Endoplasmic Reticulum/drug effects
- Endoplasmic Reticulum/metabolism
- Gene Expression Regulation/drug effects
- HEK293 Cells
- Humans
- Mice
- Models, Biological
- Neurites/drug effects
- Neurites/metabolism
- Neurites/physiology
- PC12 Cells
- Protein Transport/drug effects
- Protein Transport/physiology
- RNA, Messenger/genetics
- RNA, Messenger/metabolism
- Rats
- Receptor, Nerve Growth Factor/antagonists & inhibitors
- Receptor, Nerve Growth Factor/genetics
- Receptor, Nerve Growth Factor/immunology
- Receptor, Nerve Growth Factor/metabolism
- Recombinant Fusion Proteins/pharmacology
- bcl-X Protein/genetics
- bcl-X Protein/metabolism
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Affiliation(s)
- Congcong Zhang
- Institute for Biochemistry and Biotechnology, Technische Universität Braunschweig, Braunschweig, Germany
| | - Saskia Helmsing
- Institute for Biochemistry and Biotechnology, Technische Universität Braunschweig, Braunschweig, Germany
| | - Marta Zagrebelsky
- Zoological Institute, Technische Universität Braunschweig, Braunschweig, Germany
| | - Thomas Schirrmann
- Institute for Biochemistry and Biotechnology, Technische Universität Braunschweig, Braunschweig, Germany
| | - Andrea L. J. Marschall
- Institute for Biochemistry and Biotechnology, Technische Universität Braunschweig, Braunschweig, Germany
| | - Manuela Schüngel
- Integrated Research and Treatment Center Transplantation, Medical School of Hannover, Hannover, Germany
| | - Martin Korte
- Zoological Institute, Technische Universität Braunschweig, Braunschweig, Germany
| | - Michael Hust
- Institute for Biochemistry and Biotechnology, Technische Universität Braunschweig, Braunschweig, Germany
| | - Stefan Dübel
- Institute for Biochemistry and Biotechnology, Technische Universität Braunschweig, Braunschweig, Germany
- * E-mail:
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Abstract
Recombinant antibody fragments have a wide range of applications from research to diagnostics and therapy. Of special interest are small fragments like fragment antigen binding (Fab) or single chain fragment variables (scFv) fragments as they can be produced inexpensively in bacterial expression systems. However, recombinant production efficiencies from established production hosts vary significantly leading to inadequate yields. Gene sequences that have been synthetically adapted to match the codon preferences and respective genomic tRNA pool of the host have been used to improve yields but cannot resolve the principal problem. The development of inducible broad host range scFv expression plasmid constructs leads the way to an easy and efficient screening method for the identification of the optimal bacterial expression host.
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Affiliation(s)
- Thorben Dammeyer
- Physical & Theoretical Chemistry, NanoBioSciences, TU-Braunschweig and Helmholtz Centre for Infection Research, Braunschweig, Germany.
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29
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Geyer CR, McCafferty J, Dübel S, Bradbury ARM, Sidhu SS. Recombinant antibodies and in vitro selection technologies. Methods Mol Biol 2012; 901:11-32. [PMID: 22723092 DOI: 10.1007/978-1-61779-931-0_2] [Citation(s) in RCA: 51] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
Over the past decade, the accumulation of detailed knowledge of antibody structure and function has enabled antibody phage display to emerge as a powerful in vitro alternative to hybridoma methods for creating antibodies. Many antibodies produced using phage display technology have unique properties that are not obtainable using traditional hybridoma technologies. In phage display, selections are performed under controlled, in vitro conditions that are tailored to suit demands of the antigen and the sequence encoding the antibody is immediately available. These features obviate many of the limitations of hybridoma methodology, and because the entire process relies on scalable molecular biology techniques, phage display is also suitable for high-throughput applications. Thus, antibody phage display technology is well suited for genome-scale biotechnology and therapeutic applications. This review describes the antibody phage display technology and highlights examples of antibodies with unique properties that cannot easily be obtained by other technologies.
