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Li Y, Xu X, Wang HJ, Chen YC, Chen Y, Chiu J, Li L, Wang L, Wang J, Tang Z, Ren L, Li H, Wang X, Jin S, Wu Y, Huang M, Ju LA, Fang C. Endoplasmic Reticulum Protein 72 Regulates Integrin Mac-1 Activity to Influence Neutrophil Recruitment. Arterioscler Thromb Vasc Biol 2024; 44:e82-e98. [PMID: 38205640 DOI: 10.1161/atvbaha.123.319771] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2023] [Accepted: 12/26/2023] [Indexed: 01/12/2024]
Abstract
BACKGROUND Integrins mediate the adhesion, crawling, and migration of neutrophils during vascular inflammation. Thiol exchange is important in the regulation of integrin functions. ERp72 (endoplasmic reticulum-resident protein 72) is a member of the thiol isomerase family responsible for the catalysis of disulfide rearrangement. However, the role of ERp72 in the regulation of Mac-1 (integrin αMβ2) on neutrophils remains elusive. METHODS Intravital microscopy of the cremaster microcirculation was performed to determine in vivo neutrophil movement. Static adhesion, flow chamber, and flow cytometry were used to evaluate in vitro integrin functions. Confocal fluorescent microscopy and coimmunoprecipitation were utilized to characterize the interactions between ERp72 and Mac-1 on neutrophil surface. Cell-impermeable probes and mass spectrometry were used to label reactive thiols and identify target disulfide bonds during redox exchange. Biomembrane force probe was performed to quantitatively measure the binding affinity of Mac-1. A murine model of acute lung injury induced by lipopolysaccharide was utilized to evaluate neutrophil-associated vasculopathy. RESULTS ERp72-deficient neutrophils exhibited increased rolling but decreased adhesion/crawling on inflamed venules in vivo and defective static adhesion in vitro. The defect was due to defective activation of integrin Mac-1 but not LFA-1 (lymphocyte function-associated antigen-1) using blocking or epitope-specific antibodies. ERp72 interacted with Mac-1 in lipid rafts on neutrophil surface leading to the reduction of the C654-C711 disulfide bond in the αM subunit that is critical for Mac-1 activation. Recombinant ERp72, via its catalytic motifs, increased the binding affinity of Mac-1 with ICAM-1 (intercellular adhesion molecule-1) and rescued the defective adhesion of ERp72-deficient neutrophils both in vitro and in vivo. Deletion of ERp72 in the bone marrow inhibited neutrophil infiltration, ameliorated tissue damage, and increased survival during murine acute lung injury. CONCLUSIONS Extracellular ERp72 regulates integrin Mac-1 activity by catalyzing disulfide rearrangement on the αM subunit and may be a novel target for the treatment of neutrophil-associated vasculopathy.
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Affiliation(s)
- Yaofeng Li
- Department of Pharmacology, School of Basic Medicine, Tongji Medical College and State Key Laboratory for Diagnosis and Treatment of Severe Zoonotic Infectious Diseases (Y.L., X.X., L.L., L.W., C.F.), Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Xulin Xu
- Department of Pharmacology, School of Basic Medicine, Tongji Medical College and State Key Laboratory for Diagnosis and Treatment of Severe Zoonotic Infectious Diseases (Y.L., X.X., L.L., L.W., C.F.), Huazhong University of Science and Technology, Wuhan, Hubei, China
- Tongji-Rongcheng Center for Biomedicine (X.X., C.F.), Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Haoqing Jerry Wang
- School of Biomedical Engineering, Faculty of Engineering (H.J.W., Y.C.C., L.A.J.), The University of Sydney, New South Wales, Australia
- The University of Sydney Nano Institute Sydney Nanoscience Hub (H.J.W., Y.C.C., L.A.J.), The University of Sydney, New South Wales, Australia
| | - Yiyao Catherine Chen
- Institute of Pathology, Tongji Hospital, Tongji Medical College (Y.C.), Huazhong University of Science and Technology, Wuhan, Hubei, China
- School of Biomedical Engineering, Faculty of Engineering (H.J.W., Y.C.C., L.A.J.), The University of Sydney, New South Wales, Australia
| | - Yaobing Chen
- The University of Sydney Nano Institute Sydney Nanoscience Hub (H.J.W., Y.C.C., L.A.J.), The University of Sydney, New South Wales, Australia
| | - Joyce Chiu
- Centenary Institute (J.C.), The University of Sydney, New South Wales, Australia
| | - Li Li
- Department of Pharmacology, School of Basic Medicine, Tongji Medical College and State Key Laboratory for Diagnosis and Treatment of Severe Zoonotic Infectious Diseases (Y.L., X.X., L.L., L.W., C.F.), Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Lei Wang
- Department of Pharmacology, School of Basic Medicine, Tongji Medical College and State Key Laboratory for Diagnosis and Treatment of Severe Zoonotic Infectious Diseases (Y.L., X.X., L.L., L.W., C.F.), Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Jinyu Wang
- School of Stomatology, Tongji Medical Collage (J.W.), Huazhong University of Science and Technology, Wuhan, Hubei, China
- Hubei Province Key Laboratory of Oral and Maxillofacial Development and Regeneration of Hubei Province, Wuhan, China (J.W.)
| | - Zhaoming Tang
- Department of Clinical Laboratory, Union Hospital, Tongji Medical College (Z.T.), Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Lehao Ren
- Department of Critical Care Medicine, Union Hospital, Tongji Medical College (L.R.), Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Hongliang Li
- Laboratory of Chinese Herbal Pharmacology, Department of Pharmacy, Renmin Hospital of Wuhan University, China (H.L., X.W.)
- Biomedical Research Institute, School of Pharmaceutical Sciences and Hubei Key Laboratory of Wudang Local Chinese Medicine Research, Hubei University of Medicine, Shiyan, China (H.L., X.W.)
| | - Xuanbin Wang
- Laboratory of Chinese Herbal Pharmacology, Department of Pharmacy, Renmin Hospital of Wuhan University, China (H.L., X.W.)
