1
|
Cui Z, Ayva CE, Liew YJ, Guo Z, Mutschler R, Dreier B, Fiorito MM, Walden P, Howard CB, Ely F, Plückthun A, Pretorius C, Ungerer JP, Buckle AM, Alexandrov K. mRNA Display Pipeline for Protein Biosensor Construction. ACS Sens 2024. [PMID: 38807313 DOI: 10.1021/acssensors.3c02471] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/30/2024]
Abstract
Despite the significant potential of protein biosensors, their construction remains a trial-and-error process. The most obvious approach for addressing this is to utilize modular biosensor architectures where specificity-conferring modalities can be readily generated to recognize new targets. Toward this goal, we established a workflow that uses mRNA display-based selection of hyper-stable monobody domains for the target of choice or ribosome display to select equally stable DARPins. These binders were integrated into a two-component allosteric biosensor architecture based on a calmodulin-reporter chimera. This workflow was tested by developing biosensors for liver toxicity markers such as cytosolic aspartate aminotransferase, mitochondrial aspartate aminotransferase, and alanine aminotransferase 1. We demonstrate that our pipeline consistently produced >103 unique binders for each target within a week. Our analysis revealed that the affinity of the binders for their targets was not a direct predictor of the binder's performance in a biosensor context. The interactions between the binding domains and the reporter module affect the biosensor activity and the dynamic range. We conclude that following binding domain selection, the multiplexed biosensor assembly and prototyping appear to be the most promising approach for identifying biosensors with the desired properties.
Collapse
Affiliation(s)
- Zhenling Cui
- ARC Centre of Excellence in Synthetic Biology, Brisbane, Queensland 4001, Australia
- Centre for Agriculture and the Bioeconomy, Queensland University of Technology, Brisbane, Queensland 4001, Australia
- School of Biology and Environmental Science, Queensland University of Technology, Brisbane, Queensland 4001, Australia
| | - Cagla Ergun Ayva
- Centre for Agriculture and the Bioeconomy, Queensland University of Technology, Brisbane, Queensland 4001, Australia
- School of Biology and Environmental Science, Queensland University of Technology, Brisbane, Queensland 4001, Australia
| | - Yi Jin Liew
- CSIRO Health & Biosecurity, Westmead, New South Wales 2145,Australia
| | - Zhong Guo
- ARC Centre of Excellence in Synthetic Biology, Brisbane, Queensland 4001, Australia
- Centre for Agriculture and the Bioeconomy, Queensland University of Technology, Brisbane, Queensland 4001, Australia
- School of Biology and Environmental Science, Queensland University of Technology, Brisbane, Queensland 4001, Australia
| | - Roxane Mutschler
- Centre for Agriculture and the Bioeconomy, Queensland University of Technology, Brisbane, Queensland 4001, Australia
- School of Biology and Environmental Science, Queensland University of Technology, Brisbane, Queensland 4001, Australia
| | - Birgit Dreier
- Department of Biochemistry, University of Zurich, Winterthurerstrasse 190, Zurich CH-8057, Switzerland
| | - Maria M Fiorito
- Centre for Agriculture and the Bioeconomy, Queensland University of Technology, Brisbane, Queensland 4001, Australia
- School of Biology and Environmental Science, Queensland University of Technology, Brisbane, Queensland 4001, Australia
| | - Patricia Walden
- Centre for Agriculture and the Bioeconomy, Queensland University of Technology, Brisbane, Queensland 4001, Australia
- School of Biology and Environmental Science, Queensland University of Technology, Brisbane, Queensland 4001, Australia
| | - Christopher B Howard
- Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, Brisbane, Queensland 4072, Australia
| | | | - Andreas Plückthun
- Department of Biochemistry, University of Zurich, Winterthurerstrasse 190, Zurich CH-8057, Switzerland
| | - Carel Pretorius
- Department of Chemical Pathology, Pathology Queensland, Brisbane, Queensland 4006, Australia
- Faculty of Health and Behavioural Sciences, The University of Queensland, Brisbane, Queensland 4072, Australia
| | - Jacobus Pj Ungerer
- Department of Chemical Pathology, Pathology Queensland, Brisbane, Queensland 4006, Australia
- Faculty of Health and Behavioural Sciences, The University of Queensland, Brisbane, Queensland 4072, Australia
| | | | - Kirill Alexandrov
- ARC Centre of Excellence in Synthetic Biology, Brisbane, Queensland 4001, Australia
- Centre for Agriculture and the Bioeconomy, Queensland University of Technology, Brisbane, Queensland 4001, Australia
- School of Biology and Environmental Science, Queensland University of Technology, Brisbane, Queensland 4001, Australia
| |
Collapse
|
2
|
Guo W, Yu Y, Xin C, Jin G. Comparative study of optical fiber immunosensors based on traditional antibody or nanobody for detecting HER2. Talanta 2024; 277:126317. [PMID: 38810383 DOI: 10.1016/j.talanta.2024.126317] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2023] [Revised: 05/18/2024] [Accepted: 05/23/2024] [Indexed: 05/31/2024]
Abstract
In this study, we present a novel biomarker detection platform employing a modified S-tapered fiber coated with gold nanoparticle/graphene oxide (GNP/GO) for quantifying human epidermal growth factor receptor-2 (HER2) concentrations, using antibodies as sensing elements. The fabrication of this device involves implementing an in-situ layer-by-layer technique coupled with a chemical adsorption step to achieve the self-assembly of GNP, GO, and antibodies on the STF surface. The detection mechanism relies on monitoring the refractive index changes induced by the adsorption of HER2 onto the immobilized antibodies. For comparative analysis, both monoclonal antibody (mAb) and the novel nanobody (Nb) were employed in constructing the STF immunosensor, referred to as the mAb immunosensor and Nb immunosensor, respectively. Spectral analysis results highlight that the Nb immunosensor exhibits twice the sensitivity of the mAb immunosensor. This enhanced sensitivity is attributed to the small size, high antigen affinity, strong specificity, and structural stability of Nb. The Nb immunosensor demonstrated an impressive detection limit of 0.001 nM for HER2, surpassing the detection limit of the mAb immunosensor. These findings underscore the potential of the proposed Nb immunosensor as a promising and sensitive tool for HER2 detection, contributing to the diagnosis and prognosis of breast cancer. Furthermore, the simplicity of production and excellent optical performance position the Nb immunosensor as a prospective real-time biosensor with minimal cytotoxicity.
Collapse
Affiliation(s)
- Wanmei Guo
- Jilin Key Laboratory of Solid Laser Technology and Application, School of Science, Changchun University of Science and Technology, Changchun, 130022, China
| | - Yongsen Yu
- State Key Laboratory of Integrated Optoelectronics, College of Electronic Science and Engineering, Jilin University, Changchun, 130012, China
| | - Chao Xin
- Jilin Key Laboratory of Solid Laser Technology and Application, School of Science, Changchun University of Science and Technology, Changchun, 130022, China
| | - Guangyong Jin
- Jilin Key Laboratory of Solid Laser Technology and Application, School of Science, Changchun University of Science and Technology, Changchun, 130022, China.
| |
Collapse
|
3
|
Aoki K, Higashi K, Oda S, Manabe A, Maeda K, Morise J, Oka S, Inuki S, Ohno H, Oishi S, Nonaka M. Engineering a Low-Immunogenic Mirror-Image VHH against Vascular Endothelial Growth Factor. ACS Chem Biol 2024; 19:1194-1205. [PMID: 38695546 DOI: 10.1021/acschembio.4c00197] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/18/2024]
Abstract
Immunogenicity is a major caveat of protein therapeutics. In particular, the long-term administration of protein therapeutic agents leads to the generation of antidrug antibodies (ADAs), which reduce drug efficacy while eliciting adverse events. One promising solution to this issue is the use of mirror-image proteins consisting of d-amino acids, which are resistant to proteolytic degradation in immune cells. We have recently reported the chemical synthesis of the enantiomeric form of the variable domain of the antibody heavy chain (d-VHH). However, identifying mirror-image antibodies capable of binding to natural ligands remains challenging. In this study, we developed a novel screening platform to identify a d-VHH specific for vascular endothelial growth factor A (VEGF-A). We performed mirror-image screening of two newly constructed synthetic VHH libraries displayed on T7 phage and identified VHH sequences that effectively bound to the mirror-image VEGF-A target (d-VEGF-A). We subsequently synthesized a d-VHH candidate that preferentially bound the native VEGF-A (l-VEGF-A) with submicromolar affinity. Furthermore, immunization studies in mice demonstrated that this d-VHH elicited no ADAs, unlike its corresponding l-VHH. Our findings highlight the utility of this novel d-VHH screening platform in the development of protein therapeutics exhibiting both reduced immunogenicity and improved efficacy.