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Hust M, Frenzel A, Meyer T, Schirrmann T, Dübel S. Construction of human naive antibody gene libraries. Methods Mol Biol 2012; 907:85-107. [PMID: 22907347 DOI: 10.1007/978-1-61779-974-7_5] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Human antibodies are valuable tools for proteome research and diagnostics. Furthermore, antibodies are a rapidly growing class of therapeutic agents, mainly for inflammation and cancer therapy. The first therapeutic antibodies are of murine origin and were chimerized or humanized. The later-developed antibodies are fully human antibodies. Here, two technologies are competing the hybridoma technology using transgenic mice with human antibody gene loci and antibody phage display. The starting point for the selection of human antibodies against any target is the construction of an antibody phage display gene library.In this review we describe the construction of human naive and immune antibody gene libraries for antibody phage display.
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Affiliation(s)
- Michael Hust
- Institut für Biochemie und Biotechnologie, Techische Universität Braunschweig, Braunschweig, Germany.
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31
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Keates T, Cooper CD, Savitsky P, Allerston CK, Phillips C, Hammarström M, Daga N, Berridge G, Mahajan P, Burgess-Brown NA, Müller S, Gräslund S, Gileadi O. Expressing the human proteome for affinity proteomics: optimising expression of soluble protein domains and in vivo biotinylation. N Biotechnol 2011; 29:515-25. [PMID: 22027370 PMCID: PMC3383991 DOI: 10.1016/j.nbt.2011.10.007] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2011] [Revised: 10/10/2011] [Accepted: 10/12/2011] [Indexed: 11/17/2022]
Abstract
The generation of affinity reagents to large numbers of human proteins depends on the ability to express the target proteins as high-quality antigens. The Structural Genomics Consortium (SGC) focuses on the production and structure determination of human proteins. In a 7-year period, the SGC has deposited crystal structures of >800 human protein domains, and has additionally expressed and purified a similar number of protein domains that have not yet been crystallised. The targets include a diversity of protein domains, with an attempt to provide high coverage of protein families. The family approach provides an excellent basis for characterising the selectivity of affinity reagents. We present a summary of the approaches used to generate purified human proteins or protein domains, a test case demonstrating the ability to rapidly generate new proteins, and an optimisation study on the modification of >70 proteins by biotinylation in vivo. These results provide a unique synergy between large-scale structural projects and the recent efforts to produce a wide coverage of affinity reagents to the human proteome.
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Affiliation(s)
- Tracy Keates
- The Structural Genomics Consortium, University of Oxford, ORCRB, Roosevelt Drive, Oxford OX3 7DQ, United Kingdom
| | - Christopher D.O. Cooper
- The Structural Genomics Consortium, University of Oxford, ORCRB, Roosevelt Drive, Oxford OX3 7DQ, United Kingdom
| | - Pavel Savitsky
- The Structural Genomics Consortium, University of Oxford, ORCRB, Roosevelt Drive, Oxford OX3 7DQ, United Kingdom
| | - Charles K. Allerston
- The Structural Genomics Consortium, University of Oxford, ORCRB, Roosevelt Drive, Oxford OX3 7DQ, United Kingdom
| | - Claire Phillips
- The Structural Genomics Consortium, University of Oxford, ORCRB, Roosevelt Drive, Oxford OX3 7DQ, United Kingdom
| | - Martin Hammarström
- The Structural Genomics Consortium, Department of Biochemistry and Biophysics, Karolinska Institutet, Stockholm 171 77, Sweden
| | - Neha Daga
- The Structural Genomics Consortium, University of Oxford, ORCRB, Roosevelt Drive, Oxford OX3 7DQ, United Kingdom
| | - Georgina Berridge
- The Structural Genomics Consortium, University of Oxford, ORCRB, Roosevelt Drive, Oxford OX3 7DQ, United Kingdom
| | - Pravin Mahajan
- The Structural Genomics Consortium, University of Oxford, ORCRB, Roosevelt Drive, Oxford OX3 7DQ, United Kingdom
| | - Nicola A. Burgess-Brown
- The Structural Genomics Consortium, University of Oxford, ORCRB, Roosevelt Drive, Oxford OX3 7DQ, United Kingdom
| | - Susanne Müller
- The Structural Genomics Consortium, University of Oxford, ORCRB, Roosevelt Drive, Oxford OX3 7DQ, United Kingdom
| | - Susanne Gräslund
- The Structural Genomics Consortium, Department of Biochemistry and Biophysics, Karolinska Institutet, Stockholm 171 77, Sweden
| | - Opher Gileadi
- The Structural Genomics Consortium, University of Oxford, ORCRB, Roosevelt Drive, Oxford OX3 7DQ, United Kingdom