- Biomedical Research Institute, School of Pharmaceutical Sciences and Hubei Key Laboratory of Wudang Local Chinese Medicine Research, Hubei University of Medicine, Shiyan, China (H.L., X.W.)
| | - Si Jin
- Department of Endocrinology, Institute of Geriatric Medicine, Liyuan Hospital, Tongji Medical College (S.J.), Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Yi Wu
- Cyrus Tang Hematology Center, Soochow University, Suzhou, Jiangsu, China (Y.W.)
| | - Mingdong Huang
- College of Chemistry, Fuzhou University, Fujian, China (M.H.)
| | - Lining Arnold Ju
- School of Biomedical Engineering, Faculty of Engineering (H.J.W., Y.C.C., L.A.J.), The University of Sydney, New South Wales, Australia
- The University of Sydney Nano Institute Sydney Nanoscience Hub (H.J.W., Y.C.C., L.A.J.), The University of Sydney, New South Wales, Australia
| | - Chao Fang
- Department of Pharmacology, School of Basic Medicine, Tongji Medical College and State Key Laboratory for Diagnosis and Treatment of Severe Zoonotic Infectious Diseases (Y.L., X.X., L.L., L.W., C.F.), Huazhong University of Science and Technology, Wuhan, Hubei, China
- Tongji-Rongcheng Center for Biomedicine (X.X., C.F.), Huazhong University of Science and Technology, Wuhan, Hubei, China
- The Key Laboratory for Drug Target Researches and Pharmacodynamic Evaluation of Hubei Province, Wuhan, China (C.F.)
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2
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Akbar R, Bashour H, Rawat P, Robert PA, Smorodina E, Cotet TS, Flem-Karlsen K, Frank R, Mehta BB, Vu MH, Zengin T, Gutierrez-Marcos J, Lund-Johansen F, Andersen JT, Greiff V. Progress and challenges for the machine learning-based design of fit-for-purpose monoclonal antibodies. MAbs 2022; 14:2008790. [PMID: 35293269 PMCID: PMC8928824 DOI: 10.1080/19420862.2021.2008790] [Citation(s) in RCA: 29] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2021] [Revised: 11/04/2021] [Accepted: 11/17/2021] [Indexed: 12/15/2022] Open
Abstract
Although the therapeutic efficacy and commercial success of monoclonal antibodies (mAbs) are tremendous, the design and discovery of new candidates remain a time and cost-intensive endeavor. In this regard, progress in the generation of data describing antigen binding and developability, computational methodology, and artificial intelligence may pave the way for a new era of in silico on-demand immunotherapeutics design and discovery. Here, we argue that the main necessary machine learning (ML) components for an in silico mAb sequence generator are: understanding of the rules of mAb-antigen binding, capacity to modularly combine mAb design parameters, and algorithms for unconstrained parameter-driven in silico mAb sequence synthesis. We review the current progress toward the realization of these necessary components and discuss the challenges that must be overcome to allow the on-demand ML-based discovery and design of fit-for-purpose mAb therapeutic candidates.
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Affiliation(s)
- Rahmad Akbar
- Department of Immunology, University of Oslo and Oslo University Hospital, Oslo, Norway
| | - Habib Bashour
- School of Life Sciences, University of Warwick, Coventry, UK
| | - Puneet Rawat
- Department of Immunology, University of Oslo and Oslo University Hospital, Oslo, Norway
- Department of Biotechnology, Bhupat and Jyoti Mehta School of Biosciences, Indian Institute of Technology Madras, Chennai, India
| | - Philippe A. Robert
- Department of Immunology, University of Oslo and Oslo University Hospital, Oslo, Norway
| | - Eva Smorodina
- Faculty of Bioengineering and Bioinformatics, Lomonosov Moscow State University, Russia
| | | | - Karine Flem-Karlsen
- Department of Immunology, University of Oslo and Oslo University Hospital, Oslo, Norway
- Institute of Clinical Medicine, Department of Pharmacology, University of Oslo and Oslo University Hospital, Norway
| | - Robert Frank
- Department of Immunology, University of Oslo and Oslo University Hospital, Oslo, Norway
| | - Brij Bhushan Mehta
- Department of Immunology, University of Oslo and Oslo University Hospital, Oslo, Norway
| | - Mai Ha Vu
- Department of Linguistics and Scandinavian Studies, University of Oslo, Norway
| | - Talip Zengin
- Department of Immunology, University of Oslo and Oslo University Hospital, Oslo, Norway
- Department of Bioinformatics, Mugla Sitki Kocman University, Turkey
| | | | | | - Jan Terje Andersen
- Department of Immunology, University of Oslo and Oslo University Hospital, Oslo, Norway
- Institute of Clinical Medicine, Department of Pharmacology, University of Oslo and Oslo University Hospital, Norway
| | - Victor Greiff
- Department of Immunology, University of Oslo and Oslo University Hospital, Oslo, Norway
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3
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Siegel PM, Bojti I, Bassler N, Holien J, Flierl U, Wang X, Waggershauser P, Tonnar X, Vedecnik C, Lamprecht C, Stankova I, Li T, Helbing T, Wolf D, Anto-Michel N, Mitre LS, Ehrlich J, Orlean L, Bender I, Przewosnik A, Mauler M, Hollederer L, Moser M, Bode C, Parker MW, Peter K, Diehl P. A DARPin targeting activated Mac-1 is a novel diagnostic tool and potential anti-inflammatory agent in myocarditis, sepsis and myocardial infarction. Basic Res Cardiol 2021; 116:17. [PMID: 33721106 PMCID: PMC7960600 DOI: 10.1007/s00395-021-00849-9] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/31/2020] [Accepted: 01/18/2021] [Indexed: 12/15/2022]
Abstract
The monocyte β2-integrin Mac-1 is crucial for leukocyte–endothelium interaction, rendering it an attractive therapeutic target for acute and chronic inflammation. Using phage display, a Designed-Ankyrin-Repeat-Protein (DARPin) was selected as a novel binding protein targeting and blocking the αM I-domain, an activation-specific epitope of Mac-1. This DARPin, named F7, specifically binds to activated Mac-1 on mouse and human monocytes as determined by flow cytometry. Homology modelling and docking studies defined distinct interaction sites which were verified by mutagenesis. Intravital microscopy showed reduced leukocyte–endothelium adhesion in mice treated with this DARPin. Using mouse models of sepsis, myocarditis and ischaemia/reperfusion injury, we demonstrate therapeutic anti-inflammatory effects. Finally, the activated Mac-1-specific DARPin is established as a tool to detect monocyte activation in patients receiving extra-corporeal membrane oxygenation, as well as suffering from sepsis and ST-elevation myocardial infarction. The activated Mac-1-specific DARPin F7 binds preferentially to activated monocytes, detects inflammation in critically ill patients, and inhibits monocyte and neutrophil function as an efficient new anti-inflammatory agent.