Collapse
Affiliation(s)
- Keisuke Aoki
- Graduate School of Pharmaceutical Sciences, Kyoto University, Sakyo-ku, Kyoto 606-8501, Japan
- Laboratory of Medicinal Chemistry, Kyoto Pharmaceutical University, Yamashina-ku, Kyoto 607-8412, Japan
| | - Katsuaki Higashi
- Department of Biological Chemistry, Human Health Sciences, Graduate School of Medicine, Kyoto University, Sakyo-ku, Kyoto 606-8507, Japan
| | - Sakiho Oda
- Department of Biological Chemistry, Human Health Sciences, Graduate School of Medicine, Kyoto University, Sakyo-ku, Kyoto 606-8507, Japan
| | - Asako Manabe
- Department of Biological Chemistry, Human Health Sciences, Graduate School of Medicine, Kyoto University, Sakyo-ku, Kyoto 606-8507, Japan
| | - Kayuu Maeda
- Department of Biological Chemistry, Human Health Sciences, Graduate School of Medicine, Kyoto University, Sakyo-ku, Kyoto 606-8507, Japan
| | - Jyoji Morise
- Department of Biological Chemistry, Human Health Sciences, Graduate School of Medicine, Kyoto University, Sakyo-ku, Kyoto 606-8507, Japan
| | - Shogo Oka
- Department of Biological Chemistry, Human Health Sciences, Graduate School of Medicine, Kyoto University, Sakyo-ku, Kyoto 606-8507, Japan
| | - Shinsuke Inuki
- Graduate School of Pharmaceutical Sciences, Kyoto University, Sakyo-ku, Kyoto 606-8501, Japan
| | - Hiroaki Ohno
- Graduate School of Pharmaceutical Sciences, Kyoto University, Sakyo-ku, Kyoto 606-8501, Japan
| | - Shinya Oishi
- Graduate School of Pharmaceutical Sciences, Kyoto University, Sakyo-ku, Kyoto 606-8501, Japan
- Laboratory of Medicinal Chemistry, Kyoto Pharmaceutical University, Yamashina-ku, Kyoto 607-8412, Japan
| | - Motohiro Nonaka
- Department of Biological Chemistry, Human Health Sciences, Graduate School of Medicine, Kyoto University, Sakyo-ku, Kyoto 606-8507, Japan
| |
Collapse
|
4
|
Park KS, Park TI, Lee JE, Hwang SY, Choi A, Pack SP. Aptamers and Nanobodies as New Bioprobes for SARS-CoV-2 Diagnostic and Therapeutic System Applications. BIOSENSORS 2024; 14:146. [PMID: 38534253 DOI: 10.3390/bios14030146] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/31/2024] [Revised: 03/10/2024] [Accepted: 03/12/2024] [Indexed: 03/28/2024]
Abstract
The global challenges posed by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemic have underscored the critical importance of innovative and efficient control systems for addressing future pandemics. The most effective way to control the pandemic is to rapidly suppress the spread of the virus through early detection using a rapid, accurate, and easy-to-use diagnostic platform. In biosensors that use bioprobes, the binding affinity of molecular recognition elements (MREs) is the primary factor determining the dynamic range of the sensing platform. Furthermore, the sensitivity relies mainly on bioprobe quality with sufficient functionality. This comprehensive review investigates aptamers and nanobodies recently developed as advanced MREs for SARS-CoV-2 diagnostic and therapeutic applications. These bioprobes might be integrated into organic bioelectronic materials and devices, with promising enhanced sensitivity and specificity. This review offers valuable insights into advancing biosensing technologies for infectious disease diagnosis and treatment using aptamers and nanobodies as new bioprobes.
Collapse
Affiliation(s)
- Ki Sung Park
- Department of Biotechnology and Bioinformatics, Korea University, Sejong 30019, Republic of Korea
| | - Tae-In Park
- Department of Biotechnology and Bioinformatics, Korea University, Sejong 30019, Republic of Korea
| | - Jae Eon Lee
- Department of Biotechnology and Bioinformatics, Korea University, Sejong 30019, Republic of Korea
| | - Seo-Yeong Hwang
- Department of Biotechnology and Bioinformatics, Korea University, Sejong 30019, Republic of Korea
| | - Anna Choi
- Department of Biotechnology and Bioinformatics, Korea University, Sejong 30019, Republic of Korea
| | - Seung Pil Pack
- Department of Biotechnology and Bioinformatics, Korea University, Sejong 30019, Republic of Korea
| |
Collapse
|
5
|
Aoki K, Manabe A, Kimura H, Katoh Y, Inuki S, Ohno H, Nonaka M, Oishi S. Mirror-Image Single-Domain Antibody for a Novel Nonimmunogenic Drug Scaffold. Bioconjug Chem 2023; 34:2055-2065. [PMID: 37883660 DOI: 10.1021/acs.bioconjchem.3c00372] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2023]
Abstract
Immunogenic responses by protein therapeutics often lead to reduced therapeutic effects and/or adverse effects via the generation of neutralizing antibodies and/or antidrug antibodies (ADA). Mirror-image proteins of the variable domain of the heavy chain of the heavy chain antibody (VHH) are potential novel protein therapeutics with high-affinity binding to target proteins and reduced immunogenicity because these mirror-image VHHs (d-VHHs) are less susceptible to proteolytic degradation in antigen-presenting cells (APCs). In this study, we investigated the preparation protocols of d-VHHs and their biological properties, including stereoselective target binding and immunogenicity. Initially, we established a facile synthetic process of two model VHHs [anti-GFP VHH and PMP12A2h1 (monomeric VHH of caplacizumab)] and their mirror-image proteins by three-step native chemical ligations (NCLs) from four peptide segments. The folded synthetic VHHs (l-anti-GFP VHH and l-PMP12A2h1) bound to the target proteins (EGFP and vWF-A1 domain, respectively), while their mirror-image proteins (d-anti-GFP VHH and d-PMP12A2h1) showed no binding to the native proteins. For biodistribution studies, l-VHH and d-VHH with single radioactive indium diethylenetriamine-pentaacid (111In-DTPA) labeling at the C-terminus were designed and synthesized by the established protocol. The distribution profiles were essentially similar between l-VHH and d-VHH, in which the probes accumulated in the kidney within 15 min after intravenous administration in mice, because of the small molecular size of VHHs. Comparative assessment of the immunogenicity responses revealed that d-VHH-induced levels of ADA generation were significantly lower than those of native VHH, regardless of the peptide sequences and administration routes. The resulting scaffold investigated should be applicable in the design of d-VHHs with various C-terminal CDR3 sequences, which can be identified by screening using display technologies.
Collapse
Affiliation(s)
- Keisuke Aoki
- Graduate School of Pharmaceutical Sciences, Kyoto University, Sakyo-ku, Kyoto 606-8501, Japan
- Laboratory of Medicinal Chemistry, Kyoto Pharmaceutical University, Yamashina-ku, Kyoto 607-8412, Japan
| | - Asako Manabe
- Graduate School of Medicine, Kyoto University, Sakyo-ku, Kyoto 606-8507, Japan
| | - Hiroyuki Kimura
- Laboratory of Analytical and Bioinorganic Chemistry, Kyoto Pharmaceutical University, Yamashina-ku, Kyoto 607-8414, Japan
| | - Yohei Katoh
- Graduate School of Pharmaceutical Sciences, Kyoto University, Sakyo-ku, Kyoto 606-8501, Japan
| | - Shinsuke Inuki
- Graduate School of Pharmaceutical Sciences, Kyoto University, Sakyo-ku, Kyoto 606-8501, Japan
| | - Hiroaki Ohno
- Graduate School of Pharmaceutical Sciences, Kyoto University, Sakyo-ku, Kyoto 606-8501, Japan
| | - Motohiro Nonaka
- Graduate School of Medicine, Kyoto University, Sakyo-ku, Kyoto 606-8507, Japan
| | - Shinya Oishi
- Graduate School of Pharmaceutical Sciences, Kyoto University, Sakyo-ku, Kyoto 606-8501, Japan
- Laboratory of Medicinal Chemistry, Kyoto Pharmaceutical University, Yamashina-ku, Kyoto 607-8412, Japan
| |
Collapse
|
6
|
Hutton ARJ, Ubah O, Barelle C, Donnelly RF. Enhancing the Transdermal Delivery of 'Next Generation' Variable New Antigen Receptors Using Microarray Patch Technology: a Proof-of-Concept Study. J Pharm Sci 2022; 111:3362-3376. [PMID: 36037879 DOI: 10.1016/j.xphs.2022.08.027] [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: 07/19/2022] [Revised: 08/22/2022] [Accepted: 08/22/2022] [Indexed: 01/05/2023]
Abstract
Heavy chain only binding proteins, such as variable new antigen receptors (VNARs), have emerged as an alternative to the highly successful therapeutic monoclonal antibodies (mAb). Owing to their small size (∼ 11 kDa) and single chain only architecture, they are amenable to modular reformatting and can be produced using inexpensive expression systems. Furthermore, due to their low molecular weight (MW) and high stability, they may be suitable for alternative delivery strategies, such as microarray array patches (MAPs). In this study, the transdermal delivery of ELN22-104, a multivalent anti-hTNF-α VNAR, was examined using both dissolving and hydrogel-forming MAPs. For dissolving MAPs, the cumulative in vitro permeation of ELN22-104 reached a plateau after 2 h (12.24 ± 0.17 µg). This could be important for bolus dosing. Assessing two hydrogel-forming MAPs in vitro, PVP/PVA hydrogel-forming MAPs delivered significantly higher drug doses when compared to 'super swelling' MAPs, equivalent to 43.13 ± 10.36 µg and 23.13 ± 5.66 µg, respectively (p < 0.05). Consequently, this study has proven that by modifying the MAP system, the transdermal delivery of a VNAR across the skin can be enhanced. Furthermore, this proof-of-concept study has shown that transdermal delivery of 'next generation' biotherapeutics is achievable using MAP technology.
Collapse
Affiliation(s)
- Aaron R J Hutton
- School of Pharmacy, Queen's University Belfast, 97 Lisburn Road, Belfast BT9 7BL, United Kingdom
| | - Obinna Ubah
- Elasmogen Ltd., Liberty Building, Foresterhill Road, Aberdeen AB25 2ZP, United Kingdom
| | - Caroline Barelle
- Elasmogen Ltd., Liberty Building, Foresterhill Road, Aberdeen AB25 2ZP, United Kingdom
| | - Ryan F Donnelly
- School of Pharmacy, Queen's University Belfast, 97 Lisburn Road, Belfast BT9 7BL, United Kingdom.
| |
Collapse
|
7
|
Haueis L, Stech M, Kubick S. A Cell-free Expression Pipeline for the Generation and Functional Characterization of Nanobodies. Front Bioeng Biotechnol 2022; 10:896763. [PMID: 35573250 PMCID: PMC9096027 DOI: 10.3389/fbioe.2022.896763] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2022] [Accepted: 04/11/2022] [Indexed: 11/13/2022] Open
Abstract
Cell-free systems are well-established platforms for the rapid synthesis, screening, engineering and modification of all kinds of recombinant proteins ranging from membrane proteins to soluble proteins, enzymes and even toxins. Also within the antibody field the cell-free technology has gained considerable attention with respect to the clinical research pipeline including antibody discovery and production. Besides the classical full-length monoclonal antibodies (mAbs), so-called "nanobodies" (Nbs) have come into focus. A Nb is the smallest naturally-derived functional antibody fragment known and represents the variable domain (VHH, ∼15 kDa) of a camelid heavy-chain-only antibody (HCAb). Based on their nanoscale and their special structure, Nbs display striking advantages concerning their production, but also their characteristics as binders, such as high stability, diversity, improved tissue penetration and reaching of cavity-like epitopes. The classical way to produce Nbs depends on the use of living cells as production host. Though cell-based production is well-established, it is still time-consuming, laborious and hardly amenable for high-throughput applications. Here, we present for the first time to our knowledge the synthesis of functional Nbs in a standardized mammalian cell-free system based on Chinese hamster ovary (CHO) cell lysates. Cell-free reactions were shown to be time-efficient and easy-to-handle allowing for the "on demand" synthesis of Nbs. Taken together, we complement available methods and demonstrate a promising new system for Nb selection and validation.