- Corresponding author:
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32
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Dyson MR, Zheng Y, Zhang C, Colwill K, Pershad K, Kay BK, Pawson T, McCafferty J. Mapping protein interactions by combining antibody affinity maturation and mass spectrometry. Anal Biochem 2011; 417:25-35. [PMID: 21704603 PMCID: PMC3171153 DOI: 10.1016/j.ab.2011.05.005] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2011] [Revised: 03/27/2011] [Accepted: 05/03/2011] [Indexed: 12/24/2022]
Abstract
Mapping protein interactions by immunoprecipitation is limited by the availability of antibodies recognizing available native epitopes within protein complexes with sufficient affinity. Here we demonstrate a scalable approach for generation of such antibodies using phage display and affinity maturation. We combined antibody variable heavy (V(H)) genes from target-specific clones (recognizing Src homology 2 (SH2) domains of LYN, VAV1, NCK1, ZAP70, PTPN11, CRK, LCK, and SHC1) with a repertoire of 10(8) to 10(9) new variable light (V(L)) genes. Improved binders were isolated by stringent selections from these new "chain-shuffled" libraries. We also developed a predictive 96-well immunocapture screen and found that only 12% of antibodies had sufficient affinity/epitope availability to capture endogenous target from lysates. Using antibodies of different affinities to the same epitope, we show that affinity improvement was a key determinant for success and identified a clear affinity threshold value (60 nM for SHC1) that must be breached for success in immunoprecipitation. By combining affinity capture using matured antibodies to SHC1 with mass spectrometry, we identified seven known binding partners and two known SHC1 phosphorylation sites in epidermal growth factor (EGF)-stimulated human breast cancer epithelial cells. These results demonstrate that antibodies capable of immunoprecipitation can be generated by chain shuffling, providing a scalable approach to mapping protein-protein interaction networks.
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Affiliation(s)
- Michael R. Dyson
- Department of Biochemistry, University of Cambridge, Cambridge CB2 1QW, UK
| | - Yong Zheng
- Samuel Lunenfeld Research Institute, Mount Sinai Hospital, Toronto, Ontario, Canada M5G 1X5
| | - Cunjie Zhang
- Samuel Lunenfeld Research Institute, Mount Sinai Hospital, Toronto, Ontario, Canada M5G 1X5
| | - Karen Colwill
- Samuel Lunenfeld Research Institute, Mount Sinai Hospital, Toronto, Ontario, Canada M5G 1X5
| | - Kritika Pershad
- Department of Biological Sciences, University of Illinois at Chicago, Chicago, IL 60607, USA
| | - Brian K. Kay
- Department of Biological Sciences, University of Illinois at Chicago, Chicago, IL 60607, USA
| | - Tony Pawson
- Samuel Lunenfeld Research Institute, Mount Sinai Hospital, Toronto, Ontario, Canada M5G 1X5
- Department of Molecular and Medical Genetics, University of Toronto, Toronto, Ontario, Canada M5S 1A8
| | - John McCafferty
- Department of Biochemistry, University of Cambridge, Cambridge CB2 1QW, UK
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33
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Babel I, Barderas R, Peláez-García A, Casal JI. Antibodies on demand: a fast method for the production of human scFvs with minimal amounts of antigen. BMC Biotechnol 2011; 11:61. [PMID: 21635725 PMCID: PMC3125328 DOI: 10.1186/1472-6750-11-61] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2010] [Accepted: 06/02/2011] [Indexed: 01/10/2023] Open
Abstract
BACKGROUND Antibodies constitute a powerful tool to study protein function, protein localization and protein-protein interactions, as well as for diagnostic and therapeutic purposes. High-throughput antibody development requires faster methodologies with lower antigen consumption. RESULTS Here, we describe a novel methodology to select human monoclonal recombinant antibodies by combining in vitro protein expression, phage display antibody libraries and antibody microarrays. The application of this combination of methodologies permitted us to generate human single-chain variable fragments (scFvs) against two proteins: green fluorescent protein (GFP) and thioredoxin (Trx) in a short time, using as low as 5 μg of purified protein. These scFvs showed specific reactivity against their respective targets and worked well by ELISA and western blot. The scFvs were able to recognise as low as 31 ng of protein of their respective targets by western blot. CONCLUSION This work describes a novel and miniaturized methodology to obtain human monoclonal recombinant antibodies against any target in a shorter time than other methodologies using only 5 μg of protein. The protocol could be easily adapted to a high-throughput procedure for antibody production.
