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Tabll AA, Shahein YE, Omran MM, Hussein NA, El-Shershaby A, Petrovic A, Glasnovic M, Smolic R, Smolic M. Monoclonal IgY antibodies: advancements and limitations for immunodiagnosis and immunotherapy applications. Ther Adv Vaccines Immunother 2024; 12:25151355241264520. [PMID: 39071998 PMCID: PMC11273732 DOI: 10.1177/25151355241264520] [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: 11/30/2023] [Accepted: 06/09/2024] [Indexed: 07/30/2024] Open
Abstract
Due to their high specificity and scalability, Monoclonal IgY antibodies have emerged as a valuable alternative to traditional polyclonal IgY antibodies. This abstract provides an overview of the production and purification methods of monoclonal IgY antibodies, highlights their advantages over polyclonal IgY antibodies, and discusses their recent applications. Monoclonal recombinant IgY antibodies, in contrast to polyclonal IgY antibodies, offer several benefits. such as derived from a single B-cell clone, monoclonal antibodies exhibit superior specificity, ensuring consistent and reliable results. Furthermore, it explores the suitability of monoclonal IgY antibodies for low- and middle-income countries, considering their cost-effectiveness and accessibility. We also discussed future directions and challenges in using polyclonal IgY and monoclonal IgY antibodies. In conclusion, monoclonal IgY antibodies offer substantial advantages over polyclonal IgY antibodies regarding specificity, scalability, and consistent performance. Their recent applications in diagnostics, therapeutics, and research highlight their versatility.
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Affiliation(s)
- Ashraf A. Tabll
- Microbial Biotechnology Department, Biotechnology Research Institute, National Research Centre, Giza, Egypt
- Egypt Center for Research and Regenerative Medicine (ECRRM), Cairo, Giza, 12622, Egypt
| | - Yasser E. Shahein
- Molecular Biology Department, Biotechnology Research Institute, National Research Centre, Dokki, Giza, Egypt
| | - Mohamed M. Omran
- Chemistry Department, Faculty of Science, Helwan University, Cairo, Egypt
| | - Nahla A. Hussein
- Molecular Biology Department, Biotechnology Research Institute, National Research Centre, Dokki, Giza, Egypt
| | - Asmaa El-Shershaby
- Molecular Biology Department, Biotechnology Research Institute, National Research Centre, Dokki, Giza, Egypt
| | - Ana Petrovic
- Faculty of Dental Medicine and Health Osijek, Josip Juraj Strossmayer University of Osijek, Osijek, Croatia
| | - Marija Glasnovic
- Faculty of Dental Medicine and Health Osijek, Josip Juraj Strossmayer University of Osijek, Osijek, Croatia
| | - Robert Smolic
- Faculty of Dental Medicine and Health Osijek, Josip Juraj Strossmayer University of Osijek, Osijek, Croatia
| | - Martina Smolic
- Faculty of Dental Medicine and Health Osijek, Josip Juraj Strossmayer University of Osijek, Crkvena 21, 31000 Osijek, Croatia
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Sonnentag SJ, Jenne F, Orian-Rousseau V, Nesterov-Mueller A. High-throughput screening for cell binding and repulsion peptides on multifunctionalized surfaces. Commun Biol 2024; 7:870. [PMID: 39020032 PMCID: PMC11255233 DOI: 10.1038/s42003-024-06541-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2023] [Accepted: 07/03/2024] [Indexed: 07/19/2024] Open
Abstract
The adhesion of cells to the extracellular matrix engages cell surface receptors such as integrins, proteoglycans and other types of cell adhesion molecules such as CD44. To closely examine the determinants of cell adhesion, herein we describe the generation of high-density peptide arrays and test the growth of cells on these multifunctionalized surfaces. The peptide library used consists of over 11,000 different sequences, either random or derived from existing proteins. By applying this screen to SW620 mCherry colorectal cancer cells, we select for peptides with both maximum cell adhesion and maximum cell repulsion. All of these extreme properties are based on unique combinations of amino acids. Here, we identify peptides with maximum cell repulsion on secreted frizzled- and Dickkopf-related proteins. Peptides with strong cell repulsion are found at the poles of the TNF-alpha homotrimer. The formation of cellular patterns on alternating highly repulsive and adhesive peptides are examined. Our screen allows the identification of peptides suitable for biomedical and tissue engineering applications.
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Affiliation(s)
- Steffen J Sonnentag
- Institute of Biological and Chemical Systems - Functional Molecular Systems, Karlsruhe Institute of Technology, Kaiserstraße 12, 76131, Karlsruhe, Germany
| | - Felix Jenne
- Institute of Microstructure Technology, Karlsruhe Institute of Technology, Kaiserstraße 12, 76131, Karlsruhe, Germany
| | - Véronique Orian-Rousseau
- Institute of Biological and Chemical Systems - Functional Molecular Systems, Karlsruhe Institute of Technology, Kaiserstraße 12, 76131, Karlsruhe, Germany.
| | - Alexander Nesterov-Mueller
- Institute of Microstructure Technology, Karlsruhe Institute of Technology, Kaiserstraße 12, 76131, Karlsruhe, Germany.
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Lu J, Ding J, Liu Z, Chen T. Retrospective analysis of the preparation and application of immunotherapy in cancer treatment (Review). Int J Oncol 2022; 60:12. [PMID: 34981814 PMCID: PMC8759346 DOI: 10.3892/ijo.2022.5302] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2021] [Accepted: 12/20/2021] [Indexed: 12/11/2022] Open
Abstract
Monoclonal antibody technology plays a vital role in biomedical and immunotherapy, which greatly promotes the study of the structure and function of genes and proteins. To date, monoclonal antibodies have gone through four stages: murine monoclonal antibody, chimeric monoclonal antibody, humanised monoclonal antibody and fully human monoclonal antibody; thousands of monoclonal antibodies have been used in the fields of biology and medicine, playing a special role in the pathogenesis, diagnosis and treatment of disease. In this review, we compare the advantages and disadvantages of hybridoma technology, phage display technology, ribosome display technology, transgenic mouse technology, single B cell monoclonal antibody generation technologies, and forecast the promising applications of these technologies in clinical medicine, disease diagnosis and tumour treatment.
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Affiliation(s)
- Jiachen Lu
- Department of Obstetrics and Gynecology, The Second Affiliated Hospital of Nanchang University, Nanchang, Jiangxi 330006, P.R. China
| | - Jianing Ding
- Department of Obstetrics and Gynecology, The Second Affiliated Hospital of Nanchang University, Nanchang, Jiangxi 330006, P.R. China
| | - Zhaoxia Liu
- Department of Obstetrics and Gynecology, The Second Affiliated Hospital of Nanchang University, Nanchang, Jiangxi 330006, P.R. China
| | - Tingtao Chen
- Department of Obstetrics and Gynecology, The Second Affiliated Hospital of Nanchang University, Nanchang, Jiangxi 330006, P.R. China
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Ribosome Display Technology: Applications in Disease Diagnosis and Control. Antibodies (Basel) 2020; 9:antib9030028. [PMID: 32605027 PMCID: PMC7551589 DOI: 10.3390/antib9030028] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2020] [Revised: 06/06/2020] [Accepted: 06/08/2020] [Indexed: 12/28/2022] Open
Abstract
Antibody ribosome display remains one of the most successful in vitro selection technologies for antibodies fifteen years after it was developed. The unique possibility of direct generation of whole proteins, particularly single-chain antibody fragments (scFvs), has facilitated the establishment of this technology as one of the foremost antibody production methods. Ribosome display has become a vital tool for efficient and low-cost production of antibodies for diagnostics due to its advantageous ability to screen large libraries and generate binders of high affinity. The remarkable flexibility of this method enables its applicability to various platforms. This review focuses on the applications of ribosome display technology in biomedical and agricultural fields in the generation of recombinant scFvs for disease diagnostics and control.