Collapse
Affiliation(s)
- Lisa Haueis
- Fraunhofer Institute for Cell Therapy and Immunology (IZI), Branch Bioanalytics and Bioprocesses (IZI-BB), Potsdam, Germany.,Institute of Biochemistry and Biology, University of Potsdam, Potsdam, Germany
| | - Marlitt Stech
- Fraunhofer Institute for Cell Therapy and Immunology (IZI), Branch Bioanalytics and Bioprocesses (IZI-BB), Potsdam, Germany
| | - Stefan Kubick
- Fraunhofer Institute for Cell Therapy and Immunology (IZI), Branch Bioanalytics and Bioprocesses (IZI-BB), Potsdam, Germany.,Institute of Chemistry and Biochemistry, Freie Universität Berlin, Berlin, Germany.,Faculty of Health Sciences, Joint Faculty of the Brandenburg University of Technology Cottbus-Senftenberg, The Brandenburg Medical School Theodor Fontane and the University of Potsdam, Potsdam, Germany
| |
Collapse
|
8
|
Zhao M, Wang M, Zhang X, Zhu Y, Cao J, She Y, Cao Z, Li G, Wang J, Abd El-Aty AM. Recognition elements based on the molecular biological techniques for detecting pesticides in food: A review. Crit Rev Food Sci Nutr 2021:1-24. [PMID: 34852703 DOI: 10.1080/10408398.2021.2009762] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Abstract
Excessive use of pesticides can cause contamination of the environment and agricultural products that are directly threatening human life and health. Therefore, in the process of food safety supervision, it is crucial to conduct sensitive and rapid detection of pesticide residues. The recognition element is the vital component of sensors and methods for fast testing pesticide residues in food. Improper recognition elements may lead to defects of testing methods, such as poor stability, low sensitivity, high economic costs, and waste of time. We can use the molecular biological technique to address these challenges as a good strategy for recognition element production and modification. Herein, we review the molecular biological methods of five specific recognition elements, including aptamers, genetic engineering antibodies, DNAzymes, genetically engineered enzymes, and whole-cell-based biosensors. In addition, the application of these identification elements combined with biosensor and immunoassay methods in actual detection was also discussed. The purpose of this review was to provide a valuable reference for further development of rapid detection methods for pesticide residues.
Collapse
Affiliation(s)
- Mingqi Zhao
- Institute of Quality Standardization & Testing Technology for Agro-Products, Chinese Academy of Agricultural Sciences, Beijing, China.,Key Laboratory of Agrofood Safety and Quality (Beijing), Ministry of Agriculture and Rural Areas, Beijing, China
| | - Miao Wang
- Institute of Quality Standardization & Testing Technology for Agro-Products, Chinese Academy of Agricultural Sciences, Beijing, China.,Key Laboratory of Agrofood Safety and Quality (Beijing), Ministry of Agriculture and Rural Areas, Beijing, China
| | - Xiaoguang Zhang
- Hebei Xiangzhi Testing Technology Co., Ltd, Shijiazhuang, China.,Core Facilities and Centers of Hebei Medical University, Shijiazhuang, China
| | - Yongan Zhu
- Institute of Quality Standardization & Testing Technology for Agro-Products, Chinese Academy of Agricultural Sciences, Beijing, China.,Key Laboratory of Agrofood Safety and Quality (Beijing), Ministry of Agriculture and Rural Areas, Beijing, China
| | - Jing Cao
- Institute of Quality Standardization & Testing Technology for Agro-Products, Chinese Academy of Agricultural Sciences, Beijing, China.,Key Laboratory of Agrofood Safety and Quality (Beijing), Ministry of Agriculture and Rural Areas, Beijing, China
| | - Yongxin She
- Institute of Quality Standardization & Testing Technology for Agro-Products, Chinese Academy of Agricultural Sciences, Beijing, China.,Key Laboratory of Agrofood Safety and Quality (Beijing), Ministry of Agriculture and Rural Areas, Beijing, China
| | - Zhen Cao
- Institute of Quality Standardization & Testing Technology for Agro-Products, Chinese Academy of Agricultural Sciences, Beijing, China.,Key Laboratory of Agrofood Safety and Quality (Beijing), Ministry of Agriculture and Rural Areas, Beijing, China
| | - Guangyue Li
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Jing Wang
- Institute of Quality Standardization & Testing Technology for Agro-Products, Chinese Academy of Agricultural Sciences, Beijing, China.,Key Laboratory of Agrofood Safety and Quality (Beijing), Ministry of Agriculture and Rural Areas, Beijing, China
| | - A M Abd El-Aty
- Department of Pharmacology, Faculty of Veterinary Medicine, Cairo University, Giza, Egypt.,Department of Medical Pharmacology, Medical Faculty, Ataturk University, Erzurum, Turkey
| |
Collapse
|
9
|
Parker DM, Winkenbach LP, Parker A, Boyson S, Nishimura EO. Improved Methods for Single-Molecule Fluorescence In Situ Hybridization and Immunofluorescence in Caenorhabditis elegans Embryos. Curr Protoc 2021; 1:e299. [PMID: 34826343 PMCID: PMC9020185 DOI: 10.1002/cpz1.299] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Visualization of gene products in Caenorhabditis elegans has provided insights into the molecular and biological functions of many novel genes in their native contexts. Single-molecule fluorescence in situ hybridization (smFISH) and immunofluorescence (IF) enable the visualization of the abundance and localization of mRNAs and proteins, respectively, allowing researchers to ultimately elucidate the localization, dynamics, and functions of the corresponding genes. Whereas both smFISH and immunofluorescence have been foundational techniques in molecular biology, each protocol poses challenges for use in the C. elegans embryo. smFISH protocols suffer from high initial costs and can photobleach rapidly, and immunofluorescence requires technically challenging permeabilization steps and slide preparation. Most importantly, published smFISH and IF protocols have predominantly been mutually exclusive, preventing the exploration of relationships between an mRNA and a relevant protein in the same sample. Here, we describe protocols to perform immunofluorescence and smFISH in C. elegans embryos either in sequence or simultaneously. We also outline the steps to perform smFISH or immunofluorescence alone, including several improvements and optimizations to existing approaches. These protocols feature improved fixation and permeabilization steps to preserve cellular morphology while maintaining probe and antibody accessibility in the embryo, a streamlined, in-tube approach for antibody staining that negates freeze-cracking, a validated method to perform the cost-reducing single molecule inexpensive FISH (smiFISH) adaptation, slide preparation using empirically determined optimal antifade products, and straightforward quantification and data analysis methods. Finally, we discuss tricks and tips to help the reader optimize and troubleshoot individual steps in each protocol. Together, these protocols simplify existing workflows for single-molecule RNA and protein detection. Moreover, simultaneous, high-resolution imaging of proteins and RNAs of interest will permit analysis, quantification, and comparison of protein and RNA distributions, furthering our understanding of the relationship between RNAs and their protein products or cellular markers in early development. © 2021 Wiley Periodicals LLC. Basic Protocol 1: Sequential immunofluorescence and single-molecule fluorescence in situ hybridization Alternate Protocol: Abbreviated protocol for simultaneous immunofluorescence and single-molecule fluorescence in situ hybridization Basic Protocol 2: Simplified immunofluorescence in C. elegans embryos Basic Protocol 3: Single-molecule fluorescence in situ hybridization or single-molecule inexpensive fluorescence in situ hybridization.
Collapse
Affiliation(s)
- Dylan M Parker
- Department of Biochemistry and Molecular Biology, Colorado State University, Fort Collins, Colorado
| | - Lindsay P Winkenbach
- Department of Biochemistry and Molecular Biology, Colorado State University, Fort Collins, Colorado
| | - Annemarie Parker
- Department of Biochemistry and Molecular Biology, Colorado State University, Fort Collins, Colorado
| | - Sam Boyson
- Department of Biochemistry and Molecular Biology, Colorado State University, Fort Collins, Colorado
| | - Erin Osborne Nishimura
- Department of Biochemistry and Molecular Biology, Colorado State University, Fort Collins, Colorado
| |
Collapse
|
10
|
Kamalinia G, Grindel BJ, Takahashi TT, Millward SW, Roberts RW. Directing evolution of novel ligands by mRNA display. Chem Soc Rev 2021; 50:9055-9103. [PMID: 34165126 PMCID: PMC8725378 DOI: 10.1039/d1cs00160d] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
mRNA display is a powerful biological display platform for the directed evolution of proteins and peptides. mRNA display libraries covalently link the displayed peptide or protein (phenotype) with the encoding genetic information (genotype) through the biochemical activity of the small molecule puromycin. Selection for peptide/protein function is followed by amplification of the linked genetic material and generation of a library enriched in functional sequences. Iterative selection cycles are then performed until the desired level of function is achieved, at which time the identity of candidate peptides can be obtained by sequencing the genetic material. The purpose of this review is to discuss the development of mRNA display technology since its inception in 1997 and to comprehensively review its use in the selection of novel peptides and proteins. We begin with an overview of the biochemical mechanism of mRNA display and its variants with a particular focus on its advantages and disadvantages relative to other biological display technologies. We then discuss the importance of scaffold choice in mRNA display selections and review the results of selection experiments with biological (e.g., fibronectin) and linear peptide library architectures. We then explore recent progress in the development of "drug-like" peptides by mRNA display through the post-translational covalent macrocyclization and incorporation of non-proteogenic functionalities. We conclude with an examination of enabling technologies that increase the speed of selection experiments, enhance the information obtained in post-selection sequence analysis, and facilitate high-throughput characterization of lead compounds. We hope to provide the reader with a comprehensive view of current state and future trajectory of mRNA display and its broad utility as a peptide and protein design tool.