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Affiliation(s)
- Patrick M Siegel
- Cardiology and Angiology I, Heart Center Freiburg University, Faculty of Medicine, University of Freiburg, Freiburg, Germany.,Atherothrombosis and Vascular Biology Laboratory, Baker Heart and Diabetes Institute, Melbourne, Australia
| | - István Bojti
- Cardiology and Angiology I, Heart Center Freiburg University, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Nicole Bassler
- Atherothrombosis and Vascular Biology Laboratory, Baker Heart and Diabetes Institute, Melbourne, Australia
| | - Jessica Holien
- ACRF Rational Drug Discovery Centre, St. Vincent's Institute of Medical Research, Melbourne, Australia
| | - Ulrike Flierl
- Atherothrombosis and Vascular Biology Laboratory, Baker Heart and Diabetes Institute, Melbourne, Australia
| | - Xiaowei Wang
- Atherothrombosis and Vascular Biology Laboratory, Baker Heart and Diabetes Institute, Melbourne, Australia.,Baker Department of Cardiometabolic Health, University of Melbourne, Melbourne, Australia.,Department of Medicine, Central Clinical School, Monash University, Melbourne, Australia
| | - Philipp Waggershauser
- Cardiology and Angiology I, Heart Center Freiburg University, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Xavier Tonnar
- Cardiology and Angiology I, Heart Center Freiburg University, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Christopher Vedecnik
- Cardiology and Angiology I, Heart Center Freiburg University, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Constanze Lamprecht
- BIOSS Centre for Biological Signalling Studies/Synthetic Biology of Signalling Processes, University of Freiburg, Freiburg, Germany
| | - Ivana Stankova
- Cardiology and Angiology I, Heart Center Freiburg University, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Tian Li
- Cardiology and Angiology I, Heart Center Freiburg University, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Thomas Helbing
- Cardiology and Angiology I, Heart Center Freiburg University, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Dennis Wolf
- Cardiology and Angiology I, Heart Center Freiburg University, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Nathaly Anto-Michel
- Cardiology and Angiology I, Heart Center Freiburg University, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Lucia Sol Mitre
- Cardiology and Angiology I, Heart Center Freiburg University, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Julia Ehrlich
- Cardiology and Angiology I, Heart Center Freiburg University, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Lukas Orlean
- Cardiology and Angiology I, Heart Center Freiburg University, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Ileana Bender
- Cardiology and Angiology I, Heart Center Freiburg University, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Anne Przewosnik
- Cardiology and Angiology I, Heart Center Freiburg University, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Maximilian Mauler
- Cardiology and Angiology I, Heart Center Freiburg University, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Laura Hollederer
- Cardiology and Angiology I, Heart Center Freiburg University, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Martin Moser
- Cardiology and Angiology I, Heart Center Freiburg University, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Christoph Bode
- Cardiology and Angiology I, Heart Center Freiburg University, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Michael W Parker
- ACRF Rational Drug Discovery Centre, St. Vincent's Institute of Medical Research, Melbourne, Australia.,Baker Department of Cardiometabolic Health, University of Melbourne, Melbourne, Australia.,Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Melbourne, Australia
| | - Karlheinz Peter
- Atherothrombosis and Vascular Biology Laboratory, Baker Heart and Diabetes Institute, Melbourne, Australia. .,Baker Department of Cardiometabolic Health, University of Melbourne, Melbourne, Australia. .,Department of Medicine, Central Clinical School, Monash University, Melbourne, Australia. .,Baker Heart and Diabetes Institute, 75 Commercial Road, Melbourne, VIC, 3004, Australia.
| | - Philipp Diehl
- Cardiology and Angiology I, Heart Center Freiburg University, Faculty of Medicine, University of Freiburg, Freiburg, Germany.,Atherothrombosis and Vascular Biology Laboratory, Baker Heart and Diabetes Institute, Melbourne, Australia.,Department of Medicine, Central Clinical School, Monash University, Melbourne, Australia
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4
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Pandya P, Sayers RO, Ting JP, Morshedian S, Torres C, Cudal JS, Zhang K, Fitchett JR, Zhang Q, Zhang FF, Wang J, Durbin JD, Carrillo JJ, Espada A, Broughton H, Qian Y, Afshar S. Integration of phage and yeast display platforms: A reliable and cost effective approach for binning of peptides as displayed on-phage. PLoS One 2020; 15:e0233961. [PMID: 32479512 PMCID: PMC7263589 DOI: 10.1371/journal.pone.0233961] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2019] [Accepted: 05/16/2020] [Indexed: 12/11/2022] Open
Abstract
Hundreds of target specific peptides are routinely discovered by peptide display platforms. However, due to the high cost of peptide synthesis only a limited number of peptides are chemically made for further analysis. Here we describe an accurate and cost effective method to bin peptides on-phage based on binding region(s), without any requirement for peptide or protein synthesis. This approach, which integrates phage and yeast display platforms, requires display of target and its alanine variants on yeast. Flow cytometry was used to detect binding of peptides on-phage to the target on yeast. Once hits were identified, they were synthesized to confirm their binding region(s) by HDX (Hydrogen deuterium exchange) and crystallography. Moreover, we have successfully shown that this approach can be implemented as part of a panning process to deplete non-functional peptides. This technique can be applied to any target that can be successfully displayed on yeast; it narrows down the number of peptides requiring synthesis; and its utilization during selection results in enrichment of peptide population against defined binding regions on the target.