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Kunamneni A, Clarke EC, Ye C, Bradfute SB, Durvasula R. Generation and Selection of a Panel of Pan-Filovirus Single-Chain Antibodies using Cell-Free Ribosome Display. Am J Trop Med Hyg 2020; 101:198-206. [PMID: 31074409 PMCID: PMC6609206 DOI: 10.4269/ajtmh.18-0658] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
Abstract
Filoviruses, which include ebolaviruses and marburgvirus, can cause outbreaks of highly lethal hemorrhagic fever. This disease causes significant morbidity and mortality in humans and non-human primates, with human fatality rates reaching 90% during some outbreaks. Currently, there is lack of licensed vaccines or antivirals for these viruses. Since early symptoms of filovirus infection mimic more common diseases, there is a strong unmet public health and biodefense need for broad-spectrum filovirus rapid diagnostics. We have generated a panel of mouse single-chain Fv-antibodies (scFvs) to filovirus glycoproteins (GPs) using cell-free ribosome display and determined their cross-reactivity profiles to all known filovirus species. Two scFvs (4-2 and 22-1) were able to detect all known Ebolavirus and Marburgvirus species. This is the first report on ribosome display scFvs that can detect a broad set of filovirus GPs, which demonstrates the potential for use in diagnostics.
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Affiliation(s)
- Adinarayana Kunamneni
- Department of Medicine, Loyola University Medical Center, Chicago, Illinois.,Department of Internal Medicine, Center for Global Health, University of New Mexico, Albuquerque, New Mexico
| | - Elizabeth C Clarke
- Department of Internal Medicine, Center for Global Health, University of New Mexico, Albuquerque, New Mexico
| | - Chunyan Ye
- Department of Internal Medicine, Center for Global Health, University of New Mexico, Albuquerque, New Mexico
| | - Steven B Bradfute
- Department of Internal Medicine, Center for Global Health, University of New Mexico, Albuquerque, New Mexico
| | - Ravi Durvasula
- Department of Internal Medicine, Center for Global Health, University of New Mexico, Albuquerque, New Mexico.,Department of Medicine, Loyola University Medical Center, Chicago, Illinois
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Ren C, Wen X, Mencius J, Quan S. Selection and screening strategies in directed evolution to improve protein stability. BIORESOUR BIOPROCESS 2019. [DOI: 10.1186/s40643-019-0288-y] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
AbstractProtein stability is not only fundamental for experimental, industrial, and therapeutic applications, but is also the baseline for evolving novel protein functions. For decades, stability engineering armed with directed evolution has continued its rapid development and inevitably poses challenges. Generally, in directed evolution, establishing a reliable link between a genotype and any interpretable phenotype is more challenging than diversifying genetic libraries. Consequently, we set forth in a small picture to emphasize the screening or selection techniques in protein stability-directed evolution to secure the link. For a more systematic review, two main branches of these techniques, namely cellular or cell-free display and stability biosensors, are expounded with informative examples.
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Kravchenko Y, Ivanov SV, Kravchenko DS, Frolova EI, Chumakov SP. Combination of ribosome and phage display for fast selection of high affinity VHH antibody fragments. BULLETIN OF RUSSIAN STATE MEDICAL UNIVERSITY 2019. [DOI: 10.24075/brsmu.2019.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Selection of antibodies using phage display involves the preliminary cloning of the repertoire of sequences encoding antigen-binding domains into phagemid, which is considered the bottleneck of the method, limiting the resulting diversity of libraries and leading to the loss of poorly represented variants before the start of the selection procedure. Selection in cell-free conditions using a ribosomal display is devoid from this drawback, however is highly sensitive to PCR artifacts and the RNase contamination. The aim of the study was to test the efficiency of a combination of both methods, including pre-selection in a cell-free system to enrich the source library, followed by cloning and final selection using phage display. This approach may eliminate the shortcomings of each method and increase the efficiency of selection. For selection, alpaca VHH antibody sequences suitable for building an immune library were used due to the lack of VL domains. Analysis of immune libraries from the genes of the VH3, VHH3 and VH4 families showed that the VHH antibodies share in the VH3 and VH4 gene groups is insignificant, and selection from the combined library is less effective than from the VHH3 family of sequences. We found that the combination of ribosomal and phage displays leads to a higher enrichment of high-affinity fragments and avoids the loss of the original diversity during cloning. The combined method allowed us to obtain a greater number of different high-affinity sequences, and all the tested VHH fragments were able to specifically recognize the target, including the total protein extracts of cell cultures.
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Affiliation(s)
- YuE Kravchenko
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Moscow, Russia
| | - SV Ivanov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Moscow, Russia
| | - DS Kravchenko
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Moscow, Russia
| | - EI Frolova
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Moscow, Russia
| | - SP Chumakov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Moscow, Russia
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Lagoutte P, Lugari A, Elie C, Potisopon S, Donnat S, Mignon C, Mariano N, Troesch A, Werle B, Stadthagen G. Combination of ribosome display and next generation sequencing as a powerful method for identification of affibody binders against β-lactamase CTX-M15. N Biotechnol 2019; 50:60-69. [PMID: 30634000 DOI: 10.1016/j.nbt.2019.01.004] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2018] [Revised: 01/07/2019] [Accepted: 01/07/2019] [Indexed: 01/15/2023]
Abstract
CTX-M15 is one of the most widespread, extended spectrum β-lactamases, a major determinant of antibiotic resistance representing urgent public health threats, among enterobacterial strains infecting humans and animals. Here we describe the selection of binders to CTX-M15 from a combinatorial affibody library displayed on ribosomes. Upon three increasingly selective ribosome display iterations, selected variants were identified by next generation sequencing (NGS). Nine affibody variants with high relative abundance bearing QRP and QLH amino acid motifs at residues 9-11 were produced and characterized in terms of stability, affinity and specificity. All affibodies were correctly folded, with affinities ranging from 0.04 to 2 μM towards CTX-M15, and successfully recognized CTX-M15 in bacterial lysates, culture supernatants and on whole bacteria. It was further demonstrated that the binding of affibody molecules to CTX-M15 modulated the enzyme's kinetic parameters. This work provides an approach using ribosome display coupled to NGS for the rapid generation of protein ligands of interest in diagnostic and research applications.
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Affiliation(s)
| | - Adrien Lugari
- BIOASTER, 40 Avenue Tony Garnier, 69007 Lyon, France
| | - Céline Elie
- BIOASTER, 40 Avenue Tony Garnier, 69007 Lyon, France
| | | | | | | | | | - Alain Troesch
- BIOASTER, 40 Avenue Tony Garnier, 69007 Lyon, France
| | - Bettina Werle
- BIOASTER, 40 Avenue Tony Garnier, 69007 Lyon, France.