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Affiliation(s)
- Ingrid Babel
- Functional Proteomics Laboratory. Centro de Investigaciones Biológicas (CIB-CSIC). Ramiro de Maeztu 9, Madrid 28040, Spain
| | - Rodrigo Barderas
- Functional Proteomics Laboratory. Centro de Investigaciones Biológicas (CIB-CSIC). Ramiro de Maeztu 9, Madrid 28040, Spain
| | - Alberto Peláez-García
- Functional Proteomics Laboratory. Centro de Investigaciones Biológicas (CIB-CSIC). Ramiro de Maeztu 9, Madrid 28040, Spain
| | - J Ignacio Casal
- Functional Proteomics Laboratory. Centro de Investigaciones Biológicas (CIB-CSIC). Ramiro de Maeztu 9, Madrid 28040, Spain
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34
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Colwill K, Gräslund S. A roadmap to generate renewable protein binders to the human proteome. Nat Methods 2011; 8:551-8. [PMID: 21572409 DOI: 10.1038/nmeth.1607] [Citation(s) in RCA: 229] [Impact Index Per Article: 17.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2010] [Accepted: 04/11/2011] [Indexed: 12/16/2022]
Abstract
Despite the wealth of commercially available antibodies to human proteins, research is often hindered by their inconsistent validation, their poor performance and the inadequate coverage of the proteome. These issues could be addressed by systematic, genome-wide efforts to generate and validate renewable protein binders. We report a multicenter study to assess the potential of hybridoma and phage-display technologies in a coordinated large-scale antibody generation and validation effort. We produced over 1,000 antibodies targeting 20 SH2 domain proteins and evaluated them for potency and specificity by enzyme-linked immunosorbent assay (ELISA), protein microarray and surface plasmon resonance (SPR). We also tested selected antibodies in immunoprecipitation, immunoblotting and immunofluorescence assays. Our results show that high-affinity, high-specificity renewable antibodies generated by different technologies can be produced quickly and efficiently. We believe that this work serves as a foundation and template for future larger-scale studies to create renewable protein binders.
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Affiliation(s)
- Karen Colwill
- Samuel Lunenfeld Research Institute, Mount Sinai Hospital, Toronto, Ontario, Canada.
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35
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Bradbury ARM, Sidhu S, Dübel S, McCafferty J. Beyond natural antibodies: the power of in vitro display technologies. Nat Biotechnol 2011; 29:245-54. [PMID: 21390033 PMCID: PMC3057417 DOI: 10.1038/nbt.1791] [Citation(s) in RCA: 407] [Impact Index Per Article: 31.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
In vitro display technologies, best exemplified by phage and yeast display, were first described for the selection of antibodies some 20 years ago. Since then, many antibodies have been selected and improved upon using these methods. Although it is not widely recognized, many of the antibodies derived using in vitro display methods have properties that would be extremely difficult, if not impossible, to obtain by immunizing animals. The first antibodies derived using in vitro display methods are now in the clinic, with many more waiting in the wings. Unlike immunization, in vitro display permits the use of defined selection conditions and provides immediate availability of the sequence encoding the antibody. The amenability of in vitro display to high-throughput applications broadens the prospects for their wider use in basic and applied research.
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36
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Schirrmann T, Meyer T, Schütte M, Frenzel A, Hust M. Phage display for the generation of antibodies for proteome research, diagnostics and therapy. Molecules 2011; 16:412-26. [PMID: 21221060 PMCID: PMC6259421 DOI: 10.3390/molecules16010412] [Citation(s) in RCA: 85] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2010] [Revised: 01/04/2011] [Accepted: 01/07/2011] [Indexed: 12/15/2022] Open
Abstract
Twenty years after its development, antibody phage display using filamentous bacteriophage represents the most successful in vitro antibody selection technology. Initially, its development was encouraged by the unique possibility of directly generating recombinant human antibodies for therapy. Today, antibody phage display has been developed as a robust technology offering great potential for automation. Generation of monospecific binders provides a valuable tool for proteome research, leading to highly enhanced throughput and reduced costs. This review presents the phage display technology, application areas of antibodies in research, diagnostics and therapy and the use of antibody phage display for these applications.