Collapse
Affiliation(s)
- Golnaz Kamalinia
- Department of Chemistry, University of Southern California, Los Angeles, CA, USA.
| | | | | | | | | |
Collapse
|
11
|
Valli J, Garcia-Burgos A, Rooney LM, Vale de Melo E Oliveira B, Duncan RR, Rickman C. Seeing beyond the limit: A guide to choosing the right super-resolution microscopy technique. J Biol Chem 2021; 297:100791. [PMID: 34015334 PMCID: PMC8246591 DOI: 10.1016/j.jbc.2021.100791] [Citation(s) in RCA: 45] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2020] [Revised: 05/14/2021] [Accepted: 05/14/2021] [Indexed: 02/06/2023] Open
Abstract
Super-resolution microscopy has become an increasingly popular and robust tool across the life sciences to study minute cellular structures and processes. However, with the increasing number of available super-resolution techniques has come an increased complexity and burden of choice in planning imaging experiments. Choosing the right super-resolution technique to answer a given biological question is vital for understanding and interpreting biological relevance. This is an often-neglected and complex task that should take into account well-defined criteria (e.g., sample type, structure size, imaging requirements). Trade-offs in different imaging capabilities are inevitable; thus, many researchers still find it challenging to select the most suitable technique that will best answer their biological question. This review aims to provide an overview and clarify the concepts underlying the most commonly available super-resolution techniques as well as guide researchers through all aspects that should be considered before opting for a given technique.
Collapse
Affiliation(s)
- Jessica Valli
- Edinburgh Super Resolution Imaging Consortium (ESRIC), Institute of Biological Chemistry, Biophysics and Bioengineering, Heriot-Watt University, Edinburgh, United Kingdom.
| | - Adrian Garcia-Burgos
- Edinburgh Super Resolution Imaging Consortium (ESRIC), Institute of Biological Chemistry, Biophysics and Bioengineering, Heriot-Watt University, Edinburgh, United Kingdom
| | - Liam M Rooney
- Edinburgh Super Resolution Imaging Consortium (ESRIC), Institute of Biological Chemistry, Biophysics and Bioengineering, Heriot-Watt University, Edinburgh, United Kingdom
| | - Beatriz Vale de Melo E Oliveira
- Edinburgh Super Resolution Imaging Consortium (ESRIC), Institute of Biological Chemistry, Biophysics and Bioengineering, Heriot-Watt University, Edinburgh, United Kingdom
| | - Rory R Duncan
- Edinburgh Super Resolution Imaging Consortium (ESRIC), Institute of Biological Chemistry, Biophysics and Bioengineering, Heriot-Watt University, Edinburgh, United Kingdom
| | - Colin Rickman
- Edinburgh Super Resolution Imaging Consortium (ESRIC), Institute of Biological Chemistry, Biophysics and Bioengineering, Heriot-Watt University, Edinburgh, United Kingdom.
| |
Collapse
|
12
|
Sokullu E, Gauthier MS, Coulombe B. Discovery of Antivirals Using Phage Display. Viruses 2021; 13:v13061120. [PMID: 34200959 PMCID: PMC8230593 DOI: 10.3390/v13061120] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2021] [Revised: 06/05/2021] [Accepted: 06/07/2021] [Indexed: 02/06/2023] Open
Abstract
The latest coronavirus disease outbreak, COVID-19, has brought attention to viral infections which have posed serious health threats to humankind throughout history. The rapid global spread of COVID-19 is attributed to the increased human mobility of today's world, yet the threat of viral infections to global public health is expected to increase continuously in part due to increasing human-animal interface. Development of antiviral agents is crucial to combat both existing and novel viral infections. Recently, there is a growing interest in peptide/protein-based drug molecules. Antibodies are becoming especially predominant in the drug market. Indeed, in a remarkably short period, four antibody therapeutics were authorized for emergency use in COVID-19 treatment in the US, Russia, and India as of November 2020. Phage display has been one of the most widely used screening methods for peptide/antibody drug discovery. Several phage display-derived biologics are already in the market, and the expiration of intellectual property rights of phage-display antibody discovery platforms suggests an increment in antibody drugs in the near future. This review summarizes the most common phage display libraries used in antiviral discovery, highlights the approaches employed to enhance the antiviral potency of selected peptides/antibody fragments, and finally provides a discussion about the present status of the developed antivirals in clinic.
Collapse
Affiliation(s)
- Esen Sokullu
- Department of Translational Proteomics, Institut de Recherches Cliniques de Montréal, Montréal, QC H2W 1R7, Canada;
- Department of Biochemistry and Molecular Medicine, Université de Montréal, Montréal, QC H3C 3J7, Canada
- Correspondence: (E.S.); (B.C.)
| | - Marie-Soleil Gauthier
- Department of Translational Proteomics, Institut de Recherches Cliniques de Montréal, Montréal, QC H2W 1R7, Canada;
| | - Benoit Coulombe
- Department of Translational Proteomics, Institut de Recherches Cliniques de Montréal, Montréal, QC H2W 1R7, Canada;
- Department of Biochemistry and Molecular Medicine, Université de Montréal, Montréal, QC H3C 3J7, Canada
- Correspondence: (E.S.); (B.C.)
| |
Collapse
|
13
|
Yu S, Xiong G, Zhao S, Tang Y, Tang H, Wang K, Liu H, Lan K, Bi X, Duan S. Nanobodies targeting immune checkpoint molecules for tumor immunotherapy and immunoimaging (Review). Int J Mol Med 2020; 47:444-454. [PMID: 33416134 PMCID: PMC7797440 DOI: 10.3892/ijmm.2020.4817] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2020] [Accepted: 10/29/2020] [Indexed: 12/21/2022] Open
Abstract
The immune checkpoint blockade is an effective strategy to enhance the anti-tumor T cell effector activity, thus becoming one of the most promising immunotherapeutic strategies in the history of cancer treatment. Several immune checkpoint inhibitor have been approved by the FDA, such as anti-CTLA-4, anti-PD-1, anti-PD-L1 monoclonal antibodies. Most tumor patients benefitted from these antibodies, but some of the patients did not respond to them. To increase the effectiveness of immunotherapy, including immune checkpoint blockade therapies, miniaturization of antibodies has been introduced. A single-domain antibody, also known as nanobody, is an attractive reagent for immunotherapy and immunoimaging thanks to its unique structural characteristic consisting of a variable region of a single heavy chain antibody. This structure confers to the nanobody a light molecular weight, making it smaller than conventional antibodies, although remaining able to bind to a specific antigen. Therefore, this review summarizes the production of nanobodies targeting immune checkpoint molecules and the application of nanobodies targeting immune checkpoint molecules in immunotherapy and immunoimaging.
Collapse
Affiliation(s)
- Sheng Yu
- Department of Medicine, Guangxi University of Science and Technology, Liuzhou, Guangxi Zhuang Autonomous Region 545005, P.R. China
| | - Gui Xiong
- Department of Medicine, Guangxi University of Science and Technology, Liuzhou, Guangxi Zhuang Autonomous Region 545005, P.R. China
| | - Shimei Zhao
- Department of Medicine, Guangxi University of Science and Technology, Liuzhou, Guangxi Zhuang Autonomous Region 545005, P.R. China
| | - Yanbo Tang
- Department of Gastroenterology, The First Affiliated Hospital of Guangxi University of Science and Technology, Liuzhou, Guangxi Zhuang Autonomous Region 545001, P.R. China
| | - Hua Tang
- Department of Clinical Laboratory, The Second Clinical Medical College of Guangxi University of Science and Technology, Liuzhou, Guangxi Zhuang Autonomous Region 545006, P.R. China
| | - Kaili Wang
- Department of Medicine, Guangxi University of Science and Technology, Liuzhou, Guangxi Zhuang Autonomous Region 545005, P.R. China
| | - Hongjing Liu
- Department of Medicine, Guangxi University of Science and Technology, Liuzhou, Guangxi Zhuang Autonomous Region 545005, P.R. China
| | - Ke Lan
- Department of Medicine, Guangxi University of Science and Technology, Liuzhou, Guangxi Zhuang Autonomous Region 545005, P.R. China
| | - Xiongjie Bi
- Department of Clinical Laboratory, The First Affiliated Hospital of Guangxi University of Science and Technology, Liuzhou, Guangxi Zhuang Autonomous Region 545001, P.R. China
| | - Siliang Duan
- Department of Medicine, Guangxi University of Science and Technology, Liuzhou, Guangxi Zhuang Autonomous Region 545005, P.R. China
| |
Collapse
|
14
|
Birch J, Cheruvara H, Gamage N, Harrison PJ, Lithgo R, Quigley A. Changes in Membrane Protein Structural Biology. BIOLOGY 2020; 9:E401. [PMID: 33207666 PMCID: PMC7696871 DOI: 10.3390/biology9110401] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/14/2020] [Revised: 11/11/2020] [Accepted: 11/12/2020] [Indexed: 12/21/2022]
Abstract
Membrane proteins are essential components of many biochemical processes and are important pharmaceutical targets. Membrane protein structural biology provides the molecular rationale for these biochemical process as well as being a highly useful tool for drug discovery. Unfortunately, membrane protein structural biology is a difficult area of study due to low protein yields and high levels of instability especially when membrane proteins are removed from their native environments. Despite this instability, membrane protein structural biology has made great leaps over the last fifteen years. Today, the landscape is almost unrecognisable. The numbers of available atomic resolution structures have increased 10-fold though advances in crystallography and more recently by cryo-electron microscopy. These advances in structural biology were achieved through the efforts of many researchers around the world as well as initiatives such as the Membrane Protein Laboratory (MPL) at Diamond Light Source. The MPL has helped, provided access to and contributed to advances in protein production, sample preparation and data collection. Together, these advances have enabled higher resolution structures, from less material, at a greater rate, from a more diverse range of membrane protein targets. Despite this success, significant challenges remain. Here, we review the progress made and highlight current and future challenges that will be overcome.
Collapse
Affiliation(s)
- James Birch
- Membrane Protein Laboratory, Diamond Light Source Ltd., Harwell Science and Innovation Campus, Didcot OX11 0DE, UK; (J.B.); (H.C.); (N.G.); (P.J.H.); (R.L.)
- Research Complex at Harwell (RCaH), Harwell Science and Innovation Campus, Didcot OX11 0FA, UK
| | - Harish Cheruvara
- Membrane Protein Laboratory, Diamond Light Source Ltd., Harwell Science and Innovation Campus, Didcot OX11 0DE, UK; (J.B.); (H.C.); (N.G.); (P.J.H.); (R.L.)