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9
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Kunamneni A, Ye C, Bradfute SB, Durvasula R. Ribosome display for the rapid generation of high-affinity Zika-neutralizing single-chain antibodies. PLoS One 2018; 13:e0205743. [PMID: 30444865 PMCID: PMC6239285 DOI: 10.1371/journal.pone.0205743] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2018] [Accepted: 10/01/2018] [Indexed: 11/18/2022] Open
Abstract
Background Zika virus (ZIKV) is an emerging pathogen with no approved therapeutics and only limited diagnostics available. To address this gap, six mouse single-chain antibodies (scFvs) to ZIKV envelope (E) protein were isolated rapidly and efficiently from a ribosome-displayed antibody library constructed from the spleens of five immunized mice. Methodology/Results In this report, we have generated a panel of mouse scFvs to ZIKV E protein using ribosome display. The six scFvs demonstrated no cross-reactivity with DENV2 NGC envelope protein, suggesting specificity for ZIKV E protein. These scFvs showed differences in their affinity: two (scFv45-3, scFv63-1) of them were dominant after four rounds of panning, and showed higher affinity (an apparent Kd values from 19 to 27 nM) than the other four (scFv5-1, scFv7-2, scFv38-1, and scFv51-2). All six scFvs showed ZIKV-neutralizing activity in the plaque reduction neutralization test (PRNT) assay and their neutralizing activity was positively correlated with their affinities. Conclusions/Significance The scFvs (45–3 and 63–1) with highest affinity may have dual utility as diagnostics capable of recognizing ZIKV E subtypes and may be further developed to treat ZIKV infection. Our approach has the added advantage of generating Fc receptor-deficient antibodies, minimizing concern of antibody-dependent enhancement (ADE) of infection.
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Affiliation(s)
- Adinarayana Kunamneni
- Center for Global Health, Department of Internal Medicine, University of New Mexico, Albuquerque, New Mexico, United States of America
- Department of Medicine, Loyola University Medical Center, Chicago, United States of America
| | - Chunyan Ye
- Center for Global Health, Department of Internal Medicine, University of New Mexico, Albuquerque, New Mexico, United States of America
| | - Steven B. Bradfute
- Center for Global Health, Department of Internal Medicine, University of New Mexico, Albuquerque, New Mexico, United States of America
| | - Ravi Durvasula
- Center for Global Health, Department of Internal Medicine, University of New Mexico, Albuquerque, New Mexico, United States of America
- Department of Medicine, Loyola University Medical Center, Chicago, United States of America
- * E-mail:
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11
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Park SH, Uzawa T, Hattori F, Ogino S, Morimoto N, Tsuneda S, Ito Y. “All-in-one” in vitro selection of collagen-binding vascular endothelial growth factor. Biomaterials 2018; 161:270-278. [DOI: 10.1016/j.biomaterials.2018.01.055] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2017] [Revised: 01/29/2018] [Accepted: 01/29/2018] [Indexed: 01/08/2023]
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Galán A, Comor L, Horvatić A, Kuleš J, Guillemin N, Mrljak V, Bhide M. Library-based display technologies: where do we stand? MOLECULAR BIOSYSTEMS 2017; 12:2342-58. [PMID: 27306919 DOI: 10.1039/c6mb00219f] [Citation(s) in RCA: 76] [Impact Index Per Article: 10.9] [Reference Citation Analysis] [Abstract] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Over the past two decades, library-based display technologies have been staggeringly optimized since their appearance in order to mimic the process of natural molecular evolution. Display technologies are essential for the isolation of specific high-affinity binding molecules (proteins, polypeptides, nucleic acids and others) for diagnostic and therapeutic applications in cancer, infectious diseases, autoimmune, neurodegenerative, inflammatory pathologies etc. Applications extend to other fields such as antibody and enzyme engineering, cell-free protein synthesis and the discovery of protein-protein interactions. Phage display technology is the most established of these methods but more recent fully in vitro alternatives, such as ribosome display, mRNA display, cis-activity based (CIS) display and covalent antibody display (CAD), as well as aptamer display and in vitro compartmentalization, offer advantages over phage in library size, speed and the display of unnatural amino acids and nucleotides. Altogether, they have produced several molecules currently approved or in diverse stages of clinical or preclinical testing and have provided researchers with tools to address some of the disadvantages of peptides and nucleotides such as their low affinity, low stability, high immunogenicity and difficulty to cross membranes. In this review we assess the fundamental technological features and point out some recent advances and applications of display technologies.
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Affiliation(s)
- Asier Galán
- ERA Chair FP7, Internal diseases, Faculty of Veterinary Medicine, University of Zagreb, Heinzelova 55, 10 000 Zagreb, Croatia.
| | - Lubos Comor
- Laboratory of Biomedical Microbiology and Immunology, University of Veterinary Medicine and Pharmacy, Kosice, Slovakia
| | - Anita Horvatić
- ERA Chair FP7, Internal diseases, Faculty of Veterinary Medicine, University of Zagreb, Heinzelova 55, 10 000 Zagreb, Croatia.
| | - Josipa Kuleš
- ERA Chair FP7, Internal diseases, Faculty of Veterinary Medicine, University of Zagreb, Heinzelova 55, 10 000 Zagreb, Croatia.
| | - Nicolas Guillemin
- ERA Chair FP7, Internal diseases, Faculty of Veterinary Medicine, University of Zagreb, Heinzelova 55, 10 000 Zagreb, Croatia.
| | - Vladimir Mrljak
- ERA Chair FP7, Internal diseases, Faculty of Veterinary Medicine, University of Zagreb, Heinzelova 55, 10 000 Zagreb, Croatia.
| | - Mangesh Bhide
- ERA Chair FP7, Internal diseases, Faculty of Veterinary Medicine, University of Zagreb, Heinzelova 55, 10 000 Zagreb, Croatia. and Laboratory of Biomedical Microbiology and Immunology, University of Veterinary Medicine and Pharmacy, Kosice, Slovakia and Institute of Neuroimmunology, Slovak Academy of Sciences, Bratislava, Slovakia
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Cong C, Yu X, He Y, Dai Y, Zhang Y, Wang M, He M. Cell-free ribosome display and selection of antibodies on arrayed antigens. Proteomics 2016; 16:1291-6. [PMID: 26899874 DOI: 10.1002/pmic.201500412] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2015] [Revised: 01/05/2016] [Accepted: 02/16/2016] [Indexed: 11/09/2022]
Abstract
In vitro display technology is a powerful tool for discovery and optimisation of novel antibodies. With increasing demands on various binding molecules in proteomics studies, techniques for a large-scale generation of antibodies or antibody fragments are needed. Here, we describe a novel method for parallel generation of different antibody fragments (scFv) by integrating cell-free ribosome display with array technology. We have demonstrated the procedure by successfully isolating scFv antibodies specific to 16 different cancer biomarkers via a single process. Our results provide proof of principle for multiple production of various scFv antibodies simultaneously.
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Affiliation(s)
- Cong Cong
- Lab of Recombinant Protein Therapeutics, Chengdu Institute of Biological Products, SinoPharm, Chengdu, Sichuan, P. R. China
| | - Xin Yu
- Lab of Recombinant Protein Therapeutics, Chengdu Institute of Biological Products, SinoPharm, Chengdu, Sichuan, P. R. China
| | - Yongzhi He
- Lab of Recombinant Protein Therapeutics, Chengdu Institute of Biological Products, SinoPharm, Chengdu, Sichuan, P. R. China
| | - Yujian Dai
- Lab of Recombinant Protein Therapeutics, Chengdu Institute of Biological Products, SinoPharm, Chengdu, Sichuan, P. R. China
| | - Yongxia Zhang
- Lab of Recombinant Protein Therapeutics, Chengdu Institute of Biological Products, SinoPharm, Chengdu, Sichuan, P. R. China
| | - Mingrong Wang
- Lab of Recombinant Protein Therapeutics, Chengdu Institute of Biological Products, SinoPharm, Chengdu, Sichuan, P. R. China
| | - Mingyue He
- Lab of Recombinant Protein Therapeutics, Chengdu Institute of Biological Products, SinoPharm, Chengdu, Sichuan, P. R. China
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14
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Gan R, Jewett MC. Evolution of translation initiation sequences using in vitro yeast ribosome display. Biotechnol Bioeng 2016; 113:1777-86. [PMID: 26757179 DOI: 10.1002/bit.25933] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2015] [Revised: 12/13/2015] [Accepted: 01/07/2016] [Indexed: 11/08/2022]
Abstract
We report a novel in vitro yeast ribosome display method based on cell-free protein synthesis (CFPS) using linear DNA templates. We demonstrate that our platform can enrich a target gene from a model library by 100-fold per round of selection. We demonstrate the utility of our approach by evolving cap-independent translation initiation (CITI) sequences, which result in a 13-fold increase in CFPS yields after four rounds of selection, and a threefold further increase by placing the beneficial short sequences in tandem. We also show that 12 of the selected CITI sequences permit precise control of gene expression in vitro over a range of up to 80-fold by enhancing translation (and not as cryptic promoters). These 12 sequences are then shown to tune protein expression in vivo, though likely due to a different mechanism. Looking forward, yeast ribosome display holds promise for evolving libraries of proteins and DNA regulatory parts for protein engineering and synthetic biology. Biotechnol. Bioeng. 2016;113: 1777-1786. © 2016 Wiley Periodicals, Inc.