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Affiliation(s)
- Priyanka Pandya
- Department of Protein Engineering, Eli Lilly Biotechnology Center, San Diego, California, United States of America
| | - Robert O. Sayers
- Department of Protein Engineering, Eli Lilly Biotechnology Center, San Diego, California, United States of America
| | - Joey P. Ting
- Department of Protein Engineering, Eli Lilly Biotechnology Center, San Diego, California, United States of America
| | - Shaghayegh Morshedian
- Department of Protein Engineering, Eli Lilly Biotechnology Center, San Diego, California, United States of America
| | - Carina Torres
- Department of Protein Engineering, Eli Lilly Biotechnology Center, San Diego, California, United States of America
| | - Justine S. Cudal
- Department of Protein Engineering, Eli Lilly Biotechnology Center, San Diego, California, United States of America
| | - Kai Zhang
- Department of Protein Engineering, Eli Lilly Biotechnology Center, San Diego, California, United States of America
| | - Jonathan R. Fitchett
- Department of Protein Engineering, Eli Lilly Biotechnology Center, San Diego, California, United States of America
| | - Qing Zhang
- Department of Protein Engineering, Eli Lilly Biotechnology Center, San Diego, California, United States of America
| | - Feiyu F. Zhang
- Lilly Research Laboratories, Discovery Chemistry Research and Technologies, San Diego, California, United States of America
| | - Jing Wang
- Lilly Research Laboratories, Discovery Chemistry Research and Technologies, San Diego, California, United States of America
| | - Jim D. Durbin
- Department of Structural Biology, Discovery Chemistry Research and Technologies, Eli Lilly and Company, Indianapolis, Indiana, United States of America
| | - Juan J. Carrillo
- Department of Quantitative Biology, Discovery Chemistry Research and Technologies, Lilly Biotechnology Center, Eli Lilly and Company, Indianapolis, Indiana, United States of America
| | | | | | - Yuewei Qian
- Lilly Research Laboratories, Recombinant Protein Generation, Indianapolis, Indiana, United States of America
| | - Sepideh Afshar
- Department of Protein Engineering, Eli Lilly Biotechnology Center, San Diego, California, United States of America
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5
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von Berg L, Stern D, Pauly D, Mahrhold S, Weisemann J, Jentsch L, Hansbauer EM, Müller C, Avondet MA, Rummel A, Dorner MB, Dorner BG. Functional detection of botulinum neurotoxin serotypes A to F by monoclonal neoepitope-specific antibodies and suspension array technology. Sci Rep 2019; 9:5531. [PMID: 30940836 PMCID: PMC6445094 DOI: 10.1038/s41598-019-41722-z] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2018] [Accepted: 03/15/2019] [Indexed: 12/26/2022] Open
Abstract
Botulinum neurotoxins (BoNTs) are the most potent toxins known and cause the life threatening disease botulism. Sensitive and broad detection is extremely challenging due to the toxins' high potency and molecular heterogeneity with several serotypes and more than 40 subtypes. The toxicity of BoNT is mediated by enzymatic cleavage of different synaptic proteins involved in neurotransmitter release at serotype-specific cleavage sites. Hence, active BoNTs can be monitored and distinguished in vitro by detecting their substrate cleavage products. In this work, we developed a comprehensive panel of monoclonal neoepitope antibodies (Neo-mAbs) highly specific for the newly generated N- and/or C-termini of the substrate cleavage products of BoNT serotypes A to F. The Neo-mAbs were implemented in a set of three enzymatic assays for the simultaneous detection of two BoNT serotypes each by monitoring substrate cleavage on colour-coded magnetic Luminex-beads. For the first time, all relevant serotypes could be detected in parallel by a routine in vitro activity assay in spiked serum and food samples yielding excellent detection limits in the range of the mouse bioassay or better (0.3-80 pg/mL). Therefore, this work represents a major step towards the replacement of the mouse bioassay for botulism diagnostics.
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Affiliation(s)
- Laura von Berg
- Biological Toxins (ZBS 3), Centre for Biological Threats and Special Pathogens, Robert Koch Institute, Berlin, 13353, Germany
| | - Daniel Stern
- Biological Toxins (ZBS 3), Centre for Biological Threats and Special Pathogens, Robert Koch Institute, Berlin, 13353, Germany
| | - Diana Pauly
- Biological Toxins (ZBS 3), Centre for Biological Threats and Special Pathogens, Robert Koch Institute, Berlin, 13353, Germany
- Department of Ophthalmology, University Hospital Regensburg, Regensburg, 93053, Germany
| | - Stefan Mahrhold
- Institut für Toxikologie, Medizinische Hochschule Hannover, 30625, Hannover, Germany
| | - Jasmin Weisemann
- Institut für Toxikologie, Medizinische Hochschule Hannover, 30625, Hannover, Germany
| | - Lisa Jentsch
- Biological Toxins (ZBS 3), Centre for Biological Threats and Special Pathogens, Robert Koch Institute, Berlin, 13353, Germany
| | - Eva-Maria Hansbauer
- Biological Toxins (ZBS 3), Centre for Biological Threats and Special Pathogens, Robert Koch Institute, Berlin, 13353, Germany
| | - Christian Müller
- Spiez Laboratory, Federal Office for Civil Protection, Spiez, 3700, Switzerland
| | - Marc A Avondet
- Spiez Laboratory, Federal Office for Civil Protection, Spiez, 3700, Switzerland
| | - Andreas Rummel
- Institut für Toxikologie, Medizinische Hochschule Hannover, 30625, Hannover, Germany
| | - Martin B Dorner
- Biological Toxins (ZBS 3), Centre for Biological Threats and Special Pathogens, Robert Koch Institute, Berlin, 13353, Germany
| | - Brigitte G Dorner
- Biological Toxins (ZBS 3), Centre for Biological Threats and Special Pathogens, Robert Koch Institute, Berlin, 13353, Germany.
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6
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Zhang Q, Hu S, Wang K, Cui M, Li X, Wang M, Hu X. Engineering a yeast double-molecule carrier for drug screening. ARTIFICIAL CELLS NANOMEDICINE AND BIOTECHNOLOGY 2018; 46:386-396. [PMID: 29611428 DOI: 10.1080/21691401.2018.1457539] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
Abstract
With the advantages of unicellular eukaryotic structure and easy manipulation, yeast becomes a popular tool for biochemical, genetic and medicinal studies. In order to construct an efficient anti-inflammatory drug screening platform, we engineered yeast as a double-molecule carrier, of which an inserted domain (I domain) of lymphocyte function-associated antigen 1 was displayed on yeast surface and a green fluorescent protein (GFP) was expressed inside cytosol. The I domain specifically targeted a surface marker of mammalian cells, intercellular adhesion molecule 1, whose number is correlated with the level of cellular inflammation. Examination of GFP intensity enables swift quantification of the yeast-mammalian cell binding and thus it reflects inflammatory potency, herein the inflammatory index, of a chemical imposed to cells. The inflammatory potency of a total of 1340 chemicals was indexed. Among them, 1 inflammation-inducing and 1 inflammation-reducing compounds were verified both in vitro and in vivo. Our method demonstrated a swift, facile and high-throughput screening platform at the protein level for inflammation and related diseases drug discovery without using sophisticated instruments.