- Research Complex at Harwell (RCaH), Harwell Science and Innovation Campus, Didcot OX11 0FA, UK
| | - Nadisha Gamage
- Membrane Protein Laboratory, Diamond Light Source Ltd., Harwell Science and Innovation Campus, Didcot OX11 0DE, UK; (J.B.); (H.C.); (N.G.); (P.J.H.); (R.L.)
- Research Complex at Harwell (RCaH), Harwell Science and Innovation Campus, Didcot OX11 0FA, UK
| | - Peter J. Harrison
- Membrane Protein Laboratory, Diamond Light Source Ltd., Harwell Science and Innovation Campus, Didcot OX11 0DE, UK; (J.B.); (H.C.); (N.G.); (P.J.H.); (R.L.)
- Research Complex at Harwell (RCaH), Harwell Science and Innovation Campus, Didcot OX11 0FA, UK
| | - Ryan Lithgo
- Membrane Protein Laboratory, Diamond Light Source Ltd., Harwell Science and Innovation Campus, Didcot OX11 0DE, UK; (J.B.); (H.C.); (N.G.); (P.J.H.); (R.L.)
- Research Complex at Harwell (RCaH), Harwell Science and Innovation Campus, Didcot OX11 0FA, UK
- School of Biosciences, University of Nottingham, Sutton Bonington Campus, Loughborough LE12 5RD, Leicestershire, UK
| | - Andrew Quigley
- Membrane Protein Laboratory, Diamond Light Source Ltd., Harwell Science and Innovation Campus, Didcot OX11 0DE, UK; (J.B.); (H.C.); (N.G.); (P.J.H.); (R.L.)
- Research Complex at Harwell (RCaH), Harwell Science and Innovation Campus, Didcot OX11 0FA, UK
| |
Collapse
|
15
|
Cheloha RW, Harmand TJ, Wijne C, Schwartz TU, Ploegh HL. Exploring cellular biochemistry with nanobodies. J Biol Chem 2020; 295:15307-15327. [PMID: 32868455 PMCID: PMC7650250 DOI: 10.1074/jbc.rev120.012960] [Citation(s) in RCA: 54] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2020] [Revised: 08/27/2020] [Indexed: 12/21/2022] Open
Abstract
Reagents that bind tightly and specifically to biomolecules of interest remain essential in the exploration of biology and in their ultimate application to medicine. Besides ligands for receptors of known specificity, agents commonly used for this purpose are monoclonal antibodies derived from mice, rabbits, and other animals. However, such antibodies can be expensive to produce, challenging to engineer, and are not necessarily stable in the context of the cellular cytoplasm, a reducing environment. Heavy chain-only antibodies, discovered in camelids, have been truncated to yield single-domain antibody fragments (VHHs or nanobodies) that overcome many of these shortcomings. Whereas they are known as crystallization chaperones for membrane proteins or as simple alternatives to conventional antibodies, nanobodies have been applied in settings where the use of standard antibodies or their derivatives would be impractical or impossible. We review recent examples in which the unique properties of nanobodies have been combined with complementary methods, such as chemical functionalization, to provide tools with unique and useful properties.
Collapse
Affiliation(s)
- Ross W Cheloha
- Program in Cellular and Molecular Medicine, Boston Children's Hospital, Boston, Massachusetts, USA; Harvard Medical School, Boston, Massachusetts, USA
| | - Thibault J Harmand
- Program in Cellular and Molecular Medicine, Boston Children's Hospital, Boston, Massachusetts, USA; Harvard Medical School, Boston, Massachusetts, USA
| | - Charlotte Wijne
- Program in Cellular and Molecular Medicine, Boston Children's Hospital, Boston, Massachusetts, USA; Harvard Medical School, Boston, Massachusetts, USA
| | - Thomas U Schwartz
- Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | - Hidde L Ploegh
- Program in Cellular and Molecular Medicine, Boston Children's Hospital, Boston, Massachusetts, USA; Harvard Medical School, Boston, Massachusetts, USA.
| |
Collapse
|
16
|
Evenson WE, Lin WZS, Pang K, Czaja AT, Jalali-Yazdi F, Takahashi TT, Malmstadt N, Roberts RW. Enabling Flow-Based Kinetic Off-Rate Selections Using a Microfluidic Enrichment Device. Anal Chem 2020; 92:10218-10222. [PMID: 32633489 PMCID: PMC10368462 DOI: 10.1021/acs.analchem.0c01867] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Modern genomic sequencing efforts are identifying potential diagnostic and therapeutic targets more rapidly than existing methods can generate the peptide- and protein-based ligands required to study them. To address this problem, we have developed a microfluidic enrichment device (MFED) enabling kinetic off-rate selection without the use of exogenous competitor. We tuned the conditions of the device (bed volume, flow rate, immobilized target) such that modest, readily achievable changes in flow rates favor formation or dissociation of target-ligand complexes based on affinity. Simple kinetic equations can be used to describe the behavior of ligand binding in the MFED and the kinetic rate constants observed agree with independent measurements. We demonstrate the utility of the MFED by showing a 4-fold improvement in enrichment compared to standard selection. The MFED described here provides a route to simultaneously bias pools toward high-affinity ligands while reducing the demand for target-protein to less than a nanomole per selection.
Collapse
Affiliation(s)
- William E Evenson
- Department of Chemistry, University of Southern California, 3620 McClintock Avenue, SGM 418, Los Angeles, California 90089, United States
| | - Wan-Zhen Sophie Lin
- Mork Family Department of Chemical Engineering and Materials Science, University of Southern California, 925 Bloom Walk, HED 216, Los Angeles, California 90089, United States
| | - Kenmond Pang
- Mork Family Department of Chemical Engineering and Materials Science, University of Southern California, 925 Bloom Walk, HED 216, Los Angeles, California 90089, United States
| | - Alexander T Czaja
- Department of Biomedical Engineering, University of Southern California, 1042 Downey Way, Denney Research Center (DRB) 140, Los Angeles, California 90089, United States
| | - Farzad Jalali-Yazdi
- Mork Family Department of Chemical Engineering and Materials Science, University of Southern California, 925 Bloom Walk, HED 216, Los Angeles, California 90089, United States
| | - Terry T Takahashi
- Department of Chemistry, University of Southern California, 3620 McClintock Avenue, SGM 418, Los Angeles, California 90089, United States
| | - Noah Malmstadt
- Department of Chemistry, University of Southern California, 3620 McClintock Avenue, SGM 418, Los Angeles, California 90089, United States.,Mork Family Department of Chemical Engineering and Materials Science, University of Southern California, 925 Bloom Walk, HED 216, Los Angeles, California 90089, United States.,Department of Biomedical Engineering, University of Southern California, 1042 Downey Way, Denney Research Center (DRB) 140, Los Angeles, California 90089, United States.,USC Norris Comprehensive Cancer Center, 1441 Eastlake Avenue, Los Angeles, California 90033, United States
| | - Richard W Roberts
- Department of Chemistry, University of Southern California, 3620 McClintock Avenue, SGM 418, Los Angeles, California 90089, United States.,Mork Family Department of Chemical Engineering and Materials Science, University of Southern California, 925 Bloom Walk, HED 216, Los Angeles, California 90089, United States.,Department of Biomedical Engineering, University of Southern California, 1042 Downey Way, Denney Research Center (DRB) 140, Los Angeles, California 90089, United States.,USC Norris Comprehensive Cancer Center, 1441 Eastlake Avenue, Los Angeles, California 90033, United States.,Department of Molecular and Computational Biology, University of Southern California, 1050 Child Way, RRI 201, Los Angeles, California 90089, United States
| |
Collapse
|
17
|
Onogi Y, Khalil AEMM, Ussar S. Identification and characterization of adipose surface epitopes. Biochem J 2020; 477:2509-2541. [PMID: 32648930 PMCID: PMC7360119 DOI: 10.1042/bcj20190462] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2020] [Revised: 06/11/2020] [Accepted: 06/12/2020] [Indexed: 12/14/2022]
Abstract
Adipose tissue is a central regulator of metabolism and an important pharmacological target to treat the metabolic consequences of obesity, such as insulin resistance and dyslipidemia. Among the various cellular compartments, the adipocyte cell surface is especially appealing as a drug target as it contains various proteins that when activated or inhibited promote adipocyte health, change its endocrine function and eventually maintain or restore whole-body insulin sensitivity. In addition, cell surface proteins are readily accessible by various drug classes. However, targeting individual cell surface proteins in adipocytes has been difficult due to important functions of these proteins outside adipose tissue, raising various safety concerns. Thus, one of the biggest challenges is the lack of adipose selective surface proteins and/or targeting reagents. Here, we discuss several receptor families with an important function in adipogenesis and mature adipocytes to highlight the complexity at the cell surface and illustrate the problems with identifying adipose selective proteins. We then discuss that, while no unique adipocyte surface protein might exist, how splicing, posttranslational modifications as well as protein/protein interactions can create enormous diversity at the cell surface that vastly expands the space of potentially unique epitopes and how these selective epitopes can be identified and targeted.