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Affiliation(s)
| | | | | | | | - Michael Hust
- Technische Universität Braunschweig, Institute of Biochemistry and Biotechnology, Department of Biotechnology, Spielmannstr. 7, 38106 Braunschweig, Germany
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37
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Marschall ALJ, Frenzel A, Schirrmann T, Schüngel M, Dübel S. Targeting antibodies to the cytoplasm. MAbs 2011; 3:3-16. [PMID: 21099369 DOI: 10.4161/mabs.3.1.14110] [Citation(s) in RCA: 87] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
A growing number of research consortia are now focused on generating antibodies and recombinant antibody fragments that target the human proteome. A particularly valuable application for these binding molecules would be their use inside a living cell, e.g., for imaging or functional intervention. Animal-derived antibodies must be brought into the cell through the membrane, whereas the availability of the antibody genes from phage display systems allows intracellular expression. Here, the various technologies to target intracellular proteins with antibodies are reviewed.
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Affiliation(s)
- Andrea L J Marschall
- Technische Universität Braunschweig; Institute of Biochemistry and Biotechnology; Braunschweig, Germany
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38
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Hust M, Meyer T, Voedisch B, Rülker T, Thie H, El-Ghezal A, Kirsch MI, Schütte M, Helmsing S, Meier D, Schirrmann T, Dübel S. A human scFv antibody generation pipeline for proteome research. J Biotechnol 2010; 152:159-70. [PMID: 20883731 DOI: 10.1016/j.jbiotec.2010.09.945] [Citation(s) in RCA: 102] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2010] [Revised: 09/13/2010] [Accepted: 09/16/2010] [Indexed: 01/28/2023]
Abstract
The functional decryption of the human proteome is the challenge which follows the sequencing of the human genome. Specific binders to every human protein are key reagents for this purpose. In vitro antibody selection using phage display offers one possible solution that can meet the demand for 25,000 or more antibodies, but needs substantial standardisation and minimalisation. To evaluate this potential, three human, naive antibody gene libraries (HAL4/7/8) were constructed and a standardised antibody selection pipeline was set up. The quality of the libraries and the selection pipeline was validated with 110 antigens, including human, other mammalian, fungal or bacterial proteins, viruses or haptens. Furthermore, the abundance of VH, kappa and lambda subfamilies during library cloning and the E. coli based phage display system on library packaging and the selection of scFvs was evaluated from the analysis of 435 individual antibodies, resulting in the first comprehensive comparison of V gene subfamily use for all steps of an antibody phage display pipeline. Further, a compatible cassette vector set for E. coli and mammalian expression of antibody fragments is described, allowing in vivo biotinylation, enzyme fusion and Fc fusion.
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Affiliation(s)
- Michael Hust
- Technische Universität Braunschweig, Institut für Biochemie und Biotechnologie, Abteilung Biotechnologie, Spielmannstr. 7, 38106 Braunschweig, Germany.
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39
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Bourbeillon J, Orchard S, Benhar I, Borrebaeck C, de Daruvar A, Dübel S, Frank R, Gibson F, Gloriam D, Haslam N, Hiltker T, Humphrey-Smith I, Hust M, Juncker D, Koegl M, Konthur Z, Korn B, Krobitsch S, Muyldermans S, Nygren PÅ, Palcy S, Polic B, Rodriguez H, Sawyer A, Schlapshy M, Snyder M, Stoevesandt O, Taussig MJ, Templin M, Uhlen M, van der Maarel S, Wingren C, Hermjakob H, Sherman D. Minimum information about a protein affinity reagent (MIAPAR). Nat Biotechnol 2010; 28:650-3. [DOI: 10.1038/nbt0710-650] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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40
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Dübel S, Stoevesandt O, Taussig MJ, Hust M. Generating recombinant antibodies to the complete human proteome. Trends Biotechnol 2010; 28:333-9. [PMID: 20538360 DOI: 10.1016/j.tibtech.2010.05.001] [Citation(s) in RCA: 79] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2010] [Revised: 04/29/2010] [Accepted: 05/03/2010] [Indexed: 10/19/2022]
Abstract
In vitro antibody generation technologies have now been available for two decades. Research reagents prepared via phage display are becoming available and several recent studies have demonstrated that these technologies are now sufficiently advanced to facilitate generation of a comprehensive renewable resource of antibodies for any protein encoded by the approximately 22,500 human protein-coding genes. Antibody selection in vitro offers properties not available in animal-based antibody generation methods. By adjusting the biochemical milieu during selection, it is possible to control the antigen conformation recognized, the antibody affinity or unwanted cross-reactivity. For larger-scale antibody generation projects, the handling, transport and storage logistics and bacterial production offer cost benefits. Because the DNA sequence encoding the antibody is available, modifications, such as site-specific in vivo biotinylation and multimerization, are only a cloning step away. This opinion article summarizes opportunities for the generation of antibodies for proteome research using in vitro technologies.