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Affiliation(s)
- Qiyun Zhang
- a Laboratory of Drug Discovery and Molecular Engineering, Department of Medicinal Plants, College of Plant Science and Technology , Huazhong Agricultural University (HZAU) , Wuhan , China.,b National & Local Joint Engineering Research Center (Hubei) for Medicinal Plant Breeding and Cultivation , Wuhan , China.,c Hubei Provincial Engineering Research Center for Medicinal Plants , Wuhan , China
| | - Sheng Hu
- d Hubei Cancer Hospital , Wuhan , China
| | - Ke Wang
- e State Key Laboratory of Agricultural Microbiology , HZAU , Wuhan , China.,f College of Veterinary Medicine , HZAU , Wuhan , China
| | - Min Cui
- e State Key Laboratory of Agricultural Microbiology , HZAU , Wuhan , China.,f College of Veterinary Medicine , HZAU , Wuhan , China
| | - Xiaohua Li
- a Laboratory of Drug Discovery and Molecular Engineering, Department of Medicinal Plants, College of Plant Science and Technology , Huazhong Agricultural University (HZAU) , Wuhan , China.,b National & Local Joint Engineering Research Center (Hubei) for Medicinal Plant Breeding and Cultivation , Wuhan , China.,c Hubei Provincial Engineering Research Center for Medicinal Plants , Wuhan , China
| | - Mo Wang
- a Laboratory of Drug Discovery and Molecular Engineering, Department of Medicinal Plants, College of Plant Science and Technology , Huazhong Agricultural University (HZAU) , Wuhan , China.,b National & Local Joint Engineering Research Center (Hubei) for Medicinal Plant Breeding and Cultivation , Wuhan , China.,c Hubei Provincial Engineering Research Center for Medicinal Plants , Wuhan , China
| | - Xuebo Hu
- a Laboratory of Drug Discovery and Molecular Engineering, Department of Medicinal Plants, College of Plant Science and Technology , Huazhong Agricultural University (HZAU) , Wuhan , China.,b National & Local Joint Engineering Research Center (Hubei) for Medicinal Plant Breeding and Cultivation , Wuhan , China.,c Hubei Provincial Engineering Research Center for Medicinal Plants , Wuhan , China
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7
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Stern LA, Schrack IA, Johnson SM, Deshpande A, Bennett NR, Harasymiw LA, Gardner MK, Hackel BJ. Geometry and expression enhance enrichment of functional yeast-displayed ligands via cell panning. Biotechnol Bioeng 2016; 113:2328-41. [PMID: 27144954 DOI: 10.1002/bit.26001] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2015] [Revised: 03/23/2016] [Accepted: 04/25/2016] [Indexed: 01/10/2023]
Abstract
Yeast surface display has proven to be an effective tool in the discovery and evolution of ligands with new or improved binding activity. Selections for binding activity are generally carried out using immobilized or fluorescently labeled soluble domains of target molecules such as recombinant ectodomain fragments. While this method typically provides ligands with high affinity and specificity for the soluble molecular target, translation to binding true membrane-bound cellular target is commonly problematic. Direct selections against mammalian cell surfaces can be carried out either exclusively or in combination with soluble target-based selections to further direct towards ligands for genuine cellular target. Using a series of fibronectin domain, affibody, and Gp2 ligands and human cell lines expressing a range of their targets, epidermal growth factor receptor and carcinoembryonic antigen, this study quantitatively identifies the elements that dictate ligand enrichment and yield. Most notably, extended flexible linkers between ligand and yeast enhance enrichment ratios from 1.4 ± 0.8 to 62 ± 57 for a low-affinity (>600 nM) binder on cells with high target expression and from 14 ± 13 to 74 ± 25 for a high-affinity binder (2 nM) on cells with medium valency. Inversion of the yeast display fusion from C-terminal display to N-terminal display still enables enrichment albeit with 40-97% reduced efficacy. Collectively, this study further enlightens the conditions-while highlighting new approaches-that yield successful enrichment of yeast-displayed binding ligands via panning on mammalian cells. Biotechnol. Bioeng. 2016;113: 2328-2341. © 2016 Wiley Periodicals, Inc.
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Affiliation(s)
- Lawrence A Stern
- Department of Chemical Engineering and Materials Science, University of Minnesota-Twin Cities, Minneapolis, Minnesota, 55455
| | - Ian A Schrack
- Department of Chemical Engineering and Materials Science, University of Minnesota-Twin Cities, Minneapolis, Minnesota, 55455
| | - Sadie M Johnson
- Department of Chemical Engineering and Materials Science, University of Minnesota-Twin Cities, Minneapolis, Minnesota, 55455
| | - Aakash Deshpande
- Department of Chemical Engineering and Materials Science, University of Minnesota-Twin Cities, Minneapolis, Minnesota, 55455
| | - Nathaniel R Bennett
- Department of Chemical Engineering and Materials Science, University of Minnesota-Twin Cities, Minneapolis, Minnesota, 55455
| | - Lauren A Harasymiw
- Department of Genetics, Cell Biology, and Development, University of Minnesota-Twin Cities, Minneapolis, Minnesota
| | - Melissa K Gardner
- Department of Genetics, Cell Biology, and Development, University of Minnesota-Twin Cities, Minneapolis, Minnesota
| | - Benjamin J Hackel
- Department of Chemical Engineering and Materials Science, University of Minnesota-Twin Cities, Minneapolis, Minnesota, 55455.
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8
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Wu CY, Liang MX, Chen Q. Production and stabilization of an integrin-binding moiety of complement component 3. Mol Biol 2015. [DOI: 10.1134/s0026893315050209] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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9
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Ferrara F, D'Angelo S, Gaiotto T, Naranjo L, Tian H, Gräslund S, Dobrovetsky E, Hraber P, Lund-Johansen F, Saragozza S, Sblattero D, Kiss C, Bradbury ARM. Recombinant renewable polyclonal antibodies. MAbs 2015; 7:32-41. [PMID: 25530082 DOI: 10.4161/19420862.2015.989047] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023] Open
Abstract
Only a small fraction of the antibodies in a traditional polyclonal antibody mixture recognize the target of interest, frequently resulting in undesirable polyreactivity. Here, we show that high-quality recombinant polyclonals, in which hundreds of different antibodies are all directed toward a target of interest, can be easily generated in vitro by combining phage and yeast display. We show that, unlike traditional polyclonals, which are limited resources, recombinant polyclonal antibodies can be amplified over one hundred million-fold without losing representation or functionality. Our protocol was tested on 9 different targets to demonstrate how the strategy allows the selective amplification of antibodies directed toward desirable target specific epitopes, such as those found in one protein but not a closely related one, and the elimination of antibodies recognizing common epitopes, without significant loss of diversity. These recombinant renewable polyclonal antibodies are usable in different assays, and can be generated in high throughput. This approach could potentially be used to develop highly specific recombinant renewable antibodies against all human gene products.