Collapse
Affiliation(s)
- Yasuhiro Onogi
- RG Adipocytes and Metabolism, Institute for Diabetes and Obesity, Helmholtz Diabetes Center, Helmholtz Zentrum München, German Research Center for Environmental Health GmbH, 85764 Neuherberg, Germany
- German Center for Diabetes Research (DZD), 85764 Neuherberg, Germany
| | - Ahmed Elagamy Mohamed Mahmoud Khalil
- RG Adipocytes and Metabolism, Institute for Diabetes and Obesity, Helmholtz Diabetes Center, Helmholtz Zentrum München, German Research Center for Environmental Health GmbH, 85764 Neuherberg, Germany
- German Center for Diabetes Research (DZD), 85764 Neuherberg, Germany
| | - Siegfried Ussar
- RG Adipocytes and Metabolism, Institute for Diabetes and Obesity, Helmholtz Diabetes Center, Helmholtz Zentrum München, German Research Center for Environmental Health GmbH, 85764 Neuherberg, Germany
- German Center for Diabetes Research (DZD), 85764 Neuherberg, Germany
- Department of Medicine, Technische Universität München, Munich, Germany
| |
Collapse
|
18
|
Eom S, Bae Y, Kim S, Choi H, Park J, Kang S. Development of Recombinant Immunoglobulin G-Binding Luciferase-Based Signal Amplifiers in Immunoassays. Anal Chem 2020; 92:5473-5481. [PMID: 32142265 DOI: 10.1021/acs.analchem.0c00222] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
In general immunoassays, secondary antibodies are covalently linked with enzymes and bind to the Fc region of target-bound primary antibodies to amplify signals of low-abundant target molecules. The antibodies themselves are obtained from large mammals and are further modified with enzymes. In this study, we developed novel recombinant immunoglobulin G (IgG)-binding luciferase-based signal amplifiers (rILSAs) by genetically fusing luciferase (Nluc) with antimouse IgG1 nanobody (MG1Nb) and antibody-binding domain (ABD), individually or together, in a mix-and-match manner. We obtained three different highly pure rILSAs in large quantities using a bacterial overexpression system and one-step purification. Mouse-specific rILSA, MG1Nb-Nluc, and rabbit-specific rILSA, Nluc-ABD, selectively bound to target-molecule-bound mouse IgG1 and rabbit IgG primary antibodies, whereas the bispecific rILSA, MG1Nb-Nluc-ABD, mutually bound to both mouse IgG1 and rabbit IgG primary antibodies. All rILSAs exhibited an outstanding signal-amplifying capability comparable to those of conventional horseradish-peroxidase-conjugated secondary antibodies, regardless of the target molecules, in various immunoassay formats, such as enzyme-linked immunosorbent assay, Western blot, and lateral flow assays. Each rILSA was selected for its own individual purpose and applied to various types of target analytes, in combination with a variety of target-specific primary antibodies, effectively minimizing the use of animals as well as reducing the costs and time associated with the production and chemical conjugation of signal-amplifying enzymes.
Collapse
|
19
|
Kajiwara K, Aoki W, Ueda M. Evaluation of the yeast surface display system for screening of functional nanobodies. AMB Express 2020; 10:51. [PMID: 32180052 PMCID: PMC7076106 DOI: 10.1186/s13568-020-00983-y] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2020] [Accepted: 03/02/2020] [Indexed: 11/10/2022] Open
Abstract
Yeast surface display is a powerful technology used to isolate and engineer proteins to improve their activity, specificity, and stability. In this method, gene expression is regulated by promoters, and secretion efficiency is affected by secretion signals. Furthermore, both the accessibility and activity of the displayed proteins are affected by the length of anchor proteins. The ideal promoter, secretion signal, and anchor protein combination depend on the proteins of interest. In this study, we optimized a yeast surface display suitable for nanobody evaluation. We designed five display systems that used different combinations of promoters, secretion signals, and anchor proteins. Anti-hen egg-white lysozyme nanobody was used as the model nanobody. The amount of nanobodies displayed on yeast cells, the number of antigens bound to the displayed nanobodies, and the display efficiency were quantified. Overall, we improved the yeast display system for nanobody engineering and proposed its optimization.
Collapse
|
20
|
Affiliation(s)
- Limor Cohen
- Department of Pathology, Brigham and Women’s Hospital, Harvard Medical School, Boston, Massachusetts 02115, United States
| | - David R. Walt
- Department of Pathology, Brigham and Women’s Hospital, Harvard Medical School, Boston, Massachusetts 02115, United States
| |
Collapse
|
21
|
Zimmermann I, Egloff P, Hutter CA, Arnold FM, Stohler P, Bocquet N, Hug MN, Huber S, Siegrist M, Hetemann L, Gera J, Gmür S, Spies P, Gygax D, Geertsma ER, Dawson RJ, Seeger MA. Synthetic single domain antibodies for the conformational trapping of membrane proteins. eLife 2018; 7:34317. [PMID: 29792401 PMCID: PMC5967865 DOI: 10.7554/elife.34317] [Citation(s) in RCA: 136] [Impact Index Per Article: 22.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2017] [Accepted: 05/07/2018] [Indexed: 12/13/2022] Open
Abstract
Mechanistic and structural studies of membrane proteins require their stabilization in specific conformations. Single domain antibodies are potent reagents for this purpose, but their generation relies on immunizations, which impedes selections in the presence of ligands typically needed to populate defined conformational states. To overcome this key limitation, we developed an in vitro selection platform based on synthetic single domain antibodies named sybodies. To target the limited hydrophilic surfaces of membrane proteins, we designed three sybody libraries that exhibit different shapes and moderate hydrophobicity of the randomized surface. A robust binder selection cascade combining ribosome and phage display enabled the generation of conformation-selective, high affinity sybodies against an ABC transporter and two previously intractable human SLC transporters, GlyT1 and ENT1. The platform does not require access to animal facilities and builds exclusively on commercially available reagents, thus enabling every lab to rapidly generate binders against challenging membrane proteins.
Collapse
Affiliation(s)
- Iwan Zimmermann
- Institute of Medical Microbiology, University of Zurich, Zurich, Switzerland
| | - Pascal Egloff
- Institute of Medical Microbiology, University of Zurich, Zurich, Switzerland
| | - Cedric Aj Hutter
- Institute of Medical Microbiology, University of Zurich, Zurich, Switzerland
| | - Fabian M Arnold
- Institute of Medical Microbiology, University of Zurich, Zurich, Switzerland
| | - Peter Stohler
- Roche Pharma Research and Early Development, Therapeutic Modalities, Roche Innovation Center Basel, F. Hoffmann-La Roche Ltd, Basel, Switzerland
| | - Nicolas Bocquet
- Roche Pharma Research and Early Development, Therapeutic Modalities, Roche Innovation Center Basel, F. Hoffmann-La Roche Ltd, Basel, Switzerland
| | - Melanie N Hug
- Roche Pharma Research and Early Development, Therapeutic Modalities, Roche Innovation Center Basel, F. Hoffmann-La Roche Ltd, Basel, Switzerland
| | - Sylwia Huber
- Roche Pharma Research and Early Development, Therapeutic Modalities, Roche Innovation Center Basel, F. Hoffmann-La Roche Ltd, Basel, Switzerland
| | - Martin Siegrist
- Roche Pharma Research and Early Development, Therapeutic Modalities, Roche Innovation Center Basel, F. Hoffmann-La Roche Ltd, Basel, Switzerland
| | - Lisa Hetemann
- Roche Pharma Research and Early Development, Therapeutic Modalities, Roche Innovation Center Basel, F. Hoffmann-La Roche Ltd, Basel, Switzerland
| | - Jennifer Gera
- Roche Pharma Research and Early Development, Therapeutic Modalities, Roche Innovation Center Basel, F. Hoffmann-La Roche Ltd, Basel, Switzerland
| | - Samira Gmür
- University of Applied Sciences and Arts Northwestern Switzerland, Muttenz, Switzerland
| | - Peter Spies
- University of Applied Sciences and Arts Northwestern Switzerland, Muttenz, Switzerland
| | - Daniel Gygax
- University of Applied Sciences and Arts Northwestern Switzerland, Muttenz, Switzerland
| | - Eric R Geertsma
- Institute of Biochemistry, Goethe University Frankfurt, Frankfurt am Main, Germany
| | - Roger Jp Dawson
- Roche Pharma Research and Early Development, Therapeutic Modalities, Roche Innovation Center Basel, F. Hoffmann-La Roche Ltd, Basel, Switzerland
| | - Markus A Seeger
- Institute of Medical Microbiology, University of Zurich, Zurich, Switzerland
| |
Collapse
|
22
|
Recent advances in the selection and identification of antigen-specific nanobodies. Mol Immunol 2018; 96:37-47. [PMID: 29477934 DOI: 10.1016/j.molimm.2018.02.012] [Citation(s) in RCA: 59] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2017] [Revised: 02/12/2018] [Accepted: 02/18/2018] [Indexed: 01/21/2023]
Abstract
Nanobodies represent the next-generation antibody-derived biologics with significant advances over conventional antibodies. Several rapid and robust techniques for isolating highly specific nanobodies have been developed. Antigen specific nanobodies are selected from constructed nanobody libraries, which can be classified into 3 main types: immune library, naïve library, and semisynthetic/synthetic library. The immune library is the most widely used strategy for nanobody screening. Target specific nanobodies are highly enriched in immune libraries than in non-immune libraries; however, it is largely limited by the natural antigenicity of antigens. The naïve library is thus developed. Despite the lack of somatic maturation, protein engineering can be employed to significantly increase the affinities of selected binders. However, a substantial amount of blood samples collected from a large number of individual animals is a prerequisite to ensure the diversity of the naïve library. With this issue considered, the semisynthetic/synthetic library may be a promising path toward obtaining a limitless source of nanobodies against a variety of antigens without the need of animals. In this review, we summarize the state-of-the-art screening technologies with different libraries. The approaches presented here can further boost the diverse applications of nanobodies in biomedicine and biotechnology.
Collapse
|
23
|
Wu X, Chen S, Lin L, Liu J, Wang Y, Li Y, Li Q, Wang Z. A Single Domain-Based Anti-Her2 Antibody Has Potent Antitumor Activities. Transl Oncol 2018; 11:366-373. [PMID: 29455083 PMCID: PMC5852409 DOI: 10.1016/j.tranon.2018.01.024] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2017] [Revised: 01/27/2018] [Accepted: 01/29/2018] [Indexed: 01/07/2023] Open
Abstract
Human epidermal growth factor receptor 2 (HER2) is overexpressed in approximately 20% to 30% of breast cancers and various other types of cancers, which plays a vital role in the cancer progression. Monoclonal antibodies targeting Her2 are now used in the clinic to treat Her2 overexpression cancer patients. However, relapse or resistance is frequent with the current therapies. To generate a new treatment avenue against Her2, we immunized and selected a specific anti-Her2 single domain antibody C3 for further studies. The C3-Fc antibody drove antibody-dependent cell-mediated cytotoxicity against Her2-positive tumor cells in vitro and resulted in potent antitumor growth in vivo. These data suggest that the C3-Fc antibody may provide an alternative avenue for Her2-positive cancer therapy.