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Affiliation(s)
- Stefan Dübel
- Technische Universität Braunschweig, Institute of Biochemistry and Biotechnology, D-38106 Braunschweig, Germany.
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Pershad K, Pavlovic J, Gräslund S, Nilsson P, Colwill K, Karatt-Vellatt A, Schofield D, Dyson M, Pawson T, Kay B, McCafferty J. Generating a panel of highly specific antibodies to 20 human SH2 domains by phage display. Protein Eng Des Sel 2010; 23:279-88. [PMID: 20164216 PMCID: PMC2841545 DOI: 10.1093/protein/gzq003] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2009] [Revised: 12/31/2009] [Accepted: 01/05/2010] [Indexed: 12/02/2022] Open
Abstract
To demonstrate the utility of phage display in generating highly specific antibodies, affinity selections were conducted on 20 related Src Homology 2 (SH2) domains (ABL1, ABL2, BTK, BCAR3, CRK, FYN, GRB2, GRAP2, LYN, LCK, NCK1, PTPN11 C, PIK3R1 C, PLCgamma1 C, RASA1 C, SHC1, SH2D1A, SYK N, VAV1 and the tandem domains of ZAP70). The domains were expressed in Escherichia coli, purified and used in affinity selection experiments. In total, 1292/3800 of the resultant antibodies were shown to bind the target antigen. Of the 695 further evaluated in specificity ELISAs against all 20 SH2 domains, 379 antibodies were identified with unique specificity (i.e. monospecific). Sequence analysis revealed that there were at least 150 different clones with 1-19 different antibodies/antigen. This includes antibodies that distinguish between ABL1 and ABL2, despite their 89% sequence identity. Specificity was confirmed for many on protein arrays fabricated with 432 different proteins. Thus, even though the SH2 domains share a common three-dimensional structure and 20-89% identity at the primary structure level, we were able to isolate antibodies with exquisite specificity within this family of structurally related domains.
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Affiliation(s)
- K. Pershad
- Department of Biological Sciences, University of Illinois at Chicago, Chicago, IL 60607, USA
| | - J.D. Pavlovic
- Department of Biological Sciences, University of Illinois at Chicago, Chicago, IL 60607, USA
| | - S. Gräslund
- Structural Genomics Consortium, Department of Biochemistry and Biophysics, Karolinska Institutet, Stockholm 171 77, Sweden
| | - P. Nilsson
- Department of Proteomics, School of Biotechnology, KTH-Royal Institute of Technology, Albanova University Centre, Stockholm SE-10691, Sweden
| | - K. Colwill
- Samuel Lunenfeld Research Institute, Mount Sinai Hospital, Toronto, ON, CanadaM5G 1X5
| | - A. Karatt-Vellatt
- Department of Biochemistry, University of Cambridge, Downing Site, Cambridge CB2 1QW, UK
| | - D.J. Schofield
- Department of Biochemistry, University of Cambridge, Downing Site, Cambridge CB2 1QW, UK
| | - M.R. Dyson
- Department of Biochemistry, University of Cambridge, Downing Site, Cambridge CB2 1QW, UK
| | - T. Pawson
- Department of Molecular and Medical Genetics, University of Toronto, Toronto, ON, CanadaM5S 1A8
| | - B.K. Kay
- Department of Biological Sciences, University of Illinois at Chicago, Chicago, IL 60607, USA
| | - J. McCafferty
- Department of Biochemistry, University of Cambridge, Downing Site, Cambridge CB2 1QW, UK
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Beck A, Reichert JM, Wurch T. 5th European Antibody Congress 2009: November 30–December 2, 2009, Geneva, Switzerland. MAbs 2010; 2:108-28. [PMID: 20179425 PMCID: PMC2840230 DOI: 10.4161/mabs.2.2.11302] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2010] [Accepted: 01/26/2010] [Indexed: 12/15/2022] Open
Affiliation(s)
- Alain Beck
- Physico-Chemistry Department, Centre d’Immunologie Pierre Fabre, Saint Julien en Genevois, France.
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