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10
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Neves H, Kwok HF. Recent advances in the field of anti-cancer immunotherapy. BBA CLINICAL 2015; 3:280-8. [PMID: 26673349 PMCID: PMC4661591 DOI: 10.1016/j.bbacli.2015.04.001] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/30/2014] [Revised: 03/31/2015] [Accepted: 04/06/2015] [Indexed: 12/19/2022]
Abstract
Background The main goal of anti-cancer therapy is to specifically inhibit the malignant activity of cancer cells, while leaving healthy cells unaffected. As such, for every proposed therapy, it is important to keep in mind the therapeutic index — the ratio of the toxic dose over the therapeutic dose. The use of immunotherapy has allowed a means to both specifically block protein–protein interaction and deliver cytotoxic events to a tumor-specific antigen. Review scope It is the objective of this review to give an overview on current immunotherapy treatment for cancers using monoclonal antibodies. We demonstrate three exciting targets for immunotherapy, TNF-α Converting Enzyme (TACE), Cathepsin S and Urokinase Plasmogen Activator and go over the advances made with one of the most used monoclonal antibodies in cancer therapy, Rituximab; as well as Herceptin, which is used for breast cancer therapy. Furthermore, we touch on other venues of immunotherapy, such as adaptive cell transfer, the use of nucleic acids and the use of dendritic cells. Finally, we summarize some ongoing studies that spell tentative advancements for anti-cancer immunotherapy. General significance Immunotherapy is at the forefront of anti-cancer therapies, allying both a high degree of specificity to general high effectiveness and fewer side-effects. Current monoclonal antibodies for cancer immunotherapy have a bright future. Immunotherapy presents opportunity to eliminate tumor growth that chemotherapy can't achieve. Therapeutic antibodies for cancer immunotherapy show better results without undesirable side-effects.
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Affiliation(s)
- Henrique Neves
- Faculty of Health Sciences, University of Macau, Avenida de Universidade, Taipa, Macau
| | - Hang Fai Kwok
- Faculty of Health Sciences, University of Macau, Avenida de Universidade, Taipa, Macau
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11
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Discovering aptamers by cell-SELEX against human soluble growth factors ectopically expressed on yeast cell surface. PLoS One 2014; 9:e93052. [PMID: 24675636 PMCID: PMC3968096 DOI: 10.1371/journal.pone.0093052] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2013] [Accepted: 02/28/2014] [Indexed: 02/07/2023] Open
Abstract
SELEX, the process of selecting aptamers, is often hampered by the difficulty of preparing target molecules in their native forms and by a lack of a simple yet quantitative assay for monitoring enrichment and affinity of reactive aptamers. In this study, we sought to discover DNA aptamers against human serum markers for potential therapeutic and diagnostic applications. To circumvent soluble expression and immobilization for performing SELEX, we ectopically expressed soluble growth factors on the surface of yeast cells to enable cell-SELEX and devised a flow cytometry-based method to quantitatively monitor progressive enrichment of specific aptamers. High-throughput sequencing of selected pools revealed that the emergence of highly enriched sequences concurred with the increase in the percentage of reactive aptamers shown by flow cytometry. Particularly, selected DNA aptamers against VEGF were specific and of high affinity (K(D) = ∼ 1 nM) and demonstrated a potent inhibition of capillary tube formation of endothelial cells, comparable to the effect of a clinically approved anti-VEGF antibody drug, bevacizumab. Considering the fact that many mammalian secretory proteins have been functionally expressed in yeast, the strategy of implementing cell-SELEX and quantitative binding assay can be extended to discover aptamers against a broad array of soluble antigens.
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12
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Pepper LR, Parthasarathy R, Robbins GP, Dang NN, Hammer DA, Boder ET. Isolation of αL I domain mutants mediating firm cell adhesion using a novel flow-based sorting method. Protein Eng Des Sel 2013; 26:515-21. [PMID: 23788664 PMCID: PMC3711393 DOI: 10.1093/protein/gzt028] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2013] [Revised: 05/07/2013] [Accepted: 05/09/2013] [Indexed: 11/12/2022] Open
Abstract
The inserted (I) domain of αLβ2 integrin (LFA-1) contains the entire binding site of the molecule. It mediates both rolling and firm adhesion of leukocytes at sites of inflammation depending on the activation state of the integrin. The affinity change of the entire integrin can be mimicked by the I domain alone through mutations that affect the conformation of the molecule. High-affinity mutants of the I domain have been discovered previously using both rational design and directed evolution. We have found that binding affinity fails to dictate the behavior of I domain adhesion under shear flow. In order to better understand I domain adhesion, we have developed a novel panning method to separate yeast expressing a library of I domain variants on the surface by adhesion under flow. Using conditions analogous to those experienced by cells interacting with the post-capillary vascular endothelium, we have identified mutations supporting firm adhesion that are not found using typical directed evolution techniques that select for tight binding to soluble ligands. Mutants isolated using this method do not cluster with those found by sorting with soluble ligand. Furthermore, these mutants mediate shear-driven cell rolling dynamics decorrelated from binding affinity, as previously observed for I domains bearing engineered disulfide bridges to stabilize activated conformational states. Characterization of these mutants supports a greater understanding of the structure-function relationship of the αL I domain, and of the relationship between applied force and bioadhesion in a broader context.