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Affiliation(s)
- Rui Gan
- Department of Chemical and Biological Engineering, Northwestern University, 2145 Sheridan Road, Evanston, Illinois, 60208
| | - Michael C Jewett
- Department of Chemical and Biological Engineering, Northwestern University, 2145 Sheridan Road, Evanston, Illinois, 60208. .,Chemistry of Life Processes Institute, Northwestern University, Evanston, Illinois. .,Member, Robert H. Lurie Comprehensive Cancer Center, Northwestern University, Evanston, Illinois. .,Simpson Querrey Institute, Northwestern University, Evanston, Illinois.
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Rozenblum GT, Lopez VG, Vitullo AD, Radrizzani M. Aptamers: current challenges and future prospects. Expert Opin Drug Discov 2015; 11:127-35. [PMID: 26630462 DOI: 10.1517/17460441.2016.1126244] [Citation(s) in RCA: 55] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
INTRODUCTION Aptamers are oligonucleotide molecules raised in vitro from large combinatorial libraries of nucleic acids and developed to bind to targets with high affinity and specificity. Whereas novel target molecules are proposed for therapeutic intervention and diagnostic, aptamer technology has a great potential to become a source of lead compounds. AREAS COVERED In this review, the authors address the current status of the technology and highlight the recent progress in aptamer-based technologies. They also discuss the current major technical limitations of aptamer technology and propose original solutions based on existing technologies that could result in a solid aptamer-discovery platform. EXPERT OPINION Whereas aptamers have shown to bind to targets with similar affinities and specificities to those of antibodies, aptamers have several advantages that could outweigh antibody technology and open new opportunities for better medical and diagnostic solutions. However, the current status of the aptamer technology suffers from several technical limitations that slowdown the progression of novel aptamers into the clinic and makes the business around aptamers challenging.
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Affiliation(s)
- Guido Tomás Rozenblum
- a Departamento de Investigaciones Biomédicas y Biotecnológicas , Centro de Estudios Biomédicos, Biotecnológicos, Ambientales y Diagnóstico, CEBBAD - Universidad Maimónides , Buenos Aires , Argentina
| | - Vanina Gisela Lopez
- a Departamento de Investigaciones Biomédicas y Biotecnológicas , Centro de Estudios Biomédicos, Biotecnológicos, Ambientales y Diagnóstico, CEBBAD - Universidad Maimónides , Buenos Aires , Argentina
| | - Alfredo Daniel Vitullo
- a Departamento de Investigaciones Biomédicas y Biotecnológicas , Centro de Estudios Biomédicos, Biotecnológicos, Ambientales y Diagnóstico, CEBBAD - Universidad Maimónides , Buenos Aires , Argentina
| | - Martín Radrizzani
- b Laboratorio de Neuro y Citogenética Molecular , Centro de Estudios de Salud y Medio Ambiente, Universidad de San Martín - CONICET , Buenos Aires , Argentina
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Nevola L, Giralt E. Modulating protein-protein interactions: the potential of peptides. Chem Commun (Camb) 2015; 51:3302-15. [PMID: 25578807 DOI: 10.1039/c4cc08565e] [Citation(s) in RCA: 195] [Impact Index Per Article: 21.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Protein-protein interactions (PPIs) have emerged as important and challenging targets in chemical biology and medicinal chemistry. The main difficulty encountered in the discovery of small molecule modulators derives from the large contact surfaces involved in PPIs when compared with those that participate in protein-small molecule interactions. Because of their intrinsic features, peptides can explore larger surfaces and therefore represent a useful alternative to modulate PPIs. The use of peptides as therapeutics has been held back by their instability in vivo and poor cell internalization. However, more than 200 peptide drugs and homologous compounds (proteins or antibodies) containing peptide bonds are (or have been) on the market, and many alternatives are now available to tackle these limitations. This review will focus on the latest progress in the field, spanning from "lead" identification methods to binding evaluation techniques, through an update of the most successful examples described in the literature.
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Affiliation(s)
- Laura Nevola
- Institute for Research in Biomedicine (IRB Barcelona), C/Baldiri Reixac 10, 08028 Barcelona, Spain.
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Characterization of Anti-Citrinin Specific ScFvs Selected from Non-Immunized Mouse Splenocytes by Eukaryotic Ribosome Display. PLoS One 2015; 10:e0131482. [PMID: 26131718 PMCID: PMC4488840 DOI: 10.1371/journal.pone.0131482] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2015] [Accepted: 06/01/2015] [Indexed: 11/19/2022] Open
Abstract
Single chain variable fragments (scFvs) against citrinin (CIT) were selected from a scFv library constructed from the splenocytes of non-immunized mice by an improved eukaryotic ribosome display technology in this study. Bovine serum albumin (BSA)/ CIT-BSA and ovalbumin (OVA)/ CIT-OVA were used as the antigens to select specific anti-CIT scFvs. Eukaryotic in situ RT-PCR method was used to recover the selected mRNA after every affinity selection. After six rounds of ribosome display, expression vector pTIG-TRX carrying specific scFv DNAs were constructed and transformed into Escherichia coli BL21 (DE3) for protein expression. Thirteen positive clones were selected out of which three (designated 23, 68 and 109) showed high binding activity and specificity to CIT by indirect ELISA, while no clone showed binding activity with carrier proteins. The three scFvs showed high specificity to CIT and the cross reactivity with other mycotoxins was below 0.01% as determined by indirect competitive ELISA. These specific scFvs offer a potential novel immunoassay method for CIT residues. This study confirmed the effectiveness of the improved eukaryotic ribosome display system and could be used as a reference for the selection of scFvs specific to other small molecules using ribosome display.