Collapse
Affiliation(s)
- Xiaoqiong Wu
- School of Pharmaceutical Sciences, Sun Yat-Sen University, Guangzhou, China 510006; Center for Cellular & Structural Biology, Sun Yat-Sen University, Guangzhou, China 510006.
| | - Siqi Chen
- School of Pharmaceutical Sciences, Sun Yat-Sen University, Guangzhou, China 510006; Center for Cellular & Structural Biology, Sun Yat-Sen University, Guangzhou, China 510006.
| | - Limin Lin
- School of Pharmaceutical Sciences, Sun Yat-Sen University, Guangzhou, China 510006; Center for Cellular & Structural Biology, Sun Yat-Sen University, Guangzhou, China 510006.
| | - Jiayu Liu
- School of Pharmaceutical Sciences, Sun Yat-Sen University, Guangzhou, China 510006; Center for Cellular & Structural Biology, Sun Yat-Sen University, Guangzhou, China 510006.
| | - Yanlan Wang
- School of Pharmaceutical Sciences, Sun Yat-Sen University, Guangzhou, China 510006; Center for Cellular & Structural Biology, Sun Yat-Sen University, Guangzhou, China 510006.
| | - Yumei Li
- School of Pharmaceutical Sciences, Sun Yat-Sen University, Guangzhou, China 510006; Center for Cellular & Structural Biology, Sun Yat-Sen University, Guangzhou, China 510006.
| | - Qing Li
- School of Pharmaceutical Sciences, Sun Yat-Sen University, Guangzhou, China 510006; Center for Cellular & Structural Biology, Sun Yat-Sen University, Guangzhou, China 510006.
| | - Zhong Wang
- School of Pharmaceutical Sciences, Sun Yat-Sen University, Guangzhou, China 510006; Center for Cellular & Structural Biology, Sun Yat-Sen University, Guangzhou, China 510006.
| |
Collapse
|
24
|
Doshi R, McGrath AP, Piñeros M, Szewczyk P, Garza DM, Kochian LV, Chang G. Functional characterization and discovery of modulators of SbMATE, the agronomically important aluminium tolerance transporter from Sorghum bicolor. Sci Rep 2017; 7:17996. [PMID: 29269936 PMCID: PMC5740117 DOI: 10.1038/s41598-017-18146-8] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2017] [Accepted: 12/01/2017] [Indexed: 12/18/2022] Open
Abstract
About 50% of the world's arable land is strongly acidic (pH ≤ 5). The low pH solubilizes root-toxic ionic aluminium (Al3+) species from clay minerals, driving the evolution of counteractive adaptations in cultivated crops. The food crop Sorghum bicolor upregulates the membrane-embedded transporter protein SbMATE in its roots. SbMATE mediates efflux of the anionic form of the organic acid, citrate, into the soil rhizosphere, chelating Al3+ ions and thereby imparting Al-resistance based on excluding Al+3 from the growing root tip. Here, we use electrophysiological, radiolabeled, and fluorescence-based transport assays in two heterologous expression systems to establish a broad substrate recognition profile of SbMATE, showing the proton and/or sodium-driven transport of 14C-citrate anion, as well as the organic monovalent cation, ethidium, but not its divalent analog, propidium. We further complement our transport assays by measuring substrate binding to detergent-purified SbMATE protein. Finally, we use the purified membrane protein as an antigen to discover native conformation-binding and transport function-altering nanobodies using an animal-free, mRNA/cDNA display technology. Our results demonstrate the utility of using Pichia pastoris as an efficient eukaryotic host to express large quantities of functional plant transporter proteins. The nanobody discovery approach is applicable to other non-immunogenic plant proteins.
Collapse
Affiliation(s)
- Rupak Doshi
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California at San Diego, La Jolla, California, USA.,InhibRx LLP, 11099 N Torrey Pines Rd., Suite 280, La Jolla, San Diego, CA, 92037, USA.,Department of Electrical Engineering and Computer Science, University of California, Irvine, 2213 Engineering Hall, Irvine, CA, 92697-2625, USA
| | - Aaron P McGrath
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California at San Diego, La Jolla, California, USA
| | - Miguel Piñeros
- Robert W. Holley Center for Agriculture and Health, United States Department of Agriculture-Agricultural Research Service, Cornell University, Ithaca, NY, USA
| | - Paul Szewczyk
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California at San Diego, La Jolla, California, USA.,Cancer Metabolism and Signaling Networks Program, Sanford-Burnham Prebys Medical Discovery Institute, La Jolla, California, 92037, United States
| | - Denisse M Garza
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California at San Diego, La Jolla, California, USA
| | - Leon V Kochian
- Global Institute for Food Security, University of Saskatchewan, Saskatoon, Canada
| | - Geoffrey Chang
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California at San Diego, La Jolla, California, USA. .,Department of Pharmacology, School of Medicine, University of California at San Diego, La Jolla, California, USA.
| |
Collapse
|
25
|
Veugelen S, Dewilde M, De Strooper B, Chávez-Gutiérrez L. Screening and Characterization Strategies for Nanobodies Targeting Membrane Proteins. Methods Enzymol 2016; 584:59-97. [PMID: 28065273 DOI: 10.1016/bs.mie.2016.10.029] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/05/2022]
Abstract
The study of membrane protein function and structure requires their successful detection, expression, solubilization, and/or reconstitution, which poses a challenging task and relies on the availability of suitable tools. Several research groups have successfully applied Nanobodies in the purification, as well as the functional and structural characterization of membrane proteins. Nanobodies are small, single-chain antibody fragments originating from camelids presenting on average a longer CDR3 which enables them to bind in cavities and clefts (such as active and allosteric sites). Notably, Nanobodies generally bind conformational epitopes making them very interesting tools to stabilize, dissect, and characterize specific protein conformations. In the clinic, several Nanobodies are under evaluation either as potential drug candidates or as diagnostic tools. In recent years, we have successfully generated high-affinity, conformation-sensitive anti-γ-secretase Nanobodies. γ-Secretase is a multimeric membrane protease involved in processing of the amyloid precursor protein with high clinical relevance as mutations in its catalytic subunit (Presenilin) cause early-onset Alzheimer's disease. Advancing our knowledge on the mechanisms governing γ-secretase intramembrane proteolysis through various strategies may lead to novel therapeutic avenues for Alzheimer's disease. In this chapter, we present the strategies we have developed and applied for the screening and characterization of anti-γ-secretase Nanobodies. These protocols could be of help in the generation of Nanobodies targeting other membrane proteins.
Collapse
Affiliation(s)
- S Veugelen
- University of Leuven, Leuven, Belgium; VIB Center for Brain and Disease, Leuven, Belgium
| | - M Dewilde
- University of Leuven, Leuven, Belgium; VIB Center for Brain and Disease, Leuven, Belgium
| | - B De Strooper
- University of Leuven, Leuven, Belgium; VIB Center for Brain and Disease, Leuven, Belgium; UCL Institute of Neurology, London, United Kingdom
| | - L Chávez-Gutiérrez
- University of Leuven, Leuven, Belgium; VIB Center for Brain and Disease, Leuven, Belgium.
| |
Collapse
|
26
|
Pardee K, Slomovic S, Nguyen PQ, Lee JW, Donghia N, Burrill D, Ferrante T, McSorley FR, Furuta Y, Vernet A, Lewandowski M, Boddy CN, Joshi NS, Collins JJ. Portable, On-Demand Biomolecular Manufacturing. Cell 2016; 167:248-259.e12. [DOI: 10.1016/j.cell.2016.09.013] [Citation(s) in RCA: 223] [Impact Index Per Article: 27.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2016] [Revised: 08/16/2016] [Accepted: 09/06/2016] [Indexed: 12/12/2022]
|
27
|
Bever CS, Dong JX, Vasylieva N, Barnych B, Cui Y, Xu ZL, Hammock BD, Gee SJ. VHH antibodies: emerging reagents for the analysis of environmental chemicals. Anal Bioanal Chem 2016; 408:5985-6002. [PMID: 27209591 DOI: 10.1007/s00216-016-9585-x] [Citation(s) in RCA: 88] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2016] [Revised: 03/24/2016] [Accepted: 04/19/2016] [Indexed: 01/28/2023]
Abstract
A VHH antibody (or nanobody) is the antigen binding fragment of heavy chain only antibodies. Discovered nearly 25 years ago, they have been investigated for their use in clinical therapeutics and immunodiagnostics, and more recently for environmental monitoring applications. A new and valuable immunoreagent for the analysis of small molecular weight environmental chemicals, VHH will overcome many pitfalls encountered with conventional reagents. In the work so far, VHH antibodies often perform comparably to conventional antibodies for small molecule analysis, are amenable to numerous genetic engineering techniques, and show ease of adaption to other immunodiagnostic platforms for use in environmental monitoring. Recent reviews cover the structure and production of VHH antibodies as well as their use in clinical settings. However, no report focuses on the use of these VHH antibodies to detect small environmental chemicals (MW < 1500 Da). This review article summarizes the efforts made to produce VHHs to various environmental targets, compares the VHH-based assays with conventional antibody assays, and discusses the advantages and limitations in developing these new antibody reagents particularly to small molecule targets. Graphical Abstract Overview of the production of VHHs to small environmental chemicals and highlights of the utility of these new emerging reagents.