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Affiliation(s)
- Lauren R. Pepper
- Department of Bioengineering, University of Pennsylvania, Philadelphia, PA 19104, USA
| | | | - Gregory P. Robbins
- Department of Bioengineering, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Nicholas N. Dang
- Department of Bioengineering, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Daniel A. Hammer
- Department of Bioengineering, University of Pennsylvania, Philadelphia, PA 19104, USA
- Department of Chemical and Biomolecular Engineering, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Eric T. Boder
- Department of Chemical and Biomolecular Engineering, University of Tennessee, Knoxville, TN 37996, USA
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13
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Tillotson BJ, Cho YK, Shusta EV. Cells and cell lysates: a direct approach for engineering antibodies against membrane proteins using yeast surface display. Methods 2013; 60:27-37. [PMID: 22449570 PMCID: PMC3405166 DOI: 10.1016/j.ymeth.2012.03.010] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2011] [Accepted: 03/09/2012] [Indexed: 01/16/2023] Open
Abstract
Membrane proteins (MPs) are often desirable targets for antibody engineering. However, the majority of antibody engineering platforms depend implicitly on aqueous solubility of the target antigen which is often problematic for MPs. Recombinant, soluble forms of MPs have been successfully employed as antigen sources for antibody engineering, but heterologous expression and purification of soluble MP fragments remains a challenging and time-consuming process. Here we present a more direct approach to aid in the engineering of antibodies to MPs. By combining yeast surface display technology directly with whole cells or detergent-solubilized whole-cell lysates, antibody libraries can be screened against MP antigens in their near-native conformations. We also describe how the platform can be adapted for antibody characterization and antigen identification. This collection of compatible methods serves as a basis for antibody engineering against MPs and it is predicted that these methods will mature in parallel with developments in membrane protein biochemistry and solubilization technology.
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Affiliation(s)
- Benjamin J. Tillotson
- University of Wisconsin-Madison, Dept. of Chemical and Biological Engineering, 1415 Engineering Dr., Madison, WI 53706
| | - Yong Ku Cho
- University of Wisconsin-Madison, Dept. of Chemical and Biological Engineering, 1415 Engineering Dr., Madison, WI 53706
| | - Eric V. Shusta
- University of Wisconsin-Madison, Dept. of Chemical and Biological Engineering, 1415 Engineering Dr., Madison, WI 53706
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14
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Diversity in genetic in vivo methods for protein-protein interaction studies: from the yeast two-hybrid system to the mammalian split-luciferase system. Microbiol Mol Biol Rev 2012; 76:331-82. [PMID: 22688816 DOI: 10.1128/mmbr.05021-11] [Citation(s) in RCA: 134] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
The yeast two-hybrid system pioneered the field of in vivo protein-protein interaction methods and undisputedly gave rise to a palette of ingenious techniques that are constantly pushing further the limits of the original method. Sensitivity and selectivity have improved because of various technical tricks and experimental designs. Here we present an exhaustive overview of the genetic approaches available to study in vivo binary protein interactions, based on two-hybrid and protein fragment complementation assays. These methods have been engineered and employed successfully in microorganisms such as Saccharomyces cerevisiae and Escherichia coli, but also in higher eukaryotes. From single binary pairwise interactions to whole-genome interactome mapping, the self-reassembly concept has been employed widely. Innovative studies report the use of proteins such as ubiquitin, dihydrofolate reductase, and adenylate cyclase as reconstituted reporters. Protein fragment complementation assays have extended the possibilities in protein-protein interaction studies, with technologies that enable spatial and temporal analyses of protein complexes. In addition, one-hybrid and three-hybrid systems have broadened the types of interactions that can be studied and the findings that can be obtained. Applications of these technologies are discussed, together with the advantages and limitations of the available assays.
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15
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Hu X, Saha P, Chen X, Kim D, Devarasetty M, Varadarajan R, Jin MM. Cell surface assembly of HIV gp41 six-helix bundles for facile, quantitative measurements of hetero-oligomeric interactions. J Am Chem Soc 2012; 134:14642-5. [PMID: 22888993 DOI: 10.1021/ja301099s] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
Helix-helix interactions are fundamental to many biological signals and systems and are found in homo- or heteromultimerization of signaling molecules as well as in the process of virus entry into the host. In HIV, virus-host membrane fusion during infection is mediated by the formation of six-helix bundles (6HBs) from homotrimers of gp41, from which a number of synthetic peptides have been derived as antagonists of virus entry. Using a yeast surface two-hybrid (YS2H) system, a platform designed to detect protein-protein interactions occurring through a secretory pathway, we reconstituted 6HB complexes on the yeast surface, quantitatively measured the equilibrium and kinetic constants of soluble 6HB, and delineated the residues influencing homo-oligomeric and hetero-oligomeric coiled-coil interactions. Hence, we present YS2H as a platform for the facile characterization and design of antagonistic peptides for inhibition of HIV and many other enveloped viruses relying on membrane fusion for infection, as well as cellular signaling events triggered by hetero-oligomeric coiled coils.
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Affiliation(s)
- Xuebo Hu
- Biomedical Engineering Department, Cornell University, Ithaca, New York 14853, USA
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16
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Miersch S, Sidhu SS. Synthetic antibodies: concepts, potential and practical considerations. Methods 2012; 57:486-98. [PMID: 22750306 DOI: 10.1016/j.ymeth.2012.06.012] [Citation(s) in RCA: 89] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2012] [Revised: 06/18/2012] [Accepted: 06/21/2012] [Indexed: 01/08/2023] Open
Abstract
The last 100 years of enquiry into the fundamental basis of humoral immunity has resulted in the identification of antibodies as key molecular sentinels responsible for the in vivo surveillance, neutralization and clearance of foreign substances. Intense efforts aimed at understanding and exploiting their exquisite molecular specificity have positioned antibodies as a cornerstone supporting basic research, diagnostics and therapeutic applications [1]. More recently, efforts have aimed to circumvent the limitations of developing antibodies in animals by developing wholly in vitro techniques for designing antibodies of tailored specificity. This has been realized with the advent of synthetic antibody libraries that possess diversity outside the scope of natural immune repertoires and are thus capable of yielding specificities not otherwise attainable. This review examines the convergence of technologies that have contributed to the development of combinatorial phage-displayed antibody libraries. It further explores the practical concepts that underlie phage display, antibody diversity and the methods used in the generation of and selection from phage-displayed synthetic antibody libraries, highlighting specific applications in which design approaches gave rise to specificities that could not easily be obtained with libraries based upon natural immune repertories.
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Affiliation(s)
- S Miersch
- Banting and Best Department of Medical Research, University of Toronto, Toronto, Ontario, Canada.