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18
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Milroy LG, Grossmann TN, Hennig S, Brunsveld L, Ottmann C. Modulators of Protein–Protein Interactions. Chem Rev 2014; 114:4695-748. [DOI: 10.1021/cr400698c] [Citation(s) in RCA: 352] [Impact Index Per Article: 35.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Affiliation(s)
- Lech-Gustav Milroy
- Laboratory
of Chemical Biology and Institute of Complex Molecular Systems, Department
of Biomedical Engineering, Technische Universiteit Eindhoven, Den Dolech
2, 5612 AZ Eindhoven, The Netherlands
| | - Tom N. Grossmann
- Chemical Genomics Centre of the Max Planck Society, Otto-Hahn Straße 15, 44227 Dortmund, Germany
- Department
of Chemistry and Chemical Biology, Technical University Dortmund, Otto-Hahn-Strasse 6, 44227 Dortmund, Germany
| | - Sven Hennig
- Chemical Genomics Centre of the Max Planck Society, Otto-Hahn Straße 15, 44227 Dortmund, Germany
| | - Luc Brunsveld
- Laboratory
of Chemical Biology and Institute of Complex Molecular Systems, Department
of Biomedical Engineering, Technische Universiteit Eindhoven, Den Dolech
2, 5612 AZ Eindhoven, The Netherlands
| | - Christian Ottmann
- Laboratory
of Chemical Biology and Institute of Complex Molecular Systems, Department
of Biomedical Engineering, Technische Universiteit Eindhoven, Den Dolech
2, 5612 AZ Eindhoven, The Netherlands
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19
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Tada S, Timucin E, Kitajima T, Sezerman OU, Ito Y. Direct in vitro selection of titanium-binding epidermal growth factor. Biomaterials 2014; 35:3497-503. [DOI: 10.1016/j.biomaterials.2014.01.010] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2013] [Accepted: 01/07/2014] [Indexed: 02/01/2023]
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20
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Wada A, Hara S, Osada H. Ribosome display and photo-cross-linking techniques for in vitro identification of target proteins of bioactive small molecules. Anal Chem 2014; 86:6768-73. [PMID: 24380432 DOI: 10.1021/ac4030208] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
The identification of target proteins of bioactive small molecules as bioprobe candidates or drug seeds is indispensable for elucidating their actions and predicting their side effects. To meet the current need, we developed a scheme for detection and identification of target proteins by using ribosome display and photo-cross-linking techniques, and demonstrated the feasibility. The mRNAs encoding full-length human proteins (FHPs) were constructed and translated in vitro to prepare pools of FHP-ribosome-mRNA complexes used for ribosome display selection. Expression levels of the FHPs were confirmed by Western blot analysis, and photo-cross-linked small-molecule beads were assessed through cell-free synthesized FHP binding assay. After ribosome display selection against photo-cross-linked small-molecule beads, RT-PCR using mRNAs recovered from the selected ternary complexes and electrophoresis of the PCR products allowed specific detection of the target proteins binding to the beads. In addition, a repeat of ribosome display selection enabled us to identify the target proteins even if the molar quantity was one ten-thousandth of that of the other proteins in a cell-free synthesized FHP pool. Therefore, these results showed that ribosome display using photo-cross-linked small-molecule beads and further extended FHP pool could be one of the powerful techniques for identification of unknown target proteins of bioactive small molecules.
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Affiliation(s)
- Akira Wada
- Antibiotics Laboratory, RIKEN , 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
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21
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Zhu J, Larman HB, Gao G, Somwar R, Zhang Z, Laserson U, Ciccia A, Pavlova N, Church G, Zhang W, Kesari S, Elledge SJ. Discovery of protein interactions using parallel analysis of translated ORFs (PLATO). Nat Protoc 2014; 9:90-103. [PMID: 24336473 PMCID: PMC4129458 DOI: 10.1038/nprot.2013.167] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Parallel analysis of translated open reading frames (ORFs) (PLATO) can be used for the unbiased discovery of interactions between full-length proteins encoded by a library of 'prey' ORFs and surface-immobilized 'bait' antibodies, polypeptides or small-molecular-weight compounds. PLATO uses ribosome display (RD) to link ORF-derived mRNA molecules to the proteins they encode, and recovered mRNA from affinity enrichment is subjected to analysis using massively parallel DNA sequencing. Compared with alternative in vitro methods, PLATO provides several advantages including library size and cost. A unique advantage of PLATO is that an alternative reverse transcription-quantitative PCR (RT-qPCR) protocol can be used to test binding of specific, individual proteins. To illustrate a typical experimental workflow, we demonstrate PLATO for the identification of the immune target of serum antibodies from patients with inclusion body myositis (IBM). Beginning with an ORFeome library in an RD vector, the protocol can produce samples for deep sequencing or RT-qPCR within 4 d.
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Affiliation(s)
- Jian Zhu
- Division of Genetics, Department of Medicine, Brigham and Women’s Hospital, Boston, MA
- Department of Genetics, Harvard University Medical School, Boston, MA
- Howard Hughes Medical Institute
| | - H. Benjamin Larman
- Division of Genetics, Department of Medicine, Brigham and Women’s Hospital, Boston, MA
- Harvard-MIT Division of Health Sciences and Technology, Cambridge, MA
- Department of Materials Science and Engineering, Massachusetts Institute of Technology, Cambridge, MA
- Department of Genetics, Harvard University Medical School, Boston, MA
- Howard Hughes Medical Institute
| | - Geng Gao
- Division of Genetics, Department of Medicine, Brigham and Women’s Hospital, Boston, MA
- Department of Genetics, Harvard University Medical School, Boston, MA
- Howard Hughes Medical Institute
| | - Romel Somwar
- Human Oncology and Pathogenesis Program, Memorial Sloan-Kettering Cancer Center, New York, NY
| | - Zijuan Zhang
- Department of Chemistry, University of Massachusetts Boston, Boston, MA
| | - Uri Laserson
- Harvard-MIT Division of Health Sciences and Technology, Cambridge, MA
- Department of Genetics, Harvard University Medical School, Boston, MA
- Department of Mathematics, Massachusetts Institute of Technology, Cambridge, MA
| | - Alberto Ciccia
- Division of Genetics, Department of Medicine, Brigham and Women’s Hospital, Boston, MA
- Department of Genetics, Harvard University Medical School, Boston, MA
- Howard Hughes Medical Institute
| | - Natalya Pavlova
- Division of Genetics, Department of Medicine, Brigham and Women’s Hospital, Boston, MA
- Department of Genetics, Harvard University Medical School, Boston, MA
- Howard Hughes Medical Institute
| | - George Church
- Harvard-MIT Division of Health Sciences and Technology, Cambridge, MA
- Department of Genetics, Harvard University Medical School, Boston, MA
| | - Wei Zhang
- Department of Chemistry, University of Massachusetts Boston, Boston, MA
| | - Santosh Kesari
- Division of Neuro-Oncology, Translational Neuro-Oncology Laboratories, Department of Neurosciences, U.C. San Diego, Moores Cancer Center, La Jolla, CA
| | - Stephen J. Elledge
- Division of Genetics, Department of Medicine, Brigham and Women’s Hospital, Boston, MA
- Department of Genetics, Harvard University Medical School, Boston, MA
- Howard Hughes Medical Institute
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22
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Wang W, Uzawa T, Tochio N, Hamatsu J, Hirano Y, Tada S, Saneyoshi H, Kigawa T, Hayashi N, Ito Y, Taiji M, Aigaki T, Ito Y. A fluorogenic peptide probe developed by in vitro selection using tRNA carrying a fluorogenic amino acid. Chem Commun (Camb) 2013; 50:2962-4. [PMID: 24317094 DOI: 10.1039/c3cc47624c] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
A peptide that binds and emits fluorescence in response to conformational change in a target protein was developed by in vitro selection using tRNA carrying a fluorogenic amino acid. This technology could prove to be useful for the development of separation-free immunoassays and bio-imaging analyses.
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Affiliation(s)
- Wei Wang
- Nano Medical Engineering Laboratory, RIKEN, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan.
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23
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Wada A. Development of Next-Generation Peptide Binders Using In vitro Display Technologies and Their Potential Applications. Front Immunol 2013; 4:224. [PMID: 23914189 PMCID: PMC3730117 DOI: 10.3389/fimmu.2013.00224] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2013] [Accepted: 05/29/2013] [Indexed: 12/02/2022] Open
Abstract
During the last decade, a variety of monoclonal antibodies have been developed and used as molecular targeting drugs in medical therapies. Although antibody drugs tend to have intense pharmacological activities and negligible side effects, several issues in their development and prescription remain to be resolved. Synthetic peptides with affinities and specificities for a desired target have received significant attention as alternatives to antibodies. In vitro display technologies are powerful methods for the selection of such peptides from combinatorial peptide libraries. Various types of peptide binders are being selected with such technologies for use in a wide range of fields from bioscience to medicine. This mini review article focuses on the current state of in vitro display selection of synthetic peptide binders and compares the selected peptides with natural peptides/proteins to provide a better understanding of the target affinities and inhibitory activities derived from their amino acid sequences and structural frameworks. The potential of synthetic peptide binders as alternatives to antibody drugs in therapeutic applications is also reviewed.