Collapse
Affiliation(s)
- Candace S Bever
- Department of Entomology and Nematology and UCD Comprehensive Cancer Center, University of California Davis, One Shields Avenue, Davis, CA, 95616, USA
| | - Jie-Xian Dong
- Department of Entomology and Nematology and UCD Comprehensive Cancer Center, University of California Davis, One Shields Avenue, Davis, CA, 95616, USA
| | - Natalia Vasylieva
- Department of Entomology and Nematology and UCD Comprehensive Cancer Center, University of California Davis, One Shields Avenue, Davis, CA, 95616, USA
| | - Bogdan Barnych
- Department of Entomology and Nematology and UCD Comprehensive Cancer Center, University of California Davis, One Shields Avenue, Davis, CA, 95616, USA
| | - Yongliang Cui
- Department of Entomology and Nematology and UCD Comprehensive Cancer Center, University of California Davis, One Shields Avenue, Davis, CA, 95616, USA.,Department of Oral Biology, School of Dental Medicine, University of Buffalo, State University of New York, Buffalo, NY, 14214, USA
| | - Zhen-Lin Xu
- Department of Entomology and Nematology and UCD Comprehensive Cancer Center, University of California Davis, One Shields Avenue, Davis, CA, 95616, USA
| | - Bruce D Hammock
- Department of Entomology and Nematology and UCD Comprehensive Cancer Center, University of California Davis, One Shields Avenue, Davis, CA, 95616, USA
| | - Shirley J Gee
- Department of Entomology and Nematology and UCD Comprehensive Cancer Center, University of California Davis, One Shields Avenue, Davis, CA, 95616, USA.
| |
Collapse
|
28
|
Jullien D, Vignard J, Fedor Y, Béry N, Olichon A, Crozatier M, Erard M, Cassard H, Ducommun B, Salles B, Mirey G. Chromatibody, a novel non-invasive molecular tool to explore and manipulate chromatin in living cells. J Cell Sci 2016; 129:2673-83. [PMID: 27206857 PMCID: PMC4958301 DOI: 10.1242/jcs.183103] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2015] [Accepted: 05/13/2016] [Indexed: 12/25/2022] Open
Abstract
Chromatin function is involved in many cellular processes, its visualization or modification being essential in many developmental or cellular studies. Here, we present the characterization of chromatibody, a chromatin-binding single-domain, and explore its use in living cells. This non-intercalating tool specifically binds the heterodimer of H2A–H2B histones and displays a versatile reactivity, specifically labeling chromatin from yeast to mammals. We show that this genetically encoded probe, when fused to fluorescent proteins, allows non-invasive real-time chromatin imaging. Chromatibody is a dynamic chromatin probe that can be modulated. Finally, chromatibody is an efficient tool to target an enzymatic activity to the nucleosome, such as the DNA damage-dependent H2A ubiquitylation, which can modify this epigenetic mark at the scale of the genome and result in DNA damage signaling and repair defects. Taken together, these results identify chromatibody as a universal non-invasive tool for either in vivo chromatin imaging or to manipulate the chromatin landscape. Summary: Chromatibody is a chromatin-binding single-domain antibody, derived from llama nanobodies, that can be used as a novel non-invasive molecular tool to explore and manipulate chromatin in living cells.
Collapse
Affiliation(s)
- Denis Jullien
- Toxalim, Université de Toulouse, INRA, Université de Toulouse 3 Paul Sabatier, 31027 Toulouse, France ITAV, Université de Toulouse, CNRS, UPS, 31106 Toulouse, France
| | - Julien Vignard
- Toxalim, Université de Toulouse, INRA, Université de Toulouse 3 Paul Sabatier, 31027 Toulouse, France
| | - Yoann Fedor
- Toxalim, Université de Toulouse, INRA, Université de Toulouse 3 Paul Sabatier, 31027 Toulouse, France
| | - Nicolas Béry
- CRCT-UMR1037, Université de Toulouse, INSERM, 31037 Toulouse, France
| | - Aurélien Olichon
- CRCT-UMR1037, Université de Toulouse, INSERM, 31037 Toulouse, France
| | | | - Monique Erard
- IPBS-UMR5089, Université de Toulouse, CNRS, 31077 Toulouse, France
| | - Hervé Cassard
- IHAP, Université de Toulouse, INRA, ENVT, 31076 Toulouse, France
| | - Bernard Ducommun
- ITAV, Université de Toulouse, CNRS, UPS, 31106 Toulouse, France CHU de Toulouse, 31106 Toulouse, France
| | - Bernard Salles
- Toxalim, Université de Toulouse, INRA, Université de Toulouse 3 Paul Sabatier, 31027 Toulouse, France
| | - Gladys Mirey
- Toxalim, Université de Toulouse, INRA, Université de Toulouse 3 Paul Sabatier, 31027 Toulouse, France
| |
Collapse
|
29
|
Dodevski I, Markou GC, Sarkar CA. Conceptual and methodological advances in cell-free directed evolution. Curr Opin Struct Biol 2015; 33:1-7. [PMID: 26093059 DOI: 10.1016/j.sbi.2015.04.008] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2015] [Revised: 04/14/2015] [Accepted: 04/30/2015] [Indexed: 12/13/2022]
Abstract
Although cell-free directed evolution methods have been used to engineer proteins for nearly two decades, selections on more complex phenotypes have largely remained in the domain of cell-based engineering approaches. Here, we review recent conceptual advances that now enable in vitro display of multimeric proteins, integral membrane proteins, and proteins with an expanded amino acid repertoire. Additionally, we discuss methodological improvements that have enhanced the accessibility, efficiency, and robustness of cell-free approaches. Coupling these advances with the in vitro advantages of creating exceptionally large libraries and precisely controlling all experimental conditions, cell-free directed evolution is poised to contribute significantly to our understanding and engineering of more complex protein phenotypes.
Collapse
Affiliation(s)
- Igor Dodevski
- Department of Biomedical Engineering, University of Minnesota, Minneapolis, MN 55455, USA
| | - George C Markou
- Department of Chemical Engineering and Materials Science, University of Minnesota, Minneapolis, MN 55455, USA
| | - Casim A Sarkar
- Department of Biomedical Engineering, University of Minnesota, Minneapolis, MN 55455, USA; Department of Chemical Engineering and Materials Science, University of Minnesota, Minneapolis, MN 55455, USA.
| |
Collapse
|
30
|
Yan J, Wang P, Zhu M, Li G, Romão E, Xiong S, Wan Y. Characterization and applications of Nanobodies against human procalcitonin selected from a novel naïve Nanobody phage display library. J Nanobiotechnology 2015; 13:33. [PMID: 25944262 PMCID: PMC4475299 DOI: 10.1186/s12951-015-0091-7] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2015] [Accepted: 04/15/2015] [Indexed: 02/06/2023] Open
Abstract
BACKGROUND Nanobodies (Nbs) are single-domain antigen-binding fragments derived from the camelids heavy-chain only antibodies (HCAbs). Their unique advantageous properties make Nbs highly attractive in various applications. The general approach to obtain Nbs is to isolate them from immune libraries by phage display technology. However, it is unfeasible when the antigens are toxic, lethal, transmissible or of low immunogenicity. Naïve libraries could be an alternative way to solve the above problems. RESULTS We constructed a large camel naïve phage display Nanobody (Nb) library with great diversity. The generated library contains to 6.86 × 10(11) clones and to our best of knowledge, this is the biggest naïve phage display Nb library. Then Nbs against human procalcitonin (PCT) were isolated from this library. These Nbs showed comparable affinity and antigen-binding thermostability at 37°C and 60°C compared to the PCT Nbs from an immune phage-displayed library. Furthermore, two PCT Nbs that recognize unique epitopes on PCT have been successfully applied to develop a sandwich enzyme-linked immunosorbent assay (ELISA) to detect PCT, which showed a linear working range from 10-1000 ng/mL of PCT. CONCLUSION We have constructed a large and diverse naïve phage display Nb library, which potentially functioning as a good resource for selecting antigen-binders with high quality. Moreover, functional Nbs against PCT were successfully characterized and applied, providing great values on medical application.
Collapse
Affiliation(s)
- Junrong Yan
- The Key Laboratory of Developmental Genes and Human Disease, Ministry of Education, Institute of Life Sciences, Southeast University, Nanjing, 210096, PR China.
| | - Pingyan Wang
- The Key Laboratory of Developmental Genes and Human Disease, Ministry of Education, Institute of Life Sciences, Southeast University, Nanjing, 210096, PR China.
| | - Min Zhu
- The Key Laboratory of Developmental Genes and Human Disease, Ministry of Education, Institute of Life Sciences, Southeast University, Nanjing, 210096, PR China.
| | - Guanghui Li
- The Key Laboratory of Developmental Genes and Human Disease, Ministry of Education, Institute of Life Sciences, Southeast University, Nanjing, 210096, PR China.
| | - Ema Romão
- Laboratory of Cellular and Molecular Immunology, Vrije Universiteit Brussel, Faculty of Science, Pleinlaan 2, 1050, Brussels, Belgium.
| | - Sheng Xiong
- Institute of Biomedicine & National Engineering Research Center of Genetic Medicine, College of Life Science and Technology, Jinan University, Guangzhou, 510630, PR China.
| | - Yakun Wan
- The Key Laboratory of Developmental Genes and Human Disease, Ministry of Education, Institute of Life Sciences, Southeast University, Nanjing, 210096, PR China. .,Jiangsu Nanobody Engineering and Research Center, Nantong, 226010, PR China.
| |
Collapse
|
31
|
Desmyter A, Spinelli S, Roussel A, Cambillau C. Camelid nanobodies: killing two birds with one stone. Curr Opin Struct Biol 2015; 32:1-8. [PMID: 25614146 DOI: 10.1016/j.sbi.2015.01.001] [Citation(s) in RCA: 68] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2014] [Revised: 12/23/2014] [Accepted: 01/05/2015] [Indexed: 01/09/2023]
Abstract
In recent years, the use of single-domain camelid immunoglobulins, termed vHHs or nanobodies, has seen increasing growth in biotechnology, pharmaceutical applications and structure/function research. The usefulness of nanobodies in structural biology is now firmly established, as they provide access to new epitopes in concave and hinge regions - and stabilize them. These sites are often associated with enzyme inhibition or receptor neutralization, and, at the same time, provide favorable surfaces for crystal packing. Remarkable results have been achieved by using nanobodies with flexible multi-domain proteins, large complexes and, last but not least, membrane proteins. While generating nanobodies is still a rather long and expensive procedure, the advent of naive libraries might be expected to facilitate the whole process.
Collapse
Affiliation(s)
- Aline Desmyter
- Aix-Marseille Université, Architecture et Fonction des Macromolécules Biologiques, France; Centre National de la Recherche Scientifique, AFMB, UMR 7257, case 932, 13288 Marseille Cedex 09, France
| | - Silvia Spinelli
- Aix-Marseille Université, Architecture et Fonction des Macromolécules Biologiques, France; Centre National de la Recherche Scientifique, AFMB, UMR 7257, case 932, 13288 Marseille Cedex 09, France
| | - Alain Roussel
- Aix-Marseille Université, Architecture et Fonction des Macromolécules Biologiques, France; Centre National de la Recherche Scientifique, AFMB, UMR 7257, case 932, 13288 Marseille Cedex 09, France
| | - Christian Cambillau
- Aix-Marseille Université, Architecture et Fonction des Macromolécules Biologiques, France; Centre National de la Recherche Scientifique, AFMB, UMR 7257, case 932, 13288 Marseille Cedex 09, France.
| |
Collapse
|