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17
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Gera N, Hussain M, Rao BM. Protein selection using yeast surface display. Methods 2012; 60:15-26. [PMID: 22465794 DOI: 10.1016/j.ymeth.2012.03.014] [Citation(s) in RCA: 92] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2011] [Accepted: 03/09/2012] [Indexed: 12/16/2022] Open
Abstract
Binding proteins are typically isolated from combinatorial libraries of scaffold proteins using one of the many library screening tools available, such as phage display, yeast surface display or mRNA display. A key principle underlying these screening technologies is the establishment of a link between each unique mutant protein and its corresponding genetic code. The mutant proteins binding a desired target species are separated and subsequently identified using the genetic code. In this review, we largely focus on the use of yeast surface display for the isolation of binding proteins from combinatorial libraries. In yeast surface display, the yeast cell links the mutant protein to its coding DNA. Each yeast cell expresses the mutant proteins as fusions to a yeast cell wall protein; the yeast cell also carries plasmid DNA that codes for the mutant protein. Over the years, the yeast surface display platform has emerged as a powerful tool for protein engineering, and has been used in a variety of applications including affinity maturation, epitope mapping and biophysical characterization of proteins. Here we present a broad overview of the yeast surface display system and its applications, and compare it with other contemporary screening platforms. Further, we present detailed protocols for the use of yeast surface display to isolate de novo binding proteins from combinatorial libraries, and subsequent biophysical characterization of binders. These protocols can also be easily modified for affinity maturation of the isolated de novo binders.
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Affiliation(s)
- Nimish Gera
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, NC, USA
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18
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Boder ET, Raeeszadeh-Sarmazdeh M, Price JV. Engineering antibodies by yeast display. Arch Biochem Biophys 2012; 526:99-106. [PMID: 22450168 DOI: 10.1016/j.abb.2012.03.009] [Citation(s) in RCA: 93] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2011] [Revised: 03/09/2012] [Accepted: 03/10/2012] [Indexed: 12/19/2022]
Abstract
Since its first application to antibody engineering 15 years ago, yeast display technology has been developed into a highly potent tool for both affinity maturing lead molecules and isolating novel antibodies and antibody-like species. Robust approaches to the creation of diversity, construction of yeast libraries, and library screening or selection have been elaborated, improving the quality of engineered molecules and certainty of success in an antibody engineering campaign and positioning yeast display as one of the premier antibody engineering technologies currently in use. Here, we summarize the history of antibody engineering by yeast surface display, approaches used in its application, and a number of examples highlighting the utility of this method for antibody engineering.
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Affiliation(s)
- Eric T Boder
- Department of Chemical and Biomolecular Engineering, University of Tennessee, Knoxville, TN 37996-2200, USA.
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19
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Gu X, Vedvyas Y, Chen X, Kaushik T, Hwang CI, Hu X, Nikitin AY, Jin MM. Novel strategy for selection of monoclonal antibodies against highly conserved antigens: phage library panning against ephrin-B2 displayed on yeast. PLoS One 2012; 7:e30680. [PMID: 22292016 PMCID: PMC3264634 DOI: 10.1371/journal.pone.0030680] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2011] [Accepted: 12/21/2011] [Indexed: 12/03/2022] Open
Abstract
Ephrin-B2 is predominately expressed in endothelium of arterial origin, involved in developmental angiogenesis and neovasculature formation through its interaction with EphB4. Despite its importance in physiology and pathological conditions, it has been challenging to produce monoclonal antibodies against ephrin-B2 due to its high conservation in sequence throughout human and rodents. Using a novel approach for antibody selection by panning a phage library of human antibody against antigens displayed in yeast, we have isolated high affinity antibodies against ephrin-B2. The function of one high affinity binder (named as ‘EC8’) was manifested in its ability to inhibit ephrin-B2 interaction with EphB4, to cross-react with murine ephrin-B2, and to induce internalization into ephrin-B2 expressing cells. EC8 was also compatible with immunoprecipitation and detection of ephrin-B2 expression in the tissue after standard chemical fixation procedure. Consistent with previous reports on ephrin-B2 induction in some epithelial tumors and tumor-associated vasculatures, EC8 specifically detected ephrin-B2 in tumors as well as the vasculature within and outside of the tumors. We envision that monoclonal antibody developed in this study may be used as a reagent to probe ephrin-B2 distribution in normal as well as in pathological conditions and to antagonize ephrin-B2 interaction with EphB4 for basic science and therapeutic applications.
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Affiliation(s)
- Xiaoling Gu
- Department of Biomedical Engineering, Cornell University, Ithaca, New York, United States of America
| | - Yogindra Vedvyas
- Department of Biomedical Engineering, Cornell University, Ithaca, New York, United States of America
| | - Xiaoyue Chen
- Department of Biomedical Engineering, Cornell University, Ithaca, New York, United States of America
| | - Tanwi Kaushik
- Department of Biomedical Engineering, Cornell University, Ithaca, New York, United States of America
| | - Chang-Il Hwang
- Department of Biomedical Sciences, Cornell University, Ithaca, New York, United States of America
| | - Xuebo Hu
- Department of Biomedical Engineering, Cornell University, Ithaca, New York, United States of America
| | - Alexander Y. Nikitin
- Department of Biomedical Sciences, Cornell University, Ithaca, New York, United States of America
| | - Moonsoo M. Jin
- Department of Biomedical Engineering, Cornell University, Ithaca, New York, United States of America
- * E-mail:
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20
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Abstract
Proteolytic release from the cell surface is an essential activation event for many growth factors and cytokines. TNF-α converting enzyme (TACE) is a membrane-bound metalloprotease responsible for solubilizing many pathologically significant membrane substrates and is an attractive therapeutic target for the treatment of cancer and arthritis. Prior attempts to antagonize cell-surface TACE activity have focused on small-molecule inhibition of the metalloprotease active site. Given the highly conserved nature of metalloprotease active sites, this paradigm has failed to produce a truly specific TACE inhibitor and continues to obstruct the clinical investigation of TACE activity. We report the bespoke development of a specific TACE inhibitory human antibody using "two-step" phage display. This approach combines calculated selection conditions with antibody variable-domain exchange to direct individual antibody variable domains to desired epitopes. The resulting "cross-domain" human antibody is a previously undescribed selective TACE antagonist and provides a unique alternative to small-molecule metalloprotease inhibition.
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