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24
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Fuchs S, Nguyen HD, Phan TTP, Burton MF, Nieto L, de Vries-van Leeuwen IJ, Schmidt A, Goodarzifard M, Agten SM, Rose R, Ottmann C, Milroy LG, Brunsveld L. Proline primed helix length as a modulator of the nuclear receptor-coactivator interaction. J Am Chem Soc 2013; 135:4364-71. [PMID: 23437920 DOI: 10.1021/ja311748r] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
Nuclear receptor binding to coactivator proteins is an obligate first step in the regulation of gene transcription. Nuclear receptors preferentially bind to an LXXLL peptide motif which is highly conserved throughout the 300 or so natural coactivator proteins. This knowledge has shaped current understanding of this fundamental protein-protein interaction, and continues to inspire the search for new drug therapies. However, sequence specificity beyond the LXXLL motif and the molecular functioning of flanking residues still requires urgent addressing. Here, ribosome display has been used to reassess the estrogen receptor for new and enlarged peptide recognition motifs, leading to the discovery of a potent and highly evolved PXLXXLLXXP binding consensus. Molecular modeling and X-ray crystallography studies have provided the molecular insights on the role of the flanking prolines in priming the length of the α-helix and enabling optimal interactions of the α-helix dipole and its surrounding amino acids with the surface charge clamp and the receptor activation function 2. These findings represent new structural parameters for modulating the nuclear receptor-coactivator interaction based on linear sequences of proteinogenic amino acids and for the design of chemically modified inhibitors.
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Affiliation(s)
- Sascha Fuchs
- Laboratory of Chemical Biology, Department of Biomedical Engineering, Technische Universiteit Eindhoven, Den Dolech 2, 5612 AZ Eindhoven, The Netherlands
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25
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Barendt PA, Ng DT, McQuade CN, Sarkar CA. Streamlined protocol for mRNA display. ACS COMBINATORIAL SCIENCE 2013; 15:77-81. [PMID: 23305392 PMCID: PMC3666848 DOI: 10.1021/co300135r] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
mRNA display is a powerful method for in vitro directed evolution of polypeptides, but its time-consuming, technically demanding nature has hindered its widespread use. We present a streamlined protocol in which lengthy mRNA purification steps are replaced with faster precipitation and ultrafiltration alternatives; additionally, other purification steps are entirely eliminated by using a reconstituted translation system and by performing reverse transcription after selection, which also protects input polypeptides from thermal denaturation. We tested this procedure by performing affinity selection against Her2 using binary libraries containing a nonspecific designed ankyrin repeat protein (DARPin) doped with a Her2-binding DARPin (dopant fraction ranging from 1:10 to 1:10 000). The Her2-binding DARPin was recovered in all cases, with an enrichment factor of up to 2 orders of magnitude per selection round. The time required for 1 round is reduced from ∼4-7 days to 2 days with our protocol, thus simplifying and accelerating mRNA display experiments.
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Affiliation(s)
| | | | - Casey N. McQuade
- Department of Bioengineering, University of Pennsylvania, 240 Skirkanich Hall, 210 S.
33 Street, Philadelphia, PA 19104-6321, United States
| | - Casim A. Sarkar
- Department of Bioengineering, University of Pennsylvania, 240 Skirkanich Hall, 210 S.
33 Street, Philadelphia, PA 19104-6321, United States
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26
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Broad-specificity mRNA-rRNA complementarity in efficient protein translation. PLoS Genet 2012; 8:e1002598. [PMID: 22457640 PMCID: PMC3310771 DOI: 10.1371/journal.pgen.1002598] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2011] [Accepted: 02/03/2012] [Indexed: 12/30/2022] Open
Abstract
Studies of synthetic, well-defined biomolecular systems can elucidate inherent capabilities that may be difficult to uncover in a native biological context. Here, we used a minimal, reconstituted translation system from Escherichia coli to identify efficient ribosome binding sites (RBSs) in an unbiased, high-throughput manner. We applied ribosome display, a powerful in vitro selection method, to enrich only those mRNA sequences which could direct rapid protein translation. In addition to canonical Shine-Dalgarno (SD) motifs, we unexpectedly recovered highly efficient cytosine-rich (C-rich) sequences that exhibit unmistakable complementarity to the 16S rRNA of the small subunit of the ribosome, indicating that broad-specificity base-pairing may be an inherent, general mechanism for efficient translation. Furthermore, given the conservation of ribosomal structure and function across species, the broader relevance of C-rich RBS sequences identified through our in vitro evolution approach is supported by multiple, diverse examples in nature, including C-rich RBSs in several bacteriophage and plants, a poly-C consensus before the start codon in a lower eukaryote, and Kozak-like sequences in vertebrates. In order to maintain an appropriate balance of proteins in the cell, the protein factories (ribosomes) translate different messages (mRNAs) into protein at different rates. Many human diseases, including cancer and certain hereditary diseases, are caused by making too much or too little protein. Additionally, infections caused by bacteria and viruses are enabled by the ability of these organisms to produce protein very quickly while situated in their host. For these reasons, it is important to understand the ways in which ribosomes may recognize mRNAs and initiate translation into protein. We developed an experimental system that allowed us to uncover the inherent mRNA–binding ability of the ribosomes in a common bacterium, Escherichia coli. We found evidence that, when removed from the native cellular environment, these ribosomes are able to make protein very efficiently using previously unidentified ribosome binding sites on the mRNA that closely resemble known ribosome binding sites in diverse organisms, including plants and humans. Our results suggest a general, ubiquitous mechanism of mRNA–ribosome association during translation initiation.
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27
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Lassen KS, Schultz H, Heegaard NHH, He M. A novel DNAseq program for enhanced analysis of Illumina GAII data: a case study on antibody complementarity-determining regions. N Biotechnol 2012; 29:271-8. [PMID: 22155428 DOI: 10.1016/j.nbt.2011.11.014] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2011] [Revised: 11/09/2011] [Accepted: 11/25/2011] [Indexed: 11/16/2022]
Abstract
High-throughput DNA sequencing technologies are increasingly becoming powerful systems for the comprehensive analysis of variations in whole genomes or various DNA libraries. As they are capable of producing massive collections of short sequences with varying lengths, a major challenge is how to turn these reads into biologically meaningful information. The first stage is to assemble the short reads into longer sequences through an in silico process. However, currently available software/programs allow only the assembly of abundant sequences, which apparently results in the loss of highly variable (or rare) sequences or creates artefact assemblies. In this paper, we describe a novel program (DNAseq) that is capable of assembling highly variable sequences and displaying them directly for phylogenetic analysis. In addition, this program is Microsoft Windows-based and runs by a normal PC with 700MB RAM for a general use. We have applied it to analyse a human naive single-chain antibody (scFv) library, comprehensively revealing the diversity of antibody variable complementarity-determining regions (CDRs) and their families. Although only a scFv library was exemplified here, we envisage that this program could be applicable to other genome libraries.
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Affiliation(s)
- Klaus S Lassen
- Department of Clinical Biochemistry and Immunology, Statens Serum Institut, Artillerivej 5, 2300 Copenhagen S, Denmark.
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28
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Abstract
Ribosome display is an in vitro evolution technology for proteins. It is based on in vitro translation, but prevents the newly synthesized protein and the mRNA encoding it from leaving the ribosome. It thereby couples phenotype and genotype. Since no cells need to be transformed, very large libraries can be used directly in selections, and the in vitro amplification provides a very convenient integration of random mutagenesis that can be incorporated into the procedure. This review highlights concepts, mechanisms, and different variations of ribosome display and compares it to related methods. Applications of ribosome display are summarized, e.g., the directed evolution of proteins for higher binding affinity, for higher stability or other improved biophysical parameters and enzymatic properties. Ribosome display has developed into a robust technology used in academia and industry alike, and it has made the cell-free Darwinian evolution of proteins over multiple generations a reality.
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Affiliation(s)
- Andreas Plückthun
- Department of Biochemistry, University of Zurich, Zurich, Switzerland.
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29
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Abstract
Ribosome display is a cell-free technology which enables in vitro selection and evolution of antibodies from very large diversified DNA libraries. It operates through the following key steps: (1) generation of PCR library; (2) formation of stable antibody-ribosome-mRNA (ARM) complexes as the selection particles, (3) selection of ligand-binding ARM complexes on an immobilized ligand and (4) recovery of the selected genetic information as DNA by RT-PCR. Since PCR-based random or/and site-directed mutagenesis can be easily used to introduce mutations into the selected DNA pool in each cycle, ribosome display offers an efficient "protein evolution" tool for antibody optimization. Both prokaryotic and eukaryotic cell-free systems have been explored for ribosome display of different proteins. In this chapter, we describe the use of the eukaryotic rabbit reticulocyte ribosome display method to isolate variants of V(H) antibody fragments with improved affinities.
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Affiliation(s)
- Bryan M Edwards
- Crescendo Biologics Ltd., Babraham Research Campus, Cambridge, UK
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30
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Abstract
Ribosome display is a cell-free display technology which enables in vitro selection of antibodies from large recombinant DNA libraries. It also allows continuous introduction of mutations into the selected DNA pool by PCR-based mutagenesis in each cycle, enabling selection of antibody variants with improved affinity, specificity, and stability, thus providing a powerful "protein evolution" tool for optimizing antibody therapeutics. Ribosome display selects required molecules by linking individual proteins (phenotype) with their corresponding mRNAs (genotype) through the formation of stable Protein-Ribosome-mRNA (PRM) complexes. By affinity interaction with an immobilized ligand, the captured PRM complexes are recovered as cDNA using RT-PCR from the ribosome-attached mRNA. The DNA is then subjected to subsequent ribosome display cycles for further enrichment of rare species or cloning, expression, and sequencing to identify wanted candidates. Both prokaryotic and eukaryotic cell-free systems have been developed for ribosome display of different proteins. In this chapter, we describe ribosome display of antibodies using the eukaryotic rabbit reticulocyte system with an in situ single-primer DNA recovery method. A high-throughput Escherichia coli expression format is also described for screening of individual antibody binders from the ribosome-selected population.
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31
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Wang H, Liu R. Advantages of mRNA display selections over other selection techniques for investigation of protein-protein interactions. Expert Rev Proteomics 2011; 8:335-46. [PMID: 21679115 PMCID: PMC7103729 DOI: 10.1586/epr.11.15] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
mRNA display is a genotype–phenotype conjugation method that allows for amplification-based, iterative rounds of in vitro selection to be applied to peptides and proteins. mRNA display can be used to display both long natural protein and short synthetic peptide libraries with unusually high diversities for the investigation of protein–protein interactions. Here, we summarize the advantages of mRNA display by comparing it with other widely used peptide or protein-selection techniques, and discuss various applications of this technique in studying protein–protein interactions.
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Affiliation(s)
- Hui Wang
- University of North Carolina, Chapel Hill, NC 27599-7568, USA
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32
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Wang W, Hara S, Liu M, Aigaki T, Shimizu S, Ito Y. Polypeptide aptamer selection using a stabilized ribosome display. J Biosci Bioeng 2011; 112:515-7. [PMID: 21813322 DOI: 10.1016/j.jbiosc.2011.07.011] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2010] [Revised: 07/07/2011] [Accepted: 07/08/2011] [Indexed: 12/01/2022]
Abstract
A newly developed ribosome display protocol was applied to the in vitro selection of polypeptide aptamers to small molecular weight chemicals, 6-[hydroxy(4-nitrobenzyl)phosphonyl]hexanoic acid and vitamin B12, chosen from a peptide library of random sequences. New peptide sequences binding to the targets were found after six rounds of this protocol.
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Affiliation(s)
- Wei Wang
- Nano Medical Engineering Laboratory, RIKEN Advanced Science Institute, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
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33
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Cotten SW, Zou J, Valencia CA, Liu R. Selection of proteins with desired properties from natural proteome libraries using mRNA display. Nat Protoc 2011; 6:1163-82. [DOI: 10.1038/nprot.2011.354] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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34
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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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35
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Automation in the high-throughput selection of random combinatorial libraries--different approaches for select applications. Molecules 2010; 15:2478-90. [PMID: 20428057 PMCID: PMC6257267 DOI: 10.3390/molecules15042478] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2010] [Revised: 03/30/2010] [Accepted: 04/06/2010] [Indexed: 11/30/2022] Open
Abstract
Automation in combination with high throughput screening methods has revolutionised molecular biology in the last two decades. Today, many combinatorial libraries as well as several systems for automation are available. Depending on scope, budget and time, a different combination of library and experimental handling might be most effective. In this review we will discuss several concepts of combinatorial libraries and provide information as what to expect from these depending on the given context.
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36
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Detection of protein–protein interactions by ribosome display and protein in situ immobilisation. N Biotechnol 2009; 26:277-81. [DOI: 10.1016/j.nbt.2009.08.010] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2009] [Revised: 06/22/2009] [Accepted: 08/23/2009] [Indexed: 11/17/2022]
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37
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Qi Y, Wu C, Zhang S, Wang Z, Huang S, Dai L, Wang S, Xia L, Wen K, Cao X, Wu Y, Shen J. Selection of anti-sulfadimidine specific ScFvs from a hybridoma cell by eukaryotic ribosome display. PLoS One 2009; 4:e6427. [PMID: 19641611 PMCID: PMC2712767 DOI: 10.1371/journal.pone.0006427] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2009] [Accepted: 06/19/2009] [Indexed: 11/18/2022] Open
Abstract
BACKGROUND Ribosome display technology has provided an alternative platform technology for the development of novel low-cost antibody based on evaluating antibiotics derived residues in food matrixes. METHODOLOGY/PRINCIPAL FINDINGS In our current studies, the single chain variable fragments (scFvs) were selected from hybridoma cell lines against sulfadimidine (SM(2)) by using a ribosome library technology. A DNA library of scFv antibody fragments was constructed for ribosome display, and then mRNA-ribosome-antibody (MRA) complexes were produced by a rabbit reticulocyte lysate system. The synthetic sulfadimidine-ovalbumin (SM(2)-OVA) was used as an antigen to pan MRA complexes and putative scFv-encoding genes were recovered by RT-PCR in situ following each panning. After four rounds of ribosome display, the expression vector pCANTAB5E containing the selected specific scFv DNA was constructed and transformed into Escherichia coli HB2151. Three positive clones (SAS14, SAS68 and SAS71) were screened from 100 clones and had higher antibody activity and specificity to SM(2) by indirect ELISA. The three specific soluble scFvs were identified to be the same molecular weight (approximately 30 kDa) by Western-blotting analysis using anti-E tag antibodies, but they had different amino acids sequence by sequence analysis. CONCLUSIONS/SIGNIFICANCE The selection of anti-SM(2) specific scFv by in vitro ribosome display technology will have an important significance for the development of novel immunodetection strategies for residual veterinary drugs.
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Affiliation(s)
- Yonghua Qi
- National Center for Veterinary Drug Safety Evaluation, College of Veterinary Medicine, China Agricultural University, Beijing, China
- College of Animal Science, Henan Institute of Science and Technology, Xixiang, China
| | - Congming Wu
- National Center for Veterinary Drug Safety Evaluation, College of Veterinary Medicine, China Agricultural University, Beijing, China
| | - Suxia Zhang
- National Center for Veterinary Drug Safety Evaluation, College of Veterinary Medicine, China Agricultural University, Beijing, China
| | - Zhanhui Wang
- National Center for Veterinary Drug Safety Evaluation, College of Veterinary Medicine, China Agricultural University, Beijing, China
| | - Siyang Huang
- National Center for Veterinary Drug Safety Evaluation, College of Veterinary Medicine, China Agricultural University, Beijing, China
| | - Lei Dai
- National Center for Veterinary Drug Safety Evaluation, College of Veterinary Medicine, China Agricultural University, Beijing, China
| | - Shaochen Wang
- National Center for Veterinary Drug Safety Evaluation, College of Veterinary Medicine, China Agricultural University, Beijing, China
| | - Lining Xia
- National Center for Veterinary Drug Safety Evaluation, College of Veterinary Medicine, China Agricultural University, Beijing, China
- College of Veterinary Medicine, Xinjiang Agricultural University, Urmuqi, China
| | - Kai Wen
- National Center for Veterinary Drug Safety Evaluation, College of Veterinary Medicine, China Agricultural University, Beijing, China
| | - Xingyuan Cao
- National Center for Veterinary Drug Safety Evaluation, College of Veterinary Medicine, China Agricultural University, Beijing, China
| | - Yongning Wu
- Institute for Nutrition and Food Safety, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Jianzhong Shen
- National Center for Veterinary Drug Safety Evaluation, College of Veterinary Medicine, China Agricultural University, Beijing, China
- * E-mail:
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38
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Abstract
Ribosome display is a powerful method for selection of single-chain antibodies in vitro. It operates through the formation of libraries of antibody-ribosome-mRNA complexes that are selected on immobilized antigen, followed by recovery of the genetic information from the mRNA by RT-PCR. Both prokaryotic and eukaryotic versions are used. We describe our eukaryotic system, in which rabbit reticulocyte extracts are used for cell free transcription/translation and cDNA is recovered by in situ RT-PCR performed on the selected complexes.
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39
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Cell-free protein synthesis: applications in proteomics and biotechnology. N Biotechnol 2008; 25:126-32. [DOI: 10.1016/j.nbt.2008.08.004] [Citation(s) in RCA: 61] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2008] [Revised: 08/08/2008] [Accepted: 08/11/2008] [Indexed: 11/20/2022]
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40
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Hégarat N, François JC, Praseuth D. Modern tools for identification of nucleic acid-binding proteins. Biochimie 2008; 90:1265-72. [PMID: 18452716 DOI: 10.1016/j.biochi.2008.03.012] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2008] [Accepted: 03/21/2008] [Indexed: 11/25/2022]
Abstract
Numerous biological mechanisms depend on nucleic acid--protein interactions. The first step to the understanding of these mechanisms is to identify interacting molecules. Knowing one partner, the identification of other associated molecular species can be carried out using affinity-based purification procedures. When the nucleic acid-binding protein is known, the nucleic acid can be isolated and identified by sensitive techniques such as polymerase chain reaction followed by DNA sequencing or hybridization on chips. The reverse identification procedure is less straightforward in part because interesting nucleic acid-binding proteins are generally of low abundance and there are no methods to amplify amino acid sequences. In this article, we will review the strategies that have been developed to identify nucleic acid-binding proteins. We will focus on methods permitting the identification of these proteins without a priori knowledge of protein candidates.
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Affiliation(s)
- Nadia Hégarat
- INSERM, U565 Case Postale 26, 57 rue Cuvier, 75231 Paris Cedex 05, France
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41
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Rothe A, Nathanielsz A, Oberhäuser F, von Strandmann EP, Engert A, Hudson PJ, Power BE. Ribosome display and selection of human anti-CD22 scFvs derived from an acute lymphocytic leukemia patient. Biol Chem 2008; 389:433-9. [DOI: 10.1515/bc.2008.045] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
AbstractNovelin vitromethods for the display of antibody libraries against disease-related antigens have led to the development of powerful protein-based biotherapeutics. Eukaryotic ternary ribosome complexes can be used to display human single chain antibodies (scFvs) to isolate specific binding reagents to these antigens. Here, we present the isolation of human scFv against the immunotherapeutic target antigen CD22 from a patient-derived human scFv library using ribosome display technology. The ribosome complexes were enriched against the extra-cellular domain of human CD22 conjugated to magnetic beads. Isolated constructs were further affinity-matured and specific binding activity was demonstrated by surface plasmon resonance and validated usingin vitrocell assays. The isolated human anti-CD22 scFvs can provide a basis for the development of new immunotherapeutic strategies in CD22-expressing malignant diseases.
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42
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Abstract
Cell-free transcription and translation provides an open, controllable environment for production of correctly folded, soluble proteins and allows the rapid generation of proteins from DNA without the need for cloning. Thus it is becoming an increasingly attractive alternative to conventional in vivo expression systems, especially when parallel expression of multiple proteins is required. Through novel design and exploitation, powerful cell-free technologies of ribosome display and protein in situ arrays have been developed for in vitro production and isolation of protein-binding molecules from large libraries. These technologies can be combined for rapid detection of protein interactions.
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43
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He M, Taussig MJ. Erratum: Eukaryotic ribosome display with in situ DNA recovery. Nat Methods 2007. [DOI: 10.1038/nmeth0907-763] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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44
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Zahnd C, Amstutz P, Plückthun A. Ribosome display: selecting and evolving proteins in vitro that specifically bind to a target. Nat Methods 2007; 4:269-79. [PMID: 17327848 DOI: 10.1038/nmeth1003] [Citation(s) in RCA: 222] [Impact Index Per Article: 13.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Ribosome display is an in vitro selection and evolution technology for proteins and peptides from large libraries. As it is performed entirely in vitro, there are two main advantages over other selection technologies. First, the diversity of the library is not limited by the transformation efficiency of bacterial cells, but only by the number of ribosomes and different mRNA molecules present in the test tube. Second, random mutations can be introduced easily after each selection round, as no library must be transformed after any diversification step. This allows facile directed evolution of binding proteins over several generations. A prerequisite for the selection of proteins from libraries is the coupling of genotype (RNA, DNA) and phenotype (protein). In ribosome display, this link is accomplished during in vitro translation by stabilizing the complex consisting of the ribosome, the mRNA and the nascent, correctly folded polypeptide. The DNA library coding for a particular library of binding proteins is genetically fused to a spacer sequence lacking a stop codon. This spacer sequence, when translated, is still attached to the peptidyl tRNA and occupies the ribosomal tunnel, and thus allows the protein of interest to protrude out of the ribosome and fold. The ribosomal complexes are allowed to bind to surface-immobilized target. Whereas non-bound complexes are washed away, mRNA of the complexes displaying a binding polypeptide can be recovered, and thus, the genetic information of the binding polypeptides is available for analysis. Here we describe a step-by-step procedure to perform ribosome display selection using an Escherichia coli S30 extract for in vitro translation, based on the work originally described and further refined in our laboratory. A protocol that makes use of eukaryotic in vitro translation systems for ribosome display is also included in this issue.
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Affiliation(s)
- Christian Zahnd
- Biochemisches Institut der Universität Zürich, Winterthurerstr. 190, CH-8057 Zürich, Switzerland
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